A ✅ CORRECT: Amino acids ARE substituted methanes — α-carbon bonded to −NH₂, −COOH, −H, and −R (four substituents replacing 4H of methane).
B ❌ WRONG: Serine is a polar uncharged amino acid (−CH₂OH side chain), NOT aromatic. Aromatic = Phe, Tyr, Trp.
C ✅ CORRECT: Valine IS a neutral (non-polar, no charge on R-group at pH 7.4) amino acid. R = isopropyl group.
D ❌ WRONG: Lysine is a basic amino acid (ε-NH₂ group, pKa ~10.5, positively charged at pH 7.4), NOT acidic. Acidic = Asp, Glu.
All amino acids share a common structural backbone: a central carbon atom (α-carbon) bonded to four groups — an amino group (−NH₂), a carboxyl group (−COOH), a hydrogen atom (−H), and a variable side chain (−R group). This arrangement makes amino acids structurally analogous to substituted methane (CH₄), where three of the four hydrogen atoms are replaced by −NH₂, −COOH, and −R, with the fourth being −H. Hence, Statement A is CORRECT — amino acids ARE substituted methanes. This central α-carbon is chiral (asymmetric) in all amino acids except glycine (where R=H, making all four groups identical → no chirality). All naturally occurring amino acids are L-amino acids (based on their relationship to L-glyceraldehyde).
Amino acids are classified based on the chemical properties of their R-groups (side chains), particularly their charge at physiological pH (7.4) and their polarity. Non-polar/Hydrophobic: glycine (G), alanine (A), valine (V), leucine (L), isoleucine (I), proline (P), phenylalanine (F), tryptophan (W), methionine (M). Side chains are aliphatic (glycine through isoleucine, methionine), aromatic (phenylalanine, tryptophan), or cyclic (proline). These cluster in the protein core away from water. Polar/Uncharged: serine (S), threonine (T), cysteine (C), asparagine (N), glutamine (Q), tyrosine (Y). Side chains contain hydroxyl, thiol, or amide groups → form H-bonds with water. Acidic (negatively charged at pH 7): aspartate (D) and glutamate (E). Contain −COOH in side chain, pKa ~4. Basic (positively charged at pH 7): lysine (K, pKa ~10.5), arginine (R, pKa ~12.5), histidine (H, pKa ~6). Neutral amino acids: those with no charge at physiological pH — includes non-polar AND polar uncharged amino acids.
Statement B claims serine is an aromatic amino acid — this is INCORRECT. Serine (Ser, S) is a polar, uncharged amino acid. Its R-group is −CH₂OH (a hydroxymethyl group) — simple, aliphatic, no aromatic ring. Serine is classified as a polar uncharged amino acid because the −OH group can form hydrogen bonds with water and with other protein groups. The aromatic amino acids are: phenylalanine (Phe, F) — benzyl group, tyrosine (Tyr, Y) — para-hydroxybenzyl group, tryptophan (Trp, W) — indole group. All three have large, planar aromatic ring systems. They absorb UV light — tryptophan strongly at 280 nm, tyrosine weakly at 280 nm. This absorption is used to measure protein concentration (A₂₈₀ measurement). Serine has no aromatic ring and no UV absorption at 280 nm.
Statement C says valine is a neutral amino acid — this is CORRECT. Valine (Val, V) is a non-polar, hydrophobic amino acid. Its R-group is −CH(CH₃)₂ (isopropyl group — a branched aliphatic chain). At physiological pH (7.4), valine carries no charge on its R-group (the isopropyl group has no ionisable groups). Its α-amino group (pKa ~9.6) is protonated (−NH₃⁺) and α-carboxyl group (pKa ~2.3) is deprotonated (−COO⁻) at pH 7.4, but these are part of the backbone, not the side chain. Valine belongs to the branched-chain amino acids (BCAAs) along with leucine and isoleucine. Valine is an essential amino acid — cannot be synthesised by humans, must come from diet. It is particularly abundant in legumes, dairy, and meat.
Statement D claims lysine is an acidic amino acid — this is INCORRECT. Lysine (Lys, K) is a basic amino acid. Its R-group is −(CH₂)₄−NH₂ (a 4-carbon chain ending in an amino group, ε-amino group). At physiological pH 7.4, this ε-amino group is protonated (−NH₃⁺, pKa ~10.5) → lysine carries a +1 net charge on its R-group → it is BASIC (positively charged). The acidic amino acids are aspartate (Asp, D) and glutamate (Glu, E) — their R-groups contain carboxyl (−COOH) groups with pKa ~4 → negatively charged at pH 7.4. Lysine (along with arginine and histidine) is one of the three basic amino acids. Lysine is an essential amino acid, commonly deficient in cereal-based diets (rice, wheat) — hence, pulse-cereal combinations (dal-roti, dal-rice) provide complementary proteins.
Peptide bonds form between the α-carboxyl group of one amino acid and the α-amino group of the next, with the release of water (condensation reaction). The peptide bond (−CO−NH−) has special properties: Partial double bond character: resonance between C=O and C−N bonds → approximately 40% double bond character. This restricts rotation around the C−N bond (they are LOCKED in a plane — either cis or trans configuration). Trans configuration: predominant (R-groups on opposite sides → less steric clash). Cis configuration: rare, found with proline (its ring structure constrains geometry). The peptide backbone consists of repeating units of N−Cα−C, with the peptide bond between C and N being rigid and planar. Only the N−Cα (φ/phi) and Cα−C (ψ/psi) bonds can rotate, giving conformational flexibility to the backbone. The Ramachandran plot shows allowed φ/ψ angle combinations — different secondary structures have characteristic φ/ψ values.
Several amino acids have unique biological roles beyond protein synthesis: Glycine: smallest amino acid (R=H). Can fit in tight spaces in proteins. Major inhibitory neurotransmitter in spinal cord. Abundant in collagen (Gly-X-Y repeats essential for triple helix). Cysteine: contains −SH (thiol group). Disulfide bonds (−S−S−) form between cysteines → stabilise protein structure. Methionine: start codon AUG = methionine in eukaryotes (fMet in prokaryotes). Contains sulphur. Tryptophan: precursor of serotonin (neurotransmitter) and melatonin. Rarest amino acid in proteins. Only source via diet. Tyrosine: precursor of dopamine, noradrenaline, adrenaline (catecholamines), thyroid hormones (thyroxine T₄), and melanin pigment. Histidine: acts as acid-base catalyst in enzyme active sites (pKa ~6, can accept or donate protons near physiological pH). Glutamate: major excitatory neurotransmitter in brain. GABA (gamma-aminobutyric acid) derived from glutamate — inhibitory neurotransmitter.
The genetic code specifies which amino acid is incorporated for each codon. 64 codons for 20 amino acids → genetic code is degenerate (multiple codons for same amino acid). Synonymous codons differ mainly at the third position (wobble position). Start codon: AUG → Methionine (eukaryotes) or fMet (prokaryotes). Stop codons: UAA (ochre), UAG (amber), UGA (opal) — don't code for amino acids. Unusual amino acid properties: Proline: only cyclic amino acid. The R-group is bonded back to the α-nitrogen forming a pyrrolidine ring. This restricts φ angle → proline is a helix breaker. Found at bends/turns. Glycine: only achiral amino acid. R=H → no stereoisomers. Cysteine: its −SH group has unique chemistry → forms disulfide bonds and metal-binding sites. Selenocysteine: the 21st amino acid (UGA codon) — selenium instead of sulphur. Present in some enzymes (glutathione peroxidase). Pyrrolysine: the 22nd amino acid — in some archaea and bacteria.