Amino Acids and Peptides: Structure, Properties, and Reactions

5.1 Amino Acids

The Structure of an α-Amino Acid

Amino acids are the building blocks of proteins, each containing a central α-carbon atom bonded to four distinct groups. Their structure and properties are fundamental to understanding protein chemistry.

• α-Carbon: The central carbon atom in an amino acid, to which the following groups are attached:

  • Amino group (-NH2)

  • Carboxylic acid group (-COOH)

  • Side chain (R group): Unique to each amino acid and determines its properties

  • Hydrogen atom

• Chirality: When the α-carbon is attached to four different groups, it is a chiral center (except in glycine, where R = H).

• 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.

Example: Glycine is the only non-chiral amino acid because its R group is a hydrogen atom.

α-Amino Acid Stereochemistry

The spatial arrangement of atoms around the α-carbon leads to stereoisomerism in amino acids, which is crucial for protein structure and function.

• Chirality: All standard amino acids (except glycine) are chiral and exist as two enantiomers: L- and D-forms.

• Enantiomers: L-alanine is the mirror image of D-alanine; these are non-superimposable stereoisomers.

• Fischer Projection: A two-dimensional representation used to depict stereochemistry of amino acids.

Additional info: In biological systems, only L-amino acids are incorporated into proteins.

Classification of Naturally Occurring Amino Acids

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

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

General Properties of Amino Acids

Amino acids exhibit characteristic chemical and physical properties that are essential for protein structure and function.

• UV Absorption: Aromatic amino acids (tyrosine, 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, each with a characteristic pKa value.

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 charge on histidine varies from +2 to –1 as pH increases.

• pKa values correspond to the ionization of different groups.

• The isoelectric point (pI) is the pH at which the net charge is zero.

Example: The titration curve of histidine shows three distinct buffering regions corresponding to its three ionizable groups.

Posttranslational Modification of Amino Acids

• Posttranslational modifications (PTMs) alter amino acids after protein synthesis.

• Functions include signaling, calcium binding, stabilizing structures (e.g., collagen), and regulating gene expression.

Modification	Example	Function
Phosphorylation	Phosphoserine	Signal transduction
Hydroxylation	4-Hydroxyproline	Collagen stability
Acetylation	N-Acetyllysine	Gene regulation
Carboxylation	γ-Carboxyglutamate	Calcium binding

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 has unique structural properties due to electron delocalization.

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

• Stability: This delocalization makes the bond stable and restricts rotation around the bond.

Peptide Bond Cleavage

Peptide bonds can be hydrolyzed, but 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 (e.g., proteases).

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

Sequence Specificities for Proteases

Enzyme	Preferred Site	Source
Trypsin	R, K (Arg, Lys)	Digestive system of animals
Chymotrypsin	F, W, Y (Phe, Trp, Tyr)	Digestive system of animals
Thrombin	R (Arg)	Blood (clotting)
V8 protease	E (Glu)	Staphylococcus aureus
Cyanogen bromide	M (Met)	Chemical reagent
Additional info:	Proteases have high specificity for certain amino acid sequences, which is exploited in protein sequencing and analysis.

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.

Important Peptide Regions

Peptides and proteins have distinct regions that determine their structure and function.

• Amino (N-) terminus: The end with a free amino group.

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

• Main chain (backbone): The repeating sequence of atoms that forms the core of the peptide.

• Side chains: The variable R groups that project from the main chain and determine the properties of the peptide.

Common Modifications of Amino- and Carboxy-Termini in Peptides

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

Modification	Structure
N-formyl group	Formylation at the N-terminus
N-acetyl group	Acetylation at the N-terminus
C-terminal amide	Amidation at the C-terminus

Additional info: Such modifications can protect peptides from degradation or alter their biological activity.

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.

• The isoelectric point (pI) is the pH at which the net charge is zero.

Example: The titration curve of a tetrapeptide shows stepwise changes in charge as each ionizable group loses a proton.