Protein Structure, Classification & Properties

Classification of Proteins – Overview

• Proteins can be grouped according to several, sometimes overlapping, criteria:
  • Levels of organisation – \text{primary} \rightarrow \text{secondary} \rightarrow \text{tertiary} \rightarrow \text{quaternary}
  • Structure / morphology – fibrous vs. globular (and the special subtype “conjugated”)
  • Chemical composition – simple vs. conjugated (presence/absence of a prosthetic group)
  • Physiological / biochemical function – structural, catalytic, signalling, motility, defence, storage, transport, hormonal, receptor‐mediated, etc.

Levels of Organisation

• Four canonical structural tiers
  • Primary ➜ linear order of amino acids (covalent peptide backbone).
  • Secondary ➜ localised folding patterns stabilised mainly by hydrogen bonds.
  • Tertiary ➜ 3-D conformation of a single polypeptide (overall folding; “native state”).
  • Quaternary ➜ spatial arrangement of ≥2 polypeptide sub-units ± prosthetic groups.

Primary Structure

• Definition – unbranched “string” of amino-acid residues linked via peptide bonds.
• Covalent stability – backbone peptide bonds are rigid; side-chain chemistry confers diversity.
• Example: Lysozyme
  • 129 amino acids; full sequence given in transcript (Val–Phe–Gly–Arg–…–Arg–Leu).
  • Has a defined amino (N-) terminus and carboxyl (C-) terminus.
  • Critical for bacterial cell-wall hydrolysis ➜ illustrates that a single, precise primary sequence underpins function.

Secondary Structure

• Key driving force: intrachain H-bonding between \text{C=O} of residue i and \text{N–H} of residue (i\pm n).
• α-Helix
  • Right-handed coil (~3.6 residues/turn, pitch ≈ 0.54\,\text{nm}).
  • Stabilised by parallel H-bonds; side chains project radially outward.
  • Example: α-keratin (hair, wool) – confers elasticity & tensile strength.
• β-Pleated Sheet
  • Laterally packed strands (parallel or antiparallel) linked by inter-strand H-bonds.
  • Sheet adopts a “pleated” zig-zag; R-groups alternate above/below plane.
  • Exemplified by fibroin (silk): massive H-bond density ⇒ one silk fibre is “stronger than steel” weight-for-weight.
• Random coil / loop – irregular segments connecting helices & sheets; essential for flexibility & active/binding sites.

Tertiary Structure

• Overall folding – secondary motifs pack into compact, energetically favourable architecture (globular domain or extended fibre).
• Stabilising interactions
  • Hydrogen bonds – between polar R-groups (e.g., \text{Ser–Thr, Asn–Gln}).
  • Ionic (salt) bridges – \text{Lys/Arg}^+ ↔ \text{Asp/Glu}^-.
  • Disulfide bonds – oxidative covalent links between two cysteine \text{–SH} groups → \text{–S–S–}.
  • Hydrophobic & van der Waals interactions – non-polar side chains cluster to minimise exposure to aqueous milieu.
• Concept of folding/renaturation
  • Classic experiment: Ribonuclease unfolds with urea + reducing agent; removal of denaturant allows spontaneous refolding (shows that primary sequence encodes tertiary structure).

Quaternary Structure

• Assembly – multiple polypeptide chains (sub-units) associate non-covalently ± disulfide bridges.
• Motivations – cooperative binding, allosteric regulation, economy of genetic material, modularity.
• Example: Haemoglobin
  • 2\alpha + 2\beta globins + four haem (Fe^{2+}) groups.
  • Exhibits cooperative \text{O}2 binding (sigmoidal curve) & transports \text{CO}2 as carbaminohaemoglobin.
• Example: Collagen
  • Three left-handed α-chains form a right-handed “triple helix” → microfibrils → fibrils → fibres.
  • Rich in Gly–X–Y repeats (X = Pro, Y = Hyp) enabling tight packing & H-bond network.

Structural Classification (Morphology)

Fibrous Proteins

• Traits
  • Long, unbranched or parallel polypeptides; dominant secondary structure.
  • Water-insoluble; very stable; form fibres/sheets (structural role).
• Examples – keratin (hair, nails), collagen (connective tissue), fibroin (silk).

Globular Proteins

• Traits
  • Compact, spherical; extensive tertiary (and sometimes quaternary) folding.
  • Relatively water-soluble; can form colloidal suspensions.
  • Less structurally rigid; suited to dynamic functions (catalysis, transport).
• Examples – enzymes (amylase), haemoglobin, myoglobin, antibodies (IgG), ribonuclease.

Conjugated Proteins (overlaps fibrous/globular)

• Definition – apoprotein + non-protein prosthetic group.
• Representative list
  • Myoglobin – haem (Fe) – muscle \text{O}_2 storage.
  • Haemoglobin – haem (Fe) – erythrocyte \text{O}2/\text{CO}2 transport.
  • Glycoproteins (e.g., mucin) – carbohydrate – saliva, mucus.
  • Nucleoproteins – nucleic acid – chromosomes, ribosomes.
  • Casein – phosphoric acid – milk nutrient reservoir.
  • Cytochrome c oxidase – copper – electron transport chain.

