Question 1

Claviceps fermentation case study: phosphate inhibition of clavine alkaloid formation in Claviceps SD58 can be counteracted by adding which amino acid precursor to the process?

Accepted Answer

Introduction / Context: Clavine alkaloids (ergot-related compounds) produced by Claviceps species are sensitive to nutrient signals, notably inorganic phosphate, which can repress secondary metabolism. Process developers sometimes add specific amino acids to override or mitigate inhibitory regulatory effects and restore product titers. Given Data / Assumptions: Organism: Claviceps SD58 producing clavine alkaloids. Problem: phosphate inhibition of product formation. Task: identify which amino acid addition counteracts this inhibition. Concept / Approach: Phosphate repression can be modulated by medium formulation and sometimes by adding particular amino acids that influence pathway regulation or precursor pools. Among common candidates, methionine is reported to counteract phosphate inhibition in certain Claviceps processes, likely via effects on sulfur-containing cofactor pools and regulatory cross-talk that favor secondary metabolism. Step-by-Step Solution: Recognize target pathway: clavine alkaloid biosynthesis (ergot alkaloid branch).Recall literature reports indicating methionine supplementation alleviates phosphate repression in specific Claviceps strains.Select “methionine.” Verification / Alternative check: Process notes in fermentation development often list methionine among effective supplements; tryptophan is a general precursor for indole-derived alkaloids but is not the primary agent cited for reversing phosphate repression in this case. Why Other Options Are Wrong: Alanine and lysine: not typically associated with relief of phosphate inhibition in clavine production. Tryptophan: a biosynthetic precursor in ergot pathways but not the specific antidote to phosphate repression highlighted for SD58. Common Pitfalls: Assuming that supplying the immediate carbon–nitrogen precursor (tryptophan) always overcomes global regulatory repression. Regulation often acts upstream at the gene expression level and may require different supplements or limitation strategies. Final Answer: methionine

Question 2

Chemiosmotic ATP generation (aerobic respiration): in establishing the proton gradient used by ATP synthase, which molecule serves as the terminal electron acceptor?

Accepted Answer

Introduction / Context: In aerobic respiration, electrons derived from NADH and FADH2 flow through the electron transport chain to a terminal acceptor. This redox sequence powers proton pumping, creating a proton motive force that ATP synthase exploits to generate ATP. Given Data / Assumptions: We are specifically in the context of aerobic respiration. Question asks for the terminal electron acceptor in creating the proton gradient. Typical bacterial or mitochondrial systems apply. Concept / Approach: Under aerobic conditions, oxygen (O2) is reduced to water at the terminal oxidase complex (for example, cytochrome c oxidase). Alternative acceptors such as nitrate or sulfate characterize anaerobic respiration, not aerobic respiration. Step-by-Step Solution: Identify the mode: aerobic respiration.Recall terminal step: electrons + O2 + protons → H2O.Select “oxygen.” Verification / Alternative check: Respiratory chains in mitochondria and many bacteria culminate in oxygen reduction, a highly exergonic step that contributes to strong proton motive force. Why Other Options Are Wrong: Nitrate, sulfate, and CO2: serve as terminal acceptors in anaerobic respiration or methanogenesis, not in classic aerobic respiration. Common Pitfalls: Confusing aerobic with facultative anaerobic pathways; organisms may switch acceptors depending on oxygen availability, but under aerobic conditions, oxygen is terminal. Final Answer: oxygen

Question 3

In anoxygenic photosynthesis (as performed by green and purple bacteria), which one of the following is NOT used as the electron donor (reducing power source)?

