Chapter 7: Microbial Physiology and Genetics 1Chapter 7Microbial Physiology and GeneticsPrimary Objectives of the ChapterChapter 7 introduces aspects of microbial physiology, such as enzymes, metabolism (catabolicand anabolic reactions), oxidation–reduction reactions, biochemical pathways, aerobicrespiration, and fermentation. Microbial genetic topics discussed in Chapter 7 include mutations,the various ways in which bacteria acquire new genetic information (lysogenic conversion,transduction, transformation, conjugation), genetic engineering, and gene therapy. Theinformation in Chapter 7 is considered essential in an introductory microbiology course.Terms Introduced in This ChapterAfter reading Chapter 7, you should be familiar with the following terms. These terms aredefined in Chapter 7 and in the Glossary.Adenosine triphosphate (ATP)Ames testAnabolic reactionsAnabolismAutotrophBeneficial mutationCatabolic reactionsCatabolismChemoautotrophChemoheterotrophChemolithotrophChemoorganotrophChemosynthesisChemotrophCompetenceCompetent bacteriaDehydrogenation reactionsEcologyEcosystemElectron transport chainEndoenzymeEpisomeEssential nutrientsExoenzymeFermentationGene therapy
Chapter 7: Microbial Physiology and Genetics 2GeneticsGlycolysisHarmful mutationHeterotrophKrebs cycleLethal mutationLysogenic bacteriumLysogenic conversionLysogenyMetabolic reactionsMetaboliteMicrobial physiologyMutagenMutantMutationOxidationOxidation–reduction reactionsPhenotypePhotoautotrophPhotoheterotrophPhototrophProphageR-factorReductionSilent mutationTransductionTransformation Review of Key Points Microbial physiology is the study of the life processes of microorganisms. Scientists have learned a great deal about cells—including human cells—by studying the nutritional needs of bacteria, their metabolic pathways, and why they live, grow, multiply, or die under certain conditions. All living organisms require sources of energy and carbon so that they can produce the molecules necessary for life. In addition, organisms must be provided with certain materials (called essential nutrients) that they themselves are unable to synthesize, but are required for survival; these essential nutrients vary from species to species. The energy source for certain organisms (called phototrophs) is light and for other organisms (called chemotrophs) is organic or inorganic chemicals. Chemolithotrophs and chemoorganotrophs are subcategories of chemotrophs. Chemolithotrophs (or simply lithotrophs) use inorganic chemicals as an energy source,
Chapter 7: Microbial Physiology and Genetics 3 whereas chemoorganotrophs (or simply organotrophs) use organic chemicals as an energy source. An organism’s carbon source may be CO2 (in which case the organism is called an autotroph) or other organic compounds (in which case the organism is called a heterotroph). Humans, animals, protozoa, and fungi are heterotrophs, as are most bacteria. Interrelationships among the different nutritional types are of prime importance in the functioning of the ecosystem. Phototrophs (plants, algae, and certain bacteria) are the producers of food and oxygen for the chemoheterotrophs (animals). Dead plants and animals are recycled by the chemoheterotrophic saprophytic decomposers (certain fungi and bacteria) into nutrients for phototrophs and chemotrophs. Metabolism refers to all of the chemical reactions (metabolic reactions) that occur within a living cell, including the production of energy and the synthesis of new molecules. Metabolic reactions include catabolic reactions and anabolic reactions. Catabolic reactions (also called degradative reactions) involve the breaking of chemical bonds and the release of energy. Anabolic reactions (also called biosynthetic reactions) require energy because they involve the formation of chemical bonds. Most metabolic reactions are regulated by enzymes. Enzymes are biologic molecules (proteins) that serve as catalysts to control the rate of metabolic reactions. The enzymes produced by any particular cell are governed by the genotype of that cell, and the presence or absence of any particular enzyme is part of the phenotype of that cell. The substance upon which an enzyme acts is known at that enzyme’s substrate. All the enzymes that a cell is capable of producing need not be present in the cell at a given moment in time. They are produced to meet the metabolic needs of the cell, as determined by the internal and external environments. Endoenzymes are enzmes that remain within the cell that produced them, whereas exoenzymes are enzymes that leave the cell to catalyze reactions outside of the cell. Apoenzymes are proteins that are unable to catalyze reactions on their own. To catalyze reactions, apoenzymes must first link up with a cofactor (either a mineral ion or a coenzyme). An enzyme operates at peak efficiency within a particular pH and temperature range and when an appropriate concentration of the substrate for that enzyme exists. If the environment is too acidic, basic, hot, or cold, or contains too much or too little substrate, the enzyme will not operate at peak efficiency and the reaction will not proceed at its maximum rate. Catabolic reactions involve the breaking of chemical bonds and the release of energy. Anabolic reactions involve the formation of bonds, which requires energy. Adenosine triphosphate (ATP) is the principal energy-storing or energy-carrying molecule in the cell. Should a cell require energy, one of the high-energy bonds in an ATP molecule can be broken, producing energy, an ADP molecule, and a free phosphate. The energy can then be used for growth, reproduction, active transport of substances across membranes, sporulation, movement, anabolic reactions, and other energy- requiring activities.
