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Which amino acids are classified as nonpolar (hydrophobic)?
Answer: Glycine (G), Alanine (A), Valine (V), Leucine (L), Isoleucine (I), Proline (P), Phenylalanine (F), Methionine (M), Tryptophan (W).
Nonpolar side chains tend to cluster in the hydrophobic core of folded proteins, away from water.
Which amino acids are polar but uncharged?
Answer: Serine (S), Threonine (T), Cysteine (C), Tyrosine (Y), Asparagine (N), Glutamine (Q).
These side chains contain -OH, -SH, or amide groups that can hydrogen bond but do not fully ionize at physiological pH.
Which amino acids are acidic (negatively charged at physiological pH)?
Answer: Aspartate (D) and Glutamate (E).
Their carboxylic acid side chains deprotonate at pH 7.4, giving a net negative charge.
Which amino acids are basic (positively charged at physiological pH)?
Answer: Lysine (K), Arginine (R), Histidine (H).
Lysine's amine and arginine's guanidinium group are fully protonated at pH 7.4; histidine's imidazole is only partially protonated.
What is the isoelectric point (pI) of an amino acid?
Answer: The pH at which the amino acid carries zero net charge, existing as a zwitterion.
How does pI differ among neutral, acidic, and basic amino acids?
Answer: Acidic amino acids: low pI (~3). Neutral amino acids: pI ~5.5–6.3. Basic amino acids: high pI (~9.5–10.8).
More acidic side chains lower the pI; more basic side chains raise it.
Why is proline called a "structure breaker"?
Answer: Its side chain cyclizes back to the backbone nitrogen, creating a rigid ring with no amide H for hydrogen bonding, disrupting alpha helices and beta sheets.
What special structural role does cysteine play?
Answer: Its thiol (-SH) side chain can oxidize to form a disulfide bond (S-S) with another cysteine, stabilizing tertiary and quaternary structure.
Why is glycine structurally unique?
Answer: Its side chain is a single hydrogen, making it the smallest and most conformationally flexible residue, often found at tight turns.
Why is histidine a good physiological buffer?
Answer: Its imidazole side chain has a pKa near 6, close to physiological pH, letting it act as a proton donor/acceptor (e.g., in hemoglobin and enzyme active sites).
What is primary protein structure?
Answer: The linear sequence of amino acids joined by peptide bonds.
What is secondary protein structure?
Answer: Local folding patterns—alpha helices and beta sheets—stabilized by hydrogen bonds between backbone carbonyl and amide groups.
What is tertiary protein structure?
Answer: The overall 3D shape of a single polypeptide, stabilized by side-chain interactions: hydrophobic packing, ionic bonds, hydrogen bonds, and disulfide bonds.
What is quaternary protein structure?
Answer: The assembly of multiple polypeptide subunits into one functional protein complex (e.g., hemoglobin's four subunits).
Write the Michaelis-Menten equation.
Answer: v = (Vmax × [S]) / (Km + [S])
v = initial reaction velocity, [S] = substrate concentration, Vmax = maximum velocity at saturating substrate, Km = Michaelis constant (substrate concentration at half Vmax).
What does Km represent?
Answer: The substrate concentration at which reaction velocity equals half of Vmax; inversely related to enzyme-substrate affinity.
A low Km means high affinity (enzyme reaches half-max velocity at low [S]).
What does Vmax represent?
Answer: The maximum reaction velocity when the enzyme is fully saturated with substrate; proportional to total enzyme concentration.
What shape is a plot of velocity (v) vs substrate concentration [S] for a Michaelis-Menten enzyme?
Answer: A hyperbolic curve that rises steeply then plateaus, asymptotically approaching Vmax.
Example: with Km=10 and Vmax=100, v=50 when [S]=10, v=80 when [S]=40, approaching 100 at very high [S].
What is a Lineweaver-Burk plot and its equation?
Answer: 1/v = (Km/Vmax)(1/[S]) + 1/Vmax
v=velocity, [S]=substrate concentration, Km=Michaelis constant, Vmax=maximum velocity. Plotting 1/v vs 1/[S] linearizes the Michaelis-Menten equation.
In a Lineweaver-Burk plot, what do the x-intercept, y-intercept, and slope represent?
Answer: x-intercept = -1/Km; y-intercept = 1/Vmax; slope = Km/Vmax.
Example: if Km=10 and Vmax=100, x-intercept=-0.1, y-intercept=0.01, slope=0.1.
How does competitive inhibition affect Km and Vmax?
