Objectives1. Enumerate the attributes of living matter.2. Distinguish between prokaryotes and eukaryotes.3. Identify the important organelles of the cell.4. Name the common elements and compounds required by living organisms.
What is a Biochemistry? Biochemistry is the chemistry of biomolecules and their chemical reactions in living matter at the molecular and cellular level. biomolecules molecules involved in the survival of the living organism. chemical reactions changes within the organism’s body usually referred to as biochemical reactions or metabolism. Biochemistry seeks to describe the structure, organization, and functions of living matter in molecular terms.
Level of Organization1. Subatomic Paticles - an electron, proton, or neutron; three major particles of which atoms are composed.2. Atom - smallest unit of an element that still remains the properties of that element.3. Molecule - a unit of two or more atoms of the same or different elements bonded together.
4. Organelle - any various membraneous sacs or other compartments inside the cell that separate different metabolic reactions within the cellular space and in time. ribosome5. Cell - smallest living unit; may live independently or may be part of a multicellular organism.6. Tissue - a group of similar cells and intercellular substances functioning together in a specialized activity. red blood cell7. Organ - one or more types of of tissues interacting as a structural, functioning unit. jellyfish brain
8. Organ system - two or more organs whose separate functions are integrated int the performance of a special task. • The heart is part of the circulatory system, which carries oxygen and other materials heart throughout the body. Besides the heart, blood vessels are organs that work in your circulatory system.9. Multicellular organism - individual composed of specialized, interdependent cells arrayed in tissues, organs, and other organ system. Biochemistry asks how the remarkable properties of living organisms arise from the thousands of different lifeless biomolecules.
It can be divided into three principal areas: 1. Structural and Functional Biochemistry: Chemical structures and 3D arrangements of molecules. 2. Informational Biochemistry: Language for storing biological data and for transmitting that data in cells and organisms. 3. Bioenergetics: The flow of energy in living organisms and how it is transferred from one process to another.
When these molecules are isolated and examined individually, they conform to all the physical and chemical laws that describe the behavior of inanimate matter - as do all the processes occurring in living organisms. The study of biochemistry shows how the collections of inanimate molecules that constitute living organisms interact to maintain and perpetuate life animated solely by the physical and chemical laws that govern the nonliving universe. Physical and Chemical sciences alone may not completely explain the nature of life, but they at least provide the essential framework for such an explanation. BIOCHEMISTRY
Tools to study biochemistry: All students of life must have a fundamental understanding of general chemistry, organic chemistry and biology. Know chemical structures and reactivities of molecules that participate in cellular reactions. Know biological functions of cellular molecules. Know how all of the pieces and different chemical reactions fit together.
Interweaving of thehistorical traditions of biochemistry, cell biology, and genetics.
Biochemistry draws its major themes from: 1. Organic chemistry - which describes the properties of biomolecules. 2. Biophysics - which applies the techniques of physics to study the structures of biomolecules. 3. Medical research - which increasingly seeks to understand disease states in molecular terms. 4. Nutrition - which has illuminated metabolism by describing the dietary requirements for maintenance of health. 5. Microbiology - which has shown that single-celled organisms and viruses are ideally suited for the elucidation of many metabolic pathways and regulatory mechanisms.
6. Physiology - which investigates life processes at the tissue and organism levels.7. Cell biology - which describes the biochemical division of labor within a cell.8. Genetics - which describes mechanisms that give a particular cell or organism its biochemical identity.
Elements of Life Up to 99+% of the human body is made of the elements C (9.5%), H (25.2%), O (63%) and N (1.4%). Only 31 chemical elements occur naturally in plants and animals.
99% of the mass of the human body is made up of only six elements: oxygen, carbon, hydrogen, nitrogen, calcium, and phosphorus. Every organic molecule contains carbon. Since 65-90% of each body cell consists of water (by weight), it is not surprising that oxygen and hydrogen are major components of the body.
