Amino Acids and Proteins: Structure, Properties, and Functions

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Chapter 18: Amino Acids and Proteins

18.1 Introduction to Biochemistry

Biochemistry is the study of the molecules and chemical reactions that occur in living organisms. It focuses on understanding the structure, function, and interactions of biological macromolecules essential for life.

Major biomolecules: Proteins, lipids, carbohydrates, and nucleic acids.
Each class of biomolecule plays a unique role in the structure and function of cells and organisms.

18.2 Proteins and Their Functions

Proteins are versatile macromolecules that perform a wide range of functions in biological systems. Their three-dimensional (3D) shape is essential for their specific functions.

Structural support: Proteins provide structure to tissues and organs (e.g., collagen in connective tissue).
Hormones: Some proteins act as chemical messengers (e.g., insulin).
Enzymes: Proteins that catalyze biochemical reactions (e.g., amylase).
Storage: Proteins store essential substances (e.g., ferritin stores iron).
Transport: Proteins transport molecules in body fluids (e.g., hemoglobin transports oxygen).
Protection: Proteins are involved in immune defense (e.g., antibodies).

Note: The 3D shape of a protein is crucial for its function; loss of shape often leads to loss of function.

18.3 Amino Acids

Proteins are polymers made up of amino acids linked by amide (peptide) bonds. The sequence and properties of amino acids determine the structure and function of proteins.

Amino acid structure: Each amino acid contains an amino group (–NH2), a carboxyl group (–COOH), a hydrogen atom, and a unique side chain (R group) attached to a central (α) carbon.
α-Amino acids: The amino group is attached to the carbon atom adjacent to the carboxyl group (the α-carbon).
Chirality: Of the 20 standard amino acids, 19 are chiral (can exist as L- and D-enantiomers); glycine is achiral.
L-amino acids: Only L-enantiomers are used in proteins in living organisms.

Classification of Amino Acids

Amino acids are classified based on the properties of their side chains (R groups):

Nonpolar (hydrophobic): Side chains are mostly hydrocarbons (e.g., alanine, valine).
Polar (hydrophilic): Side chains contain groups that can form hydrogen bonds (e.g., serine, threonine, cysteine, glutamine, tyrosine).
Acidic: Side chains contain a carboxyl group (e.g., aspartic acid, glutamic acid).
Basic: Side chains contain an amino group (e.g., lysine, arginine, histidine).

Intermolecular Forces Between Amino Acids

Noncovalent forces: Include hydrogen bonding, van der Waals forces, and ionic interactions.
Disulfide bonds: Covalent bonds formed between cysteine residues, stabilizing protein structure.

18.4 Acid-Base Properties of Amino Acids

Amino acids exhibit both acidic and basic properties due to their amino and carboxyl groups. In aqueous solution, they can exist as zwitterions—molecules with both positive and negative charges.

Zwitterion: A dipolar ion with a positively charged amino group (–NH3+) and a negatively charged carboxylate group (–COO–).
In acidic solution: The amino acid accepts a proton, becoming positively charged.
In basic solution: The amino acid loses a proton, becoming negatively charged.
Isoelectric point (pI): The pH at which the amino acid has no net charge (equal number of positive and negative charges). The pI value is unique for each amino acid.

18.5 Peptides

Peptides are short chains of amino acids linked by peptide (amide) bonds. The sequence of amino acids in a peptide or protein is critical for its identity and function.

Peptide bond: An amide bond formed between the carboxyl group of one amino acid and the amino group of another, releasing water.
Dipeptide: Contains two amino acids.
Tripeptide: Contains three amino acids.
Polypeptide: Contains many amino acids (usually more than 10).
Oligopeptide: Short peptide with a few amino acids (typically 2–20).
Protein: A polypeptide with more than 50 amino acids, folded into a functional shape.
Amino (N-) terminal: The end of the peptide with a free amino group.
Carboxyl (C-) terminal: The end of the peptide with a free carboxyl group.
Residue: Each amino acid unit within a peptide or protein.

Example: The sequence Ser–Ala–Gly–Phe represents a tetrapeptide with serine at the N-terminal and phenylalanine at the C-terminal.

18.6–18.9 Protein Structure

Proteins have four levels of structural organization, each contributing to their overall shape and function.

Primary structure: The linear sequence of amino acids in a protein chain, held together by peptide bonds. The precise order is crucial for protein identity and function.
Secondary structure: Local folding patterns stabilized by hydrogen bonds. The two main types are:
- α-helix: A right-handed coil stabilized by hydrogen bonds every fourth amino acid.
- β-sheet: Flat, sheet-like structures formed by hydrogen bonding between backbone atoms of adjacent chains.
Fibrous proteins: Form fibers or sheets, generally insoluble in water (e.g., collagen).
Globular proteins: Compact, generally water-soluble (e.g., enzymes, hemoglobin).
Tertiary structure: The overall 3D folding of a single polypeptide chain, stabilized by interactions between side chains (R groups), including hydrogen bonds, ionic interactions, hydrophobic interactions, and disulfide bonds.
Native protein: A protein in its functional, folded shape.
Simple protein: Composed only of amino acid residues.
Conjugated protein: Contains non-amino acid components (e.g., myoglobin contains a heme group).
Quaternary structure: The arrangement of two or more polypeptide chains (subunits) in a large, ordered structure (e.g., hemoglobin, collagen).
Cellular proteins: Found inside cells.
Mobile proteins: Found in extracellular fluids.

18.10 Chemical Properties of Proteins

Proteins can undergo chemical changes such as hydrolysis and denaturation, affecting their structure and function.

Protein hydrolysis: The cleavage of peptide bonds by water, yielding individual amino acids. This process is catalyzed by enzymes called endoproteases (e.g., chymotrypsin, trypsin).
Chymotrypsin: Hydrolyzes peptide bonds at the C-terminal side of aromatic amino acids (phenylalanine, tyrosine).
Trypsin: Hydrolyzes peptide bonds at the C-terminal side of basic amino acids (lysine, arginine).
Denaturation: The loss of secondary, tertiary, and quaternary structure (but not primary structure) due to external factors such as heat, mechanical agitation, detergents, organic solvents, pH changes, or inorganic salts. Denaturation usually results in loss of protein function.

Key Equations and Concepts

Peptide bond formation:

Zwitterion formation:

Isoelectric point (pI):

Additional info: The pI formula above applies to amino acids with non-ionizable side chains. For amino acids with ionizable side chains, the pI is calculated using the two pKa values that correspond to the neutral zwitterion form.

Table: Classification of Amino Acids by Side Chain Properties

Type	Properties	Examples
Nonpolar (Hydrophobic)	Hydrocarbon side chains, do not interact with water	Alanine, Valine, Leucine, Isoleucine, Methionine, Phenylalanine, Tryptophan, Proline, Glycine
Polar (Hydrophilic)	Side chains can form hydrogen bonds	Serine, Threonine, Cysteine, Tyrosine, Asparagine, Glutamine
Acidic	Side chains contain carboxyl groups, negatively charged at pH 7	Aspartic acid, Glutamic acid
Basic	Side chains contain amino groups, positively charged at pH 7	Lysine, Arginine, Histidine