BIOL 111 Chapter 9

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Review

See BIOL 111 Chapter 8#Vocabulary

• $\Delta G$ is Gibbs Free Energy
• Exergonic is spontaneous ($-\Delta G$)
• Endergonic is NOT spontaneous ($+\Delta G$)
• Anabolic metabolism creates molecular structure, catabolic metabolism breaks things down. (cats are destructive)
• Metabolic disequilibrium mandates that there will always be reactants for other reactions
• Energy Coupling or phosphorylation makes an endergonic reaction into an exergonic reaction
• Redox Reactions: 6O₂ + C₆H₁₂O₆ → 6CO₂ + 6H₂O (OIL RIG)
  • Glucose becomes oxidized (loses electrons when bound to electronegative O atoms) into CO₂
  • Oxygen becomes reduced (gains electrons from other atoms) by binding with hydrogen and carbon

Catabolic Pathways: Obtaining Energy from Redox Reactions

1. Organic "fuels" are broken down in steps
2. Electrons stripped in each stage
3. Result is a systematic, controlled release of energy in form of ATP via phosphorylation
   1. Substrate level - Enzymes transfer energy directly to ADP
   2. Oxidative - uses O₂ as an electron acceptor

NAD+/NADH: Systematic removal of electrons

Dehydrogenase ("enzyme that removes hydrogen") removes pairs of hydrogen atoms:

2H⁺ + 2e^–

NAD+ acts as a coenzyme and e^– acceptor:

NAD⁺ + 2[H] →reduced→ NADH + H⁺ + 1/2O₂ →oxidized→ NAD⁺ + H₂O

NAD+ becomes reduced to NADH (gains electrons)

ΔG_NADH = -52.6 kcal/mol

In theory: -52.6/-7.3 = 7.205479452054795 mol ATP from 1 mol NADH

In reality: = 3 ATP because energy is lost to heat

Summary

• Many small steps trap electrons
• Electrons transferred to O₂ by electron transport
• Energy captured in process

Cellular Respiration

1. Break down "fuel" into monomers (fuel can be anything: proteins [amino acids], carbohydrates, fats [glycerol and fatty acids])
2. Glycolysis breaks glucose into 2 pyruvate (C₃H₆O₃)
   • forms NADH and ATP
   • occurs in cytosol
3. Citric Acid Cycle converts pyruvate into CO₂
   • forms NADH, ATP, FADH₂
   • occurs in Mitochondrial Matrix
4. Oxidative Phosphorylation (electron transport chain)
   • Takes electrons from NADH and FADH₂
   • forms O₂→H₂O and lots of ATP
   • occurs in inner membrane of mitochondria

Glycolysis

1. Energy Investment: 2 ATP used
2. Energy Payoff: 4 ATP + 2 NADH

Result is 2 Pyruvate + 2 H₂O

Net Gain: 2 ATP, 2 NADH, 2 Pyruvate

Detailed view (Figure 9.9)

kinase transfers phosphate groups: (bolded items are all that I need to know)

1. Glucose + ATP + Hexokinase → Glucose-6-phosphate + ADP
2. ...
3. Fructose-6-phosphate + ATP + Phophofructokinase → Fructose-1, 6-biphosphate + ADP
4. Fructose-1, 6-biphosphate + Aldolase → DHAP + G3P
5. G3P is used directly, and [DHAP + Isomerase → G3P] happens due to metabolic disequilibrium; ∴ ⇒ 2 G3P net product
6. 2 G3P + 2 NAD+ + Triose phosphate dehydrogenase → 2 × (1, 3-bisphosphoglycerate) + 2 NADH
7. 2 (1, 3-bisphosphoglycerate) + 2 ADP + Phosphoglycerokinase → 2 3-Phosphoglycerate + 2 ATP
8. ...
9. 2 Phosphoenolpyruvate + 2 ADP + Pyruvate kinase → 2 Pyruvate + 2 ATP

Know the following

• Enzymes: Dehydrogenase, Kinase, and Isomerase
• Substrates: Glucose, DHAP, G3P, Pyruvate

NADH is transported into Mitochondrion straight as NADH or as FADH₂

If Oxygen is present, then Pyruvate also goes into Mitochondrion. Otherwise, fermentation occurs (ethanol or lactate)

Junction Reaction

Figure 9.10 Conversion of pyruvate into acetyl CoA, the junction between glycolysis and the citric acid cycle.