Question What property unites H, O, C and N and renders these atoms so appropriate to the chemistry of life? Their ability to form covalent bonds by electron-pair sharing. Bond Energy (kJ/mol) H-H 436 C-H 414 C-C 343 C-O 351
The elements of Life C, the hybridizer Fe, the O2 carrier H, placeholder and water Na,K depolarizers builder P, the energy carrier O, the oxidizer and hydrogen Cl, the neutralizer bonder S, the linker N, protein builder Mg, Zn, Cu, Ni, Mo Ca, the skeletizer enzyme coordinators Lithium, Strontium, Oxygen (65%) Sulfur (0.25%) Aluminum, Silicon, Carbon (18%) Sodium (0.15%) Lead, Vanadium, Hydrogen (10%) Magnesium (0.05%) Arsenic, Bromine Nitrogen (3%) (trace amounts) Calcium (1.5%) Copper, Zinc, Selenium, Molybdenum, Phosphorus (1.0%) Fluorine, Chlorine, Iodine, Manganese, Potassium (0.35%) Cobalt, Iron (0.70%)
Biomolecules of Life1. Proteins - these are polymers of amino acids linked by peptide bonds. - they are also called polypetides. - they function as transport proteins, structural proteins, enzymes, antibodies, cell receptors.2. Nucelic acids - classified as RNA and DNA, are polymers of nucleotides linked by phosphodiester bonds.
- the nucleotide sequence in these polymers spells out the genetic information that directs growth, development and reproduction.3. Carbohydrates - also known as polysaccharides which are polymers of monosaccharides. - function as storage sources of energy in plants (starch) and animals (glycogen) and as structural elements in plants. - function as storage sources of energy in plants (starch) and animals (glycogen), as structural elements in plants, supply carbon for synthesis of other compounds and used in intercellular communications..
4. Lipids - storage of energy in the form of fat - responsible for the integrity of cellular membranes (phospholipids), synthesis of hormones and vitamins, and act as insulator (thermal blanket). Livingthings are composed of lifeless molecules. When these molecules are considered individually, they are found to conform to all the physical and chemical laws that describe the behavior of inanimate matter. But when put together in a particular manner, this collection of lifeless molecules start to exhibit the different attributes of life.
What is Life? Hard to define! Let’s list some of its properties. Necessary Properties highly organized and complicated - all organisms are consist of one or more cells (atoms connect to form molecules, molecules make organelles, and organelles make cells. Cells make up tissue, tissues organized into organs, and organs into organ systems. uses energy - all organisms acquire and use energy to perform many kinds of work.
sensitive (interacts with its environment) - plants grow toward light, an animal’s pupils dilate in darkness, amoeba and paramecia move toward food. metabolism - ability to change substances into different substances to get energy. evolutionary adaptation - all organisms interact with the environment and other organisms in ways that influence their survival to better adapt to their environment. homeostasis - all organisms maintain ‘relatively’ constant internal conditions like ion concentration, body fluid, temperature, glucose in the bloodstream, blood pH, blood pressure, etc. excretion - removal of waste products Likely (but maybe not be necessary) Properties grows and develops - normally, all forms of life must grow to allow development and reproduction
reproduces - heriditary molecules (RNA and DNA) ensures production of offspring similar to previous generation. mutates and evolves - long term adaptation, new forms of life are formed from life itself
Requirements for Life1. Energy (need food to function) a. Autotrophs = make their own food (plants are autotrophs) b. Heterotrophs = cannot make their own food (animals, people, dogs, lizards, are heterotrophs).2. Water – all living things need water to survive.3. Living Space – need a place to get food, water, and shelter.4. Homeostasis = Stable Internal Conditions – so when the temperature gets too cold or hot, or too wet or dry where they live, their body still stays the same inside.
The Cell All living organisms on earth are made of cells except viruses. The smallest unit that is capable of life. multicellur organism, Human one-celled organism, Bacteria (at least 1014 cells)
There are many different types of cells that are usually highly specialized. The differences could be according to shape and function.
Examples of Cells Amoeba Proteus Plant StemBacteria Red Blood Cell Nerve Cell
All cells are relatively small. They vary in length from 2 µm to 30 µm.
