cellular energetics

🧬 SECTION 1: ENZYMES

1. How enzymes lower activation energy (Ea)

Enzymes are catalysts: they speed up reactions without being used up.

They lower activation energy by:

1. Correctly orienting substrates

   • Enzyme holds substrates in the right position so collisions are effective.

2. Stabilizing the transition state

   • Active site can form temporary bonds or interactions that make the “in-between” state easier to reach.

3. Straining/bending bonds

   • Enzyme may physically distort bonds so they’re easier to break.

4. Providing a special microenvironment

   • Example: acidic R-groups in active site create a lower pH than the rest of the cell.

5. Forming temporary covalent bonds with substrate

   • Enzyme briefly reacts with substrate, then returns to original state.

2. Substrate specificity (“induced fit”)

• The active site has a specific shape + chemical environment that fits only certain substrates.

• It’s not a rigid “lock-and-key”—it’s induced fit:

  • Substrate binding causes a subtle shape change in the enzyme.

  • This improves binding and catalysis.

3. Factors that regulate enzyme activity

a. Temperature

• Low T: molecules move slowly → fewer collisions → low rate (enzyme still intact).

• Optimal T: highest rate; enzyme shape is intact.

• High T: enzyme denatures (H-bonds, ionic bonds disrupted) → active site destroyed.

b. pH

• Each enzyme has an optimal pH.

• Too acidic or too basic → alters charges on R-groups → disrupts H-bonds/ionic bonds → denaturation.

c. Substrate concentration

• At low [substrate] → increasing [substrate] increases rate.

• When all enzymes are working (active sites full) → saturation → rate plateaus (Vmax).

d. Enzyme concentration

• More enzyme = more active sites → higher rate (if substrate isn’t limiting).

e. Inhibitors (see below)

• Competitive, noncompetitive/allosteric.

4. Inhibitors

Competitive inhibitor

• Resembles substrate.

• Binds active site, blocking substrate.

• DOES NOT change enzyme shape.

• Can be overcome by adding more substrate.

Noncompetitive (allosteric) inhibitor

• Binds a different site (allosteric site).

• Changes enzyme shape → active site no longer fits substrate.

• Cannot be overcome by extra substrate.

5. Allosteric regulation

• Any regulation where a molecule binds away from the active site and changes enzyme activity.

Types:

• Allosteric activator: stabilizes active form → increases activity.

• Allosteric inhibitor: stabilizes inactive form → decreases activity.

Common in multi-subunit enzymes (like those in pathways).

6. Feedback regulation (feedback inhibition)

• End product of a metabolic pathway binds to an enzyme early in the pathway (often the first step).

• Usually binds allosterically → inhibits enzyme.

• Prevents overproduction and waste of energy/resources.

Classic example:

• Amino acid synthesis pathways where the final amino acid inhibits the first enzyme.

🔋 SECTION 2: CELLULAR RESPIRATION

1. Redox reactions and energy

• Oxidation = loss of electrons (often loss of H or gain of O).

• Reduction = gain of electrons (often gain of H).

• “OIL RIG” or “LEO the lion says GER.”

In respiration:

• Glucose is oxidized → CO₂

• O₂ is reduced → H₂O
  Electrons move from higher energy (C-H bonds in glucose) to lower energy (O-H bonds in water), releasing energy used to make ATP.

2. Three types of phosphorylation

1. Substrate-level phosphorylation

   • Directly transfers a phosphate from a substrate to ADP → ATP.

   • Happens in glycolysis and citric acid cycle.

2. Oxidative phosphorylation

   • Uses ETC + chemiosmosis in mitochondria.

   • Energy from electrons → proton gradient → ATP synthase makes ATP.

   • Most ATP in respiration comes from here.

3. Photophosphorylation

   • Same idea as oxidative, but powered by light in chloroplast thylakoids (photosynthesis).

