exam 1 quiz questions + sample questions

why is glucose the preferred source of carbon

glucose is the fastest, easiest fuel. the cell does not have to waste time building enzymes. glucose feeds straight into glycolysis, provides high ATP yeild and rapid uptake and metabolism. it is also very versitile, and supplies ATP energy, NADH/NADPH reducing power, and biosynthetic precursers like AAs, nucleotides, and lipids

explain diauxic growth

diauxic growth is the two-phase growing pattern that occurs when microorganisms are grown in a medium containing two carbon sources- glucose + another sugar (like lactose).

the growth curve is a lag → exponential growth on glucose → second lag (because catabolite repression needs to be turned off, cAMP rises, and new enzymes must be made)→ exponential growth on second sugar → stationary → death

what are the glycolysis phases

1. energy investment phase

   1. glucose uses 2 ATP to convert to glucose-6-phosphate

2. energy payoff phase

   1. glyceraldehyde-3-phosphate is oxidized, energy is harvested and 2 ATP and 1 NADH and pyruvate result

what are the oxidative alternative glycolysis pathways in bacteria

1. Entner-Doudoroff Pathway

   1. glucose → 6-phosphogluconate → KDPG

   2. KDPG → pyruvate and glyceraldehyde-3-phosphate

   3. yeilds 1 ATP, 1 NADH, 1 NADPH

2. Pentose Phosphate Pathway

   1. glucose-6-phosphate is oxidized, producing NADPH and ribose-5-phosphate

*both these alt pathways generate reducing power (esp NADPH) with fewer enzymes, which is essential for biosynthesis.

what is gluconeogenesis pathway

the reverse of glycolysis. a metabolic pathway that synthesizes (makes) glucose from non-carbohydrate carbon sources. uses ATP and GTP and pulls carbon from the citric acid cycle. feeds glucose back into glycolysis, PPP, and biosynthesis. bypasses irriversible glycolysis steps

differentiate between catabolism and anabolism

catabolism: breakdown molecules to release energy. produces ATP, NADH/FADH2, metabolic intermediates. examples include glycolysis, citric acid cycle, respiration

anabolism: building up molecules using energy. uses ATP, NADPH. examples include calvin cycle, gluconeogenesis, amino acid biosynthesis

how are catabolism and anabolism connected through central metabolism

catabolism powers anabolism by providing ATP and reducing power. anabolism uses this energy to synthesize (make) cellular components.

net energy yield per molecule of glucose in glyolysis

2 ATP, 2 NADH

explain the role of NAD+/NADH in glycolysis and why fermentation is required under anaerobic conditions

during glycolysis, NAD+ acts as an electron carrier and is reduced to NADH in the payoff phase when G3P is oxidized. NADH is oxidized back to NAD+ by the ETC (oxygn is the terminal electron acceptor)

when oxygen is absent and there is no usable ETC so the cell must use fermentation to regenerate NAD+. in fermentation an organic molecule (like pyruvate) is the terminal e- acceptor and yeilds low ATP

compare respiration and fermentation in terms of oxygen use and ATP production

Oxygen Use

1. respiration: oxygen is used in aerobic respiration, but not anaerobic

2. fermentation: occurs in the absence of oxygen

ATP Production

1. respiration: produces large amounts of ATP through substrate level phosphorylation and oxidative phosphorylation

2. fermentation: produces low ATP only through substrate-level phosphorylation

what is the pentose phosphate pathway and why is it essential for biosynthesis

the pentose phosphate pathway is a metabolic pathway for g-6-p that oxidizes glucose, does not primarily make ATP, and produces molecules needed for anabolic reactions. its two phases are:

1. oxidative phase: G6P is oxidized producing NADPH, ribulose-5-phosphate, and CO2

2. non-oxidative phase: sugars are rearranged, producing ribose-5-phosphate and glycolytic intermediates (F6P, G3P). this is important as r5p is used for nucleotide synthesis and carbon can re-enter glycolysis or glyconeogenisis

explain how pyruvate links glycolysis to the citric acid cycle and when this link can function

pyruvate (glycolysis end product) is converted to acetyl-CoA + CO2 + NADH. this acetyl-CoA enters the citric acid cycle. this link only functions when there is an active electron trnasport chain and anaerobic/aerobic respiration is occuring. as NAD+ must be regenerated for the pyruvate dehydrogenase complex that converts pyruvate into its products to work.

describe the main functions and products of the citric acid cycle

1. oxidation of carbon

   1. oxidizes acetyl-CoA to CO2

2. energy carrier production

   1. generates reduced e- carriers that feed the ETC

   2. drives ATP synthesis during respiration

3. supply of biosynthetic precursors

   1. provides intermediates for AA, nucleotide, lipid synthesis

main products- 3 NADH, 1 FADH2, 1GTP or ATP, 2 CO2

what is the electron transport chain (ETC) and why is it essential for energy production

the electron transport chain is a series of membrane-bound protein complexes and carriers that transfer electrons from NADH and FADH2 and pass them to a terminal electron acceptor. energy is released and a proton motive force is created.

