Bio lectures 7-9, Enzymes, energy metabolism

Good for learning definitions, and getting facts down [does not replace learners manual, theres just a lot of content so this is to help drill it/compile so we arent tryning hard to remember when we do learners manual]

What is an enzyme?

A protein catalyst that speeds up a chemical reaction without being consumed.

What is activation energy?

The energy required to reach the transition state; determines reaction speed.

What does a catalyst do to activation energy?

Lowers activation energy and increases reaction rate.

Does an enzyme change ΔG or the equilibrium constant?

No. It changes the rate, not the overall free energy difference or equilibrium.

What determines reaction direction versus reaction speed?

ΔG determines favored direction; activation energy determines speed.

What is a substrate?

A reactant that binds to an enzyme and is acted upon.

What is the active site?

The region of an enzyme where substrate binding and catalysis occur.

What is the enzyme-substrate (ES) complex?

An enzyme temporarily bound to its substrate.

Why are enzymes specific?

Their binding sites recognize particular substrate structures and chemical groups.

How do enzymes facilitate reactions?

They bring substrates together, orient them, strain bonds, and stabilize transition states.

What is initial velocity (V0)?

The initial rate of product formation: V0 = d[P]/dt = -d[S]/dt.

What is Vmax?

The maximum initial reaction rate at saturating substrate concentration.

What causes the V0 versus [S] curve to plateau?

Enzyme active sites become saturated; adding substrate no longer appreciably increases rate.

What is the Michaelis-Menten mechanism?

E + S ⇌ ES → E + P.

What is the steady-state assumption?

ES concentration remains approximately constant because its formation and breakdown rates balance.

How is steady state different from equilibrium?

Steady state allows net flow through the reaction; equilibrium has no net flow.

What is the Michaelis-Menten equation?

V0 = Vmax[S]/(Km + [S]).

How is Vmax related to k3 and total enzyme concentration?

Vmax = k3[E0].

What is Km in terms of rate constants?

Km = (k2 + k3)/k1.

What does Km tell you on a Michaelis-Menten curve?

Km is the substrate concentration where V0 = Vmax/2.

When does Km approximate the dissociation constant Kd?

When k3 is much smaller than k2; then Km ≈ k2/k1.

What is the turnover number k3?

The maximum number of substrate molecules converted to product per enzyme molecule per unit time.

What happens when [S] is much smaller than Km?

V0 ≈ (Vmax/Km)[S]; rate is approximately proportional to substrate concentration.

What happens when [S] is much larger than Km?

V0 ≈ Vmax; rate becomes nearly independent of substrate concentration.

What happens if total enzyme concentration doubles?

Vmax doubles and V0 doubles at a given [S], while Km stays the same.

What is competitive inhibition?

An inhibitor competes with substrate for binding at the substrate binding site.

How does competitive inhibition affect Km and Vmax?

Apparent Km increases; Vmax stays the same because high [S] can overcome inhibition.

What is noncompetitive inhibition in the lecture example?

An inhibitor prevents catalysis even though the substrate can still bind.

How does noncompetitive inhibition affect the kinetic curve?

Vmax decreases; adding more substrate does not restore the original maximum rate.

What is allosteric inhibition and feedback inhibition?

Allosteric inhibition occurs through binding at another site; feedback inhibition occurs when a pathway end product inhibits an earlier enzyme, usually at the first committed step.

What does ΔG represent?

The free energy change under the actual conditions of a reaction.

What does ΔG < 0 mean?

The forward reaction is thermodynamically favored (exergonic).

What does ΔG > 0 mean?

The forward reaction is unfavorable (endergonic).

What does ΔG = 0 mean?

The reaction is at equilibrium with no net direction.

What is the Gibbs free energy equation?

ΔG = ΔG° + RT ln(Q).

What is Q for A + B ⇌ C + D?

Q = [C][D]/([A][B]) using current concentrations.

What is ΔG°?

Standard free energy change; an intrinsic constant for a reaction under specified standard conditions.

When does ΔG equal ΔG°?

When Q = 1, so RT ln(Q) = 0.

How are ΔG° and Keq related?

ΔG° = -RT ln(Keq).

What is Q at equilibrium?

Q = Keq.

What happens to ΔG° when a reaction is reversed?

Its sign reverses.

What happens to ΔG when product concentration decreases?

Q decreases, making ΔG more negative and favoring forward reaction.

What approximate value of RT is used at room temperature?

RT ≈ 0.6 kcal/mol, using T ≈ 300 K.

What standard H+ concentration is used in biochemistry?

10^-7 M (pH 7), giving the biochemical standard free energy ΔG°'.

What is ATP's role in the cell?

Transfers usable chemical energy to energy-requiring processes.

What is ATP hydrolysis?

ATP + H2O → ADP + Pi.

What is the approximate standard free energy change of ATP hydrolysis in these lectures?

About -7 kcal/mol.

Why is ATP hydrolysis energetically favorable?

Among other factors, hydrolysis relieves electrostatic repulsion between phosphate groups.

What is reaction coupling?

Combining an unfavorable reaction with a favorable reaction so their total ΔG is negative.

