Theme B

What is metabolism?

Sum of all chemical reactions in a living cell/organism that obtain and use free energy required for life.

What catalyses metabolic reactions?

Enzymes.

What are metabolites?

Small molecules that are intermediates, substrates, or products in metabolic pathways.

What are the two main categories of metabolism?

Catabolism (degradation) and Anabolism (synthesis).

What does catabolism do to molecules in terms of complexity and oxidation state?

Breaks complex, reduced molecules → simple, oxidised molecules; produces energy.

What does anabolism do to molecules in terms of complexity and oxidation state?

Builds simple, oxidised molecules → complex, reduced molecules; consumes energy.

Which coenzyme do catabolic enzymes generally use?

NAD⁺ (dehydrogenases).

Which coenzyme do anabolic enzymes generally use?

NADPH (reductases).

What is oxidation in metabolism?

Loss of electrons (e⁻) or hydrogen (H⁺ + e⁻).

What is reduction in metabolism?

Gain of electrons (e⁻) or hydrogen (H⁺ + e⁻).

In a redox reaction, what is the electron donor called?

Reducing agent (reductant).

In a redox reaction, what is the electron acceptor called?

Oxidising agent (oxidant).

Write the oxidation half-reaction of NADH.

NADH ⇋ NAD⁺ + 2e⁻ + H⁺

Write the reduction half-reaction for 1,3-bisphosphoglycerate.

1,3-bisphosphoglycerate + 2e⁻ + H⁺ ⇋ glyceraldehyde-3-phosphate + Pi

What does a [NADH]/[NAD⁺] ratio < 1 promote?

Metabolite oxidation.

What does a [NADPH]/[NADP⁺] ratio > 1 promote?

Metabolite reduction.

What is the main use of NADH in metabolism?

Oxidative phosphorylation → ATP production.

What is the main use of NADPH in metabolism?

Reductive biosynthesis (anabolism).

What are the six questions to ask when analyzing a metabolic pathway?

1. Beginning substrate(s)? 2. End product(s)? 3. Net ATP consumption/production? 4. Net reducing equivalents consumption/production? 5. Net chemical process: oxidising or reducing? 6. Is the pathway anabolic or catabolic?

If 1 ATP is consumed and 2 are produced, what is the net ATP?

1 ATP produced.

If 2 ATP are consumed and 2 are produced, what is the net ATP?

None; no net ATP.

If a pathway consumes reducing equivalents, what is its chemical process?

Reductive.

If a pathway produces reducing equivalents, what is its chemical process?

Oxidative.

A pathway that builds complex molecules from simple ones is:

Anabolic.

A pathway that breaks down complex molecules to simple ones is:

Catabolic.

What is functional coupling in metabolism?

Functional coupling is the linkage between catabolism and anabolism, where energy and reducing equivalents produced in catabolism are used for anabolic reactions.

What are primary coupling agents?

Agents that directly couple catabolism and anabolism, e.g., ADP/ATP and NADP+/NADPH.

What are secondary coupling agents?

Agents produced during catabolism that are used for energy (ATP) production, e.g., NAD+/NADH, FMN/FMNH2, FAD/FADH2.

What are key metabolites or general coupling agents?

Metabolites produced during catabolism that serve as building blocks during anabolism, e.g., triose, tetrose, pentose, hexose phosphates, PEP, acetyl-CoA, succinyl-CoA, pyruvate, α-ketoglutarate, oxaloacetate.

Give an example of a primary coupling agent for energy.

ATP/ADP

Give an example of a primary coupling agent for reducing equivalents.

NADP+/NADPH

Give an example of a secondary coupling agent.

NAD+/NADH

What is the ATP coupling coefficient?

The number of moles of ATP (or ATP equivalents) produced or consumed during the conversion of 1 mole of substrate to product.

What is the ATP equivalent?

The energy value associated with converting ATP ↔ ADP or vice versa, or similar conversions for NADH, NADPH, FADH2.

ATP → ADP conversion corresponds to how many ATP equivalents?

1

ATP → AMP conversion corresponds to how many ATP equivalents?

2

NADPH → NADP+ conversion corresponds to how many ATP equivalents?

3

NADH → NAD+ conversion corresponds to how many ATP equivalents?

2.5 (mitochondrial) / 1.5 (cytoplasmic, glycerol-3-phosphate shuttle)

FADH2 → FAD conversion corresponds to how many ATP equivalents?

1

How do catabolism and anabolism relate to key metabolites?

Catabolism provides building blocks for anabolism; these are the key metabolites or general coupling agents.

Name the three types of functional coupling agents.

1. Primary coupling agents, 2. Secondary coupling agents, 3. Key metabolites.

How are primary and secondary coupling agents regenerated?

By group-conserved cycles, e.g., ADP + Pi → ATP, FAD + [2H] → FADH2.

What is the net reaction for glucose + ATP → glucose-6-phosphate + ADP?

ATP coupling coefficient = -1

Calculate the ATP coupling coefficient for C6H12O6 + 6 O2 + 32 ADP + 32 Pi ⇌ 6 CO2 + 6 H2O + 32 ATP.

32

In a reaction producing 2 NADH in cytoplasm via malate-aspartate shuttle, how many ATP equivalents are generated?

2 x 2.5 = +5

In a reaction producing 2 NADH in cytoplasm via glycerol-3-phosphate shuttle, how many ATP equivalents are generated?

2 x 1.5 = +3

Compare primary and secondary coupling agents to key metabolites.