Chemical Composition Classification

Simple Proteins

• Pure polypeptides; no prosthetic group.
• Sub-classes & examples:
  • Albumins – egg white albumin.
  • Globulins – immunoglobulins (antibodies).
  • Histones – DNA packaging.
  • Scleroproteins – keratin, collagen.

Conjugated Proteins

• Covered above; emphasise diversity of prosthetic groups (metal ions, lipids, carbohydrates, phosphates, etc.).

Physicochemical Properties

• Amphoteric nature – can act as acid or base due to \text{–NH}_3^+ and \text{–COO}^- groups.
• Zwitterionic form – at the isoelectric point pI, net charge =0.
• Buffering capacity – resist pH changes around pK_a values of side chains.
• Colloidal behaviour – large size ⇒ do not dialyse easily; scatter light (Tyndall effect).

Effect of pH & Temperature – Denaturation

• Definition – loss of native secondary, tertiary, (quaternary) structure without breaking primary covalent backbone.
• Agents
  • Extreme heat (≥ 40^{\circ}\text{C} for many mammalian proteins).
  • Extreme pH:
  • Acid: excess \text{H}^+ protonates \text{–COO}^- → \text{–COOH}.
  • Alkali: \text{OH}^- deprotonates \text{–NH}3^+ → \text{–NH}2.
  • Urea, guanidinium, detergents, heavy metals, organic solvents.
• Consequence – disruption of H-bonds, ionic interactions, disulfide bridges; protein unfolds ➜ loss of function.
• Renaturation – some proteins (e.g., ribonuclease) can refold if denaturant removed; many transformations are irreversible.
• Enzyme sensitivity – active site geometry collapses when tertiary structure fails → catalytic activity lost.

Functional Classification (Selected)

• Structural – collagen (connective tissue), keratin (hair).
• Storage – casein (milk), ovalbumin (egg), ferritin (iron).
• Transport – haemoglobin (\text{O}2/\text{CO}2), albumin (fatty acids), membrane pumps.
• Hormonal/signalling – insulin, growth hormone.
• Receptor – rhodopsin, cytokine receptors.
• Contractile/movement – actin, myosin, tubulin (cilia/flagella).
• Defensive – antibodies, complement proteins, thrombin (clotting).
• Enzymatic/catalytic – vast majority of metabolic catalysts.

Collagen – Structure–Function Correlation

• Quaternary architecture – triple helix (three α-chains) → microfibrils → fibrils → fibres.
• Chemical composition – Gly-X-Y repeat (X ≈ Pro, Y ≈ 4-Hydroxy-Pro); every third residue glycine fits sterically at helix centre.
• Cross-linking – covalent inter-chain links (lysyl oxidase) add tensile strength.
• Resultant properties
  • Insoluble, high tensile strength (≈ steel per weight) – resists stretching in tendons, ligaments, skin.
  • Slight flexibility provides skin elasticity.

Haemoglobin – Structure–Function Correlation

• Globular tetramer – \alpha2\beta2 each with haem (Fe^{2+}) prosthetic group.
• **Each haem binds one \text{O}2 ➜ total capacity = 4 \text{O}2 per molecule.
• Allosteric co-operativity – binding of first \text{O}_2 increases affinity for subsequent molecules (sigmoidal curve; essential for efficient loading/unloading in lungs/tissues).
• Also transports \text{CO}_2 – N-termini of globin chains form carbamates (carbaminohaemoglobin).

Polar vs. Non-Polar Amino Acids – Key Differences

• Side-chain chemistry
  • Polar: possess reactive functional groups (–OH, –SH, –CONH2, –COOH, –NH2, etc.) → hydrophilic.
  • Non-polar: alkyl or aromatic groups → hydrophobic, chemically inert.
• Hydrogen bonding
  • Polar residues form H-bonds with water/other polar residues.
  • Non-polar cannot (no suitable electronegative atoms).
• Spatial orientation in proteins
  • Polar outward (surface) interacting with aqueous environment.
  • Non-polar inward (core) – stabilised by hydrophobic interactions.
• Unique capability – Cysteine (polar) forms disulfide bonds; no non-polar residue forms such covalent cross-links.

Concept Integration & Exam Tips

• Hierarchy logic – primary dictates secondary, which influences tertiary, culminating in quaternary assemblies.
• Chemical principles – recognise how polarity, charge, hydrophobicity govern folding & stability.
• Real-world link – silk’s β-sheet strength enables biomimetic materials; haemoglobin mutations (e.g., sickle cell) show how single-residue changes disrupt quaternary behaviour.
• Ethical/medical aspect – protein denaturation in fevers (>40^{\circ}\text{C}) can be life-threatening; collagen degradation in scurvy underscores vitamin C’s role in post-translational hydroxylation.