b. The number of ATP produced by oxidative phosphorylation would be reduced,
      although not to 0. Since some H⁺ would move into the matrix through UCP1 rather than
      through ATP synthase, fewer ATP would be made, but how many fewer is unknown.    

2. a. The a subunit has two half channels, one open to the P side and the other open to the N
    side of the inner membrane. The 10-12 c subunits form a rotating ring; each c subunit
    has an Asp side chain that can enter the half channels of the a subunit. When the Asp⁻
    enters the P side half channel, it can accept H⁺ and become Asp⁰, which can rotate into
    the neutral membrane. Rotation eventually causes it to enter the N side half channel,
    where it donates the H⁺.

     b. F₁ has three β subunits, each with an active site. At any one time, the three subunits have
    three different conformations: L conformation binds ADP and P_i, T conformation forms
    ATP and binds it tightly, and O conformation releases ATP.

     c. Rotation of the c ring causes the conformation changes in the β subunits.

3.

b. Substrates and products are not shown, as that information is readily available.
c. Citrate synthase always adds AcCoA to the same face of oxaloacetate (creates a pro-chiral molecule). The reaction is irreversivle, and this is the only condensation reaction.
Aconitase is an isomerase that always attacks the bond that had been part of oxaloacetate. The reaction is reversible and includes removing and adding a water molecule.
Succinyl-CoA synthetase is a ligase that catalyzes a reversible substrate phosphorylation reaction. The enzyme has a His side chain in the active site that can accept a phosphoryl group and then transfer it to GDP, making GTP.

4. a. Phosphorylase kinase b + ATP → phosphorylase kinase a – P + ADP.
    Phosphorylase kinase b is less active (T conformation), and becomes more active (R conformation stabilized) as a result of the reaction.
    Glycogen synthase a + ATP → glycogen synthase b – P + ADP.
    Glycogen synthase a is more active (R conformation) and becomes less active (T conformation stabilized) as a result of the reaction.
     b. Phosphorylase kinase:
     glycogen phosphorylase b + (2) ATP → glycogen phosphorylase a – (P)₂ + (2) ADP.
    You didn't need to have the 2 for credit.
     Glycogen synthase: glycogen_n + UDP-glucose → glycogen_(n+1) + UDP
     c. PKA indirectly increases glycogen degradation and decreases glycogen synthesis by
catalyzing these two reactions.

5. a. Asp-Glu, because their side chains bracket pH 4.0 .
    b. Since the Glu α-COOH has a pK_a that is closer (slightly) to 4, it is a little bit better to
          have the sequence be Asp-Glu rather than Glu-Asp.
    c.

6. a. ΔG°′ = − R T ln K_eq, so ln K_eq= − ΔG°′/RT = 29,700 J/mol/(8.315 J/mol-K)(298 K)
         ln K_eq= 11.9875                         K_eq= 160,000
     b. The reaction in the matrix is malate + NAD⁺ ↔ oxaloacetate + NADH + H⁺ .
    As long as the concentrations of malate and NAD⁺ are significantly greater than the
    concentrations of NADH and oxaloacetate, the reaction can still occur.
     Remember, ΔG = ΔG°′ + R T ln ([products]/[reactants]).
      In addition, the next reaction (citrate synthase) is very favorable. Since ΔG is additive,
      adding a large negative ΔG to the positive ΔG can still result in a negative ΔG.

7. a. The receptor causes a conformation change that results in release of GDP and separation
    from Gβγ.
     b. Gα activates AC (adenylyl cyclase) by binding it.
     c. Gα is active while it has GTP in its active site, but once Gα converts GTP to GDP, Gα is no longer active.

Answers to multiple choice questions:

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