Microbiology: Trying to simplify and memorize hard concepts

When in photosynthesis is NADP⁺ actually regenerated — when it's being reduced to NADPH, or when NADPH is later used to power carbon fixation?

NADP⁺ → NADPH (reduction) happens in light reactions, consuming NADP⁺.

NADPH → NADP⁺ (oxidation) happens in the Calvin cycle or biosynthesis, recycling the coenzyme.Answer: Recycling occurs during oxidation in the Calvin cycle, not during its reduction.

What is the name of the bacterial system that uses phosphoenolpyruvate (PEP) to transport sugars across the membrane and phosphorylate them at the same time?

This is a group translocation mechanism — energy from PEP transfers a phosphate group to the sugar during transport.Answer: Phosphotransferase System (PTS).

For one molecule of acetyl-CoA entering the TCA cycle, what energy carriers and byproducts are formed, and what is regenerated to keep the cycle going?

Each cycle turn yields energy carriers and CO₂ from oxidation, while regenerating oxaloacetate (OAA).Answer: 3 NADH, 1 FADH₂, 1 ATP (or GTP), 2 CO₂; OAA is regenerated.

How can you tell which molecule serves as the final electron acceptor in aerobic respiration, anaerobic respiration, or fermentation?

Aerobic = O₂ → H₂O

Anaerobic = Inorganic molecule other than O₂ (e.g., NO₃⁻, SO₄²⁻, CO₂)

Fermentation = Organic molecule (e.g., pyruvate, acetaldehyde)Tip: If the final acceptor is organic → fermentation; if inorganic → respiration.

Does the cyclic light reaction make O₂ or NADPH like the non-cyclic pathway does?

In cyclic flow, electrons return to PSI — no photolysis, no O₂, no NADPH. Only ATP is made.Answer: ATP only; no O₂ or NADPH.

What types of bonds hold the DNA backbone together, and what bonds connect the bases between the two strands?

Backbone → Covalent phosphodiester bonds (strong).

Bases → Hydrogen bonds (weak, for strand separation).Answer: Backbone = phosphodiester; Bases = hydrogen.

When a bacterial ribosome begins translating mRNA, what amino acid is used first, and how does it differ from eukaryotes?

Prokaryotes start with formyl-methionine (fMet); eukaryotes start with methionine.Answer: Formyl-methionine (fMet).

What three independent variables determine how fast a metabolic pathway runs?

Enzyme amount (gene expression level)

Enzyme activity (allosteric regulation, covalent modification)

Substrate availability (mass-action effect)Answer: Enzyme amount, enzyme activity, and substrate concentration.

Aerobic Respiration

Meaning: Respiration that requires oxygen.

Oxygen role: Final electron acceptor in the electron transport chain.

ATP yield: High (around 36–38 ATP per glucose).

Example organisms: Humans, animals, most plants, many bacteria.

Also called:

Cellular respiration (in the presence of oxygen)

Oxidative respiration

Anaerobic Respiration

Meaning: Respiration that does not use oxygen but still uses an electron transport chain.

Alternative final electron acceptors: Nitrate (NO₃⁻), sulfate (SO₄²⁻), or carbon dioxide (CO₂).

ATP yield: Moderate (less than aerobic respiration).

Example organisms: Some bacteria (like those in oxygen-poor soil or intestines).

Also called:

Non-oxygen respiration

Anoxic respiration

Fermentation

Meaning: Energy production without oxygen and without an electron transport chain.

ATP source: Only from substrate-level phosphorylation (glycolysis).

ATP yield: Low (only 2 ATP per glucose).

Types:

Lactic acid fermentation: In muscle cells and some bacteria.

Alcoholic fermentation: In yeast and some plants.

Also called:

Anaerobic metabolism (in casual use)

Glycolytic fermentation

Are fermentation and anaerobic respiration the same thing?

No. Both occur without oxygen, but they are different processes. Fermentation makes ATP only through glycolysis and does not use an electron transport chain, producing just 2 ATP per glucose. Anaerobic respiration still uses an electron transport chain but with a final electron acceptor other than oxygen (like nitrate or sulfate), producing more ATP than fermentation but less than aerobic respiration.

How are fermentation and anaerobic respiration alike

Both occur when oxygen is not available.

Both start with glycolysis, where glucose is split into pyruvate and a small amount of ATP is made

Fermentation: electron transport chain? final electron receptor? ATP yield? Organisms?