1. 3-Carbon Pyruvate loses a carbon to CO₂, leaving 2-Carbon Acetate (Pyruvate + O₂ → Acetate + CO₂)
2. A NADH molecule is generated from 2e^– in acetate
3. Coenzyme A (CoA) forms unstable bond to acetate, forming Acetyl CoA

Citric Acid Cycle

Figure 9.12 The citric acid cycle

(Also called Tricarboxylic Acid Cycle and Kreb's Cycle)

• It's a cycle: Starting molecule eventually becomes ending molecule
• Follow the carbons and where they're going
• Where is the energy payoff?
• This occurs for each Pyruvate (2 times for every 1 molecule of glucose)

Addition Phase

2-carbon Acetyl CoA bonds with 4-carbon Oxaloacetate to form 6-carbon Citrate

Acetyl CoA + Oxaloacetate → Citrate + CoA

Removal Phase

Two COO^– groups are lost to 2 CO₂ and 2 NADH

Now at 4 carbons

Regeneration Phase

CoA is added temporarily to generate a GTP, which transfers its P_i to an ATP molecule, then CoA is removed

FADH₂ carries away two more Hydrogen atoms ∴ 2e^– from 4-carbon structure

One more NADH gained as water is added to convert 4-carbon structure back into oxaloacetate

What I Need to Know

1 Acetyl CoA ⇒ 3 NADH + 1 FADH₂ + 1 ATP + 2 CO₂

6O₂ + C₆H₁₂O₆ → 6CO₂ + 6H₂O + Energy

We've currently accounted for the entire C6H12O6 molecule, the 6CO2, a little energy, and a little water

The rest of the energy is generated in the next step...

Oxidative Phosphorylation

Figure 9.16 Oxidative Phosphorylation

Figure 9.13 Free energy change during electron transport

Figure 9.14 ATP synthase, a molecular mill

Electron transport chain

• Located in/on the inner mitochondrial membrane
• Composed of 4 multiprotein complexes with cofactors Fe-S complex OR heme (Fe) groups; the irons in the proteins help move the electrons along
• e^– transferred to cofactors by series of redox reactions (don't need to know them)
• O₂ is the final acceptor of the electrons → H₂O

ΔG NADH ≈ –53 kcal/mol; ΔG FADH₂ ≈ –40 kcal/mol;

Many poisons target the proteins used during this phase.

Chemiosmosis

• H⁺ from matrix is pumped into area between membranes
• Proteins and energy from electron transport chain provides active transport for H⁺
• Creates a lot of potential energy: H⁺ ions want to flow down concentration gradient back into matrix
• ATP Synthase ("turbine") captures energy from H⁺ movement and generates ATP

ATP Synthase

• Powered by H⁺ gradient
• Proteins: Stator (channel), rotor, rod, knob
• H⁺ flows through stator and rotor, which turns the rod, which activates catalytic sites on knob, which forms ATP

Summary of Respiration

Given yields

NADH = 3 ATP

FADH₂ = 2 ATP

Glycolysis

–2 ATP invested + 4 ATP = 2 ATP (substrate)

2 NADH × 3 ATP/NADH = 6 ATP (oxidative)

Junction Reaction

2 Pyruvate × 1 NADH × 3 ATP/NADH = 6 ATP (oxidative)

Citric Acid Cycle

2 Pyruvate × 1 ATP = 2 ATP (substrate)

2 Pyruvate × 3 NADH × 3 ATP/NADH = 18 ATP (oxidative)

2 Pyruvate × 1 FADH₂ × 2 ATP/FADH₂ = 4 ATP (oxidative)

TOTAL = 38 ATP from 1 Glucose (or 36 ATP if NADH produced in Glycolysis is actually FADH₂)

40% efficiency Recall that ΔG Glucose ≈ –686 kcal/mol