Question 1

Hydrogen bonding capacity — Which amino acids listed can form hydrogen bonds through their side-chain (R-group) functional groups in aqueous proteins?

Accepted Answer

Introduction / Context: Hydrogen bonds are critical for protein folding, enzyme–substrate recognition, and macromolecular assemblies. Side-chain functional groups that can donate or accept hydrogen bonds frequently determine specificity and stability. Given Data / Assumptions: Asparagine (amide), aspartic acid (carboxylate), and glutamine (amide) are considered. We evaluate their R-groups for hydrogen bond donor/acceptor roles. Physiological pH context applies. Concept / Approach: Asparagine and glutamine have carboxamide side chains capable of donating (via –NH) and accepting (via C=O) hydrogen bonds. Aspartic acid, when protonated (–COOH), can donate; when deprotonated (–COO−), it can accept hydrogen bonds through its carboxylate oxygens and engage in electrostatic interactions. Step-by-Step Solution: Examine Asn: side-chain amide supports both donor and acceptor interactions.Examine Asp: side-chain carboxyl participates as an acceptor (COO−) or donor (COOH) depending on microenvironment and pH.Examine Gln: analogous to Asn but with a longer chain; robust H-bonding capacity.Therefore, all listed residues can form hydrogen bonds via their side chains. Verification / Alternative check: Protein crystal structures show these residues frequently located at active sites or solvent-exposed regions making H-bond networks. Why Other Options Are Wrong: Asparagine only or glutamine only: incomplete; ignores aspartate's roles. Aspartic acid only: incomplete; amides are strong H-bond participants too. Common Pitfalls: Assuming deprotonated carboxylates cannot hydrogen bond; while less effective donors, they are strong acceptors and engage in intricate networks. Final Answer: All of these

Question 2

Standard vs. nonstandard amino acids — Identify the nonstandard (post-translationally derived) amino acid among the following choices.

Accepted Answer

Introduction / Context: Nonstandard amino acids arise through post-translational modification or occur as metabolic intermediates but are not directly encoded by the universal genetic code. Recognizing them is vital for interpreting protein composition and stability. Given Data / Assumptions: Cysteine, isoleucine, and histidine are among the 20 standard amino acids. Hydroxyproline is a hydroxylated derivative of proline found prominently in collagen. Question targets the “nonstandard” residue present in proteins owing to modification. Concept / Approach: Hydroxylation of proline to hydroxyproline is catalyzed by prolyl hydroxylase and requires vitamin C as a cofactor. This modification is essential for collagen triple-helix stability through enhanced hydrogen bonding. The others are encoded directly by codons and incorporated during translation. Step-by-Step Solution: List standard residues: cysteine, isoleucine, histidine.Identify hydroxyproline as post-translationally modified proline.Select hydroxyproline as the nonstandard amino acid. Verification / Alternative check: Protein hydrolysate analyses from collagen reveal abundant hydroxyproline; genetic code tables do not list it as a primary residue. Why Other Options Are Wrong: Cysteine, isoleucine, histidine: all are standard proteinogenic amino acids. Common Pitfalls: Confusing “nonstandard” with “non-protein”; hydroxyproline is nonstandard yet a genuine component of proteins after modification. Final Answer: Hydroxyproline

Question 3

Protein assays — In the Bradford (Coomassie Brilliant Blue G-250) method, the dye binds most strongly to which feature of proteins to produce the characteristic blue shift?

Accepted Answer

Introduction / Context: The Bradford assay is a rapid colorimetric method for estimating protein concentration. It relies on the binding of Coomassie Brilliant Blue G-250 to proteins, causing a spectral shift from reddish to blue. Understanding what the dye recognizes helps interpret assay variability across proteins. Given Data / Assumptions: Dye–protein interactions involve electrostatic and hydrophobic forces. Proteins differ in amino-acid composition; the assay response can vary accordingly. We seek the dominant binding determinant. Concept / Approach: Coomassie G-250 preferentially binds to basic and aromatic residues, with the strongest affinity for arginine due to the guanidinium group forming strong electrostatic and stacking interactions with the dye's sulfonated aromatic system. Lesser contributions arise from lysine, histidine, and hydrophobic contacts with aromatic residues, but arginine content best predicts assay response. Step-by-Step Solution: Identify principal interaction: dye in anionic form complexes with protonated sites.Arginine's guanidinium group provides strong binding and stabilizes the blue form.Other interactions (aromatic, lysine, histidine) are secondary; peptide bonds alone are not the main determinant.Therefore, select “arginine residues.” Verification / Alternative check: Comparative calibration using proteins with known arginine content (e.g., BSA vs. IgG) shows differing responses per mass, consistent with arginine-driven binding. Why Other Options Are Wrong: Free C-termini: present once per chain; not the main binding site. Peptide bonds: Lowry/Biuret assays target peptide bonds; Bradford relies primarily on side chains. Aromatic ring: contributes, but less decisive than arginine's guanidinium interactions. Common Pitfalls: Assuming all proteins yield identical absorbance per mass; composition differences, especially arginine content, alter the assay response, necessitating matched standards when possible. Final Answer: arginine residues

