Amino Acids and Peptides: Structure, Properties, and Biochemical Roles

5.1 Amino Acids

Structure of an α-Amino Acid

Amino acids are the fundamental building blocks of proteins, each containing a central α-carbon atom to which four distinct groups are attached: an amino group, a carboxylic acid group, a side chain (R group), and a hydrogen atom. The unique properties of each amino acid are determined by its side chain.

• α-Carbon: The central carbon atom in amino acids; it is an asymmetric center (chiral) when the R group is not hydrogen.

• Functional Groups: Amino group (–NH2), carboxylic acid group (–COOH), and a variable side chain (R group).

• Zwitterion: At neutral pH, the amino group is protonated (–NH3+) and the carboxylic acid group is deprotonated (–COO−), resulting in a molecule with both positive and negative charges.

• Example: Glycine is the simplest amino acid, with R = H.

α-Amino Acid Stereochemistry

The stereochemistry of amino acids is crucial for protein structure and function. Most amino acids are chiral, meaning they exist as non-superimposable mirror images (enantiomers).

• Chirality: When four different groups are attached to the α-carbon, it is chiral (a stereocenter).

• Fischer Projection: A 2D representation used to depict stereochemistry.

• L- and D-forms: L-alanine is the mirror image of D-alanine; these are enantiomers. Proteins in nature are composed almost exclusively of L-amino acids.

• Exception: Glycine is achiral because its R group is hydrogen.

Classification of Naturally Occurring Amino Acids

The 20 common amino acids found in proteins are classified based on the properties of their side chains.

• Nonpolar Aliphatic: Glycine, Alanine, Valine, Leucine, Isoleucine, Proline, Methionine

• Nonpolar Aromatic: Phenylalanine, Tyrosine, Tryptophan

• Polar Uncharged: Serine, Threonine, Asparagine, Glutamine, Cysteine

• Positively Charged (Basic): Lysine, Arginine, Histidine

• Negatively Charged (Acidic): Aspartic acid, Glutamic acid

General Properties of Amino Acids

Amino acids exhibit distinct chemical properties, including UV absorbance and ionization behavior.

• UV Absorption: Aromatic amino acids (tyrosine and tryptophan) absorb UV light at 280 nm, allowing protein quantification. Nucleic acids absorb most strongly at 260 nm.

• Ionizable Groups: Amino acids contain groups that can gain or lose protons, characterized by their pKa values.

Group Type	Typical pKa Range
α-Carboxyl	3.5–4.0
Side-chain carboxyl (Asp, Glu)	4.0–4.8
Imidazole (His)	6.5–7.4
Cysteine (–SH)	8.0–9.0
Phenolic (Tyr)	9.5–10.5
α-Amino	8.0–9.0
Side-chain amino (Lys)	9.8–10.4
Guanidinium (Arg)	>12

Titration Curve of Histidine

The titration curve of histidine illustrates how its charge changes with pH due to ionizable groups.

• Charge Variation: Histidine's charge ranges from +2 to –1 as pH increases.

• pKa Values: Each ionizable group has a characteristic pKa value, marked on the curve.

• Isoelectric Point (pI): The pH at which the net charge is zero.

Posttranslational Modification of Amino Acids

Posttranslational modifications alter amino acids after protein synthesis, affecting protein function and regulation.

• Functions: Signaling pathways, calcium binding, stabilizing structures (e.g., collagen), gene expression/suppression.

• Examples: Phosphoserine, 4-hydroxyproline, N-acetyllysine, γ-carboxyglutamate.

5.2 Peptides and the Peptide Bond

Peptide Bond Formation between Amino Acids

Peptide bonds link amino acids to form peptides and proteins through a condensation reaction that releases water.

• Condensation Reaction: Two amino acids join, forming a peptide bond and releasing H2O.

• Energetics: The reaction is not thermodynamically favorable and is coupled to ATP hydrolysis during protein biosynthesis.

• Equation: $\text{Amino acid}_1 + \text{Amino acid}_2 \rightarrow \text{Dipeptide} + H_2O$

Structure of the Peptide Bond

The peptide bond is characterized by electron delocalization, which imparts planarity and stability to the bond.

• Planar Structure: The peptide bond is rigid and planar due to resonance between the carbonyl and amide nitrogen.

• Stability: Delocalization of electrons prevents free rotation around the bond.

Peptide Bond Cleavage

Peptide bonds can be hydrolyzed under specific conditions, either chemically or enzymatically.

• Hydrolysis: $\Delta G^\circ$ for peptide bond hydrolysis is about –10 kJ/mol.

• Stability: Peptides are stable unless exposed to strong acid at high temperature or a catalyst.

• Proteases: Enzymes that cleave specific peptide bonds.

Sequence Specificities for Proteases

Enzyme	Preferred Site	Source
Trypsin	R, K (Arg, Lys)	Digestive systems of animals
Chymotrypsin	F, Y, W (Phe, Tyr, Trp)	Digestive systems of animals
Thrombin	R	Blood, clotting cascade
V-8 protease	E, D (Glu, Asp)	Staphylococcus aureus
Cyanogen bromide	M (Met)	Chemical reagent
Additional info: Other proteases may have different specificities.

Oligopeptides

Peptides are classified by the number of amino acid residues they contain.

• Oligopeptides: Chains of 3–15 amino acid residues.

• Polypeptides: Chains containing more than 15 residues.

• Example: A tetrapeptide consists of four amino acids linked by peptide bonds.

Important Peptide Regions

Peptides and proteins have distinct regions, including the amino (N-) terminus, carboxy (C-) terminus, main chain, and side chains.

• N-terminus: The end of the peptide with a free amino group.

• C-terminus: The end with a free carboxyl group.

• Main Chain: The repeating backbone of the peptide.

• Side Chains: The variable R groups extending from the main chain.

Common Modifications of Amino- and Carboxy-Termini in Peptides

Peptide termini can be chemically modified, affecting protein stability and function.

• N-formyl group: Blocks the N-terminus.

• N-acetyl group: Another N-terminal modification.

• C-terminal amide: Blocks the C-terminus.

Peptides and Proteins as Polyampholytes

Peptides and proteins contain multiple ionizable groups, making them polyampholytes—molecules with both acidic and basic groups.

• Ionization Behavior: As pH increases, the overall charge on a peptide becomes more negative; as pH decreases, it becomes more positive.

• Isoelectric Point (pI): The pH at which the net charge is zero.

• Application: This property is important for techniques such as isoelectric focusing and protein purification.