Accepted Answer

Introduction / Context: Green and purple photosynthetic bacteria carry out anoxygenic photosynthesis. Unlike plants, algae, and cyanobacteria, these bacteria do not split water and therefore do not release oxygen. The question probes which electron donor is not used by these organisms. Given Data / Assumptions: Organisms considered: green sulfur bacteria and purple bacteria. Process: anoxygenic photosynthesis (no oxygen evolution). Common bacterial electron donors include reduced sulfur compounds and hydrogen gas. Concept / Approach: Anoxygenic phototrophs harvest light with bacteriochlorophylls and reduce their electron transport chains using donors other than water. Typical donors are hydrogen sulfide (H2S), elemental sulfur (S), thiosulfate, and molecular hydrogen (H2). Water is the hallmark donor in oxygenic photosynthesis only. Step-by-Step Solution: List donors used by anoxygenic phototrophs: H2S, S, H2, organic acids.Recall oxygenic phototrophs (plants/cyanobacteria) use H2O, releasing O2.Therefore, the donor not used by green/purple bacteria is H2O. Verification / Alternative check: Presence of photosystem architecture lacking the strong oxidant required to split water confirms these bacteria cannot oxidize water; many oxidize sulfide to elemental sulfur or sulfate instead. Why Other Options Are Wrong: H2: Common bacterial donor. H2S: Classic donor for sulfur phototrophs. S (elemental sulphur): Can serve as donor or intermediate in many of these bacteria. Common Pitfalls: Equating all photosynthesis with oxygen release. Only oxygenic photosynthesis splits water. Final Answer: H2O

Question 4

Photosynthesis and oxygen evolution: which of the following does NOT produce molecular oxygen (O2) as a product of photosynthesis?

Accepted Answer

Introduction / Context: Photosynthesis can be oxygenic or anoxygenic. Oxygenic photosynthesis splits water to release oxygen, whereas anoxygenic photosynthesis uses other electron donors and does not generate oxygen. The question checks recognition of anoxygenic phototrophs. Given Data / Assumptions: Oak trees and most phytoplankton (including many algae) perform oxygenic photosynthesis. Cyanobacteria are oxygenic prokaryotes. Purple sulfur bacteria are classic anoxygenic phototrophs. Concept / Approach: Organisms that use water as the electron donor produce O2. Purple sulfur bacteria instead oxidize reduced sulfur compounds such as H2S, depositing elemental sulfur and ultimately sulfate, without splitting water. Step-by-Step Solution: Identify oxygenic groups: plants (oak trees), cyanobacteria, many phytoplankton.Identify anoxygenic group: purple sulfur bacteria.Select the group that does not release O2: purple sulfur bacteria. Verification / Alternative check: Stromatolite formation and sulfur granules in purple sulfur bacteria confirm H2S usage and absence of oxygen evolution. Why Other Options Are Wrong: Oak trees / Phytoplankton / Cyanobacteria: All perform oxygenic photosynthesis and release O2. Common Pitfalls: Assuming all bacteria are anoxygenic; cyanobacteria are an important exception that are oxygenic. Final Answer: Purple sulfur bacteria

Question 5

Thermodynamics in biochemistry: express the relationship between the standard free energy change (ΔG°) and the equilibrium constant (Keq). Choose the correct formula.

Accepted Answer

Introduction / Context: Connecting free energy changes to equilibrium constants is essential for predicting reaction directionality and coupling reactions in metabolism. This relationship holds for standard conditions and is widely used in bioenergetics. Given Data / Assumptions: R is the gas constant and T is absolute temperature in kelvins. Keq is the thermodynamic equilibrium constant. Standard state conditions are assumed. Concept / Approach: The canonical relationship is ΔG° = -R * T * ln(Keq). A large Keq > 1 implies negative ΔG° (favorable forward direction), while Keq < 1 implies positive ΔG°. Step-by-Step Solution: Recall definition: ΔG = ΔG° + RT ln Q; at equilibrium, ΔG = 0 and Q = Keq.Rearrange to obtain: ΔG° = -RT ln Keq.Select the matching expression. Verification / Alternative check: Dimensional analysis and sign logic: if Keq > 1, ln Keq positive → ΔG° negative, aligning with exergonic reactions. Why Other Options Are Wrong: RTlnkeq (positive sign): Wrong sign. R/T * lnkeq: Incorrect dimensionality. -RT/lnkeq: Algebraically incorrect. Common Pitfalls: Confusing ln with log10 and misplacing the minus sign; both errors reverse the interpretation of spontaneity. Final Answer: ΔG° = -RTlnkeq

Question 6

Distribution of central carbon pathways: the Entner–Doudoroff (ED) pathway is typically absent from which group of organisms?