Fermentation:

No electron transport chain

final electron acceptor = organic molecule like pyruvate or acetaldehyde

ATP: only 2 ATP per glucose via glycolysis

Organisms: yeast, muscle cells

Purpose: regenerate NAD+ so glycolysis can continue

Example: lactic acid fermentation, alcohol fermentation

Anaerobic Respiration: electron transport chain; ATP yield; Organisms; Main Purpose; Examples

Anaerobic Respiration:

Electron transport chain: YES

Final Electron Receptor: INORGANIC molecule such as Nitrate, sulfate, carbon dioxide

ATP Yield: moderate

organisms: some bacteria, archea

Main purpose: Generate ATP through ETC without using oxygen

Examples: nitrate respiration in E Coli, sulfate respiration in some marine bacteria

Easy fermentation vs anaerobic respiration

Fermentation = No ETC, only glycolysis → 2 ATP.

Anaerobic respiration = Uses an ETC, just no oxygen at the end.

Glucose → 2 Lactic acid + 2 ATP

Fermentation (lactic acid)

Glucose + Nitrate → Carbon dioxide + Nitrite + ATP

Anaerobic Respiration (with nitrate)

What does ATP actually do for the cell?

Transfers energy to reactions that need it; it doesn’t store energy long-term.→ ATP links catabolism and anabolism by transferring phosphate energy.

Photoautotroph vs chemoheterotroph — what's the energy source?

Photoautotroph → light energy; chemoheterotroph → chemical energy from organic molecules.

Where do carbohydrate, fat, and protein catabolism overlap?

All intersect in the citric acid (TCA/Krebs) cycle.→ Shared intermediates connect macronutrient metabolism.

Cellular Respiration and Fermentation; how alike?

both processes that generate ATP, the energy currency of the cell.

Cellular respiration and fermentation: how different?

cellular respiration is an aerobic process that requires oxygen and is highly efficient, producing up to 38 ATP molecules per glucose molecule. Fermentation is an anaerobic process that occurs without oxygen and is much less efficient, producing only 2 ATP molecules per glucose molecule, with common byproducts like lactic acid or ethanol.

Type of phosphorylation used to generate ATP: aerobic respiration versus anaerobic respiration versus fermentation

Anaerobic respiration: oxidative and substrate level

Aerobic respiration: oxidative and substrate level

Fermentation: substrate level

Substrate level phosphorylation

Definition: ATP is made directly from a reaction where a phosphate group is transferred from a substrate molecule to ADP.

Example: In glycolysis and the Krebs (citric acid) cycle.

Oxygen requirement: No oxygen needed for this type of ATP production.

oxidative phosphorylation

Definition: ATP is made indirectly using energy from electrons that pass down the electron transport chain (ETC) to oxygen (or another final electron acceptor).

This process uses the proton gradient created across a membrane to power ATP synthase.

Oxygen requirement: Usually requires oxygen (aerobic), but some anaerobes use other acceptors like nitrate or sulfate.

Stages of the Respiration Cycle

1. Glycolysis

2. Krebs Cycle (Citric Acid Cycle)

3. Electron Transport Chain (oxidative phosphorylation)

Cellular respiration: process, oxygen requirement, location, energy yield, byproducts

Process: Converts nutrients into ATP through a series of reactions.

Oxygen requirement: Aerobic (requires oxygen).

Location: Starts with glycolysis in the cytoplasm, then moves to the mitochondria for the Krebs cycle and electron transport chain.

Energy yield: Highly efficient, producing approximately 38 ATP per glucose molecule.

Byproducts: Carbon dioxide and water.

Glycolysis

Location: Cytoplasm (or cytosol).

Process: A molecule of glucose is broken down into two molecules of pyruvate.

Products: Some ATP and NADH (an electron carrier) are produced.

Oxygen Requirement: Glycolysis does not require oxygen.

Krebs Cycle (Citric Acid Cycle)

Location: Mitochondrial matrix.

Process: Pyruvate is converted to acetyl-CoA and then enters a cycle of reactions where it is further broken down.

Products: Carbon dioxide, ATP, and more NADH and FADH2 (another electron carrier) are generated.

Oxygen Requirement: This stage requires oxygen.

Electron Transport Chain (Oxidative Phosphorylation)

Location: Inner mitochondrial membrane.

Process: NADH and FADH2 from the previous stages deliver electrons to the ETC. These electrons are used to create a proton gradient, which drives ATP synthesis.

Products: Large amounts of ATP are produced, and oxygen combines with electrons and hydrogen to form water.

Oxygen Requirement: This is an aerobic process that requires oxygen to function

Fermentation

Process: A partial breakdown of sugars to generate ATP without oxygen.

Oxygen requirement: Anaerobic (does not require oxygen).

Location: Occurs entirely in the cytoplasm.

Energy yield: Less efficient, producing only 2 ATP per glucose molecule.

