Amino Acids, Peptides, and Proteins: Structure, Properties, and Function

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AMINO ACIDS, PEPTIDES, AND PROTEINS

Overview of Protein Functions

Proteins are essential macromolecules that perform a vast array of functions in biological systems. Their diversity in structure allows them to catalyze reactions, provide structural support, transport molecules, and more.

Enzymatic proteins: Catalyze biochemical reactions, e.g., digestive enzymes hydrolyze food molecules.
Defensive proteins: Protect against disease, e.g., antibodies neutralize pathogens.
Storage proteins: Store amino acids, e.g., casein in milk, ovalbumin in eggs.
Transport proteins: Move substances, e.g., hemoglobin transports oxygen, membrane proteins transport molecules across membranes.
Hormonal proteins: Coordinate activities, e.g., insulin regulates blood sugar.
Receptor proteins: Respond to chemical stimuli, e.g., nerve cell receptors detect signaling molecules.
Contractile and motor proteins: Enable movement, e.g., actin and myosin in muscles.
Structural proteins: Provide support, e.g., keratin in hair, collagen in connective tissue.

Overview of protein functions (enzymatic, defensive, storage, transport)

AMINO ACIDS: BUILDING BLOCKS OF PROTEINS

General Structure and Properties

Amino acids are the monomeric units of proteins. Each amino acid contains a central (α) carbon atom bonded to an amino group, a carboxyl group, a hydrogen atom, and a unique side chain (R group).

α-carbon: Tetrahedral geometry with four different substituents (except glycine).
Functional groups: Acidic carboxyl group, basic amino group, hydrogen, and variable R group.
Polymerization: Amino acids link via peptide bonds to form polypeptides.

General structure of an alpha-amino acid

Classification of Amino Acids

Amino acids are classified based on the properties of their R groups:

Nonpolar, aliphatic: Glycine, Alanine, Proline, Valine, Leucine, Isoleucine, Methionine
Aromatic: Phenylalanine, Tyrosine, Tryptophan
Polar, uncharged: Serine, Threonine, Cysteine, Asparagine, Glutamine
Positively charged (basic): Lysine, Arginine, Histidine
Negatively charged (acidic): Aspartate, Glutamate

v Aromatic R groups Polar, uncharged R groups Positively charged R groups Negatively charged R groups

Properties and Notation

Three-letter and one-letter codes: Used for shorthand notation in sequences (e.g., Gly, G).
Chirality: All amino acids (except glycine) are chiral; proteins contain only L-amino acids.

Chirality of amino acids (L- and D- forms)

Ionization and Acid-Base Properties

Amino acids contain at least two ionizable groups (α-carboxyl and α-amino), each with its own pKa value. The ionization state depends on the pH of the environment.

At low pH: Amino acids are fully protonated (cationic form).
At high pH: Amino acids are fully deprotonated (anionic form).
Zwitterion: At intermediate pH, amino acids exist as zwitterions (net charge = 0).
Buffering: Amino acids can act as buffers near their pKa values.

Titration curve of glycine showing buffer regions and pI

Isoelectric Point (pI)

The isoelectric point is the pH at which the net charge of the amino acid is zero. For amino acids without ionizable side chains:

Formula:
At pI: Amino acid is least soluble and does not migrate in an electric field.

For amino acids with ionizable side chains, the pI is calculated using the two pKa values that surround the zwitterionic form.

Titration curve of histidine showing pI calculation Structure of aspartate (negatively charged R group)

Properties Table of Amino Acids

The following tables summarize the properties, abbreviations, pKa values, and occurrence of the common amino acids found in proteins.