Chapter 7: Microbial Physiology and Genetics 4 Nutrients should be thought of as energy sources, and chemical bonds should be thought of as stored energy. A common pathway by which bacteria catabolize glucose is aerobic respiration, which consists of three phases: glycolysis, the Krebs cycle, and the electron transport chain. Most of the energy that is produced by aerobic respiration is produced by the electron transport chain. The breakdown of one molecule of glucose by aerobic respiration yields either 36 ATP molecules (procaryotic cells) or 38 ATP molecules (eucaryotic cells). Aerobes and facultative anaerobes are able to produce more energy than anaerobes, because they can catabolize glucose molecules via aerobic pathways. Anaerobes must catabolize glucose by fermentation, a relatively inefficient method that yields only two ATP molecules from a molecule of glucose. Oxygen does not participate in fermentation reactions. Oxidation reactions involve the loss of an electron, whereas reduction reactions involve the gain of an electron. Phototrophic organisms (algae, plants, and photosynthetic bacteria) derive their energy from the sun by photosynthesis. Chemosynthetic organisms use a chemical source of energy and raw materials to synthesize metabolites and macromolecules for growth and function of the organisms. As with humans, animals, and plants, the genetics of microbes involves DNA, genes, the genetic code, chromosomes, DNA replication, transcription, and translation—all part of molecular genetics. An organism’s genotype (or genome) is its complete collection of genes, whereas an organism’s phenotype is all the physical traits, attributes, or characteristics of the organism. Genes direct all functions of the cell, providing it with its own particular traits and individuality. An organism’s phenotype is the manifestation of that organism’s genotype. Constitutive genes are expressed at all times, whereas inducible genes are expressed only when the products that they code for (gene products) are needed. The base sequence of any gene on a chromosome may be altered accidentally in many ways, resulting in a mutation. Mutations are expressed not only in the cell in which the mutation occurred, but in subsequent generations as well. The altered genetic code will result in an altered protein, which could affect any of a number of different phenotypic characteristics (e.g., changes in colony characteristics, cell shape, biochemical activities, nutritional needs, antigenic sites, virulence, pathogenicity, drug resistance). Mutant bacteria are used in genetic and medical research and the production of vaccines. Mutations may be beneficial, harmful, or of no consequence to the cell or organism containing the mutation. Those of no consequence are called silent or neutral mutations. Beneficial mutations are of benefit to an organism, whereas harmful mutations result in the production of structurally altered proteins (often, nonfunctional enzymes). Some harmful mutations are lethal to the organism. Physical or chemical agents that cause an increased mutation rate are called mutagens.
Chapter 7: Microbial Physiology and Genetics 5 In addition to mutations, genetic changes in a bacterial cell may be the result of lysogenic conversion, transduction, transformation, or conjugation, all of which occur in nature as well as in the laboratory. Lysogenic conversion involves temperate bacteriophages. In lysogenic conversion, bacteria gain new genetic information in the form of viral genes. Transduction also involves bacteriophages. In lysogenic conversion, bacteria gain new genetic information in the form of bacterial genes. In transformation, a bacterial cell becomes genetically transformed following uptake of DNA fragments (―naked DNA‖) from the environment. Conjugation involves the transfer of genetic material (usually a plasmid) from a donor cell to a recipient cell through a hollow sex pilus. A plasmid that contains multiple genes for antibiotic resistance is called a resistance factor or R-factor. The field of genetic engineering involves the introduction of new genes into cells. When a cell receives a new gene, it can produce the gene product that is coded for by that gene. Genetically engineered bacteria are used to produce products such as insulin, interferon, human growth hormone, and materials for use as vaccines. Gene therapy involves the use of viruses and plasmids to introduce normal genes into cells that contain abnormal genes. InsightWhy Anaerobes Die in the Presence of OxygenWhen molecular oxygen (O2) is reduced (i.e., when O2 gains electrons; as in certain oxidation–reduction reactions), extremely reactive substances are produced (as shown in the followingequations). O2 + e– –O2 (superoxide anion) O2 + 2e– H2O2 (hydrogen peroxide) O2 + 3e– H2O + OH– (hydroxyl radical) These reduction products (superoxide anion, hydrogen peroxide, and hydroxyl radicals)are capable of causing severe damage to enzymes and cell membranes; they are potentially lethalto cells. To survive in the presence of oxygen, organisms must possess enzymes (e.g., superoxidedismutase and catalase) that can neutralize these toxic substances. Obligate anaerobes are killedin the presence of oxygen because they lack one or more of these enzymes. Aerotolerantanaerobes produce these enzymes, but not in high enough concentrations to enable the organismsto survive in high concentrations of oxygen.
