micro exam 3

what are the two main divisions of metabolism? compare.

catabolism: breaks down molecules

anabolism: assembles macromolecules

how are catabolism and anabolism coupled processes?

catabolism: provides ATP, reducing power, and building blocks

anabolism: uses them to build cellular components

what are the 12 key precursor metabolites?

• glycolysis (6): G6P, F6P, G3P, 3PG, PEP, pyruvate

• TCA (4): acetyl-CoA, a-ketoglutarate, succinyl-CoA, oxaloacetate

• PPP (2): E4P, R5P

which precursors are involved in peptidoglycan synthesis?

• NAM-NAG

• F6P, PEP, acetyl-CoA

what does a negative vs. positive reduction potential signify?

negative (-) reduction potential: donates electrons

positive (+) reduction potential: accepts electrons

what are the sources of energy for catabolism?

phototroph: uses light to generate ATP via. photophosphorylation (e.g., photosynthesis) (light → excited electrons → PMF → ATP)

chemotroph: uses chemicals to generate ATP via. oxidation reactions (electron carriers → ETC → PMF → ATP)

what are sources of electrons for catabolism?

lithotroph: inorganic electron donors; low energy yield; may require reverse electron flow to make NADH (e.g., H₂, NH₃, H₂S, Fe²⁺)

organotrophs: organic electron donors; high energy yield; (e.g., glucose)

what are sources of carbon for catabolism?

autotroph: CO₂, carbon fully oxidized; requires ATP and NADH for carbon fixation

heterotroph: organic carbon; carbon already reduced and easily used in biosynthesis

what type of metabolism type are humans?

chemoorganoheterotrophs

• chemo-

• organo-breaks down nutrients for energy

• heterotrophs-

Compare and contrast respiration and fermentation as chemoorganotrophic fueling processes.

key similarities:

• use organic compounds for energy + electrons

• both start with glycolysis → pyruvate

• both must regenerate NAD⁺

key differences:

• uses external electron acceptor vs. uses internal electron acceptor (e.g., pyruvate)

• oxidative phosphorylation & substrate-level phosphorylation (presence of ETC) vs. ONLY substrate-level phosphorylation (absence of ETC)

• PMF generated from ETC vs. ATPase (reverse)

• high vs. low ATP yield

• fully functional vs. horseshoe TCA cycle

• fully oxidized carbon vs. partially oxidized

what are the three glycolytic pathways?

**all glycolytic pathways lead to producing pyruvate

**pyruvate can feed into TCA cycle, fermentation products, amino acid synthesis, fatty acid synthesis, etc

• Embden-Meyerhof-Parnas (EMP) Pathway

• Pentose Phosphate Pathway (PPP)

• Entner-Doudoroff (ED) Pathway

What is Embden-Meyerhof-Parnas (EMP) Pathway?

• purpose: energy production (main pathway); produce precursor metabolites that contribute to anabolic/biosynthetic pathways (e.g., amino acids, phospholipids, NAM-NAG)

• input: glucose, 2 ADP + 2 Pi, 2 NAD⁺

• output: 2 pyruvate, 2 ATP (net), 2 NADH

• 6C Phase (investment): glucose (C₆) → 2 phosphoglyceraldehydes (aka PGALD, G3P, C₃)

• 3C Phase (payoff): oxidation of G3P → pyruvate

What is Pentose Phosphate Pathway (PPP)?

• purpose: biosynthesis of precursors for nucleotides + amino acids  & reducing power (NADPH)

  • does not directly generate ATP but can feed intermediates (F6P, G3P) into glycolysis

• input: glucose-6-phosphate (G6P), NADP⁺

• output: ribose-5-phosphate (R5P), NADPH (major product-reducing power), CO₂, intermediates (F6P, G3P) **NO ATP production

Stage 1. oxidation-decarboxylation of G6P → Ru5P

Stage 2: isomerization of ribulose Ru5P → Xu5P + R5P

Stage 3: sugar rearrangement reactions → F6P + G3P (glycolysis), R5P (nucleotides, histidine), E4P (aromatic amino acids)

What is Entner-Doudoroff (ED) pathway

• purpose: alternative glycolysis pathway (similar to EMP) specific to prokaryotes; mix of energy synthesis + biosynthesis

• input: glucose, ADP + Pi, NAD⁺ + NADP⁺

• output: 2 pyruvate, 1 ATP (less efficient), 1 NADH, 1 NADPH

• used when growing on aldonic acids (gluconate, galactonate)

1. glucose → G6P → 6-phosphogluconate

2. 6-phosphogluconate → KDPG

3. KDPG splits into 1 pyruvate (amino acid synthesis) + 1 G3P (lipid synthesis)

4. G3P enters bottom half of EMP → pyruvate

what is pyruvate oxidation?