How do free energy changes combine in coupled reactions?

Add the individual ΔG values.

What is the directly coupled glucose phosphorylation reaction?

Glucose + ATP → glucose-6-phosphate + ADP.

What is the ΔG° for coupled glucose phosphorylation in lecture?

-3.4 kcal/mol, from -7 + 3.6.

Why is separate ATP hydrolysis insufficient for direct coupling?

Energy released as heat does not automatically drive another reaction; a shared coupled reaction is needed.

How can removing a reaction product drive an unfavorable reaction?

It lowers Q and can make ΔG negative, pulling the reaction forward.

What is glycolysis?

A metabolic pathway converting one glucose into two pyruvate molecules.

What is the net ATP yield of glycolysis per glucose?

2 ATP.

How many ATP are consumed and produced in glycolysis?

2 ATP consumed and 4 ATP produced.

How many NADH are generated in glycolysis per glucose?

2 NADH (called NADH2 in lecture).

What is substrate-level phosphorylation?

Direct ATP formation by transfer of a phosphate group from a metabolic intermediate to ADP.

Why must NADH be reoxidized to NAD+?

Glycolysis requires NAD+ as an electron acceptor; without regeneration glycolysis stops.

What happens during lactate fermentation?

Pyruvate is reduced to lactate while NADH is oxidized back to NAD+.

What happens during alcoholic fermentation in yeast?

Pyruvate is converted to acetaldehyde and CO2; acetaldehyde is reduced to ethanol while NAD+ is regenerated.

Does fermentation itself produce additional ATP beyond glycolysis?

No. Its essential role is NAD+ regeneration, allowing glycolysis to continue.,

What is the overall reaction for complete glucose oxidation?

Glucose + 6 O2 → 6 CO2 + 6 H2O.

What is the approximate ΔG° for complete glucose oxidation?

-686 kcal/mol of glucose.

What happens to pyruvate before entering the Krebs cycle?

Pyruvate is converted to acetyl-CoA, releasing CO2 and producing NADH.

What is the yield of pyruvate oxidation per glucose?

2 acetyl-CoA, 2 NADH, and 2 CO2.

What is acetyl-CoA?

A two-carbon acetyl group attached to coenzyme A through a high-energy thioester linkage.

What are the other names of the Krebs cycle?

Citric acid cycle and tricarboxylic acid (TCA) cycle.

What enters the Krebs cycle?

Acetyl-CoA combines with oxaloacetate to form citrate.

How many carbons are in acetyl-CoA, oxaloacetate, and citrate?

2, 4, and 6 carbons respectively.

What is the function of oxaloacetate in the Krebs cycle?

Accepts the acetyl group and is regenerated at the end of the cycle.

What is the Krebs cycle yield per acetyl-CoA?

3 NADH, 1 FADH2, 1 GTP, and 2 CO2.

What is the Krebs cycle yield per glucose?

6 NADH, 2 FADH2, 2 GTP, and 4 CO2.

What is the relationship between GTP and ATP?

They are energetically equivalent; GTP + ADP ⇌ GDP + ATP.

What is FAD?

Flavin adenine dinucleotide, an electron carrier reduced to FADH2.

At which Krebs cycle step is FADH2 produced?

Succinate → fumarate.

At which Krebs cycle step is oxaloacetate regenerated?

Malate → oxaloacetate, producing NADH.

How many NADH are generated before the ETC per glucose?

10 NADH: 2 from glycolysis, 2 from pyruvate oxidation, and 6 from the Krebs cycle.

How many FADH2 are generated before the ETC per glucose?

2 FADH2 from the Krebs cycle.

What is the main function of the electron transport chain (ETC)?

Transfers electrons to oxygen while pumping H+ across a membrane.

What is the final electron acceptor in aerobic respiration?

Oxygen, which is reduced to water.

Where is the ETC located in mitochondria?

Inner mitochondrial membrane.

Where does the Krebs cycle occur in eukaryotes?

Mitochondrial matrix.

Where does glycolysis occur?

Cytoplasm.

Where is the ETC located in E. coli?

Plasma membrane.

Which ETC complexes pump protons?

Complexes I, III, and IV.

Which ETC complex does FADH2 bypass?

Complex I; its electrons enter through Complex II.

What is the proton motive force?

Electrochemical potential energy from the H+ concentration and electrical gradients across a membrane.

What is chemiosmosis?

Movement of H+ down its electrochemical gradient through ATP synthase to drive ATP production.

What is ATP synthase (F0F1)?

A rotary molecular machine that uses proton flow to synthesize ATP from ADP and Pi.

What is oxidative phosphorylation?

ATP synthesis driven by the proton gradient established through electron transport.

How many ATP are produced per NADH and FADH2 according to the lecture model?

3 ATP per NADH and 2 ATP per FADH2.

What is the total ATP yield per glucose in the lecture's model?

38 ATP in E. coli and 36 ATP in eukaryotes; the lecture subtracts 2 ATP for transfer of glycolytic reducing equivalents.

How can fats enter energy metabolism?

Glycerol can enter glycolysis through DHAP; fatty acids are oxidized to produce acetyl-CoA and reduced electron carriers.