Biochem Metabolism & Enzyme Mechanisms

FInal Exam

Catabolism

Degradation; in which the cell nutrients and constituents are broken down to salvage their components and/ or to generate energy; usually energy-yielding; oxidative (substrates lose reducing equivalents usually H:- ions

Fuels(Carbs, fats) ——> CO2 +H2O + useful energy

Metabolism

The overall processes through which the living organism acquire and use the free energy to carry out their various functions. (Catabolism+Anabolism)

Autotrophs

Use CO2; Organisms that produce their own food using light or chemical energy to fix inorganic carbon (CO2)

Heterotrophs

Use organic carbon; catabolism produces ATP which drives activities of cells; Organisms that cannot produce their own food and must consume organic carbon for growth

Phototrophs

Use light to drive synthesis of organic molecules (ATP); Organisms that carry out photon capture to acquire energy, using light to perform cellular functions.

Chemotrophs

Use Glc, inorganics & S; Organisms that obtain energy by the oxidation of electron donors in their environment (chemical energy).

Anabolism

Biosynthetic pathways; energy-requiring; reductive- NADPH provides the reducing power (electrons) for anabolic processes

Anaplerotic

Metabolic reactions that replenish intermediates in a central metabolic cycle, most commonly the Citric Acid Cycle (TCA cycle), allowing it to continue operating.

Anaerobic

Processes that occur in the absence of oxygen, such as anaerobic respiration or fermentation

Aerobic

Processes the require oxygen, such as aerobic respiration

Substrate-Level Phosphorylation

A direct mechanism of ATP production where a phosphate group is transferred from a high-energy substrate molecule to ADP, occurring in both glycolysis and the TCA cycle.

NADH/ NAD+/ NADPH Chemical Core

Nicotinamide ring (a pyridine derivative)

NADH/ NAD+/ NADPH Redox States

Oxidized: NAD+, NADP+ (positively charged nitrogen)

Reduced: NADH, NADPH (neutralized ring)

NADH/ NAD+/ NADPH Electron Transfer

-2-Electron Reduction/ Oxidation: They work strictly as 2-electron transfers, transferring a hydride anion (H^-)

-does NOT participate in1-electron (radical) chemistry

Flavins (FMN/FAD) Chemical Core

Isoalloxazine ring

Flavins (FMN/FAD) Redox States

• Oxidized (Quinone): FAD, FMN

• 1-Electron Reduced (Semiquinone): FADH, FMNH (radical intermediate)

• 2-Electron Reduced (Hydroquinone): FADH₂, FMNH₂

Flavins (FMN/FAD) Redox States Electron Transfer

Both 1 and 2 Electrons: Flavins are unique in their ability to act as intermediaries, accepting 2 electrons at once (from donors like NADH) and passing them 1-by-1 to other acceptors.

Coenzyme Q (Ubiquinone) Chemical Core

Benzoquinone ring

Coenzyme Q (Ubiquinone) Redox States

• Oxidized (Quinone): Ubiquinone (Q)

• 1-Electron Reduced (Semiquinone): Ubisemiquinone (Q^-)

• 2-Electron Reduced (Hydroquinone): Ubiquinol (QH₂)

Coenzyme Q (Ubiquinone) Electron Transfer

Both 1 and 2 Electrons: CoQ accepts 2 electrons and 2 protons sequentially (often in Complex I/Complex III) to move between ubiquinone and ubiquinol. The semiquinone radical is an essential part of the Q-cycle mechanism.

Glycolysis Aerobic (With Oxygen) Products

2 Pyruvate, 2 ATP (net), 2 NADH

Glycolysis Anaerobic (Without Oxygen) Products

2 Pyruvate, 2 ATP (net), 2 NADH

Glycolysis Aerobic (With Oxygen) Fate

Pyruvate is converted into Acetyl-CoA and enters the mitochondria for the TCA cycle, followed by oxidative phosphorylation to produce ~32–34 ATP.

Glycolysis Anaerobic (Without Oxygen) Fate

To continue generating ATP, the cell must regenerate by converting pyruvate into waste products (fermentation).

