Microbiology - Test III

What are the two energy units to know?

calorie (cal) and joule (J)

Provide the calorie-joule conversion.

1 cal = 4.184 J

What family of compounds act as the energy currency of biosynthesis?

Nucleoside triphosphates (NTPs)

• ATP

• GTP

• CTP

• UTP

Does ATP possess a high or low phosphate transfer potential, and what does this mean?

ATP has a high phosphate transfer potential meaning that it readily donates to a phosphoryl group.

In what biosynthesis process is GTP used?

Guanosine 5’-triphosphate (GTP) is used in protein synthesis and translation.

In what biosynthesis process is CTP used?

Cytidine 5’-triphosphate (CTP) is used in lipid, especially phospholipid, biosynthesis.

In what biosynthesis process is UTP used?

Uridine 5’-triphosphate is used in carbohydrate metabolism and peptidoglycan biosynthesis.

Differentiate oxidation and reduction.

Oxidation involves a substance losing electrons while reduction involves a substance gaining electrons.

Differentiate oxidants and reductants.

Oxidants cause another substance to be oxidised (lose electrons), resulting in the oxidant getting reduced (gaining electrons).

Reductants cause another substance to be reduced (gain electrons), resulting in the reductant getting oxidised (losing electrons).

What does a more negative or more positive standard redox potential (E’₀) mean?

More negative = better electron donor (reductant)

More positive = better electron acceptor (oxidant)

Provide the formula for calculating standard redox potential (E’₀).

E’₀ = E’_{0, ox} - E’_{0, red}

Provide the formula for calculating free energy (ΔG^’0) from standard redox potential (E’₀).

ΔG^’0 = -n F ΔE’₀

• n is number of electrons

• F is Faraday constant (23 kcal/volt eq. or 96.5 kJ/volt eq.)

• E’₀ = E’_{0, ox} - E’_{0, red}

List the five main electron carriers and how many electrons and/or protons they donate.

• NADH and NADPH

  • 2 e^-, 1 H⁺

• FAD and FMN

  • 2 e^-, 2 H⁺

• CoQ / ubiquionine

  • 2 e^-, 2 H⁺

• cytochromes

  • 1 e^-

• non-haem iron-sulphur proteins

  • 1 e^-

What molecules are the electron carriers of FAD and FMN often associated with?

Flavoproteins

What molecules are the electron carriers of CoQ/ubiquinone often associated with?

Lipids

What molecules are the electron carriers of cytochromes often associated with?

the iron of a haem group

What molecules are the electron carriers of non-haem iron-sulphur proteins often associated with?

ferredoxin (iron not part of haem group)

Differentiate between an apoenzyme, cofactor, and holoenzyme.

An apoenzyme involves the inactive protein components, a cofactor involves the necessary non-protein components, and the holoenzyme is the coupled version of the two.

Differentiate between a prosthetic group and a coenzyme.

A prosthetic group is tightly bound to an apoenzyme, while the coenzyme is weakly bound.

What are the three major mechanisms of metabolism regulation?

1. Metabolic channeling

2. Gene expression

3. Post-translational regulation

Describe phototrophs.

Use light to generate energy.

Describe chemotrophs.

Use the oxidation of chemical compounds to generate energy.

Describe organotrophs.

Use organic compounds as their electron source.

Describe lithotrophs.

Use inorganic molecules as their electron source.

Describe autotrophs.

Use carbon dioxide as their carbon source.

Describe heterotrophs.

Use organic molecules for their carbon source, and often also as their energy source.

Describe the catabolic processes that chemoorganoheterotrophs and chemolithotrophs can perform.

Chemoorganoheterotrophs:

• Aerobic respiration

• Anaerobic respiration

• Fermentation

Chemolithotrophs:

• Aerobic respiration

• Anaerobic respiration

Aerobic and anaerobic respiration utilise electron acceptors. Which ones do each use?

Aerobic respiration uses oxygen, while anaerobic respiration uses an exogenous receptor like NO₃^- or CO₂.

What electron acceptor does fermentation use?

An endogenous electron acceptor like pyruvate.

Which of the following does fermentation use?: the electron transport chain, proton motive force, oxidative phosphorylation, substate-level phosphorylation.

Fermentation only uses substrate-level phosphorylation.

What are the three steps of aerobic respiration?

1. Glycolysis to produce pyruvate.

2. TCA (citric acid, Krebs) cycle to oxidise pyruvate into CO₂.

3. Electron transport chain with oxygen as final electron acceptor.

What are the three pathways commonly seen in the glycolysis step for aerobic respiration? What do all three have in common?

1. Embden-Meyerhof pathway

2. Entner-Duodoroff pathway

3. Pentose phosphate (hexose monophosphate) pathway

All three convert glucose to glyceraldehyde-3-phosphate to pyruvate.