ETC is essential for energy production as it produces the most ATP, regenerates NAD+ and FAD, and allows for complete oxidation of fuels

how do NADH and FADH2 contribute to electron transport and ATP synthesis?

NADH and FADH2 are electron courriers that carry energy (e-) from glycolysis and citric acid cycle to the electron transport chain where that energy is converted into ATP. each NADH ~2.5 ATP and FADH2 ~1.5 ATP

how does electron flow through the ETC create a proton motive force?

1. NADH and FADH2 donate electrons and each transfer releases some energy

2. energy is used by ETC complexes to pump H+ from one side of the membrane to the other, creating a proton concentration gradient and an electrical gradient that together form a proton motive force

how do aerobic and anaerobic respiration differ in their terminal electron acceptors?

aerobic respiration terminal electron acceptor is O2

• highest ATP yeild

anaerobic respiration terminal electron accpetor is not oxygen. instead uses alternative inorganic molecules like nitrate, sulfate, iron, etc.

• lower ATP yeild

how does ATP synthase use the proton gradient to produce ATP?

protons flow through ATP synthase (the gate) as they move from high H+ to low H+ concentration. this proton flow causes the F0 rotor to spin, and this rotation is transmitted to the F1 head. The F1 head has catalytic sites that change shape and conformational changes bind ADP and PI, forming ATP.

why is ATP synthase considered a rotary motor?

proton flow causes rotatoin which forces the F1 catalytic head to change shape and each 120 degree turn changes how tightly ADP and Pi are bound which results in the release of ATP

why are metabolic pathways an ATP synthase attractive targets for antimicrobial drugs?

metabolic pathways are good drug targets because if you shut down energy and biosynthesis the cell does not survive. ATP synthase makes most cellular ATP and blocking it causes rapid energy depletion

what challenges exist in targeting bacterial metabolism for drug development?

1. many metaolic pathways are conserved between bacteria and humans. risk of host toxicity if drugs hit human enzymes too

2. metabolic flexibility of bacteria. bacteria can use alternative pathways, switch carbon sources. blocking one pathway may not kill the cell

3. some metabolic functions can be bypassed through different routes or compensated by alternative enzymes

4. rapid evolution of resistance

how do bacteria benefit from using multiple ETCs?

it gives them metabolic flexibility- they can keep making energy even when conditions change.

• different ETCs use different e- donors and acceptors, allowing growth under aerobic and anaerbic conditions

• some ETCs generate lots of ATP but use lots of oxygen while others can conserve oxygen and generate less ATP

• certain ETC components are resistant to inhibitors

• resistance to stress and toxins

what is a microbe-powered battery and what is its current stage of development?

a microbe powered battery is a bio-electrochemical device that uses the metabolism of microorganisms to generate electrical current. microbes oxidize organic compounds and the electrons released are routed through an electrode to do useful work. powered by living cells

besides glucose, what alternative carbohydrates can bacteria metabolize?

lactose, sucrose, maltose, starch, gylcerol, etc.

what is catabolite repression and why is it important?

regulatory mechanism where the cell shuts off genes for using alternative energy sources when glucose is availible, letting bacteria use the best carbon source first. this is important as it maximizes energy efficiency, ensures hierarchical carbon use and improves survival

what is the lac operon and what is its biological significance?

the lac operon is a gene-regulation system that controls lactose metabolism. it is a cluster of genes in E. coli that includes lac Z, Y, A, L, and a promoter and operator. when lactose is present, the operon is on. this helps so enzymes are made only when needed, and enables bacteria to metabolize lactose only when its available and glucose is absent, optimizing energy use

how does lactose induce expression of the lac operon?

when lactose is present, the Iac repressor is inactive. cAMP levels rise and cAMP-CRP activates transcription, turning on the lac operon and triggering lactose metabolism

what is diauxic growth and when does it occur?

diauxic growth is the two phase growth pattern that occurs when bacteria are grown in the presence of two different carbon sources (preffered, glucose and less preferred). it occurs when catabolite repression is in effect and both carbon sources are present at the same time

once glucose is depleted, repression is lifted and the second carbon source is activated. follows the growth model (lag exponential etc)

why is glucose preferentially used over other carbon sources?

what is chitin and which bacteria can use it as a carbon source?

chitin is a structural polysaccharide and an abundant biopolymer on earth found in arthropod exoskeletons, fungal cell walls, and some algae. bacteria that make chitinases (enzymes that break down chitin) can use it. this includes marine and soil bacteria like vibrio species and streptomyces.

chitin is broken down by chitinases and produces N-acetylglucosamine which enters central metabolism and links carbon and nitrogen cycling.

how does Vibrio cholerae utilize chitin in the environment?