• purpose: produce precursor (Acetyl-CoA) for TCA cycle

• input: pyruvate, NAD⁺, CoA

• output: acetyl-CoA (precursor metabolite for TCA cycle), NADH, CO₂

• enzyme complex: pyruvate dehydrogenase

what is TCA cycle?

• purpose: regenerate reducing power (NADH, FADH₂) for ETC; provides intermediates for biosynthesis/anabolic pathways (e.g., amino acids)

• input: 1 acetyl-CoA (2C), 3 NAD⁺, FAD, GDP/ADP+Pi, oxaloacetate (regenerated, not consumed)

• output: 2 CO₂, 3 NADH, 1 FADH₂, 1 GTP/ATP, CoA (recycled)

what are anaplerotic pathways?

Anaplerotic pathways: replenish TCA cycle intermediates that have been used in biosynthesis, ensuring the cycle can continue functioning

• **pyruvate → oxaloacetate

• amino acid → TCA intermediates (e.g., glutamate → a-ketoglutarate)

what are the two types of respiration?

**terminal electron acceptor differs but both use ETC

aerobic respiration: final electron acceptor = O₂, high energy yield

anaerobic respiration: final electron acceptors = NO₃⁻, SO₄²⁻, Fe³⁺, CO₂, etc; lower energy yield

compare aerobic respiration in eukaryotes vs. e.coli

how does e.coli switch pathways depending on O₂ levels?

high O₂ levels (log phase) → bo₃ branch → high ATP yield, promotes growth

low O₂ levels (stationary phase) → bd branch (minimal proton pumping) → low ATP yield, promotes survival

what is electron transport chain?

series of membrane-bound carriers that transfer electrons to terminal electron acceptor

what is proton pumping?

pumping H⁺ across the membrane (cytoplasm → outside) as electrons are being transferred

what is PMF?

protein motive force: gradient of protons across the membrane that stores potential energy

what is chemiosmosis?

movement of protons back across the membrane (outside → inside) down their gradient

what is oxidative phosphorylation?

protons flowing through the ATP synthase that drives ATP synthesis

what is the purpose of fermentation?

• to regenerate NAD⁺ to feed back into glycolysis

• reduces pyruvate and reoxidizes NADH

what type of species undergo fermentation?

• aerotolerant anaerobes — ALWAYS ferments bc no ETC; can tolerate O₂ but does not use O₂

• facultative anaerobes — flexible; switches between aerobic respiration, anaerobic respiration, and fermentation

what are the possibilities of metabolism that a facultative anaerobe undergoes when in an anoxic environment?

• fermentation

• anaerobic respiration

• uses anaerobic respiration first, then switches to fermentation when terminal electron acceptor runs out

what are the different types of fermentation?

• alcohol fermentation

• lactic acid fermentation

• mixed acid fermentation

• ABE (acetone-butanol-ethanol)

what are the steps of alcohol fermentation?

1. pyruvate → acetaldehyde + CO₂ 

2. acetaldehyde + NADH + H⁺ → ethanol + NAD⁺

what are the steps of lactic acid fermentation?

pyruvate + NADH + H⁺ → lactate + NAD⁺

what is homofermentative vs. heterofermentative?

homofermentative: produces only lactate

heterofermentative: can do both alcohol and lactic acid fermentation; yields lactate + CO₂ + ethano

what is mixed acid fermentation?

• occurs when multiple pathways are active at once, yielding diverse products

1. lactic acid fermentation (LDH) → forms lactate

2. alcohol fermentation (ADH) → forms alcohol

3. pyruvate formate lyase (PFL) → forms acetyl-CoA + formate

4. formate hydrogen lyase (FHL) breaks down formate → CO₂ + H₂ gas

what is ABE?

• mainly carried out by a certain species of clostridia (strict anaerobe)

• pathway triggered by acid stress, nutrient depletion, waste accumulation, etc → stationary phase → sporulation

• mechanism:

1. acid-producing phase - produces acetate, butyrate, ATP; pH drops

2. solvent-producing phase - acids converted into acetone, butanol (main product), ethanol; regenerates NAD⁺

• products: acetone, butanol (main product), ethanol, NAD⁺

what are two problems that arise from fermentation? what is the cause and solution?