3. Three stages of cellular respiration

🌟 Stage 1: Glycolysis

• Location: Cytosol

• Input: Glucose

• Output per glucose:

  • 2 pyruvate

  • 2 ATP (net; 4 made – 2 used) via substrate-level phosphorylation

  • 2 NADH

🌟 Stage 2: Pyruvate oxidation + Citric Acid Cycle (Krebs)

Pyruvate oxidation (per glucose → 2 pyruvate)

• Location: Mitochondrial matrix

• Each pyruvate → acetyl-CoA + CO₂ + NADH

• Per glucose: 2 acetyl-CoA, 2 CO₂, 2 NADH

• Transport into mitochondria

  • Pyruvate (a 3‑carbon molecule from glycolysis) is moved from the cytosol into the mitochondrial matrix.

• Decarboxylation

  • One carbon atom is removed from pyruvate as CO₂.

  • This reduces pyruvate from a 3‑carbon molecule to a 2‑carbon molecule.

• Oxidation

  • The remaining 2‑carbon fragment is oxidized.

  • Electrons are transferred to NAD⁺, forming NADH, which will later feed into the electron transport chain.

• Formation of Acetyl-CoA

  • The 2‑carbon fragment is attached to Coenzyme A (CoA), forming acetyl-CoA.

  • Acetyl-CoA is the molecule that enters the citric acid cycle (Krebs cycle)

simple terms

• The 2‑carbon fragment (acetyl group) is oxidized.

• Electrons (and a proton) are released.

• NAD⁺ is waiting nearby as an electron carrier.

• NAD⁺ accepts 2 electrons and 1 proton (H⁺), becoming NADH.

Citric Acid Cycle (per glucose → 2 turns)

• Location: Matrix

• Per glucose:

  • 4 CO₂

  • 2 ATP (substrate-level)

  • 6 NADH

  • 2 FADH₂

• Starting Point

  • From pyruvate oxidation, you now have acetyl-CoA (a 2‑carbon molecule attached to CoA).

  • This acetyl-CoA enters the mitochondrial matrix and fuels the citric acid cycle.

🌟 Stage 3: Oxidative phosphorylation (ETC + chemiosmosis)

• Location: Inner mitochondrial membrane (cristae)

• Inputs: NADH, FADH₂, O₂

• Outputs: ~26–28 ATP, H₂O, NAD⁺, FAD

4. Role of the electron transport chain (ETC)

• Series of protein complexes that pass electrons from NADH/FADH₂ → O₂.

• As electrons move “downhill,” energy released is used to:

  • Pump H⁺ from matrix to intermembrane space.

• Final electron acceptor = O₂, forming water.

5. How the proton gradient is created

• ETC complexes I, III, and IV pump H⁺ into the intermembrane space.

• Creates:

  • pH gradient (more acidic outside)

  • Charge gradient (more positive outside)

• This electrochemical gradient = proton motive force.

ATP synthase lets H⁺ flow back into matrix → uses energy to form ATP from ADP + Pi (chemiosmosis).

6. ATP yield calculations (per 1 glucose)

Glycolysis:

• 2 ATP (substrate-level)

• 2 NADH → ~5 ATP (in many AP texts: 3–5 depending on shuttle; use 5 if they say 2.5 per NADH)

Pyruvate oxidation:

• 2 NADH → ~5 ATP

Citric acid cycle:

• 2 ATP (substrate-level)

• 6 NADH → ~15 ATP

• 2 FADH₂ → ~3 ATP

Total:

• Substrate-level = 4 ATP

• Oxidative phosphorylation = ~28 ATP

• Overall ≈ 30–32 ATP per glucose (AP usually accepts a range).

Fermentation:

• Only glycolysis works.

• Net: 2 ATP per glucose (substrate-level only).

7. Fermentation vs anaerobic respiration

Fermentation

• No ETC, no O₂.

• Purpose: regenerate NAD⁺ so glycolysis can continue.