Question 4

Isoelectric point (pI) — By definition, at which pH condition does an amino acid exhibit no net electric charge and therefore shows minimal electrophoretic mobility in an electric field?

Accepted Answer

Introduction / Context: The isoelectric point (pI) is fundamental to techniques such as isoelectric focusing, protein purification, and prediction of solubility. At pI, a molecule's positive and negative charges balance to give zero net charge. Given Data / Assumptions: Amino acids exist as zwitterions over a range of pH values. At a specific pH (pI), net charge becomes zero. Mobility in an electric field depends on net charge. Concept / Approach: The pI is the pH at which the sum of positive charges equals the sum of negative charges; the molecule still bears internal charges but migrates minimally in an electric field because the net force is near zero. For simple amino acids, pI approximates the midpoint between relevant pKa values; for polyionic proteins, pI depends on the distribution of all ionizable side chains. Step-by-Step Solution: Relate pI to net charge neutrality.Recognize that individual groups may be charged, but overall charge sums to zero.Therefore, choose the definition referencing “no net electric charge.” Verification / Alternative check: In isoelectric focusing, proteins stop migrating when they reach the gel region where pH equals their pI, confirming minimized mobility at zero net charge. Why Other Options Are Wrong: “Carboxyl group uncharged” or “amino group uncharged”: oversimplify; multiple ionizable groups influence pI. “Maximum electrolytic mobility”: incorrect; mobility is minimized near pI. Common Pitfalls: Confusing “uncharged groups” with “no net charge”; even at pI, groups can remain ionized in a zwitterionic state. Final Answer: where the molecule carries no electric charge

Question 5

One-letter amino-acid code — The peptide abbreviation “WYQN” corresponds to which sequence of amino-acid names in order from N- to C-terminus?

Accepted Answer

Introduction / Context: One-letter codes are widely used in bioinformatics, structural biology, and sequence annotation. Accurate decoding ensures correct interpretation of motifs, domains, and mutational data across databases. Given Data / Assumptions: Sequence given: W Y Q N. Standard one-letter codes: W = tryptophan, Y = tyrosine, Q = glutamine, N = asparagine. We must match each letter to the correct full name. Concept / Approach: Memorized mappings (e.g., “Queen Q = glutamine,” “New N = asparagine,” “Why Y = tyrosine,” “Double ring W = tryptophan”) help recall. Care must be taken not to confuse Q (glutamine) with E (glutamic acid) or N (asparagine) with D (aspartic acid). Step-by-Step Solution: Map W → tryptophan.Map Y → tyrosine.Map Q → glutamine (amide form).Map N → asparagine (amide form).Thus, the full sequence is tryptophan, tyrosine, glutamine, asparagine. Verification / Alternative check: Compare with standard IUPAC tables of one-letter amino-acid codes; W, Y, Q, N are unambiguous. Why Other Options Are Wrong: Option (a) uses E (glutamic acid) instead of Q. Option (c) duplicates tryptophan and misplaces glutamine. Option (d) begins with glutamine and ends with aspartic acid (D), not N. Common Pitfalls: Confusing amide forms (Q, N) with their acidic counterparts (E, D). The side-chain amides are neutral at physiological pH, unlike their acidic forms. Final Answer: Tryptophan, tyrosine, glutamine, asparagine

Question 6

Essential amino acids — From the list below, which option correctly identifies essential amino acids for humans?