Prokaryotic Cell Do not have structures surrounded by membranes Few internal structures No nucleus
• Nucleoid region contains the DNA• Cell membrane and cell wall• Contain ribosomes (no membrane) to make proteins in their cytoplasm
Eukaryotic Cell (Animal) Contain organelles such as a nucleus surrounded by membranes Most living organisms Contain 3 basic cell structures: • Nucleus • Cell Membrane • Cytoplasm with organelles
Functions of Organelles Cell Membrane A lipid/protein/carbohydrate complex, providing a barrier and containing transport and signaling systems. (Serves as security guards or gate keeprs. Decides what can enter or leaves the cell. It lets in useful substances and lets out waste.) Cell wall Plants have a rigid cell wall in addition to their cell membranes Cytoplasm enclosed by the plasma membrane, liquid portion called cytosol and it houses the membranous organelles. Nucleus Double membrane surrounding the chromosomes and the nucleolus. Pores allow specific communication with the cytoplasm. The nucleolus is a site for synthesis of RNA making up the ribosome (Serves as the control center. All the activities inside the cell are controlled by instructions which comes from the nucleus.)
MitochondrionSurrounded by a double membrane with a series of foldscalled cristae. Functions in energy production through metabolism.Contains its own DNA, and is believed to have originated as acaptured bacterium.(Serves as the power house of the cell. The mitochondira releasesenergy from food.)Chloroplasts (plastids)Surrounded by a double membrane, containing stacked thylakoidmembranes. Responsible for photosynthesis, the trapping of lightenergy for the synthesis of sugars. Contains DNA, and likemitochondria is believed to have originated as a capturedbacterium.Endoplasmic reticulum (RER)A network of interconnected membranes forming channels within thecell. Covered with ribosomes (causing the "rough" appearance) whichare in the process of synthesizing proteins for secretion orlocalization in membranes. (Serves as the construction team of the cell.)
Golgi bodyA series of stacked membranes. Vesicles (small membranesurrounded bags) carry materials from the RER to the Golgiapparatus. Vesicles move between the stacks while the proteins are"processed" to a mature form. Vesicles then carry newly formedmembrane and secreted proteins to their final destinations includingsecretion or membrane localization.(Serves as the assembly and storage point of the cell. Some of thesubstances made in the cells are assembled and stored in the Golgibody.)LysosymesA membrane bound organelle that is responsible for degradingproteins and membranes in the cell, and also helps degrade materialsingested by the cell.(Serves as the waste disposal unit of the cell. The lysozomes eatup waste materials and old worn out parts of the cell.)VacuolesMembrane surrounded "bags" that contain water and storagematerials in plants.
Peroxisomes or MicrobodiesProduce and degrade hydrogen peroxide, a toxic compound thatcan be produced during metabolism. Cytoskeleton Arrays of protein filaments in the cytosol. Gives the cell its shape and provides basis for movement. E.g. microtubules and microfilaments.
AssignmentPurpose: To compare the structure and function of cells with a familiar system.DIRECTIONS: You will create an analogy (comparison) for a cell using a factory.
Your analogy will include a(1) drawing or model where you label each part of the city/house/body/station and its corresponding cell part (organelle), and a(2) written description of each city/house/body/station part andhow it is similar to its corresponding organelle.
Biomolecules in Cells
Biochemical Reactions • Metabolism - total sum of the chemical reaction happening in a living organism (highly coordinated and purposeful activity) Anabolism – biosynthesis of small molecules to larger molecules which requires energy. Catabolism - degradation of fuel molecules and the production of energy for cellular function All biochemical reactions occur inside the cell and are catalyzed by enzymes. Both anabolism and catabolism may occur simultaneously not only because they involve different enzymes but also because they ma be separated in their location within the cell.
catabolic • For example: the degradation of fatty acids to acetyl CoA occurs by way of exnzym located within the mitochondria, whereas the anabolic conversion of acetyl CoA to anabolic fatty acids occurs in the cytoplasm by way oif a separate system. FUNCTIONS OF METABOLISM 1. Acquistion and utilization of energy. 2. Synthesis of molecules needed for cell structure and functioning (i.e., proteins, nucleic acids, lipids, etc. 3. Removal of waste products.
