Biology book1
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  • 1. Table of ContentsBiology: The Science of Our Lives. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .3Science and the Scientific Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .3Theories Contributing to Modern Biology. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4Development of the Theory of Evolution. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5The Modern View of the Age of the Earth. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5Development of the Modern View of Evolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6Darwinian Evolution. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7The Diversity of Life . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8Characteristics of Living things . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11Levels of Organization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11Review Questions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13Structure of Water . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14Organic Molecules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15Review Questions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26Origin of the Earth and Life. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27Is There Life on Mars, Venus, Anywhere Else?? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 29Terms Applied to Cells. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30Components of Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31The Origins of Multicellularity. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31Microscopes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31Review Questions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34Cell Size and Shape. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35The Cell Membrane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36The Nucleus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36Ribosomes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38Endoplasmic Reticulum. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38Golgi Apparatus and Dictyosomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38Mitochondria . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39Cell Movement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40Review Questions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42Water and Solute Movement. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43Cells and Diffusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46Active and Passive Transport. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47Carrier-assisted Transport. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47Types of transport molecules. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48Vesicle-mediated transport. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48The Cell Cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49Prokaryotic Cell Division. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50Eukaryotic Cell Division. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50Mitosis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50Meiosis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .53Life Cycles. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53Phases of Meiosis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53Comparison of Mitosis and Meiosis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .57Laws of Thermodynamics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59Potential vs. Kinetic energy. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59 1
  • 2. Table of Contents ContinuedEndergonic and exergonic. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60Oxidation/Reduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60Enzymes: Organic Catalysts. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61The Nature of ATP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64Glycolysis, the Universal Process. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66Anaerobic Pathways . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66Aerobic Respiration. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67What is Photosynthesis? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69Leaves and Leaf Structure. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69The Nature of Light. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70Chlorophyll and Accessory Pigments. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .70Stages of Photosynthesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72C-4 Pathway. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .74The Carbon Cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75Review Questions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76Heredity, historical perspectives. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79The Monk and his peas. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79Principle of segregation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .80Dihybrid Crosses. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82Mutations. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85Genetic Terms. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85The modern view of the gene. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87Interactions among genes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88Polygenic inheritance. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89Genes and chromosomes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90Chromosome abnormalities. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91The physical carrier of inheritance. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92The structure of DNA. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94DNA Replication. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96Protein Synthesis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99The structure of hemoglobin. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .101Transcription: making an RNA copy of a DNA sequence. . . . . . . . . . . . . . . . . . . . . . . . . 103Ecology. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109Population Growth. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109Mutualism. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113Parasitism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113Commensalism. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .113Altering Population Growth. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115Range and Density. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116Ecology Definitions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117Community Structure. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117Classification of Communities. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .117Change in Communities Over Time. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126Ecosystems and Communities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .127Biogeochemical Cycles. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130 2
  • 3. INTRODUCTION: THE NATURE OF SCIENCE AND BIOLOGYBiology: The Science of Our LivesBiology literally means "the study of life". Biology is such a broad field, covering the minute workings of chemicalmachines inside our cells, to broad scale concepts of ecosystems and global climate change. Biologists study intimatedetails of the human brain, the composition of our genes, and even the functioning of our reproductive system. Biologistsrecently all but completed the deciphering of the human genome, the sequence of deoxyribonucleic acid (DNA) bases thatmay determine much of our innate capabilities and predispositions to certain forms of behavior and illnesses. DNAsequences have played major roles in criminal cases (O.J. Simpson, as well as the reversal of death penalties for manywrongfully convicted individuals), as well as the impeachment of President Clinton. We are bombarded with headlinesabout possible health risks from favorite foods (Chinese, Mexican, hamburgers, etc.) as well as the potential benefits ofeating other foods such as cooked tomatoes. Infomercials tout the benefits of metabolism-adjusting drugs for weight loss.Many Americans are turning to herbal remedies to ease arthritis pain, improve memory, as well as improve our moods.Can a biology book give you the answers to these questions? No, but it will enable you learn how to sift through thebiases of investigators, the press, and others in a quest to critically evaluate the question. To be honest, five years after youare through with this class it is doubtful you would remember all the details of metabolism. However, you will knowwhere to look and maybe a little about the process of science that will allow you to make an informed decision. Will yoube a scientist? Yes, in a way. You may not be formally trained as a science major, but you can think critically, solveproblems, and have some idea about what science can and cannot do. I hope you will be able to tell the shoe from theshinola.Science and the Scientific MethodScience is an objective, logical, and repeatable attempt to understand the principles and forces operating in the naturaluniverse. Science is from the Latin word, scientia, to know. Good science is not dogmatic, but should be viewed as anongoing process of testing and evaluation. One of the hoped-for benefits of students taking a biology course is that theywill become more familiar with the process of science.Humans seem innately interested in the world we live in. Young children drive their parents batty with constant "why"questions. Science is a means to get some of those whys answered. When we shop for groceries, we are conducting a kindof scientific experiment. If you like Brand X of soup, and Brand Y is on sale, perhaps you try Brand Y. If you like it youmay buy it again, even when it is not on sale. If you did not like Brand Y, then no sale will get you to try it again.In order to conduct science, one must know the rules of the game (imagine playing Monopoly and having to discover therules as you play! Which is precisely what one does with some computer or videogames (before buying the cheat book).The scientific method is to be used as a guide that can be modified. In some sciences, such as taxonomy and certain typesof geology, laboratory experiments are not necessarily performed. Instead, after formulating a hypothesis, additionalobservations and/or collections are made from different localities.Steps in the scientific method commonly include: 1. Observation: defining the problem you wish to explain. 2. Hypothesis: one or more falsifiable explanations for the observation. 3. Experimentation: Controlled attempts to test one or more hypotheses. 4. Conclusion: was the hypothesis supported or not? After this step the hypothesis is either modified or rejected, which causes a repeat of the steps above.After a hypothesis has been repeatedly tested, a hierarchy of scientific thought develops. Hypothesis is the most common,with the lowest level of certainty. A theory is a hypothesis that has been repeatedly tested with little modification, e.g. TheTheory of Evolution. A Law is one of the fundamental underlying principles of how the Universe is organized, e.g. TheLaws of Thermodynamics, Newtons Law of Gravity. Science uses the word theory differently than it is used in the 3
  • 4. general population. Theory to most people, in general nonscientific use, is an untested idea. Scientists call this ahypothesis.Scientific experiments are also concerned with isolating the variables. A good science experiment does not simultaneouslytest several variables, but rather a single variable that can be measured against a control. Scientific controlled experimentsare situations where all factors are the same between two test subjects, except for the single experimental variable.Consider a commonly conducted science fair experiment. Sandy wants to test the effect of gangsta rap music on pea plantgrowth. She plays loud rap music 24 hours a day to a series of pea plants grown under light, and watered every day. At theend of her experiment she concludes gangsta rap is conducive to plant growth. Her teacher grades her project very low,citing the lack of a control group for the experiment. Sandy returns to her experiment, but this time she has a separategroup of plants under the same conditions as the rapping plants, but with soothing Led Zeppelin songs playing. She comesto the same conclusion as before, but now has a basis for comparison. Her teacher gives her project a better grade.Theories Contributing to Modern BiologyModern biology is based on several great ideas, or theories: 1. The Cell Theory 2. The Theory of Evolution by Natural Selection 3. Gene Theory 4. HomeostasisRobert Hooke (1635-1703), one of the first scientists to use a microscope to examine pond water, cork and other things,referred to the cavities he saw in cork as "cells", Latin for chambers. Mattias Schleiden (in 1838) concluded all planttissues consisted of cells. In 1839, Theodore Schwann came to a similar conclusion for animal tissues. Rudolf Virchow, in1858, combined the two ideas and added that all cells come from pre-existing cells, formulating the Cell Theory. Thusthere is a chain-of-existence extending from your cells back to the earliest cells, over 3.5 billion years ago. The cell theorystates that all organisms are composed of one or more cells, and that those cells have arisen from pre-existing cells. James Watson (L) and Francis Crick (R), and the model they built of the structure of deoxyribonucleic acid, DNA. While a model may seem a small thing, their development of the DNA model fostered increased understanding of how genes work. Image from the Internet.In 1953, American scientist James Watson and British scientist Francis Crick developed the model for deoxyribonucleicacid (DNA), a chemical that had (then) recently been deduced to be the physical carrier of inheritance. Crick hypothesizedthe mechanism for DNA replication and further linked DNA to proteins, an idea since referred to as the central dogma.Information from DNA "language" is converted into RNA (ribonucleic acid) "language" and then to the "language" ofproteins. The central dogma explains the influence of heredity (DNA) on the organism (proteins).Homeostasis is the maintenance of a dynamic range of conditions within which the organism can function. Temperature,pH, and energy are major components of this concept. Thermodynamics is a field of study that covers the laws governingenergy transfers, and thus the basis for life on earth. Two major laws are known: the conservation of matter and energy, 4
  • 5. and entropy. These will be discussed in more detail in a later chapter. The universe is composed of two things: matter(atoms, etc.) and energy.These first three theories are very accepted by scientists and the general public. The theory of evolution is well acceptedby scientists and most of the general public. However, it remains a lightening rod for school boards, politicians, andtelevision preachers. Much of this confusion results from what the theory says and what it does not say.Development of the Theory of EvolutionModern biology is based on several unifying themes, such as the cell theory, genetics and inheritance, Francis Crickscentral dogma of information flow, and Darwin and Wallaces theory of evolution by natural selection. In this first unit wewill examine these themes and the nature of science.The Ancient Greek philosopher Anaxiamander (611-547 B.C.) and the Roman philosopher Lucretius (99-55 B.C.) coinedthe concept that all living things were related and that they had changed over time. The classical science of their time wasobservational rather than experimental. Another ancient Greek philosopher, Aristotle developed his Scala Naturae, orLadder of Life, to explain his concept of the advancement of living things from inanimate matter to plants, then animalsand finally man. This concept of man as the "crown of creation" still plagues modern evolutionary biologists. Post-Aristotlean "scientists" were constrained by the prevailing thought patterns of the Middle Ages -- the inerrancy ofthe biblical book of Genesis and the special creation of the world in a literal six days of the 24-hour variety. ArchbishopJames Ussher of Ireland, in the late 1600s calculated the age of the earth based on the genealogies from Adam and Evelisted in the biblical book of Genesis. According to Usshers calculations, the earth was formed on October 22, 4004 B.C.These calculations were part of Usshers book, History of the World. The chronology he developed was taken as factual,and was even printed in the front pages of bibles. Usshers ideas were readily accepted, in part because they posed nothreat to the social order of the times; comfortable ideas that would not upset the linked apple carts of church and state.Often new ideas must "come out of left field", appearing as wild notions, but in many cases prompting investigationwhich may later reveal the "truth". Usshers ideas were comfortable, the Bible was viewed as correct, therefore the earthmust be only 5000 years old.Geologists had for some time doubted the "truth" of a 5,000 year old earth. Leonardo da Vinci (painter of the Last Supper,and the Mona Lisa, architect and engineer) calculated the sedimentation rates in the Po River of Italy. Da Vinci concludedit took 200,000 years to form some nearby rock deposits. Galileo, convicted heretic for his contention that the Earth wasnot the center of the Universe, studied fossils (evidence of past life) and concluded that they were real and not inanimateartifacts. James Hutton, regarded as the Father of modern geology, developed the Theory of Uniformitarian’s, the basis ofmodern geology and paleontology. According to Huttons work, certain geological processes operated in the past in muchthe same fashion as they do today, with minor exceptions of rates, etc. Thus many geological structures and processescannot be explained if the earth was only a mere 5000 years old.The Modern View of the Age of the EarthRadiometric age assignments based on the rates of decay of radioactive isotopes, not discovered until the late 19thcentury, suggest the earth is over 4.5 billion years old. The Earth is thought older than 4.5 billion years, with the oldestknown rocks being 3.96 billion years old. Geologic time divides into eons, eras, and smaller units. The geologic time scale, highlighting some of the firsts in the evolution of life. One way to represent geological time. Note the break during the Precambrian. If the vertical scale was truly to scale the Precambrian would account for 7/8 of the graphic.Development of the modern view of Evolution 5
  • 6. Erasmus Darwin (1731-1802; grandfather of Charles Darwin) a British physician and poet in the late 1700s, proposed thatlife had changed over time, although he did not present a mechanism. Georges-Louis Leclerc, Comte de Buffon(pronounced Bu-fone; 1707-1788) in the middle to late 1700s proposed that species could change. This was a major breakfrom earlier concepts that species were created by a perfect creator and therefore could not change because they wereperfect, etc.Swedish botanist Carl Linne (more popularly known as Linneus, after the common practice of the day which was toLatinize names of learned men), attempted to pigeon-hole all known species of his time (1753) into immutable categories.Many of these categories are still used in biology, although the underlying thought concept is now evolution and notimmutability of species. Linnean hierarchical classification was based on the premise that the species was the smallestunit, and that each species (or taxon) belonged to a higher category.Linnean Hierarchical for Classification of SpeciesKingdom AnimaliaPhylum (Division is used for plants) ChordataClass MammaliaOrder PrimatesFamily HominidaeGenus HomoSpecies sapiensPneumonic: King Phillip Crossed Over For Ginger Snaps Linneus also developed the concept of binomial nomenclature, whereby scientists speaking and writing different languages could communicate clearly. For example Man in English is Hombre in Spanish, Mensch in German, and Homo in Latin. Linneus settled on Latin, which was the language of learned men at that time. If a scientist refers to Homo, all scientists know what he or she means. William "Strata" Smith (1769-1839), employed by the English coal mining industry, developed the first accurate geologic map of England. He also, from his extensive travels, developed the Principle of Biological Succession. This idea states that each period of Earth history has its own unique assemblages of fossils. In essence Smith fathered the science of stratigraphy, the correlation of rock layers based on (among other things) their fossil contents. He also developedan idea that life had changed over time, but did not overtly state that.Abraham Gottlob Werner and Baron Georges Cuvier (1769-1832) were among the foremost proponents of catastrophism,the theory that the earth and geological events had formed suddenly, as a result of some great catastrophe (such as Noahsflood). This view was a comfortable one for the times and thus was widely accepted. Cuvier eventually proposed thatthere had been several creations that occurred after catastrophes. Louis Agassiz (1807-1873) proposed 50-80 catastrophesand creations.Jean Baptiste de Lamarck (1744-1829) developed one of the first theories on how species changed. He proposed theinheritance of acquired characteristics to explain, among other things, the length of the giraffe neck. The Lamarckian viewis that modern giraffes have long necks because their ancestors progressively gained longer necks due to stretching toreach food higher and higher in trees. According to the 19th century concept of use and disuse the stretching of necksresulted in their development, which was somehow passed on to their progeny. Today we realize that only bacteria areable to incorporate non-genetic (nonheritable) traits. Lamarcks work was a theory that plainly stated that life had changedover time and provided (albeit an erroneous) mechanism of change.Darwinian evolution 6
  • 7. Charles Darwin, former divinity student and former medical student, secured (through the intercession of his geologyprofessor) an unpaid position as ships naturalist on the British exploratory vessel H.M.S. Beagle. The voyage wouldprovide Darwin a unique opportunity to study adaptation and gather a great deal of proof he would later incorporate intohis theory of evolution. On his return to England in 1836, Darwin began (with the assistance of numerous specialists) tocatalog his collections and ponder the seeming "fit" of organisms to their mode of existence. He eventually settled on fourmain points of a radical new hypothesis: 1. Adaptation: all organisms adapt to their environments. 2. Variation: all organisms are variable in their traits. 3. Over-reproduction: all organisms tend to reproduce beyond their environments capacity to support them (this is based on the work of Thomas Malthus, who studied how populations of organisms tended to grow geometrically until they encountered a limit on their population size). 4. Since not all organisms are equally well adapted to their environment, some will survive and reproduce better than others -- this is known as natural selection. Sometimes this is also referred to as "survival of the fittest". In reality this merely deals with the reproductive success of the organisms, not solely their relative strength or speed.Unlike the upper-class Darwin, Alfred Russel Wallace (1823-1913) came from a different social class. Wallace spentmany years in South America, publishing salvaged notes in Travels on the Amazon and Rio Negro in 1853. In 1854,Wallace left England to study the natural history of Indonesia, where he contracted malaria. During a fever Wallacemanaged to write down his ideas on natural selection.In 1858, Darwin received a letter from Wallace, in which Darwins as-yet-unpublished theory of evolution and adaptationwas precisely detailed. Darwin arranged for Wallaces letter to be read at a scientific meeting, along with a synopsis of hisown ideas. To be correct, we need to mention that both Darwin and Wallace developed the theory, although Darwinsmajor work was not published until 1859 (the book On the Origin of Species by Means of Natural Selection, consideredby many as one of the most influential books written). While there have been some changes to the theory since 1859, mostnotably the incorporation of genetics and DNA into what is termed the "Modern Synthesis" during the 1940s, mostscientists today acknowledge evolution as the guiding theory for modern biology.Recent revisions of biology curricula stressed the need for underlying themes. Evolution serves as such a universal theme.An excellent site devoted to Darwins thoughts and work is available by clicking here. At that same site is a timelineshowing many of the events mentioned above in their historical contexts. The Diversity of Life Evolutionary theory and the cell theory provide us with a basis for the interrelation of all living things. We also utilize Linneus hierarchical classification system, adopting (generally) five kingdoms of living organisms. Viruses, as discussed later, are not considered living.. Recent studies suggest that there might be a sixth Kingdom, the Archaea. A simple phylogenetic representation of three domains of life" Archaea, Bacteria (Eubacteria), and Eukaryota (all eukaryotic groups: Protista, Plantae, Fungi, and Animalia). 7
  • 8. The Five Kingdoms. Methods of Kingdom Organization Environmental Significance Examples Nutrition Photosynthesis, Single-celled, Monerans play various roles in almost Bacteria (E. coli), chemosynthesis, filament, or colony all food chains, including cyanobacteria (Oscillatoria), decomposer, of cells; all producer,consumer, and decomposer. methanogens, and parasitic. prokaryotic. thermacidophiles.Monera Cyanobacteria are important oxygen producers.(in the broadest sense,including organisms Many Monerans also produce nitrogen,usually placed in the vitamins, antibiotics, and are importantDomain Archaea). compoents in human and animal intestines. Photosynthesis, Single-celled, Important producers in ocean/pond Plankton (both absorb food from filamentous, food chain. phytoplankton and environment, or colonial, and zooplankton), algae (kelp,Protista trap/engulf smaller multicelled; all Source of food in some human cultures. diatoms, dinoflagellates),and organisms. eukaryotic. Protozoa (Amoeba, Phytoplankton component that is one of Paramecium). the major producers of oxygen Absorb food from a Single-celled, Decomposer, parasite, and consumer. Mushrooms (Agaricus host or from their filamentous, to campestris, the commercial environment. multicelled; all Produce antibiotics,help make bread mushroom), molds,Fungi eukaryotic. and alcohol. mildews, rusts and smuts All heterotrophic. (plant parasites), yeasts Crop parasites (Dutch Elm Disease, (Saccharomyces cerevisae, Karnal Bunt, Corn Smut, etc.). the brewers yeast). Almost all All multicelled, Food source, medicines and drugs, Angiosperms (oaks, tulips, photosynthetic, photosynthetic, dyes, building material, fuel. cacti),gymnosperms (pines, although a few autotrophs.. spuce, fir), mosses,Plantae parasitic plants are Producer in most food chains. ferns,liverworts, horsetails known. (Equisetum, the scouring rush) All heterotrophic. Multicelled Consumer level in most food chains Sponges, worms,molluscs, heterotrophs (herbivores,carnivores,omnivores). insects, starfish,mammals, capable of amphibians,fish, birds,Animalia movement at some Food source, beasts of burden and reptiles, and dinosaurs, and stage during their transportation, recreation, and people. life history (even companionship. couch potatoes).Monera, the most primitive kingdom, contain living organisms remarkably similar to ancient fossils. Organisms in thisgroup lack membrane-bound organelles associated with higher forms of life. Such organisms are known as prokaryotes.Bacteria (technically the Eubacteria) and blue-green bacteria (sometimes called blue-green algae, or cyanobacteria) are themajor forms of life in this kingdom. The most primitive group, the archaebacteria, are today restricted to marginal habitatssuch as hot springs or areas of low oxygen concentration. 8
  • 9. Protista were the first of the eukaryotic kingdoms, these organisms and all others have membrane-bound organelles,which allow for compartmentalization and dedication of specific areas for specific functions. The chief importance ofProtista is their role as a stem group for the remaining Kingdoms: Plants, Animals, and Fungi. Major groups within theProtista include the algae, euglenoids, ciliates, protozoa, and flagellates. Scanning electron micrographs of diatoms (Protista).There are two basic types of diatoms: bilaterally symmetrical (left) and radially symmetrical (right). Light micrographs of some protistans.Fungi are almost entirely multicellular (with yeast, Saccharomyces cerviseae, being a prominent unicellular fungus),heterotrophic (deriving their energy from another organism, whether alive or dead), and usually having some cells withtwo nuclei (multinucleate, as opposed to the more common one, or uninucleate) per cell. Ecologically this kingdom isimportant (along with certain bacteria) as decomposers and recyclers of nutrients. Economically, the Fungi provide uswith food (mushrooms; Bleu cheese/Roquefort cheese; baking and brewing), antibiotics (the first of the wonder drugs,penicillin, was isolated from a fungus Penicillium), and crop parasites (doing several billion dollars per year of damage).Plantae include multicelled organisms that are all autotrophic (capable of making their own food by the process ofphotosynthesis, the conversion of sunlight energy into chemical energy). Ecologically, this kingdom is generally (alongwith photosynthetic organisms in Monera and Protista) termed the producers, and rest at the base of all food webs. A foodweb is an ecological concept to trace energy flow through an ecosystem. Economically, this kingdom is unparalleled, withagriculture providing billions of dollars to the economy (as well as the foundation of "civilization"). Food, buildingmaterials, paper, drugs (both legal and illegal), and roses, are plants or plant-derived products.Animalia consists entirely of multicellular heterotrophs that are all capable (at some point during their life history) ofmobility. Ecologically, this kingdom occupies the level of consumers, which can be subdivided into herbivore (eaters ofplants) and carnivores (eaters of other animals). Humans, along with some other organisms, are omnivores (capable offunctioning as herbivores or carnivores). Economically, animals provide meat, hides, beasts of burden, pleasure (pets),transportation, and scents (as used in some perfumes). 9
  • 10. Characteristics of living thingsLiving things have a variety of common characteristics. • Organization. Living things exhibit a high level of organization, with multicellular organisms being subdivided into cells, and cells into organelles, and organelles into molecules, etc. • Homeostasis. Homeostasis is the maintenance of a constant (yet also dynamic) internal environment in terms of temperature, pH, water concentrations, etc. Much of our own metabolic energy goes toward keeping within our own homeostatic limits. If you run a high fever for long enough, the increased temperature will damage certain organs and impair your proper functioning. Swallowing of common household chemicals, many of which are outside the pH (acid/base) levels we can tolerate, will likewise negatively impact the human bodys homeostatic regime. Muscular activity generates heat as a waste product. This heat is removed from our bodies by sweating. Some of this heat is used by warm-blooded animals, mammals and birds, to maintain their internal temperatures. • Adaptation. Living things are suited to their mode of existence. Charles Darwin began the recognition of the marvelous adaptations all life has that allow those organisms to exist in their environment. • Reproduction and heredity. Since all cells come from existing cells, they must have some way of reproducing, whether that involves asexual (no recombination of genetic material) or sexual (recombination of genetic material). Most living things use the chemical DNA (deoxyribonucleic acid) as the physical carrier of inheritance and the genetic information. Some organisms, such as retroviruses (of which HIV is a member), use RNA (ribonucleic acid) as the carrier. The variation that Darwin and Wallace recognized as the wellspring of evolution and adaptation, is greatly increased by sexual reproduction. • Growth and development. Even single-celled organisms grow. When first formed by cell division, they are small, and must grow and develop into mature cells. Multicellular organisms pass through a more complicated process of differentiation and organogenesis (because they have so many more cells to develop). • Energy acquisition and release. One view of life is that it is a struggle to acquire energy (from sunlight, inorganic chemicals, or another organism), and release it in the process of forming ATP (adenosine triphosphate). • Detection and response to stimuli (both internal and external). • Interactions. Living things interact with their environment as well as each other. Organisms obtain raw materials and energy from the environment or another organism. The various types of symbioses (organismal interactions with each other) are examples of this.Levels of OrganizationBiosphere: The sum of all living things taken in conjunction with their environment. In essence, where life occurs, fromthe upper reaches of the atmosphere to the top few meters of soil, to the bottoms of the oceans. We divide the earth intoatmosphere (air), lithosphere (earth), hydrosphere (water), and biosphere (life). Ecosystem: The relationships of a smaller groups of organisms with each other and their environment. Scientists often speak of the interrelatedness of living things. Since, according to Darwins theory, organisms adapt to their environment, they must also adapt to other organisms in that environment. We can discuss the flow of energy through an ecosystem from photosynthetic autotrophs to herbivores to carnivores. Community: The relationships between groups of different species. For example, the desert communities consist of rabbits, coyotes, snakes, birds, miceand such plants as sahuaro cactus (Carnegia gigantea), Ocotillo, creosote bush, etc. Community structure can be disturbedby such things as fire, human activity, and over-population.Species: Groups of similar individuals who tend to mate and produce viable, fertile offspring. We often find speciesdescribed not by their reproduction (a biological species) but rather by their form (anatomical or form species). 10