Accepted Answer

Introduction / Context: Essential amino acids cannot be synthesized de novo by humans and must be obtained from dietary sources. Their adequate intake is crucial for growth, repair, and nitrogen balance, especially in children, pregnancy, and illness. Given Data / Assumptions: Candidates: tryptophan, methionine, lysine. We apply the standard human essential amino-acid list. No special clinical exceptions are invoked. Concept / Approach: The essential amino acids are histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine (with histidine especially important in growing individuals). Tryptophan, methionine, and lysine are all on this list. Step-by-Step Solution: Confirm tryptophan: essential; precursor to serotonin and niacin.Confirm methionine: essential sulfur donor; precursor to S-adenosylmethionine.Confirm lysine: essential basic amino acid, often limiting in cereals.Therefore, “All of these” is correct. Verification / Alternative check: Nutrition references and WHO/FAO guidelines agree on these three as essential, with defined daily intake recommendations based on age and physiological state. Why Other Options Are Wrong: Any single choice omits the other essential residues listed; the comprehensive answer is all three. Common Pitfalls: Confusing conditional essentiality (e.g., tyrosine when phenylalanine is deficient) with absolute essentiality; misremembering sulfur metabolism and methionine/cysteine interchangeability limits. Final Answer: All of these

Question 7

Intrinsic protein fluorescence — Fluorescence from native proteins in the near-UV arises predominantly from which aromatic amino-acid residue?

Accepted Answer

Introduction / Context: Intrinsic protein fluorescence is a powerful probe of protein folding, conformational changes, and ligand binding. It mainly originates from aromatic residues excited in the near-UV, with emission sensitive to the local environment. Given Data / Assumptions: Three aromatic residues exist in proteins: phenylalanine, tyrosine, and tryptophan. Quantum yield and sensitivity differ dramatically among them. We assume typical excitation around 280 nm and emission monitoring near 320–350 nm. Concept / Approach: Tryptophan has the highest quantum yield and the most environment-sensitive emission maximum, often dominating total protein fluorescence even when present at low abundance. Tyrosine fluoresces weakly and is often quenched or energy-transferred to tryptophan. Phenylalanine has very low quantum yield and minimal contribution under standard conditions. Arginine is non-aromatic and non-fluorescent in this context. Step-by-Step Solution: Compare intrinsic fluorescence efficiencies: Trp > Tyr > Phe.Consider typical measurement wavelengths: excitation at 280 nm efficiently excites Trp and Tyr; emission is dominated by Trp.Select tryptophan as the principal emitter. Verification / Alternative check: Empirical spectra of purified proteins show that mutating or quenching tryptophan residues drastically reduces fluorescence, validating its dominant role. Why Other Options Are Wrong: Tyrosine: contributes, but far weaker and often quenched. Phenylalanine: weakest fluorescence among aromatics. Arginine: aliphatic, non-aromatic; does not fluoresce in the near-UV. Common Pitfalls: Assuming the most abundant aromatic determines intensity; a single buried tryptophan can dominate over multiple tyrosines due to higher quantum yield. Final Answer: Tryptophan

Question 8

In stereochemistry of amino acids: D-alanine and L-alanine are technically classified as which type of stereoisomers (considering the mirror-image relationship of their chiral centers)?

Accepted Answer

Introduction / Context: Understanding the stereochemistry of amino acids is fundamental in biochemistry because enzyme recognition, peptide folding, and receptor binding depend on precise 3-D arrangements. Naturally occurring proteins overwhelmingly use L-amino acids, while the D-forms are their mirror images and can display very different biological behavior. Given Data / Assumptions: Alanine has one chiral center at the alpha carbon (Cα). D-alanine and L-alanine differ only in the spatial arrangement around this single stereocenter. No ring closures or cyclic sugar contexts are involved. Concept / Approach: Stereoisomers that are non-superimposable mirror images are called enantiomers. Epimers differ at one stereocenter but are not mirror images. Anomers are a special case of epimers formed upon cyclization of sugars (α/β at the anomeric carbon), not relevant to amino acids. Polymers refer to macromolecules composed of repeating units and are not a stereochemical class. Step-by-Step Solution: Identify the chiral center in alanine → the alpha carbon attached to H, CH3, NH2, and COOH. Recognize D vs L as mirror-image configurations around the same stereocenter. Classify mirror-image, non-superimposable pairs → enantiomers. Exclude epimer/anomer/polymer definitions as inapplicable here. Verification / Alternative check: Enantiomers rotate plane-polarized light equally and oppositely and interconvert only by bond breaking at the stereocenter. D- and L-alanine meet this criterion. Why Other Options Are Wrong: Anomers apply to cyclic sugars; epimers are not mirror images; polymers describe chain length, not stereochemistry; diastereomers are stereoisomers that are not mirror images (need ≥2 stereocenters), which alanine lacks. Common Pitfalls: Confusing epimer with enantiomer; extending sugar terminology (anomer) to amino acids. Final Answer: Enantiomers.

