Chapter 11 micro

What are the requirements for Carbon (C), Hydrogen (H), and Oxygen (O) in organisms?

They are often satisfied together through the assimilation of organic molecules

Do all microbes have fixed nutritional requirements?

No, some organisms possess great metabolic flexibility, which allows them to change their metabolic strategy depending on the environment.

How are organisms categorized based on their Energy source?

Phototrophs: Use light.

Chemotrophs: Obtain energy from the oxidation of chemical compounds (organic or inorganic).

How are organisms categorized based on their Electron source?

Organotrophs: Use organic compounds.

Lithotrophs: Use reduced inorganic substances.

How are organisms categorized based on their Carbon source?

Heterotrophs: Use organic molecules (which often also serve as their energy source).

Autotrophs: Use CO2 molecules as their sole or principal source

What are the three majority classes of known microorganisms?

1. Photolithoautotrophs / Photoautotrophs. 2. Chemolithoautotrophs (considered the oldest microbes). 3. Chemoorganoheterotrophs / Chemoheterotrophs / Chemoorganotrophs

Why are chemoorganoheterotrophs uniquely efficient regarding nutrients, and what major group do they include?

A single organic nutrient can satisfy all three of their requirements (carbon, electrons, and energy). This group contains the majority of pathogens.

What role do photolithoautotrophs and chemolithoautotrophs play in ecosystems?

They are known as primary producers

What are the three basic needs shared by all organisms (Fueling Reactions)?

1. ATP as an energy currency. 2. Reducing power ($\text{NADPH}$ and $\text{NADH}$) to supply electrons for chemical reactions. 3. Precursor metabolites for biosynthesis

What metabolic fueling processes can Chemoorganotrophs perform?

Fermentation, Aerobic respiration, and Anaerobic respiration.

What metabolic fueling processes can Chemolithotrophs perform?

They can only perform Aerobic respiration and Anaerobic respiration (no fermentation).

In chemoorganotrophic catabolism, where do the released electrons initially go?

They are accepted by electron carriers, reducing them to NADH or FADH

What determines whether an organic catabolic process is classified as respiration or fermentation?

Respiration: If the electrons are donated to an Electron Transport Chain (ETC).

Fermentation: If the electrons are donated to an endogenous electron acceptor.

What basic mechanism defines Respiration? And what can preform it?

It involves the use of an electron transport chain (ETC) that passes electrons to an external (exogenous) final electron acceptor. Chemolitho and Chemorgano

What is the final electron acceptor in Aerobic respiration?

Oxygen O2

What are examples of exogenous final electron acceptors in Anaerobic respiration?

NO3-, SO42-,

CO2, Fe3+, or SeO42

How is ATP generated during respiration?

Electrons passing through the ETC generate a Proton Motive Force (PMF), which powers ATP synthesis via Oxidative Phosphorylation (OP).

What is the role of electron acceptors in Fermentation?

It uses an endogenous electron acceptor (an internal intermediate generated by the pathway, such as pyruvate) to recycle electron carriers.

Does Fermentation use an ETC or Oxidative Phosphorylation?

No. It does not involve an ETC, does not generate a PMF, and no oxidative phosphorylation occurs ($\text{NO OP!}$)

How is ATP made during Fermentation?

Exclusively via Substrate-Level Phosphorylation (SLP) during the breakdown of the organic compound.

What is the broad goal of central metabolic pathways?

To provide the essential precursor metabolites to all other biosynthetic pathways in the cell.

What are the three stages/components of Aerobic Respiration?

1. Glycolytic pathways: Completely break down glucose to pyruvate, generating NADH and/or FADH. 2. TCA cycle: Pyruvate is completely oxidized to CO2, yielding GTP, NADH, and FADH. 3. Electron Transport Chain (ETC): Uses oxygen as the final electron acceptor to generate the bulk of ATP.

What are the three common routes used by microbes to convert glucose to pyruvate?

1. Embden-Meyerhof pathway (EMP) 2. Entner-Doudoroff pathway (ED) 3. Pentose phosphate pathway (PPP)

What major intersection point is shared by the EMP, ED, and PPP pathways?

All three convert glucose into glyceraldehyde 3-phosphate (G3P), which is then oxidized to pyruvate in the exact same manner across all three routes.

What is the significance of the Embden-Meyerhof Pathway (EMP)?

It is the most common pathway for glucose degradation to pyruvate, yielding precursor metabolites, NADH, and ATP. It can function in both the presence or absence of O2

What are the two distinct phases of the EMP?

1. Six-carbon phase: Consumes/uses ATP to prime glucose. 2. Three-carbon phase: Yields ATP and NADH via substrate-level phosphorylation and oxidation steps.

Which groups of organisms utilize the Entner-Doudoroff (ED) Pathway, and which group notably does not?

It is used by Gram-negative soil bacteria and some Gram-positives (often under aerobic conditions, e.g., E. coli and Enterococcus faecalis). It is NOT used by eukaryotes.