Metabolic Pathway Metabolism generally occurs by orderly, stepwise, series or sequence of individual chemical reactions that are dependent on the basic laws of thermodynamics called as metabolic pathways. • Also called biochemical pathway, is a multistep reaction within a cell that is catalyzed by enzymes An example of a simple metabolic pathway is the single step conversion of a precursor A to a given product B. an enzymatic reaction A enzyme B is reversible.
In a multi-steps metabolic pathway, product B could become a substrate of the second reaction to yield product C and so on. E1 E2 E3 E4 E5 A B C D E Product linear metabolic pathway E’s are enzymes B, C, D, E are intermediate substances also called metabolites. E5 E8 E11 E2 C D E Product 1 E1 E3 E6 E9 E12 A B F G H Product 2 E4 E7 E10 E13 I J K Product 3 branched metabolic pathway
Primary Metabolic Pathway A series of metabolism or biochemical reactions that encompasses reactions involving primary compounds which are formed as part of the normal anabolic and catabolic processes of plants and animals. Primary metabolites are compounds commonly produced from primary metabolic pathways such as proteins, carbohydrates, lipids, nucleic acid that are directly used for growth and devlopment. Absence of primary metabolites will cause cells and the whole organism to die. Examples: Glycolysis Electron Transport Chain Citric Acid Cylce Oxydation of Fatty Acids
GLYCOLYSIS reverse steps not shown
Secondary Metabolic Pathway A metabolism of secondary compounds or secondary metabolites other than primary compunds. A compound is classified as secondary metabolite if it does not seem to to directly function in the processes of growth and devlopment of the animal or plant. Even though secondary compounds are a normal part of the metabolism of an organism, they are often produced in specialized cells and tend to be more complex than primary compounds. Examples of secondary metabolites antibiotics alkaloids
Even though thousands of reactions sound very large and complex inside a tiny cell: 1. The type of reactions are small. 2. Mechanisms of biochemical reactions are simple. 3. Reactions of central importance (for energy production and synthesis and degradation of major cell components) are relatively few in number. Frequent reactions encountered in biochemical processes: 1. Nucleophilic substitution • one atom or group of atoms substituted for another. 2. Elimination reactions • double bond is formed when atoms in a molecule is removed. 3. Addition reactions • two molecules combine to form a single product. • hydration reactions - water added to alkene > alcohol (common addition reaction).
4. Isomerization reactions • involve intramolecular shift of atoms or groups5. Oxidation-Reduction (redox) reactions • occur when there is transfer of electron from a donor to an electron acceptor.6. Hydrolysis reactions • cleavage of double bond by water.
Requirement for Life MATTER: PRODUCED IN BIG BANG (H & He) AND STARS ( (HEAVIER ELEMENTS) ARE CERTAIN ELEMENTS NEEDED? STABLE ENERGY SOURCE: LOW MASS MAIN SEQUENCE STARS (OR SOMETHING E ELSE?) PROTECTED ENVIRONMENT: PLANETARY OR LUNAR SURFACES PLANETARY OR LUNAR INTERIORS THICK PLANETARY OR LUNAR ATMOSPHERES CHEMICAL SOLVENT (LIQUID): W WATER (OR SOMETHING ELSE?)