Accepted Answer

Introduction / Context: The Entner–Doudoroff pathway is an alternative to glycolysis (Embden–Meyerhof–Parnas) for glucose catabolism. Understanding where ED occurs helps in microbial physiology and metabolic engineering. Given Data / Assumptions: ED is common in many Gram-negative bacteria and some archaea. Eukaryotes overwhelmingly use the Embden–Meyerhof–Parnas pathway for cytosolic glycolysis. Some prokaryotes are aerobic, some anaerobic; ED occurs in both depending on species. Concept / Approach: ED pathway enzymes (e.g., 6-phosphogluconate dehydratase, KDPG aldolase) are characteristically prokaryotic. Eukaryotic cytosol lacks the canonical ED route, relying on classic glycolysis. Step-by-Step Solution: Identify organism classes known to have ED: prokaryotes (aerobic and anaerobic species).Identify the class lacking ED: eukaryotes.Choose the option indicating absence: eukaryotes. Verification / Alternative check: Genome annotations of bacteria such as Pseudomonas and Zymomonas show ED enzymes; standard eukaryotic glycolysis lacks them. Why Other Options Are Wrong: Aerobic/anaerobic prokaryotes: ED is present in many of these. Both (a) and (b): Incorrect because ED is not restricted by oxygen preference. Common Pitfalls: Assuming ED is rare or specific to anaerobes; it is widespread among diverse bacteria. Final Answer: eukaryotes

Question 7

High-energy transfer compounds (such as ATP and acetyl-CoA) are characterized by their ability to:

Accepted Answer

Introduction / Context: High-energy compounds are central to metabolism. They act as energy currency, coupling exergonic and endergonic processes. Recognizing their defining property is crucial for understanding bioenergetics. Given Data / Assumptions: Examples include ATP, GTP, acetyl-CoA, and phosphoenolpyruvate. They contain bonds with large negative free energy of hydrolysis. Focus is on what they do functionally in pathways. Concept / Approach: Such molecules transfer free energy to other molecules by group transfer reactions (e.g., phosphoryl transfer from ATP). The large negative ΔG of hydrolysis drives coupled reactions forward. Step-by-Step Solution: Identify function: donate phosphoryl or acyl groups.Assess impact: transfer of chemical potential (free energy) to acceptor reactions.Select statement matching this: transfer large amounts of free energy. Verification / Alternative check: Coupling ATP hydrolysis to unfavorable biosyntheses (e.g., aminoacyl-tRNA formation) exemplifies energy transfer. Why Other Options Are Wrong: Accept large energy: Vague and not the defining feature. Measure free energy: Measurement is an analytical concept, not molecular function. None: Incorrect since a correct description exists. Common Pitfalls: Misinterpreting “high-energy bond” as a store to be “accepted” rather than transferred in a chemical reaction. Final Answer: transfer large amounts of free energy

Question 8

In anoxygenic photosynthesis, what is the primary role of bacteriochlorophyll within the reaction center and antenna complexes?

Accepted Answer

Introduction / Context: Bacteriochlorophyll is the photopigment in many anoxygenic phototrophs. Understanding its fundamental photophysical role helps differentiate pigment function from downstream redox chemistry. Given Data / Assumptions: Organisms: green and purple bacteria. Pigment: bacteriochlorophyll in reaction centers and light-harvesting complexes. Process: conversion of light energy into excited electronic states. Concept / Approach: Upon absorbing photons, bacteriochlorophyll elevates an electron to an excited state. This energized electron is transferred through the reaction center, initiating cyclic or noncyclic electron flow. Direct reduction of NADP or ferredoxin is typically mediated by specific dehydrogenases or electron carriers downstream. Step-by-Step Solution: Identify the primary photochemical event: photon absorption by bacteriochlorophyll.Result: creation of an excited electron capable of charge separation.Therefore, the correct role is energizing an electron using light. Verification / Alternative check: Flash photolysis and spectroscopy show rapid charge separation following excitation of the special pair in reaction centers. Why Other Options Are Wrong: Reduce ferredoxin/NADP directly: These are downstream redox steps involving carriers and enzymes. Transfer to sulfide intermediate: Sulfide oxidation involves separate enzymes; bacteriochlorophyll initiates, but does not specifically perform this transfer. Common Pitfalls: Confusing the initial photochemical excitation with later electron-transport steps and terminal reductant formation. Final Answer: use light energy to energize an electron

Question 9

Energy conservation in fermentation: the acquisition of ATP during glucose fermentation occurs primarily via which mechanism?