How does the ED pathway structurally fit into glucose catabolism?

It replaces the 6-carbon phase of the Embden-Meyerhof pathway (EMP).

What is an alternative name for the Pentose Phosphate Pathway (PPP), and what is its chemical baseline?

Also called the hexose monophosphate pathway, it oxidizes glucose-6P →ribulose-5P + CO2.

Is the Pentose Phosphate Pathway dependent on oxygen, and where is it absent?

It is not oxygen dependent and works simultaneously with the ED or EMP pathways. Notably, it is not found in Archaea.

Why is the Pentose Phosphate Pathway needed, and what unique precursors does it yield?

It serves both biosynthesis and catabolism. It is a major source of NADPH and produces essential sugars like erythrose 4-phosphate (E4P) and ribose 5-phosphate. Its intermediates can also be funneled to produce ATP

What are the two possible metabolic fates for intermediates generated in the PPP?

1. They can be degraded to pyruvate using EMP enzymes. 2. They can regenerate glucose-6P via gluconeogenesis.

What is an Amphibolic Pathway?

A metabolic pathway that functions in both anabolic (biosynthesis) and catabolic (degradation) directions

How do cells regulate amphibolic pathways, and what pathways are included?

Decisions depend on the levels of multiple regulatory signals that modulate pacemaker enzymes. Examples include the EMP/gluconeogenesis loop, the TCA cycle, and the PPP.

What are alternative names for the TCA Cycle, and where is it common?

Citric acid cycle or Krebs cycle. It is common in aerobic bacteria, free-living protozoa, most algae, and fungi.

Beyond producing energy carriers, what is a key biosynthetic purpose of the TCA cycle?

It acts as a major source of carbon skeletons for use in biosynthesis.

How does pyruvate enter the TCA cycle?

The pyruvate dehydrogenase complex (PDH) oxidizes and cleaves pyruvate into acetyl-CoA and $\text{CO}_2$

What molecular feature of acetyl-CoA and succinyl-CoA fuels metabolic work?

They both contain a high-energy thioester bond, the hydrolysis of which yields significant energy.

How does the ETC make the majority of cellular ATP?

By re-oxidizing the reduced electron carriers NADH and FADH2

: What is the driving potential difference E'_0 between NADH and O2?

It is 1.14 volts.

How are electron carriers organized structurally within an ETC?

They form a sequential series moving from carriers with more negative reduction potentials to those with more positive reduction potentials

Which specific components of the ETC carry both electrons and protons

Flavoproteins (Fp)

Ubiquinone (UQ) / Coenzyme Q

Which specific components of the ETC carry electrons only?

Cytochromes

Nonheme iron-sulfur proteins (FeS)

Outline the complexes and mobile links of the Mitochondrial ETC.

Complex I: NADH-ubiquinone oxidoreductase (coupling site).

• Mobile Link: CoQ connects Complex I and II to Complex III.

• Complex II: Succinate dehydrogenase.

• Complex III: Ubiquinol-cytochrome c oxidoreductase (coupling site).

• Mobile Link: Cyt c connects Complex III to Complex IV.

• Complex IV: Cytochrome c oxidase (coupling site; transfers electrons directly to O2

How does electron movement through the ETC generate ATP?

As electrons flow down the chain, coupling sites pump protons across the inner mitochondrial membrane (IMM), creating a proton motive force (PMF) that drives Oxidative Phosphorylation (OP)

What are five key features that differentiate Bacterial and Archaeal ETCs from Mitochondrial ETCs?

1. Different cellular location (plasma membrane/periplasm vs. inner mitochondrial membrane). 2. Use different electron carriers. 3. They may be branched. 4. They may be shorter. 5. They generally exhibit a lower P/O ratio.

What is the metabolic identity of Escherichia coli, and how does its ETC adapt to oxygen levels?

It is a facultative anaerobic bacterium with a branched pathway featuring two terminal branches:

• bd branch: Active during stationary phase/low aeration; high affinity for O2 but moves fewer protons.

• bo branch: Active during log phase/high aeration; lower affinity forO2 but pumps more protons.

What type of organism is Paracoccus denitrificans, and how versatile is its aerobic respiration?

A Gram-negative, non-fermenting, facultative anaerobic soil bacterium. It is extremely versatile:

• On Glucose: Uses NADH to donate electrons to NADH dehydrogenase.

• On 1-Carbon Molecules (e.g., Methanol): No NADH is involved; electrons are donated directly to cytochrome c via methanol dehydrogenase (MD).

What enzyme complex synthesizes ATP using the PMF, and what are its two primary functional parts?

ATP Synthase (best studied is F1 F0 ATP synthase).

• F0: The proton-conducting channel embedded in the membrane.

F1: The spherical complex that physically catalyzes ATP synthesis. (Note: It can also run backward to catalyze ATP hydrolysis)

What are the theoretical maximum total yields of ATP per glucose during aerobic respiration across domains?