  • 11. Populations: Groups of similar individuals who tend to mate with each other in a limited geographic area. This can be assimple as a field of flowers, which is separated from another field by a hill or other area where none of these flowersoccur.Individuals: One or more cells characterized by a unique arrangement of DNA "information". These can be unicellular ormulticellular. The multicellular individual exhibits specialization of cell types and division oflabor into tissues, organs, and organ systems.Organ System: (in multicellular organisms). A group of cells, tissues, and organs that perform aspecific major function. For example: the cardiovascular system functions in circulation ofblood.Organ: (in multicellular organisms). A group of cells or tissues performing an overall function.For example: the heart is an organ that pumps blood within the cardiovascular system. Tissue: (in multicellular organisms). A group of cells performing a specific function. For example heart muscle tissue is found in the heart and its unique contraction properties aid the hearts functioning as a pump. . Cell: The fundamental unit of living things. Each cell has some sort of hereditary material (either DNA or more rarely RNA), energy acquiring chemicals, structures, etc. Living things, by definition, must have the metabolic chemicals plus a nucleic acid hereditary information molecule.Organelle: A subunit of a cell, an organelle is involved in a specific subcellularfunction, for example the ribosome (the site of protein synthesis) ormitochondrion (the site of ATP generation in eukaryotes).Molecules, atoms, and subatomic particles: The fundamental functional levels ofbiochemistry.It is thus possible to study biology at many levels, from collections of organisms (communities), to the inner workings ofa cell (organelle).Learning Objectives • Name the special molecule that sets living things apart from the nonliving world and be able to explain why this molecule is important. • The cell is considered to be the basic living unit. Be able to distinguish between single-celled organisms and multicelled organisms. • Be able to arrange in order, from smallest to largest, the levels of organization that occur in nature and to write a brief description of each. • What does the term metabolism mean to the cell and the organism. • Organisms use a molecule known as ATP to transfer chemical energy from one molecule to another. Why is this essential for living things to exist. • Homeostasis is defined as a state in which the conditions of an organisms internal environment are maintained within tolerable limits. What mechanisms in your body are involved with homeostasis? • Reproduction is the means by which each new organism arises. Why is this an essential characteristic of life? • How are DNA and cellular reproduction linked in the process of inheritance? • A trait that assists an organism in survival and reproduction in a certain environment is said to be adaptive. What sorts of adaptive traits do you have? How do they aid your survival? • List the five kingdoms of life that are currently recognized by most scientists; tell generally what kinds of organisms are classified in each kingdom, and discuss the new ideas about Domains and how they may alter the five kingdom approach. 11
  • 12. • Arrange in order, from the fewer to the greater numbers of organisms included, the following categories of classification: class, family, genus, kingdom, order, phylum, and species. • Explain what the term biological diversity means to you, and speculate about what caused the great diversity of life on Earth. • Define natural selection and briefly describe what is occurring when a population is said to evolve. • Outline a set of steps that might be used in the scientific method of investigating a problem. • Explain why a control group is used in an experiment. • Define what is meant by a theory; cite an actual example that is significant to biology.Review Questions 1. Which of these scientific terms has the greatest degree of certainty? a) hypothesis; b) theory; c) law; d) guess. 2. The purpose of a control in a scientific experiment is to ___. a) provide a basis of comparison between experimental and nonexperimental; b) indicate the dependent variable; c) indicate the independent variable; d) provide a baseline from which to graph the data. 3. Which of these theories is not a basis for modern biology? a) evolution; b) creationism; c) cell theory; d) gene theory. 4. The molecule that is the physical carrier of inheritance is known as ___. a) ATP; b) RNA; c) DNA; d) NADH 5. Bacteria belong to the taxonomic kingdom ____. a) Plantae; b) Protista; c) Animalia; d) Fungi; e) Monera 6. Mushrooms belong to which of these taxonomic kingdoms? a) Plantae; b) Protista; c) Animalia; d) Fungi; e) Monera 7. Papaver somniferum, the opium poppy, belongs to which of these taxonomic kingdoms? a) Plantae; b) Protista; c) Animalia; d) Fungi; e) Monera 8. The sum of all energy transfers within a cell is known as _____. a) photosynthesis; b) cellular respiration; c) metabolism; d) replication; e) conjugation. 9. The molecule that is the energy coin of the cell is ___. a) ATP; b) RNA; c) DNA; d) NADH 10. Which of these is NOT a living organism? a) cactus; b) cat; c) algae; d) virus; e) yeast 11. Which of the following is the least inclusive (smallest) unit of classification? a) kingdom; b) species; c) genus; d) class; e) phylum 12. The scientist(s) credited with developing the theory of evolution by natural selection were ____. a) James Watson and Francis Crick; b) Aristotle and Lucretius; c) Charles Darwin and Alfred Wallace; d) Robert Hooke and Rudolph Virchow; e) James Watson and Charles Darwin 13. When an organism consists of a single cell, the organism is referred to as ___. a) uninucleate; b) uniport; c) unisexual; d) unicellular 14. According to science, the Earth is ___ years old. a) 4.5 billion; b) 4.5 million; c) 10 billion; d) 10,000; e) 450 million 15. Which of these is not an economic use of bacteria? a) food; b) biotechnology; c) mushrooms; d) food spoilage 12
  • 13. WATER AND ORGANIC MOLECULESStructure of WaterIt can be quite correctly argued that life exists on Earth because of the abundant liquid water. Other planets havewater, but they either have it as a gas (Venus) or ice (Mars). Recent studies of Mars reveal the presencesometime in the past of running fluid, possibly water. The chemical nature of water is thus one we mustexamine as it permeates living systems: water is auniversal solvent, and can be too much of a goodthing for some cells to deal with.Water is polar covalently bonded within themolecule. This unequal sharing of the electronsresults in a slightly positive and a slightly negativeside of the molecule. Other molecules, such asEthane, are nonpolar, having neither a positive nor anegative side.The difference between a polar (water) andnonpolar (ethane) molecule is due to the unequalsharing of electrons within the polar molecule.Nonpolar molecules have electrons equally sharedwithin their covalent bonds.These link up by the hydrogen bond discussed earlier. Consequently, water has a great interconnectivity ofindividual molecules, which is caused by the individually weak hydrogen bonds, that can be quite strong whentaken by the billions.Water has been referred to as the universal solvent. Living things are composed of atoms and molecules withinaqueous solutions (solutions that have materials dissolved in water). Solutions are uniform mixtures of themolecules of two or more substances. The solvent isusually the substance present in the greatest amount (andis usually also a liquid). The substances of lesser amountsare the solutes.The solubility of many molecules is determined by theirmolecular structure. You are familiar with the phrase"mixing like oil and water." The biochemical basis forthis phrase is that the organic macromolecules known as 13
  • 14. lipids (of which fats are an important, although often troublesome, group) have areas that lack polar covalentbonds. The polar covalently bonded water molecules act to exclude nonpolar molecules, causing the fats toclump together. The structure of many molecules can greatly influence their solubility. Sugars, such as glucose,have many hydroxyl (OH) groups, which tend to increase the solubility of the molecule.Water tends to disassociate into H+ and OH- ions. In this disassociation, the oxygen retains the electrons andonly one of the hydrogens, becoming a negatively charged ion known as hydroxide. Pure water has the samenumber (or concentration) of H+ as OH- ions. Acidic solutions have more H+ ions than OH- ions. Basic solutionshave the opposite. An acid causes an increase in the numbers of H+ ions and a base causes an increase in thenumbers of OH- ions.The pH scale is a logarithmic scale representing the concentration of H+ ions in a solution. Remember that asthe H+ concentration increases the OH- concentration decreases and vice versa . If we have a solution with onein every ten molecules being H+, we refer to the concentration of H+ ions as 1/10. Remember from algebra thatwe can write a fraction as a negative exponent, thus 1/10 becomes 10-1. Conversely 1/100 becomes 10-2 , 1/1000becomes 10-3, etc. Logarithms are exponents to which a number (usually 10) has been raised. For example log10 (pronounced "the log of 10") = 1 (since 10 may be written as 101). The log 1/10 (or 10-1) = -1. pH, a measureof the concentration of H+ ions, is the negative log of the H+ ion concentration. If the pH of water is 7, then theconcentration of H+ ions is 10-7, or 1/10,000,000. In the case of strong acids, such as hydrochloric acid (HCl), anacid secreted by the lining of your stomach, [H+] (the concentration of H+ ions, written in a chemical shorthand)is 10-1; therefore the pH is 1.Organic moleculesOrganic molecules are those that: 1) formed by the actions of living things; and/or 2) have a carbon backbone.Methane (CH4) is an example of this. If we remove the H from one of the methane units below, and begin 14
  • 15. linking them up, while removing other H units, we begin toform an organic molecule. (NOTE: Not all methane isorganically derived, methane is a major component of theatmosphere of Jupiter, which we think is devoid of life).When two methanes are combined, the resultant moleculeis Ethane, which has a chemical formula C2H6. Moleculesmade up of H and C are known as hydrocarbons.Scientists eventually realized that specific chemicalproperties were a result of the presence of particularfunctional groups. Functional groups are clusters of atoms with characteristic structure and functions. Polar molecules (with +/- charges) are attracted to water molecules and are hydrophilic. Nonpolar molecules are repelled by water and do not dissolve in water; are hydrophobic. Hydrocarbon is hydrophobic except when it has an attached ionized functional group such as carboxyl (acid) (COOH), then molecule is hydrophilic. Since cells are 70-90% water, the degree to which organic molecules interact with water affects their function. One of the most common groups is the -OH (hydroxyl) group. Its presence will enable a molecule to be water soluble.Isomers are molecules with identical molecular formulas but differ in arrangement of their atoms (e.g.,glyceraldehyde and dihydroxyacetone)..Functional groups in organic molecules. 15
  • 16. Carbon has four electrons in outer shell, and can bond with up to four other atoms (usually H, O, N, or anotherC). Since carbon can make covalent bonds with another carbon atom, carbon chains and rings that serve as thebackbones of organic molecules are possible.Chemical bonds store energy. The C-C covalent bond has 83.1 Kcal (kilocalories) per mole, while the C=Cdouble covalent bond has 147 Kcal/mole. Energy is in two forms: kinetic, or energy in use/motion; andpotential, or energy at rest or in storage. Chemical bonds are potential energy, until they are converted intoanother form of energy, kinetic energy (according to the two laws of thermodynamics).Each organic molecule group has small molecules (monomers) that are linked to form a larger organic molecule(macromolecule). Monomers can be joined together to form polymers that are the large macromolecules madeof three to millions of monomer subunits.Macromolecules are constructed by covalently bonding monomers by condensation reactions where water isremoved from functional groups on the monomers. Cellular enzymes carry out condensation (and the reversal ofthe reaction, hydrolysis of polymers). Condensation involves a dehydration synthesis because a water isremoved (dehydration) and a bond is made (synthesis). When two monomers join, a hydroxyl (OH) group isremoved from one monomer and a hydrogen (H) is removed from the other. This produces the water given offduring a condensation reaction. Hydrolysis (hydration) reactions break down polymers in reverse ofcondensation; a hydroxyl (OH) group from water attaches to one monomer and hydrogen (H) attaches to theother. 16
  • 17. There are four classes of macromolecules (polysaccharides, triglycerides, polypeptides, nucleic acids). Theseclasses perform a variety of functions in cells.1. Carbohydrates have the general formula [CH2O]n where n is a number between 3 and 6.. Carbohydratesfunction in short-term energy storage (such as sugar); as intermediate-term energy storage (starch for plants andglycogen for animals); and as structural components in cells (cellulose in the cell walls of plants and manyprotists), and chitin in the exoskeleton of insects and other arthropods.Sugars are structurally the simplest carbohydrates. They are the structural unit which makes up the other typesof carbohydrates. Monosaccharides are single (mono=one) sugars. Important monosaccharides include ribose(C5H10O5), glucose (C6H12O6), and fructose (same formula but different structure than glucose).We classify monosaccharides by the number of carbon atoms and the types of functional groups present in thesugar. For example, glucose and fructose, have the same chemical formula (C6H12O6), but a different structure:glucose having an aldehyde (internal hydroxyl shown as: -OH) and fructose having a keto group (internaldouble-bond O, shown as: =O). This functional group difference, as small as it seems, accounts for the greatersweetness of fructose as compared to glucose. 17
  • 18. In an aqueous solution, glucose tends to have two structures, α (alpha) and β (beta), with an intermediatestraight-chain form. The α form and β form differ in the location of one -OH group. Glucose is a commonhexose, six carbon sugar, in plants. The products of photosynthesis are assembled to form glucose. Energy fromsunlight is converted into and stored as C-C covalent bond energy. This energy is released in living organismsin such a way that not enough heat is generated at once to incinerate the organisms. One mole of glucose yields673 Kcal of energy. (A calorie is the amount of heat needed to raise one gram of water one degree C. A Kcalhas 1000 times as much energy as a cal.). Glucose is also the form of sugar measured in the humanbloodstream. Monosaccarides: Glucose, Fructose, Galactose, Ribose, and Deoxyribose Disaccharides are formed when two monosaccharides are chemically bonded together. Sucrose, a common plant disaccharide is composed of the monosaccharides glucose and fructose. Lactose, milk sugar, is a disaccharide composed of glucose and the monosaccharide galactose. The maltose that flavors a maltedmilkshake (and other items) is also a disaccharide made of two glucose molecules bonded together as shown in.Polysaccharides are large molecules composed of individual monosaccharide units. A common plantpolysaccharide is starch which is made up of many glucoses (in a polypeptide these are referred to as glucans).Two forms of polysaccharide, amylose and amylopectin makeup what we commonly call starch. The formationof the ester bond by condensation (the removal of water from a molecule) allows the linking ofmonosaccharides into disaccharides and polysaccharides. Glycogen is an animal storage product thataccumulates in the vertebrate liver. 18
  • 19. Cellulose, is a polysaccharide found in plant cell walls. Cellulose forms the fibrous part of the plant cell wall. Interms of human diets, cellulose is indigestible, and thus forms an important, easily obtained part of dietary fiber. As compared to starch and glycogen, which are each made up of mixtures of α and β glucoses, cellulose (and the animal structural polysaccharide chitin) are made up of only β glucoses. The three-dimensional structure of these polysaccharides is thus constrained into straight microfibrils by the uniform nature of the glucoses, which resist the actions of enzymes (such as amylase) that breakdown storage polysaccharides (such a starch).2. Lipids are involved mainly with long-term energy storage. They are generally insoluble in polar substancessuch as water. Secondary functions of lipids include structural components (as in the case of phospholipids thatare the major building block in cell membranes) and "messengers" (hormones) that play roles incommunications within and between cells. Lipids are composed of three fatty acids (usually) covalently bondedto a 3-carbon glycerol. The fatty acids are composed of CH2 units, and are hydrophobic/not water soluble.Fatty acids can be saturated (meaning they have as many hydrogens bonded to their carbons as possible) orunsaturated (with one or more double bonds connecting their carbons, hence fewer hydrogens). A fat is solid atroom temperature, while an oil is a liquid under the same conditions. The fatty acids in oils are mostlyunsaturated, while those in fats are mostly saturated.Saturated (palmitic and stearic) and unsaturated (next page Oleic) fatty acids. The term saturated refers to the"saturation" of the molecule by hydrogen atoms. The presence of a double C=C covalent bond reduces thenumber of hydrogens that can bond to the carbon chain, hence the application of therm "unsaturated". 19
  • 20. Fats and oils function in long-term energy storage. Animals convert excess sugars (beyond their glycogenstorage capacities) into fats. Most plants store excess sugars as starch, although some seeds and fruits haveenergy stored as oils (e.g. corn oil, peanut oil, palm oil, canola oil, and sunflower oil). Fats yield 9.3 Kcal/gm,while carbohydrates yield 3.79 Kcal/gm. Fats thus store six times as much energy as glycogen.Diets are attempts to reduce the amount of fats present in specialized cells known as adipose cells thataccumulate in certain areas of the human body. By restricting the intakes of carbohydrates and fats, the body isforced to draw on its own stores to makeup the energy debt. The body responds to this by lowering its metabolicrate, often resulting in a drop of "energy level." Successful diets usually involve three things: decreasing theamounts of carbohydrates and fats; exercise; and behavior modification.Another use of fats is as insulators and cushions. The human body naturally accumulates some fats in the"posterior" area. Subdermal ("under the skin") fat plays a role in insulation.Phospholipids and glycolipids are important structural components of cell membranes. Phospholipids, aremodified so that a phosphate group (PO4-) is added to one of the fatty acids. The addition of this group makes apolar "head" and two nonpolar "tails". Waxes are an important structural component for many organisms, suchas the cuticle, a waxy layer covering the leaves and stems of many land plants; and protective coverings on skinand fur of animals.Cholesterol and steroids: Most mention of these two types of lipids in the news is usually negative.Cholesterol, has many biological uses, it occurs in cell membranes, and its forms the sheath of some types ofnerve cells. However, excess cholesterol in the blood has been linked to atherosclerosis, hardening of thearteries. Recent studies suggest a link between arterial plaque deposits of cholesterol, antibodies to thepneumonia-causing form of Chlamydia, and heart attacks. The plaque increases blood pressure, much the wayblockages in plumbing cause burst pipes in old houses.Structure of four steroids.. 20
  • 21. 3. Proteins are very important in biological systems as control and structural elements. Control functions ofproteins are carried out by enzymes and proteinaceous hormones. Enzymes are chemicals that act as organiccatalysts (a catalyst is a chemical that promotes but is not changed by a chemical reaction). Structural proteinsfunction in the cell membrane, muscle tissue, etc.The building block of any protein is the amino acid, which has anamino end (NH2) and a carboxyl end (COOH). The R indicatesthe variable component (R-group) of each amino acid. Alanineand Valine, for example, are both nonpolar amino acids, but theydiffer, as do all amino acids, by the composition of their R-groups. All living things (and even viruses) use variouscombinations of the same twenty amino acids. A very powerfulbit of evidence for the phylogenetic connection of all livingthings. 21
  • 22. Amino acids are linked together by joining the amino end of one molecule to the carboxyl end of another.Removal of water allows formation of a type of covalent bond known as a peptide bond.Formation of a peptide bond between two amino acids by the condensation (dehydration) of the amino end ofone amino acid and the acid end of the other amino acid.Amino acids are linked together into a polypeptide, the primary structure in the organization of proteins. Theprimary structure of a protein is the sequence of amino acids, which is directly related to the sequence ofinformation in the RNA molecule, which in turn is a copy of the information in the DNA molecule. Changes inthe primary structure can alter the proper functioning of the protein. Protein function is usually tied to theirthree-dimensional structure. The primary structure is the sequence of amino acids in a polypeptide..The secondary structure is the tendency of the polypeptide to coil or pleat due to H-bonding between R-groups.The tertiary structure is controlled by bonding (or in some cases repulsion) between R-groups.. Many proteins,such as hemoglobin, are formed from one or more polypeptides. Such structure is termed quaternary structure.Structural proteins, such as collagen, have regular repeated primary structures. Like the structuralcarbohydrates, the components determine the final shape and ultimately function. Collagens have a variety offunctions in living things, such as the tendons, hide, and corneas of a cow. Keratin is another structural protein.It is found in fingernails, feathers, hair, and rhinoceros horns. Microtubules, important in cell division andstructures of flagella and cilia (among other things), are composed of globular structural proteins.4. Nucleic acids are polymers composed of monomer units known as nucleotides. There are a very fewdifferent types of nucleotides. The main functions of nucleotides are information storage (DNA), proteinsynthesis (RNA), and energy transfers (ATP and NAD). Nucleotides, consist of a sugar, a nitrogenous base, anda phosphate. The sugars are either ribose or deoxyribose. They differ by the lack of one oxygen in deoxyribose.Both are pentoses usually in a ring form. There are five nitrogenous bases. Purines (Adenine and Guanine) aredouble-ring structures, while pyrimidines (Cytosine, Thymine and Uracil) are single-ringed. 22
  • 23. Deoxyribonucleic acid (better known as DNA) is the physical carrier of inheritance for 99% of livingorganisms. The bases in DNA are C, G, A and T.Structure of a segment of a DNA double helix.DNA functions in information storage. The English alphabet has 26 letters that can be variously combined toform over 50,000 words. DNA has four letters (C, G, A, and T, the nitrogenous bases) that code for twentywords (the twenty amino acids found in all living things) that can make an infinite variety of sentences(polypeptides). Changes in the sequences of these bases information can alter the meaning of a sentence.For example take the sentence: I saw Elvis. This implies certain knowledge (that Ive been out in the sun toolong without a hat, etc.).If we alter the sentence by inverting the middle word, we get: I was Elvis (thank you, thank you very much).Now we have greatly altered the information.A third alteration will change the meaning: I was Levis. Clearly the original sentences meaning is now greatlychanged.Changes in DNA information will be translated into changes in the primary structure of a polypeptide, and fromthere to the secondary and tertiary structures. A mutation is any change in the DNA base sequence. Mostmutations are harmful, few are neutral, and a very few are beneficial and contribute the organisms reproductivesuccess. Mutations are the wellspring of variation, variation is central to Darwin and Wallaces theory ofevolution by natural selection.Ribonucleic acid (RNA), was discovered after DNA. DNA, with exceptions in chloroplasts and mitochondria, isrestricted to the nucleus (in eukaryotes, the nucleoid region in prokaryotes). RNA occurs in the nucleus as wellas in the cytoplasm (also remember that it occurs as part of the ribosomes that line the rough endoplasmicreticulum). There are three types of RNA: 23
  • 24. Messenger RNA (mRNA) is the blueprint for construction of a protein.Ribosomal RNA (rRNA) is the construction site where the protein is made.Transfer RNA (tRNA) is the truck delivering the proper amino acid to the site at the right time.Adenosine triphosphate, better known as ATP the energy currency or coin of the cell, transfers energy fromchemical bonds to endergonic (energy absorbing) reactions within the cell. Structurally, ATP consists of theadenine nucleotide (ribose sugar, adenine base, and phosphate group, PO4-2) plus two other phosphate groups.Energy is stored in the covalent bonds between phosphates, with the greatest amount of energy (approximately7 kcal/mole) in the bond between the second and third phosphate groups. This covalent bond is known as apyrophosphate bond.Learning Objectives • Dissolved substances are called solutes; a fluid in which one or more substances can dissolve is called a solvent. Describe several solutions that you use everyday in terms of what is the solvent and what is the solute. • Define acid and base and be able to cite an example of each. • The concentration of free hydrogen ions in solutions is measured by the pH scale.. • Nearly all large biological molecules have theory organization influenced by interactions with water. Describe this interaction as it exists with carbohydrate molecules. • Be able to list the three most abundant elements in living things. • Each carbon atom can form as many as four covalent bonds with other carbon atoms as well as with other elements. Be able to explain why this is so. • Be able to list the four main groups of organic molecules and their functions in living things. • Enzymes are a special class of proteins that speed up chemical reactions in cells. What about the structure of proteins allows for the reaction specificity that occurs with most enzymes. • Condensation reactions result in the formation of covalent bonds between small molecules to form larger organic molecules. Be able to describe a condensation reaction in words. • Be able to describe what occurs during a hydrolysis reaction. • Be able to define carbohydrates and list their functions. • The simplest carbohydrates are sugar monomers, the monosaccharides. Be able to give examples and their functions. • A polysaccharide is a straight or branched chain of hundreds or thousands of sugar monomers, of the same or different kinds. Be able to give common examples and their functions. • Be able to define lipids and to list their functions. • Distinguish between a saturated fat and an unsaturated fat. Why is such a distinction a life and death matter for many people? • A phospholipid has two fatty acid tails attached to a glycerol backbone. What is the importance of these molecules. • Define steroids and describe their chemical structure. Be able to discuss the importance of the steroids known as cholesterol and hormones. • Be able to describe proteins and cite their general functions. • Be prepared to make a sketch and name the three parts of every amino acid. 24
  • 25. • Describe the complex structure of a protein through its primary, secondary, tertiary, and quaternary structure. How does this relate to the three-dimensional structure of proteins? • Describe the three parts of every nucleotide.. • Be able to give the general functions of DNA and RNA molecules.Review Questions 1. The chemical reaction where water is removed during the formation of a covalent bond linking two monomers is known as ___. a) dehydration; b) hydrolysis; c) photosynthesis; d) protein synthesis 2. The monomer that makes up polysaccharides is ____. a) amino acids; b) glucose; c) fatty acids; d) nucleotides; e) glycerol 3. Proteins are composed of which of these monomers? a) amino acids; b) glucose; c) fatty acids; d) nucleotides; e) glycerol 4. Which of these is not a function of lipids? a) long term energy storage; b) structures in cells; c) hormones; d) enzymes; e) sex hormones 5. All living things use the same ___ amino acids. a) 4; b) 20; c) 100; d) 64 6. The sequence of ___ bases determines the ___ structure of a protein. a) RNA, secondary; b) DNA, quaternary; c) DNA, primary; d) RNA, primary 7. Which of these is not a nucleotide base found in DNA? a) uracil; b) adenine; c) guanine; d) thymine; e) cytosine 8. Which of these carbohydrates constitutes the bulk of dietary fiber? a) starch; b) cellulose; c) glucose; d) fructose; e) chitin 9. A diet high in _____ is considered unhealthy, since this type of material is largely found in animal tissues. a) saturated fats; b) testosterone; c) unsaturated fats; d) plant oils 10. The form of RNA that delivers information from DNA to be used in making a protein is ____. a) messenger RNA; b) ribosomal RNA; c) transfer RNA; d) heterogeneous nuclear RNA 11. The energy locked inside an organic molecule is most readily accessible in a ___ molecule. a) fat; b) DNA; c) glucose; d) chitin; e) enzyme 12. Phospholipids are important components in ____. a) cell walls; b) cytoplasm; c) DNA; d) cell membranes; e) cholesterol 25
  • 26. CELLS: ORIGINSOrigin of the Earth and LifeScientific estimates place the origin of the Universe at between 10 and 20 billion years ago. The theory currently with themost acceptance is the Big Bang Theory, the idea that all matter in the Universe existed in a cosmic egg (smaller than thesize of a modern hydrogen atom) that exploded, forming the Universe. Recent discoveries from the Space Telescope andother devices suggest this theory may need some modification. Evidence for the Big Bang includes:1) The Red Shift: when stars/galaxies are moving away from us the energy they emit is shifted to the red side of thevisible-light spectrum. Those moving towards us are shifted to the violet side. This shift is an example of the Dopplereffect. Similar effects are observed when listening to a train whistle-- it will sound higher (shorter wavelengths)approaching and lower (longer wavelengths) as it moves away. Likewise red wavelengths are longer than violet ones.Most galaxies appear to be moving away from ours.2) Background radiation: two Bell Labs scientists discovered that in interstellar space there is a slight backgroundradiation, thought to be the residual after blast remnant of the Big Bang.Soon after the Big Bang the major forces (such as gravity, weak nuclear force, strong nuclear force, etc.) differentiated.While in the cosmic egg, scientists think that matter and energy as we understand them did not exist, but rather theyformed soon after the bang. After 10 million to 1 billion years the universe became clumpy, with matter beginning toaccumulate into solar systems. One of those solar systems, ours, began to form approximately 5 billion years ago, with alarge "protostar" (that became our sun) in the center. The planets were in orbits some distance from the star, theirincreasing gravitational fields sweeping stray debris into larger and larger planetesimals that eventually formed planets.The processes of radioactive decay and heat generated by the impact of planetesimals heated the Earth, which then beganto differentiate into a "cooled" outer cooled crust (of silicon, oxygen and other relatively light elements) and increasinglyhotter inner areas (composed of the heavier and denser elements such as iron and nickel). Impact (asteroid, comet,planetismals) and the beginnings of volcanism released water vapor, carbon dioxide, methane, ammonia and other gasesinto a developing atmosphere. Sometime "soon" after this, life on Earth began.Where did life originate and how?Extra-terrestrial: In 1969, a meteorite (left-over bits from the origin of the solar system) landed near Allende, Mexico.The Allende Meteorite (and others of its sort) have been analyzed and found to contain amino acids, the building blocks ofproteins, one of the four organic molecule groups basic to all life. The idea of panspermia hypothesized that life originatedout in space and came to Earth inside a meteorite. Recently, this idea has been revived as Cosmic Ancestry. The aminoacids recovered from meteorites are in a group known as exotics: they do not occur in the chemical systems of livingthings. The ET theory is now not considered by most scientists to be correct, although the August 1996 discovery of theMartian meteorite and its possible fossils have revived thought of life elsewhere in the Solar System.Supernatural: Since science is an attempt to measure and study the natural world, this theory is outside science (at leastour current understanding of science). Science classes deal with science, and this idea is in the category of not-science.Organic Chemical Evolution: Until the mid-1800s scientists thought organic chemicals (those with a C-C skeleton)could only form by the actions of living things. A French scientist heated crystals of a mineral (a mineral is by definitioninorganic), and discovered that they formed urea (an organic chemical) when they cooled. Russian scientist andacademician A.I. Oparin, in 1922, hypothesized that cellular life was preceded by a period of chemical evolution. Thesechemicals, he argued, must have arisen spontaneously under conditions existing billions of years ago (and quite unlikecurrent conditions). 26
  • 27. In 1950, then-graduate student Stanley Miller designed an experimental test for Oparins hypothesis. Oparins originalhypothesis called for : 1) little or no free oxygen (oxygen not bonded to other elements); and 2) C H O and N inabundance. Studies of modern volcanic eruptions support inference of the existence of such an atmosphere. Millerdischarged an electric spark into a mixture thought to resemble the primordial composition of the atmosphere. From thewater receptacle, designed to model an ancient ocean, Miller recovered amino acids. Subsequent modifications of theatmosphere have produced representatives or precursors of all four organic macromolecular classes.. The primordial Earth was a very different place than today, with greater amounts of energy, stronger storms, etc. The oceans were a "soup" of organic compounds that formed by inorganic processes (although this soup would not taste umm ummm good). Millers (and subsequent) experiments have not proven life originated in this way, only that conditions thought to have existed over 3 billion years ago were such that the spontaneous (inorganic) formation of organic macromolecules could have taken place..The interactions of these molecules would have increased as their concentrations increased. Reactions would have led tothe building of larger, more complex molecules. A pre-cellular life would have began with the formation of nucleic acids.Chemicals made by these nucleic acids would have remained in proximity to the nucleic acids. Eventually the pre-cellswould have been enclosed in a lipid-protein membrane, which would have resulted in the first cells.Biochemically, living systems are separated from other chemical systems by three things. 1. The capacity for replication from one generation to another. Most organisms today use DNA as the hereditary material, although recent evidence (ribosome) suggests that RNA may have been the first nucleic acid system to have formed. Nobel laureate Walter Gilbert refers to this as the RNA world. Recent studies suggest a molecular 2. The presence of enzymes and other complex molecules essential to the processes needed by living systems. Millers experiment showed how these could possibly form. 3. A membrane that separates the internal chemicals from the external chemical environment. This also delimits the cell from not-cell areas. The work of Sidney W. Fox has produced proteinoid spheres, which while not cells, suggest a possible route from chemical to cellular life. 27
