Microbiology Lecture 3 Review: Chapter 6,10 Microbial Metabolism and Taxonomy

Lecture Review - By: Amma Genfi

Chapter 6 - Microbial Metabolism: Fueling Cell Growth

1.    [06-01] What are metabolism and its two branches? How are they coupled? – Lecture 3, Slides 2, 5 –

Metabolism = Sum of all chemical reactions in the cell (Catabolism + Anabolism).

Catabolism = Sum of catabolic (exergonic) reactions that break down energy-rich, complex molecules and harvest energy as ATP.

Anabolism = Sum of anabolic (endergonic) reactions consume energy (mainly in form of ATP) and build up complex molecules out of simpler ones.

Both catabolism and anabolism are coupled (interconnected) via ATP molecules, which allow flow of energy from catabolic reactions to anabolic reactions.

2.     [06-03] What is metabolic pathway? What are the roles of enzymes and ATP in metabolic pathway? – Lecture 3, Slide 6 –

Metabolic pathway – Series of chemical reactions in which product of one chemical reaction becomes the reactant of the next one.

Enzymes – Protein catalysts speed up rate of chemical reaction by reducing activation energy needed for chemical reaction.

ATP – Energy currency of cell. ATP is build of adenine, ribose, and 3 phosphate groups. Carries the energy stored in third phosphate group in immediately available form.

3.    [06-05] Describe reduction-oxidation (redox) reaction. Describe electron carriers and give examples – Lecture 3, Slide 7 –

Redox reaction – Transfer of electrons from one compound to another. The compound that loses electrons becomes oxidized and is called electron donor. The compound that accepts electrons becomes reduced and is called electron acceptor. OIL RIG → Oxidation is loss, Reduction is gain (of electrons).

4.    [06-06] Describe the mechanisms of enzyme action – Lecture 3, Slide 9 – 

Mostly proteins, some are RNAs. Function as catalysts, speed up reaction w/o being consumed in the process: Enzyme binds to substrate at active site forming enzyme-substrate complex (lock and key model). → Active site provides local conditions that reduce activation energy (EA) and promote chemical reaction. → Substrate converted to product and product is released from enzyme active site. → Enzyme available for another round of enzymatic reaction.

5.    [06-08] Compare competitive and non-competitive inhibitors of enzymes. Why is sulfanilamide effective in treatment of bacterial infections? – Lecture 3, Slide 12 –

Competitive: Enzyme inhibitor that competes with substrate for the active site of enzyme. Effect can be reduced by increasing concentration of substrate.

Non-competitive: Enzyme inhibitor that binds to enzyme at site different from active site, does NOT compete with substrate. Effect is NOT reduced by increasing concentration of substrate.

Sulfanilamide drugs acts as a competitive inhibitor for enzyme involved in synthesis of folic acid in bacteria. Metabolic pathway not present in human cells. So drug will not affect human cells.

6.    [06-10] Describe allosteric regulation of metabolic pathways – Lecture 3, Slide 13 –

Allosteric regulation = End product of metabolic pathway acts as reversible non-competitive inhibitor of first enzyme of the same metabolic pathway.

Example of non-competitive inhibition of enzymatic activity that is used in regulation of some metabolic pathways in the cell. End product inhibition of first enzyme shuts down metabolic pathway, allows cells to quickly adjust depending end product concentration and conserve cellular resources.

7.    [06-11] Describe the outcomes of glycolysis, transitional step and TCA cycle in glucose catabolism – Lecture 3, Slides 14, 15, and 16 –

Glycolysis: Glucose → 2 Pyruvic acid, 2 ATP + 2 NADH also formed.
Transitional Step: 2Pyruvic acid → 2 acetyl-CoA, 2 CO₂ + 2 NADH also formed.

TCA cycle (Critic Acid Cycle): Cycle of carbon → 2 ATP + 6 NADH + 2 FADH2

Total Overall: 4 ATP + [ 10 NADH + 2 FADH2 ] to be used in electron transport chain.

8.    [06-12] Describe the role of electron transport chain and chemiosmosis in cellular respiration – Lecture 3, Slide 17 –

Electron transport chain (ETC) set of membrane proteins that utilize the energy rich electrons from 10 NADH + 2 FADH2 to create proton gradient. Proton gradient is used during chemiosmosis to produce ATP.

9.    [06-13] What is the difference between aerobic and anaerobic cellular respiration? – Lecture 3, Slide 17 –

Aerobic respiration = Oxygen is used as terminal acceptor of electrons.

Anaerobic respiration = Terminal acceptor is metal (Fe, Mn, Co, U, S, CO2, NO3, or organic molecule.

