MCAT Organic Chemistry Syllabus

What are the four levels of protein structure?

Primary: linear amino acid sequence (peptide bonds). Secondary: local folding into $\alpha$-helices and $\beta$-pleated sheets (H-bonds in backbone). Tertiary: overall 3D shape of one polypeptide (R-group interactions). Quaternary: assembly of multiple subunits.

Which interactions stabilize tertiary protein structure?

Hydrophobic interactions (core), hydrogen bonds, ionic (salt) bridges, disulfide bonds ($\ce{-S-S-}$ between cysteines), and van der Waals forces among side chains.

How do enzymes accelerate reactions in thermodynamic terms?

Enzymes lower the activation energy $E_a$ of a reaction by stabilizing the transition state. They do NOT change $\Delta G$ of the overall reaction or the equilibrium position; they only speed the approach to equilibrium.

Contrast the lock-and-key and induced-fit models of enzyme action.

Lock-and-key: the active site is a rigid, pre-formed complement to the substrate. Induced fit: substrate binding causes a conformational change in the enzyme that molds the active site around the substrate for optimal catalysis.

State the Michaelis-Menten equation and define each term.

$$v_0 = \frac{V_{max}[S]}{K_M + [S]}$$ where $v_0$ is initial velocity, $V_{max}$ the maximum rate, $[S]$ substrate concentration, and $K_M$ the Michaelis constant (the $[S]$ at which $v_0 = \tfrac{1}{2}V_{max}$).

What does $K_M$ indicate about enzyme-substrate affinity?

$K_M$ equals the substrate concentration at half $V_{max}$. A low $K_M$ indicates high affinity (enzyme reaches half-max at low $[S]$); a high $K_M$ indicates low affinity.

Write the Lineweaver-Burk (double-reciprocal) equation and state what its intercepts give.

$$\frac{1}{v_0} = \frac{K_M}{V_{max}}\cdot\frac{1}{[S]} + \frac{1}{V_{max}}$$ The y-intercept $= \frac{1}{V_{max}}$, the x-intercept $= -\frac{1}{K_M}$, and the slope $= \frac{K_M}{V_{max}}$.

Define $k_{cat}$ and the catalytic efficiency of an enzyme.

$k_{cat}$ (turnover number) is the maximum number of substrate molecules converted per active site per unit time: $k_{cat} = \frac{V_{max}}{[E]_T}$. Catalytic efficiency is $\frac{k_{cat}}{K_M}$, with a diffusion limit near $10^{8}$–$10^{9}\ \text{M}^{-1}\text{s}^{-1}$.

How does a competitive inhibitor affect $K_M$ and $V_{max}$?

A competitive inhibitor binds the active site and competes with substrate. It increases apparent $K_M$ but leaves $V_{max}$ unchanged, because high $[S]$ can outcompete the inhibitor.

How does a pure noncompetitive inhibitor affect $K_M$ and $V_{max}$?

A noncompetitive inhibitor binds an allosteric site on free enzyme or enzyme-substrate complex equally. It decreases $V_{max}$ but leaves $K_M$ unchanged.

How does an uncompetitive inhibitor affect $K_M$ and $V_{max}$?

An uncompetitive inhibitor binds only the enzyme-substrate complex. It decreases both $K_M$ and $V_{max}$, keeping their ratio $\frac{V_{max}}{K_M}$ roughly constant.

Contrast allosteric regulation with feedback inhibition.

Allosteric regulation: effectors bind sites other than the active site, changing enzyme conformation and activity (activators or inhibitors). Feedback inhibition: the end product of a pathway allosterically inhibits an early (often committed-step) enzyme to prevent overproduction.

Describe how cooperativity produces sigmoidal kinetics.

In multi-subunit allosteric enzymes, binding of substrate to one subunit increases affinity of others (positive cooperativity), giving an S-shaped (sigmoidal) $v_0$ vs $[S]$ curve rather than the hyperbolic Michaelis-Menten curve.

Compare reversible covalent modification and zymogen activation as regulatory mechanisms.

Covalent modification (e.g., phosphorylation by kinases, removal by phosphatases) reversibly toggles activity. Zymogen activation is an irreversible proteolytic cleavage that converts an inactive precursor (e.g., trypsinogen) into an active enzyme.

Distinguish a cofactor from a coenzyme.

A cofactor is any non-protein helper required for enzyme activity; the term includes inorganic metal ions (e.g., $\ce{Zn^{2+}}$, $\ce{Mg^{2+}}$). A coenzyme is a specifically organic cofactor (often vitamin-derived), such as $\ce{NAD+}$ or FAD.