Secondary metabolism:Metabolism of secondary compounds, defined simply ascompounds other than primary compounds. A compound isclassified as a secondary metabolite if it does not seem todirectly function in the processes of growth anddevelopment. Even though secondary compounds are anormal part of the metabolism of an organism, they areoften produced in specialized cells, and tend to be morecomplex than primary compounds. Examples of secondarycompounds include antibiotics, and plant chemicaldefenses such as alkaloids and steroids.MetaCyc (www.metacyc.org)Taiz, Lincoln, and Eduardo Zeiger. "Surface Protection and SecondaryDefense Compounds." Plant Physiology. New York: Benjamin/CummingsPublishing Company, Inc., 1991: 320-345.[item in sorceforge, should be readdressed via sourceforge]
Secondary metabolism:Processes that result in many of the chemical changes ofcompounds that are not required for growth andmaintenance of cells, and are often unique to a taxon. Inmulticellular organisms secondary metabolism is generallycarried out in specific cell types, and may be useful for theorganism as a whole. In unicellular organisms, secondarymetabolism is often used for the production of antibiotics orfor the utilization and acquisition of unusual nutrients.MetaCyc (www.metacyc.org)Taiz, Lincoln, and Eduardo Zeiger. "Surface Protection and SecondaryDefense Compounds." Plant Physiology. New York: Benjamin/CummingsPublishing Company, Inc., 1991: 320-345.[item in sorceforge, should be readdressed via sourceforge]
Main Players Enzymes: polymers of amino acids that act as catalysts that regulate speed of many chemical reactions in the metabolism of living organisms; ex. Phosphoglucoisomerase, aldolase Metabolites: substance involved or by- product of metabolism; ex. erythrose 4- phosphate, sedoheptulose 7-phosphate
Protein Carbohydrates LipidsAmino Acids
. Ribosomes Protein and RNA complex responsible for protein synthesis Smooth endoplasmic reticulum (SER) A network of interconnected membranes forming channels within the cell. A site for synthesis and metabolism of lipids. Also contains enzymes for detoxifying chemicals including drugs and pesticides. Golgi apparatus A series of stacked membranes. Vesicles (small membrane surrounded bags) carry materials from the RER to the Golgi apparatus. Vesicles move between the stacks while the proteins are "processed" to a mature form. Vesicles then carry newly formed membrane and secreted proteins to their final destinations including secretion or membrane localization.
Primary (1°) Metabolism- Construct common biological macromolecules from simple building blocks found within every cell- Typically a process of polymerization, stringing monomers together into a macromolecule that performs a cellular function sugars polysaccharides amino acids proteins fats phospholipid bilayers- Block production: cell dies (primary metabolites are essential)
Metabolism andEnergy Production Citric Acid Cycle Electron Transport Chain ATP Energy from Glucose Oxidation of Fatty Acids Metabolic Pathways for Amino Acids
Cell Membrane Outer membrane of cell that controls movement in and out of the cell Double layer
Cell Wall Most commonly found in plant cells & bacteria Supports & protects cellshttp://library.thinkquest.org/12413/structures.html
Inside the Cell
Nucleus Directs cell activities Separated from cytoplasm by nuclear membrane Contains genetic material - DNA
Nuclear Membrane Surrounds nucleus Made of two layers Openings allow material to enter and leave nucleushttp://library.thinkquest.org/12413/structures.html
Chromosomes In nucleus Made of DNA Contain instructions for traits & characteristicshttp://library.thinkquest.org/12413/structures.html
Nucleolus Inside nucleus Contains RNA to build proteinshttp://library.thinkquest.org/12413/structures.html
Cytoplasm Gel-like mixture Surrounded by cell membrane Contains hereditary material
Endoplasmic Reticulum Moves materials around in cell Smooth type: lacks ribosomes Rough type (pictured): ribosomes embedded in surfacehttp://library.thinkquest.org/12413/structures.html
Ribosomes Each cell contains thousands Make proteins Found on ribosomes & floating throughout the cellhttp://library.thinkquest.org/12413/structures.html
Mitochondria Produces energy through chemical reactions – breaking down fats & carbohydrates Controls level of water and other materials in cell Recycles and decomposes proteins, fats, and carbohydrateshttp://library.thinkquest.org/12413/structures.html
Golgi Bodies Protein packaging plant Move materials within the cell Move materials out of the cellhttp://library.thinkquest.org/12413/structures.html
Lysosome Digestive plant for proteins, fats, and carbohydrates Transports undigested material to cell membrane for removal Cell breaks down if lysosome explodeshttp://library.thinkquest.org/12413/structures.html
Vacuoles Membrane-bound sacs for storage, digestion, and waste removal Contains water solution Help plants maintain shapehttp://library.thinkquest.org/12413/structures.html
Chloroplast Usually found in plant cells Contains green chlorophyll Where photosynthesis takes placehttp://library.thinkquest.org/12413/structures.html
What is Life Made of? Physical and Chemical sciences alone may not completely explain the nature of life, but they at least provide the essential framework for such an explanation. All students of life must have a fundamental understanding of organic chemistry and biology
BOTTOM LINE:THE ELEMENTS THAT MAKE UP TERRESTRIAL LIVING ORGANISMS ARE VERY COMMON IN STARS AND IN THE INTERSTELLAR MATERIAL FROM WHICH STARS AND PLANETS ARE FORMED.IN LIVING THINGS, THE ATOMS OF THESE ELEMENTS ARE ORGANIZED IN ORGANIC MOLECULES, MANY OF WHICH ARE LARGE AND COMPLEX.