• Types:

  • Lactic acid fermentation (pyruvate → lactate)

  • Alcohol fermentation (pyruvate → ethanol + CO₂)

• ATP made = 2 ATP from glycolysis only.

Anaerobic respiration

• Uses an ETC with a different final electron acceptor (not O₂), e.g., nitrate, sulfate.

• More ATP than fermentation, less than aerobic.

8. Obligate vs facultative anaerobes

• Obligate anaerobes

  • Cannot live with O₂ (toxic).

  • Use anaerobic respiration or fermentation.

• Facultative anaerobes

  • Can use O₂ if present (aerobic), or fermentation if not.

  • Example: many yeast, some bacteria, muscle cells under heavy exercise.

9. Mitochondria structure for each step

• Outer membrane – boundary.

• Inner membrane (cristae) – location of ETC and ATP synthase.

• Intermembrane space – where H⁺ accumulates.

• Matrix – inside inner membrane:

  • pyruvate oxidation

  • citric acid cycle

Where each step happens:

• Glycolysis – cytosol

• Pyruvate oxidation – matrix

• Krebs – matrix

• ETC & chemiosmosis – inner membrane + intermembrane space

10. Factors that affect cellular respiration

• O₂ availability

• Glucose/food availability

• Temperature (affects enzyme activity)

• Presence of inhibitors/uncouplers

• Hormonal regulation (e.g., insulin/glucagon in multicellular organisms—big picture).

11. Decoupling ETC from chemiosmosis & uncouplers

Decoupling = ETC keeps running and pumping protons, but ATP synthase doesn’t use the gradient → energy is released as heat instead of ATP.

Natural decoupler: Brown fat / Thermogenin

• In infants and hibernating animals.

• Thermogenin forms a proton channel that lets H⁺ leak back into matrix without ATP synthase → generates heat.

Uncouplers (general idea)

• Chemicals that make inner mitochondrial membrane leaky to H⁺ or otherwise disrupt gradient.

• Result:

  • Less ATP

  • More heat

  • Increased oxygen consumption (ETC keeps running)

AP-level questions usually ask:

🌱 SECTION 3: PHOTOSYNTHESIS

1. Chloroplast structure

• Outer and inner membrane

• Thylakoids – flattened sacs; contain chlorophyll, ETC, ATP synthase.

• Grana – stacks of thylakoids.

• Stroma – fluid surrounding thylakoids; site of Calvin cycle.

2. Absorption vs action spectrum

• Absorption spectrum – how strongly pigments absorb different wavelengths (colors).

• Action spectrum – how effective each wavelength is at driving photosynthesis (O₂ production, sugar).

They overlap because wavelengths that pigments absorb best generally drive photosynthesis best (blue and red).

3. Linear electron flow (light-dependent reactions)

Location: Thylakoid membrane
Goal: Make ATP + NADPH + O₂

Steps:

1. Light excites PSII → high-energy electrons.

2. Water splits: H₂O → 2 e⁻ + 2 H⁺ + ½ O₂

3. Electrons → PSII primary acceptor → ETC (plastoquinone, cytochrome complex, plastocyanin).

4. ETC pumps H⁺ into thylakoid lumen → proton gradient.

5. H⁺ flows back via ATP synthase → ATP (photophosphorylation).

6. Electrons reach PSI, are re-energized by light.

7. Electrons passed to ferredoxin → NADP⁺ reductase → NADP⁺ + H⁺ + 2 e⁻ → NADPH.

Outputs: ATP, NADPH, O₂

4. Cyclic electron flow

• Electrons from PSI cycle back through the cytochrome complex instead of reducing NADP⁺.

• Makes ATP only, no NADPH, no O₂.

• Used when the Calvin cycle needs more ATP than NADPH (balances energy budget).