Chapter 7: Microbial Physiology and Genetics 6Genetically Engineered Bacteria and YeastsThe term genetic engineering refers to the manufacture and manipulation of genetic material invitro (in the laboratory). Genetic engineering has been possible only since the late 1960s, when ascientist named Paul Berg demonstrated that fragments of human or animal DNA can be attachedto bacterial DNA. Such a hybrid DNA molecule is referred to as recombinant DNA. When amolecule of recombinant DNA is inserted into a bacterial cell, the bacterium is able to producethe gene product, usually a protein. Thus, microorganisms (primarily bacteria) can be geneticallyengineered to produce substances (gene products) that they would not normally manufacture.Paul Berg won a Nobel Prize in 1980 for his pioneering genetic engineering experiments. Molecules of self-replicating, extrachromosomal DNA, called plasmids, are frequentlyused in genetic engineering and are referred to as vectors. A particular gene of interest is firstinserted into the vector DNA, forming a molecule of recombinant DNA. The recombinant DNAis then inserted into or taken up by a bacterial cell. The cell is next allowed to multiply, creatingmany genetically identical bacteria (clones), each of which is capable of producing the geneproduct. From the clone culture, a genetic engineer may then remove (―harvest‖) the geneproduct. The Gram-negative bacillus, Escherichia coli, has often been used because it can beeasily grown in the laboratory, has a relatively short generation time (about 20 minutes underideal conditions), and its genetics are well understood by researchers. A Gram-positive bacterium(Bacillus subtilis), a yeast (Saccharomyces cerevisiae), and cultured plant and mammalian cellshave also been used by genetic engineers to produce desired gene products. An example of a product produced by genetic engineering is insulin, a hormoneproduced in E. coli cells and used to treat diabetic patients. Human growth hormone(somatotropin), bovine growth hormone (BGH), porcine growth hormone (PGH), somatostatin (ahormone used to limit growth), tissue growth factors, clotting factors, and interferon are alsoproduced by genetically engineered E. coli. Genetically engineered bacteria are being used toproduce industrial enzymes, citric acid, and ethanol, and to degrade pollutants and toxic wastes.The hepatitis B vaccine that is administered to healthcare workers is produced by a geneticallyengineered yeast, called Saccharomyces cerevisiae. New uses for recombinant DNA and genetic engineering are being discovered every day,causing profound changes in medicine, agriculture, and other areas of science. Increase Your Knowledge1. A Closer Look at Transduction. There are actually two types of transduction:specialized and generalized. The explanation in Chapter 7 describes specialized transduction, inwhich the infecting phage integrates into the bacterial chromosome or a plasmid. As the virusgenome breaks away to replicate and produce more viruses, it carries one or more bacterial geneswith it to the newly infected cell. In this way, genetic capabilities involving the fermentation ofcertain sugars, antibiotic resistance, and other phenotypic characteristics can be transduced toother bacteria. This process has been shown in the laboratory (in vitro) to occur in species of
Chapter 7: Microbial Physiology and Genetics 7Bacillus, Pseudomonas, Haemophilus, Salmonella, and Escherichia, and it is assumed to occurin nature. In generalized transduction, the bacteriophage is a virulent lytic phage that does notincorporate into the bacterial genome or plasmid. Rather, it picks up fragments of bacterial DNAduring the assembly of new virus particles and carries these bacterial genes to other cells that thenew viruses infect. Generalized transduction has been observed in species of Streptococcus,Staphylococcus, and Salmonella, and in Vibrio cholerae.2. A Closer Look at Fertility Factors. Bacteria possessing F+ or Hfr+ genes have theability to produce sex pili and become donor cells. If the fertility factor is on a plasmid, it iscalled an F+ gene, whereas if it is incorporated into the chromosome, it is referred to as an HFr+gene. A complete copy of the F plasmid (the plasmid containing the F+ gene) usually moves tothe recipient (F-) cell; therefore, the recipient cell usually becomes F+ (i.e., the recipient cellbecomes capable of producing a sex pilus and becoming a donor cell). On the other hand, therecipient cell usually receives only a portion of the chromosome from an HFr+ cell, and thatportion does not include the HFr+ gene; therefore, in this case, the recipient cell remains Hfr–,does not produce a sex pilus, and cannot become a donor cell.3. Learn more about enzymes at: