Amino Acids and Peptides: Structure, Properties, and Reactions

5.1 Amino Acids

The Structure of an Amino Acid

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

• α-Carbon: The central carbon atom to which all other groups are attached.

• Amino Group (–NH2): Basic group, typically protonated at physiological pH.

• Carboxylic Acid Group (–COOH): Acidic group, typically deprotonated at physiological pH.

• R Group (Side Chain): Determines the identity and properties of the 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 overall neutral.

Example: Glycine is the simplest amino acid, with its R group being a hydrogen atom.

Stereochemistry of Amino Acids

Most amino acids (except glycine) have a chiral α-carbon, making them optically active. The spatial arrangement of the four groups around the α-carbon leads to stereoisomerism.

• Chirality: A carbon atom with four different groups is called a chiral or asymmetric carbon.

• Stereoisomers: L- and D- forms; in proteins, only L-amino acids are found.

• Enantiomers: L-alanine and D-alanine are non-superimposable mirror images.

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

Example: L-alanine is the mirror image of D-alanine; both are enantiomers.

Classification of Naturally Occurring Amino Acids

The 20 standard amino acids are classified based on the properties of their side chains:

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

• Aromatic: Phenylalanine, Tyrosine, Tryptophan

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

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

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

Example: Tyrosine is an aromatic amino acid with a polar side chain.

General Properties of Amino Acids

Amino acids exhibit unique chemical properties due to their ionizable groups and side chains.

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

• pKa Values: Each ionizable group has a characteristic pKa value, influencing its protonation state at different pH levels.

• Titration Curves: The charge on amino acids (e.g., histidine) varies with pH, with the isoelectric point (pI) being the pH at which the net charge is zero.

• Posttranslational Modifications: Amino acids can be covalently modified after translation, affecting protein function (e.g., phosphorylation, hydroxylation, acetylation).

Example: Phosphorylation of serine introduces a phosphate group, altering protein activity.

Table: Typical pKa Ranges for Ionizable Groups in Proteins

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)	8.5–9.0
Phenolic (Tyr)	9.5–10.5
α-Amino	8.0–9.0
Side-chain amino (Lys)	9.8–10.4
Guanidinium (Arg)	~12

Additional info: For calculations, use pKa ≈ 2.0 for α-carboxyl and pKa ≈ 9.0 for α-amino groups.

5.2 Peptides and the Peptide Bond

Peptide Bond Formation between Amino Acids

Peptide bonds link amino acids together to form peptides and proteins. This bond forms via a condensation (dehydration synthesis) reaction, releasing water.

• Reaction: The carboxyl group of one amino acid reacts with the amino group of another, forming a peptide bond and releasing H2O.

• Energetics: Peptide bond formation 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 resonance between the carbonyl and amide nitrogen.

• Planarity: The peptide bond is planar and stable due to electron delocalization.

• Partial Double Bond Character: Restricts rotation around the bond, influencing protein structure.

Peptide Bond Cleavage

Peptide bonds can be hydrolyzed by strong acid at high temperature or by specific enzymes called proteases.

• Hydrolysis: Peptide bonds are stable under physiological conditions; hydrolysis requires harsh conditions or enzymatic catalysis.

• Proteases: Enzymes that cleave peptide bonds at specific sequences.

Equation:

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

Table: Sequence Specificities for Proteolytic Enzymes and Cyanogen Bromide

Enzyme	Preferred Site	Source
Trypsin	After Lys (K), Arg (R)	Digestive system of animals
Chymotrypsin	After Phe (F), Trp (W), Tyr (Y), sometimes Leu (L), Met (M)	Digestive system of animals
Thrombin	After Arg (R)	Blood, vertebrates
V8 protease	After Glu (E)	Staphylococcus aureus
Cyanogen bromide	After Met (M)	Chemical reagent

Additional info: Trypsin does not cleave if Proline follows the cleavage site.

Oligopeptides and Polypeptides

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

• Oligopeptides: Chains of 3–15 amino acids.

• Polypeptides: Chains with more than 15 amino acids.

Important Peptide Regions

Peptides have two termini: the amino (N-) terminus and the carboxy (C-) terminus. Side chains project from the main chain and determine peptide properties.

• N-terminus: Free amino group at one end.

• C-terminus: Free carboxyl group at the other end.

• Side Chains: Project from the peptide backbone and confer unique chemical properties.

Common Modifications of Amino- and Carboxy-Termini in Peptides

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

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

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

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

Ionization Behavior of Peptides

Peptides contain multiple ionizable groups, and their overall charge depends on the pH of the environment.

• Each ionizable group (N-terminus, C-terminus, side chains) has a characteristic pKa.

• As pH increases, the peptide becomes more negatively charged; as pH decreases, it becomes more positively charged.

• The isoelectric point (pI) is the pH at which the peptide has no net charge.

Example: A tetrapeptide with Glu and Lys side chains will have four ionizable groups, each contributing to the overall charge as pH changes.

Table: Ionizable Groups in a Tetrapeptide Example

Group	pKa
α-COOH of Glu	~2.0
Side chain COOH of Glu	~4.2
α-NH3+ of N-terminus	~9.0
Side chain NH3+ of Lys	~10.0

Additional info: Understanding the ionization states at different pH values is essential for predicting peptide behavior in biological systems.