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

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:

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:

Table: Sequence Specificities for Proteolytic Enzymes and Cyanogen Bromide

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

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