Proteins

Definition and Overview

Concept

Proteins: polymers of amino acids linked by peptide bonds. Function: catalysis, structure, signaling, transport, immune response. Diversity: >20,000 human proteins known.

Classification

Fibrous proteins: structural, insoluble, e.g., collagen, keratin. Globular proteins: functional, soluble, e.g., enzymes, hemoglobin.

Importance

Essential in cellular machinery, metabolic pathways, and genetic expression. Target molecules for drugs and biotechnological applications.

Amino Acids: Building Blocks

Structure

General formula: NH₂-CHR-COOH. Central α-carbon, amino group, carboxyl group, side chain (R-group).

Classification

Polar, nonpolar, acidic, basic, aromatic side chains. 20 standard amino acids encoded genetically.

Properties

Amphoteric: act as acid/base. Zwitterions at physiological pH. Side chains determine chemical behavior and interactions.

Peptide Bonds and Polymerization

Chemical Nature

Peptide bond: amide linkage between carboxyl of one amino acid and amino group of another. Covalent, planar, partial double-bond character.

Formation

Condensation reaction: elimination of water molecule. Enzymatic catalysis in ribosomes during translation.

Properties

Rigid bond restricts rotation, influences protein conformation. Backbone polarity: N-terminus to C-terminus directionality.

R1-COOH + H2N-R2 → R1-CONH-R2 + H2O

Primary Structure

Definition

Sequence of amino acids linked by peptide bonds. Unique to each protein.

Determination

Edman degradation, mass spectrometry used for sequencing. Genetic code specifies sequence.

Role

Defines all higher order structures. Mutations lead to functional changes or diseases.

Secondary Structure

Types

α-Helix: right-handed coil stabilized by hydrogen bonds. β-Sheet: aligned strands forming sheet via interchain hydrogen bonds. Turns and loops also present.

Stabilization

Hydrogen bonding between backbone amide hydrogen and carbonyl oxygen. No side chain involvement.

Examples

Keratin rich in α-helices. Silk fibroin dominated by β-sheets.

Tertiary Structure

Definition

Three-dimensional folding of a single polypeptide chain. Spatial arrangement of secondary structures.

Interactions

Hydrophobic interactions, hydrogen bonds, ionic bonds, disulfide bridges between cysteine residues.

Significance

Determines protein functionality and specificity. Misfolding causes aggregation and diseases.

Quaternary Structure

Definition

Association of multiple polypeptide subunits into a functional protein complex.

Examples

Hemoglobin: tetramer of two α and two β chains. DNA polymerase complexes with multiple subunits.

Stabilization

Non-covalent interactions: hydrophobic patches, electrostatic forces. Sometimes disulfide bonds.

Protein Folding and Stability

Mechanisms

Spontaneous folding driven by hydrophobic collapse and local interactions. Chaperones assist complex folding.

Energy Landscape

Folding funnels to minimum energy conformation. Misfolding traps lead to aggregates.

Denaturation

Loss of structure due to heat, pH, chemicals. Reversible or irreversible depending on conditions.

Biological Functions

Structural

Support and shape: collagen in connective tissue, keratin in hair and nails.

Transport

Carrier proteins: hemoglobin transports oxygen. Membrane channels regulate ion flow.

Regulatory

Hormones: insulin regulates glucose metabolism. Transcription factors control gene expression.

Enzymatic Activity

Catalysis

Enzymes accelerate biochemical reactions by lowering activation energy.

Specificity

Active site complements substrate shape and chemistry. High selectivity.

Regulation

Allosteric modulation, covalent modification, feedback inhibition control activity.

Protein Synthesis

Transcription

DNA template transcribed to mRNA in nucleus. RNA polymerase catalyzes synthesis.

Translation

Ribosomes decode mRNA into polypeptide chain. tRNA delivers amino acids matching codons.

Post-translational Modifications

Phosphorylation, glycosylation, ubiquitination alter activity, localization, stability.

DNA → mRNA → ProteinCodon (3 nucleotides) → Amino AcidRibosome catalyzes peptide bond formation

Analytical Techniques

Chromatography

Separation by size, charge, hydrophobicity: ion exchange, gel filtration, affinity chromatography.

Electrophoresis

SDS-PAGE separates proteins by molecular weight. Isoelectric focusing separates by pI.

Spectroscopy

UV absorbance for concentration. Circular dichroism for secondary structure. NMR and X-ray crystallography for 3D structures.

References

• Alberts B., Johnson A., Lewis J., et al., Molecular Biology of the Cell, 6th ed., Garland Science, 2014, pp. 1-1465.
• Lehninger A.L., Nelson D.L., Cox M.M., Principles of Biochemistry, 7th ed., W.H. Freeman, 2017, pp. 1-1304.
• Berg J.M., Tymoczko J.L., Gatto G.J., Stryer L., Biochemistry, 8th ed., W.H. Freeman, 2015, pp. 1-1152.
• Branden C., Tooze J., Introduction to Protein Structure, 2nd ed., Garland Publishing, 1999, pp. 1-302.
• Voet D., Voet J.G., Biochemistry, 4th ed., Wiley, 2011, pp. 1-1118.