Accepted Answer

Introduction / Context: Fermentation enables ATP production without external electron acceptors. Recognizing how ATP is generated in fermentation is key to distinguishing it from respiration. Given Data / Assumptions: No functional electron transport chain is used to conserve energy in classic fermentation. NADH produced in glycolysis is reoxidized by internal organic acceptors. ATP yield is modest compared to respiration. Concept / Approach: Fermentative pathways generate ATP directly by substrate-level phosphorylation, where a high-energy phosphate from a metabolic intermediate is transferred to ADP. Electron transport phosphorylation (oxidative phosphorylation) requires an external terminal acceptor and a membrane-linked chain, which fermentation lacks. Step-by-Step Solution: Identify ATP-producing steps in glycolysis (e.g., PEP → pyruvate via pyruvate kinase).Confirm absence of electron transport-linked phosphorylation in fermentation.Select substrate-level phosphorylation as the mechanism. Verification / Alternative check: Measured fermentation yields (e.g., 2 ATP per glucose in lactic fermentation) match substrate-level phosphorylation accounting. Why Other Options Are Wrong: Electron transport from NADH: Defines respiration, not classical fermentation. Fatty acid oxidation: Catabolic but not the basis of fermentative ATP gain. Formic-hydrogen lyase: Enzyme present in some bacteria for redox balance, not the ATP-conserving step. Common Pitfalls: Assuming any NADH reoxidation implies electron transport; in fermentation, reoxidation is substrate-linked. Final Answer: substrate-level phosphorylation

Question 10

Regulatory genetics: a phosphate-deregulated mutant (Pho– derepressed) is best described as being:

Accepted Answer

Introduction / Context: Phosphate regulation systems (e.g., Pho regulon in bacteria) control expression of genes in response to phosphate availability. Mutations can alter the sensitivity of this control, affecting metabolite uptake and enzyme production. Given Data / Assumptions: A deregulated mutant exhibits constitutive or reduced-control expression. Environmental phosphate usually represses certain genes; scarcity derepresses them. Terminology: deregulated/derepressed implies diminished responsiveness. Concept / Approach: In deregulated (derepressed) mutants, the normal repression by phosphate is weakened or lost, so target genes are expressed even when phosphate would ordinarily repress them. This corresponds to being less sensitive to phosphate-mediated regulation. Step-by-Step Solution: Define normal regulation: repression at high phosphate.Define mutant state: expression persists despite phosphate → reduced sensitivity.Choose description: less sensitive to phosphate regulation. Verification / Alternative check: Phenotypes such as constitutive alkaline phosphatase activity in the presence of phosphate exemplify deregulation. Why Other Options Are Wrong: Moderately or highly sensitive: Opposite of deregulated behavior. None of these: Incorrect because a precise description exists. Common Pitfalls: Confusing derepression (reduced control) with hypersensitivity (increased control). Final Answer: less sensitive to phosphate regulation

Question 11

Phosphate assimilation: to incorporate inorganic phosphate (Pi) into organic compounds inside the cell, phosphate is added via which process(es)?

Accepted Answer

Introduction / Context: Cells convert inorganic phosphate into organic phosphates through phosphoryl-transfer reactions. This powers metabolism and builds key biomolecules like ATP, nucleotides, and phospholipids. Given Data / Assumptions: Pi can be incorporated during ATP synthesis and during direct group transfers from high-energy intermediates. Two major routes: substrate-level phosphorylation and oxidative phosphorylation. DNA is an organic phosphate-containing product, not the mechanism of incorporation. Concept / Approach: Substrate-level phosphorylation transfers a phosphate from a high-energy intermediate to ADP (e.g., PEP to ATP). Oxidative phosphorylation uses a proton motive force to drive ATP synthase to add Pi to ADP, forming ATP. Both routes convert inorganic phosphate into organic phosphate esters. Step-by-Step Solution: Identify mechanisms that attach Pi to organic molecules: substrate-level and oxidative phosphorylation.Confirm both are bona fide cellular processes of Pi incorporation.Select “both (a) and (b).” Verification / Alternative check: Biochemical assays measure ATP formation from ADP + Pi via ATP synthase (oxidative) and directly via kinases (substrate-level). Why Other Options Are Wrong: Only one mechanism: Incomplete. DNA: A molecule containing phosphate, not the mechanism of incorporation. Common Pitfalls: Confusing products (nucleic acids) with the pathways that generate the phosphate donors (ATP) used to build them. Final Answer: both (a) and (b)