Question 9

Aromatic amino acids and hydrophobicity: Which listed amino acid is aromatic but not purely hydrophobic under physiological conditions (due to a polar substituent)?

Accepted Answer

Introduction / Context: Aromatic amino acids (phenylalanine, tyrosine, tryptophan) contribute to protein spectroscopy, stacking interactions, and hydrophobic cores. However, not all aromatics behave identically with respect to polarity and hydrogen bonding—substituents on the ring can change solubility and reactivity. Given Data / Assumptions: Phenylalanine has a benzyl side chain (nonpolar). Tyrosine has a phenolic side chain (ring plus –OH). Tryptophan has an indole ring (largely hydrophobic with a weakly polar NH). Concept / Approach: Hydrophobicity is reduced by polar groups that can hydrogen bond with water. Tyrosine’s phenolic –OH increases polarity and enables hydrogen bonding, making it less hydrophobic (often categorized as aromatic, polar). Phenylalanine lacks heteroatoms in the ring and is strongly hydrophobic. Tryptophan is mostly hydrophobic despite its indole NH because the large aromatic system dominates. Step-by-Step Solution: Evaluate side chains: Phe → nonpolar benzyl; Tyr → phenol; Trp → indole. Assess polarity: Tyr’s –OH contributes measurable polarity and H-bonding. Rank hydrophobicity: Phe ≈ Trp > Tyr (most polar of the three aromatics). Select amino acid that is aromatic yet not purely hydrophobic → Tyrosine. Verification / Alternative check: Hydropathy index commonly lists Tyr as less hydrophobic than Phe and Trp. Tyrosine often locates at protein surfaces or interfaces where its –OH can interact with solvent. Why Other Options Are Wrong: Phenylalanine is strongly hydrophobic; tryptophan is largely hydrophobic; “None of these/All of these” contradict the polarity differences. Common Pitfalls: Assuming all aromatics are equally hydrophobic; ignoring the phenolic –OH in tyrosine. Final Answer: Tyrosine.

Question 10

Zwitterionic behavior: When alanine (R = CH3) is placed in an aqueous solution at pH 7.3, what is its predominant ionic form?

Accepted Answer

Introduction / Context: Amino acids are amphoteric and commonly exist as zwitterions in water near physiological pH. Recognizing their protonation states is key to predicting solubility, electrophoresis behavior, and interactions in proteins. Given Data / Assumptions: Alanine pKa values: pKa_carboxyl ≈ 2–3; pKa_amino ≈ 9–10. Solution pH = 7.3, slightly above alanine’s isoelectric point (≈ 6.0). No extreme ionic strength or denaturants present. Concept / Approach: At pH between the two pKa values, the carboxyl is deprotonated (COO−) and the amino group remains protonated (NH3+), producing a dipolar ion (zwitterion) with roughly zero net charge. Slightly above the pI, the population may skew marginally toward the anionic side, but the dominant microstate remains zwitterionic. Step-by-Step Solution: Compare pH (7.3) to pKa_carboxyl (~2.3) → fully deprotonated COO−. Compare pH (7.3) to pKa_amino (~9.7) → predominantly protonated NH3+. Combine → NH3+ and COO− on the same molecule (zwitterion). Net charge near zero → consistent with electrophoretic behavior around neutral pH. Verification / Alternative check: Henderson–Hasselbalch calculations confirm species distribution: at pH between pKa values, the zwitterionic form dominates for simple amino acids like alanine. Why Other Options Are Wrong: Fully cationic form occurs near very low pH; fully anionic form near high pH; “nonpolar neutral without charges” ignores the internal ionic character; isotope is unrelated to acid–base chemistry. Common Pitfalls: Equating “net zero charge” with “uncharged”; the zwitterion is charged internally. Final Answer: A zwitterion (NH3+ and COO− present, net ~0).

Question 11

Side-chain charge at basic pH: Which pair of amino acids carries a net negative charge on the side chain at pH 8.0?

