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1A. Structure and Function of Proteins and Their Constituent Amino Acids

Twenty side chains, four levels of folding, and the kinetic curves the MCAT keeps drawing: enzymes, inhibitors, and hemoglobin's sigmoid.

21 topics · 87 questions

Each topic is a path, not a menu: work down it in order and every question builds on the one above. Click any of them to watch the answer draw itself.

1A. Amino Acid Structure and Absolute Configuration

  1. How it worksHow does the alpha carbon end up with four different groups and a handedness you can see?
  2. Worked exampleFind whether L-alanine is R or S by ranking the four groups around its alpha carbon.
  3. Common mistakeWhy isn't every L amino acid automatically S in the R and S naming system?
  4. Going furtherWhat makes glycine the one amino acid with no handedness at all?
Your turneasy1 of 3
A linear peptide is built from 8 amino acid residues. Every residue has one chiral alpha carbon and no chiral atom anywhere in its side chain. How many stereoisomers of this peptide are possible?

1A. Classification of the Twenty Side Chains

  1. How it worksHow does a side chain's polarity decide whether it faces water or hides in the protein's core?
  2. How it worksWalk me through which side chains carry a charge at pH 7 and which only get one when pH moves.
  3. Worked exampleFind which of valine, glutamate, lysine and serine sits buried in a folded protein's greasy core.
  4. Common mistakeWhy isn't histidine simply a basic amino acid the way lysine and arginine are?
Your turnmedium1 of 3
A protein contains 15 lysine, 11 arginine, 21 aspartate and 8 glutamate residues; every other residue in it has an uncharged side chain. Ignoring the two termini, what is the net charge on this protein at pH 7.4?

1A. Amino Acids as Dipolar Ions: pKa and Titration

  1. How it worksHow does a titration curve of glycine grow two flat shelves with one steep jump between them?
  2. How it worksWalk me through which group gives up its proton first as you titrate an amino acid from pH 1 upward.
  3. Common mistakeWhy isn't an amino acid uncharged at pH 7 just because the pH happens to be neutral?
  4. Going furtherWhat happens to the titration curve when the side chain itself can be protonated, as in glutamate?
  5. Worked exampleFind the net charge on lysine at pH 9.7 given pKa values of 2.2, 9.0 and 10.5.
Your turnhard1 of 3
Glutamate has pKa values of 2.2 for its alpha-carboxyl group, 4.3 for its side-chain carboxyl group and 9.7 for its alpha-amino group. What is the net charge on a glutamate molecule at pH 9?

1A. The Isoelectric Point and Protein Electrophoresis

  1. How it worksHow does averaging two pKa values land you on the pH where net charge comes out zero?
  2. Worked exampleFind the isoelectric point of glutamate from pKa values of 2.2, 4.3 and 9.7.
  3. Worked exampleFind which electrode lysine travels toward in a gel buffered at pH 7 when its pI is 9.7.
  4. Common mistakeWhy isn't the isoelectric point simply the average of every pKa in the molecule?
  5. Going furtherWhat changes about a protein's migration when the gel is run in SDS instead of a plain buffer?
Your turneasy1 of 3
An amino acid with an uncharged side chain has an alpha-carboxyl pKa of 2.47 and an alpha-amino pKa of 9.77. What is its isoelectric point?

1A. The Peptide Bond and Primary Structure

  1. How it worksHow does resonance give the peptide bond partial double-bond character and lock six atoms flat?
  2. Worked exampleDraw the tripeptide Ala-Gly-Ser and mark its two peptide bonds and both charged ends.
  3. Going furtherWhat happens to a polypeptide boiled in 6 molar hydrochloric acid for a full day?
  4. Common mistakeWhy isn't a protein sequence written from whichever end you happen to start reading?
Your turneasy1 of 3
A linear polypeptide is 178 residues long. How many peptide bonds does it contain?

1A. Cysteine, Cystine and the Disulfide Bond

  1. How it worksHow do two cysteine thiols lose their hydrogens and become a single covalent cystine bridge?
  2. How it worksWalk me through why disulfides show up in secreted proteins but almost never inside the cytosol.
  3. Going furtherWhat happens to a folded protein the moment a reducing agent snaps every disulfide it has?
Your turneasy1 of 3
A secreted protein contains 22 cysteine residues in total, 5 of which are paired into intramolecular disulfide bonds - that is, it contains 5 disulfide bridges. How many free thiol groups remain?

1A. Secondary Structure: the Alpha Helix and the Beta Sheet

  1. How it worksHow do backbone hydrogen bonds four residues apart build one turn of an alpha helix?
  2. How it worksWalk me through how parallel and antiparallel beta sheets line their strands up differently.
  3. Worked exampleFind how long a 36-residue alpha helix is at 3.6 residues and 5.4 angstroms per turn.
  4. Going furtherWhat happens to a helix when a proline turns up in the middle of it?
  5. Common mistakeWhy isn't secondary structure held together by the side chains?
Your turneasy1 of 3
An alpha helix contains 47 residues. At 3.6 residues per turn and a rise of 5.4 angstroms per turn, how long is the helix along its axis?