Vibrio cholerae binds to chitin using surface proteins and produces chitinases that break chitin into: N-acetylglucosamine (GlcNAc). This is taken up and funneled into central metabolism and provides both carbon and nitrogen. growth on chitin also promotes biofilm formation and explains how V. cholerae persists in aquatic reservoirs.

what is bioremediation?

bioremediation is the use of living organisms, usually microbes, to clean up ennvironmental pollutants by breaking them down, transforming them, or immobilizing them into less harmful forms.

give one example of a bacterium used in bioremediation and explain its role?

Psudomonas putida is a bacterium found in soil and water. it degrades petrolium hydrocarbons through oxidative pathways and uses these pollutants as carbon and energy sources

briefly explain how the emergence of photosynthesis changed life on earth

the emergence of photosynthesis transformed earth ~2.4bya by introducing oxygn into the atmosphere. this enabled aerobic respiration, increased enegy yield, and led to the evolution of complex life

what role do microbial photoautotrophs play in global carbon and oxygen cycles?

microbial photoautotrophs such as cyanobacteria and algae capture carbon and produce oxygen, helping to sustain life on earth.

they use light energy to convert CO2 into organic compounds via photosynthesis, removing carbon from the atmosphere helping to regulate global climate. they also produce O2, enabling aerobic respiration and supporting life on earth.

what is the key difference between oxygenic and anoxygenic photosynthesis?

whether oxygn is produced as a byproduct

why is having a broad range of photosynthetic pigments beneficial for microbes?

because microbes can capture more light energy across different wavelengths, increasing their efficiency in photosynthesis.

they can use light that other organisms might not absorb, adapt to different aquatic or shaded environements, and protect from harmful UV or excess liight

how do purple and green bacteria differ from cyanobacteria in photosynthesis?

cyanobacteria split water and produce oxygen while purple and green bacteria use other electron donors and do not produce oxygen, allowing them to thrive in anaerobic environments

what is the role of RuBisCO in photosynthesis and why is it considered inefficient?

RuBisCO converts inorganic CO2 into organic molecules which are then used to make sugars. RuBisCo though has a slow catalytic rate, can mistakenly bind O2 instead of CO2 and high enzyme abundance

why are microbial phototrophs important in modern ecosystems?

microbial phototrophs are fundamental because they form the base of energy flow and nutrient cycling. they are primary producers that convert sunlight into chemical energy, produce organic matter, release O2 as a byproduct, fix CO2 from the atmosphere

give one example of how microbial photosynthetic organisms are used in biotechnology or bioenergy

cyanobacteria/microalgae convert sunlight, CO2, and water into lipids (oils) or carbs through photosynthesis. these lipids can be processed into biodiesel, a renewable biofuel and carbs can be fermented to produce bioethanol. they provide a sustainable alternative to fossil fuels while also fixing CO2

why is inorganic metabolism essential for global nutrient cycling?

Inorganic metabolism involves microbes using inorganic compounds (like NH4+, NO2-, H2S) as energy sources or e- donors. they have roles in the nitrogen, sulfur, and iron cycle. this maintains the balance of essential elements, supports primary production, and without, ecosystems would run out of usale elements, stalling life cycles.

how do microbes drive the sulfur and nitrogen cycles in nature?

microbes carry out chemical transformations that recycle these essential elements in ecosystems. microbes transform nitrogen between atmospheric, organic, and inorganic forms, making it available for plants and returning it to the air. microbes also convert sulfur between reduced and oxidized forms, maintaining uslfur availibility in soils, sediments, and aquatic ecosystems.

without microbial tansformations, nitrogen anf sulfur would remain locked in unusable forms.

what is the difference between assimilation and dissimilation in inorganic metabolism?

assimilation is making biomass from inorganic nutrients (build)

dissimilation is using inorganic compounds for energy (burn)

why are chemolithotrophs ecologically important?