Amino acid	Abbreviation	Mr	pK1 (COOH)	pK2 (NH3+)	pKR	pI	Occurrence (%)
Glycine	Gly, G	75	2.34	9.60	-	5.97	7.2
Alanine	Ala, A	89	2.34	9.69	-	6.01	8.3
Phenylalanine	Phe, F	165	1.83	9.13	-	5.48	3.9
Serine	Ser, S	105	2.21	9.15	-	5.68	6.8
Lysine	Lys, K	146	2.18	8.95	10.53	9.74	5.9
Aspartate	Asp, D	133	1.88	9.60	3.65	2.77	5.3

Amino acid properties table (part 1)

PEPTIDES AND PROTEINS

Peptide Bond Formation

Peptides are formed by the condensation of amino acids, resulting in an amide (peptide) bond. The peptide bond is planar due to resonance, restricting rotation and contributing to protein structure.

Directionality: Peptide chains are written from the N-terminus (amino end) to the C-terminus (carboxyl end).
Primary structure: The unique sequence of amino acids in a protein.

Peptide bond formation (condensation reaction) Primary structure of a peptide (sequence)

Protein Synthesis

Proteins are synthesized in cells using mRNA as a template. Ribosomes facilitate the assembly of amino acids into polypeptides via tRNA molecules.

Transcription: DNA is transcribed to mRNA.
Translation: mRNA is translated into a polypeptide chain.

Protein synthesis: translation on ribosome Protein synthesis: elongation and termination Protein synthesis: peptide bond formation tRNA structure and aminoacylation

PROTEIN STRUCTURE: HIERARCHY AND STABILIZATION

Levels of Protein Structure

Primary structure: Linear sequence of amino acids.
Secondary structure: Local folding into α-helices and β-sheets, stabilized by hydrogen bonds.
Tertiary structure: Overall 3D shape of a single polypeptide, stabilized by hydrophobic interactions, hydrogen bonds, ionic interactions, and disulfide bonds.
Quaternary structure: Assembly of multiple polypeptide subunits into a functional protein complex.

Hierarchy of protein structure: primary, secondary, tertiary, quaternary

Peptide Bond Properties

The peptide bond is a resonance hybrid, making it planar and rigid. This restricts rotation and influences the folding of the polypeptide chain.

Peptide bond resonance structures Peptide backbone geometry and bond angles

Secondary Structure: α-Helix and β-Sheet

α-Helix: Right-handed coil stabilized by hydrogen bonds between every fourth amino acid. Side chains project outward.
β-Sheet: Extended strands connected laterally by hydrogen bonds. Can be parallel or antiparallel.

α-helix structure and properties β-sheet structure and properties Parallel and antiparallel β-sheets

Tertiary and Quaternary Structure

Tertiary structure is the overall 3D arrangement of a polypeptide, while quaternary structure refers to the assembly of multiple polypeptides. Stabilizing forces include hydrophobic interactions, hydrogen bonds, ionic interactions, and disulfide bridges.

Tertiary structure: forces and disulfide bonds Disulfide bridge in protein structure Quaternary structure: assembly of subunits

FIBROUS PROTEINS AND STRUCTURE-FUNCTION RELATIONSHIPS

Fibrous Proteins

Fibrous proteins have structural roles and are characterized by regular secondary structures. Examples include α-keratin (hair, nails), collagen (connective tissue), and silk fibroin (spider silk).

Structure	Characteristics	Examples
α-Helix, cross-linked by disulfide bonds	Tough, insoluble, variable hardness	α-Keratin (hair, feathers, nails)
β-Conformation	Soft, flexible filaments	Silk fibroin
Collagen triple helix	High tensile strength, no stretch	Collagen (tendons, bone)

Structure of α-keratin in hair Collagen triple helix structure Collagen fibrils (cross-linking)

Protein Analysis Techniques

Purification: Based on charge, size, affinity, solubility, or hydrophobicity.
Sequencing: Edman degradation (classical), mass spectrometry (modern).

SUMMARY

Proteins are polymers of amino acids with diverse structures and functions.
Amino acids are classified by their side chains and have characteristic ionization properties.
Protein structure is hierarchical: primary, secondary, tertiary, and quaternary levels.
Fibrous proteins illustrate the relationship between structure and function.
Modern techniques allow for the purification and sequencing of proteins.