1A. Tertiary Structure and the Hydrophobic Core

  1. How it worksHow do nonpolar side chains get pushed together by water rather than pulled together by each other?
  2. Common mistakeWhy isn't the hydrophobic effect an attraction between the oily side chains themselves?
  3. Worked exampleFind which substitution wrecks a protein core more: valine to isoleucine or valine to aspartate.
  4. Going furtherWhat changes about tertiary structure when a protein folds inside a lipid membrane instead of water?
Your turnhard1 of 3
Folding a 236-residue protein buries its nonpolar side chains and is accompanied by an increase in the total entropy of the system. Where does that entropy increase come from?

1A. Quaternary Structure and Subunit Assembly

  1. How it worksHow do separate folded subunits lock together using the same forces that made each one fold?
  2. Worked exampleFind the subunit composition of adult hemoglobin and count the heme groups it carries.
  3. Ties togetherHow does having four subunits make cooperative oxygen binding possible in the first place?
Your turneasy1 of 3
A sample contains 29 molecules of adult hemoglobin, every one of them fully saturated with oxygen. How many oxygen molecules are bound in the sample in total?

1A. Conformational Stability, Denaturation and Chaperones

  1. How it worksHow do heat, urea and extreme pH each unfold a protein by attacking a different force?
  2. Common mistakeWhy doesn't denaturation break a single peptide bond in the chain?
  3. Common mistakeWhy isn't folding a search through every possible shape until the best one turns up?
  4. Going furtherWhat happens inside a chaperone barrel that a crowded cytosol would never allow outside it?
Your turnmedium1 of 3
Levinthal's estimate: a chain of 16 residues in which each residue can adopt 3 backbone conformations has how many possible conformations in total?

1A. Nonenzymatic Protein Function: Binding, Immune, Motor and Structural

  1. How it worksHow does an antibody's Y shape let two identical arms grab the same antigen twice?
  2. How it worksWalk me through how myosin walks along actin by gripping, pulling and letting go.
  3. Common mistakeWhy isn't a binding protein just an enzyme that forgot to do any chemistry?
  4. Worked exampleFind how far a kinesin motor travels along a microtubule in 50 steps of 8 nanometers.
  5. Ties togetherHow does collagen's triple helix turn the same folding rules into a rope instead of a globule?
Your turneasy1 of 3
A kinesin motor takes 91 steps along a microtubule, each step advancing it 8 nanometers. How far does it travel?

1A. Hemoglobin and the Cooperative Binding Curve

  1. How it worksHow does one oxygen landing on one subunit make the other three easier to fill?
  2. Worked exampleFind how much oxygen hemoglobin unloads going from 100 torr in the lung to 25 torr in muscle.
  3. Common mistakeWhy isn't the sigmoid shape caused simply by hemoglobin holding four oxygens instead of one?
  4. Going furtherWhat happens to the curve when hemoglobin is locked permanently in its high-affinity R state?
  5. Ties togetherHow does cooperative oxygen binding follow the same logic as an allosteric enzyme's kinetics?
Your turnmedium1 of 3
Hemoglobin leaves the lungs 96 percent saturated with oxygen and returns from an exercising muscle bed 58 percent saturated. On average, how many oxygen molecules does each hemoglobin tetramer deliver on one pass?

1A. The Bohr Effect and 2,3-BPG

  1. How it worksHow do rising carbon dioxide and falling pH slide the whole oxygen curve to the right?
  2. Going furtherWhat happens to the curve at altitude when red cells crank out extra 2,3-BPG?
  3. Common mistakeWhy doesn't a right shift mean hemoglobin picks up less oxygen in the lungs?
  4. Worked exampleFind how P50 moves when blood pH drops from 7.4 to 7.2 in an exercising muscle bed.
Your turnmedium1 of 3
In a hard-working muscle bed the hydrogen ion concentration of the capillary blood rises by a factor of 3.59. By how many units does the pH fall?

1A. What Enzymes Do: Lowering Activation Energy and the Six Classes

  1. How it worksHow does stabilizing the transition state lower the hill a reaction has to climb?
  2. Going furtherWhat happens to the reverse reaction's rate when an enzyme lowers the forward activation energy?
  3. Worked exampleFind which of the six enzyme classes moves a phosphate from ATP onto glucose.
  4. Common mistakeWhy doesn't an enzyme change how much product you end up with at equilibrium?
Your turnmedium1 of 3
An uncatalysed reaction has a standard free energy change of -38 kJ per mole. An enzyme is added that lowers the activation energy of the forward step by 30 kJ per mole. What is the standard free energy change of the catalysed reaction, in kJ per mole?

