Amino Acids and Peptides: Structure, Properties, and Modifications

5.1 Amino Acids

The Structure of an α-Amino Acid

All amino acids share a common structure centered around the α-carbon, which is bonded to four distinct groups: an amino group, a carboxylic acid group, a hydrogen atom, and a variable side chain (R group). This structure is fundamental to protein biochemistry.

• α-Carbon: The central carbon atom in amino acids, except for glycine, is asymmetric (chiral), allowing for stereoisomerism.

• Functional Groups: The amino group (–NH2), carboxylic acid group (–COOH), and side chain (R group) define the chemical properties of each amino acid.

• Zwitterion: At neutral pH, the amino group is protonated (–NH3+) and the carboxyl group is deprotonated (–COO–), resulting in a molecule with both positive and negative charges but an overall neutral charge.

Example: Glycine is the simplest amino acid, with R = H, and is the only achiral amino acid.

α-Amino Acid Stereochemistry

The spatial arrangement of the four groups attached to the α-carbon gives rise to stereoisomerism in amino acids.

• Chirality: When four different groups are attached to the α-carbon, the amino acid is chiral and exists as two enantiomers (L and D forms).

• Biological Relevance: Proteins are composed almost exclusively of L-amino acids.

• Fischer Projection: A two-dimensional representation used to distinguish between L- and D- isomers.

Example: L-alanine and D-alanine are non-superimposable mirror images (enantiomers).

Classification of Naturally Occurring Amino Acids

The 20 standard amino acids found in proteins are classified based on the properties of their side chains (R groups).

Class	Examples	Properties
Nonpolar Aliphatic	Glycine, Alanine, Valine, Leucine, Isoleucine, Proline, Methionine	Hydrophobic, found in protein interiors
Nonpolar Aromatic	Phenylalanine, Tyrosine, Tryptophan	Aromatic rings, absorb UV light
Polar Uncharged	Serine, Threonine, Cysteine, Asparagine, Glutamine	Hydrophilic, can form hydrogen bonds
Positively Charged (Basic)	Lysine, Arginine, Histidine	Basic side chains, often protonated at physiological pH
Negatively Charged (Acidic)	Aspartic acid, Glutamic acid	Acidic side chains, often deprotonated at physiological pH

General Properties of Amino Acids

Amino acids possess unique chemical and physical properties that are essential for protein structure and function.

• UV Absorption: Aromatic amino acids (tyrosine and tryptophan) absorb UV light strongly at 280 nm, which is used to quantify protein concentration. Nucleic acids absorb maximally 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
Guanidino (Arg)	>12

• Titration Curves: The titration curve of an amino acid (e.g., histidine) shows how its charge changes with pH. The isoelectric point (pI) is the pH at which the net charge is zero.

Example: Histidine's charge varies from +2 to –1 as pH increases; the pI is where the net charge is zero.

Posttranslational Modification of Amino Acids

After translation, amino acids in proteins can be chemically modified, affecting protein function and regulation.

• Functions: Modifications can play roles in signaling pathways, calcium binding, stabilizing structures (e.g., collagen), and gene expression or 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 together to form peptides and proteins through a condensation reaction.

• Condensation Reaction: The carboxyl group of one amino acid reacts with the amino group of another, releasing water and forming a peptide bond.

• Energetics: This 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 resonance, which imparts partial double-bond character, making it planar and stable.

• Planarity: The peptide bond is rigid and planar due to electron delocalization between the carbonyl oxygen and the amide nitrogen.

• Stability: This stability is crucial for maintaining protein structure.

Peptide Bond Cleavage

Peptide bonds can be hydrolyzed, but they are generally stable under physiological conditions.

• Hydrolysis: The standard free energy change ($\Delta G^\circ'$) for peptide bond hydrolysis is about –10 kJ/mol.

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

• Proteases: Enzymes that catalyze the cleavage of specific peptide bonds.

Equation:

$\text{Peptide} + H_2O \rightarrow \text{Amino acid}_1 + \text{Amino acid}_2$

Sequence Specificities for Proteases

Different proteases cleave peptide bonds at specific amino acid sequences.

Enzyme	Preferred Site	Source
Trypsin	After Lys, Arg	Digestive systems of animals
Chymotrypsin	After Trp, Tyr, Phe, Leu, Met	Digestive systems of animals
Thrombin	After Arg	Blood (clotting)
V8 protease	After Glu	Staphylococcus aureus
Cyanogen bromide	After Met	Chemical reagent

Oligopeptides and Polypeptides

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

• Oligopeptides: Chains of 3–15 amino acids.

• Polypeptides: Chains containing more than 15 amino acids.

Important Peptide Regions

Peptides have distinct regions, including the amino (N-) terminus, carboxy (C-) terminus, main chain, and side chains. These regions are critical for peptide function and interactions.

Common Modifications of Amino- and Carboxy-Termini in Peptides

The N- and C-termini of peptides can be chemically modified, affecting peptide stability and function.

• N-formyl group

• N-acetyl group

• C-terminal amide

Peptides and Proteins as Polyampholytes

Peptides and proteins contain multiple ionizable groups, allowing them to act as polyampholytes (molecules with both acidic and basic groups).

• As pH increases, the overall charge on a peptide becomes more negative.

• As pH decreases, the overall charge becomes more positive.

Additional info: The isoelectric point (pI) is a key property for protein purification and characterization, as it is the pH at which the molecule carries no net charge.