परासरण

What Are Proteins?

Proteins are the most structurally and functionally diverse biological macromolecules. They are polymers of amino acids linked by peptide bonds. A single protein can consist of dozens to thousands of amino acid units, and the human body contains an estimated 100,000 different protein types.

Proteins perform an astounding range of biological functions: - Enzymes: catalyze biochemical reactions (amylase, DNA polymerase, hemoglobin) - Structural proteins: collagen (connective tissue), keratin (hair, nails), actin and myosin (muscle) - Transport proteins: hemoglobin (oxygen), transferrin (iron), lipoproteins (cholesterol) - Signaling molecules: insulin, growth hormone, antibodies - Defense: immunoglobulins (antibodies), fibrinogen (blood clotting) - Motor proteins: kinesin, dynein (intracellular transport)

Amino Acids: The Building Blocks

Amino acids are the monomers of proteins. All 20 standard amino acids share the same core structure:

• A central α-carbon (Cα)
• An amino group (–NH₂) attached to Cα
• A carboxyl group (–COOH) attached to Cα
• A hydrogen atom attached to Cα
• A unique side chain (R group) that distinguishes each amino acid

The general structure can be written as: H₂N–CαHR–COOH

At physiological pH (~7.4), amino acids exist as zwitterions — the amino group is protonated (–NH₃⁺) and the carboxyl group is deprotonated (–COO⁻), giving an overall neutral charge.

Chirality of Amino Acids

All 20 standard amino acids (except glycine, which has H as its R group) are chiral — they have four different groups on Cα. All naturally occurring amino acids in proteins are L-amino acids (S configuration at the α-carbon, with one exception). D-amino acids occur in some bacterial cell walls and certain antibiotics.

The 20 Standard Amino Acids

Amino acids are classified by the chemical nature of their R groups:

Nonpolar, Aliphatic

• Glycine (Gly, G): R = –H; smallest amino acid; no chiral center; found in tight turns
• Alanine (Ala, A): R = –CH₃; very common; found in helices
• Valine (Val, V): R = –CH(CH₃)₂; branched; hydrophobic core packing
• Leucine (Leu, L): R = –CH₂CH(CH₃)₂; very common in proteins
• Isoleucine (Ile, I): branched; two stereocenters
• Proline (Pro, P): cyclic structure — N is part of a ring; disrupts α-helices (creates kinks)
• Methionine (Met, M): contains sulfur; always the initiator amino acid (start codon AUG)

Aromatic

• Phenylalanine (Phe, F): hydrophobic benzyl group
• Tyrosine (Tyr, Y): has –OH on benzene ring; can be phosphorylated (signal transduction)
• Tryptophan (Trp, W): largest amino acid; indole ring; precursor to serotonin

Polar, Uncharged

• Serine (Ser, S): –CH₂OH; can be phosphorylated; found in active sites
• Threonine (Thr, T): –CH(OH)CH₃; can be phosphorylated
• Cysteine (Cys, C): –CH₂SH; forms disulfide bonds (–S–S–) that stabilize protein structure
• Asparagine (Asn, N): –CH₂CONH₂; N-glycosylation site
• Glutamine (Gln, Q): –(CH₂)₂CONH₂; most common amino acid in blood

Charged (Acidic)

• Aspartate (Asp, D): –CH₂COO⁻; negatively charged at pH 7; enzyme active sites
• Glutamate (Glu, E): –(CH₂)₂COO⁻; neurotransmitter (glutamic acid)

Charged (Basic)

• Lysine (Lys, K): –(CH₂)₄NH₃⁺; positively charged; histone proteins
• Arginine (Arg, R): guanidinium group; strongly basic; DNA binding
• Histidine (His, H): imidazole ring; near-neutral pKₐ (~6); critical in enzyme catalysis (proton shuttling)

The Peptide Bond

Amino acids join through peptide bond formation — a condensation reaction between the carboxyl group of one amino acid and the amino group of another, releasing water:

–COOH + H₂N– → –CO–NH– + H₂O

The peptide bond has partial double-bond character due to resonance delocalization of the nitrogen lone pair into the carbonyl. This means: - Rotation around the C–N bond is restricted - The four atoms C, O, N, H of the peptide bond are coplanar - The bond is usually in the trans configuration (R groups on opposite sides)

A chain of amino acids is a polypeptide. By convention, the free amino end is the N-terminus and the free carboxyl end is the C-terminus. Amino acid sequence is written N→C.

Levels of Protein Structure

Protein structure is described at four hierarchical levels:

Primary Structure

The primary structure is the linear sequence of amino acids, determined by the gene. Even a single amino acid substitution can dramatically alter protein function — sickle cell anemia results from valine replacing glutamate at position 6 of hemoglobin β-chain, causing the hemoglobin to polymerize under low oxygen conditions.

Secondary Structure

Secondary structures are local, regular patterns of folding stabilized by hydrogen bonds between backbone amide N–H and carbonyl C=O groups:

• α-helix: a right-handed coil with 3.6 amino acids per turn. The side chains point outward. Stabilized by H-bonds between residue i and residue i+4. Common in globular and membrane proteins. Keratin (hair) is mainly α-helical.

• β-sheet: extended strands running side by side (parallel or antiparallel) with H-bonds between strands. Antiparallel β-sheets are more stable. Silk fibroin and amyloid fibrils are mainly β-sheet structures.

• β-turn: a short loop that reverses the direction of the polypeptide chain.

• Random coil: regions without defined regular secondary structure (but not disordered — position is still defined in the folded protein).

Tertiary Structure

Tertiary structure is the overall three-dimensional fold of a single polypeptide chain. It is stabilized by: - Hydrophobic interactions: nonpolar side chains cluster in the protein core, away from water - Disulfide bonds: covalent S–S bonds between cysteine residues (important in extracellular proteins) - Ionic interactions (salt bridges): between oppositely charged side chains - Hydrogen bonds: between polar side chains - Van der Waals interactions: throughout the protein core

The protein folds to minimize free energy — the hydrophobic core with polar/charged residues on the surface (aqueous phase).

Quaternary Structure

Quaternary structure describes the arrangement of multiple polypeptide chains (subunits) in a multi-subunit protein. Not all proteins have quaternary structure.

Hemoglobin is a tetramer: 2 α subunits + 2 β subunits. The subunits interact cooperatively — oxygen binding to one subunit increases the affinity of the others (cooperative binding), creating the sigmoidal oxygen dissociation curve critical for oxygen transport.

Protein Denaturation

Denaturation is the loss of native three-dimensional structure without breaking peptide bonds. It destroys biological activity. Denaturing agents include: - Heat: disrupts H-bonds and hydrophobic packing (cooking an egg is irreversible denaturation) - Extremes of pH: disrupts ionic interactions - Detergents (SDS): disrupts hydrophobic interactions - Urea, guanidinium chloride: form H-bonds with the backbone, competing with intramolecular bonds - Reducing agents (β-mercaptoethanol): break disulfide bonds

Most denaturation in cells is irreversible. Chaperone proteins help newly synthesized polypeptides fold correctly and prevent inappropriate aggregation.

Protein Synthesis and the Genetic Code

Proteins are synthesized at ribosomes according to instructions encoded in mRNA (translation). Each codon (three nucleotides) specifies an amino acid. The genetic code is: - Degenerate: most amino acids are encoded by more than one codon - Universal: essentially the same in all living organisms - Unambiguous: each codon specifies exactly one amino acid