Byproducts: Depends on the type of fermentation. Lactic acid fermentation: Produces lactic acid (occurs in human muscle cells during strenuous exercise). Alcoholic fermentation: Produces ethanol and carbon dioxide (occurs in yeast).

Can carbohydrates become amino acids?

Yes — via intermediates of glycolysis/TCA (e.g., pyruvate → alanine). NOT DIRECTLY

Can fatty acids become glycogen?

No — fatty acids are oxidized for energy, not stored as glycogen.

Glycolysis: where does it occur?

Cytoplasm of ALL cells

Glycolysis used when? Does it need oxygen?

without or with oxygen

Glycolysis input and output

Glucose (6 carbon hexose) →

2 pyruvate (carboxylic acid) + 2 ATP (net) + 2 NADH.

Glycolysis input and output

Glucose → 2 pyruvate + 2 ATP (net) + 2 NADH.

Glycolysis other names

Embden-Meyerhof-Parnas pathway (EMP); glycolytic pathway; anaerobic glucose breakdown.

Glycolysis type of ATP formation

Substrate-level phosphorylation (direct).

Glycolysis net ATP yield reasoning

4 made - 2 used = 2 net.

Glycolysis organic acid product

Pyruvate (3 Carbon) — gateway to fermentation or respiration.

It's a carboxylic acid

What happens if no oxygen is present?

fermentation

Cells regenerate NAD⁺ by transferring electrons from NADH to organic acceptors.

Fermentation

A catabolic process that makes a limited amount of ATP from glucose without an electron transport chain and that produces a characteristic end product, such as ethyl alcohol or lactic acid. Fermentation is a way for organisms to regenerate NAD+ from NADH, which is produced during glycolysis. It does this by converting pyruvate into other organic molecules, such as lactic acid or ethanol. This conversion "recycles" the NAD+ so that glycolysis can continue, allowing the organism to produce a small amount of ATP even in an anaerobic environment.

Fermentation hub

Pyruvate → various products (lactate, ethanol → acetaldehyde, acetate, formate).

Fermentation energy yield

Only ATP from glycolysis (2 per glucose).

Amino acids → lactic acid directly?

No — they first enter central metabolism, then feed into glycolysis intermediates.

Fermentation electron acceptor

Organic molecule (e.g., pyruvate or acetaldehyde).

Respiration

The process by which cells break down simple food molecules to release the energy they contain.

Respiration final electron acceptor (aerobic)

Oxygen

Oxygen → H₂O.

Respiration Final electron acceptor (anaerobic):

Inorganic molecule other than O₂ (e.g., nitrate, nitrite, sulfate).

Respiration ATP yield summary (aerobic)

36-38 ATP per glucose (prokaryote vs eukaryote).

Respiration Pyruvate → Acetyl-CoA step:

2 NADH = 6 ATP (eq. old 3 P/O).

Respiration TCA (citric acid) per turn

3 NADH + 1 FADH₂ + 1 ATP (GTP); 2 CO₂ released.

Respiration Yield (from 2 turns per glucose)

6 NADH + 2 FADH₂ + 2 ATP + 4 CO₂.

Why is respiration called a cycle?

Oxaloacetate (OAA) is regenerated.

Oxidative Phosphorylation

final stage of cellular respiration in which energy from electrons transferred through the electron transport chain is used to produce ATP. It occurs in the inner mitochondrial membrane and involves the transfer of electrons from NADH and FADH₂ to oxygen, forming water.

Chemiosmosis

couples this electron transport to ATP synthesis.

As electrons move through the transport chain, protons (H⁺ ions) are pumped across the inner mitochondrial membrane, creating a proton gradient.

The return flow of protons through ATP synthase drives the phosphorylation of ADP to ATP.

Where does oxidative phosphorylation take place in eukaryotes?

inner mitochondrial membrane

Where does oxidative phosphorylation take place in prokaryotes?

cell membrane (prokaryotes).

Oxidative Phosphorylation & Chemiosmosis Inputs

NADH, FADH₂, O₂, ADP + Pi.

Oxidative Phosphorylation & Chemiosmosis Output

ATP, H₂O, recycled NAD⁺ and FAD.

Oxidative Phosphorylation & Chemiosmosis Process Summary

electrons flow → protons pumped → gradient powers ATP synthase.

proton (concentration) gradient.

The product of the electron transport chain. A higher concentration of protons outside the inner membrane of the mitochondria than inside the membrane is the driving force behind ATP synthesis.

electrical potential gradient.

in the context of resting and action potentials, a difference in electrical potential between the inside of a cell and its surrounding, extracellular space

proton motive force (PMF).

potential energy stored across a membrane; its the combination of proton concentration gradient and the electrical potential gradient