Theoretical maximum: 32 ATP.

• In Eukaryotes: 30 ATP (using standard P/O ratios: 2.5 for NADH, 1.5 for FADH2.

• In Prokaryotes: Lower than eukaryotes due to shorter electron transport chains and reduced P/O efficiencies.

Why does Anaerobic Respiration yield less energy than Aerrial Respiration?

Because the standard reduction potential (E0) of the alternative exogenous electron acceptors is less positive than that of O2, and the ETCs are typically shorter.

What domain(s) perform anaerobic respiration, and what states are the electron acceptors in?

It is performed by all three domains of life. The final electron acceptors are always oxidized molecules that become reduced during the process

What happens to Paracoccus denitrificans under anoxic conditions?

It switches to dissimilatory nitrate reduction / denitrification (NO3→NO2→NO→N2O→N2). These specialized enzymes are strictly inhibited by the presence of O2

What is the environmental consequence of denitrification by soil bacteria?

Because nitrate is reduced to nitrogen gas N2, it escapes into the atmosphere and becomes unavailable for plant assimilation, causing a loss of soil fertility.

Name two other genera of facultative anaerobes besides Paracoccus that carry out denitrification.

Pseudomonas and Bacillus.

What are the major physiological features of Fermentation?

The energy source is only partially oxidized.

• Oxygen is not needed.

• There is no ETC and no PMF.

• Oxidative phosphorylation does not occur; ATP is generated only by SLP.

• NADH produced during glycolysis must be converted back to NAD+ by reducing pyruvate or a derivative.

How are fermentation pathways named?

They are named after the major acid or alcohol that they produce.

Provide examples of microbial fermenters and their specific pathways.

Mixed acid fermenters: E. coli.

• Butanediol fermenters: Enterobacter.

• Alcoholic acid fermenters: S. cerevisiae

What are the commercial and ecological roles of fermentation?

It causes food spoilage but is extensively harnessed to manufacture alcoholic beverages, yogurt, cheese, bread, and alternative fuels.

If strictly fermenting cells lack an ETC, how do they generate the PMF needed for other cellular functions?

y utilizing end-product efflux mechanisms.

• In strictly fermentative conditions, their F1 F0 ATP synthase operates reversibly, hydrolyzing ATP to pump protons out of the cell and generate a PMF.

How do complex carbohydrates (disaccharides and polysaccharides) enter microbial catabolism?

They are broken down into monosaccharides either outside the cell via hydrolases or inside the cell via phosphorylases.

How are Triglycerides catabolized by chemoorganotrophs?

They are cleaved by lipases into glycerol and fatty acids:

• Glycerol: Converted into dihydroxyacetone phosphate (DHAP) and funneled into the glycolytic pathway as glyceraldehyde-3P.

• Fatty acids: Oxidized via the $\beta$-oxidation pathway, where they are shortened by 2 carbons at a time and released as acetyl-CoA

How are proteins processed for energy production?

Proteases hydrolyze proteins into amino acids (proteolysis). The amino acids undergo deamination (often followed by transamination) to remove nitrogen, producing organic acids.

Where do the organic acids derived from amino acid catabolism enter central metabolism?

They are converted into pyruvate, acetyl-CoA, or directly into intermediates of the TCA cycle.

Where do Chemolithotrophs obtain their electrons, and how do they pass them on?

Electrons are released from inorganic molecules (e.g., reduced nitrogen, reduced sulfur, or Fe2+) and are donated directly to the ETC.

What are the terminal electron acceptors for chemolithotrophs, and what carbon source do they require?

Acceptors include oxygen, sulfate, and nitrate. Because they cannot use organic carbon, they must utilize CO2 as their carbon source via CO2 fixation pathways.

Why can't chemolithotrophs perform fermentation?

Because they do not use or have an organic molecule to oxidize, making fermentation biochemically impossible.

Why is significantly less energy available from the oxidation of inorganic molecules compared to organic ones?

Inorganic molecules have much more positive redox potentials, leaving a very small potential gap when paired with terminal acceptors

What are the three ecologically important major groups of Chemolithotrophs?

1. Hydrogen-oxidizing microbes: Oxidize H2 to reduce NAD+ or donate directly to the ETC.

2. Nitrifying bacteria: Carry out nitrification by oxidizing ammonia (NH3) to nitrate (NO3) in a process involving one or two distinct microbes.

3. Sulfur-oxidizing microbes: Oxidize reduced sulfur compounds (like H2S, S0, or thiosulfate) to sulfuric acid (H2SO4).

What is Reverse Electron Flow, and why do many chemolithotrophs need it?

Since many chemolithotrophs are autotrophs, they need NAD(P)H and ATP to reduce CO2. However, their inorganic substrates often cannot donate electrons directly to NAD(P)+ because their redox potentials are too positive. They must use energy to push electrons backward up the ETC to generate reducing power.