Question 12

Use of radioactive phosphorus (³²P) in cell studies: after growing an Escherichia coli culture for 48 hours in medium containing radioactive phosphate, where would you expect the label to be found?

Accepted Answer

Introduction / Context: Radioisotopic tracers are widely used to follow the incorporation of atoms into cellular macromolecules. Phosphorus is a core component of many biological molecules, so ³²P labeling reveals biosynthetic destinations in living cells. Given Data / Assumptions: The medium supplies inorganic phosphate that cells assimilate. E. coli will be actively growing and dividing over 48 hours. Cellular macromolecules synthesized during growth will incorporate phosphate groups where chemically appropriate. Concept / Approach: Phosphate is incorporated into nucleic acids (DNA and RNA backbones as phosphodiester linkages) and phospholipids (phosphatidyl headgroups). Proteins (enzymes) generally lack phosphorus in their backbone, but many bacterial proteins undergo phosphorylation (post-translational modification) or bind tightly to phosphorylated metabolites, and some enzymes form covalent phospho-enzyme intermediates during catalysis. Over extended growth, detectable ³²P becomes associated with multiple cellular fractions. Step-by-Step Solution: Identify macromolecules with obligatory phosphate: nucleic acids (RNA) and membrane phospholipids.Consider proteins: phosphorylation events and transient phospho-intermediates can incorporate ³²P into enzymes.Therefore, the label will be found in all listed categories. Verification / Alternative check: Fractionation experiments show strong ³²P signals in nucleic acids and membranes; phosphoproteomics and autoradiography detect ³²P in proteins after kinase-mediated labeling. Why Other Options Are Wrong: Picking only one class (RNA or phospholipids) ignores other major phosphate pools. Selecting only enzymes or only one macromolecule underestimates cellular phosphate distribution during growth. Common Pitfalls: Assuming proteins never contain phosphorus. While peptide backbones do not, phosphorylation and covalent intermediates can carry ³²P on proteins in vivo. Final Answer: all of these

Question 13

Microbial metabolism and carbon assimilation When acetate is provided as the sole source of carbon, which specialized metabolic cycle do many microorganisms use to assimilate carbon efficiently without losing it as carbon dioxide?

Accepted Answer

Introduction / Context: Some bacteria, yeasts, and plants can grow when acetate or other two-carbon (C2) compounds are the only carbon source. To conserve carbon for biosynthesis, they avoid losing carbon as CO2 in the tricarboxylic acid (TCA) cycle by engaging a variant called the glyoxylate pathway (glyoxylate shunt). This question tests recognition of that specific cycle and why it is used. Given Data / Assumptions: Carbon source available: acetate (C2), no sugars provided. Organism must assimilate acetate into cell material while generating some reducing power and precursors. Objective: identify the pathway that enables net carbon conservation from C2 units. Concept / Approach: The classic TCA cycle decarboxylates isocitrate and alpha-ketoglutarate, causing carbon loss as CO2. The glyoxylate shunt bypasses these steps via two hallmark enzymes, isocitrate lyase and malate synthase, allowing two molecules of acetyl-CoA to be converted into malate and succinate without decarboxylation. This conserves carbon skeletons for gluconeogenesis and anabolism. Step-by-Step Solution: Note carbon economy requirement: from acetyl-CoA to C4 intermediates without CO2 loss.Recall the glyoxylate shunt: isocitrate lyase forms succinate + glyoxylate; malate synthase condenses glyoxylate + acetyl-CoA to malate.Conclude the pathway used with acetate as sole carbon source is the glyoxylate pathway. Verification / Alternative check: Mutants lacking isocitrate lyase or malate synthase fail to grow on acetate as the only carbon source, confirming the essential role of the glyoxylate pathway for C2 growth. Why Other Options Are Wrong: Pentose phosphate pathway: Generates NADPH and pentoses; not sufficient for C2 assimilation. Glycolysis: Catabolizes hexoses; not applicable with acetate alone. Oxaloacetate pathway: Not a standard, named cycle for C2 growth. Entner–Doudoroff pathway: An alternative to glycolysis for sugars, not acetate assimilation. Common Pitfalls: Assuming any central pathway works for all substrates; acetate requires bypass of TCA decarboxylation. Confusing “glyoxylate cycle” with “anaplerotic reactions”; they are related but distinct concepts. Final Answer: glyoxylate pathway (glyoxylate shunt)