www.northland.cc.mn.us/biology/biology1111/animations/enzyme.swf4. View the following animations on the TCA Cycle and Electron Transport: Click here to view TCA Cycle Click here to view Electron Transport5. Learn more about transduction, conjugation and transformation at: www.emunix.emich.edu/~rwinning/genetics/bactrec.htm6. Try your hand at some advanced microbial genetic problems at: www.sci.sdsu.edu/~smaloy/MicrobialGenetics/problems/7. There are many good videos on genetics on YouTube. For example, try this one: www.youtube.com/watch?v=t4i0Q_irM8o8. The HowStuffWorks website also has many good videos on bacterial mutations andgenetics. Check it out at: videos.howstuffworks.com/discovery/28648-assignment-discovery-bacteria-mutations- video.htm9. Learn more about gene therapy at: www.ornl.gov/sci/techresources/Human_Genome/medicine/genetherapy.shtml
Chapter 7: Microbial Physiology and Genetics 8 Critical Thinking1. What are some possible reasons why an obligate anaerobe is unable to live in the presence of oxygen?2. Assume that you are a microbiologist who has been doing research on a penicillin- sensitive strain of Staphylococcus aureus for many months. One day you discover that the organism is now resistant to penicillin. You know that it has not come in contact with any other species of bacteria, nor has it come in contact with the DNA from any other species of bacteria. What are two possible explanations for its sudden change from penicillin susceptibility to penicillin resistance?3. Several products were mentioned in this chapter that are being produced by genetically engineered bacteria and yeasts. Using the Internet, can you find others?Answers to the Chapter 7 Self-Assessment Exercises in the Text 1. C 2. A 3. D 4. A 5. C 6. D 7. D 8. B 9. C10. A Additional Chapter 7 Self-Assessment Exercises(Note: Don’t peek at the answers before you attempt to solve these self-assessment exercises.)
Chapter 7: Microbial Physiology and Genetics 9Matching QuestionsA. autotrophs _____ 1. _______________ are chemotrophs thatB. heterotrophs use inorganic chemicals as their energyC. lithotrophs source.D. organotrophsE. phototrophs _____ 2. Organisms that use organic compounds as their source of carbon are called _______________. _____ 3. Organisms that use organic compounds as their energy source are called _______________. _____ 4. Organisms that use carbon dioxide as their source of carbon are called _______________. _____ 5. Organisms that use light as their energy source are called _______________.A. conjugation _____ 6. In _______________, bacteria acquireB. lysogenic conversion new genetic information in the form ofC. mutation viral genes.D. transductionE. transformation _____ 7. Oswald Avery and his colleagues discovered that DNA is the hereditary molecule while performing _______________ experiments with Streptococcus pneumoniae. _____ 8. In _______________, bacteria acquire new genetic information as a result of absorbing pieces of naked DNA from their environment. _____ 9. In _______________, genetic information is passed from one bacterial cell to another via a hollow sex pilus. _____ 10. In _______________, bacteria acquire new genetic information when bacteriophages inject bacterial genes.True/False Questions
Chapter 7: Microbial Physiology and Genetics 10_____ 1. Dehydration synthesis reactions always involve the removal of a molecule of water._____ 2. The biosynthesis of polysaccharides, polypeptides, and nucleic acids are examples of catabolic reactions._____ 3. Oxidation–reduction reactions are paired reactions that involve the transfer of electrons._____ 4. Breaking a disaccharide down into its two monosaccharide components is an example of a hydrolysis reaction._____ 5. Anabolic reactions are a cell’s major source of energy._____ 6. The majority of energy produced in aerobic respiration is produced by the Krebs cycle._____ 7. In glycolysis, a 6-carbon glucose molecule is broken down into two 3-carbon molecules of pyruvic acid._____ 8. Aerobic respiration is a more efficient method of breaking down glucose than is fermentation._____ 9. Virulent bacteriophages are responsible for lysogenic conversion._____ 10. Mutations are always harmful.Answers to the Additional Chapter 7 Self-Assessment Exercises
Chapter 7: Microbial Physiology and Genetics 11Matching Questions 1. C 2. B 3. D 4. A 5. E 6. B 7. E 8. E 9. A10. DTrue/False Questions 1. True 2. False (these are examples of anabolic reactions) 3. True 4. True 5. False (catabolic reactions are a cell’s major source of energy) 6. False (the majority of the energy is produced by the electron transport chain) 7. True 8. True 9. False (temperate bacteriophages are responsible for lysogenic conversion)10. False (mutations may be harmful, beneficial, or ―silent‖)