MCAT Biochemistry — Amino Acids & Proteins flashcards
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The 20 amino acids by code, side-chain class, charge and pKa, then peptide bonds, the four levels of protein structure, denaturation, pI calculations, protein separation and analysis, and hemoglobin versus myoglobin.
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Which standard amino acid is achiral, and what feature of its structure makes it so?Glycine. Its side chain is just a hydrogen atom, so the α-carbon carries two identical substituents and has no stereocenter.Amino Acid Structure
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Which stereochemical family (D or L) do the amino acids found in human proteins belong to?L-amino acids only. D-amino acids do occur in some bacterial cell walls and antibiotics, but ribosomes never incorporate them.Amino Acid Structure
Watch out: D/L is a configurational label inherited from glyceraldehyde, not a statement about which way the molecule rotates plane-polarized light. -
Which three amino acids are the branched-chain amino acids (BCAAs)?Valine (Val, V), leucine (Leu, L) and isoleucine (Ile, I) — all nonpolar and aliphatic, and typically buried in a protein's hydrophobic core.Side-Chain Classes
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What are the approximate pKa values of the α-carboxyl and α-amino groups of a free amino acid?The α-carboxyl group has a pKa of about 2 and the α-amino group about 9 to 10. The electron-withdrawing ammonium group next door makes the carboxyl far more acidic than an ordinary carboxylic acid (pKa about 4.8).Acid-Base & pKa
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How do you calculate the isoelectric point of an amino acid whose side chain does not ionize, such as alanine?Average the two backbone pKa values: pI = (pKa of α-COOH + pKa of α-NH₃⁺)/2, which is about (2.3 + 9.7)/2, so roughly 6. At that pH the molecule is a neutral zwitterion.Isoelectric Point
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What type of reaction forms a peptide bond, and what small molecule is released?A condensation (dehydration) reaction: the carboxyl carbon of one amino acid is joined to the amino nitrogen of the next, releasing one molecule of water. In cells the ribosome's peptidyl transferase, an rRNA, drives it.Peptide Bonds
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Which level of protein structure is defined by the sequence of amino acids, and what bonds hold it together?Primary structure, held together by covalent peptide bonds. It is the only level that survives denaturation, and it ultimately dictates all of the higher levels.Protein Structure
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What is protein denaturation, and which level of structure survives it?The loss of secondary, tertiary and quaternary structure, and with it function, without breaking peptide bonds, so the primary structure stays intact. Causes include heat, pH extremes, urea, detergents and organic solvents.Denaturation & Folding
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In SDS-PAGE, what single property determines how far a protein migrates, and why?Molecular mass alone. SDS gives every chain the same charge-to-mass ratio and the same rod-like shape, so the only remaining difference is how easily each chain threads through the gel: smaller proteins travel farther toward the positive electrode.Separation & Analysis
Watch out: native PAGE keeps proteins folded and separates by size, shape and intrinsic charge together. -
How do the oxygen-binding curves of myoglobin and hemoglobin differ in shape, and what explains the difference?Myoglobin's curve is hyperbolic: its single heme binds oxygen independently with high affinity. Hemoglobin's is sigmoidal because its four subunits bind cooperatively; the first oxygen binds weakly, and each binding event raises the affinity of the remaining sites.Hemoglobin & Myoglobin
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Review status: Second-reader reviewed, with corrections applied.
Checked against:
- OpenStax Biology 2e and OpenStax Anatomy and Physiology 2e, consulted as references; no text copied.
- Facts cross-checked against Lehninger Principles of Biochemistry, 8th ed. (reference only; no text copied).
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