Answer: Apparent Km increases (lower apparent affinity); Vmax is unchanged because excess substrate can outcompete the inhibitor.
Competitive inhibitors bind the active site and compete directly with substrate.
How does noncompetitive inhibition affect Km and Vmax?
Answer: Km is unchanged; Vmax decreases because the inhibitor binds an allosteric site regardless of substrate binding.
How does uncompetitive inhibition affect Km and Vmax?
Answer: Both Km and Vmax decrease because the inhibitor binds only the enzyme-substrate complex, trapping it.
How do the three classic inhibition types shift the Lineweaver-Burk plot relative to no inhibitor?
Answer: Competitive: same y-intercept (Vmax unchanged), steeper slope, x-intercept closer to zero (higher Km). Noncompetitive: same x-intercept (Km unchanged), higher y-intercept (lower Vmax). Uncompetitive: parallel line shifted up and left (Km and Vmax both decrease).
What is cooperativity in ligand binding?
Answer: Binding of a ligand at one site increases (positive cooperativity) or decreases (negative cooperativity) affinity at other sites on a multi-subunit protein.
Classic example: oxygen binding to hemoglobin shows positive cooperativity.
How does a cooperative binding curve differ from a Michaelis-Menten curve?
Answer: Cooperative binding produces a sigmoidal (S-shaped) curve, while non-cooperative Michaelis-Menten kinetics produce a hyperbolic curve.
The sigmoidal shape reflects low affinity at low ligand concentration that rises sharply as binding at other sites increases affinity.
What is the rate-limiting enzyme of glycolysis?
Answer: Phosphofructokinase-1 (PFK-1), which converts fructose-6-phosphate to fructose-1,6-bisphosphate.
What regulates PFK-1 activity?
Answer: Activated by AMP and fructose-2,6-bisphosphate; inhibited by ATP and citrate.
These signals reflect the cell's energy charge: high ATP/citrate signal abundant energy and shut glycolysis down.
What is the rate-limiting enzyme of gluconeogenesis?
Answer: Fructose-1,6-bisphosphatase, which converts fructose-1,6-bisphosphate back to fructose-6-phosphate.
It is reciprocally regulated with PFK-1 (inhibited by AMP, activated by citrate).
What is the rate-limiting enzyme of the citric acid cycle?
Answer: Isocitrate dehydrogenase, which converts isocitrate to alpha-ketoglutarate, producing NADH and CO2.
Activated by ADP/Ca2+, inhibited by ATP and NADH.
What is the rate-limiting enzyme of fatty acid synthesis?
Answer: Acetyl-CoA carboxylase, which converts acetyl-CoA to malonyl-CoA.
Activated by citrate and insulin; inhibited by palmitoyl-CoA and glucagon/epinephrine (via phosphorylation).
What is the approximate net ATP yield per glucose via aerobic respiration?
Answer: ~30–32 ATP (older estimates cite 36–38), the difference reflecting the cost of shuttling cytosolic NADH into mitochondria.
How much net ATP does glycolysis produce directly?
Answer: 2 net ATP (4 produced minus 2 invested) plus 2 NADH per glucose.
How much ATP/GTP does the citric acid cycle produce directly per glucose?
Answer: 2 GTP/ATP total (1 per acetyl-CoA, 2 acetyl-CoA per glucose), plus 6 NADH and 2 FADH2.
How many ATP equivalents does one NADH vs one FADH2 yield via oxidative phosphorylation?
Answer: NADH ≈ 2.5 ATP; FADH2 ≈ 1.5 ATP.
FADH2 enters the chain at Complex II, bypassing Complex I, so it yields fewer protons pumped and less ATP.
What does Complex I of the electron transport chain do?
Answer: NADH dehydrogenase: oxidizes NADH to NAD+, passes electrons to ubiquinone (CoQ), and pumps H+ into the intermembrane space.
What does Complex II of the electron transport chain do?
Answer: Succinate dehydrogenase: oxidizes FADH2 (from succinate→fumarate in the citric acid cycle) and passes electrons to ubiquinone; does not pump protons.
What does Complex III of the electron transport chain do?
Answer: Cytochrome bc1 complex: transfers electrons from ubiquinol to cytochrome c and pumps protons into the intermembrane space via the Q cycle.
What does Complex IV of the electron transport chain do?
Answer: Cytochrome c oxidase: transfers electrons from cytochrome c to O2, forming H2O, while pumping protons.
What does Complex V (ATP synthase) do?
Answer: Uses the proton-motive force generated by Complexes I, III, and IV to phosphorylate ADP to ATP as protons flow back into the mitochondrial matrix.
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