Burton's Microbiology for the Health Sciences

Chapter 7. Microbial Physiology and Genetics

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Chapter 7 Outline
Microbial Physiology
Introduction Microbial Nutritional Requirements Categorizing Microorganisms According to Their Energy and Carbon Sources Metabolic Enzymes Biologic Catalysts Factors That Affect the Efficiency of Enzymes

Metabolism
Catabolism Anabolism Bacterial Genetics

Mutations
Ways in Which Bacteria Acquire New Genetic Information Genetic Engineering Gene Therapy

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Microbial Physiology
Introduction
Physiology is the study of the vital life processes of organisms. Microbial physiology concerns the vital life processes of microorganisms. Scientists can learn about human cells by studying the nutritional needs of bacteria, their metabolic pathways, and why they live, grow, multiply, or die under certain conditions. Bacteria, fungi, and viruses are used extensively in genetic studies because they produce generation after generation so rapidly.
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Microbial Physiology

Nutritional Requirements
All living protoplasm contains 6 major chemical elements: carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur.

Combinations of these and other elements make up vital macromolecules of life, including carbohydrates, lipids, proteins, and nucleic acids.
Materials that organisms are unable to synthesize, but are required for building macromolecules and sustaining life, are termed essential nutrients (e.g., certain essential amino acids and essential fatty acids).

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Microbial Physiology

Categorizing Microorganisms According to Their Energy and Carbon Sources

Terms relating to an organisms energy source.

Phototrophs use light as an energy source.

Chemotrophs use either inorganic or organic chemicals as an energy source.

Chemolithotrophs use inorganic chemicals as an energy source.

Chemoorganotrophs use organic chemicals as an energy source.

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Microbial Physiology

Categorizing Microorganisms According to Their Energy and Carbon Sources, cont.

Terms relating to an organisms carbon source:
Autotrophs use carbon dioxide (CO2) as their sole source of carbon. Heterotrophs use organic compounds other than CO2 as carbon sources. Photoautotrophs use light as a carbon source and CO2 as an energy source. Chemoautotrophs use chemicals as a carbon source and CO2 as an energy source. Chemoheterotrophs use chemicals as a carbon source and organic compounds other than CO2 as an energy source.

Terms that combine both energy and carbon source:

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Microbial Physiology

Categorizing Microorganisms According to Their Energy and Carbon Sources, cont.

Ecology is the study of the interactions between living organisms and the world around them. Ecosystem refers to the interactions between living organisms and their nonliving environment. Interrelationships among the different nutritional types are of prime importance in the functioning of the ecosystem. Example: Phototrophs, such as algae and plants, are the producers of food and oxygen for chemoheterotrophs, such as animals.
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Metabolic Enzymes
Metabolism refers to all the chemical reactions that occur in a cell. The chemical reactions are referred to as metabolic reactions.

Metabolic reactions are enhanced and regulated by enzymes known as metabolic enzymes.
Biologic Catalysts

Enzymes are biologic catalysts; they are proteins that either cause a particular chemical reaction to occur or accelerate it.

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Metabolic Enzymes

Biologic Catalysts, cont.

Enzymes are specific in that they only catalyze one particular chemical reaction. A particular enzyme can only exert its effect on one particular substance, known as the substrate for that enzyme. The unique 3-dimensional shape of an enzyme enables it to fit the combining site of the substrate like a key fits into a lock. An enzyme does not become altered during the chemical reaction it catalyzes. (They dont last forever, however!)
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Action of specific enzyme (E1) breaking down a substrate (S1) molecule

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Metabolic Enzymes

Biologic Catalysts, cont.

Endoenzymes are enzymes produced within a cell that remain within the cell to catalyze reactions. Example: digestive enzymes within phagocytes Exoenzymes are produced within a cell and then released outside of the cell to catalyze extracellular reactions. Examples: cellulase and pectinase, which are secreted by saprophytic fungi to break down cellulose and pectin, respectively Hydrolases and polymerases are examples of metabolic enzymes.
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Metabolic Enzymes

Factors That Affect the Efficiency of Enzymes

Many factors affect the efficiency or effectiveness of enzymes; enzymes function best under optimum conditions.

pH - extreme acidity for example

Temperature - heat can denature enzymes by breaking bonds

Concentration of enzyme and/or substrate may be too high or too low

Inhibitors, for example heavy metals like lead, zinc, mercury and arsenic
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Metabolism
As previously stated, metabolism refers to all of the chemical reactions within a cell - reactions known as metabolic reactions.

A metabolite is any molecule that is a nutrient, an intermediary product, or an end product in a metabolic reaction.
Metabolic reactions fall into 2 categories: catabolism and anabolism. Catabolism refers to all catabolic reactions in a cell. Anabolism refers to all anabolic reactions in a cell.
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Metabolism, cont.
Catabolic reactions involve the breaking down of larger molecules into smaller ones. Whenever chemical bonds are broken, energy is released. Catabolic reactions are a cells major source of energy.