Aerobic respiration > anaerobic respiration because more energy extracted, allowing aerobes to grow quicker.

10. [06-14] Compare fermentation to cellular respiration – Lecture 3, Slides 18, 19 and 20 –

Respiration

- Taking place in mitochondrial inner membrane/bacterial plasma membrane

- Requires presence of electron transport chain (ETC)

- Up to 38 ATP

Fermentation

- Alternative that requires not oxygen, and takes place in cytoplasm.

- Uses organic molecule as final electron acceptor

- 2 NAD+ regenerated to allow continual fermentation.

Chapter 10 - Identifying and Classifying Microorganisms

11. [10-01] Explain binominal nomenclature and taxonomic hierarchy. Give examples – Lecture 3, Slides 24, 25 – Binominal nomenclature is a system of assigning Latin two worded names to each biological species. First word describes genus, second word describes the species itself. In bacterial name Escherichia coli, “Escherichia” is the name of genus to which the species belong, “coli” describes the species itself. Taxonomic hierarchy is a system of taxa (classification units) of various ranks. The high ranked taxon may include multiple taxa of lower ranks. Taxa from highest to lowest: Domain à Kingdom à Phylum à Class à Order à Family à Genus à Species. These taxa are used to classify biological species. The closer two species related to each other, the lower taxon they will share.

12. [10-03] Describe The three-domain system of classification of Life – Lecture 3, Slides 26, 27, 28 – The system is based on differences in nucleotide sequences of 16S (in prokaryotes) and 18S (in eukaryotes) ribosomal RNA genes. It divides all cellular forms of life into 3 domains, Archaea, Bacteria, and Eukaryota. All three domains have common ancestor. The first two domains, Archaea and Bacteria, include prokaryotic organisms. The third domain, Eukarya, include all eukaryotic organisms and is divided into four kingdoms Protista, Plantae, Fungi, and Animalia. Domains Archaea and Eukarya are closer related to each other than domains Archaea and Bacteria. Domain Archaea includes oldest prokaryotic organisms that have cell wall built of pseudopeptidoglycan and proteins. In plasma (cytoplasmic) membrane, they are using hydrocarbons not fatty acids linked by glycerol. They are often living in extreme conditions – high temperatures, high salt concentrations, extreme pH. Domain Bacteria includes prokaryotic organisms that have cell wall built of peptidoglycan. In plasma (cytoplasmic) membrane, they are using fatty acids linked by glycerol (lipids).

13. [10-04] Describe the identification of bacteria based on phenotype – Lecture 3, Slide 29-36 –  Phenotype is the physical and biochemical appearance of an organism. Identification of bacteria starts with culture characterization, which includes the description of bacterial colony morphology (shape, surface, texture, color, elevation, margin) grown at standard conditions and on standard culture medium. Note that the appearance of bacterial colony can be affected by culture medium used, temperature and time of incubation, atmospheric conditions. Then, bacterial culture is subjected to microscopic characterization. The culture is used to prepare stained slide that are studied under the microscope. Microscopic description includes cell shape and arrangement, type of cell wall, ability of bacterium produce endospores and ability to move. Finally, the bacterial culture is subjected to metabolic characterization. Various biochemical tests are run to characterize metabolic capabilities of bacterial culture by growing it on various growth media. For example, bacterial culture can be tested for its ability to use different sugars as a source of carbon and energy. These studies establish the biochemical profile of the bacterial culture. All these characterizations of phenotype helps to identify the unknown bacterial culture and establish to which bacterial species the culture in question belongs to.   

14. [10-06] Name bacterial genera that are source of antibiotics and belong to the following bacterial phyla: Proteobacteria, Firmicutes, and Actinobacteria – Lecture 3, Slide 39 (notes) –

Phylum Proteobacteria – NO bacteria produces antibiotics useful to humans.

Phylum Firmicutes – Some bacteria of Bacillus genus produce some antibiotics that have limited use b/c their high toxicity to humans (polymyxin, bacitracin).

Phylum Actinobacteria – Genera Streptomyces and Actinomyces are major sources of antibiotics for humans (streptomycin, neomycin).

15. [10-07] Name bacterial genera of human pathogens from the following bacterial phyla: Proteobacteria, Firmicutes, and Actinobacteria – Lecture 3, Slide 39 and see also Lecture 4 –
Proteobacteria (Gram-negative bacteria): Escherichia Neisseria, Pseudomonas, Salmonella, Shigella, Yersinia
Firmicutes (Gram-positive bacteria):Clostridium, Mycoplasma, Staphylococcus, Streptococcus, Ureaplasma
Actinobacteria (Gram-positive and acid-fast bacteria):Mycobacterium, Nocardia