Yeast (Alcohol) Fermentation Conditions

Anaerobic

Yeast (Alcohol) Fermentation Pathway

Pyruvate —> Acetaldehyde —> Ethanol

Yeast (Alcohol) Fermentation Key Enzyme

Alcohol Dehydrogenase

Yeast (Alcohol) Fermentation Final Products

Ethanol + Carbon Dioxide (CO₂)+ NAD⁺

Yeast (Alcohol) Fermentation Significance

Produces alcohol/bread; regenerates

Mammals (Lactate Production) Conditions

Anaerobic (e.g. strenuous exercise)

Mammals (Lactate Production) Pathway

Pyruvate —> Lactate

Mammals (Lactate Production) Key Enzyme

Lactate Dehydrogenase (LDH)

Mammals (Lactate Production) Final Products

Lactate + NAD⁺

Mammals (Lactate Production) Significance

Rapid energy; regenerates NAD⁺

Glycolysis (per Glucose)

NET ATP: 2 (4 produced, 2 consumed)

NADH: 2

FADH₂:0

Pyruvate Oxidation (Transition Step)

NET ATP:0

NADH: 2 (1 per pyruvate)

FADH₂:0

TCA/Krebs Cycle (Per Glucose)

(2 turns per glucose)

Net ATP (or GTP):2

NADH: 6 (3 per turn)

FADH₂: 2 (1 per turn)

Electron Transport Chain (ETC) # of ATP produced

~ 30 to 32 ATP per Glucose (eukaryotes) [DOUBLE CHECK]

Electron Transport Pathway Complexes

4 main protein complexes

1. Complex I (NADH-ubiquinone oxdoreductase)

2. Complex II (Succinate-ubiquinone reductase)

3. Complex III (Ubiquinone-cytochrome c oxidoreductase)

4. Complex IV (cytochrome c oxidase)

Complex I (NADH-ubiquinone oxdoreductase)

Uses NADH, pumps protons (H⁺)

Complex II (Succinate-ubiquinone reductase)

Uses FADH2, does NOT pump protons

Complex III (Ubiquinone-cytochrome c oxidoreductase)

Pumps protons

Complex IV (cytochrome c oxidase)

Pumps protons and reduces O₂ to H₂O

pH gradient of Electron Transport Pathway

Protons are pumped from the matrix (low concentration, high pH) to the intermembrane space (high concentration, low pH)

Electron Transport Pathway Mobile Coenzymes

Ubiquinone (Q) (within the membrane) and cytochrome c (intermembrane space) transfer electrons.

ATP Synthase (Complex V) Location

Embedded in the inner mitochondrial membrane

ATP Synthase (Complex V) Mechanism

Uses the proton-motive force (H⁺ gradient) to drive the rotation of F_o component, transferring energy to the F₁ component to phosphorylate ADP to ATP

ATP Synthase (Complex V) ATP Yield

Approximately 2.5 ATP per NADH and 1.5 ATP per . Total yield per glucose is roughly 30-32 ATP

ATP Synthase (Complex V) Three Intermediate States (Binding Change Mechanism)

The Catalytic β-subunits cycle between three conformations:

• Open (O): Very low affinity; releases ATP or binds ADP+Pi.

• Loose (L): Binds ADP and Pi loosely.

• Tight (T): Catalyzes ATP synthesis

Effect of Uncouplers on Electron Transport

Increases (accelerates) because the inhibition caused by the high proton gradient is removed

Effect of uncouplers on ATP Synthesis

Decreases or stops because the proton gradient necessary to drive ATP synthase is dissipated

Outcome of the effect of uncouplers

Energy is released as heat rather than stored in ATP

NADH generated in the cytosol during glycolysis cannot pass through the inner mitochondrial membrane (impermeable) to reach the ETC

SO protein shuttles are used

Protein Shuttles involved in electron transfer between glycolysis and TCA/electron transport

• Malate-Aspartate Shuttle

• Glycerol-3-Phosphate Shuttle

Malate-Aspartate Shuttle

Transports electrons from cytosolic NADH into the matrix to produce NADH in the mitochondria (higher energy yield)

Glycerol-3-Phosphate Shuttle

Transports electrons from cytosolic NADH to Q in the ETC, reducing FAD to (lower energy yield)