Question 14

Distribution of the Entner–Doudoroff (ED) pathway In which groups of organisms is the Entner–Doudoroff pathway found as an alternative catabolic route for glucose?

Accepted Answer

Introduction / Context: The Entner–Doudoroff (ED) pathway is an alternative to the Embden–Meyerhof–Parnas (EMP) glycolytic route. It occurs in diverse bacteria and some archaea and is important in microbial physiology, diagnostics, and ecology. Knowing where ED occurs helps predict metabolic capabilities across taxa. Given Data / Assumptions: We are comparing organismal groups: prokaryotes (aerobic/anaerobic) versus eukaryotes. Looking for where ED is present as a functional pathway. ED is not the dominant sugar catabolism in most eukaryotes. Concept / Approach: The ED pathway is widespread among prokaryotes, including aerobic bacteria such as Pseudomonas and anaerobes like Zymomonas. It is rare or absent in typical eukaryotes, which primarily use EMP and the pentose phosphate pathway. Thus, ED spans both aerobic and anaerobic prokaryotes, depending on species and niche. Step-by-Step Solution: Identify ED pathway distribution: largely prokaryotic.Recognize it occurs under aerobic and anaerobic conditions in different species.Select “both (a) and (b)”. Verification / Alternative check: Examples: Pseudomonas putida (aerobic) and Zymomonas mobilis (anaerobic) both use ED prominently, demonstrating presence across oxygen regimes in prokaryotes. Why Other Options Are Wrong: A or B alone: Too narrow; ED is not exclusive to one oxygen condition. Aerobic eukaryotes/animal mitochondria: Eukaryotes do not commonly possess a canonical ED pathway. Common Pitfalls: Assuming ED equals fermentation only; it can operate in aerobes as well. Final Answer: both (a) and (b)

Question 15

Alternate names of central sugar pathways The hexose monophosphate pathway (HMP) is also known by which name in microbial biochemistry?

Accepted Answer

Introduction / Context: The hexose monophosphate (HMP) pathway, more commonly called the pentose phosphate pathway (PPP), is a major route for generating NADPH and ribose-5-phosphate. Knowing synonymous names helps map literature references and exam questions that use alternate terminology such as the “phosphogluconate pathway.” Given Data / Assumptions: HMP = PPP, emphasizing oxidation of glucose-6-phosphate via 6-phosphogluconate. The question seeks the accepted alias used in textbooks. Other listed pathways relate to TCA intermediates, not to HMP/PPP. Concept / Approach: In the oxidative branch of PPP, glucose-6-phosphate is converted to 6-phosphogluconate and then to ribulose-5-phosphate, producing NADPH. Because 6-phosphogluconate is a key intermediate, the HMP route has historically been called the phosphogluconate pathway. Step-by-Step Solution: Recognize HMP = pentose phosphate pathway.Recall synonymous name derived from the central intermediate: phosphogluconate pathway.Select the matching option. Verification / Alternative check: Biochemistry references list PPP synonyms as “hexose monophosphate shunt” and “phosphogluconate pathway,” confirming the correct alias. Why Other Options Are Wrong: Oxaloacetate/malate/fumarate pathways: These terms are associated with TCA cycle or shuttles, unrelated to HMP. Glyoxylate pathway: A TCA bypass for C2 growth, not sugar oxidation for NADPH. Common Pitfalls: Confusing the PPP with glycolysis due to shared hexose substrates; focuses differ (NADPH and pentoses vs. ATP). Final Answer: phosphogluconate pathway

Microbial Metabolism Questions