Accepted Answer

Introduction / Context: Protein charge depends heavily on side-chain ionization. Correctly identifying acidic versus basic residues at a given pH helps predict protein folding, salt bridges, enzyme catalysis, and migration in electrophoresis. Given Data / Assumptions: Side-chain pKa values: Asp/Glu carboxyl groups ≈ 4; Lys ε-NH3+ ≈ 10.5; His imidazole ≈ 6; Asn/Gln amides are nonionizable under normal conditions. pH under consideration is 8.0 (mildly basic). Concept / Approach: For acidic residues (Asp, Glu), at pH well above their pKa the side chains are deprotonated and negatively charged (–COO−). Basic residues (Lys, Arg) tend to be positively charged below their pKa; histidine is partially protonated near pH 6 and largely neutral at pH 8. Step-by-Step Solution: Compare pH 8 to pKa(Asp/Glu ~4) → deprotonated, −1 charge. Asn/Gln have amide side chains → do not ionize under these conditions. His/Lys at pH 8: His mostly neutral, Lys mostly still protonated (+). Therefore, only Aspartate and Glutamate are negatively charged at pH 8. Verification / Alternative check: Charge calculations using Henderson–Hasselbalch confirm near-complete deprotonation for Asp/Glu at pH 8. Why Other Options Are Wrong: Asn/Gln side chains do not carry charge; Leu/Gly are nonpolar/neutral; His/Lys are not negatively charged at pH 8. Common Pitfalls: Confusing amides (Asn/Gln) with their acidic counterparts (Asp/Glu); assuming histidine is always positively charged. Final Answer: Aspartate and Glutamate.

Question 12

Analytical color test: Which amino acid yields a characteristic yellow–brown color with the ninhydrin reaction due to its imino (secondary amine) nature?

Accepted Answer

Introduction / Context: Ninhydrin is a classic reagent for detecting amino acids in chromatography and electrophoresis. Most α-amino acids yield a deep purple product (Ruhemann’s purple). However, imino acids behave differently and generate a distinct color, which is diagnostically useful. Given Data / Assumptions: Proline is an imino acid: its α-amino group is secondary (incorporated in a pyrrolidine ring). Standard ninhydrin conditions are used (heating, mildly acidic aqueous/organic medium). Other listed amino acids have primary α-amino groups. Concept / Approach: The ninhydrin reaction mechanism involves oxidative deamination of primary amino groups to an aldehyde and formation of a chromophore (Ruhemann’s purple). Secondary amino groups (as in proline/hydroxyproline) cannot follow the same pathway and instead form a yellow to yellow-brown product. Step-by-Step Solution: Classify amino groups: primary vs secondary. Predict color outcome: primary → purple; secondary (imino) → yellow-brown. Identify imino acid → Proline (also hydroxyproline, not listed). Therefore the amino acid giving brownish/yellow product is proline. Verification / Alternative check: Textbook TLC plates show proline spots as yellow compared to purple for most amino acids, confirming the diagnostic difference. Why Other Options Are Wrong: Asparagine, alanine, valine, and glycine have primary amino groups and produce the purple chromophore. Common Pitfalls: Assuming all amino acids turn the same color with ninhydrin; forgetting that proline’s ring makes the amino group secondary. Final Answer: Proline.

Question 13

Disulfide chemistry: Which amino acid name is used when referring to a ‘‘half-cystine’’ residue participating in a disulfide bond within proteins?

Accepted Answer

Introduction / Context: Disulfide bonds stabilize protein tertiary and quaternary structures. The terminology around cysteine/cystine and “half-cystine” can be confusing but is routinely used in biochemistry, structural biology, and proteomics. Given Data / Assumptions: Cysteine side chain contains a thiol (–SH). Two cysteine residues can oxidize to form a disulfide bond (–S–S–), commonly called cystine. “Half-cystine” refers to each cysteine residue within a disulfide linkage. Concept / Approach: When a disulfide forms, the individual residues are still cysteine residues by sequence, but in structural/analytical contexts each partner within the –S–S– is often called a half-cystine. The term cystine names the covalent dimer, not the individual amino acid. Step-by-Step Solution: Identify residue forming disulfides → cysteine. Name of the oxidized dimer → cystine (two cysteines linked). Each participant within the disulfide → “half-cystine.” Therefore, the amino acid referred to is cysteine. Verification / Alternative check: Protein sequence annotations and mass-spec modifications list “cysteine (disulfide-linked)” or “half-cystine” for residues engaged in disulfides. Why Other Options Are Wrong: Isoleucine, valine, histidine cannot form disulfides; “cystine” denotes the linked pair, not a single residue. Common Pitfalls: Confusing the term cystine with half-cystine; assuming half-cystine is a different amino acid. Final Answer: Cysteine.

Structure and Properties of Amino Acids Questions