BASIC FACTS ABOUT LIFE ON EARTH LIVING ORGANISMS ON EARTH ARE MADE OF CELLS. EXCEPTION: VIRUSES A CELL IS TINY DROP OF WATER AND VARIOUS ORGANIC MOLECULES, SURROUNDED BY A MEMBRANE. SOME CELLS CONTAIN CERTAIN STRUCTURES, TO BE DISCUSSED LATER. SOME ORGANISMS (BACTERIA, FOR EXAMPLE) ARE SINGLE-CELLED, AND OTHER ORGANISMS (HUMANS, FOR EXAMPLE) ARE MULTICELLULAR. A CELL CAN DIVIDE, RESULTING IN TWO CELLS.
Bio-molecules Just like cells are building blocks of tissues likewise molecules are building blocks of cells. Animal and plant cells contain approximately 10, 000 kinds of molecules (bio-molecules) Water constitutes 50-95% of cells content by weight. Ions like Na+, K+ and Ca+ may account for another 1% Almost all other kinds of bio-molecules are organic (C, H, N, O, P, S) Infinite variety of molecules contain C. Most bio-molecules considered to be derived from hydrocarbons. The chemical properties of organic bio-molecules are determined by their functional groups. Most bio-molecules have more than one.
Major Classes of small Bio-molecules • Building blocks of proteins. 1. Amino • 20 commonly occurring. acids: • Contains amino group and carboxyl group function groups (behavioral properties) • R Group (side chains) determines the chemical properties of each amino acids. • Also determines how the protein folds and its biological function. • Individual amino acids in protein connected by peptide bond. • Functions as transport proteins, structural proteins, enzymes, antibodies, cell receptors.
Sugars Carbohydrates most abundant organic molecule found in nature. Initially synthesized in plants from a complex series of reactions involving photosynthesis. Basic unit is monosaccharides. Monosaccharides can form larger molecules e.g. glycogen, plant starch or cellulose.Functions Store energy in the form of starch (photosynthesis in plants) or glycogen (in animals and humans). Provide energy through metabolism pathways and cycles. Supply carbon for synthesis of other compounds. Form structural components in cells and tissues. Intercellular communications
Fatty acids Are monocarboxylic acid contains even number C atoms Two types: saturated (C-C sb) and unsaturated (C-C db) Fatty acids are components of several lipid molecules. E,g. of lipids are triacylglycerol, streiods (cholestrol, sex hormones), fat soluble vitamins.Functions Storage of energy in the form of fat Membrane structures Insulation (thermal blanket) Synthesis of hormones
Energy for Cells Living cells are inherently unstable. Constant flow of energy prevents them from becoming disorganized. Cells obtains energy mainly by the oxidation of bio- molecules (e- transferred from 1 molecule to another and in doing so they lose energy) This energy captured by cells & used to maintain highly organized cellular structure and functions
How do complex structure of cells maintain high internal order?n Synthesis of bio-molecules2. Transport Across Membranes- Cell membranes regulate the passage of ions and molecules from one compartment to another.3. Cell Movement- Organised movement- most obvious characteristics of living cells. The intricate and coordinated activities required to sustain life require the movement of cell components.4. Waste Removal- Animal cells convert food molecules into CO2, H20 & NH3. If these not disposed properly can be toxic.
Year 1944 Proteins were thought to carry genetic information 1897 Mie s c he r d is c o ve re d D NA 1828 Interweaving of the historical traditions of biochemistry, cell biology, and genetics.
Living things are composed of lifeless molecules. When these molecules are considered individually, they are found to conform to all the physical and chemical laws that describe the behavior of inanimate matter.