  • 28. Fossil evidence supports the origins of life on Earth earlier than 3.5 billion years ago. The North Pole microfossils fromAustralia, are complex enough that more primitive cells must have existed earlier. From rocks of the Ishua Super Group inGreenland come possibly the earliest cells, as much as 3.8 billion years old. The oldest known rocks on Earth are 3.96billion years old and are from Arctic Canada. Thus, life appears to have begun soon after the cooling of the Earth andformation of the atmosphere and oceans.Microfossils from the Apex Chert, North Pole, Australia. These organisms are Archean in age, approximately 3.465 billionyears old, and resemble filamentous cyanobacteria.These ancient fossils occur in marine rocks, such as limestones and sandstones, that formed in ancient oceans. Theorganisms living today that are most similar to ancient life forms are the archaebacteria. This group is today restricted tomarginal environments. Recent discoveries of bacteria at mid-ocean ridges add yet another possible origin for life: at thesemid-ocean ridges where heat and molten rock rise to the Earths surface.Archaea and Eubacteria are similar in size and shape. When we do recover "bacteria" as fossils those are the two featureswe will usually see: size and shape. How can we distinguish between the two groups: the use of molecular fossils that willpoint to either (but not both) groups. Such a chemical fossil has been found and its presence in the Ishua rocks ofGreenland (3.8 billion years old) suggests that the archeans were present at that time.Is there life on Mars, Venus, anywhere else??The proximity of the Earth to the sun, the make-up of the Earths crust (silicate mixtures, presence of water, etc.) and thesize of the Earth suggest we may be unique in our own solar system, at least. Mars is smaller, farther from the sun, has alower gravitational field (which would keep the atmosphere from escaping into space) and does show evidence of runningwater sometime in its past. If life did start on Mars, however, there appears to be no life (as we know it) today. Venus, thesecond planet, is closer to the sun, and appears similar to Earth in many respects. Carbon dioxide build-up has resulted ina "greenhouse planet" with strong storms and strongly acidic rain. Of all planets in the solar system, Venus is most likelyto have some form of carbon-based life. The outer planets are as yet too poorly understood, although it seems unlikely thatJupiter or Saturn harbor life as we know it. Like Goldilocks would say "Venus is too hot, Mars is too cold, the Earth isjust right!" 28
  • 29. Mars: In August 1996, evidence of life on Mars (or at least the chemistry of life), was announced.. The results of years ofstudy are inconclusive at best. The purported bacteria are much smaller than any known bacteria on Earth, were nothollow, and most could possibly have been mineral in origin. However, many scientists consider that the chemistry of lifeappears to have been established on Mars. Search for martian life (or its remains) continues.Terms applied to cellsHeterotroph (other-feeder): an organism that obtains its energy from another organism. Animals, fungi, bacteria, and mantprotistans are heterotrophs.Autotroph (self-feeder): an organism that makes its own food, it converts energy from an inorganic source in one of twoways. Photosynthesis is the conversion of sunlight energy into C-C covalent bonds of a carbohydrate, the process bywhich the vast majority of autotrophs obtain their energy. Chemosynthesis is the capture of energy released by certaininorganic chemical reactions. This is common in certain groups of likely that chemosynthesis predates photosynthesis. Atmid-ocean ridges, scientists have discovered black smokers, vents that release chemicals into the water. These chemicalreactions could have powered early ecosystems prior to the development of an ozone layer that would have permitted lifeto occupy the shallower parts of the ocean. Evidence of the antiquity of photosynthesis includes: a) biochemicalprecursors to photosynthesis chemicals have been synthesized in experiments; and b) when placed in light, thesechemicals undergo chemical reactions similar to some that occur in primitive photosynthetic bacteria.Prokaryotes are among the most primitive forms of life on Earth. Remember that primitive does not necessarily equate tooutdated and unworkable in an evolutionary sense, since primitive bacteria seem little changed, and thus may be viewedas well adapted, for over 3.5 Ga. Prokaryote (pro=before, karyo=nucleus): these organisms lack membrane-boundorganelles. Some internal membrane organization is observable in a few prokaryotic autotrophs, such as thephotosynthetic membranes associated with the photosynthetic chemicals in the photosynthetic bacterium Prochloron..The Cell Theory is one of the foundations of modern biology. Its major tenets are: • All living things are composed of one or more cells; • The chemical reactions of living cells take place within cells; • All cells originate from pre-existing cells; and • Cells contain hereditary information, which is passed from one generation to another. 29
  • 30. Components of CellsCell Membrane (also known as plasma membrane or plasmalemma) is surrounds all cells. It: 1) separates the inner partsof the cell from the outer environment; and 2) acts as a selectively permeable barrier to allow certain chemicals, namelywater, to pass and others to not pass. In multicellular organisms certain chemicals on the membrane surface act in therecognition of self. Antigens are substances located on the outside of cells, viruses and in some cases other chemicals.Antibodies are chemicals (Y-shaped) produced by an animal in response to a specific antigen. This is the basis ofimmunity and vaccination.Hereditary material (both DNA and RNA) is needed for a cell to be able to replicate and/or reproduce. Most organismsuse DNA. Viruses and viroids sometimes employ RNA as their hereditary material. Retroviruses include HIV (HumanImmunodefficiency Virus, the causative agent of AIDS) and Feline Leukemia Virus (the only retrovirus for which asuccessful vaccine has been developed). Viroids are naked pieces of RNA that lack cytoplasm, membranes, etc. They areparasites of some plants and also as possible glimpses of the functioning of pre-cellular life forms. Prokaryotic DNA isorganized as a circular chromosome contained in an area known as a nucleoid. Eukaryotic DNA is organized in linearstructures, the eukaryotic chromosomes, which are associations of DNA and histone proteins contained within a doublemembrane nuclear envelope, an area known as the cell nucleus.Organelles are formed bodies within the cytoplasm that perform certain functions. Some organelles are surrounded bymembranes, we call these membrane-bound organelles.Ribosomes are the tiny structures where proteins synthesis occurs. They are not membrane-bound and occur in all cells,although there are differences between the size of subunits in eukaryotic and prokaryotic ribosomes.The Cell Wall is a structure surrounding the plasma membrane. Prokaryote and eukaryote (if they have one) cell wallsdiffer in their structure and chemical composition. Plant cells have cellulose in their cell walls, other organisms havedifferent materials comprising their walls. Animals are distinct as a group in their lack of a cell wall.Membrane-bound organelles occur only in eukaryotic cells. They will be discussed in detail later. Eukaryotic cells aregenerally larger than prokaryotic cells. Internal complexity is usually greater in eukaryotes, with their compartmentalizedmembrane-bound organelles, than in prokaryotes. Some prokaryotes, such as Anabaena azollae, and Prochloron, haveinternal membranes associated with photosynthetic pigments.The Origins of MulticellularityThe oldest accepted prokaryote fossils date to 3.5 billion years; Eukaryotic fossils to between 750 million years andpossibly as old as 1.2-1.5 billion years. Multicellular fossils, purportedly of animals, have been recovered from 750Marocks in various parts of the world. The first eukaryotes were undoubtedly Protistans, a group that is thought to have givenrise to the other eukaryotic kingdoms. Multicellularity allows specialization of function, for example muscle fibers arespecialized for contraction, neuron cells for transmission of nerve messages.MicroscopesMicroscopes are important tools for studying cellular structures. In this class we will use light microscopes for ourlaboratory observations. Your text will also show light photomicrographs (pictures taken with a light microscope) andelectron micrographs (pictures taken with an electron microscope). There are many terms and concepts which will helpyou in maximizing your study of microscopy.There are many different types of microscopes used in studying biology. These include the light microscopes (dissecting,compound brightfield, and compound phase-contrast), electron microscopes (transmission and scanning), and atomicforce microscope. 30
  • 31. The microscope is an important tool used by biologists to magnify small objects. There are several concepts fundamentalto microscopy.Magnification is the ratio of enlargement (or eduction) between the specimen and its image (either printed photograph orthe virtual image seen through the eyepiece). To calculate magnification we multiply the power of each lens throughwhich the light from the specimen passes, indicating that product as GGGX, where GGG is the product. For example: ifthe light passes through two,lenses (an objective lens and an ocular lens) we multiply the 10X ocular value by the value ofthe objective lens (say it is 4X): 10 X 4=40, or 40X magnification.Resolution is the ability to distinguish between two objects (or points). The closer the two objects are, the easier it is todistinguish recognize the distance between them. What microscopes do is to bring small objects "closer" to the observerby increasing the magnification of the sample. Since the sample is the same distance from the viewer, a "virtual image" isformed as the light (or electron beam) passes through the magnifying lenses. Objects such as a human hair appear smooth(and feel smooth) when viewed with the unaided or naked) eye. However, put a hair under a microscope and it takes on aVERY different look!Working distance is the distance between the specimen and the magnifying lens.Depth of field is a measure of the amount of a specimen that can be in focus.Magnification and resolution are terms used frequently in the study of cell biology, often without an accurate definition oftheir meanings. Magnification is a ratio of the enlargement (or reduction) of an image (drawing or photomicrograph),usually expressed as X1, X1/2, X430, X1000, etc. Resolution is the ability to distinguish between two points. Generallyresolution increases with magnification, although there does come a point of diminishing returns where you increasemagnification beyond added resolution gain.Scientists employ the metric system to measure the size and volume of specimens. The basic unit of length is the meter(slightly over 1 yard). Prefixes are added to the "meter" to indicate multiple meters (kilometer) or fractional meters(millimeter). Below are the values of some of the prefixes used in the metric system. kilo = one thousand of the basic unit meter = basic unit of length centi = one hundreth (1/100) of the basic unit milli = one thousandth (1/1000) of the basic unit micro = one millionth (1/1,000,000) of the basic unit nano = one billionth (1/1,000,000,000) of the basic unitThe basic unit of length is the meter (m), and of volume it is the liter (l). The gram (g). Prefixes listed above can beapplied to all of these basic units, abbreviated as km, kg, ml, mg, nm....etc. The Greek letter micron (µ) is applied to smallmeasurements (thousandths of a millimeter), producing the micrometer (symbolized as µm). Measurements in microscopyare usually expressed in the metric system. General units you will encounter in your continuing biology careers includemicrometer (µm, 10-6m), nanometer (nm, 10-9m), and angstrom (Å, 10-10m).Light microscopes were the first to be developed, and still the most commonly used ones. The best resolution of lightmicroscopes (LM) is 0.2 µm. Magnification of LMs is generally limited by the properties of the glass used to makemicroscope lenses and the physical properties of their light sources. The generally accepted maximum magnifications inbiological uses are between 1000X and 1250X. Calculation of LM magnification is done by multiplying objective valueby eyepiece value.The compound light microscope, uses two ground glass lenses to form the image. The lenses in this microscope, however,are aligned with the light source and specimen so that the light passes through the specimen, rather than reflects off thesurface. The compound microscope provides greater magnification (and resolution), but only thin specimens (or thinslices of a specimen) can be viewed with this type of microscope. 31
  • 32. Parts of a Nikon compound microscope. Image courtesy of Nikon Co.Electron microscopes, are more rarely encountered by beginning biology students. However, the images gathered fromthese microscopes reveal a greater structure of the cell, so some familiarity with the strengths and weaknesses of each typeis useful. Instead of using light as an imaging source, a high energy beam of electrons (between five thousand and onebillion electron volts) is focused through electromagnetic lenses (instead of glass lenses used in the light microscope). Theincreased resolution results from the shorter wavelength of the electron beam, increasing resolution in the transmissionelectron microscope (TEM) to a theoretical limit of 0.2 nm. The magnifications reached by TEMs are commonly over100,000X, depending on the nature of the sample and the operating condition of the TEM. The other type of electronmicroscope is the scanning electron microscope (SEM). It uses a different method of electron capture and displays imageson high resolution television monitors. The resolution and magnification of the SEM are less than that of the TEMalthough still orders of magnitude above the LM.Learning Objectives • Describe the major scientific ideas on the origin of life and the evidence supporting each one. • List the basic physical and biological requirements for life. What planet(s) would these be available on? • Be able to cite the main components of the Cell Theory. • What did Millers experiment prove? What did it NOT prove? How does this experiment fit with each of the hypotheses of the origin of life discussed here? • Describe these basic cellular features and their functions: plasma membrane, cytoplasm, and nucleus (nucleoid in prokaryotes). • A micrometer is one-millionth of a meter long. A nanometer is one-billionth of a meter long. • Describe the basic structure of prokaryotic cells and cite an example of these cells. • Describe the types of microscopes and the types of information scientists can obtain using each one. 32
  • 33. Review Questions 1. Which of these is not a type of cell? a) bacterium; b) amoeba; c) sperm; d) virus 2. The Earths early atmosphere apparently lacked ___. a) oxygen; b) carbon dioxide; c) water vapor; d) ammonia 3. The oldest fossil forms of life are most similar to _____. a) animals; b) modern bacteria; c) archaebacteria; d) fungi 4. A prokaryotic cell would not have which of these structures? a) ribosome; b) nucleus; c) cell membrane; d) cell wall 5. Heterotrophic organisms obtain their food ____. a) from another creature; b) by photosynthesis; c) by chemical synthesis; d) by ATP synthesis. 6. Ribosomes are cellular structures involved in ____. a) photosynthesis; b) chemosynthesis; c) protein synthesis; d) carbohydrate synthesis 7. The earliest microscopes used _____ to image the specimens. a) high energy electron beams; b) interatomic forces; c) low energy electron beams; d) light 33
  • 34. CELLS II: CELLULAR ORGANIZATIONLife exhibits varying degrees of organization. Atoms are organized into molecules, molecules into organelles, andorganelles into cells, and so on. According to the Cell Theory, all living things are composed of one or more cells, and thefunctions of a multicellular organism are a consequence of the types of cells it has. Cells fall into two broad groups:prokaryotes and eukaryotes. Prokaryotic cells are smaller (as a general rule) and lack much of the internalcompartmentalization and complexity of eukaryotic cells. No matter which type of cell we are considering, all cells havecertain features in common, such as a cell membrane, DNA and RNA, cytoplasm, and ribosomes. Eukaryotic cells have agreat variety of organelles and structures.Cell Size and ShapeThe shapes of cells are quite varied with some, such as neurons, being longer than they are wide and others, such asparenchyma (a common type of plant cell) and erythrocytes (red blood cells) being equidimensional. Some cells areencased in a rigid wall, which constrains their shape, while others have a flexible cell membrane (and no rigid cell wall).The size of cells is also related to their functions. Eggs (or to use the latin word, ova) are very large, often being thelargest cells an organism produces. The large size of many eggs is related to the process of development that occurs afterthe egg is fertilized, when the contents of the egg (now termed a zygote) are used in a rapid series of cellular divisions,each requiring tremendous amounts of energy that is available in the zygote cells. Later in life the energy must beacquired, but at first a sort of inheritance/trust fund of energy is used.Cells range in size from small bacteria to large, unfertilized eggs laid by birds and dinosaurs. In science we use the metricsystem for measuring. Here are some measurements and conversions that will aid your understanding of biology.1 meter = 100 cm = 1,000 mm = 1,000,000 µm = 1,000,000,000 nm1 centimeter (cm) = 1/100 meter = 10 mm1 millimeter (mm) = 1/1000 meter = 1/10 cm1 micrometer (µm) = 1/1,000,000 meter = 1/10,000 cm1 nanometer (nm) = 1/1,000,000,000 meter = 1/10,000,000 cm 34
  • 35. The Cell MembraneThe cell membrane functions as a semi-permeable barrier, allowing a very few molecules across it while fencing themajority of organically produced chemicals inside the cell. Electron microscopic examinations of cell membranes haveled to the development of the lipid bilayer model (also referred to as the fluid-mosaic model). The most common moleculein the model is the phospholipid, which has a polar (hydrophilic) head and two nonpolar (hydrophobic) tails. Thesephospholipids are aligned tail to tail so the nonpolar areas form a hydrophobic region between the hydrophilic heads onthe inner and outer surfaces of the membrane. This layering is termed a bilayer since an electron microscopic techniqueknown as freeze-fracturing is able to split the bilayer.Cholesterol is another important component of cell membranes embedded in the hydrophobic areas of the inner (tail-tail)region. Most bacterial cell membranes do not contain cholesterol. Cholesterol aids in the flexibility of a cell membrane.Proteins, are suspended in the inner layer, although the more hydrophilic areas of these proteins "stick out" into the cellsinterior as well as outside the cell. These proteins function as gateways that will allow certain molecules to cross into andout of the cell by moving through open areas of the protein channel. These integral proteins are sometimes known asgateway proteins. The outer surface of the membrane will tend to be rich in glycolipids, which have their hydrophobictails embedded in the hydrophobic region of the membrane and their heads exposed outside the cell. These, along withcarbohydrates attached to the integral proteins, are thought to function in the recognition of self, a sort of cellularidentification system.The contents (both chemical and organelles) of the cell are termed protoplasm, and are further subdivided into cytoplasm(all of the protoplasm except the contents of the nucleus) and nucleoplasm (all of the material, plasma and DNA etc.,within the nucleus).The Cell WallNot all living things have cell walls, most notably animals and many of the more animal-like protistans. Bacteria have cellwalls containing the chemical peptidoglycan. Plant cells, have a variety of chemicals incorporated in their cell walls.Cellulose, a nondigestible (to humans anyway) polysaccharide is the most common chemical in the plant primary cellwall. Some plant cells also have lignin and other chemicals embedded in their secondary walls.The cell wall is located outside the plasma membrane. Plasmodesmata are connections through which cells communicatechemically with each other through their thick walls. Fungi and many protists have cell walls although they do not containcellulose, rather a variety of chemicals (chitin for fungi).The nucleusThe nucleus, occurs only in eukaryotic cells. It is the location for most of the nucleic acids a cell makes, such as DNAand RNA. Danish biologist Joachim Hammerling carried out an important experiment in 1943. His work showed the roleof the nucleus in controlling the shape and features of the cell. Deoxyribonucleic acid, DNA, is the physical carrier ofinheritance and with the exception of plastid DNA (cpDNA and mDNA, found in the chloroplast and mitochondrionrespectively) all DNA is restricted to the nucleus. Ribonucleic acid, RNA, is formed in the nucleus using the DNA basesequence as a template. RNA moves out into the cytoplasm where it functions in the assembly of proteins. The nucleolusis an area of the nucleus (usually two nucleoli per nucleus) where ribosomes are constructed.Structure of the nucleus. Note the chromatin, uncoiled DNA that occupies the space within the nuclear envelope. 35
  • 36. The nuclear envelope, is a double-membrane structure. Numerous pores occur in the envelope, allowing RNA and otherchemicals to pass, but the DNA not to pass.Structure of the nuclear envelope and nuclear pores.CytoplasmThe cytoplasm was defined earlier as the material between the plasma membrane (cell membrane) and the nuclearenvelope. Fibrous proteins that occur in the cytoplasm, referred to as the cytoskeleton maintain the shape of the cell aswell as anchoring organelles, moving the cell and controlling internal movement of structures. Microtubules function incell division and serve as a "temporary scaffolding" for other organelles. Actin filaments are thin threads that function incell division and cell motility. Intermediate filaments are between the size of the microtubules and the actin filaments.Vacuoles and vesiclesVacuoles are single-membrane organelles that are essentially part of the outside that is located within the cell. The singlemembrane is known in plant cells as a tonoplast. Many organisms will use vacuoles as storage areas. Vesicles are muchsmaller than vacuoles and function in transporting materials both within and to the outside of the cell.Ribosomes 36
  • 37. Ribosomes are the sites of protein synthesis. They are not membrane-bound and thus occur in both prokaryotes and eukaryotes. Eukaryotic ribosomes are slightly larger than prokaryotic ones. Structurally, the ribosome consists of a small and larger subunit. Biochemically, the ribosome consists of ribosomal RNA (rRNA) and some 50 structural proteins. Often ribosomes cluster on the endoplasmic reticulum, in which case they resemble a series of factories adjoining a railroad line. Endoplasmic reticulumEndoplasmic reticulum, is a mesh of interconnected membranes that serve a function involving protein synthesis andtransport. Rough endoplasmic reticulum (Rough ER) is so-named because of its rough appearance due to the numerousribosomes that occur along the ER. Rough ER connects to the nuclear envelope through which the messenger RNA(mRNA) that is the blueprint for proteins travels to the ribosomes. Smooth ER; lacks the ribosomes characteristic ofRough ER and is thought to be involved in transport and a variety of other functions. Golgi Apparatus and Dictyosomes Golgi Complexes, are flattened stacks of membrane-bound sacs. Italian biologist Camillo Golgi discovered these structures in the late 1890s, although their precise role in the cell was not deciphered until the mid-1900s . Golgi function as a packaging plant, modifying vesicles produced by the rough endoplasmic reticulum. New membrane material is assembled in various cisternae (layers) of the golgi. Lysosomes Lysosomes, are relatively large vesicles formed by the Golgi. They contain hydrolytic enzymes that could destroy the cell. Lysosome contents function in the extracellular breakdown of materials. They are commonly known in the cell as the suicide sac.MitochondriaMitochondria contain their own DNA (termed mDNA) and are thought to represent bacteria-like organisms incorporatedinto eukaryotic cells over 700 million years ago (perhaps even as far back as 1.5 billion years ago). They function as the sites of energy release (following glycolysis in the cytoplasm) and ATP formation (by chemiosmosis). The mitochondrion has been termed the powerhouse of the cell. Mitochondria are bounded by two membranes. The inner membrane folds into a series of cristae, which are the surfaces on which adenosine triphosphate (ATP) is generated. The matrix is the 37
  • 38. area of the mitochondrion surrounded by the inner mitochondrial membrane. Ribosomes and mitochondrial DNA arefound in the matrix. The significance of these features will be discussed below..Mitochondria and endosymbiosisDuring the 1980s, Lynn Margulis proposed the theory of endosymbiosis to explain the origin of mitochondria andchloroplasts from permanent resident prokaryotes.According to this idea, a larger prokaryote (or perhapsearly eukaryote) engulfed or surrounded a smallerprokaryote some 1.5 billion to 700 million years ago..Instead of digesting the smaller organisms the largeone and the smaller one entered into a type ofsymbiosis known as mutualism, wherein bothorganisms benefit and neither is harmed. The larger organism gained excess ATP provided by the "protomitochondrion"and excess sugar provided by the "protochloroplast", while providing a stable environment and the raw materials theendosymbionts required. This is so strong that now eukaryotic cells cannot survive without mitochondria (likewisephotosynthetic eukaryotes cannot survive without chloroplasts), and the endosymbionts can not survive outside theirhosts. Nearly all eukaryotes have mitochondria. Mitochondrial division is remarkably similar to the prokaryotic methodsthat will be studied later in this course.PlastidsPlastids are also membrane-bound organelles that only occur in plants and photosynthetic eukaryotes. Leucoplasts, alsoknown as amyloplasts store starch, as well as sometimes protein or oils. Chromoplasts store pigments associated with thebright colors of flowers and/or fruits.Chloroplasts, are the sites of photosynthesis in eukaryotes. They contain chlorophyll, thegreen pigment necessary for photosynthesis to occur, and associated accessory pigments(carotenes and xanthophylls) in photosystems embedded in membranous sacs, thylakoids(collectively a stack of thylakoids are a granum [plural = grana) floating in a fluid termedthe stroma. Chloroplasts contain many different types of accessory pigments, dependingon the taxonomic group of the organism being observed.Chloroplasts and endosymbiosisLike mitochondria, chloroplasts have their own DNA, termed cpDNA. Chloroplasts of Green Algae (Protista) and Plants(descendants of some of the Green Algae) are thought to have originated by endosymbiosis of a prokaryotic alga similarto living Prochloron (the sole genus present in the Prochlorobacteria,). Chloroplasts of Red Algae (Protista) are verysimilar biochemically to cyanobacteria (also known as blue-green bacteria [algae to chronologically enhanced folks likemyself :)]). Endosymbiosis is also invoked for this similarity, perhaps indicating more than one endosymbiotic eventoccurred.Cell MovementCell movement; is both internal, referred to as cytoplasmic streaming, and external, referred to as motility. Internalmovements of organelles are governed by actin filaments and other components of the cytoskeleton. These filamentsmake an area in which organelles such as chloroplasts can move. Internal movement is known as cytoplasmic streaming.External movement of cells is determined by special organelles for locomotion. 38
  • 39. The cytoskeleton is a network of connected filaments and tubules. It extends from the nucleus to the plasma membrane.Electron microscopic studies showed the presence of an organized cytoplasm. Immunofluorescence microscopy identifiesprotein fibers as a major part of this cellular feature. The cytoskeleton components maintain cell shape and allow the celland its organelles to move.Actin filaments, are long, thin fibers approximately seven nm in diameter. These filaments occur in bundles or meshlikenetworks. These filaments are polar, meaning there are differences between the ends of the strand. An actin filamentconsists of two chains of globular actin monomers twisted to form a helix. Actin filaments play a structural role, forming adense complex web just under the plasma membrane. Actin filaments in microvilli of intestinal cells act to shorten the celland thus to pull it out of the intestinal lumen. Likewise, the filaments can extend the cell into intestine when food is to beabsorbed. In plant cells, actin filaments form tracts along which chloroplasts circulate.Actin filaments move by interacting with myosin, The myosin combines with and splits ATP, thus binding to actin andchanging the configuration to pull the actin filament forward. Similar action accounts for pinching off cells during celldivision and for amoeboid movement.Intermediate filaments are between eight and eleven nm in diameter. They are between actin filaments and microtubulesin size. The intermediate fibers are rope-like assemblies of fibrous polypeptides. Some of them support the nuclearenvelope, while others support the plasma membrane, form cell-to-cell junctions.Microtubules are small hollow cylinders (25 nm in diameter and from 200 nm-25 µm in length). These microtubules arecomposed of a globular protein tubulin. Assembly brings the two types of tubulin (alpha and beta) together as dimers,which arrange themselves in rows.In animal cells and most protists, a structure known as a centrosome occurs. The centrosome contains two centrioles lyingat right angles to each other. Centrioles are short cylinders with a 9 + 0 pattern of microtubule triplets. Centrioles serve asbasal bodies for cilia and flagella. Plant and fungal cells have a structure equivalent to a centrosome, although it does notcontain centrioles.Cilia are short, usually numerous, hairlike projections that can move in an undulating fashion (e.g., the protzoanParamecium, the cells lining the human upper respiratory tract). Flagella are longer, usually fewer in number, projectionsthat move in whip-like fashion (e.g., sperm cells). Cilia and flagella are similar except for length, cilia being much shorter.They both have the characteristic 9 + 2 arrangement of microtubules.Cilia from an epithelial cell in cross section (TEM x199,500). Note the 9 + 2 arrangement of cilia. 39
  • 40. Cilia and flagella move when the microtubules slide past one another. Both of these locomotion structures have a basalbody at base with thesame arrangement of microtubule triples as centrioles. Cilia and flagella grow by the addition oftubulin dimers to their tips.Flagella work as whips pulling (as inChlamydomonas or Halosphaera) orpushing (dinoflagellates, a group ofsingle-celled Protista) the organismthrough the water. Cilia work like oars ona viking longship (Paramecium has17,000 such oars covering its outersurface).Not all cells use cilia or flagella formovement. Some, such as Amoeba, Chaos(Pelomyxa) and human leukocytes (whiteblood cells), employ pseudopodia to movethe cell. Unlike cilia and flagella,pseudopodia are not structures, but ratherare associated with actin near the movingedge of the cell..Learning Objectives • Give the function and cellular location of the following basic eukaryotic organelles and structures: cell membrane, nucleus, endoplasmic reticulum, Golgi bodies, lysosomes, mitochondria, ribosomes, chloroplasts, vacuoles, and cell walls. • A micrometer is one-millionth of a meter long. A nanometer is one-billionth of a meter long. How many micrometers tall are you? • Describe the function of the nuclear envelope and nucleolus. • Describe the details of the structure of the chloroplast, the site of photosynthesis. • Mature, living plant cells often have a large, fluid-filled central vacuole that can store amino acids, sugars, ions, and toxic wastes. Animal cells generally lack large vacuoles. How do animal cells perform these functions? • Microtubules, microfilaments, and intermediate filaments are all main components of the cytoskeleton. • Flagella and cilia propel eukaryotic cells through their environment; the microtubule organization in these organelles is a 9+2 array.Review Questions 1. There are ____ micrometers (µm) in one millimeter (mm). a) 1; b) 10; c) 100; d) 1000; e) 1/1000 2. Human cells have a size range between ___ and ___ micrometers (µm). a) 10-100; b) 1-10; c) 100-1000; d) 1/10-1/1000 3. Chloroplasts and bacteria are ___ in size. a) similar; b) at different ends of the size range; c) exactly the same; d) none of these. 4. The plasma membrane does all of these except ______. a) contains the hereditary material; b) acts as a boundary or border for the cytoplasm; c) regulates passage of material in and out of the cell; d) functions in the recognition of self 5. Which of these materials is not a major component of the plasma membrane? a) phospholipids; b) glycoproteins; c) proteins; d) DNA 6. Cells walls are found in members of these kingdoms, except for ___, which all lack cell walls. a) plants; b) animals; c) bacteria; d) fungi 7. The polysaccharide ___ is a major component of plan cell walls. a) chitin; b) peptidoglycan; c) cellulose; d) mannitol; e) cholesterol 40
  • 41. 8. Plant cells have ___ and ___, which are not present in animal cells. a) mitochondria, chloroplasts; b) cell membranes, cell walls; c) chloroplasts, nucleus; d) chloroplasts, cell wall9. The ___ is the membrane enclosed structure in eukaryotic cells that contains the DNA of the cell. a) mitochondrion; b) chloroplast; c) nucleolus; d) nucleus10. Ribosomes are constructed in the ___. a) endoplasmic reticulum; b) nucleoid; c) nucleolus; d) nuclear pore11. Rough endoplasmic reticulum is the area in a cell where ___ are synthesized. a) polysaccharides; b) proteins; c) lipids; d) DNA12. The smooth endoplasmic reticulum is the area in a cell where ___ are synthesized. a) polysaccharides; b) proteins; c) lipids; d) DNA13. The mitochondrion functions in ____. a) lipid storage; b) protein synthesis; c) photosynthesis; d) DNA replication; e) ATP synthesis14. The thin extensions of the inner mitochondrial membrane are known as _____. a) cristae; b) matrix; c) thylakoids; d) stroma15. The chloroplast functions in ____. a) lipid storage; b) protein synthesis; c) photosynthesis; d) DNA replication; e) ATP synthesis16. Which of these cellular organelles have their own DNA? a) chloroplast; b) nucleus; c) mitochondrion; d) all of these17. The theory of ___ was proposed to explain the possible origin of chloroplasts and mitochondria. a) evolution; b) endosymbiosis; c) endocytosis; d) cells18. Long, whiplike microfibrils that facilitate movement by cells are known as ___. a) cilia; b) flagella; c) leather; d) pseudopodia 41