chemolithotrophs are microbes that obtain energy by oxidizing inorgnic compounds (like NH4, H2S, Fe2+) to use it to fix CO2 without needing light. they are important because they can be used in extreme environments and maintain chemical balance an sustain life in places sunlight cannot reach.

how does denitrification affect agriculture and fertilizer efficiency?

denitrification is the process where microbes convert nitrate (NO3-) in soil into gaseous forms such as N2 or N2O. denitrification reduces soil nitrate and making plants unable to access it, reducing fertilizer efficiency and depleting soil nitrogen.

why does tillage help perserve nitrate in agricultural soils?

tilliage aereates the soil as plowing/turning soil increases oxygen penetration, reducing anaerobic zones. with more oxygen, denitrifying bacteria are less active and less nitrate is lost as gas. tilliage also helps prevent waterlogging, which also limits anaerobic conditions and mixes organic matter and fertilizer, making nutrients more evenly distributed and accesible to plants.

how can microbial metabolism be harnessed for bioremediation?

microbes can break down, transform, or immobilize pollutants, turning harmful compounds into less toxic or harmless forms and thereby cleaning contaminated environments naturally

give one example of a bacterium used in biodegradation or bioremediation and explain its role

how does central metabolism provide precursors for amino acid biosynthesis in bacteria?

central metabolism pathways like glycolysis, PPP, and krebs cycle provide intermediates that are starting materials for amino acids like 3Pg, pyruvate, a-ketoglutarate ,R5p, etc. they are all converted into amino acids, connecting energy metabolism with protein synthesis

why are glutamate and glutamine essential for inorganic nitrogen assimilation?

glutamate and glutamine act as key amino group donors in bacteria, incorperating inorganic nitrogen (ammonia and NH4+) into organic molecules. without them, bacteria cannot effectivley convert inorganic nitrogen into these forms eneded for growth to form other amino acids, nucleotides, and nitrogen-containing compounds.

what roles do amino acids play in microbes besides protein synthesis?

1. precursors for other biomolecules

   1. precursors for nucleotides, coenzymes, vitamins, and cell wall components

2. energy and carbon sources

   1. some AA’s can be degraded to feed central metabolism when nutrients are limited

3. nitrogen storage and transport

   1. glutamine and glutamate act as nitrogen carriers, storing and distributing nitrogen within the cell

4. signaling and reguIation

   1. AA’s can function as signals for gene regulation

5. stress protection

   1. certain AAs help microbes survive osmotic or oxidative stress by stabilizing proteins and membranes

what are aromatic amino acids and from what precursor are they synthesized?

aromatic amino acids contain an aromatic ring in their side chain: phenylalanine, tyrosine, and tryptophan

these amino acids are synthesized via the shikimate pathway and their starting precursur is Phosphoenolpyruvate (PEP) from glycolysis and erythrose-4-phosphate from PPP

aromatic AAs are esseential for protein synthesis and serve as precursors for cofactors, neurotransmitters, and secondary metabolites

why are branch points in amino acid biosynthesis key sites of regulation?

a branch point is a metabolic intermediate that can be channeled into multiple biosynthetic pathways. they control the distribution of intermediates, prevent energy waste, and maintain balanced AA synthesis via feedback mechanisms

what is an auxotrophic mutant, and how is it used to study amino acid biosynthesis?

an auxotrophic mutant is a microbe that cannot synthesize a specific compound that it normally would, instead it requires that compiund from its environment to grow. (ex- an E.coli mutant that cannot make tryptophan is called a tryptophan auxotroph)

by observing which compounds the mutant cannot grow without, researchers c an determine which steps or enzymes are missing (ex a tryptophan auxotroph cant grow unless tryptophan is supplied, indicating a block in the tryptophan biosynthetic pathway)

• they can reveal how biosynthesis is regulated, which genes encode the pathway enzymes, and map the sequence of enzymatic steps in AA synthesis

how does glyphosate affect aromatic amino acid synthesis?

glyphosate inhibits EPSP synthase in the shikimate pathway, blocking the production of aromatic amino acids (phenylalanine, tyrosine, tryptophan) and preventing protein synthesis in plants and microbes

what is the gut-brain axis, and how are microbial amino acid metabolites involved?

the gut-brain axis is a bidirectional communication network between the gut microbiota, the gastrointestinal tract, and the central nervous system. communication occurs via neural pathways, immune signaling, endocrine/hormonal signaling, metabolites produced by gut microbes.

gut microbes metabolize dietary and host derived amino acids to produce bioactive compounds that affect brain function. these metabolites can cross the gut barrier, influence, neuronal signaling, or modulate immune responses that impact brain function.