Amino Acids, Peptides, and Protein Structure (5D) - Chem & Physics

Which amino acids have side chains that are positively charged (basic) near pH $7$ ?

Lys, Arg, His. Basic side chains have high pKa values, remaining protonated and positively charged near neutral pH.
What covalent bond links amino acids in a polypeptide chain?

Peptide (amide) bond. The peptide bond is an amide linkage formed between the carboxyl group of one amino acid and the amino group of another.
Which interaction is the primary driving force for burying nonpolar side chains in globular proteins?

Hydrophobic effect. The hydrophobic effect drives nonpolar residues into the protein core to minimize water contact and maximize entropy.
What is the net charge for a peptide with no ionizable side chains at $pH = pI$ ?

Net charge $0$ . The isoelectric point (pI) is the pH where the peptide's average net charge is zero due to balanced ionization states.
What is released during peptide bond formation between two amino acids?

$H_2O$ (condensation/dehydration). Peptide bond formation is a dehydration reaction where water is eliminated from the carboxyl and amino groups.
Which amino acid is commonly phosphorylated on its phenolic hydroxyl group?

Tyrosine. Tyrosine's phenolic hydroxyl is a target for kinases in signal transduction due to its aromatic nature.
Which amino acids are classified as nonpolar, aliphatic side chains on the MCAT?

Gly, Ala, Val, Leu, Ile, Met, Pro. These amino acids have hydrocarbon side chains that lack polarity, making them hydrophobic and aliphatic in classification.
Which amino acids are most commonly phosphorylated on aliphatic hydroxyl groups?

Serine and threonine. Aliphatic hydroxyl groups on serine and threonine are accessible for phosphorylation in regulatory processes.
Which amino acid has an imidazole side chain and can be neutral or positive near pH $7$ ?

Histidine. Histidine's imidazole has a pKa near 6, allowing it to act as a buffer by protonating or deprotonating around pH 7.
Which direction is a peptide written and synthesized: from which terminus to which terminus?

$N$ -terminus to $C$ -terminus. Peptides are conventionally written and biosynthesized from the amino terminus to the carboxyl terminus, reflecting ribosomal synthesis direction.
What is the definition of a zwitterion for an amino acid in water?

Molecule with both $+ $ and $-$ charges, net $0$ . Amino acids form zwitterions at physiological pH where the carboxylic acid deprotonates and the amino group protonates, balancing charges.
Which amino acid side chain is an amide derived from glutamate?

Glutamine. Glutamine results from amidation of glutamate's side chain carboxyl, providing a longer polar amide group.
What is the defining feature of quaternary structure in proteins?

Association of multiple polypeptide subunits. Quaternary structure arises from non-covalent interactions between separate polypeptide chains in multimeric proteins.
Which amino acid is achiral among the standard $20$ amino acids?

Glycine. Glycine lacks a side chain on its alpha carbon, preventing chirality unlike other amino acids with four different substituents.
Which equation relates $pH$ , $pK_a$ , and the conjugate base/acid ratio for an amino acid group?

Henderson–Hasselbalch: $pH=pK_a+\log\frac{[A^-]}{[HA]}$ . The Henderson-Hasselbalch equation describes the ionization equilibrium of weak acids, applied to amino acid functional groups.
Which amino acid side chain is a thiol that can form disulfide bonds upon oxidation?

Cysteine. The thiol group in cysteine can oxidize to form covalent disulfide bridges, stabilizing protein structure.
What is the defining feature of tertiary structure in proteins?

Overall $3$ D fold of one polypeptide chain. Tertiary structure involves the spatial arrangement of a single chain, stabilized by side chain interactions.
Which amino acid side chain is an amide derived from aspartate?

Asparagine. Asparagine is formed by amidation of aspartate's carboxyl group, adding a polar, uncharged amide.
Identify the major intermolecular force that stabilizes protein secondary structure (alpha helix and beta sheet).

Backbone hydrogen bonding. Hydrogen bonds between backbone carbonyls and amides stabilize regular secondary structures like alpha helices and beta sheets.
Which amino acid has a side chain that cyclizes onto the backbone nitrogen (a secondary amine)?

Proline. Proline's side chain forms a ring with the alpha-amino group, restricting conformational flexibility in proteins.
Which amino acids have carboxylate side chains (acidic functional groups)?

Aspartate and glutamate. Carboxylate groups in aspartate and glutamate ionize at physiological pH, contributing acidity.
Which amino acids are polar, uncharged at physiological pH?

Ser, Thr, Asn, Gln, Cys, Tyr. These side chains have polar groups like hydroxyls, amides, or thiols that do not ionize at physiological pH.
Which amino acids have side chains that are negatively charged (acidic) near pH $7$ ?

Asp, Glu. Acidic side chains have low pKa values, deprotonating to form negatively charged carboxylates near pH 7.
Which amino acids have aromatic side chains on the MCAT classification scheme?

Phe, Tyr, Trp. Aromatic side chains contain benzene-like rings, distinguishing them from aliphatic or other polar groups.
What does primary structure mean for a protein?

Linear amino acid sequence (covalent connectivity). Primary structure refers to the covalent sequence of amino acids in a protein, determining higher-level folding.

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