  • 42. TRANSPORT IN AND OUT OF CELLSWater and Solute MovementCell membranes act as barriers to most, but not all, molecules. Development of a cell membrane that could allow somematerials to pass while constraining the movement of other molecules was a major step in the evolution of the cell. Cellmembranes are differentially (or semi-) permeable barriers separating the inner cellular environment from the outercellular (or external) environment.Water potential is the tendency of water to move from an area of higher concentration to one of lower concentration.Energy exists in two forms: potential and kinetic. Water molecules move according to differences in potential energybetween where they are and where they are going. Gravity and pressure are two enabling forces for this movement. Theseforces also operate in the hydrologic (water) cycle. Remember in the hydrologic cycle that water runs downhill (likewiseit falls from the sky, to get into the sky it must be acted on by the sun and evaporated, thus needing energy input to powerthe cycle).Diffusion is the net movement of a substance (liquid or gas) from an area of higher concentration to one of lowerconcentration. You are on a large (10 ft x 10 ft x10 ft) elevator. An obnoxious individual with a lit cigar gets on at thethird floor with the cigar still burning. You are also unfortunate enough to be in a very tall building and the person says"Hey were both going to the 62nd floor!" Disliking smoke you move to the farthest corner you can. Eventually you areunable to escape the smoke! An example of diffusion in action. Nearer the source the concentration of a given substanceincreases. You probably experience this in class when someone arrives freshly doused in perfume or cologne, especiallythe cheap stuff.Since the molecules of any substance (solid, liquid, or gas) are in motion when that substance is above absolute zero (0degrees Kelvin or -273 degrees C), energy is available for movement of the molecules from a higher potential state to alower potential state, just as in the case of the water discussed above. The majority of the molecules move from higher tolower concentration, although there will be some that move from low to high. The overall (or net) movement is thus fromhigh to low concentration. Eventually, if no energy is input into the system the molecules will reach a state of equilibriumwhere they will be distributed equally throughout the system. 42
  • 43. The Cell MembraneThe cell membrane functions as a semi-permeable barrier, allowing a very few molecules across it while fencing themajority of organically produced chemicals inside the cell. Electron microscopic examinations of cell membranes haveled to the development of the lipid bilayer model (also referred to as the fluid-mosaic model). The most common moleculein the model is the phospholipid, which has a polar (hydrophilic) head and two nonpolar (hydrophobic) tails. Thesephospholipids are aligned tail to tail so the nonpolar areas form a hydrophobic region between the hydrophilic heads onthe inner and outer surfaces of the membrane. This layering is termed a bilayer since an electron microscopic techniqueknown as freeze-fracturing is able to split the bilayer.Phospholipids and glycolipids are important structural components of cell membranes. Phospholipids are modified so thata phosphate group (PO4-) replaces one of the three fatty acids normally found on a lipid. The addition of this group makesa polar "head" and two nonpolar "tails".Structure of a phospholipid, space-filling model (left) and chain model (right). 43
  • 44. Diagram of a cell membrane.Cell Membranes from Opposing Neurons (TEM x436,740). 44
  • 45. Cholesterol is another important component of cell membranes embedded in the hydrophobic areas of the inner (tail-tail)region. Most bacterial cell membranes do not contain cholesterol.Proteins are suspended in the inner layer, although the more hydrophilic areas of these proteins "stick out" into the cellsinterior as well as the outside of the cell. These integral proteins are sometimes known as gateway proteins. Proteins alsofunction in cellular recognition, as binding sites for substances to be brought into the cell, through channels that will allowmaterials into the cell via a passive transport mechanism, and as gates that open and close to facilitate active transport oflarge molecules.The outer surface of the membrane will tend to be rich in glycolipids, which have their hydrophobic tails embedded in thehydrophobic region of the membrane and their heads exposed outside the cell. These, along with carbohydrates attachedto the integral proteins, are thought to function in the recognition of self. Multicellular organisms may have somemechanism to allow recognition of those cells that belong to the organism and those that are foreign. Many, but not all,animals have an immune system that serves this sentry function. When a cell does not display the chemical markers thatsay "Made in Mike", an immune system response may be triggered. This is the basis for immunity, allergies, andautoimmune diseases. Organ transplant recipients must have this response suppressed so the new organ will not beattacked by the immune system, which would cause rejection of the new organ. Allergies are in a sense an over reactionby the immune system. Autoimmune diseases, such as rheumatoid arthritis and systemic lupus erythmatosis, happen whenfor an as yet unknown reason, the immune system begins to attack certain cells and tissues in the body.Cells and DiffusionWater, carbon dioxide, and oxygen are among the few simple molecules that can cross the cell membrane by diffusion (ora type of diffusion known as osmosis ). Diffusion is one principle method of movement of substances within cells, as wellas the method for essential small molecules to cross the cell membrane. Gas exchange in gills and lungs operates by thisprocess. Carbon dioxide is produced by all cells as a result of cellular metabolic processes. Since the source is inside thecell, the concentration gradient is constantly being replenished/re-elevated, thus the net flow of CO2 is out of the cell.Metabolic processes in animals and plants usually require oxygen, which is in lower concentration inside the cell, thus thenet flow of oxygen is into the cell.Osmosis is the diffusion of water across a semi-permeable (or differentially permeable or selectively permeable)membrane. The cell membrane, along with such things as dialysis tubing and cellulose acetate sausage casing, is such amembrane. The presence of a solute decreases the water potential of a substance. Thus there is more water per unit ofvolume in a glass of fresh-water than there is in an equivalent volume of sea-water. In a cell, which has so manyorganelles and other large molecules, the water flow is generally into the cell.Hypertonic solutions are those in which more solute(and hence lower water potential) is present.Hypotonic solutions are those with less solute (againread as higher water potential). Isotonic solutions haveequal (iso-) concentrations of substances. Waterpotentials are thus equal, although there will still beequal amounts of water movement in and out of thecell, the net flow is zero.Water relations and cell shape in blood cells. 45
  • 46. One of the major functions of blood in animals is the maintain an isotonic internal environment. This eliminates theproblems associated with water loss or excess water gain in orout of cells. Again we return to homeostasis. Parameciumand other single-celled freshwater organisms have difficultysince they are usually hypertonic relative to their outsideenvironment. Thus water will tend to flow across the cellmembrane, swelling the cell and eventually bursting it. Notgood for any cell! The contractile vacuole is theParameciums response to this problem. The pumping ofwater out of the cell by this method requires energy since thewater is moving against the concentration gradient. Sinceciliates (and many freshwater protozoans) are hypotonic,removal of water crossing the cell membrane by osmosis is asignificant problem. One commonly employed mechanism is a contractile vacuole. Water is collected into the central ringof the vacuole and actively transported from the cell.Active and Passive Transport Passive transport requires no energy from the cell. Examples include the diffusion of oxygen and carbon dioxide, osmosis of water, and facilitated diffusion. Active transport requires the cell to spend energy, usually in the form of ATP. Examples include transport of large molecules (non-lipid soluble) and the sodium-potassium pump.Carrier-assisted TransportThe transport proteins integrated into the cell membrane are often highly selective about the chemicals they allow to cross.Some of these proteins can move materials across the membrane only when assisted by the concentration gradient, a typeof carrier-assisted transport known as facilitated diffusion. Both diffusion and facilitated diffusion are driven by thepotential energy differences of a concentration gradient. Glucoseenters most cells by facilitated diffusion. There seem to be alimiting number of glucose-transporting proteins. The rapidbreakdown of glucose in the cell (a process known as glycolysis)maintains the concentration gradient. When the externalconcentration of glucose increases, however, the glucose transportdoes not exceed a certain rate, suggesting the limitation ontransport.In the case of active transport, the proteins are having to moveagainst the concentration gradient. For example the sodium-potassium pump in nerve cells. Na+ is maintained at lowconcentrations inside the cell and K+ is at higher concentrations.The reverse is the case on the outside of the cell. When a nerve message is propagated, the ions pass across the membrane,thus sending the message. After the message has passed, the ions must be actively transported back to their "startingpositions" across the membrane. This is analogous to setting up 100 dominoes and then tipping over the first one. To resetthem you must pick each one up, again at an energy cost. Up to one-third of the ATP used by a resting animal is used toreset the Na-K pump. 46
  • 47. Types of transport molecules |Uniport transports one solute at a time. Symport transports the solute and a cotransported solute at the same time in thesame direction. Antiport transports the solute in (or out) and the co-transported solute the opposite direction. One goes inthe other goes out or vice-versa.Vesicle-mediated transportVesicles and vacuoles that fuse with the cell membrane may be utilized to release or transport chemicals out of the cell orto allow them to enter a cell. Exocytosis is the term applied when transport is out of the cell.Endocytosis is the case when a molecule causes the cell membrane to bulge inward, forming a vesicle. Phagocytosis is thetype of endocytosis where an entire cell is engulfed. Pinocytosis is when the external fluid is engulfed. Receptor-mediatedendocytosis occurs when the material to be transported binds to certain specific molecules in the membrane. Examplesinclude the transport of insulin and cholesterol into animal cells.Learning Objectives • Materials are exchanged between the cytoplasm and external cell environment across the plasma membrane by several different processes, some require energy, some do not.. • Describe the general structure of a phospholipid molecule and what makes it suitable as a major component of cell membranes. • Explain the behavior of a great number of phospholipid molecules in water. • Describe the most recent version of the fluid mosaic model of membrane structure. • Molecules moving to regions where they are less concentrated are moving down their concentration gradient. • Random movement of like molecules or ions down a concentration gradient is called simple diffusion. • When salt is dissolved in water, which is the solute and which is the solvent? • Explain osmosis in terms of a differentially permeable membrane. • Define tonicity and be able to use the terms isotonic, hypertonic, and hypotonic. • When water moves into a plant cell by osmosis, the internal turgor pressure developed pushes on the wall. What does this do to your understanding of a neglected houseplant? 47
  • 48. CELL DIVISION: BINARY FISSION AND MITOSISThe Cell CycleDespite differences between prokaryotes and eukaryotes, there are several common features in their cell divisionprocesses. Replication of the DNA must occur. Segregation of the "original" and its "replica" follow. Cytokinesis ends thecell division process. Whether the cell was eukaryotic or prokaryotic, these basic events must occur.Cytokinesis is the process where one cell splits off from its sister cell. It usually occurs after cell division. The Cell Cycleis the sequence of growth, DNA replication, growth and cell division that all cells go through. Beginning after cytokinesis,the daughter cells are quite small and low on ATP. They acquire ATP and increase in size during the G1 phase ofInterphase. Most cells are observed in Interphase, the longest part of the cell cycle. After acquiring sufficient size andATP, the cells then undergo DNA Synthesis (replication of the original DNA molecules, making identical copies, one"new molecule" eventually destined for each new cell) which occurs during the S phase. Since the formation of new DNAis an energy draining process, the cell undergoes a second growth and energy acquisition stage, the G2 phase. The energyacquired during G2 is used in cell division (in this case mitosis).The cell cycle.Regulation of the cell cycle is accomplished in several ways. Some cells divide rapidly (beans, for example take 19 hoursfor the complete cycle; red blood cells must divide at a rate of 2.5 million per second). Others, such as nerve cells, losetheir capability to divide once they reach maturity. Some cells, such as liver cells, retain but do not normally utilize theircapacity for division. Liver cells will divide if part of the liver is removed. The division continues until the liver reachesits former size.Cancer cells are those which undergo a series of rapid divisions such that the daughter cells divide before they havereached "functional maturity". Environmental factors such as changes in temperature and pH, and declining nutrient levelslead to declining cell division rates. When cells stop dividing, they stop usually at a point late in the G1 phase, the R point(for restriction). 48
  • 49. Prokaryotic Cell DivisionProkaryotes are much simpler in their organization than are eukaryotes. There are a great many more organelles ineukaryotes, also more chromosomes. The usual method of prokaryote cell division is termed binary fission. Theprokaryotic chromosome is a single DNA molecule that first replicates, then attaches each copy to a different part of thecell membrane. When the cell begins to pull apart, the replicate and original chromosomes are separated. Following cellsplitting (cytokinesis), there are then two cells of identical genetic composition (except for the rare chance of aspontaneous mutation).The prokaryote chromosome is much easier to manipulate than the eukaryotic one. We thus know much more about thelocation of genes and their control in prokaryotes.One consequence of this asexual method of reproduction is that all organisms in a colony are genetic equals. Whentreating a bacterial disease, a drug that kills one bacteria (of a specific type) will also kill all other members of that clone(colony) it comes in contact with.Eukaryotic Cell DivisionDue to their increased numbers of chromosomes, organelles and complexity, eukaryote cell division is more complicated,although the same processes of replication, segregation, and cytokinesis still occur.MitosisMitosis is the process of forming (generally) identical daughter cells by replicating and dividing the originalchromosomes, in effect making a cellular xerox. Commonly the two processes of cell division are confused. Mitosis dealsonly with the segregation of the chromosomes and organelles into daughter cells.Eukaryotic chromosomes occur in the cell in greater numbers than prokaryotic chromosomes. The condensed replicatedchromosomes have several points of interest. The kinetochore is the point where microtubules of the spindle apparatusattach. Replicated chromosomes consist of two molecules of DNA (along with their associated histone proteins) known aschromatids. The area where both chromatids are in contact with each other is known as the centromere the kinetochoresare on the outer sides of the centromere. Remember that chromosomes are condensed chromatin (DNA plus histoneproteins). During mitosis replicated chromosomes are positioned near themiddle of the cytoplasm and then segregated so that each daughtercell receives a copy of the original DNA (if you start with 46 in theparent cell, you should end up with 46 chromosomes in each 49
  • 50. daughter cell). To do this cells utilize microtubules (referred to as the spindle apparatus) to "pull" chromosomes into each"cell". The microtubules have the 9+2 arrangement discussed earlier. Animal cells (except for a group of worms known asnematodes) have a centriole. Plants and most other eukaryotic organisms lack centrioles. Prokaryotes, of course, lackspindles and centrioles; the cell membrane assumes this function when it pulls the by-then replicated chromosomes apartduring binary fission. Cells that contain centrioles also have a series of smaller microtubules, the aster, that extend fromthe centrioles to the cell membrane. The aster is thought to serve as a brace for the functioning of the spindle fibers.The phases of mitosis are sometimes difficult to separate. Remember that the process is a dynamic one, not the staticprocess displayed of necessity in a textbook.ProphaseProphase is the first stage of mitosis proper. Chromatin condenses (remember that chromatin/DNA replicate duringInterphase), the nuclear envelope dissolves, centrioles (if present) divide and migrate, kinetochores and kinetochore fibersform, and the spindle forms. 50
  • 51. MetaphaseMetaphase follows Prophase. The chromosomes (which at this point consist of chromatids held together by a centromere)migrate to the equator of the spindle, where the spindles attach to the kinetochore fibers.AnaphaseAnaphase begins with the separation of the centromeres, and the pulling of chromosomes (we call them chromosomesafter the centromeres are separated) to opposite poles of the spindle.TelophaseTelophase is when the chromosomes reach the poles of their respective spindles, the nuclear envelope reforms,chromosomes uncoil into chromatin form, and the nucleolus (which had disappeared during Prophase) reform. Wherethere was one cell there are now two smaller cells each with exactly the same genetic information. These cells may thendevelop into different adult forms via the processes of development.CytokinesisCytokinesis is the process of splitting the daughter cells apart. Whereas mitosis is the division of the nucleus, cytokinesisis the splitting of the cytoplasm and allocation of the golgi, plastids and cytoplasm into each new cell. 51
  • 52. CELL DIVISION: MEIOSIS AND SEXUAL REPRODUCTIONMeiosisSexual reproduction occurs only in eukaryotes. During the formation of gametes, the number of chromosomes is reducedby half, and returned to the full amount when the two gametes fuse during fertilization.PloidyHaploid and diploid are terms referring to the number of sets of chromosomes in a cell. Gregor Mendel determined hispeas had two sets of alleles, one from each parent. Diploid organisms are those with two (di) sets. Human beings (exceptfor their gametes), most animals and many plants are diploid. We abbreviate diploid as 2n. Ploidy is a term referring to thenumber of sets of chromosomes. Haploid organisms/cells have only one set of chromosomes, abbreviated as n. Organismswith more than two sets of chromosomes are termed polyploid. Chromosomes that carry the same genes are termedhomologous chromosomes. The alleles on homologous chromosomes may differ, as in the case of heterozygousindividuals. Organisms (normally) receive one set of homologous chromosomes from each parent.Meiosis is a special type of nuclear division which segregates one copy of each homologous chromosome into each new"gamete". Mitosis maintains the cells original ploidy level (for example, one diploid 2n cell producing two diploid 2ncells; one haploid n cell producing two haploid n cells; etc.). Meiosis, on the other hand, reduces the number of sets ofchromosomes by half, so that when gametic recombination (fertilization) occurs the ploidy of the parents will bereestablished.Most cells in the human body are produced by mitosis. These are the somatic (or vegetative) line cells. Cells that becomegametes are referred to as germ line cells. The vast majority of cell divisions in the human body are mitotic, with meiosisbeing restricted to the gonads.Life CyclesLife cycles are a diagrammatic representation of the events in the organisms development and reproduction. Wheninterpreting life cycles, pay close attention to the ploidy level of particular parts of the cycle and where in the life cyclemeiosis occurs. For example, animal life cycles have a dominant diploid phase, with the gametic (haploid) phase being arelative few cells. Most of the cells in your body are diploid, germ line diploid cells will undergo meiosis to producegametes, with fertilization closely following meiosis.Plant life cycles have two sequential phases that are termed alternation of generations. The sporophyte phase is "diploid",and is that part of the life cycle in which meiosis occurs. However, many plant species are thought to arise by polyploidy,and the use of "diploid" in the last sentence was meant to indicate that the greater number of chromosome sets occur inthis phase. The gametophyte phase is "haploid", and is the part of the life cycle in which gametes are produced (by mitosisof haploid cells). In flowering plants (angiosperms) the multicelled visible plant (leaf, stem, etc.) is sporophyte, whilepollen and ovaries contain the male and female gametophytes, respectively. Plant life cycles differ from animal ones byadding a phase (the haploid gametophyte) after meiosis and before the production of gametes.Many protists and fungi have a haploid dominated life cycle. The dominant phase is haploid, while the diploid phase isonly a few cells (often only the single celled zygote, as in Chlamydomonas ). Many protists reproduce by mitosis untiltheir environment deteriorates, then they undergo sexual reproduction to produce a resting zygotic cyst.Phases of MeiosisTwo successive nuclear divisions occur, Meiosis I (Reduction) and Meiosis II (Division). Meiosis produces 4 haploidcells. Mitosis produces 2 diploid cells. The old name for meiosis was reduction/ division. Meiosis I reduces the ploidy 52
  • 53. level from 2n to n (reduction) while Meiosis II divides the remaining set of chromosomes in a mitosis-like process(division). Most of the differences between the processes occur during Meiosis I.Prophase IProphase I has a unique event -- the pairing (by an as yet undiscovered mechanism) of homologous chromosomes.Synapsis is the process of linking of the replicated homologous chromosomes. The resulting chromosome is termed atetrad, being composed of two chromatids from each chromosome, forming a thick (4-strand) structure. Crossing-overmay occur at this point. During crossing-over chromatids break and may be reattached to a different homologouschromosome.The alleles on this tetrad:ABCDEFGABCDEFGabcdefgabcdefgwill produce the following chromosomes if there is a crossing-over event between the 2nd and 3rd chromosomes from thetop:ABCDEFGABcdefgabCDEFGabcdefgThus, instead of producing only two types of chromosome (all capital or alllower case), four different chromosomes are produced. This doubles thevariability of gamete genotypes. The occurrence of a crossing-over isindicated by a special structure, a chiasma (plural chiasmata) since therecombined inner alleles will align more with others of the same type (e.g.a with a, B with B). Near the end of Prophase I, the homologouschromosomes begin to separate slightly, although they remain attached atchiasmata.Events of Prophase I (save for synapsis and crossing over) are similar tothose in Prophase of mitosis: chromatin condenses into chromosomes, thenucleolus dissolves, nuclear membrane is disassembled, and the spindleapparatus forms. 53
  • 54. Metaphase IMetaphase I is when tetrads line-up along the equator of the spindle. Spindle fibers attach to the centromere region of eachhomologous chromosome pair. Other metaphase events as in mitosis.Anaphase IAnaphase I is when the tetrads separate, and are drawn to opposite poles by the spindle fibers. The centromeres inAnaphase I remain intact.Telophase ITelophase I is similar to Telophase of mitosis, except that only one set of (replicated) chromosomes is in each "cell".Depending on species, new nuclear envelopes may or may not form. Some animal cells may have division of thecentrioles during this phase. 54
  • 55. Prophase IIDuring Prophase II, nuclear envelopes (if they formed during Telophase I) dissolve, and spindle fibers reform. All else isas in Prophase of mitosis. Indeed Meiosis II is very similar to mitosis.Metaphase IIMetaphase II is similar to mitosis, with spindles moving chromosomes into equatorial area and attaching to the oppositesides of the centromeres in the kinetochore region.Anaphase IIDuring Anaphase II, the centromeres split and the former chromatids (now chromosomes) are segregated into oppositesides of the cell.Telophase IITelophase II is identical to Telophase of mitosis. Cytokinesis separates the cells. 55
  • 56. Comparison of Mitosis and MeiosisMitosis maintains ploidy level, while meiosis reduces it. Meiosis may be considered a reduction phase followed by aslightly altered mitosis. Meiosis occurs in a relative few cells of a multicellular organism, while mitosis is more common. 56
  • 57. GametogenesisGametogenesis is the process of forming gametes (bydefinition haploid, n) from diploid cells of the germ line.Spermatogenesis is the process of forming sperm cellsby meiosis (in animals, by mitosis in plants) inspecialized organs known as gonads (in males these aretermed testes). After division the cells undergodifferentiation to become sperm cells. Oogenesis is theprocess of forming an ovum (egg) by meiosis (inanimals, by mitosis in the gametophyte in plants) inspecialized gonads known as ovaries. Whereas inspermatogenesis all 4 meiotic products develop intogametes, oogenesis places most of the cytoplasm into thelarge egg. The other cells, the polar bodies, do notdevelop. This all the cytoplasm and organelles go intothe egg. Human males produce 200,000,000 sperm per day, while the female produces one egg (usually) each menstrualcycle. Spermatogenesis Sperm production begins at puberty at continues throughout life, with several hundred million sperm being produced each day. Once sperm form they move into the epididymis, where they mature and are stored.OogenesisThe ovary contains many follicles composed of a developing egg surroundedby an outer layer of follicle cells. Each egg begins oogenesis as a primaryoocyte. At birth each female carries a lifetime supply of developing oocytes,each of which is in Prophase I. A developing egg (secondary oocyte) isreleased each month from puberty until menopause, a total of 400-500 eggs. 57
  • 58. LAWS OF THERMODYNAMICSLaws of ThermodynamicsEnergy exists in many forms, such as heat, light, chemical energy, and electrical energy. Energy is the ability to bringabout change or to do work. Thermodynamics is the study of energy.First Law of Thermodynamics: Energy can be changed from one form to another, but it cannot be created or destroyed.The total amount of energy and matter in the Universe remains constant, merely changing from one form to another. TheFirst Law of Thermodynamics (Conservation) states that energy is always conserved, it cannot be created or destroyed. Inessence, energy can be converted from one form into another.The Second Law of Thermodynamics states that "in all energy exchanges, if no energy enters or leaves the system, thepotential energy of the state will always be less than that of the initial state." This is also commonly referred to as entropy.A watchspring-driven watch will run until the potential energy in the spring is converted, and not again until energy isreapplied to the spring to rewind it. A car that has run out of gas will not run again until you walk 10 miles to a gas stationand refuel the car. Once the potential energy locked in carbohydrates is converted into kinetic energy (energy in use ormotion), the organism will get no more until energy is input again. In the process of energy transfer, some energy willdissipate as heat. Entropy is a measure of disorder: cells are NOT disordered and so have low entropy. The flow of energymaintains order and life. Entropy wins when organisms cease to take in energy and die.Potential vs. Kinetic energyPotential energy, as the name implies, is energy that has not yet been used, thus the term potential. Kinetic energy isenergy in use (or motion). A tank of gasoline has a certain potential energy that is converted into kinetic energy by theengine. When the potential is used up, youre outta gas! Batteries, when new or recharged, have a certain potential. Whenplaced into a tape recorder and played at loud volume (the only settings for such things), the potential in the batteries istransformed into kinetic energy to drive the speakers. When the potential energy is all used up, the batteries are dead. Inthe case of rechargeable batteries, their potential is reelevated or restored.In the hydrologic cycle, the sun is the ultimate source of energy, evaporating water (in a fashion raising its potentialabove water in the ocean). When the water falls as rain (or snow) it begins to run downhill toward sea-level. As the waterget closer to sea-level, its potential energy is decreased. Without the sun, the water would eventually still reach sea-level,but never be evaporated to recharge the cycle.Chemicals may also be considered from a potential energy or kinetic energy standpoint. One pound of sugar has a certainpotential energy. If that pound of sugar is burned the energy is released all at once. The energy released is kinetic energy(heat). So much is released that organisms would burn up if all the energy was released at once. Organisms must releasethe energy a little bit at a time.Energy is defined as the ability to do work. Cells convert potential energy, usually in the from of C-C covalent bonds orATP molecules, into kinetic energy to accomplish cell division, growth, biosynthesis, and active transport, among otherthings.Learning Objectives 1. Define energy; be able to state the first and second laws of thermodynamics. 2. Entropy is a measure of the degree of randomness or disorder of systems. Explain how life maintains a high degree of organization. 58
  • 59. REACTIONS AND ENZYMESEndergonic and exergonicEnergy releasing processes, ones that "generate" energy, are termed exergonic reactions. Reactions that require energy toinitiate the reaction are known as endergonic reactions. All natural processes tend to proceed in such a direction that thedisorder or randomness of the universe increases (the second law of thermodynamics).Oxidation/ReductionBiochemical reactions in living organisms are essentially energy transfers. Often they occur together, "linked", in what arereferred to as oxidation/reduction reactions. Reduction is the gain of an electron. Sometimes we also have H ions along forthe ride, so reduction also becomes the gain of H. Oxidation is the loss of an electron (or hydrogen). Inoxidation/reduction reactions, one chemical is oxidized, and its electrons are passed (like a hot potato) to another(reduced, then) chemical. Such coupled reactions are referred to as redox reactions. The metabolic processes glycolysis,Krebs Cycle, and Electron Transport Phosphorylation involve the transfer of electrons (at varying energy states) by redoxreactions. 59
  • 60. Catabolism and AnabolismAnabolism is the total series of chemical reactions involved in synthesis of organic compounds. Autotrophs must be ableto manufacture (synthesize) all the organic compounds they need. Heterotrophs can obtain some of their compounds intheir diet (along with their energy). For example humans can synthesize 12 of the 20 amino acids, we must obtain theother 8 in our diet. Catabolism is the series of chemical reactions that breakdown larger molecules. Energy is released thisway, some of it can be utilized for anabolism. Products of catabolism can be reassembled by anabolic processes into newanabolic molecules. 60
  • 61. Enzymes: Organic CatalystsEnzymes allow many chemical reactions to occur within the homeostasis constraints of a living system. Enzymes functionas organic catalysts. A catalyst is a chemical involved in, but notchanged by, a chemical reaction. Many enzymes function bylowering the activation energy of reactions. By bringing thereactants closer together, chemical bonds may be weakened andreactions will proceed faster than without the catalyst.Enzymes can act rapidly, as in the case of carbonic anhydrase(enzymes typically end in the -ase suffix), which causes thechemicals to react 107 times faster than without the enzymepresent. Carbonic anhydrase speeds up the transfer of carbondioxide from cells to the blood. There are over 2000 knownenzymes, each of which is involved with one specific chemical reaction. Enzymes are substrate specific. The enzymepeptidase (which breaks peptide bonds in proteins) will not work on starch (which is broken down by human-producedamylase in the mouth).Enzymes are proteins. The functioning of the enzyme is determined by the shape of the protein. The arrangement ofmolecules on the enzyme produces an area known as the active site within which the specific substrate(s) will "fit". Itrecognizes, confines and orients the substrate in a particular direction.The induced fit hypothesis suggests that the binding of the substrate to the enzyme alters the structure of the enzyme,placing some strain on the substrate and further facilitating the reaction. Cofactors are nonproteins essential for enzymeactivity. Ions such as K+ and Ca+2 are cofactors. Coenzymesare nonprotein organic molecules bound to enzymes near theactive site. NAD (nicotinamide adenine dinucleotide).Enzymatic pathways form as a result of the commonoccurrence of a series of dependent chemical reactions. Inone example, the end product depends on the successfulcompletion of five reactions, each mediated by a specific enzyme. The enzymes in a series can be located adjacent to each other (in an organelle or in the membrane of an organelle), thus speeding the reaction process. Also, intermediate products tend not to accumulate, making the process more efficient. By removing intermediates (and by inference end products) from the reactive pathway, equilibrium (the tendency of reactions to reverse when concentrations of the products build up to a certain level) effects are minimized, since equilibrium is not attained, and so the reactions will proceed in the "preferred" direction.Temperature: Increases in temperature will speed up the rate of nonenzyme mediated reactions, and so temperatureincrease speeds up enzyme mediated reactions, but only to a point. When heated too much, enzymes (since they areproteins dependent on their shape) become denatured. When the temperature drops, the enzyme regains its shape.Thermolabile enzymes, such as those responsible for the color distribution in Siamese cats and color camouflage of theArctic fox, work better (or work at all) at lower temperatures.Concentration of substrate and product also control the rate of reaction,providing a biofeedback mechanism. 61