What is the difference between an apoenzyme, a holoenzyme, and a prosthetic group?

An apoenzyme is the inactive protein lacking its cofactor. A holoenzyme is the complete, active enzyme + cofactor. A prosthetic group is a cofactor tightly (often covalently) bound to the enzyme, e.g., heme or FAD.

Which vitamins give rise to $\ce{NAD+}$ and FAD, and what is their role?

$\ce{NAD+}$ derives from niacin (vitamin $\text{B}_3$); FAD derives from riboflavin (vitamin $\text{B}_2$). Both are electron carriers that accept hydrides/electrons during oxidation reactions in metabolism.

State the overall net equation for glycolysis.

$$\ce{Glucose + 2NAD+ + 2ADP + 2P_i -> 2Pyruvate + 2NADH + 2H+ + 2ATP + 2H2O}$$ It occurs in the cytoplasm and does not require oxygen.

What are the two phases of glycolysis and their ATP balance?

Energy-investment phase consumes 2 ATP (phosphorylating glucose and fructose-6-phosphate). Energy-payoff phase produces 4 ATP (substrate-level) and 2 NADH. Net yield: 2 ATP and 2 NADH per glucose.

Which three enzymes catalyze the irreversible, regulated steps of glycolysis?

Hexokinase (glucose $\to$ G6P), phosphofructokinase-1 (PFK-1, F6P $\to$ F1,6BP), and pyruvate kinase (PEP $\to$ pyruvate). PFK-1 is the rate-limiting, committed step.

How is PFK-1 regulated?

PFK-1 is inhibited by high ATP and citrate (energy abundance) and activated by AMP and fructose-2,6-bisphosphate. It is the key control point of glycolysis.

What is the fate of pyruvate under aerobic versus anaerobic conditions?

Aerobic: pyruvate enters the mitochondrion and is oxidatively decarboxylated to acetyl-CoA (pyruvate dehydrogenase), feeding the citric acid cycle. Anaerobic: pyruvate is reduced to lactate (or ethanol in yeast) to regenerate $\ce{NAD+}$ for glycolysis to continue.

Write the reaction catalyzed by the pyruvate dehydrogenase complex.

$$\ce{Pyruvate + NAD+ + CoA-SH -> Acetyl\text{-}CoA + NADH + CO2}$$ It is irreversible and links glycolysis to the citric acid cycle; it requires cofactors including TPP, lipoic acid, FAD, $\ce{NAD+}$, and CoA.

Per turn of the citric acid cycle, how many $\ce{NADH}$, $\ce{FADH2}$, $\ce{GTP}$, and $\ce{CO2}$ are produced?

Per acetyl-CoA (one turn): 3 NADH, 1 $\ce{FADH2}$, 1 GTP (or ATP), and 2 $\ce{CO2}$. Per glucose (two turns), double these values.

Name the regulated enzymes of the citric acid cycle and their common inhibitors.

Citrate synthase, isocitrate dehydrogenase (major control point), and $\alpha$-ketoglutarate dehydrogenase. All are inhibited by high ATP/NADH; isocitrate dehydrogenase is activated by ADP.

What is the approximate current-consensus ATP yield of complete aerobic oxidation of one glucose?

About 30–32 ATP total: roughly 2 (glycolysis) + 2 (citric acid cycle GTP) + ~26–28 from oxidative phosphorylation of the NADH and $\ce{FADH2}$ produced.

What are the modern P/O ratios (ATP yield) for NADH and $\ce{FADH2}$ in oxidative phosphorylation?

Each NADH yields about 2.5 ATP and each $\ce{FADH2}$ about 1.5 ATP, because they enter the electron transport chain at complex I versus complex II, pumping different numbers of protons.

Why does cytoplasmic NADH from glycolysis yield variable ATP?

Cytoplasmic NADH cannot cross the inner mitochondrial membrane directly. Via the malate-aspartate shuttle it delivers electrons to NADH (~2.5 ATP each); via the glycerol-3-phosphate shuttle it delivers to FAD/$\ce{FADH2}$ (~1.5 ATP each), lowering total yield.

Compare the ATP yield and speed of aerobic respiration versus anaerobic fermentation per glucose.

Aerobic respiration yields ~30–32 ATP per glucose but is slower and requires $\ce{O2}$. Anaerobic fermentation yields only 2 net ATP per glucose (substrate-level only) but rapidly regenerates $\ce{NAD+}$, sustaining glycolysis without oxygen.