1. internal acidification

• cause: fermentation produces organic acids (lactate, acetate, etc)

• solution: pump H⁺ out of cytoplasm via. reverse ATPase; hydrolyzes ATP to ADP

2. struggle to produce enough biosynthetic precursors

• cause: no functional ETC bc no terminal electron acceptor → NADH not efficiently reoxidized → TCA cycle can’t run fully → lack of TCA intermediates for biosynthesis

• solutions: horseshoe TCA cycle (run partial pathways to generate needed intermediates), anaplerotic pathways

what is horseshoe TCA cycle?

horseshoe TCA cycle: split TCA cycle into two partial pathways to generate needed intermediates

• oxidative branch: acetyl CoA + oxaloacetate → a-ketoglutarate → biosynthetic precursors for amino acids

• reductive branch: oxaloacetate → malate → fumarate → succinate; regenerates NAD⁺ and prevents NADH buildup

how does the goal of anaplerotic pathways differ between respiration and fermentation?

respiration: refill intermediates to keep TCA cycle running

fermentation: refill intermediates to be used for anabolic/biosynthetic pathways, not to run full TCA cycle?

compare and contrast between chemoorganotrophs and chemolithotrophs

similarities:

• use chemical compounds for energy instead of light

• use redox reactions and ETC

• generate ATP, reducing power, and proton motive force

• support biosynthesis

differences

• organic molecule provides energy, electrons, and carbon

• inorganic molecules provides energy + electrons but need to fix CO₂ (require ATP + NADPH)

• energy yield: higher vs. lower

what are chemolithotrophs?

• uses inorganic material to provide energy and electrons

• CO₂ (inorganic carbon) needs to be fixed to be used in anabolic pathways

• weak electron donors requires reverse electron flow to make NADH

what are examples of chemolithotrophy?

• hydrogen oxidation

• nitrification (ammonia oxidation, nitrite oxidation)

• sulfur oxidation

• iron oxidation

what are the relative energy yields of chemolithotrophy?

• energy yield depends on difference in reduction potential

• bigger difference = more energy release + more ATP produced

• H₂ = strong electron donor → high energy yield

• NO₂^-/Fe²⁺ = weak electron donor → low energy yield

what is hydrogen bacteria?

• chemolithotroph

• hydrogen oxidation: H₂ + ½ O₂ → H₂O

• high energy yield (strong donor + O₂ acceptor)

• need to find environment with presence of hydrogen and oxygen

  • problem: H₂ is scare in oxygen-rich environment

what is sulfur bacteria?

• chemolithotroph

• electron donors: H₂S (hydrogen sulfide), S⁰ (elemental sulfur), S₂O₃^2- (thiosulfate), SO₃^2- (sulfite)

• final oxidation product: SO₄^2- (sulfate)

• pathways

  • Sox system (Sulfite oxidase): direct oxidation → electrons → ETC

  • APS pathway (adenosine 5’ triphosphate): produce ATP via. substrate-level phosphorylation

• species found in very acidic environments

what is nitrifying bacteria?

• chemolithotroph

• low energy yield → slow growth

• requires reverse electron flow to generate NADH

• ammonia oxidizers: NH₄⁺ + O₂ → NH₂OH → NO₂^- ; bacteria & archaea

• nitrite oxidizers: NO₂^- (nitrite) → NO₃^- (nitrate); bacteria

• anammox (anaerobic ammonium oxidation): NH₄⁺ + NO₂^- → N₂ + 2 H₂O ; bacteria

what is iron bacteria

• electron donor: Fe²⁺

• very low energy yield

• common in iron-rich environments

• requires reverse electron flow to generate NADH

when is reverse electron flow vs. reverse atpase used?

reverse electron flow: in chemolithotrophs to generates NADH bc electron donors are weak; pushes electrons “uphill” to make NADH

reverse ATPase : used in fermentation when no ETC and no external electron acceptor to pump out acids

compare and contrast photolithoautotrophy and photoorganoheterotrophy

similiarities:

• phototrophs - use light as energy source → ETC → PMF → ATP

differences:

• Photolithoautotrophs: inorganic electron & carbon source; undergoes carbon fixation to make carbon source usable for biosynthesis

  • chlorophyll-based phototrophy

• Photoorganoheterotrophs: uses organic carbon from environment that is ready for biosynthesis

  • rhodopsin-based phototrophy → does not form NADPH, requires reverse electron flow

compare chlorophyll vs. rhodopsin-based phototrophy

chlorophyll system: uses ETC, makes ATP + NADPH, supports autotrophy (CO₂ fixation)

rhodopsin systems: uses light-driven proton pump directly, makes only ATP, only supports heterotrophs

what is oxygenic vs. anoxygenic photosynthesis?