  • 62. Activation, as in the case of chymotrypsin, protects a cell from the hazards or damage the enzyme might cause.Changes in pH will also denature the enzyme by changing the shape of the enzyme. Enzymes are also adapted to operateat a specific pH or pH range.Allosteric Interactions may allow an enzyme to be temporarily inactivated. Binding of an allosteric effector changes theshape of the enzyme, inactivating it while the effector is still bound. Such a mechanism is commonly employed infeedback inhibition. Often one of the products, either an end or near-end product act as an allosteric effector, blocking orshunting the pathway.Competitive Inhibition works by the competition of the regulatory compound and substrate for the binding site. Ifenough regulatory compound molecules bind to enough enzymes, the pathway is shut down or at least slowed down.PABA, a chemical essential to a bacteria that infects animals, resembles a drug, sulfanilamide, that competes with PABA,shutting down an essential bacterial (but not animal) pathway.Noncompetitive Inhibition occurs when the inhibitory chemical, which does not have to resemble the substrate, binds tothe enzyme other than at the active site. Lead binds to SH groups in this fashion. Irreversible Inhibition occurs when thechemical either permanently binds to or massively denatures the enzyme so that the tertiary structure cannot be restored.Nerve gas permanently blocks pathways involved in nerve message transmission, resulting in death. Penicillin, the first ofthe "wonder drug" antibiotics, permanently blocks the pathways certain bacteria use to assemble their cell wallcomponents.Learning Objectives • Reactions that show a net loss in energy are said to be exergonic; reactions that show a net gain in energy are said to be endergonic. Describe an example of each type of chemical reaction from everyday life. • What is meant by a reversible reaction? How might this be significant to living systems? • What is the function of metabolic pathways in cellular chemistry? Want more? Try Metabolic Pathways of Biochemistry. • What are enzymes? Explain their importance. • Explain what happens when enzymes react with substrates. 62
  • 63. ATP AND BIOLOGICAL ENERGYThe Nature of ATPAdenosine triphosphate (ATP), the energy currency, transfers energy from chemical bonds to endergonic (energyabsorbing) reactions within the cell. Structurally, ATP consists of the adenine nucleotide (ribose sugar, adenine base, andphosphate group, PO4-2) plus two other phosphate groups.Energy is stored in the covalent bonds between phosphates, with the greatest amount of energy (approximately 7kcal/mole) in the bond between the second and third phosphate groups. This covalent bond is known as a pyrophosphatebond.We can write the chemical reaction for the formation of ATP as:a) in chemicalese: ADP + Pi + energy ----> ATPb) in English: Adenosine diphosphate + inorganic Phosphate + energy produces Adenosine TriphosphateThe chemical formula for the expenditure/release of ATP energy can be written as:a) in chemicalese: ATP ----> ADP + energy + Pib) in English Adenosine Triphosphate produces Adenosine diphosphate + energy + inorganic PhosphateAn analogy between ATP and rechargeable batteries is appropriate. The batteries are used, giving up their potentialenergy until it has all been converted into kinetic energy and heat/unusable energy. Recharged batteries (into whichenergy has been put) can be used only after the input of additional energy. Thus, ATP is the higher energy form (therecharged battery) while ADP is the lower energy form (the used battery). When the terminal (third) phosphate is cutloose, ATP becomes ADP (Adenosine diphosphate; di= two), and thestored energy is released for some biological process to utilize. Theinput of additional energy (plus a phosphate group) "recharges" ADPinto ATP (as in my analogy the spent batteries are recharged by theinput of additional energy).How to Make ATPTwo processes convert ADP into ATP: 1) substrate-levelphosphorylation; and 2) chemiosmosis. Substrate-level 63
  • 64. phosphorylation occurs in the cytoplasm when an enzyme attaches a third phosphate to the ADP (both ADP and thephosphates are the substrates on which the enzyme acts).Chemiosmosis, involves more than the single enzyme ofsubstrate-level phosphorylation. Enzymes in chemiosmoticsynthesis are arranged in an electron transport chain that isembedded in a membrane. In eukaryotes this membrane is ineither the chloroplast or mitochondrion. According to thechemiosmosis hypothesis proposed by Peter Mitchell in 1961, aspecial ATP-synthesizing enzyme is also located in themembranes. Mitchell would later win the Nobel Prize for hiswork.During chemiosmosis in eukaryotes, H+ ions are pumped across anorganelle membrane by membrane "pump proteins" into aconfined space (bounded by membranes) that containsnumerous hydrogen ions. The energy for the pumping comesfrom the coupled oxidation-reduction reactions in the electron transport chain. Electrons are passed from one membrane- bound enzyme to another, losing some energy with each transfer (as per the second law of thermodynamics). This "lost" energy allows for the pumping of hydrogen ions against the concentration gradient (there are fewer hydrogen ions outside the confined space than there are inside the confined space). The confined hydrogens cannot pass back through the membrane. Their only exit is through the ATP synthesizing enzyme that is located in the confining membrane. As the hydrogen passes through the ATP synthesizing enzyme, energy from the enzyme is used to attach a third phosphate to ADP, converting it to ATP. Usually the terminal phosphate is not simply removed, but instead is attached to another molecule. This process is known as phosphorylation.W + ATP -----> W~P + ADP where W is any compound, for example:glucose + ATP -----> glucose~P + ADPGlucose can be converted into Glucose-6-phosphate by the addition of thephosphate group from ATP.ATP serves as the biological energy company, releasing energy for bothanabolic and catabolic processes and being recharged by energy generatedfrom other catabolic reactions.Learning Objectives • Describe the components, organization, and functions of an electron transport system. • ATP is composed of ribose, a five-carbon sugar, three phosphate groups, and adenine , a nitrogen-containing compound (also known as a nitrogenous base). What class of organic macromolecules is composed of monomers similar to ATP? • ATP directly or indirectly delivers energy to almost all metabolic pathways. Explain the functioning of the ATP/ADP cycle. 64
  • 65. • Adding a phosphate to a molecule is called phosphorylation. What two methods do cells use to phosphorylate ADP into ATP?CELLULAR METABOLISM AND FERMENTATIONGlycolysis, the Universal ProcessNine reactions, each catalyzed by a specific enzyme, makeup the process we call glycolysis. ALL organisms haveglycolysis occurring in their cytoplasm.At steps 1 and 3 ATP is converted into ADP, inputtingenergy into the reaction as well as attaching a phosphate tothe glucose. At steps 6 and 9 ADP is converted into thehigher energy ATP. At step 5 NAD+ is converted intoNADH + H+.The process works on glucose, a 6-C, until step 4 splitsthe 6-C into two 3-C compounds. Glyceraldehydephosphate (GAP, also known as phosphoglyceraldehyde,PGAL) is the more readily used of the two.Dihydroxyacetone phosphate can be converted into GAPby the enzyme Isomerase. The end of the glycolysisprocess yields two pyruvic acid (3-C) molecules, and anet gain of 2 ATP and two NADH per glucose.Anaerobic PathwaysUnder anaerobic conditions, the absence of oxygen, pyruvic acid can be routed by the organism into one of threepathways: lactic acid fermentation, alcohol fermentation, or cellular (anaerobic) respiration. Humans cannot fermentalcohol in their own bodies, we lack the genetic information to do so. These biochemical pathways, with their myriadreactions catalyzed by reaction-specific enzymes all under genetic control, are extremely complex. We will only skim thesurface at this time and in this course.Alcohol fermentation is the formation of alcohol from sugar. Yeast, when under anaerobic conditions, convert glucose topyruvic acid via the glycolysis pathways, then go one step farther, converting pyruvic acid into ethanol, a C-2 compound.Many organisms will also ferment pyruvic acid into, other chemicals, suchas lactic acid. Humans ferment lactic acid in muscles where oxygenbecomes depleted, resulting in localized anaerobic conditions. This lacticacid causes the muscle stiffness couch-potatoes feel after beginning exerciseprograms. The stiffness goes away after a few days since the cessation ofstrenuous activity allows aerobic conditions to return to the muscle, and thelactic acid can be converted into ATP via the normal aerobic respirationpathways. 65
  • 66. Aerobic RespirationWhen oxygen is present (aerobic conditions), most organisms will undergo two more steps, Krebs Cycle, and ElectronTransport, to produce their ATP. In eukaryotes, these processes occur in the mitochondria, while in prokaryotes theyoccur in the cytoplasm.Acetyl Co-A: The Transition ReactionPyruvic acid is first altered in the transition reaction by removal of a carbon and two oxygens (which form carbondioxide). When the carbon dioxide is removed, energy is given off, and NAD+ is converted into the higher energy formNADH. Coenzyme A attaches to the remaining 2-C (acetyl) unit, forming acetyl Co-A. This process is a prelude to theKrebs Cycle.Krebs Cycle (aka Citric Acid Cycle)The Acetyl Co-A (2-C) is attached to a 4-C chemical (oxaloacetic acid). The Co-A is released and returns to await anotherpyruvic acid. The 2-C and 4-C make another chemical known as Citric acid, a 6-C. Krebs Cycle is also known as theCitric Acid Cycle. The process after Citric Acid is essentially removing carbon dioxide, getting out energy in the form ofATP, GTP, NADH and FADH2, and lastly regenerating the cycle. Between Isocitric Acid and α-Ketoglutaric Acid,carbon dioxide is given off and NAD+ is converted into NADH. Between α-Ketoglutaric Acid and Succinic Acid therelease of carbon dioxide and reduction of NAD+ into NADH happens again, resulting in a 4-C chemical, succinic acid.GTP (Guanine Triphosphate, which transfers its energy to ATP) is also formed here (GTP is formed by attaching aphosphate to GDP).The remaining energy carrier-generating steps involve the shifting of atomic arrangements within the 4-C molecules.Between Succinic Acid and Fumaric Acid, the molecularshifting releases not enough energy to make ATP or NADHoutright, but instead this energy is captured by a new energycarrier, Flavin adenine dinucleotide (FAD). FAD is reduced bythe addition of two Hs to become FADH2. FADH2 is not asrich an energy carrier as NADH, yielding less ATP than thelatter.The last step, between Malic Acid and Oxaloacetic Acidreforms OA to complete the cycle. Energy is given off andtrapped by the reduction of NAD+ to NADH. The carbondioxide released by cells is generated by the Krebs Cycle, asare the energy carriers (NADH and FADH2) which play a rolein the next step. 66
  • 67. Electron Transport PhosphorylationWhereas Krebs Cycle occurs in the matrix of the mitochondrion, the Electron Transport System (ETS) chemicals areembedded in the membranes known as the cristae. Krebs cycle completely oxidized the carbons in the pyruvic acids,producing a small amount of ATP, and reducing NAD and FAD into higher energy forms. In the ETS those higher energyforms are cashed in, producing ATP. Cytochromes are molecules that pass the "hot potatoes" (electrons) along the ETSchain. Energy released by the "downhill" passage of electrons is captured as ATP by ADP molecules. The ADP is reducedby the gain of electrons. ATP formed in this way is made by the process ofoxidative phosphorylation. The mechanism for the oxidative phosphorylationprocess is the gradient of H+ ions discovered across the inner mitochondrialmembrane. This mechanism is known as chemiosmotic coupling. Thisinvolves both chemical and transport processes. Drops in the potential energyof electrons moving down the ETS chain occur at three points. These pointsturn out to be where ADP + P are converted into ATP. Potential energy iscaptured by ADP and stored in the pyrophosphate bond. NADH enters theETS chain at the beginning, yielding 3 ATP per NADH. FADH2 enters at Co-Q, producing only 2 ATP per FADH2.Catabolism and AnabolismCatabolism is the breaking down of complex molecules (triglycerides and polysaccharides). Anabolism is the building upof molecules for energy storage. 67
  • 68. PHOTOSYNTHESISWhat is Photosynthesis?Photosynthesis is the process by which plants, some bacteria, and some protistans use the energy from sunlight to producesugar, which cellular respiration converts into ATP, the "fuel" used by all living things. The conversion of unusablesunlight energy into usable chemical energy, is associated with the actions of the green pigment chlorophyll. Most of thetime, the photosynthetic process uses water and releases the oxygen that we absolutely must have to stay alive. Oh yes, weneed the food as well!We can write the overall reaction of this process as: 6H2O + 6CO2 ----------> C6H12O6+ 6O2Most of us dont speak chemicalese, so the above chemical equation translates as:six molecules of water plus six molecules of carbon dioxide produce one molecule ofsugar plus six molecules of oxygenLeaves and Leaf StructurePlants are the only photosynthetic organisms to have leaves (and not all plants have leaves). A leaf may be viewed as asolar collector crammed full of photosynthetic cells.The raw materials of photosynthesis, water and carbon dioxide, enter the cells of the leaf, and the products ofphotosynthesis, sugar and oxygen, leave the leaf. 68
  • 69. Water enters the root and is transported up to the leaves through specialized plant cells known as xylem (pronounces zigh-lem). Land plants must guard against drying out (desiccation) and so have evolved specialized structures known asstomata to allow gas to enter and leave the leaf. Carbon dioxide cannot pass through the protective waxy layer coveringthe leaf (cuticle), but it can enter the leaf through an opening (the stoma; plural = stomata; Greek for hole) flanked by twoguard cells. Likewise, oxygen produced during photosynthesis can only pass out of the leaf through the opened stomata.Unfortunately for the plant, while these gases are moving between the inside and outside of the leaf, a great deal water isalso lost. Cottonwood trees, for example, will lose 100 gallons of water per hour during hot desert days. Carbon dioxideenters single-celled and aquatic autotrophs through no specialized structures.The Nature of LightWhite light is separated into the different colors (=wavelengths) of light by passing it through a prism. Wavelength isdefined as the distance from peak to peak (or trough to trough). The energy of is inversely proportional to the wavelength:longer wavelengths have less energy than do shorter ones.The order of colors is determined by the wavelength of light.Visible light is one small part of the electromagnetic spectrum.The longer the wavelength of visible light, the more red the color.Likewise the shorter wavelengths are towards the violet side of thespectrum. Wavelengths longer than red are referred to as infrared,while those shorter than violet are ultraviolet. Light behaves both as a wave and a particle. Wave properties of light include the bending of the wave path when passing from one material (medium) into another (i.e. the prism, rainbows, pencil in a glass-of-water, etc.). The particle properties are demonstrated by the photoelectric effect. Zinc exposed to ultraviolet light becomes positively charged because light energy forces electrons from the zinc. These electrons can create an electrical current. Sodium, potassium and selenium have critical wavelengths in the visible light range. The critical wavelength is the maximum wavelength of light (visible or invisible) that creates a photoelectric effect.Chlorophyll and Accessory PigmentsA pigment is any substance that absorbs light. The color of the pigment comes from the wavelengths of light reflected (inother words, those not absorbed). Chlorophyll, the green pigment common to all photosynthetic cells, absorbs allwavelengths of visible light except green, which it reflects to be detected by our eyes. Black pigments absorb all of thewavelengths that strike them. White pigments/lighter colors reflect all or almost all of the energy striking them. Pigmentshave their own characteristic absorption spectra, the absorption pattern of a given pigment. 69
  • 70. Chlorophyll is a complex molecule. Several modifications of chlorophyll occur among plants and other photosyntheticorganisms. All photosynthetic organisms (plants, certain protistans, prochlorobacteria, and cyanobacteria) havechlorophyll a. Accessory pigments absorb energy that chlorophyll a does not absorb. Accessory pigments includechlorophyll b (also c, d, and e in algae and protistans), xanthophylls, and carotenoids (such as beta-carotene). Chlorophylla absorbs its energy from the Violet-Blue and Reddish orange-Red wavelengths, and little from the intermediate (Green-Yellow-Orange) wavelengths.Carotenoids and chlorophyll b absorb some of the energy in the green wavelength. Why not so much in the orange andyellow wavelengths? Both chlorophylls also absorb in the orange-red end of the spectrum (with longer wavelengths andlower energy). The origins of photosynthetic organisms in the sea may account for this. Shorter wavelengths (with moreenergy) do not penetrate much below 5 meters deep in sea water. The ability to absorb some energy from the longer(hence more penetrating) wavelengths might have been an advantage to early photosynthetic algae that were not able to bein the upper (photic) zone of the sea all the time. The action spectrum of photosynthesis is the relative effectiveness of different wavelengths of light at generating electrons. If a pigment absorbs light energy, one of three things will occur. Energy is dissipated as heat. The energy may be emitted immediately as a longer wavelength, a phenomenon known as fluorescence. Energy may trigger a chemical reaction, as in photosynthesis. Chlorophyll only triggers a chemical reaction when it is associated with proteins embedded in a membrane (as in a chloroplast) or the membrane infoldings found in photosynthetic prokaryotes such as cyanobacteria and prochlorobacteria. 70
  • 71. The structure of the chloroplast and photosynthetic membranesThe thylakoid is the structural unit of photosynthesis. Both photosyntheticprokaryotes and eukaryotes have these flattened sacs/vesicles containingphotosynthetic chemicals. Only eukaryotes have chloroplasts with asurrounding membrane.Thylakoids are stacked like pancakes in stacks known collectively as grana. Theareas between grana are referred to as stroma. While the mitochondrion has twomembrane systems, the chloroplast has three, forming three compartments.Stages of PhotosynthesisPhotosynthesis is a two stage process. The first process is the Light Dependent Process (Light Reactions), requires thedirect energy of light to make energy carrier molecules that are used in the second process. The Light Independent Process(or Dark Reactions) occurs when the products of the Light Reaction are used to form C-C covalent bonds ofcarbohydrates. The Dark Reactions can usually occur in the dark, if the energy carriers from the light process are present.Recent evidence suggests that a major enzyme of the Dark Reaction is indirectly stimulated by light, thus the term DarkReaction is somewhat of a misnomer. The Light Reactions occur in the grana and the Dark Reactions take place in thestroma of the chloroplasts.Light ReactionsIn the Light Dependent Processes (Light Reactions) light strikeschlorophyll a in such a way as to excite electrons to a higher energystate. In a series of reactions the energy is converted (along an electrontransport process) into ATP and NADPH. Water is split in the process,releasing oxygen as a by-product of the reaction. The ATP andNADPH are used to make C-C bonds in the Light Independent Process(Dark Reactions).In the Light Independent Process, carbon dioxide from the atmosphere(or water for aquatic/marine organisms) is captured and modified bythe addition of Hydrogen to form carbohydrates (general formula ofcarbohydrates is [CH2O]n). The incorporation of carbon dioxide intoorganic compounds is known as carbon fixation. The energy for thiscomes from the first phase of the photosynthetic process. Livingsystems cannot directly utilize light energy, but can, through acomplicated series of reactions, convert it into C-C bond energy that can be released by glycolysis and other metabolic processes. Photosystems are arrangements of chlorophyll and other pigments packed into thylakoids. Many Prokaryotes have only one photosystem, Photosystem II (so numbered because, while it was most likely the first to evolve, it was the second one discovered). Eukaryotes have Photosystem II plus Photosystem I. Photosystem I uses chlorophyll a, in the form referred to as P700. Photosystem II uses a form of chlorophyll a known as P680. Both "active" forms of chlorophyll a function inphotosynthesis due to their association with proteins in the thylakoid membrane. 71
  • 72. Photophosphorylation is the process of converting energy from a light-excited electron into the pyrophosphate bond of anADP molecule. This occurs when the electrons from water are excited by the light in the presence of P680. The energytransfer is similar to the chemiosmotic electron transport occurring in the mitochondria. Light energy causes the removalof an electron from a molecule of P680 that is part of Photosystem II. The P680 requires an electron, which is taken froma water molecule, breaking the water into H+ ions and O-2 ions. These O-2 ions combine to form the diatomic O2 that isreleased. The electron is "boosted" to a higher energy state and attached to a primary electron acceptor, which begins aseries of redox reactions, passing the electron through a series of electron carriers, eventually attaching it to a molecule inPhotosystem I. Light acts on a molecule of P700 in Photosystem I, causing an electron to be "boosted" to a still higherpotential. The electron is attached to a different primary electron acceptor (that is a different molecule from the oneassociated with Photosystem II). The electron is passed again through a series of redox reactions, eventually beingattached to NADP+ and H+ to form NADPH, an energy carrier needed in the Light Independent Reaction. The electronfrom Photosystem II replaces the excited electron in the P700 molecule. There is thus a continuous flow of electrons fromwater to NADPH. This energy is used in Carbon Fixation. Cyclic Electron Flow occurs in some eukaryotes and primitivephotosynthetic bacteria. No NADPH is produced, only ATP. This occurs when cells may require additional ATP, or whenthere is no NADP+ to reduce to NADPH. In Photosystem II, the pumping to H ions into the thylakoid and the conversionof ADP + P into ATP is driven by electron gradients established in the thylakoid membrane.Chemiosmosis as it operates in photophosphorylation within a chloroplastHalobacteria, which grow in extremely salty water, are facultative aerobes, they can grow when oxygen is absent. Purplepigments, known as retinal (a pigment also found in the human eye) act similar to chlorophyll. The complex of retinal andmembrane proteins is known as bacteriorhodopsin, which generates electrons which establish a proton gradient thatpowers an ADP-ATP pump, generating ATP from sunlight without chlorophyll. This supports the theory thatchemiosmotic processes are universal in their ability to generate ATP.Dark ReactionCarbon-Fixing Reactions are also known as the Dark Reactions (or Light Independent Reactions). Carbon dioxide enterssingle-celled and aquatic autotrophs through no specialized structures, diffusing into the cells. Land plants must guardagainst drying out (desiccation) and so have evolved specialized structures known as stomata to allow gas to enter andleave the leaf. The Calvin Cycle occurs in the stroma of chloroplasts (where would it occur in a prokaryote?). Carbondioxide is captured by the chemical ribulose biphosphate (RuBP). RuBP is a 5-C chemical. Six molecules of carbondioxide enter the Calvin Cycle, eventually producing one molecule of glucose. The reactions in this process were workedout by Melvin Calvin (shown below). 72
  • 73. The first steps in the Calvin cycle.The first stable product of the Calvin Cycle is phosphoglycerate (PGA), a 3-C chemical. The energy from ATP andNADPH energy carriers generated by the photosystems is used to attach phosphates to (phosphorylate) the PGA.Eventually there are 12 molecules of glyceraldehyde phosphate (also known as phosphoglyceraldehyde or PGAL, a 3-C),two of which are removed from the cycle to make a glucose. The remaining PGAL molecules are converted by ATPenergy to reform 6 RuBP molecules, and thus start the cycle again. Remember the complexity of life, each reaction in thisprocess, as in Krebs Cycle, is catalyzed by a different reaction-specific enzyme.C-4 PathwaySome plants have developed a preliminary step to the Calvin Cycle (which is also referred to as a C-3 pathway), thispreamble step is known as C-4. While most C-fixation begins with RuBP, C-4 begins with a new molecule,phosphoenolpyruvate (PEP), a 3-C chemical that is converted into oxaloacetic acid (OAA, a 4-C chemical) when carbondioxide is combined with PEP. The OAA is converted to Malic Acid and then transported from the mesophyll cell into thebundle-sheath cell, where OAA is brokendown into PEP plus carbon dioxide. Thecarbon dioxide then enters the CalvinCycle, with PEP returning to the mesophyllcell. The resulting sugars are now adjacentto the leaf veins and can readily betransported throughout the plant.The capture of carbon dioxide by PEP isediated by the enzyme PEP carboxylase,which has a stronger affinity for carbondioxide than does RuBP carboxylase Whencarbon dioxide levels decline below the threshold for RuBP carboxylase, RuBP is catalyzed with oxygen instead of carbon dioxide. The product of that reaction forms glycolic acid, a chemical that can be broken down by photorespiration, producing neither NADH nor ATP, in effect dismantling the Calvin Cycle. C-4 plants, which often grow close together, have had to adjust to decreased levels of carbon dioxide by artificially raising the carbon dioxide concentration in certain cells to prevent photorespiration. C-4 plants evolved in the tropics and are adapted to higher temperatures than are the C-3 plants found at higher latitudes. Common C-4 plants include crabgrass, corn, and sugar cane. Note that OAA and Malic Acid also have functions in other processes, thus the chemicals would havebeen present in all plants, leading scientists to hypothesize that C-4 mechanisms evolved several times independently inresponse to a similar environmental condition, a type of evolution known as convergent evolution. 73
  • 74. We can see anatomical differences between C3 and C4 leaves.The Carbon CyclePlants may be viewed as carbon sinks, removing carbon dioxide from the atmosphere and oceans by fixing it into organicchemicals. Plants also produce some carbon dioxide by their respiration, but this is quickly used by photosynthesis. Plantsalso convert energy from light into chemical energy of C-C covalent bonds. Animals are carbon dioxide producers thatderive their energy from carbohydrates and other chemicals produced by plants by the process of photosynthesis.The balance between the plant carbon dioxide removal and animal carbon dioxide generation is equalized also by theformation of carbonates in the oceans. This removes excess carbon dioxide from the air and water (both of which are inequilibrium with regard to carbon dioxide). Fossil fuels, such as petroleum and coal, as well as more recent fuels such aspeat and wood generate carbon dioxide when burned. Fossil fuels are formed ultimately by organic processes, andrepresent also a tremendous carbon sink. Human activity has greatly increased the concentration of carbon dioxide in air.This increase has led to global warming, an increase in temperatures around the world, the Greenhouse Effect. Theincrease in carbon dioxide and other pollutants in the air has also led to acid rain, where water falls through polluted airand chemically combines with carbon dioxide, nitrous oxides, and sulfur oxides, producing rainfall with pH as low as 4.This results in fish kills and changes in soil pH which can alter the natural vegetation and uses of the land. The GlobalWarming problem can lead to melting of the ice caps in Greenland and Antarctica, raising sea-level as much as 120meters. Changes in sea-level and temperature would affect climate changes, altering belts of grain production and rainfallpatterns.Learning ObjectivesAfter completing this chapter you should be able to: • Study the general equation for photosynthesis and be able to indicate in which process each reactant is used and each product is produced. • List the two major processes of photosynthesis and state what occurs in those sets of reactions. • Distinguish between organisms known as autotrophs and those known as heterotrophs as pertains to their modes of nutrition. • Explain the significance of the ATP/ADP cycle. • Describe the nature of light and how it is associated with the release of electrons from a photosystem. • Describe how the pigments found on thylakoid membranes are organized into photosystems and how they relate to photon light energy. 74
  • 75. • Describe the role that chlorophylls and the other pigments found in chloroplasts play to initiate the light- dependent reactions. • Describe the function of electron transport systems in the thylakoid membrane. • Explain the role of the two energy-carrying molecules produced in the light-dependent reactions (ATP and NADPH) in the light-independent reactions. • Describe the Calvin-Benson cycle in terms of its reactants and products. • Explain how C-4 photosynthesis provides an advantage for plants in certain environments. • Describe the phenomenon of acid rain, and how photosynthesis relates to acid rain and the carbon cycle..Review Questions1. The organic molecule produced directly by photosynthesis is: a) lipids; b) sugar; c) amino acids; d) DNA2. The photosynthetic process removes ___ from the environment. a) water; b) sugar; c) oxygen; d) chlorophyll; e) carbondioxide3. The process of splitting water to release hydrogens and electrons occurs during the _____ process. a) light dependent;b) light independent; c) carbon fixation; d) carbon photophosphorylation; e) glycolysis4. The process of fixing carbon dioxide into carbohydrates occurs in the ____ process. a) light dependent; b) lightindependent; c) ATP synthesis; d) carbon photophosphorylation; e) glycolysis5. Carbon dioxide enters the leaf through ____. a) chloroplasts; b) stomata: c) cuticle; d) mesophyll cells; e) leaf veins6. The cellular transport process by which carbon dioxide enters a leaf (and by which water vapor and oxygen exit) is ___.a) osmosis; b) active transport; c. co- transport; d) diffusion; e) bulk flow7. Which of the following creatures would not be an autotroph? a) cactus; b) cyanobacteria; c) fish; d) palm tree; e)phytoplankton8. The process by which most of the worlds autotrophs make their food is known as ____. a) glycolysis; b)photosynthesis; c) chemosynthesis; d) herbivory; e) C-4 cycle9. The process of ___ is how ADP + P are converted into ATP during the Light dependent process. a) glycolysis; b)Calvin Cycle; c) chemiosmosis; d) substrate-level phosphorylation; e) Krebs Cycle10. Once ATP is converted into ADP + P, it must be ____. a) disassembled into components (sugar, base, phosphates) andthen ressembled; b) recharged by chemiosmosis; c) converted into NADPH; d) processed by the glycolysis process; e)converted from matter into energy.11. Generally speaking, the longer the wavelenght of light, the ___ the available energy of that light. a) smaller; b)greater; c) same12. The section of the electromagnetic spectrum used for photosynthesis is ___. a) infrared; b) ultraviolet; c) x-ray; d)visible light; e) none of the above13. The colors of light in the visible range (from longest wavelength to shortest) is ___. a) ROYGBIV; b) VIBGYOR; c)GRBIYV; d) ROYROGERS; e) EBGDF14. The photosynthetic pigment that is essential for the process to occur is ___. a) chlorophyll a; b) chlorophyll b; c) betacarotene; d) xanthocyanin; e) fucoxanthin 75
  • 76. 15. When a pigment reflects red light, _____. a) all colors of light are absorbed; b) all col;ors of light are reflected; c)green light is reflected, all others are absorbed; d) red light is reflected, all others are absorbed; e) red light is absorbedafter it is reflected into the internal pigment molecules.16. Chlorophyll a absorbs light energy in the ____color range. a) yellow-green; b) red-organge; c) blue violet; d) a and b;e) b and c.17. A photosystem is ___. a) a collection of hydrogen-pumping proteins; b) a collection of photosynthetic pigmentsarranged in a thylakjoid membrane; c) a series of electron-accepting proteins arranged in the thylakoid membrane; d.found only in prokaryotic organisms; e) multiple copies of chlorophyll a located in the stroma of the chloroplast.18. The individual flattened stacks of membrane material inside the chloroplast are known as ___. a) grana; b) stroma; c)thylakoids; d) cristae; e) matrix19. The fluid-filled area of the chloroplast is the ___. a) grana; b) stroma; c) thylakoids; d) cristae; e) matrix20. The chloroplast contains all of these except ___. a) grana; b) stroma; c) DNA; d) membranes; e) endoplasmicreticulum21. The chloroplasts of plants are most close in size to __. a) unfertilized human eggs; b) human cheek cells; c) humannerve cells; d) bacteria in the human mouth; e) viruses22. Which of these photosynthetic organisms does not have a chloroplast? a) plants; b) red algae; c) cyanobacteria; d)diatoms; e) dinoflagellates23. The photoelectric effect refers to ____. a) emission of electrons from a metal when energy of a critical wavelengthstrikes the metal; b) absorbtion of electrons from the surrounding environment when energy of a critical wavelength isnearby; c) emission of electrons from a metal when struck by any wavelength of light; d) emission of electrons stored inthe daytime when stomata are open at night; e) release of NADPH and ATP energy during the Calvin Cycvle when lightiof a specific wavelength strikes the cell.24. Light of the green wavelengths is commonly absorbed by which accessory pigment? a) chlorophyll a; b) chlorophyllb; c) phycocyanin; d) beta carotene25. The function of the electron transport proteins in the thyakoid membranes is ___. a) production of ADP bychemiosmosis; b) production of NADPH by substrate-level phosphorylation; c) pumping of hydrogens into the thylakoidspace for later generation of ATP by chemiosmosis; d) pumping of hydrogens into the inner cristae space for latergeneration of ATP by chemiosmosis; e) preparation of water for eventual incorporation into glucose26. ATP is known as the energy currency of the cell because ____. a) ATP is the most readily usable form of energy forcells; b) ATP passes energy along in an electron transport chain; c) ATP energy is passed to NADPH; d) ATP traps moreenergy than is produced in its formation; e) only eukaryotic cells use this energy currency.27. Both cyclic and noncyclic photophosphorylation produce ATP. We can infer that the purpose of ATP inphotosynthesis is to ____. a) supply hydrogen to the carbohydrate; b) supply carbon to the carbohydrate; c) supply energythat can be used to form a carbohydrate; d) transfer oxygens from the third phosphate group to the carbohydrate molecule;e) convert RuBP into PGA28. The role of NADPH in oxygen-producing photosynthesis is to ____. a) supply hydrogen to the carbohydrate; b)supply carbon to the carbohydrate; c) supply energy that can be used to form a carbohydrate; d) transfer oxygens from thethird phosphate group to the carbohydrate molecule; e) convert RuBP into PGA. 76