Anabolic reactions involve the assembly of smaller molecules into larger molecules, requiring the formation of bonds. Once formed, the bonds represent stored energy. Much of the energy released during catabolic reactions is used to drive anabolic reactions.
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Metabolism, cont.
Energy can be temporarily stored in high-energy bonds in special molecules, usually adenosine triphosphate (ATP). ATP molecules are the major energy-storing or energy-carrying molecules in a cell. ATP molecules are found in all cells because they are used to transfer energy from energy-yielding molecules like glucose, to energy-requiring reactions. When ATP is used as an energy source, it is hydrolyzed to adenosine diphosphate (ADP). ADP can be used as an energy source by hydrolysis to adenosine monophosphate (AMP).
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Interrelationships among ATP, ADP, and AMP molecules.

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Metabolism, cont.
Energy is required not only for metabolic pathways, but also for growth, reproduction, sporulation, and movement of the organism, as well as active transport of substances across membranes. Some organisms (e.g., marine dinoflagellates) use energy for bioluminescence. Cellular mechanisms that release small amounts of energy as the cell needs it usually involve a sequence of catabolic and anabolic reactions.

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Metabolism
Catabolism
Catabolic reactions release energy (by breaking bonds) and are a cells major source of energy. Some energy is lost as heat in catabolic reactions.

Biochemical pathways are a series of linked biochemical reactions occurring in a stepwise manner, from a starting material to an end product.
Think of nutrients as energy sources for organisms and think of chemical bonds as stored energy. Glucose, for example, can be catabolized by one of 2 common biochemical pathways: aerobic respiration and fermentation.
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A biochemical pathway with 4 steps. Compound A is ultimately converted to compound E. Four enzymes are required in this biochemical pathway. Compound A is the substrate for Enzyme 1, Compound B for Enzyme 2, etc.

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Metabolism

Catabolism, cont.
Catabolism of glucose by aerobic respiration occurs in 3 phases (each is a biochemical pathway): Glycolysis

The Krebs cycle

The electron transport chain The 1st phase (glycolysis) is actually anaerobic, but the other 2 phases are aerobic. Glycolysis (also called the glycolytic pathway, the Embden-Meyerhof pathway and the Meyerhof-Parnas pathway) is a 9-step biochemical pathway. Each step requires a specific enzyme.
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Aerobic Respiration of Glucose: First Step = Glycolysis.

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Catabolism

Aerobic Respiration of Glucose, cont.

The Krebs Cycle (also known as the citric acid cycle, the tricarboxylic acid cycle and the TCA cycle): A biochemical pathway consisting of 8 separate reactions, each controlled by a different enzyme. Only 2 ATP molecules are produced, but a number of products (e.g., NADH, H+, FADH2) are formed, which enter the electron transport chain.

In eucaryotes, the TCA cycle and the electron transport chain occur in mitochondria.
In procaryotes, both occur at the inner surface of the cell membrane.
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The Krebs Cycle.

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Catabolism

Aerobic Respiration of Glucose, cont.

The electron transport chain (also referred to as the electron transport system or respiratory chain): A series of oxidation-reduction reactions, whereby energy is released as electrons which are transferred from one compound to another. Many enzymes are involved in the electron transport chain, including cytochrome oxidase, which transfers electrons to oxygen (the final acceptor). A large number of ATP molecules are produced by oxidative phosphorylation. Aerobic respiration is very efficient!
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Catabolism

Fermentation of Glucose
Fermentation reactions do not involve oxygen. They take place in anaerobic environments. There are many industrial applications of fermentation reactions.

First step is glycolysis (anaerobic).

The next step is conversion of pyruvic acid into an end product. The end product varies from one organism to another. Example: yeasts are used to make wine and beer; the end product is ethanol. Fermentation reactions produce very little energy (~ 2 ATP molecules).
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Catabolism

Oxidation-Reducton (Redox) Reactions

Oxidation-reduction reactions are paired reactions in which electrons are transferred from one compound to another.

Oxidation occurs whenever an atom, ion, or molecule loses one or more electrons in a reaction; in which case, the molecule is said to be oxidized.
The gain of one or more electrons by a molecule is called reduction and the molecule is said to be reduced. Within a cell, an oxidation reaction is always paired with a reduction reaction; hence the term, oxidation-reduction reaction.
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Catabolism

Oxidation-Reduction (Redox) Reactions, cont.

In a redox reaction, the electron donor (compound A) is the reducing agent, and the electron acceptor (compound B) is the oxidizing agent. Many biologic oxidations are referred to as dehydrogenation reactions because hydrogen ions, as well as electrons, are removed.