• oxygenic:

  • uses H₂O → O₂

  • 2 photosystems (PSII + PSI)

  • produces ATP + NADPH

• anoxygenic:

  • uses H₂S, S⁰, organic compounds

  • 1 photosystem

  • produces ATP only; must use reverse electron flow to make NADPH

compare the pigments used in photosynthesis?

• chlorophyll (680nm):

  • higher energy light

  • oxygenic (H₂O  splitting forms O₂)

  • 2 photosystems

  • direct NADPH generated

• bacteriochlorophyll (860 nm):

  • lower energy light

  • anoxygenic (no H₂O splitting, does not form O₂)

  • 1 photosystem

  • reverse electron flow

how does oxygenic photolithotrophy work?

• photosynthesis: light hits chlorophyll → electron excites and leaves PSII → H₂O splits to O₂ → ETC (generates PMF → ATP) →  light excites PSI→ NADPH formation 

• PSII → splits water to form O₂

• PSI → makes NADPH (direct process)

how does anoxygenic photolithtrophy work?

anoxygenic photolithotrophy: couples photosynthesis with sulfur oxidation (getting electrons from sulfur); 

• anoxygenic photosynthesis: light excites bacteriochlorophyll → electrons flow through ETC → PMF is generated → protons flow back through ATP synthase → ATP is produced

• electrons from sulfur oxidation reduces NADP⁺ to NADPH (separate process)

How do autotrophic microorganisms fix CO₂ (in general)?

1. obtain energy (ATP) and reducing power (NADPH or NADH → NADPH) from light (phototrophs) or chemical reactions (chemolithotrophs)

2. CO₂ is reduced and incorporated into an organic molecule

How does Calvin Cycle work?

1. carbon fixation: CO₂ attached to RuBP (5C) → two 3-PG ; enzyme-Rubisco

2. reduction: 3PG → 1,3BPG → G3P

3. regeneration of RuBP

what is the difference between assimilatory vs. dissimilatory processes?

Assimilatory = for building biomass (anabolism/biosynthesis), requires ATP, incorporates end product into cell

Dissimilatory = for generating energy (catabolism), produces ATP, releases end product as waste

what is the assimilatory mechanism of inorganic sulfate?

• reduce sulfate SO₄^2- (inorganic, unusable) → sulfite SO₃^2-, → H₂S (organic, usable) → cysteine

what is the assimilatory mechanism of inorganic sulfate?

• sulfur acts as a terminal electron acceptor in anaerobic respiration

• SO₄^2- → H₂S (released)

what is the assimilatory process of inorganic nitrogen?

• use nitrate reductase NAS enzyme (located in cytoplasm)

• nitrate NO₃^- → nitrite NO₂^- → nitroxyl (NOH) → hydroxylamine (NH₂OH) → NH₃

• after assimilatory process, can use ammonia (NH₃) for amino acid synthesis

what is the dissimilatory mechanism of inorganic nitrogen?

• use nitrate reductase NAR enzyme

• NO₃^-​→ N₂ (denitrification)

what is nitrogen fixation?

• converting nitrogen gas N₂ to ammonia NH₃ for biosynthesis

• enzyme: nitrogenase—O₂ sensitive, requires lots of ATP and electrons

what are mechanisms to shield nitrogenase enzymes from O₂?

*nitrogenase are O₂ sensitive; enzyme complex deactivates in the presence if O₂

• physical separation—heterocyst (cyanobacteria)

• spatial separation (symbiosis)—leghemoglobin (produced in nodulation of plant roots)

• high respiration rates—ex: Azotobacter species

how do heterocysts work?

• separates photosynthesis from nitrogen fixation (either via. compartment or cell differentiating into specialized cell) → limits the effects of O₂

how do leghemoglobin work?

• leghemoglobin: O₂ binding protein

• produced in Rhizobium bacteria (found in root nodules of plant)

• keeps O₂ levels low enough to protect nitrogenase but high enough for respiration

how does Azotobacter protect nitrogenase?

• rapidly consumes O₂ via. respiration → keeps intracellular O₂ low

• accumulate PHB (polymer) reserve when low O₂

• mobilizes PHB polymers and secrete alginate (thick slime layer) → prevents/slows diffusion of oxygen into the cell

what is carboxysome?

• compartmentalizes carbon fixation process