  • 77. 29. The dark reactions require all of these chemicals to proceed except ___. a) ATP; b) NADPH; c) carbon dioxide; d)RUBP; e) oxygen30. The first stable chemical formed by the Calvin Cycle is _____. a) RUBP; b) RU/18; c) PGA; d) PGAL; e) Rubisco31. The hydrogen in the carbohydrate produced by the Calvin Cycle comes from ___ a.) ATP; b) NADPH; c) theenvironment if the pH is very acidic; d) a and b; e) a and c32. The carbon incorporated into the carbohydrate comes from ___. a) ATP; b) NADPH; c) carbon dioxide; d) glucose; e)organic molecules33. C-4 photosynthesis is so named because _____. a) it produces a three carbon compound as the first stable product ofphotosynthesis; b) it produces a four carbon compound as the first stable produc of photosynthesis; c) it produces fourATP and four NADPH molecules for carbon fixation.; d) there are only four steps in this form of carbon fixation intocarbohydrate. 77
  • 78. INTRODUCTION TO GENETICSHeredity, Historical PerspectiveFor much of human history people were unaware of the scientific details of how babies were conceived and how heredityworked. Clearly they were conceived, and clearly there was some hereditary connection between parents and children, butthe mechanisms were not readily apparent. The Greek philosophers had a variety of ideas: Theophrastus proposed thatmale flowers caused female flowers to ripen; Hippocrates speculated that "seeds" were produced by various body partsand transmitted to offspring at the time of conception, and Aristotle thought that male and female semen mixed atconception. Aeschylus, in 458 BC, proposed the male as the parent, with the female as a "nurse for the young life sownwithin her".During the 1700s, Dutch microscopist Anton van Leeuwenhoek (1632-1723) discovered "animalcules" in the sperm ofhumans and other animals. Some scientists speculated they saw a "little man" (homunculus) inside each sperm. Thesescientists formed a school of thought known as the "spermists". They contended the only contributions of the female tothe next generation were the womb in which the homunculus grew, and prenatal influences of the womb. An opposingschool of thought, the ovists, believed that the future human was in the egg, and that sperm merely stimulated the growthof the egg. Ovists thought women carried eggs containing boy and girl children, and that the gender of the offspring wasdetermined well before conception.Pangenesis was an idea that males and females formed "pangenes" in every organ. These pangenes subsequently movedthrough their blood to the genitals and then to the children. The concept originated with the ancient Greeks and influencedbiology until little over 100 years ago. The terms "blood relative", "full-blooded", and "royal blood" are relicts ofpangenesis. Francis Galton, Charles Darwins cousin, experimentally tested and disproved pangenesis during the 1870s.Blending theories of inheritance supplanted the spermists and ovists during the 19th century. The mixture of sperm andegg resulted in progeny that were a "blend" of two parents characteristics. Sex cells are known collectively as gametes(gamos, Greek, meaning marriage). According to the blenders, when a black furred animal mates with white furredanimal, you would expect all resulting progeny would be gray (a color intermediate between black and white). This isoften not the case. Blending theories ignore characteristics skipping a generation. Charles Darwin had to deal with theimplications of blending in his theory of evolution. He was forced to recognize blending as not important (or at least notthe major principle), and suggest that science of the mid-1800s had not yet got the correct answer. That answer came froma contemporary, Gregor Mendel, although Darwin apparently never knew of Mendels work.The Monk and his peasAn Austrian monk, Gregor Mendel, developed the fundamental principles that would becomethe modern science of genetics. Mendel demonstrated that heritable properties are parceled outin discrete units, independently inherited. These eventually were termed genes.Mendel reasoned an organism for genetic experiments should have: 1. a number of different traits that can be studied 2. plant should be self-fertilizing and have a flower structure that limits accidental contact 3. offspring of self-fertilized plants should be fully fertile.Mendels experimental organism was a common garden pea (Pisum sativum), which has a flower that lends itself to self-pollination. The male parts of the flower are termed the anthers. They produce pollen, which contains the male gametes(sperm). The female parts of the flower are the stigma, style, and ovary. The egg (female gamete) is produced in theovary. The process of pollination (the transfer of pollen from anther to stigma) occurs prior to the opening of the peaflower. The pollen grain grows a pollen tube which allows the sperm to travel through the stigma and style, eventually 78
  • 79. reaching the ovary. The ripened ovary wall becomes the fruit (in this case the pea pod). Most flowers allow cross-pollination, which can be difficult to deal with in genetic studies if the male parent plant is not known. Since pea plantsare self-pollinators, the genetics of the parent can be more easily understood. Peas are also self-compatible, allowing self-fertilized embryos to develop as readily as out-fertilized embryos. Mendel tested all 34 varieties of peas available to himthrough seed dealers. The garden peas were planted and studied for eight years. Each character studied had two distinctforms, such as tall or short plant height, or smooth or wrinkled seeds. Mendels experiments used some 28,000 pea plants.Some of Mendels traits as expressed in garden peasMendels contribution was unique because of his methodical approach to a definite problem, use of clear-cut variables andapplication of mathematics (statistics) to the problem. Gregor Using pea plants and statistical methods, Mendel was ableto demonstrate that traits were passed from each parent to their offspring through the inheritance of genes.Mendels work showed: 1. Each parent contributes one factor of each trait shown in offspring. 2. The two members of each pair of factors segregate from each other during gamete formation. 3. The blending theory of inheritance was discounted. 4. Males and females contribute equally to the traits in their offspring. 5. Acquired traits are not inherited.Principle of SegregationMendel studied the inheritance of seed shape first. A cross involving only one trait is referred to as a monohybrid cross.Mendel crossed pure-breeding (also referred to as true-breeding) smooth-seeded plants with a variety that had alwaysproduced wrinkled seeds (60 fertilizations on 15 plants). All resulting seeds were smooth. The following year, Mendelplanted these seeds and allowed them to self-fertilize. He recovered 7324 seeds: 5474 smooth and 1850 wrinkled. To helpwith record keeping, generations were labeled and numbered. The parental generation is denoted as the P1 generation. 79
  • 80. The offspring of the P1 generation are the F1 generation (first filial). The self-fertilizing F1 generation produced the F2 generation (second filial). Inheritance of two alleles, S and s, in peas.Punnett square explaining the behavior of the S and s alleles. P1: smooth X wrinkledF1 : all smoothF2 : 5474 smooth and 1850 wrinkledMeiosis, a process unknown in Mendels day, explains how the traits are inherited. 80
  • 81. Mendel studied seven traits which appeared in two discrete forms, rather than continuous characters which are oftendifficult to distinguish. When "true-breeding" tall plants were crossed with "true-breeding" short plants, all of theoffspring were tall plants. The parents in the cross were the P1 generation, and the offspring represented the F1generation. The trait referred to as tall was considered dominant, while short was recessive. Dominant traits were definedby Mendel as those which appeared in the F1 generation in crosses between true-breeding strains. Recessives were thosewhich "skipped" a generation, being expressed only when the dominant trait is absent. Mendels plants exhibited completedominance, in which the phenotypic expression of alleles was either dominant or recessive, not "in between".When members of the F1 generation were crossed, Mendel recovered mostly tall offspring, with some short ones alsooccurring. Upon statistically analyzing the F2 generation, Mendel determined the ratio of tall to short plants wasapproximately 3:1. Short plants have skipped the F1 generation, and show up in the F2 and succeeding generations.Mendel concluded that the traits under study were governed by discrete (separable) factors. The factors were inherited inpairs, with each generation having a pair of trait factors. We now refer to these trait factors as alleles. Having traitsinherited in pairs allows for the observed phenomena of traits "skipping" generations.Summary of Mendels Results: 1. The F1 offspring showed only one of the two parental traits, and always the same trait. 2. Results were always the same regardless of which parent donated the pollen (was male). 3. The trait not shown in the F1 reappeared in the F2 in about 25% of the offspring. 4. Traits remained unchanged when passed to offspring: they did not blend in any offspring but behaved as separate units. 5. Reciprocal crosses showed each parent made an equal contribution to the offspring.Mendels Conclusions: 1. Evidence indicated factors could be hidden or unexpressed, these are the recessive traits. 81
  • 82. 2. The term phenotype refers to the outward appearance of a trait, while the term genotype is used for the genetic makeup of an organism. 3. Male and female contributed equally to the offsprings genetic makeup: therefore the number of traits was probably two (the simplest solution). 4. Upper case letters are traditionally used to denote dominant traits, lower case letters for recessives.Mendel reasoned that factors must segregate from each other during gamete formation (remember, meiosis was not yetknown!) to retain the number of traits at 2. The Principle of Segregation proposes the separation of paired factors duringgamete formation, with each gamete receiving one or the other factor, usually not both. Organisms carry two alleles forevery trait. These traits separate during the formation of gametes.Dihybrid CrosseWhen Mendel considered two traits per cross (dihybrid, as opposed to single-trait-crosses, monohybrid), The resulting(F2) generation did not have 3:1 dominant:recessive phenotype ratios. The two traits, if considered to inheritindependently, fit into the principle of segregation. Instead of 4 possible genotypes from a monohybrid cross, dihybridcrosses have as many as 16 possible genotypes.Mendel realized the need to conduct his experiments on more complex situations. He performed experiments tracking twoseed traits: shape and color. A cross concerning two traits is known as a dihybrid cross.Crosses With Two TraitsSmooth seeds (S) are dominant over wrinkled (s) seeds.Yellow seed color (Y) is dominant over green (g).Again, meiosis helps us understand the behavior of alleles. 82
  • 83. Methods, Results, and ConclusionsMendel started with true-breeding plants that had smooth, yellow seeds and crossed them with true-breeding plants havinggreen, wrinkled seeds. All seeds in the F1 had smooth yellow seeds. The F2 plants self-fertilized, and produced fourphenotypes:315 smooth yellow108 smooth green101 wrinkled yellow32 wrinkled greenMendel analyzed each trait for separate inheritance as if the other trait were not present. The 3:1 ratio was seen separatelyand was in accordance with the Principle of Segregation. The segregation of S and s alleles must have happenedindependently of the segregation of Y and y alleles. The chance of any gamete having a Y is 1/2; the chance of any onegamete having a S is 1/2.The chance of a gamete having both Y and S is the product of their individual chances (or 1/2 X1/2 = 1/4). The chance of two gametes forming any given genotype is 1/4 X 1/4 (remember, the product of their individualchances). Thus, the Punnett Square has 16 boxes. Since there are more possible combinations to produce a smooth yellowphenotype (SSYY, SsYy, SsYY, and SSYy), that phenotype is more common in the F2. 83
  • 84. From the results of the second experiment, Mendel formulated the Principle of Independent Assortment -- that whengametes are formed, alleles assort independently. If traits assort independent of each other during gamete formation, theresults of the dihybrid cross can make sense. Since Mendels time, scientists have discovered chromosomes and DNA. Wenow interpret the Principle of Independent Assortment as alleles of genes on different chromosomes are inheritedindependently during the formation of gametes. This was not known to Mendel.Punnett squares deal only with probability of a genotype showing up in the next generation. Usually if enough offspringare produced, Mendelian ratios will also be produced.Step 1 - definition of alleles and determination of dominance.Step 2 - determination of alleles present in all different types of gametes.Step 3 - construction of the square.Step 4 - recombination of alleles into each small square.Step 5 - Determination of Genotype and Phenotype ratios in the next generation.Step 6 - Labeling of generations, for example P1, F1, etc.While answering genetics problems, there are certain forms and protocols that will make unintelligible problems easier todo. The term "true-breeding strain" is a code word for homozygous. Dominant alleles are those that show up in the nextgeneration in crosses between two different "true-breeding strains". The key to any genetics problem is the recessivephenotype (more properly the phenotype that represents the recessive genotype). It is that organism whose genotype canbe determined by examination of the phenotype. Usually homozygous dominant and heterozygous individuals haveidentical phenotypes (although their genotypes are different). This becomes even more important in dihybrid crosses.MutationsHugo de Vries, one of three turn-of-the-century scientists who rediscovered the work of Mendel, recognized thatoccasional abrupt, sudden changes occurred in the patterns of inheritance in the primrose plant. These sudden changes hetermed mutations. De Vries proposed that new alleles arose by mutations. Charles Darwin, in his Origin of Species, wasunable to describe how heritable changes were passed on to subsequent generations, or how new adaptations arose.Mutations provided answers to problems of the appearance of novel adaptations. The patterns of Mendelian inheritanceexplained the perseverance of rare traits in organisms, all of which increased variation, as you recall that was a major facetof Darwins theory.Mendels work was published in 1866 but not recognized until the early 1900s when three scientists independentlyverified his principles, more than twenty years after his death. Ignored by the scientific community during his lifetime,Mendels work is now a topic enjoyed by generations of biology students (;))Genetic TermsDefinitions of terms. While we are discussing Mendel, we need to understand the context of his times as well as how hiswork fits into the modern science of genetics.Gene - a unit of inheritance that usually is directly responsible for one trait or character.Allele - an alternate form of a gene. Usually there are two alleles for every gene, sometimes as many a three or four. 84
  • 85. Homozygous - when the two alleles are the same.Heterozygous - when the two alleles are different, in such cases the dominant allele is expressed.Dominant - a term applied to the trait (allele) that is expressed irregardless of the second allele.Recessive - a term applied to a trait that is only expressed when the second allele is the same (e.g. short plants arehomozygous for the recessive allele).Phenotype - the physical expression of the allelic composition for the trait under study.Genotype - the allelic composition of an organism.Punnett squares - probability diagram illustrating the possible offspring of a mating. 85
  • 86. GENE INTERACTIONSFinding the GenesBetween 1884 (the year Mendel died) and 1888 details of mitosis and meiosis were reported, the cell nucleus wasidentified as the location of the genetic material, and "qualities" were even proposed to be transmitted on chromosomes todaughter cells at mitosis. In 1903 Walter Sutton and Theodore Boveri formally proposed that chromosomes contain thegenes. The Chromosome Theory of Inheritance is one of the foundations of genetics and explains the physical reality ofMendels principles of inheritance.The location of many genes (Mendels factors) was determined by Thomas Hunt Morgan and his coworkers in the early1900s. Morgans experimental organism was the fruit fly (Drosophila melanogaster). Fruit flies are ideal organisms forgenetics, having a small size, ease of care, susceptibility to mutations, and short (7-9 day) generation time. The role ofchromosomes in determination of sex was deduced by Morgan from work on fruit flies.During Metaphase I, homologous chromosomes will line up. A karyotype can be made by cutting and arrangingphotomicrographs of the homologous chromosomes thus revealed at Metaphase I. Two types of chromosome pairs occur.Autosomes resemble each other in size and placement of the centromere, for example pairs of chromosome 21 are thesame size, while pairs of chromosome 9 are of a different size from pair 21. Sex chromosomes may differ in their size,depending on the species of the organism they are from. In humans and Drosophila, males have a smaller sexchromosome, termed the Y, and a larger one, termed the X. Males are thus XY, and are termed heterogametic. Femalesare XX, and are termed homogametic. In grasshoppers, which Sutton studied in discovering chromosomes, there is no Y,only the X chromosome in males. Females are XX, while males are denoted as XO. Other organisms (notably birds,moths and butterflies) have males homogametic and females heterogametic. Males (if heterogametic) contribute either anX or Y to the offspring, while females contribute either X. The male thus determines the sex of the offspring. Rememberthat in meiosis, each chromosome is replicated and one copy sent to each gamete.Morgan discovered a mutant eye color and attempted to use this mutant as a recessive to duplicate Mendels results. Hefailed, instead of achieving a 3:1 F2 ratio the ratio was closer to 4:1 (red to white). Most mutations are usually recessive,thus the appearance of the white mutant presented Morgan a chance to test Mendels ratios on animals. The F1 generationalso had no white eyed females. Morgan hypothesized that the gene for eye color was only on the X chromosome,specifically in that region of the X that had no corresponding region on the Y. White eyed fruit flies were also more likelyto die prior to adulthood, thus explaining the altered ratios. Normally eyes are red, but a variant (white) eyed was detectedand used in genetic study. Cross a homozygous white eyed male with a homozygous red eyed female, and all the offspringhave red eyes. Red is dominant over white. However, cross a homozygous white eyed female with a red eyed male, andthe unexpected results show all the males have white eyes and all the females red eyes. This can be explained if the eyecolor gene is on the X chromosome.ExplanationIf the gene for eye color is on the X chromosome, the red eyed male in the second cross will pass his red eyed X to onlyhis daughters, who in turn received only a recessive white-carrying Xfrom their mother. Thus all females had red eyes like their father. Sincethe male fruit fly passes only the Y to his sons, their eye color isdetermined entirely by the single X chromosome they receive from theirmother (in this case white). Thus all the males in the second cross werewhite eyed.These experiments introduced the concept of sex-linkage, theoccurrence of genes on that part of the X that lack a correspondinglocation on the Y. Sex-linked recessives (such as white eyes in fruit 86
  • 87. flies, hemophilia, baldness, and colorblindness in humans) occur more commonly in males, since there is no chance ofthem being heterozygous. Such a condition is termed hemizygous.Characteristics of X-linked Traits1. Phenotypic expression more common in males2. Sons cannot inherit the trait from their fathers, but daughterscan.Sons inherit their Y chromosome from their father.Only a few genes have been identified on the Y chromosome, among them the testis-determining factor (TDF) thatpromotes development of the male phenotype.Barr bodies are interpreted as inactivated X chromosomes in mammalian females. Since females have two Xchromosomes, the Lyon hypothesis suggests that one or the other X is inactivated in each somatic (non-reproductive) cellduring embryonic development. Cells mitotically produced from these embryonic cells likewise have the same inactivatedX chromosome.Calico cats (sometimes called tortoiseshell) are almost always female since the calico trait is caused by some areas of thecats fur expressing one allele and others expressing the other color. Can there be a male tortoiseshell cat? How wouldsuch a cat get its genes? Remember that fur color in cats is a sex-linked feature. Would the male calico be fertile orsterile?The Modern View of the GeneWhile Mendel discussed traits, we now know that genes are segments of the DNA that code for specific proteins. Theseproteins are responsible for the expression of the phenotype. The basic principles of segregation and independentassortment as worked out by Mendel are applicable even for sex-linked traits.Codominant allelesCodominant alleles occur when rather than expressing an intermediate phenotype, the heterozygotes express bothhomozygous phenotypes. An example is in human ABO blood types, the heterozygote AB type manufactures antibodiesto both A and B types. Blood Type A people manufacture only anti-B antibodies, while type B people make only anti-Aantibodies. Codominant alleles are both expressed. Heterozygotes for codominant alleles fully express both alleles. Blood 87
  • 88. type AB individuals produce both A and B antigens. Since neither A nor B is dominant over the other and they are bothdominant over O they are said to be codominant.Incomplete dominanceIncomplete dominance is a condition when neither allele is dominant over the other.condition is recognized by the heterozygotes expressing an intermediate phenotyperelative to the parental phenotypes. If a red flowered plant is crossed with a whiteflowered one, the progeny will all be pink. When pink is crossed with pink, theprogeny are 1 red, 2 pink, and 1 white.Flower color in snapdragons is an example of this pattern. Cross a true-breeding red strain with a true-breeding white strain and the F1 are allpink (heterozygotes). Self-fertilize the F1 and you get an F2 ratio of 1red: 2 pink: 1 white. This would not happen if true blending hadoccurred (blending cannot explain traits such as red or white skipping ageneration and pink flowers crossed with pink flowers should produceONLY pink flowers).Multiple allelesMany genes have more than two alleles (even though any one diploid individual can only have at most two alleles for anygene), such as the ABO blood groups in humans, which are an example of multiple alleles. Multiple alleles result fromdifferent mutations of the same gene. Coat color in rabbits is determined by four alleles. Human ABO blood types aredetermined by alleles A, B, and O. A and B are codominants which are both dominant over O. The only possible genotypefor a type O person is OO. Type A people have either AA or AO genotypes. Type B people have either BB or BOgenotypes. Type AB have only the AB (heterozygous) genotype. The A and B alleles of gene I produce slightly differentglycoproteins (antigens) that are on the surface of each cell. Homozygous A individuals have only the A antigen,homozygous B individuals have only the B antigen, homozygous O individuals produce neither antigen, while a fourthphenotype (AB) produces both A and B antigens.Interactions among genesWhile one gene may make only one protein, the effects of those proteins usually interact (for example widows peak maybe masked by expression of the baldness gene). Novel phenotypes often result from the interactions of two genes, as in thecase of the comb in chickens. The single comb is produced only by the rrpp genotype. Rose comb (b) results from R_pp.(_ can be either R or r). Pea comb (c) results from rrP_. Walnut comb, a novel phenotype, is produced when the genotypehas at least one dominant of each gene (R_P_).EpistasisEpistasis is the term applied when one gene interferes with the expression of another (as in the baldness/widows peakmentioned earlier). Bateson reported a different phenotypic ratio in sweet pea than could be explained by simpleMendelian inheritance. This ratio is 9:7 instead of the 9:3:3:1 one would expect of a dihybrid cross betweenheterozygotes. Of the two genes (C and P), when either is homozygous recessive (cc or pp) that gene is epistatic to (orhides) the other. To get purple flowers one must have both C and P alleles present.Environment and Gene ExpressionPhenotypes are always affected by their environment. In buttercup (Ranunculus peltatus), leaves below water-level arefinely divided and those above water-level are broad, floating, photosynthetic leaf-like leaves. Siamese cats are darker on 88
  • 89. their extremities, due to temperature effects on phenotypic expression. Expression of phenotype is a result of interactionbetween genes and environment. Siamese cats and Himalayan rabbits both animals have dark colored fur on theirextremities. This is caused by an allele that controls pigment production being able only to function at the lowertemperatures of those extremities. Environment determines the phenotypic pattern of expression.Polygenic InheritancePolygenic inheritance is a pattern responsible for many features that seem simple on the surface. Many traits such asheight, shape, weight, color, and metabolic rate are governed by the cumulative effects of many genes. Polygenic traits arenot expressed as absolute or discrete characters, as was the case with Mendels pea plant traits. Instead, polygenic traits arerecognizable by their expression as a gradation of small differences (a continuous variation). The results form a bellshaped curve, with a mean value and extremes in either direction.Height in humans is a polygenic trait, as is color in wheat kernels. Height in humans is NOT discontinuous. If you line upthe entire class a continuum of variation is evident, with an average height and extremes in variation (very short[vertically challenged?] and very tall [vertically enhanced]). Traits showing continuous variation are usually controlled bythe additive effects of two or more separate gene pairs. This is an example of polygenic inheritance. The inheritance ofEACH gene follows Mendelian rules.Usually polygenic traits are distinguished by 1. Traits are usually quantified by measurement rather than counting. 2. Two or more gene pairs contribute to the phenotype. 3. Phenotypic expression of polygenic traits varies over a wide range.Human polygenic traits include 1. Height 2. SLE (Lupus) Weight 3. Eye Color) 4. Intelligence 5. Skin Color 6. Many forms of behavior 89
  • 90. PleiotropyPleiotropy is the effect of a single gene on more than one characteristic. An example is the "frizzle-trait" in chickens. Theprimary result of this gene is the production of defective feathers. Secondary results are both good and bad; good includeincreased adaptation to warm temperatures, bad include increased metabolic rate, decreased egg-laying, changes in heart,kidney and spleen. Cats that are white with blue eyes are often deaf, white cats with a blue and an yellow-orange eye aredeaf on the side with the blue eye. Sickle-cell anemia is a human disease originating in warm lowland tropical areas wheremalaria is common. Sickle-celled individuals suffer from a number of problems, all of which are pleiotropic effects of thesickle-cell allele.Genes and Chromosomes 90
  • 91. Linkage occurs when genes are on the same chromosome. Remember that sex-linked genes are on the X chromosome,one of the sex chromosomes. Linkage groups are invariably the same number as the pairs of homologous chromosomes anorganism possesses. Recombination occurs when crossing-over has broken linkage groups, as in the case of the genes forwing size and body color that Morgan studied. Chromosome mapping was originally based on the frequencies ofrecombination between alleles.Since mutations can be induced (by radiation or chemicals), Morgan and his coworkers were able to cause new alleles toform by subjecting fruit flies to mutagens (agents of mutation, or mutation generators). Genes are located on specificregions of a certain chromosome, termed the gene locus (plural: loci). A gene therefore is a specific segment of the DNAmolecule.Alfred Sturtevant, while an undergraduate student in Morgans lab, postulated that crossing-over would be less commonbetween genes adjacent to each other on the same chromosome and that it should be possible to plot the sequence of genesalong a fruit fly chromosome by using crossing-over frequencies. Distances on gene maps are expressed in map units (onemap unit = 1 recombinant per 100 fertilized eggs; or a 1% chance of recombination).The map for Drosophila melanogaster chromosomes is well known Note that eye color and aristae length are far apart, asindicated by the occurrence of more recombinants (crossing-overs) between them, while wing length is closer to eyeshape (as indicated by the low frequency of recombination between these two features).Figure A illustrates the fruit fly chromosomes at metaphase; figure B shows a polytene chromosome.Chromosome AbnormalitiesChromosome abnormalities include inversion, insertion, duplication, and deletion. These are types of mutations. SinceDNA is information, and information typically has a beginning point, an inversion would produce an inactive or alteredprotein. Likewise deletion or duplication will alter the gene product. 91
  • 92. 92
  • 93. DNA AND MOLECULAR GENETICSThe physical carrier of inheritanceWhile the period from the early 1900s to World War II has been considered the "golden age" of genetics, scientists stillhad not determined that DNA, and not protein, was the hereditary material. However, during this time a great manygenetic discoveries were made and the link between genetics and evolution was made.Friedrich Meischer in 1869 isolated DNA from fish sperm and the pus of open wounds. Since it came from nuclei,Meischer named this new chemical, nuclein. Subsequently the name was changed to nucleic acid and lastly todeoxyribonucleic acid (DNA). Robert Feulgen, in 1914, discovered that fuchsin dye stained DNA. DNA was then foundin the nucleus of all eukaryotic cells.During the 1920s, biochemist P.A. Levene analyzed the components of the DNA molecule. He found it contained fournitrogenous bases: cytosine, thymine, adenine, and guanine; deoxyribose sugar; and a phosphate group. He concluded thatthe basic unit (nucleotide) was composed of a base attached to a sugar and that the phosphate also attached to the sugar.He (unfortunately) also erroneously concluded that the proportions of bases were equal and that there was atetranucleotide that was the repeating structure of the molecule. The nucleotide, however, remains as the fundemantal unit(monomer) of the nucleic acid polymer. There are four nucleotides: those with cytosine (C), those with guanine (G), thosewith adenine (A), and those with thymine (T). 93
  • 94. During the early 1900s, the study of genetics began in earnest: the link between Mendels work and that of cell biologistsresulted in the chromosomal theory of inheritance; Garrod proposed the link between genes and "inborn errors ofmetabolism"; and the question was formed: what is a gene? The answer came from the study of a deadly infectiousdisease: pneumonia. During the 1920s Frederick Griffith studied the difference between a disease-causing strain of thepneumonia causing bacteria (Streptococcus peumoniae) and a strain that did not cause pneumonia. The pneumonia- 94
  • 95. causing strain (the S strain) was surrounded by a capsule. The other strain (the R strain) did not have a capsule and alsodid not cause pneumonia. Frederick Griffith (1928) was able to induce a nonpathogenic strain of the bacteriumStreptococcus pneumoniae to become pathogenic. Griffith referred to a transforming factor that caused the non-pathogenic bacteria to become pathogenic. Griffith injected the different strains of bacteria into mice. The S strain killedthe mice; the R strain did not. He further noted that if heat killed S strain was injected into a mouse, it did not causepneumonia. When he combined heat-killed S with Live R and injected the mixture into a mouse (remember neither alonewill kill the mouse) that the mouse developed pneumonia and died. Bacteria recovered from the mouse had a capsule andkilled other mice when injected into them!Hypotheses:1. The dead S strain had been reanimated/resurrected.2. The Live R had been transformed into Live S by some "transforming factor".Further experiments led Griffith to conclude that number 2 was correct.In 1944, Oswald Avery, Colin MacLeod, and Maclyn McCarty revisited Griffiths experiment and concluded thetransforming factor was DNA. Their evidence was strong but not totally conclusive. The then-current favorite for thehereditary material was protein; DNA was not considered by many scientists to be a strong candidate.The breakthrough in the quest to determine the hereditary material came from the work of Max Delbruck and SalvadorLuria in the 1940s. Bacteriophage are a type of virus that attacks bacteria, the viruses that Delbruck and Luria workedwith were those attacking Escherichia coli, a bacterium found in human intestines. Bacteriophages consist of protein coatscovering DNA. Bacteriophages infect a cell by injecting DNA into the host cell. This viral DNA then "disappears" whiletaking over the bacterial machinery and beginning to make new virus instead of new bacteria. After 25 minutes the hostcell bursts, releasing hundreds of new bacteriophage. Phages have DNA and protein, making them ideal to resolve thenature of the hereditary material.In 1952, Alfred D. Hershey and Martha Chase (click the link to view details of their experiment) conducted a series ofexperiments to determine whether protein or DNA was the hereditary material. By labeling the DNA and protein withdifferent (and mutually exclusive) radioisotopes, they would be able to determine which chemical (DNA or protein) wasgetting into the bacteria. Such material must be the hereditary material (Griffiths transforming agent). Since DNAcontains Phosphorous (P) but no Sulfur (S), they tagged the DNA with radioactive Phosphorous-32. Conversely, proteinlacks P but does have S, thus it could be tagged with radioactive Sulfur-35. Hershey and Chase found that the radioactiveS remained outside the cell while the radioactive P was found inside the cell, indicating that DNA was the physical carrierof heredity. 95
  • 96. The Structure of DNAErwin Chargaff analyzed the nitrogenous bases in many different forms of life, concluding that the amount of purinesdoes not always equal the amount of pyrimidines (as proposed by Levene). DNA had been proven as the genetic materialby the Hershey-Chase experiments, but how DNA served as genes was not yet certain. DNA must carry information fromparent cell to daughter cell. It must contain information for replicating itself. It must be chemically stable, relativelyunchanging. However, it must be capable of mutational change. Without mutations there would be no process ofevolution.Many scientists were interested in deciphering the structure of DNA, among them were Francis Crick, James Watson,Rosalind Franklin, and Maurice Wilkens. Watson and Crick gathered all available data in an attempt to develop a modelof DNA structure. Franklin took X-ray diffraction photomicrographs of crystalline DNA extract, the key to the puzzle.The data known at the time was that DNA was a long molecule, proteins were helically coiled (as determined by the workof Linus Pauling), Chargaffs base data, and the x-ray diffraction data of Franklin and Wilkens. 96
