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5.1 Amino Acids

The Structure of an α-Amino Acid

All amino acids share a common structure centered around the α-carbon, to which four distinct groups are attached: an amino group, a carboxylic acid group, a hydrogen atom, and a unique 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).

• Functional Groups: The amino group (–NH2), carboxylic acid group (–COOH), hydrogen, and R group are bonded to the α-carbon.

• 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 a hydrogen as its R group.

α-Amino Acid Stereochemistry

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

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

• Enantiomers: Amino acids (except glycine) exist as L- and D- forms; 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 are classified based on the properties of their side chains (R groups), which influence protein structure and function.

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

• Nonpolar 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 and tryptophan are aromatic amino acids that absorb UV light.

General Properties of Amino Acids

Amino acids possess unique chemical 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, 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

Example: The titration curve of histidine shows three distinct ionization steps, with the isoelectric point (pI) 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.

• Signaling Pathways: Phosphorylation (e.g., phosphoserine) is crucial for cell signaling.

• Calcium Binding: γ-carboxyglutamate binds calcium ions in blood clotting proteins.

• Structural Stability: Hydroxyproline stabilizes collagen structure.

• Gene Expression: Acetylation can regulate gene expression by modifying histones.

Example: N-acetyllysine is found in histone proteins and is involved in epigenetic regulation.

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 in cells.

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 oxygen and the amide nitrogen.

• Stability: This delocalization makes the bond stable and restricts rotation, influencing protein folding.

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 specific catalysts (proteases).

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

Sequence Specificities for Proteases

Enzyme	Preferred Site	Source
Trypsin	R, K (Arg, Lys)	Digestive systems of animals
Chymotrypsin	F, Y, W, L, M (Phe, Tyr, Trp, Leu, Met)	Digestive systems of animals
Thrombin	R (Arg)	Blood (clotting cascade)
V8 protease	E (Glu)	Staphylococcus aureus
Cyanogen bromide	M (Met)	Chemical reagent
Additional info: Table entries inferred for completeness.

Oligopeptides

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.

Example: A tetrapeptide consists of four amino acid residues linked by peptide bonds.

Important Peptide Regions

Peptides and proteins have distinct regions that determine their chemical and biological properties.

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

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

• Main Chain: The repeating backbone of the peptide.

• Side Chains: The variable R groups that project from the main chain and determine function.

Common Modifications of Amino- and Carboxy-Termini in Peptides

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

• N-formyl group: Blocks the N-terminus, common in bacterial proteins.

• N-acetyl group: Acetylation of the N-terminus, common in eukaryotic proteins.

• C-terminal amide: Amidation of the C-terminus, often found in peptide hormones.

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).

• pH Dependence: 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 of the peptide is zero.

Example: The titration curve of a tetrapeptide shows stepwise ionization of its groups, with the pI indicated where the net charge is zero.