Describe the Embden-Meyerhof pathway.

• most common pathway for glucose-pyruvate conversion.

• Provides precursor metabolites, NADH, and ATP.

• Functions with or without oxygen.

• Two phases are a six-carbon phase (uses ATP) and a three-carbon phase (makes ATP).

Describe the Entner-Duodoroff pathway.

• used by G(-) soil bacteria, some G(+) bacteria, E. coli, and Enterococcus faecalis.

• Not used by eukaryotes

• Replaces the six-carbon phase in the Embden-Meyerhof pathway

Describe the pentose phosphate (hexose monophosphate) pathway.

• oxidises glucose-6-phosphate to ribulose-5-phosphate and CO₂.

• Not oxygen dependent

• Works with the Embden-Meyerhof and Entner-Duodoroff pathways

• Absent from archaea

• Needed for both biosynthesis and catabolism; major source of NADPH, E4P, ribulose-5-P, and intermediates used for ATP

Describe the mitochondrial ETC.

Complex I: NADH-ubiquinone oxidoreductase, CoQ connects I to III.

Complex II: Succinate dehydrogenase (not a coupling site), CoQ connects II to III.

Complex III: ubiquinol-cytochrome c oxidoreductase, cytochrome c connects III to IV.

Complex IV: cytochrome c oxidase, transfers electrons to oxygen

ATP is generated from pmf-powered oxidative phosphorylation.

Describe the ETC of E. coli.

Involves a branched ETC pathway dependent on oxygen level:

• bd branch occurs during the stationary phase and low aeration, higher affinity for oxygen, moves fewer protons.

• bo branch occurs during the log phase and high aeration, lower affinity for oxygen.

Describe the ETC of Paracoccus denitrificans.

Very versatile ETC:

• Glucose can use NADH to donate electrons to NADH dehydrogenase.

• Methanol donates its electrons to cytochrome c with methanol dehydrogenase (no NADH used).

What is the theoretical maximum total yield of ATP from aerobic respiration in eukaryotes?

32 ATP

What two pathways do autotrophs mainly fix carbon through?

• Calvin (reductive pentose phosphate) cycle

• reductive TCA cycle

What is the main product of the Calvin cycle?

Glyceraldehyde-3-P

Where does the Calvin cycle occur between eukaryotes and prokaryotes?

In eukaryotes, the stroma of the chloroplasts; in prokaryotes, the carboxysomes.

What are the inputs of the Calvin cycle?

3 ATP and 2 NADPH per 1 CO₂

What are the three phases of the Calvin cycle?

1. Carboxylation where RuBisCO catalyses the conversion of CO₂ and RuBP into two 3-phosphoglycerates.

2. Reduction where 3-phosphoglycerate is reduced to glyceraldehyde-3-P.

3. Regeneration where RuBP is regenerated.

Describe the reductive TCA cycle.

Converts four CO₂ to oxaloacetate, and requires fumarate reductase, a-ketoglutarate synthase, and ATP-dependent citrate lyase.

• Used by some chemolithoautotrophs and depends on ferredoxin.

What is the universal intermediate for the synthesis of sugars like glycogen?

Uridine diphosphate glucose (UDP-G)

Differentiate assimilatory and dissimilatory pathways.

Assimilatory pathways involve reducing inorganic ions to allow them to be incorporated into biosynthetic pathways; dissimilatory pathways involve using inorganic compounds as electron acceptors rather than oxygen.

Describe assimilatory nitrate reduction in bacteria.

• Occurs in the cytoplasm.

• Nitrate is reduced to nitrite by nitrate reductase.

• Nitrite is reduced to ammonia by nitrite reductase.

Describe nitrogen fixation.

• Exergonic reduction of atmospheric nitrogen gas to ammonia by nitrogenase.

• Highly sensitive to oxygen.

• Requires 8 electrons and 16 ATP.

• Only carried out by a few diazotrophs

What two mechanisms allow for ammonia incorporation?

1. Reductive amination

2. Glutamine synthetase-glutamate synthase (GS-GOGAT)

Describe reductive amination

Ammonia incorporation mechanism in bacteria and fungi performed under high ammonia concentration with no ATP required; a-ketoglutarate is converted to glutamate by glutamate dehydrogenase.

Describe glutamine synthetase-glutamate synthase (GS-GOGAT)

Ammonia incorporation mechanism performed under low ammonia concentration with ATP; glutamate is converted to glutamine by glutamine synthetase while a-ketoglutarate and glutamine are converted to glutamate by glutamate synthase.

Describe assimilatory sulphate reduction.

Sulphate is converted into H₂S.