  • 97. Ball and stick model of DNA.X-ray diffraction photograph of the DNA double helix.James Watson (L) and Francis Crick (R), and the model they built of the structure of DNA.DNA is a double helix, with bases to the center (like rungs on a ladder) and sugar-phosphate units along the sides of thehelix (like the sides of a twisted ladder). The strands are complementary (deduced by Watson and Crick from Chargaffsdata, A pairs with T and C pairs with G, the pairs held together by hydrogen bonds). Notice that a double-ringed purine isalways bonded to a single ring pyrimidine. Purines are Adenine (A) and Guanine (G). We have encountered Adenosinetriphosphate (ATP) before, although in that case the sugar was ribose, whereas in DNA it is deoxyribose. Pyrimidines areCytosine (C) and Thymine (T). The bases are complementary, with A on one side of the molecule you only get T on theother side, similarly with G and C. If we know the base sequence of one strand we know its complement. 97
  • 98. The ribbon model of DNA.DNA ReplicationDNA was proven as the hereditary material and Watson et al. had deciphered its structure. What remained was todetermine how DNA copied its information and how that was expressed in the phenotype. Matthew Meselson andFranklin W. Stahl designed an experiment to determine the method of DNA replication. Three models of replication wereconsidered likely.1. Conservative replication would somehow produce an entirely new DNAstrand during replication.2. Semiconservative replication would produce two DNA molecules, each ofwhich was composed of one-half of the parental DNA along with an entirelynew complementary strand. In other words the new DNA would consist of onenew and one old strand of DNA. The existing strands would serve ascomplementary templates for the new strand. 98
  • 99. 3. Dispersive replication involved the breaking of the parental strands duringreplication, and somehow, a reassembly of molecules that were a mix of old and newfragments on each strand of DNA.The Meselson-Stahl experiment involved the growth of E.coli bacteria on a growth medium containing heavy nitrogen(Nitrogen-15 as opposed to the more common, but lightermolecular weight isotope, Nitrogen-14). The first generationof bacteria was grown on a medium where the sole source ofN was Nitrogen-15. The bacteria were then transferred to amedium with light (Nitrogen-14) medium. Watson and Crickhad predicted that DNA replication was semi-conservative.If it was, then the DNA produced by bacteria grown on lightmedium would be intermediate between heavy and light. Itwas.DNA replication involves a great many building blocks,enzymes and a great deal of ATP energy (remember thatafter the S phase of the cell cycle cells have a G phase to regenerate energy for cell division). Only occurring in a cellonce per (cell) generation, DNA replication in humans occurs at a rate of 50 nucleotides per second, 500/second inprokaryotes. Nucleotides have to be assembled and available in the nucleus, along with energy to make bonds betweennucleotides. DNA polymerases unzip the helix by breaking the H-bonds between bases. Once the polymerases haveopened the molecule, an area known as the replication bubble forms (always initiated at a certain set of nucleotides, theorigin of replication). New nucleotides are placed in the fork and link to the corresponding parental nucleotide alreadythere (A with T, C with G). Prokaryotes open a single replication bubble, while eukaryotes have multiple bubbles. Theentire length of the DNA molecule is replicated as the bubbles meet. 99
  • 100. Since the DNA strands are antiparallel, and replication proceeds in the 5 to 3 direction on EACH strand, one strand willform a continuous copy, while the other will form a series of short Okazaki fragments. 100
  • 101. PROTEIN SYNTHESISOne-gene-one-proteinDuring the 1930s, despite great advances, geneticists had several frustrating questions yet to answer:What exactly are genes?How do they work?What produces the unique phenotype associated with a specific allele?Answers from physics, chemistry, and the study of infectious disease gave rise to the field of molecular biology.Biochemical reactions are controlled by enzymes, and often are organized into chains of reactions known as metabolicpathways. Loss of activity in a single enzyme can inactivate an entire pathway.Archibald Garrod, in 1902, first proposed the relationship through his study of alkaptonuria and its association with largequantities "alkapton". He reasoned unaffected individuals metabolized "alkapton" (now called homogentistic acid) toother products so it would not buildup in the urine. Garrod suspected a blockage of the pathway to break this chemicaldown, and proposed that condition as "an inborn error of metabolism". He also discovered alkaptonuria was inherited as arecessive Mendelian trait.George Beadle and Edward Tatum during the late 1930s and early 1940s established the connection Garrod suspectedbetween genes and metabolism. They used X rays to cause mutations in strains of the mold Neurospora. These mutationsaffected a single genes and single enzymes in specific metabolic pathways. Beadle and Tatum proposed the "one gene oneenzyme hypothesis" for which they won the Nobel Prize in 1958.Since the chemical reactions occurring in the body are mediated by enzymes, and since enzymes are proteins and thusheritable traits, there must be a relationship between the gene and proteins. George Beadle, during the 1940s, proposedthat mutant eye colors in Drosophila was caused by a change in one protein in a biosynthetic pathway.In 1941 Beadle and coworker Edward L. Tatum decided to examine step by step the chemical reactions in a pathway.They used Neurospora crassa as an experimental organism. It had a short life-cycle and was easily grown. Since it ishaploid for much of its life cycle, mutations would be immediately expressed. The meiotic products could be easilyinspected. Chromosome mapping studies on the organism facilitated their work. Neurospora can be grown on a minimalmedium, and its nutrition could be studied by its ability to metabolize sugars and other chemicals the scientist could addor delete from the mixture of the medium. It was able to synthesize all of the amino acids and other chemicals needed forit to grow, thus mutants in synthetic pathways would easily show up. X-rays induced mutations in Neurospora, and themutated spores were placed on growth media enriched with all essential amino acids. Crossing the mutated fungi withnon-mutated forms produced spores which were then grown on media supplying only one of the 20 essential amino acids.If a spore lacked the ability to synthesize a particular amino acid, such as Pro (proline), it would only grow if the Prolinewas in the growth medium. Biosynthesis of amino acids (the building blocks of proteins) is a complex process with manychemical reactions mediated by enzymes, which if mutated would shut down the pathway, resulting in no-growth. Beadleand Tatum proposed the "one gene one enzyme" theory. One gene codes for the production of one protein. "One gene oneenzyme" has since been modified to "one gene one polypeptide" since many proteins (such as hemoglobin) are made ofmore than one polypeptide. 101
  • 102. 102
  • 103. The Structure of HemoglobinLinus Pauling used electrophoresis to separate hemoglobin molecules. Sickle-cell anemia (h) is a recessive allele in whicha defective hemoglobin is made, ultimately causing pain and death to those individuals homozygous recessive for the trait.Pauling reasoned that if Beadle and Tatum were correct, there should be a slight (but detectable) difference between thestructure of a normal (HH) and sickle cell (hh) hemoglobin due to genetic differences. Heterozygotes (Hh, also sampledby Pauling) make both normal and "sickle cell" hemoglobins. Later, Vernon Ingram discovered that the normal andsickle-cell hemoglobins differ by only 1 (out of a total of 300) amino acids.Viruses Contain DNAThe coats of viruses act as antigens, initiating an antigen-specific antibody response. Remember that vaccines work byeither prompting the immune system to make antibodies or by supplying antibodies. If a virus (or anything else for thatmatter) mutates its antigens, the immune system is forever playing catch-up.RNA Links the Information in DNA to the Sequence of Amino Acids in ProteinRibonucleic acid (RNA) was discovered after DNA. DNA, with exceptions in chloroplasts and mitochondria, is restrictedto the nucleus (in eukaryotes, the nucleoid region in prokaryotes). RNA occurs in the nucleus as well as in the cytoplasm(also remember that it occurs as part of the ribosomes that line the rough endoplasmic reticulum).Scientists for some time had suspected such a link between DNA and proteins. Cells of developing embryos contain highlevels of RNA. Rapidly growing E. coli has half its mass as ribosomes. Ribosomes are 2/3 RNA (a type of RNA known asribosomal RNA or rRNA) and 1/3 protein. RNA is synthesized from viral DNA in an infected cell before proteinsynthesis begins. Some viruses, for example Tobacco Mosaic Virus (TMV) have RNA in place of DNA. If RNA extractedfrom a virus was injected into a host cell the cell began to make new viruses. Clearly RNA was involved in proteinsynthesis.Cricks central dogma. Information flow (with the exception of reverse transcription) is from DNA to RNA via the processof transcription, and thence to protein via translation. Transcription is the making of an RNA molecule off a DNAtemplate. Translation is the construction of an amino acid sequence (polypeptide) from an RNA molecule. Althoughoriginally called dogma, this idea has been tested repeatedly with almost no exceptions to the rule being found (saveretroviruses). 103
  • 104. Messenger RNA (mRNA) is the blueprint for construction of a protein. Ribosomal RNA (rRNA) is the construction sitewhere the protein is made. Transfer RNA (tRNA) is the truck delivering the proper amino acid to the site at the right time.RNA has ribose sugar instead of deoxyribose sugar. The base uracil (U) replaces thymine (T) in RNA. Most RNA issingle stranded, although tRNA will form a "cloverleaf" structure due to complementary base pairing.Transcription: making an RNA copy of a DNA sequenceRNA polymerase opens the part of the DNA to be transcribed. Only one strand of DNA (the template strand) istranscribed. RNA nucleotides are available in the region of the chromatin (this process only occurs during Interphase) andare linked together similar to the DNA process. 104
  • 105. The Genetic Code: Translation of RNA code into proteinThe code consists of at least three bases, according to astronomer George Gamow. To code for the 20 essential aminoacids a genetic code must consist of at least a 3-base set (triplet) of the 4 bases. If one considers the possibilities ofarranging four things 3 at a time (4X4X4), we get 64 possible code words, or codons (a 3-base sequence on the mRNAthat codes for either a specific amino acid or a control word).The genetic code was broken by Marshall Nirenberg and Heinrich Matthaei, a decade after Watson and Cricks work.Nirenberg discovered that RNA, regardless of its source organism, could initiate protein synthesis when combined withcontents of broken E. coli cells. By adding poly-U to each of 20 test-tubes (each tube having a different "tagged" aminoacid) Nirenberg and Matthaei were able to determine that the codon UUU (the only one in poly-U) coded for the aminoacid phenylalanine. 105
  • 106. Likewise, an artificial mRNA consisting of alternating A and C bases would code for alternating amino acids histidine andthreonine. Gradually, a complete listing of the genetic code codons was developed.The genetic code consists of 61 amino-acid coding codonsand three termination codons, which stop the process oftranslation. The genetic code is thus redundant (degeneratein the sense of having multiple states amounting to thesame thing), with, for example, glycine coded for by GGU,GGC, GGA, and GGG codons. If a codon is mutated, sayfrom GGU to CGU, is the same amino acid specified?Protein SynthesisProkaryotic gene regulation differs from eukaryotic regulation, but since prokaryotes are much easier to work with, wefocus on prokaryotes at this point. Promoters are sequences of DNA that are the start signals for the transcription ofmRNA. Terminators are the stop signals. mRNA molecules are long (500- 10,000 nucleotides).Ribosomes are the organelle (in all cells) where proteins are synthesized. They consist of two-thirds rRNA and one-thirdprotein. Ribosomes consist of a small (in E. coli , 30S) and larger (50S) subunits. The length of rRNA differs in each. The30S unit has 16S rRNA and 21 different proteins. The 50S subunit consists of 5S and 23S rRNA and 34 different proteins.The smaller subunit has a binding site for the mRNA. The larger subunit has two binding sites for tRNA. 106
  • 107. Transfer RNA (tRNA) is basically cloverleaf-shaped. tRNA carries the proper amino acid to the ribosome when the codons call for them. At the top of the large loop are three bases, the anticodon, which is the complement of the codon. There are 61 different tRNAs, each having a different binding site for the amino acid and a different anticodon. For the codon UUU, the complementary anticodon is AAA. Amino acid linkage to the proper tRNA is controlled by the aminoacyl-tRNA synthetases. Energy for binding the amino acid to tRNA comes from ATP conversion to adenosine monophosphate (AMP).Translation is the process of converting the mRNA codon sequences into an amino acid sequence. The initiator codon(AUG) codes for the amino acid N-formylmethionine (f-Met). No transcription occurs without the AUG codon. f-Met isalways the first amino acid in a polypeptide chain, although frequently it is removed after translation. The intitator tRNA/mRNA/small ribosomal unit is called the initiation complex. The larger subunit attaches to the initiation complex. Afterthe initiation phase the message gets longer during the elongation phase. 107
  • 108. 108
  • 109. New tRNAsbring theiramino acids tothe openbinding siteon theribosome/mRNA complex, forming a peptide bond between the amino acids. The complex then shifts along the mRNA tothe next triplet, opening the A site. The new tRNA enters at the A site. When the codon in the A site is a terminationcodon, a releasing factor binds to the site, stopping translation and releasing the ribosomal complex and mRNA.Often many ribosomes will read the same message, a structure known as a polysome forms. In this way a cell may rapidlymake many proteins. 109
  • 110. Mutations RedefinedWe earlier defined mutations as any change in the DNA. We now can refine that definition: a mutation is a change in theDNA base sequence that results in a change of amino acid(s) in the polypeptide coded for by that gene. Alleles arealternate sequences of DNA bases (genes), and thus at the molecular level the products of alleles differ (often by only a 110
  • 111. single amino acid, which can have a ripple effect on an organism by changing ). Addition, deletion, or addition ofnucleotides can alter the polypeptide. Point mutations are the result of the substitution of a single base. Frame-shiftmutations occur when the reading frame of the gene is shifted by addition or deletion of one or more bases. With theexception of mitochondria, all organisms use the same genetic code. Powerful evidence for the common ancestry of allliving things. 111
  • 112. POPULATION ECOLOGYEcologyIn previous chapters/units we have concentrated on the biology of the individual cell, tissue, and organism.There are levels of organization above the individual organism that will be the subject of this unit. Individualorganisms are grouped into populations, which in turn form communities, which form ecosystems. Ecosystemsmake up the biosphere, which includes all life on Earth. If there is life on other planets, will we need anotherlevel of organization?Biosphere: The sum of all living things taken in conjunction with their environment. In essence, where lifeoccurs, from the upper reaches of the atmosphere to the top few meters of soil, to the bottoms of the oceans. Wedivide the earth into atmosphere (air), lithosphere (earth), hydrosphere (water), and biosphere (life).Ecosystem: The relationships of a smaller groups of organisms with each other and their environment. Scientistsoften speak of the interrelatedness of living things. Since, according to Darwins theory, organisms adapt to theirenvironment, they must also adapt to other organisms in that environment. We can discuss the flow of energythrough an ecosystem from photosynthetic autotrophs to herbivores to carnivores.Community: The relationships between groups of different species. For example, the desert communitiesconsist of rabbits, coyotes, snakes, birds, mice and such plants as sahuaro cactus (Carnegia gigantea), Ocotillo,creosote bush, etc. Community structure can be disturbed by such things as fire, human activity, and over-population.Species: Groups of similar individuals who tend to mate and produce viable, fertile offspring. We often findspecies described not by their reproduction (a biological species) but rather by their form (anatomical or formspecies).Populations: Groups of similar individuals who tend to mate with each other in a limited geographic area. Thiscan be as simple as a field of flowers, which is separated from another field by a hill or other area where none ofthese flowers occur.Individuals: One or more cells characterized by a unique arrangement of DNA "information". These can beunicellular or multicellular. The multicellular individual exhibits specialization of cell types and division oflabor into tissues, organs, and organ systems.Ecology is the study how organisms interact with each other and their physical environment. These interactionsare often quite complex. Human activity frequently disturbs living systems and affects these interactions.Ecological predictions are, of a consequence, often more general than we would like.Population GrowthA population is a group of individuals of the same species living in the same geographic area. The study offactors that affect growth, stability, and decline of populations is population dynamics. All populations undergothree distinct phases of their life cycle: 1. growth 2. stability 112
  • 113. 3. declinePopulation growth occurs when available resources exceed the number of individuals able to exploit them.Reproduction is rapid, and death rates are low, producing a net increase in the population size.Population stability is often proceeded by a "crash" since the growing population eventually outstrips itsavailable resources. Stability is usually the longest phase of a populations life cycle.Decline is the decrease in the number of individuals in a population, and eventually leads to populationextinction.Factors Influencing Population GrowthNearly all populations will tend to grow exponentially as long as there are resources available. Most populationshave the potential to expand at an exponential rate, since reproduction is generally a multiplicative process. Twoof the most basic factors that affect the rate of population growth are the birth rate, and the death rate. Theintrinsic rate of increase is the birth rate minus the death rate.Two modes of population growth. The Exponential curve (also known as a J-curve) occurs when there is nolimit to population size. The Logistic curve (also known as an S-curve) shows the effect of a limiting factor (inthis case the carrying capacity of the environment).Population Growth Potential Is Related to Life HistoryThe age within its individual life cycle at which an organism reproduces affects the rate of population increase.Life history refers to the age of sexual maturity, age of death, and other events in that individuals lifetime thatinfluence reproductive traits. Some organisms grow fast, reproduce quickly, and have abundant offspring eachreproductive cycle. Other organisms grow slowly, reproduce at a late age, and have few offspring per cycle.Most organisms are intermediate to these two extremes. 113
  • 114. Age structure refers to the relative proportion of individuals in each age group of a population. Populations withmore individuals aged at or before reproductive age have a pyramid-shaped age structure graph, and can expandrapidly as the young mature and breed. Stable populations have relatively the same numbers in each of the ageclasses.Comparison of the population age structure in the United States and Mexico. Note the demographic bulge in theMexican population. The effects of this bulge will be felt for generations.Human populations are in a growth phase. Since evolving about 200,000 years ago, our species has proliferatedand spread over the Earth. Beginning in 1650, the slow population increases of our species exponentiallyincreased. New technologies for hunting and farming have enabled this expansion. It took 1800 years to reach atotal population of 1 billion, but only 130 years to reach 2 billion, and a mere 45 years to reach 4 billion.Despite technological advances, factors influencing population growth will eventually limit expansion of humanpopulation. These will involve limitation of physical and biological resources as world population increased toover six billion in 1999. The 1987 population was estimated at a puny 5 billion. 114
  • 115. Human population growth over the past 10,000 years. Note the effects of worldwide disease (the Black death)and technological advances on the population size.Populations Transition Between Growth and StabilityLimits on population growth can include food supply, space, and complex interactions with other physical andbiological factors (including other species). After an initial period of exponential growth, a population willencounter a limiting factor that will cause the exponential growth to stop. The population enters a slower growthphase and may eventually stabilize at a fairly constant population size within some range of fluctuation. Thismodel fits the logistic growth model. The carrying capacity is the point where population size levels off.Several Basic Controls Govern Population SizeThe environment is the ultimate cause of population stabilization. Two categories of factors are commonlyused: physical environment and biological environment. Three subdivisions of the biological environment arecompetition, predation, and symbiosis.Physical environment factors include food, shelter, water supply, space availability, and (for plants) soil andlight. One of these factors may severely limit population size, even if the others are not as constrained. The Lawof the Minimum states that population growth is limited by the resource in the shortest supply.The biological role played by a species in the environment is called a niche. Organisms/populations incompetition have a niche overlap of a scarce resource for which they compete. Competitive exclusion occursbetween two species when competition is so intense that one species completely eliminates the second speciesfrom an area. In nature this is rather rare. While owls and foxes may compete for a common food source, thereare alternate sources of food available. Niche overlap is said to be minimal.Paramecium aurelia has a population nearly twice as large when it does not have to share its food source with acompeting species. Competitive release occurs when the competing species is no longer present and itsconstraint on the winners population size is removed.Predators kill and consume other organisms. Carnivores prey on animals, herbivores consume plants. Predatorsusually limit the prey population, although in extreme cases they can drive the prey to extinction. There arethree major reasons why predators rarely kill and eat all the prey: 115
  • 116. 1. Prey species often evolve protective mechanisms such as camouflage, poisons, spines, or large size to deter predation. 2. Prey species often have refuges where the predators cannot reach them. 3. Often the predator will switch its prey as the prey species becomes lower in abundance: prey switching.Fluctuations in predator (wolf) and prey (moose) populations over a 40-year span. Note the effects of declinesin the wolf population in the late 1960s and again in the early 1980s on the moose population.Symbiosis has come to include all species interactions besides predation and competition. Mutualism is a symbiosis where both parties benefit, for example algae (zooxanthellae) inside reef-buildingcoral. Parasitism is a symbiosis where one species benefits while harming the other. Parasites act more slowly thanpredators and often do not kill their host.Commensalism is a symbiosis where one species benefits and the other is neither harmed nor gains a benefit:Spanish moss on trees, barnacles on crab shells. Amensalism is a symbiosis where members of one population inhibit the growth of another while beingunaffected themselves.The Real World Has a Complex Interaction of Population ControlsNatural populations are not governed by a single control, but rather have the combined effects of many controlssimultaneously playing roles in determining population size. If two beetle species interact in the laboratory, oneresult occurs; if a third species is introduced, a different outcome develops. The latter situation is more likenature, and changes in one population may have a domino effect on others.Which factors, if either, is more important in controlling population growth: physical or biological? Physicalfactors may play a dominant role, and are called density independent regulation, since population density is nota factor The other extreme has biological factors dominant, and is referred to as density dependent regulation, 116
  • 117. since population density is a factor. It seems likely that one or the other extreme may dominate in someenvironments, with most environments having a combination control.Population Decline and ExtinctionExtinction is the elimination of all individuals in a group. Local extinction is the loss of all individuals in apopulation. Species extinction occurs when all members of a species and its component populations go extinct.Scientists estimate that 99% of all species that ever existed are now extinct. The ultimate cause of decline andextinction is environmental change. Changes in one of the physical factors of the environment may cause thedecline and extinction; likewise the fossil record indicates that some extinctions are caused by migration of acompetitor.Dramatic declines in human population happen periodically in response to an infectious disease. Bubonicplague infections killed half of Europes population between 1346 and 1350, later plagues until 1700 killed onequarter of the European populace. Smallpox and other diseases decimated indigenous populations in North andSouth America.Human ImpactHuman populations have continued to increase, due to use of technology that has disrupted natural populations.Destabilization of populations leads to possible outcomes: • population growth as previous limits are removed • population decline as new limits are imposedAgriculture and animal domestication are examples of population increase of favored organisms. In Englandalone more than 300,000 cats are put to sleep per year, yet before their domestication, the wild cat ancestorswere rare and probably occupied only a small area in the Middle East.PollutionPollutants generally are (unplanned?) releases of substances into the air and water. Many lakes often havenitrogen and phosphorous as limiting nutrients for aquatic and terrestrial plants. Runoff from agriculturalfertilizers increases these nutrients, leading to runaway plant growth, or eutrophication. Increased plantpopulations eventually lead to increased bacterial populations that reduce oxygen levels in the water, causingfish and other organisms to suffocate.Pesticides and CompetitionRemoval of a competing species can cause the ecological release of a population explosion in that speciescompetitor. Pesticides sprayed on wheat fields often result in a secondary pest outbreak as more-tolerant-to-pesticide species expand once less tolerant competitors are removed.Removal of PredatorsPredator release is common where humans hunt, trap, or otherwise reduce predator populations, allowing theprey population to increase. Elimination of wolves and panthers have led to increase in their natural prey: deer.There are more deer estimated in the United States than there were when Europeans arrived. Large deerpopulations often cause over grazing that in turn leads to starvation of the deer. 117
  • 118. Introduction of New SpeciesIntroduction of exotic or alien non-native species into new areas is perhaps the greatest single factor to affectnatural populations. More than 1500 exotic insect species and more than 25 families of alien fish have beenintroduced into North America; in excess of 3000 plant species have also been introduced. The majority ofaccidental introductions may fail, however, once an introduced species becomes established, its populationgrowth is explosive. Kudzu, a plant introduced to the American south from Japan, has taken over large areas ofthe countryside.Altering Population GrowthHumans can remove or alter the constraints on population sizes, with both good and bad consequences. On thenegative side, about 17% of the 1500 introduced insect species require the use of pesticides to control them. Forexample, African killer bees are expanding their population and migrating from northward from South America.These killer bees are much more aggressive than the natives, and destroy native honeybee populations.On a positive note, human-induced population explosions can provide needed resources for growing humanpopulations. Agriculture now produces more food per acre, allowing and sustaining increased human populationsize.Human action is causing the extinction of species at thousands of times the natural rate. Extinction is caused byalteration of a populations environment in a harmful way. Habitat disruption is the disturbance of the physicalenvironment of a species, for example cutting a forest or draining wetlands. Habitat disruption in currently theleading cause of extinction.Changes in the biological environment occur in three ways. 1. Species introduction: An exotic species is introduced into an area where it may have no predfators to control its population size, or where it can gratly out compete native organisms. Examples include zebra mussels introduced into Lake Erie, and lake trout released into Yellowstone Lake where they are threatening the native cutthroat trout populations. 2. Overhunting: When a predator population increases or becomes more efficient at killing the prey, the prey population may decline or go extinct. Examples today include big game hunting, which has in many places reduced the predator (or in this case prey) population. In human prehistory we may have caused the extinction of the mammoths and mastodons due to increased human hunting skill. 3. Secondary extinction: Loss of food species can cause migration or extinction of any species that depends largely or solely on that species as a food source.Overkill is the shooting, trapping, or hunting of a species usually for sport or economic reasons. Unfortunately,this cannot eliminate "pest" species like cockroaches and mice due to their large population sizes and capacityto reproduce more rapidly than we can eliminate them. However, many large animals have been eliminated orhad their populations drastically reduced (such as tigers, elephants, and leopards).The death of one species or population can cause the decline or elimination of others, a process known assecondary extinction. Destruction of bamboo forests in China, the food for the giant panda, may cause theextinction of the panda. The extinction of the dodo bird has caused the Calviera tree to become unable toreproduce since the dodo ate the fruit and processed the seeds of that tree. 118
  • 119. Giant pandas eat an estimated 10,000 pounds of bamboo per panda per year.Populations Have a Minimum Viable SizeEven if a number of individuals survive, the population size may become toosmall for the species to continue. Small populations may have breedingproblems. They are susceptible to random environmental fluctuationsand genetic drift to a greater degree than are larger populations. Thechance of extinction increases exponentially with decreasing populationsize.The minimum viable population (MVP) is the smallest population sizethat can avoid extinction by the two reasons listed above. If no severeenvironmental fluxes develop for a long enough time, a small populationwill recover. The MVP depends heavily on reproductive rates of thespecies.Range and DensityPopulations tend to have a maximum density near the center of their geographic range. Geographic range is thetotal area occupied by the species. Outlying zones, where conditions are less optimal, include the zone ofphysiological stress (where individuals are rare), and eventually the zone of intolerance (where individuals arenot found).The environment is usually never uniform enough to support uniform distribution of a species. Species thushave a dispersion pattern. Three patterns found include uniform, clumped, and random.Geographic ranges of species are dynamic, over time they can contract or expand due to environmental changeor human activity. Often a species will require another species presence, for example Drosophila in Hawaii.Species ranges can also expand due to human actions: brown trout are now found worldwide because of thespread of trout fishing. 119
  • 120. COMMUNITY AND ECOSYSTEM DYNAMICSDefinitionsA community is the set of all populations that inhabit a certain area. Communities can have different sizes andboundaries. These are often identified with some difficulty.An ecosystem is a higher level of organization the community plus its physical environment. Ecosystemsinclude both the biological and physical components affecting the community/ecosystem. We can studyecosystems from a structural view of population distribution or from a functional view of energy flow and otherprocesses.Community StructureEcologists find that within a community many populations are not randomly distributed. This recognition thatthere was a pattern and process of spatial distribution of species was a major accomplishment of ecology. Twoof the most important patterns are open community structure and the relative rarity of species within acommunity.Do species within a community have similar geographic range and density peaks? If they do, the community issaid to be a closed community, a discrete unit with sharp boundaries known as ecotones. An open community,however, has its populations without ecotones and distributed more or less randomly.In a forest, where we find an open community structure, there is a gradient of soil moisture. Plants havedifferent tolerances to this gradient and occur at different places along the continuum. Where the physicalenvironment has abrupt transitions, we find sharp boundaries developing between populations. For example, anecotone develops at a beach separating water and land.Open structure provides some protection for the community. Lacking boundaries, it is harder for a communityto be destroyed in an all or nothing fashion. Species can come and go within communities over time, yet thecommunity as a whole persists. In general, communities are less fragile and more flexible than some earlierconcepts would suggest.Most species in a community are far less abundant than the dominant species that provide a community itsname: for example oak-hickory, pine, etc. Populations of just a few species are dominant within a community,no matter what community we examine. Resource partitioning is thought to be the main cause for thisdistribution.Classification of CommunitiesThere are two basic categories of communities: terrestrial (land) and aquatic (water). These two basic types ofcommunity contain eight smaller units known as biomes. A biome is a large-scale category containing manycommunities of a similar nature, whose distribution is largely controlled by climate • Terrestrial Biomes: tundra, grassland, desert, taiga, temperate forest, tropical forest. • Aquatic Biomes: marine, freshwater. 120
