MCAT Chemical and Physical Foundations of Biological Systems Flashcards: 5d Amino Acids Peptides Protein Structure

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This deck focuses on 5d Amino Acids Peptides Protein Structure, giving you a quick way to review the definitions, rules, and examples that matter most for MCAT Chemical and Physical Foundations of Biological Systems.

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Work through these flashcards in short sessions. Try to answer each prompt before flipping the card, then revisit any cards you miss until the explanation feels automatic.

Flashcard 1: Which amino acid has an imidazole side chain and can be neutral or positive near pH $7$?

Answer: Histidine. Histidine's imidazole has a pKa near 6, allowing it to act as a buffer by protonating or deprotonating around pH 7.

Flashcard 2: Which amino acids are classified as nonpolar, aliphatic side chains on the MCAT?

Answer: Gly, Ala, Val, Leu, Ile, Met, Pro. These amino acids have hydrocarbon side chains that lack polarity, making them hydrophobic and aliphatic in classification.

Flashcard 3: Which amino acids have aromatic side chains on the MCAT classification scheme?

Answer: Phe, Tyr, Trp. Aromatic side chains contain benzene-like rings, distinguishing them from aliphatic or other polar groups.

Flashcard 4: Which amino acids are polar, uncharged at physiological pH?

Answer: Ser, Thr, Asn, Gln, Cys, Tyr. These side chains have polar groups like hydroxyls, amides, or thiols that do not ionize at physiological pH.

Flashcard 5: Which amino acids have side chains that are positively charged (basic) near pH $7$?

Answer: Lys, Arg, His. Basic side chains have high pKa values, remaining protonated and positively charged near neutral pH.

Flashcard 6: Which amino acids have side chains that are negatively charged (acidic) near pH $7$?

Answer: Asp, Glu. Acidic side chains have low pKa values, deprotonating to form negatively charged carboxylates near pH 7.

Flashcard 7: Which amino acid is achiral among the standard $20$ amino acids?

Answer: Glycine. Glycine lacks a side chain on its alpha carbon, preventing chirality unlike other amino acids with four different substituents.

Flashcard 8: Which amino acid has a side chain that cyclizes onto the backbone nitrogen (a secondary amine)?

Answer: Proline. Proline's side chain forms a ring with the alpha-amino group, restricting conformational flexibility in proteins.

Flashcard 9: Which amino acid side chain is a thiol that can form disulfide bonds upon oxidation?

Answer: Cysteine. The thiol group in cysteine can oxidize to form covalent disulfide bridges, stabilizing protein structure.

Flashcard 10: Which amino acid is commonly phosphorylated on its phenolic hydroxyl group?

Answer: Tyrosine. Tyrosine's phenolic hydroxyl is a target for kinases in signal transduction due to its aromatic nature.

Flashcard 11: Which amino acids are most commonly phosphorylated on aliphatic hydroxyl groups?

Answer: Serine and threonine. Aliphatic hydroxyl groups on serine and threonine are accessible for phosphorylation in regulatory processes.

Flashcard 12: Which amino acid side chain is an amide derived from aspartate?

Answer: Asparagine. Asparagine is formed by amidation of aspartate's carboxyl group, adding a polar, uncharged amide.

Flashcard 13: Which amino acid side chain is an amide derived from glutamate?

Answer: Glutamine. Glutamine results from amidation of glutamate's side chain carboxyl, providing a longer polar amide group.

Flashcard 14: Which amino acids have carboxylate side chains (acidic functional groups)?

Answer: Aspartate and glutamate. Carboxylate groups in aspartate and glutamate ionize at physiological pH, contributing acidity.

Flashcard 15: What is the definition of a zwitterion for an amino acid in water?

Answer: 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.

Flashcard 16: Which direction is a peptide written and synthesized: from which terminus to which terminus?

Answer: $N$-terminus to $C$-terminus. Peptides are conventionally written and biosynthesized from the amino terminus to the carboxyl terminus, reflecting ribosomal synthesis direction.

Flashcard 17: What covalent bond links amino acids in a polypeptide chain?

Answer: 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.

Flashcard 18: What is released during peptide bond formation between two amino acids?

Answer: $H_2O$ (condensation/dehydration). Peptide bond formation is a dehydration reaction where water is eliminated from the carboxyl and amino groups.

Flashcard 19: What is the net charge for a peptide with no ionizable side chains at $pH = pI$?

Answer: Net charge $0$. The isoelectric point (pI) is the pH where the peptide's average net charge is zero due to balanced ionization states.

Flashcard 20: Which equation relates $pH$, $pK_a$, and the conjugate base/acid ratio for an amino acid group?

Answer: 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.

Flashcard 21: Identify the major intermolecular force that stabilizes protein secondary structure (alpha helix and beta sheet).

Answer: Backbone hydrogen bonding. Hydrogen bonds between backbone carbonyls and amides stabilize regular secondary structures like alpha helices and beta sheets.

Flashcard 22: What does primary structure mean for a protein?

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

Flashcard 23: What is the defining feature of tertiary structure in proteins?

Answer: Overall $3$D fold of one polypeptide chain. Tertiary structure involves the spatial arrangement of a single chain, stabilized by side chain interactions.

Flashcard 24: What is the defining feature of quaternary structure in proteins?

Answer: Association of multiple polypeptide subunits. Quaternary structure arises from non-covalent interactions between separate polypeptide chains in multimeric proteins.

Flashcard 25: Which interaction is the primary driving force for burying nonpolar side chains in globular proteins?

Answer: Hydrophobic effect. The hydrophobic effect drives nonpolar residues into the protein core to minimize water contact and maximize entropy.