Proteins, DNA & RNA – Comprehensive Study Notes

Protein Shape & Functional Importance

• Proper folding is essential; mis-folded proteins lose or alter function (e.g., disease‐causing prions, cystic-fibrosis protein CFTR).
• Folding is intrinsically guided by the amino-acid sequence ("Anfinsen’s dogma") and assisted by cellular chaperones.
• Environmental factors (temperature, $pH$, ionic strength) stabilize or destabilize weak bonds (H-bonds, Van-der-Waals, hydrophobic interactions) that hold the structure.

Four Hierarchical Levels of Protein Structure

• Primary Structure
  • Linear sequence of amino acids linked by peptide bonds.
  • Sequence dictates higher-order folding; even a single residue change (e.g., Glu→Val in sickle-cell haemoglobin) may be catastrophic.
  • Usually written from N-terminus → C-terminus.

• Secondary Structure
  • Localized, repetitive conformations stabilized mainly by backbone H-bonds.
  • Main motifs: $\alpha$-helix (3.6 residues/turn; side chains project outward) and $\beta$-pleated sheet (parallel or antiparallel strands, side chains alternate above/below plane).
  • Turns/loops connect motifs and position functional residues.

• Tertiary Structure
  • Overall 3-D folding of an entire single polypeptide chain.
  • Stabilized by disulfide bridges (Cys-Cys), hydrophobic core packing, salt bridges, H-bonds.
  • Produces domains with specific activities (e.g., enzyme active sites, ligand-binding pockets).
  • Example: globular proteins often show hydrophobic interiors and polar surfaces; membrane proteins invert this distribution in trans-membrane segments.

• Quaternary Structure
  • Spatial arrangement of multiple polypeptide subunits into a functional oligomer.
  • Can be homomeric (identical subunits) or heteromeric (different).
  • Cooperative and allosteric behaviour (e.g., haemoglobin) emerges only at this level.

Conjugated Proteins (Glycoproteins & Lipoproteins)

• Some proteins are covalently linked to non-protein moieties:
  • Carbohydrate → glycoproteins (e.g., cell-surface receptors, antibodies).
  • Lipid → lipoproteins (e.g., LDL, membrane anchors).
• Conjugation alters solubility, targeting, and recognition.

Protein Denaturation, Renaturation & Practical Implications

• Denaturation = loss of native conformation without breaking primary peptide bonds.
  • Causes: Heat (cooking egg whites), extreme $pH$, high [NaCl] $\Rightarrow$ disrupt weak interactions.
  • Affects secondary $\rightarrow$ quaternary structure; primary remains intact.
• Renaturation: Some proteins refold spontaneously once the denaturant is removed (proof of sequence-encoded folding). Others require chaperones or are irreversibly denatured.
• Real-world relevance: sterilization by heat, fever-induced enzyme malfunction, desalting proteins during purification.

DNA – Blueprint Molecule

• Double-stranded helix held by complementary base pairing.
  • Sugar: deoxyribose $(C<em>5H</em>{10}O_4)$
  • Phosphate backbone (negatively charged)
  • Nitrogenous bases: Adenine (A), Thymine (T), Cytosine (C), Guanine (G).
• Nucleotide = deoxyribose + phosphate + base.
• Base pairing rules (Chargaff): $A$ pairs with $T$ (2 H-bonds), $G$ pairs with $C$ (3 H-bonds).
• Functions: Long‐term information storage, replication, hereditary transmission.

RNA – Working Copy of Genetic Information

• Single-stranded, generally shorter; transcribed only for the "gene of interest."
  • Sugar: ribose $(C<em>5H</em>{10}O_5)$ (one extra $O$ vs. DNA).
  • Bases: Adenine (A), Uracil (U), Cytosine (C), Guanine (G) – $U$ replaces $T$.
• Complementary base-pairing used during transcription: DNA template $\rightarrow$ RNA, with $A\leftrightarrow U$ and $G\leftrightarrow C$.
• Three major functional classes:
  • mRNA – messenger; carries coding sequence to ribosome.
  • tRNA – transfer; adaptor that brings amino acids during translation.
  • rRNA – ribosomal; structural & catalytic core of ribosomes.
• Additional forms: snRNA, miRNA, lncRNA (regulatory roles).

DNA vs. RNA – Key Differences (Quick Reference)

• Sugar: Deoxyribose vs. Ribose.
• Strand: Double vs. Single (usually).
• Base: Thymine vs. Uracil.
• Length: Entire genome vs. short gene-specific segments.
• Stability: DNA more chemically stable (lacks $2'$-OH), RNA more reactive $\rightarrow$ suitable for transient roles.

Connections & Broader Context

• Protein synthesis workflow: $\text{DNA} \xrightarrow{\text{transcription}} \text{RNA} \xrightarrow{\text{translation}} \text{Protein}$.
• Errors in any stage (mutation, misfolding, denaturation) lead to disease; therapeutic strategies include chaperone modulators and mRNA vaccines.
• Ethical / societal aspect: Genetic editing (CRISPR) alters DNA, indirectly influencing the proteome; must weigh benefits vs. potential off-target effects.