5. Oxidative phosphorylation vs photophosphorylation

Similarities:

• ETC + chemiosmosis

• Proton gradient → ATP synthase → ATP

• Membrane-bound complexes

Differences:

• Location:

  • Oxidative: inner mitochondrial membrane

  • Photo: thylakoid membrane

• Energy source:

  • Oxidative: energy from oxidation of food

  • Photo: light energy excites electrons

• Final electron acceptor:

  • Oxidative: O₂ → H₂O

  • Photo: NADP⁺ → NADPH

• Side of gradient:

  • Mitochondria: H⁺ pumped out of matrix → intermembrane space; flow back into matrix.

  • Chloroplast: H⁺ pumped into thylakoid lumen; flow into stroma.

6. Leaky mutants of proton channel proteins

• If proton channels are leaky, H⁺ diffuses across membrane without going through ATP synthase.

• Result: Lower ATP production, weaker proton motive force.

• Some energy lost as heat.

(Same concept as mitochondrial uncoupling.)

7. Photophosphorylation & ATP synthase

• H⁺ gradient in lumen → flows through ATP synthase into stroma.

• ATP synthase spins and makes ATP from ADP + Pi.

• This ATP is used in the Calvin cycle.

8. NADP⁺ reductase & feedback

• Enzyme at end of PSI pathway.

• Receives electrons → reduces NADP⁺ to NADPH.

• NADPH used in Calvin cycle; when it builds up (Calvin slows), electron flow may shift more to cyclic flow and less NADPH is produced → prevents over-reduction.

9. RuBisCO & CO₂ fixation

• Enzyme that starts Calvin cycle.

• Adds CO₂ to RuBP (5C) → unstable 6C → splits to 3-PGA.

• Carbon fixation = incorporating inorganic CO₂ into organic molecules.

10. Role of ATP & NADPH in Calvin cycle

Calvin cycle (in stroma) has 3 phases:

1. Carbon fixation (RuBisCO + CO₂ + RuBP).

2. Reduction:

   • ATP phosphorylates 3-PGA.

   • NADPH reduces it → G3P (a 3-carbon sugar).

3. Regeneration of RuBP:

   • ATP used to rearrange G3P → RuBP.

So:

• ATP provides energy.

• NADPH provides electrons (reducing power).

11. Photorespiration

• Happens when RuBisCO binds O₂ instead of CO₂ (hot, dry conditions when stomata close).

• RuBP + O₂ → one 3-PGA + one 2-carbon molecule that must be recycled.

• Consequences:

  • Uses ATP.

  • Releases CO₂.

  • No sugar made.

  • Decreases efficiency of photosynthesis.

12. C₄ and CAM plants (photorespiration adaptations)

C₄ Plants (corn, sugarcane)

• Spatial separation of steps.

• CO₂ initially fixed in mesophyll cells by PEP carboxylase (doesn’t bind O₂).

• Forms 4C compound → moved to bundle-sheath cells → releases CO₂ for Calvin cycle.

• Keeps CO₂ high around RuBisCO → reduces photorespiration.

CAM Plants (cacti, succulents)

• Temporal separation of steps.

• Night: stomata open, CO₂ fixed into organic acids.

• Day: stomata close, CO₂ released from acids for Calvin cycle.

• Saves water, reduces photorespiration.

13. Structural components of chloroplasts per step

• Thylakoid membrane:

  • PSII, PSI, ETC, ATP synthase, NADP⁺ reductase

  • Light-dependent reactions

• Thylakoid lumen:

  • H⁺ accumulation for gradient

• Stroma:

  • Calvin cycle, RuBisCO

  • Where ATP & NADPH are used and sugars produced

14. Factors affecting rate of photosynthesis

• Light intensity (increases → rate rises then plateaus)

• CO₂ concentration (more CO₂ → faster until enzymes max out)

• Temperature (enzyme activity; too hot → RuBisCO and others denature)

• Water (needed for PSII; drought closes stomata → less CO₂ → more photorespiration)