Primary and secondary agents are regenerated rapidly; key metabolites are synthesised de novo and used as building blocks for anabolism.

What is the main goal of studying functional coupling agents?

To understand the ATP/ADP cycle, functional coupling agents, key metabolites, group-conserved cycles, ATP equivalents, and ATP coupling coefficients.

Give examples of key metabolites.

G6P, pyruvate (Pyr), GAP, PEP, acetyl-CoA, succinyl-CoA, α-ketoglutarate, oxaloacetate.

What is the main focus of metabolism in cells?

The organization, regulation, and interdependence of chemical reactions in living cells/organisms.

What are the three main phases of metabolism?

Catabolism (breakdown of polymers → monomers → key metabolites → inorganic compounds), Anabolism (synthesis of monomers → polymers), Energy transfer (ATP and reducing equivalents [H])

Give an example of the three main phases in carbohydrate metabolism.

Glycogen → Glucose → Pyruvate → CO2

What are the types of metabolic pathways?

Linear (e.g., amino acid biosynthesis), Cyclic (e.g., citric acid cycle), Spiral (e.g., fatty acid biosynthesis/degradation)

Catabolic and anabolic pathways for carbohydrates?

Catabolic: glycogenolysis/starch degradation → glucose → glycolysis → pyruvate → TCA cycle; Anabolic: gluconeogenesis, glycogen/starch synthesis

Catabolic and anabolic pathways for lipids?

Catabolic: lipid catabolism → fatty acids + glycerol → Acetyl-CoA → TCA cycle; Anabolic: lipid anabolism → fatty acids + glycerol

Catabolic and anabolic pathways for proteins?

Catabolic: protein → amino acids → deamination → pyruvate/Acetyl-CoA/TCA intermediates; Anabolic: amino acids → proteins via amination

Why are separate biosynthetic and degradation pathways important?

Prevent futile cycles, allow regulation, usually involve different enzymes, may occur in different compartments, irreversible steps determine direction

What is compartmentalisation of metabolic pathways?

Segregation of pathways into organelles or regions of the cell to increase efficiency, regulate reactions, and prevent interference

Examples of metabolic pathways by compartment?

Mitochondrion: TCA cycle, β-oxidation, oxidative phosphorylation, amino acid degradation; Cytoplasm: glycolysis, pentose phosphate pathway, fatty acid biosynthesis, gluconeogenesis; Rough ER: protein synthesis; Smooth ER: lipid/steroid synthesis

What is a substrate cycle?

When opposing metabolic pathways (e.g., glycolysis and gluconeogenesis) operate simultaneously, allowing fine regulation of flux

Why are highly exergonic reactions important in metabolism?

They drive the direction of irreversible steps and are often key regulatory points

How are opposing enzymes in biosynthesis and degradation regulated?

In a coordinated but opposite manner to prevent futile cycling

Which energy carriers are commonly involved in metabolism?

ATP, NADH, FADH2, GTP, and reducing equivalents [H]

Give an example of spiral, cyclic, and linear pathways.

Spiral: fatty acid synthesis/degradation; Cyclic: citric acid cycle; Linear: amino acid biosynthesis

Why do metabolic pathways often share metabolites and enzymes?

To integrate pathways efficiently and allow flexibility, while regulated steps prevent conflict

What are the main strategies for regulating metabolic pathways?

Thermodynamic regulation and kinetic regulation

What is thermodynamic regulation in metabolism?

Using the free energy change (∆G) of reactions to drive irreversible steps and determine pathway direction

Why are irreversible reactions important for regulation?

They act as key control points that determine the flux and direction of metabolic pathways

What is kinetic regulation in metabolism?

Control of pathway flux through modulation of enzyme activity by effectors, inhibitors, activators, or covalent modifications

What is allosteric regulation?

Regulation of enzyme activity by molecules binding at sites other than the active site, affecting enzyme conformation and activity

Give an example of allosteric regulation.

Phosphofructokinase-1 (PFK-1) in glycolysis is activated by AMP and inhibited by ATP and citrate

What is covalent modification of enzymes?

Reversible chemical changes (e.g., phosphorylation, acetylation) that alter enzyme activity

What is feedback inhibition?

The end product of a pathway inhibits an enzyme earlier in the pathway to prevent overproduction

What is feedforward activation?

An intermediate or substrate activates a downstream enzyme to prepare the pathway for increased flux

What role do energy carriers play in metabolic regulation?

ATP, ADP, AMP, NADH, NAD+, and other carriers act as signals of energy status, influencing enzyme activity

How does ∆G <<< 0 relate to metabolic control?

Highly exergonic reactions are irreversible and serve as key regulatory points in pathways

Why is compartmentalization important for regulation?

Segregates pathways into organelles or regions of the cell to increase efficiency, regulate reactions, and prevent interference

What is a substrate cycle?

Simultaneous operation of opposing pathways (e.g., glycolysis vs gluconeogenesis) that allows fine-tuned metabolic control

Why are substrate cycles important?

They allow precise regulation of metabolic flux and prevent sudden energy imbalances

How are opposing enzymes in anabolic and catabolic pathways coordinated?

They are often regulated in opposite directions to prevent futile cycling

What is the difference between kinetic and thermodynamic control?

Thermodynamic control: direction of reaction based on ∆G; Kinetic control: rate of reaction based on enzyme activity

Give an example of a pathway regulated by allosteric effectors.

Glycolysis: PFK-1 activated by AMP, inhibited by ATP and citrate; TCA cycle: isocitrate dehydrogenase activated by ADP