1. Chapter 7 Microbial Physiology and Genetics

2. Microbial Physiology Introduction
Physiology is the study of the vital life processes of organisms.
Microbial physiology concerns the vital life processes of microorganisms.

3. Microbial Physiology Microbial Nutritional Requirements
All living protoplasm contains six 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).

4. Microbial Physiology Categorizing Microorganisms According to Their Energy and Carbon Sources
Terms relating to an organism’s 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.

5. Microbial Physiology Categorizing Microorganisms According to Their Energy and Carbon Sources (cont.)
Terms relating to an organism’s carbon source:
Autotrophs use carbon dioxide (CO2) as their sole source of carbon.
Heterotrophs use organic compounds other than CO2 as carbon sources.
Terms that combine both energy and carbon source:
Photoautotrophs use light as an energy source and CO2 as a carbon source.
Photoheterotrophs use light as an energy source and organic compounds other than CO2 as a carbon source.
Chemoautotrophs use chemicals as an energy source and CO2 as a carbon source.
Chemoheterotrophs use chemicals as an energy source and organic compounds other than CO2 as a carbon source.

6. 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, including 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.

7. Metabolic Enzymes
Metabolism refers to all of 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.
An enzyme does not become altered during the chemical reaction it catalyzes. (They don’t last forever, however!)

8. Metabolism
As previously stated, metabolism refers to all of the chemical reactions within a cell. These reactions known as metabolic reactions.
Metabolic reactions fall into two categories: catabolism and anabolism.
Catabolism refers to all catabolic reactions in a cell.
Anabolism refers to all anabolic reactions in a cell.
Catabolic reactions involve the breaking down of larger molecules into smaller ones.
Whenever chemical bonds are broken, energy is released. Catabolic reactions are a cell’s 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.

9. Anabolic and Catabolic Reactions

10. 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, such as glucose, to energy-requiring reactions.

11. 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.

12. Metabolism Catabolism (cont.)
Catabolic reactions release energy (by breaking bonds) and are a cell’s major source of energy.
Some energy is lost as heat in catabolic reactions.
Catabolism of glucose by aerobic respiration occurs in three phases (each is a biochemical pathway):
Glycolysis
The Krebs cycle
The electron transport chain
The first phase (glycolysis) is actually anaerobic, but the other two phases are aerobic.

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

14. Catabolism Oxidation–Reduction (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.

15. Anabolism
Anabolic reactions require energy because chemical bonds are being formed.
The energy that is required comes from catabolic reactions, which are occurring simultaneously.

16. Bacterial Genetics Genetics is the study of heredity.
An organism’s genotype (or genome) is its complete collection of genes.
An organism’s phenotype refers to its physical traits (e.g., hair and eye color in humans).
An organism’s phenotype is the manifestation of that organism’s genotype.
Genes direct all functions of the cell.
A particular segment of the chromosome constitutes a gene.

17. Bacterial Genetics Mutations
A change in a DNA molecule (genetic alteration) that is transmissible to offspring is called a mutation.
There are three 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.

18. 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.

19. Bacterial Genetics Ways in Which Bacteria Acquire New Genetic Information (cont.)
Lysogenic conversion
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.
The bacterial cell exhibits new properties, directed by the viral genes. This is referred to as lysogenic conversion.

20. Bacterial Genetics Ways in Which Bacteria Acquire New Genetic Information, cont.
Transduction (“to carry across”):
This 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.

21. 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.

22. Bacterial Genetics Ways in Which Bacteria Acquire New Genetic Information (cont.)
Conjugation
This 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 from the donor cell to the recipient cell through a conjugative pore.
A plasmid that contains multiple genes for antibiotic resistance is known as a resistance factor or R-factor. A bacterial cell that receives an R-factor becomes a “superbug.”

23. Genetic Engineering
Genetic engineering or recombinant DNA technology involves techniques to transfer eukaryotic 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, as well as synthesis of important enzymes and hormones for treatment of diseases.