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Anabolism
Anabolic reactions require energy because chemical bonds are being formed. The energy that is required comes from catabolic reactions, which are occurring simultaneously. Anabolic reactions are also called biosynthetic reactions. Biosynthesis of organic compounds requires energy. The energy may be obtained through photosynthesis (from light) or chemosynthesis (from chemicals). Photosynthetic reactions trap the radiant energy of light and convert it into chemical bond energy in ATP and carbohydrates (e.g., glucose).
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Bacterial Genetics
Genetics = the study of heredity. An organisms genotype is its complete collection of genes. An organisms phenotype refers to its physical traits (e.g., includes hair and eye color in humans). An organisms phenotype is the manifestation of that organisms genotype. Genes direct all functions of the cell. A particular segment of the chromosome constitutes a gene.
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Bacterial Genetics
Mutations
A change in a DNA molecule (genetic alteration) that is transmissible to offspring is called a mutation.

3 categories of mutations:
Beneficial mutations Harmful mutations (some are lethal mutations)

Silent mutations
Mutation rate (the rate at which mutations occur) can be increased by exposing cells to physical or chemical agents called mutagens.

The organism containing the mutation is called a mutant.

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Bacterial Genetics

Ways in Which Bacteria Acquire New Genetic Information

Ways in which bacteria acquire new genetic information (i.e., acquire new genes):
Lysogenic Conversion Transduction

Transformation
Conjugation An extrachromosomal DNA molecule is called a plasmid. An organism that acquires a plasmid acquires new genes. A plasmid that can either exist by itself or can integrate into the chromosome is called an episome.
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(A) A disrupted E. coli cell, in which the DNA has spilled out. A plasmid can be seen slightly to the left of top center (arrow). (B) Enlargement of plasmid.

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Bacterial Genetics
Lysogenic Conversion

Ways in Which Bacteria Acquire New Genetic Information, cont.

Temperate phages (or lysogenic phages) inject their DNA into a bacterial cell.

The phage DNA integrates into the bacterial chromosome, but does not cause the lytic cycle to occur this is known as lysogeny.
A phage is called a prophage when all that remains of it is its DNA. The bacterial cell containing the prophage is referred to as a lysogenic cell. The bacterial cell exhibits new properties, directed by the viral genes this is referred to as lysogenic conversion.
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Bacterial Genetics

Ways in Which Bacteria Acquire New Genetic Information, cont.

Transduction (to carry across): Also involves bacteriophages.

In transduction, bacterial genetic material is carried across from one bacterial cell to another by a bacterial virus; thus, in transduction, bacteria acquire new bacterial genes. Note how this differs from lysogenic conversion, wherein bacteria acquire new genetic information in the form of viral genes.
Only small amounts of genetic material are transferred by transduction.
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Generalized Transduction

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Bacterial Genetics

Ways in Which Bacteria Acquire New Genetic Information, cont.

Transformation A bacterial cell becomes genetically transformed following the uptake of DNA fragments (naked DNA) from its environment. The ability to absorb naked DNA into the cell is called competence and bacteria capable of absorbing naked DNA are said to be competent bacteria. Transformation is probably not widespread in nature.

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Transformation

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Bacterial Genetics
Conjugation

Ways in Which Bacteria Acquire New Genetic Information, cont.

Involves a specialized type of pilus called a sex pilus.
A bacterial cell with a sex pilus (called the donor cell) attaches by means of the sex pilus to another bacterial cell (called the recipient cell). Some genetic material (usually a plasmid) is transferred through the hollow sex pilus from the donor cell to the recipient cell. A plasmid that contains multiple genes for antibiotic resistance is known as a resistance factor or Rfactor. A bacterial cell that receives a R-factor becomes a superbug.
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Conjugation

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Conjugation in Escherichia coli.

Sex pilus

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Genetic Engineering
Genetic engineering or recombinant DNA technology involves techniques to transfer eucaryotic genes (particularly human genes) into easily cultured cells to manufacture important gene products (mostly proteins). Plasmids are frequently used as vehicles for inserting genes into cells.
There are many industrial and medical benefits from genetic engineering.

Examples: synthesis of antibodies, antibiotics, drugs and vaccines; also, for synthesis of important enzymes and hormones for treatment of diseases.
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Gene Therapy
Gene therapy of human diseases involves the insertion of a normal gene into cells to correct a specific genetic disorder caused by a defective gene.

Viral delivery is the most common method for inserting genes into cells; specific viruses are selected to target the DNA of specific cells.
Genes may someday be regularly prescribed as drugs in the treatment of diseases (e.g., autoimmune diseases, sickle cell anemia, cancer, cystic fibrosis, heart disease, etc.)

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