  • 121. Major terrestrial biomes.Terrestrial BiomesTundra and DesertThe tundra and desert biomes occupy the most extreme environments, with little or no moisture and extremes oftemperature acting as harsh selective agents on organisms that occupy these areas. These two biomes have thefewest numbers of species due to the stringent environmental conditions. In other words, not everyone can livethere due to the specialized adaptations required by the environment.Tropical Rain ForestsTropical rain forests occur in regions near the equator. The climate is always warm (between 20° and 25° C)with plenty of rainfall (at least 190 cm/year). The rain forest is probably the richest biome, both in diversity andin total biomass. The tropical rain forest has a complex structure, with many levels of life. More than half of allterrestrial species live in this biome. While diversity is high, dominance by a particular species is low.While some animals live on the ground, most rain forest animals live in the trees. Many of these animals spendtheir entire life in the forest canopy. Insects are so abundant in tropical rain forests that the majority have not yetbeen identified. Charles Darwin noted the number of species found on a single tree, and suggested the richnessof the rain forest would stagger the future systematist with the size of the catalogue of animal species foundthere. Termites are critical in the decomposition and nutrient cycling of wood. Birds tend to be brightly colored,often making them sought after as exotic pets. Amphibians and reptiles are well represented. Lemurs, sloths,and monkeys feed on fruits in tropical rain forest trees. The largest carnivores are the cats (jaguars in SouthAmerica and leopards in Africa and Asia). Encroachment and destruction of habitat put all these animals andplants at risk. 121
  • 122. Epiphytes are plants that grow on other plants. These epiphytes have their own roots to absorb moisture andminerals, and use the other plant more as an aid to grow taller. Some tropical forests in India, Southeast Asia,West Africa, Central and South American are seasonal and have trees that shed leaves in dry season. The warm,moist climate supports high productivity as well as rapid decomposition of detritus.With its yearlong growing season, tropical forests have a rapid cycling of nutrients. Soils in tropical rain foreststend to have very little organic matter since most of the organic carbon is tied up in the standing biomass of theplants. These tropical soils, termed laterites, make poor agricultural soils after the forest has been cleared.About 17 million hectares of rain forest are destroyed each year (an area equal in size to Washington state).Estimates indicate the forests will be destroyed (along with a great part of the Earths diversity) within 100years. Rainfall and climate patterns could change as a result.Temperate ForestsThe temperate forest biome occurs south of the taiga in eastern North America, eastern Asia, and much ofEurope. Rainfall is abundant (30-80 inches/year; 75-150 cm) and there is a well-defined growing season ofbetween 140 and 300 days. The eastern United States and Canada are covered (or rather were once covered) bythis biomes natural vegetation, the eastern deciduous forest. Dominant plants include beech, maple, oak; andother deciduous hardwood trees. Trees of a deciduous forest have broad leaves, which they lose in the fall andgrow again in the spring..Sufficient sunlight penetrates the canopy to support a well-developed understory composed of shrubs, a layer ofherbaceous plants, and then often a ground cover of mosses and ferns. This stratification beneath the canopyprovides a numerous habitats for a variety of insects and birds. The deciduous forest also contains manymembers of the rodent family, which serve as a food source for bobcats, wolves, and foxes. This area also is ahome for deer and black bears. Winters are not as cold as in the taiga, so many amphibian and reptiles are ableto survive.Shrubland (Chaparral)The shrubland biome is dominated by shrubs with small but thick evergreen leaves that are often coated with athick, waxy cuticle, and with thick underground stems that survive the dry summers and frequent fires.Shrublands occur in parts of South America, western Australia, central Chile, and around the MediterraneanSea. Dense shrubland in California, where the summers are hot and very dry, is known as chaparral. ThisMediterranean-type shrubland lacks an understory and ground litter, and is also highly flammable. The seeds ofmany species require the heat and scarring action of fire to induce germination.GrasslandsGrasslands occur in temperate and tropical areas with reduced rainfall (10-30 inches per year) or prolonged dryseasons. Grasslands occur in the Americas, Africa, Asia, and Australia. Soils in this region are deep and richand are excellent for agriculture. Grasslands are almost entirely devoid of trees, and can support large herds ofgrazing animals. Natural grasslands once covered over 40 percent of the earths land surface. In temperate areaswhere rainfall is between 10 and 30 inches a year, grassland is the climax community because it is too wet fordesert and too dry for forests. 122
  • 123. Most grasslands have now been utilized to grow crops, especially wheat and corn. Grasses are the dominantplants, while grazing and burrowing species are the dominant animals. The extensive root systems of grassesallows them to recover quickly from grazing, flooding, drought, and sometimes fire.Temperate grasslands include the Russian steppes, the South American pampas, and North American prairies. Atall-grass prairie occurs where moisture is not quite sufficient to support trees.Animal life includes mice, prairie dogs, rabbits, and animals that feed on them (hawks and snakes). Prairiesonce contained large herds of buffalo and pronghorn antelope, but with human activity these once great herdshave dwindled.The savanna is a tropical grassland that contains some trees. The savanna contains the greatest variety andnumbers of herbivores (antelopes, zebras, and wildebeests, among others). This environment supports a largepopulation of carnivores (lions, cheetahs, hyenas, and leopards). Any plant litter not consumed by grazers isattacked by termites and other decomposers. Once again, human activities are threatening this biome, reducingthe range for herbivores and carnivores. Will extinction of the great cats be a result?DesertsDeserts are characterized by dry conditions (usually less than 10 inches per year; 25 cm) and a wide temperaturerange. The dry air leads to wide daily temperature fluctuations from freezing at night to over 120 degrees duringthe day. Most deserts occur at latitudes of 30o N or S where descending air masses are dry. Some deserts occurin the rainshadow of tall mountain ranges or in coastal areas near cold offshore currents. Plants in this biomehave developed a series of adaptations (such as succulent stems, and small, spiny, or absent leaves) to conservewater and deal with these temperature extremes. Photosynthetic modifications (CAM) are another strategy tolife in the drylands.The Sahara and a few other deserts have almost no vegetation. Most deserts, however, are home to a variety ofplants, all adapted to heat and lack of abundant water (succulents and cacti).. Animal life of the Sonoran desertincludes arthropods (especially insects and spiders), reptiles (lizards and snakes), running birds (the roadrunnerof the American southwest and Warner Brothers cartoon fame), rodents (kangaroo rat and pack rat), and a fewlarger birds and mammals (hawks, owls, and coyotes).Taiga (Boreal Forest)The taiga (pronounced "tie-guh") is a coniferous forest extending across most of the northern area of northernEurasia and North America. This forest belt also occurs in a few other areas, where it has different names: themontane coniferous forest when near mountain tops; and the temperate rain forest along the Pacific Coast as farsouth as California. The taiga receives between 10 and 40 inches of rain per year and has a short growingseason. Winters are cold and short, while summers tend to be cool. The taiga is noted for its great stands ofspruce, fir, hemlock, and pine. These trees have thick protective leaves and bark, as well as needlelike(evergreen) leaves can withstand the weight of accumulated snow. Taiga forests have a limited understory ofplants, and a forest floor covered by low-lying mosses and lichens. Conifers, alders, birch and willow arecommon plants; wolves, grizzly bears, moose, and caribou are common animals. Dominance of a few species ispronounced, but diversity is low when compared to temperate and tropical biomes. 123
  • 124. TundraThe tundra, covers the northernmost regions of North America and Eurasia, about 20% of the Earths land area.This biome receives about 20 cm (8-10 inches) of rainfall annually. Snow melt makes water plentiful duringsummer months. Winters are long and dark, followed by very short summers. Water is frozen most of the time,producing frozen soil, permafrost. Vegetation includes no trees, but rather patches of grass and shrubs; grazingmusk ox, reindeer, and caribou exist along with wolves, lynx, and rodents. A few animals highly adapted tocold live in the tundra year-round (lemming, ptarmigan). During the summer the tundra hosts numerous insectsand migratory animals. The ground is nearly completely covered with sedges and short grasses during the shortsummer. There are also plenty of patches of lichens and mosses. Dwarf woody shrubs flower and produce seedsquickly during the short growing season. The alpine tundra occurs above the timberline on mountain ranges,and may contain many of the same plants as the arctic tundra.Climate, Altitude and Terrestrial BiomesClimate controls biome distribution byan altitudinal gradient and a latitudinalgradient. With increases of eitheraltitude or latitude, cooler and drierconditions occur. Cooler conditions cancause aridity since cooler air can holdless water vapor than can warmer air.Deserts can occur in warm areas due to ablockage of air circulation patterns thatform a rain shadow, or from atmosphericcirculation patters. Warm air rises,producing low pressure areas. Cooler airsinks, producing high pressure areas.The tropics tend to be atmospheric lowpressure zones the arctic areasatmospheric highs. Relative humidity isa measure of how much water an air mass at a given temperature can hold. In short, warm air can hold moremoisture than can cold air. This basic physical feature of air helps explain the distribution of some of the worldsgreat deserts.The warm, moist air masses in the tropics rise upward in the atmosphere as they heat. The pressure of air risingforces air in the upper atmosphere to flow away north and south. This air at higher elevations is cooler and losesmuch of its moisture as rainfall. When the air masses begin to descend they heat up and begin to draw moisturefrom the lands they descend upon, at 30 degrees north and south of the equator. Many of the worlds deserts areat approximately 30 degrees latitude.Rain shadow deserts also form when cool, dry air masses descend after passing over a tall mountain range, suchas the Coast Range and Sierras in California. The Sonoran desert in Arizona is a doubly caused desert, being at30 degrees latitude as well as in the rain shadow of California mountains. 124
  • 125. Global Wind Patterns 125
  • 126. Aquatic BiomesConditions in water are generally less harsh than those on land. Aquatic organisms are buoyed by water support,and do not usually have to deal with desiccation. Despite covering 71% of the Earths surface, areas of the openocean are a vast aquatic desert containing few nutrients and very little life. Clear-cut biome distinctions inwater, like those on land, are difficult to make. Dissolved nutrients controls many local aquatic distributions.Aquatic communities are classified into: freshwater (inland) communities and marine (saltwater or oceanic) communities. The Marine Biome The marine biome contains more dissolved minerals than the freshwater biome. Over 70% of the Earths surface is covered in water, by far the vast majority of that being saltwater. There are two basic categories to this biome: benthic and pelagic. Benthic communities (bottom dwellers) are subdivided by depth: the shore/shelf and deep sea. Pelagic communities (swimmers or floaters suspended in the water column) include planktonic (floating) andnektonic (swimming) organisms. The upper 200 meters of the water column is the euphotic zone to which lightcan penetrate.Coastal CommunitiesEstuaries are bays where rivers empty into the sea. Erosion brings down nutrients and tides wash in salt water;forms nutrient trap. Estuaries have high production for organisms that can tolerate changing salinity. Estuariesare called "nurseries of the sea" because many young marine fish develop in this protected environment beforemoving as adults into the wide open seas.SeashoresRocky shorelines offer anchorage for sessile organisms. Seaweeds are main photosynthesizers and use holdfaststo anchor. Barnacles glue themselves to stone. Oysters and mussels attach themselves by threads. Limpets andperiwinkles either hide in crevices or fasten flat to rocks.Sandy beaches and shores are shifting strata. Permanent residents therefore burrow underground. Worms livepermanently in tubes. Amphipods and ghost crabs burrow above high tide and feed at night.Coral ReefsAreas of biological abundance in shallow, warm tropical waters. Stony corals have calcium carbonateexoskeleton and may include algae. Most form colonies; may associate with zooxanthellae dinoflagellates. Reefis densely populated with animal life. The Great Barrier Reef of Australia suffers from heavy predation bycrown-of-thorns sea star, perhaps because humans have harvested its predator, the giant triton. 126
  • 127. OceansOceans cover about three-quarters of the Earths surface. Oceanic organisms are placed in either pelagic (openwater) or benthic (ocean floor) categories. Pelagic division is divided into neritic and three levels of pelagicprovinces. Neritic province has greater concentration of organisms because sunlight penetrates; nutrients arefound here. Epipelagic zone is brightly lit, has much photosynthetic phytoplankton, that support zooplanktonthat are food for fish, squid, dolphins, and whales. Mesopelagic zone is semi-dark and contains carnivores;adapted organisms tend to be translucent, red colored, or luminescent; for example: shrimps, squids, lantern andhatchet fishes. The bathypelagic zone is completely dark and largest in size; it has strange-looking fish. Benthicdivision includes organisms on continental shelf (sublittoral), continental slope (bathyal), and the abyssal plain.Sublittoral zone harbors seaweed that becomes sparse where deeper; most dependent on slow rain of planktonand detritus from sunlit water above. Bathyal zone continues with thinning of sublittoral organisms. Abyssalzone is mainly animals at soil-water interface of dark abyssal plain; in spite of high pressure, darkness andcoldness, many invertebrates thrive here among sea urchins and tubeworms.Thermal vents along oceanic ridges form a very unique community. Molten magma heats seawater to 350oC,reacting with sulfate to form hydrogen sulfide (H2S). Chemosynthetic bacteria obtain energy by oxidizinghydrogen sulfide. The resulting food chain supports a community of tubeworms and clams.The Freshwater Biome 127
  • 128. The freshwater biome is subdivided into two zones: running waters and standing waters. Larger bodies offreshwater are less prone to stratification (where oxygen decreases with depth). The upper layers have abundantoxygen, the lowermost layers are oxygen-poor. Mixing between upper and lower layers in a pond or lake occursduring seasonal changes known as spring and fall overturn.Lakes are larger than ponds, and are stratified in summer andwinter. The epilimnion is the upper surface layer. It is warm insummer. The hypolimnion is the cold lower layer. A suddendrop in temperature occurs at the middle of the thermocline.Layering prevents mixing between the lower hypolimnion (richin nutrients) and the upper epilimnion (which has oxygenabsorbed from its surface). The epilimnion warms in spring andcools in fall, causing a temporary mixing. As a consequence,phytoplankton become more abundant due to the increased amounts of nutrients. Life zones also exist in lakes and ponds. The littoral zone is closest to shore. The limnetic zone is the sunlit body of the lake. Below the level of sunlight penetration is the dark profundal zone. At the soil-water interface we find the benthic zone. The term benthos is applied to animals and other organisms that live on or in the benthic zone. Rapidly flowing, bubbling streams have insects and fish adapted to oxygen-rich water. Slow moving streams have aquatic life more similar to lake and pond life.Community Density and StabilityCommunities are made up of species adapted to the conditions of that community. Diversity and stability helpdefine a community and are important in environmental studies. Species diversity decreases as we move awayfrom the tropics. Species diversity is a measure of the different types of organisms in a community (alsoreferred to as species richness). Latitudinal diversity gradient refers to species richness decreasing steadilygoing away from the equator. A hectare of tropical rain forest contains 40-100 tree species, while a hectare oftemperate zone forest contains 10-30 tree species. In marked contrast, a hectare of taiga contains only a paltry1-5 species! Habitat destruction in tropical countries will cause many more extinctions per hectare than it wouldin higher latitudes.Environmental stability is greater in tropical areas, where a relatively stable/constant environment allows moredifferent kinds of species to thrive. Equatorial communities are older because they have been less disturbed byglaciers and other climate changes, allowing time for new species to evolve. Equatorial areas also have a longergrowing season.The depth diversity gradient is found in aquatic communities. Increasing species richness with increasing waterdepth. This gradient is established by environmental stability and the increasing availability of nutrients.Community stability refers to the ability of communities to remain unchanged over time. During the 1950s and1960s, stability was equated to diversity: diverse communities were also stable communities. Mathematical 128
  • 129. modeling during the 1970s showed that increased diversity can actually increase interdependence amongspecies and lead to a cascade effect when a keystone species is removed. Thus, the relation is more complexthan previously thought.Change in Communities Over TimeBiological communities, like the organisms that comprise them, can and do change over time. Ecological timefocuses on community events that occur over decades or centuries. Geological time focuses on events lastingthousands of years or more.Community succession is the sequential replacement of species by immigration of new species and localextinction of older ones following a disturbance that creates unoccupied habitats for colonization. The initialrapid colonizer species are the pioneer community. Eventually a climax community of more or less stable butslower growing species eventually develops.During succession productivity declines and diversity increases. These trends tend to increase the biomass (totalweight of living tissue) in a community. Succession occurs because each community stage prepares theenvironment for the stage following it.Primary succession begins with bare rock and takes a very long time to occur. Weathering by wind and rain plusthe actions of pioneer species such as lichens and mosses begin the buildup of soil. Herbaceous plants,including the grasses, grow on deeper soil and shade out shorter pioneer species. Pine trees or deciduous treeseventually take root and in most biomes will form a climax community of plants that are stabile in theenvironment. The young produced by climax species can live in that environment, unlike the young producedby successional species.Secondary succession occurs when an environment has been disturbed, such as by fire, geological activity, orhuman intervention (farming or deforestation in most cases). This form of succession often begins in anabandoned field with soil layers already in place. Compared to primary succession, which must take longperiods of time to build or accumulate soil, secondary succession occurs rapidly. The herbaceous pioneeringplants give way to pines, which in turn may give way to a hardwood deciduous forest (in the classical old fieldsuccession models developed in the eastern deciduous forest biome).Early researchers assumed climax communities were determined for each environment. Today we recognize theoutcome of competition among whatever species are present as establishing the climax community.Climax communities tend to be more stable than successional communities. Early stages of succession show themost growth and are most productive. Pioneer communities lack diversity, make poor use of inputs, and loseheat and nutrients. As succession proceeds, species variety increases and nutrients are recycled more. Climaxcommunities make fuller use of inputs and maintain themselves, thus, they are more stable. Human activity(such as clearing a climax forest community to establish a farm field consisting of a cultivated pioneeringspecies, say corn or wheat) replaces climax communities with simpler communities.Communities are composed of species that evolve, so the community must also evolve. Comparing marinecommunities of 500 million years ago with modern communities shows modern communities composed ofquite different organisms. Modern communities also tend to be more complex, although this may be a reflectionof the nature of the fossil record as well as differences between biological and fossil species.Disturbance of a Community 129
  • 130. The basic effect of human activity on communities is community simplification, an overall reduction of speciesdiversity. Agriculture is a purposeful human intervention in which we create a monoculture of a single favored(crop) species such as corn. Most of the agricultural species are derived from pioneering communities.Inadvertent human intervention can simplify communities and produce stressed communities that have fewerspecies as well as a superabundance of some species. Disturbances favor early successional (pioneer) speciesthat can grow and reproduce rapidly.Ecosystems and CommunitiesEcosystems include both living and nonliving components. These living, or biotic, components include habitatsand niches occupied by organisms. Nonliving, or abiotic, components include soil, water, light, inorganicnutrients, and weather. An organisms place of residence, where it can be found, is its habitat. A niche is is oftenviewed as the role of that organism in the community, factors limiting its life, and how it acquires food.Producers, a major niche in all ecosystems, are autotrophic, usually photosynthetic, organisms. In terrestrialecosystems, producers are usually green plants. Freshwater and marine ecosystems frequently have algae as thedominant producers.Consumers are heterotrophic organisms that eat food produced by another organism. Herbivores are a type ofconsumer that feeds directly on green plants (or another type of autotroph). Since herbivores take their fooddirectly from the producer level, we refer to them as primary consumers. Carnivores feed on other animals (oranother type of consumer) and are secondary or tertiary consumers. Omnivores, the feeding method used byhumans, feed on both plants and animals. Decomposers are organisms, mostly bacteria and fungi that recyclenutrients from decaying organic material. Decomposers break down detritus, nonliving organic matter, intoinorganic matter. Small soil organisms are critical in helping bacteria and fungi shred leaf litter and form richsoil.Even if communities do differ in structure, they have some common uniting processes such as energy flow andmatter cycling. Energy flows move through feeding relationships. The term ecological niche refers to how anorganism functions in an ecosystem. Food webs, food chains, and food pyramids are three ways of representingenergy flow.Producers absorb solar energy and convert it to chemical bonds from inorganic nutrients taken fromenvironment. Energy content of organic food passes up food chain; eventually all energy is lost as heat,therefore requiring continual input. Original inorganic elements are mostly returned to soil and producers; canbe used again by producers and no new input is required. 130
  • 131. Energy flow in ecosystems, as with all other energy, must follow the two laws of thermodynamics. Recall thatthe first law states that energy is neither created nor destroyed, but instead changes from one form to another(potential to kinetic). The second law mandates that when energy is transformed from one form to another,some usable energy is lost as heat. Thus, in any food chain, some energy must be lost as we move up the chain.The ultimate source of energy for nearly all life is the Sun. Recently, scientists discovered an exception to thisonce unchallenged truism: communities of organisms around ocean vents where food chain begins withchemosynthetic bacteria that oxidize hydrogen sulfide generated by inorganic chemical reactions inside theEarths crust. In this special case, the source of energy is the internal heat engine of the Earth.Food chains indicate who eats whom in an ecosystem. Represent one path of energy flow through an ecosystem.Natural ecosystems have numerous interconnected food chains. Each level of producer and consumers is atrophic level. Some primary consumers feed on plants and make grazing food chains; others feed on detritus.The population size in an undisturbed ecosystem is limited by the food supply, competition, predation, andparasitism. Food webs help determine consequences of perturbations: if titmice and vireos fed on beetles andearthworms, insecticides that killed beetles would increase competition between birds and probably increasepredation of earthworms, etc.The trophic structure of an ecosystem forms an ecological pyramid. The base of this pyramid represents theproducer trophic level. At the apex is the highest level consumer, the top predator. Other pyramids can berecognized in an ecosystem. A pyramid of numbers is based on how many organisms occupy each trophic level.The pyramid of biomass is calculated by multiplying the average weight for organisms times the number oforganisms at each trophic level. An energy pyramid illustrates the amounts of energy available at eachsuccessive trophic level. The energy pyramid always shows a decrease moving up trophic levels because: • Only a certain amount of food is captured and eaten by organisms on the next trophic level. • Some of food that is eaten cannot be digested and exits digestive tract as undigested waste. • Only a portion of digested food becomes part of the organisms body; rest is used as source of energy. 131
  • 132. • Substantial portion of food energy goes to build up temporary ATP in mitochondria that is then used to synthesize proteins, lipids, carbohydrates, fuel contraction of muscles, nerve conduction, and other functions. • Only about 10% of the energy available at a particular trophic level is incorporated into tissues at the next level. Thus, a larger population can be sustained by eating grain than by eating grain-fed animals since 100 kg of grain would result in 10 human kg but if fed to cattle, the result, by the time that reaches the human is a paltry 1 human kg!A food chain is a series of organisms each feeding on the one preceding it. There are two types of food chain:decomposer and grazer. Grazer food chains begin with algae and plants and end in a carnivore. Decomposerchains are composed of waste and decomposing organisms such as fungi and bacteria.Energy flow and the relative proportions of various levels in the food chain..Food chains are simplifications of complex relationships. A food web is a more realistic and accurate depictionof energy flow. Food webs are networks of feeding interactions among species.The food pyramid provides a detailed view of energy flow in an ecosystem. The first level consists of theproducers (usually plants). All higher levels are consumers. The shorter the food chain the more energy isavailable to organisms.Most humans occupy a top carnivore role, about 2% of all calories available from producers ever reach thetissues of top carnivores. Leakage of energy occurs between each feeding level. Most natural ecosystemstherefore do not have more than five levels to their food pyramids. Large carnivores are rare because there is solittle energy available to them atop the pyramid.Food generation by producers varies greatly between ecosystems. Net primary productivity (NPP) is the rate atwhich producer biomass is formed. Tropical forests and swamps are the most productive terrestrial ecosystems. 132
  • 133. Reefs and estuaries are the most productive aquatic ecosystems. All of these productive areas are in danger fromhuman activity. Humans redirect nearly 40% of the net primary productivity and directly or indirectly usenearly 40% of all the land food pyramid. This energy is not available to natural populations.Learning Objectives • Be able to describe the major terrestrial biomes and the types of plants and animals occurring there. • Relate the effect of increasing altitude as one goes up a mountain to biome changes seen as one moves north of the equator toward the polar regions. • Distinguish the different regions within the marine ecosystems. • Be able to describe a food chain in detail, with some indication of the relative proportions of organisms at each trophic level.Biogeochemical CyclesMore than thirty chemical elements are cycled through the environment by biogeochemical cycles. There are siximportant biogeochemical cycles that transport carbon, hydrogen, oxygen, nitrogen, sulfur, and phosphorous.Recall that these six elements comprise the bulk of atoms in living things. Carbon, the most abundant element inthe human body, is not the most common element in the crust, silicon is.The Phosphorus CycleWeathering of rocks makes phosphateions (PO4= and HPO4=) available toplants through uptake from the soil. Themineral apatite contains a small amountof phosphorous, although this is enoughfor all living things to utilize. Runoffreturns phosphates to aquatic systemsand sediment. Organisms use phosphatein phospholipids, ATP, teeth, bones, andshells. Phosphate is a limiting nutrientbecause most of it is being currentlyused in organisms. The inorganic source,apatite, is a rare mineral, further limitingthe input of this essential nutrient.Humans mine phosphate ores for use infertilizer, as an animal feed supplement, and for detergents. Detergents, untreated human and animal wastes,and fertilizers from cropland add excess phosphate to water often causing population explosions (algal blooms)in lakes.. 133
  • 134. The Nitrogen CycleAtmospheric nitrogen gas (N2), the majorportion of our modern atmosphere, isunfortunately in a form that is not usable byplants and most other organisms. Plantstherefore depend on various types of nitrogen-fixing bacteria to take up nitrogen gas and makeit available to them as some form of organicnitrogen. Nitrogen fixation occurs whennitrogen gas is chemically reduced and nitrogenis added to organic compounds. Atmosphericnitrogen is converted to ammonium (NH4+) bysome cyanobacteria in aquatic ecosystems andby nitrogen-fixing bacteria in the nodules onroots of legume (beans, peas, clover, etc.) plantsin terrestrial ecosystems. Plants take up both NH4+ and nitrate (NO3-) from soil. The nitrate (NO3-) isenzymatically reduced to ammonium (NH4+) and used in the production of both amino acids and nucleic acids.Nitrification is the inorganic production of nitrates. Nitrogen gas (N2) is converted to nitrate (NO3-) by cosmicradiation, meteor trails, and lightning in the atmosphere. Human technology can now manufacture nitrates foruse in fertilizers. In soil, bacteria convert ammonium (NH4+) to nitrate (NO3-) by a two-step process. Nitrite-producing bacteria convert ammonia to nitrite (NO2-). Next, nitrate-producing bacteria convert nitrite to nitrate.These two groups of bacteria are called nitrifying bacteria.Denitrification is conversion of nitrate to nitrous oxide and nitrogen gas back to atmosphere. This is done bydenitrifying bacteria in both aquatic and terrestrial ecosystems. The process of denitrification almost, but notcompletely, counterbalances nitrogen fixation.The Carbon CycleThere is a relationship between the two major metabolic processes of photosynthesis and cellular respiration.Cellular respiration releases carbon dioxide, which is used as a raw material in photosynthesis. Photosynthesisin turn releases oxygen used in respiration. Animals and other heterotrophs depend on green organisms fororganic food, energy, and oxygen. In the carbon cycle, organisms exchange carbon dioxide with theatmosphere. On land, plants take up carbon dioxide via photosynthesis and incorporate it into food used bythemselves and heterotrophs. When organisms respire, some of this carbon is returned to the atmosphere in themolecules of carbon dioxide. In aquatic ecosystems, carbon dioxide from air combines with water to givecarbonic acid, which breaks down to bicarbonate ions. Bicarbonate ions are a source of carbon for algae. Whenaquatic organisms respire, they release carbon dioxide that becomes bicarbonate (HCO3). The amount ofbicarbonate in water is in equilibrium with amount of carbon dioxide in air.Living and dead organisms are reservoirs of carbon in carbon cycle. More than 800 billion tons of carbon are inthe worlds biota, mainly in cells of trees. An additional 1,000 to 3,000 billion tons of carbon occurs in plant andanimal remains in the soil. Fossil fuels, such as coal, petroleum, and natural gas, were formed during varioustimes of the geologic past when exceptional amount of organic matter were rapidly buried in an environmentthat locally lacked biologic activity. Inorganic calcium carbonate (the minerals calcite and aragonite, CaCO3)accumulates in limestone and the calcite of shells. 134
  • 135. Human burning of fossil fuels and wood has increased the amount of carbon dioxide released into atmosphereto 42 billion metric tons in only 22 years. Since human activity in 22 years probably released 78 billion metrictons, 36 billion metric tons were probably absorbed in oceans. Increased carbon dioxide levels may increase thegreenhouse effect, where such gases allow the Suns radiant energy to pass through to Earth where it is absorbedand reradiated as heat. Instead of radiating from the earth back into space, this heat is then trapped on Earth,perhaps causing or contributing to global warming.. The global carbon cycle..Excess output occurs when biomass is suddenly released, such as in slash and burn agriculture. Excess inputcommonly occurs from agricultural increase in organic fertilizer and other nutrients into an ecosystem.Generally speaking, the faster matter cycles, the faster it can recover from human intervention.Recently, speculation has centered on the interconnection of biogeochemical cycles and their possible roles in a"superorganism" that James Lovelock has called Gaia, after the ancient Greek Earth goddess. While anintriguing notion, the degree of organization of these cycles is not as complex or integrated as the cells in abody. Gaia remains controversial hypothesis that continues to generate speculation and research both pro andcon. 135