Proteins and Amino Acids Lecture

Composition & Basic Structure of Proteins

• Composed of the elements C, H, O, N and occasionally S & P.

• Polymer is called polypeptide; monomeric unit is an amino acid.

• Generalised amino-acid backbone:

  • Central (α) carbon attached to four different groups:

  • \text{NH}_2 (amino group)

  • \text{COOH} (carboxyl group)

  • H (hydrogen atom)

  • R (variable side-chain that defines the amino acid)

• "R" side-chain also termed residual chain; determines polarity, charge, size & reactivity.

Diversity & Sources of Amino Acids

• > 20 naturally occurring amino acids share the same backbone but differ in R.

• Nutritional classification:

  • Essential – cannot be synthesised in the body; must be supplied by diet.

  • Non-essential – synthesised endogenously.

Classification by R-Group Properties

1. Non-Polar (Hydrophobic)

• Insoluble in water; generally non-reactive.

• Side-chains dominated by hydrocarbons or sulphur:

  • Glycine (Gly)

  • Alanine (Ala)

  • Valine (Val)

  • Leucine (Leu)

  • Isoleucine (Ile)

  • Methionine (Met) – contains S but remains non-polar.

  • Phenylalanine (Phe) – aromatic ring.

  • Tryptophan (Trp) – indole ring.

  • Proline (Pro) – cyclic structure; introduces kinks in polypeptides.

2. Polar (Uncharged, Hydrophilic)

• Increase protein solubility; capable of H-bonding.

• Examples & salient functional groups:

  • Serine (Ser) – \text{OH}

  • Threonine (Thr) – \text{OH}

  • Cysteine (Cys) – \text{SH} (forms disulphide bridges)

  • Tyrosine (Tyr) – aromatic \text{OH}

  • Asparagine (Asn) – amide \text{CONH}_2

  • Glutamine (Gln) – amide \text{CONH}_2

3. Basic (Positively Charged, Strongly Hydrophilic)

• R contains additional amino/guanidino groups; net + charge at physiological pH.

  • Lysine (Lys) – \text{NH}_3^+ terminal.

  • Arginine (Arg) – \text{=NH}_2^+ in guanidinium.

  • Histidine (His) – imidazole ring; pKa ~ 6.0, key in enzyme active sites.

4. Acidic (Negatively Charged, Strongly Hydrophilic)

• R has extra carboxyl giving net - charge.

  • Aspartic acid (Asp) – one-carbon side-chain.

  • Glutamic acid (Glu) – two-carbon side-chain.

Peptide Bond Formation (Condensation)

• Condensation (dehydration) reaction: removal of 1 molecule of H_2O.

  • \text{COOH} (of AA₁) + \text{NH}2 (of AA₂) \rightarrow peptide bond + H2O.

• Resulting bond is called an amide or peptide bond.

• Terminology:

  • 2 amino acids → dipeptide.

  • Many amino acids → polypeptide (primary structure of protein).

Peptide Bond Hydrolysis (Breakdown)

• Hydrolysis: addition of H_2O splits peptide bond.

  • H attaches to \text{NH}; OH attaches to carbonyl C=O.

• Biologically catalysed by proteases; industrially by acid/alkali treatment.

Acid-Base Behaviour of Amino Acids

Amphoteric Nature

• Contain both acidic (carboxyl) and basic (amino) groups → can donate or accept H^+.

• Act as intrinsic buffers in aqueous media.

Zwitterions & Isoelectric Point (pI)

• In neutral water: amino acids exist as zwitterions (dipolar ions) with internal salt linkage.

  • Carboxyl deprotonated (\text{COO}^-), amino protonated (\text{NH}_3^+).

  • Net charge 0 at specific pH = pI.

• Behaviour in pH extremes:

  • pH < pI: excess H^+ → amino acid gains H^+ → net positive.

  • pH > pI: excess OH^- → amino acid loses H^+ → net negative.

• Each amino acid possesses a unique pI that governs solubility & electrophoretic mobility.

Biological Buffering

• Amino acids & proteins resist small pH changes via reversible ionisation of \text{NH}_3^+ / \text{COO}^-.

• Help stabilise body fluid pH (e.g., blood at pH \approx 7.4).

• Haemoglobin acts similarly, complementing bicarbonate buffer system.

Colloidal Properties of Proteins

• Colloid = dispersed phase (protein particles 1–100 nm) + continuous medium (water).

• Protein surfaces carry charge, attracting hydration shells → remain suspended.

• Biological relevance:

  • Cytoplasm – colloidal matrix providing large reactive surface area.

  • Plasma proteins (albumin, globulins, fibrinogen) create oncotic (colloid osmotic) pressure, regulating water exchange across capillaries.

• Polysaccharides can form analogous colloids (e.g., starch paste).

Summary of Key Physicochemical Properties of Proteins

• Amphoteric – possess both acidic & basic reactive groups.

• Zwitterionic – net zero charge at pI; influences solubility & migration in electric fields.

• Buffer capacity – mitigate pH fluctuations; crucial for enzyme stability & metabolic homeostasis.

• Colloidal behaviour – do not fully dissolve; remain dispersed, impacting osmotic & rheological properties.

Applied & Integrative Notes

• Disulphide bonds (Cys ↔ Cys) stabilise tertiary & quaternary structures; redox-sensitive (e.g., insulin maturation).

• Hydrophobic vs. hydrophilic distribution drives protein folding (core burial of non-polar residues).

• Charged residues participate in salt bridges, active-site catalysis & substrate recognition.

• Nutritional balance depends on obtaining all essential amino acids (e.g., combining legumes & cereals).

• Denaturation (heat, pH, chemicals) disrupts non-covalent interactions without breaking peptide bonds, leading to loss of biological function – highlights criticality of proper buffering.

• Electrophoresis & isoelectric focusing exploit pI values to separate proteins; diagnostic tool (e.g., serum protein electrophoresis for multiple myeloma).

Ethical / Health & Practical Considerations

• Protein malnutrition (kwashiorkor, marasmus) underscores essential nature of dietary amino acids.

• Understanding colloidal & buffering properties informs pharmaceutical formulation (e.g., stable protein therapeutics, IV albumin).

• Environmental pH shifts can denature enzymes, impacting ecosystems; emphasises buffer systems’ ecological importance.

• Advances in synthetic biology enable design of novel polypeptides with tailored R-groups for biomaterials, raising biosecurity discussions.