1A. The Active Site, Specificity and the Induced-Fit Model

  1. How it worksHow does an active site reshape itself around a substrate instead of waiting as a rigid keyhole?
  2. Common mistakeWhy isn't the lock-and-key picture good enough to explain how enzymes really work?
  3. Going furtherWhat changes about specificity when an enzyme has a second site far away from the active one?
Your turnhard1 of 3
An enzyme binds its natural substrate with a dissociation constant of 35 micromolar but binds an analogue differing by one methyl group about a thousand times more weakly. What does induced fit add to the lock-and-key picture here?

1A. Cofactors, Coenzymes and Water-Soluble Vitamins

  1. How it worksHow does NAD plus shuttle electrons out of one reaction and into another as a coenzyme?
  2. Worked exampleFind which vitamin is missing when a cell cannot build either NAD plus or FAD.
  3. Going furtherWhat happens to an apoenzyme's activity the instant its cofactor binds and makes a holoenzyme?
Your turneasy1 of 3
A dehydrogenase reduces 22 molecules of NAD plus to NADH. Each reduction transfers a hydride ion, which carries two electrons. How many electrons have been moved onto the coenzyme in total?

1A. Effects of pH and Temperature on Enzyme Activity

  1. How it worksHow does changing pH flip the charge on active-site residues and shut catalysis down?
  2. Going furtherWhat happens to reaction rate as temperature climbs past an enzyme's optimum?
  3. Common mistakeWhy doesn't a faster reaction at 50 degrees C mean the enzyme is happier there?
  4. Ties togetherHow does an enzyme's optimum-pH curve echo the titration curves of its active-site side chains?
Your turnmedium1 of 3
Below its optimum, an enzyme's reaction rate doubles for every 10 degree C rise in temperature. If the rate at 27 degrees C is taken as 1, what is the relative rate at 45 degrees C, assuming the enzyme has not begun to denature?

1A. Michaelis-Menten Kinetics and the Lineweaver-Burk Plot

  1. How it worksHow does the Michaelis-Menten curve rise steeply and then flatten into a hard ceiling?
  2. How it worksWalk me through why flipping both axes turns that curve into a line with readable intercepts.
  3. Worked exampleFind Vmax and Km from a double-reciprocal line with y-intercept 0.02 and x-intercept -0.5.
  4. Common mistakeWhy isn't a low Km the same thing as a fast enzyme?
  5. Ties togetherHow does a sigmoid kinetic curve break the assumption that every active site acts independently?
Your turnmedium1 of 3
An enzyme has Vmax = 69 micromoles per minute and Km = 8 micromolar. What is the initial velocity, in micromoles per minute, at a substrate concentration of 37 micromolar?

1A. The Four Types of Enzyme Inhibition

  1. How it worksHow does a competitive inhibitor raise Km while leaving Vmax exactly where it was?
  2. Common mistakeWhy doesn't piling on more substrate rescue an enzyme from a noncompetitive inhibitor?
  3. Going furtherWhat happens to both Km and Vmax when an inhibitor binds only the enzyme-substrate complex?
  4. Worked exampleFind the inhibition type at work when Vmax falls from 100 to 50 and Km stays at 4.
  5. Ties togetherHow do the four inhibition patterns show up as four different families of double-reciprocal lines?
Your turnhard1 of 3
A competitive inhibitor is present at 14 micromolar and has an inhibition constant Ki of 8 micromolar. The enzyme's true Km is 8 micromolar. What is the apparent Km in the presence of the inhibitor, in micromolar?

1A. Allosteric Enzymes and Feedback Inhibition

  1. How it worksHow does a molecule binding far from the active site change the active site's shape?
  2. Common mistakeWhy isn't feedback inhibition the same thing as competitive inhibition?
  3. Going furtherWhat happens to an allosteric enzyme's sigmoid curve when an activator binds instead of an inhibitor?
  4. Ties togetherHow does the tense-to-relaxed shift in an allosteric enzyme match what goes on inside hemoglobin?
Your turneasy1 of 3
An allosteric activator raises the velocity of a regulated enzyme from 23 to 76 micromoles per minute at a fixed substrate concentration. By what factor has the velocity risen?

1A. Covalent Modification, Phosphorylation and Zymogens

  1. How it worksHow does clipping a short peptide off a zymogen let its active site finally take shape?
  2. Going furtherWhat happens when a single trypsin molecule activates too early inside the pancreas?
  3. Worked exampleFind how one kinase turns a single hormone molecule into millions of activated enzymes.
  4. Ties togetherHow does adding one phosphate flip an enzyme between two states the way an allosteric ligand does?
Your turnmedium1 of 3
One hormone molecule activates one receptor, which activates 45 molecules of a G protein; each G protein activates 45 molecules of adenylate cyclase, and each cyclase activates 45 molecules of protein kinase A. How many kinase molecules does the single hormone molecule end up activating?

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