Amino Acids

🧪 Amino Acids & Peptides: Master Guide

CSIR-NET | GATE | DBT-JRF PREPARATION

1. Standard Amino Acids & Basic Properties

• Stereochemistry: All standard amino acids are L-α-amino acids. In the absolute (R/S) system, almost all are (S), except Cysteine which is (R).
• Chirality: 19 of the 20 amino acids have a chiral alpha-carbon. Glycine is achiral (has two H atoms). Isoleucine and Threonine have two chiral centers.
• UV Absorbance (280 nm): Aromatic amino acids absorb UV light. Order of absorbance: Tryptophan (Trp) > Tyrosine (Tyr) > Phenylalanine (Phe). Trp has the highest molar extinction coefficient.

🔥 CSIR-NET EXAM POINT: Disulfide bonds are formed strictly by the oxidation of the sulfhydryl (-SH) groups of two Cysteine residues. Methionine contains sulfur but cannot form disulfide bridges.

2. Classification of Standard Amino Acids

A highly tested area is the side-chain properties and the pKr (side-chain pKa) of the 7 ionizable amino acids.

Category	Amino Acids (3-Let / 1-Let)	Key Structural Features / pKr
Aliphatic (Non-polar)	Gly(G), Ala(A), Val(V), Leu(L), Ile(I), Pro(P)	Hydrophobic. Proline is an imino acid (secondary amine), forms rigid kinks (helix breaker).
Aromatic (Non-polar)	Phe(F), Trp(W)	Hydrophobic base stacking. Trp has an indole ring.
Polar Uncharged	Ser(S), Thr(T), Cys(C), Tyr(Y), Asn(N), Gln(Q)	Form H-bonds. Cys pKr ~8.3 (sulfhydryl), Tyr pKr ~10.0 (phenol).
Acidic (-ve charge)	Aspartate(D), Glutamate(E)	Carboxyl side chains. Asp pKr ~3.9, Glu pKr ~4.2.
Basic (+ve charge)	Lys(K), Arg(R), His(H)	His pKr ~6.0 (imidazole, physio buffer). Lys pKr ~10.5. Arg pKr ~12.5 (guanidinium).

3. The Peptide Bond

The peptide bond is an amide linkage formed by a dehydration (condensation) reaction between the carboxyl group of one AA and the amino group of another.

• Partial Double Bond Character: Due to resonance between the carbonyl oxygen and amide nitrogen, the C-N bond is shorter than a normal single bond. It cannot rotate.
• Trans Configuration: Nearly all peptide bonds are in the trans configuration to minimize steric hindrance. Exception: Proline can form cis peptide bonds (approx 6% of the time).
• Torsion Angles: Rotation only occurs around the N-Cα bond (φ Phi angle) and the Cα-C bond (ψ Psi angle). These dictate protein folding (Ramachandran Plot).
• UV Absorption: The peptide backbone itself absorbs UV light strongly at 210 - 220 nm.

4. Molecular Weight (MW) of Peptides

CSIR-NET highly favors numericals on this.

• Average MW of a free amino acid = 128 Da (Daltons)
• When forming a peptide bond, 1 molecule of Water (MW = 18 Da) is lost.
• Average MW of an amino acid residue in a chain = 128 - 18 = 110 Da.

Formula: MW of protein = Number of residues × 110 Da

5. Charge on a Peptide

To calculate net charge at a given pH, you only care about:

1. The free N-terminal amino group (pK_a ~ 8.0 - 9.0)
2. The free C-terminal carboxyl group (pK_a ~ 2.0 - 3.0)
3. The 7 ionizable side chains (D, E, H, C, Y, K, R). Internal peptide bonds do not ionize!

Golden Rule:
If pH < pKa → Protonated state (H⁺ attached).
If pH > pKa → Deprotonated state (H⁺ lost).

6. Isoelectric Point (pI) Calculation

The Isoelectric Point (pI) is the specific pH at which the net charge of the molecule is exactly zero (the Zwitterion form). At this pH, the molecule will not move in an electric field.

• Neutral Amino Acids: Average of the two pKa values. Formula: pI = (pK₁ + pK₂) / 2
• Acidic Amino Acids (Asp, Glu): Average of the carboxyl pKa and the side-chain pKr. Formula: pI = (pK₁ + pK_R) / 2
• Basic Amino Acids (Lys, Arg, His): Average of the amino pKa and the side-chain pKr. Formula: pI = (pK₂ + pK_R) / 2

💡 ULTIMATE TRICK FOR PEPTIDES: To find the pI of a multi-residue peptide, list all pKa values of the peptide from lowest to highest. Find the pH range where the net charge is exactly 0. The pI is strictly the average of the two pKa values that flank this zero-charge region!