Protein Folding, Bonds & Nucleic Acid Structure – Key Vocabulary

Protein Basics and Folding Rationale

• Proteins = functional workhorses inside cells; activity depends on their 3-D conformation.
• Construction pipeline
  • DNA sequence ➜ mRNA (transcription) ➜ amino-acid chain on ribosome (translation) ➜ spontaneous or assisted folding in aqueous cytoplasm.
• Key bond linking amino acids = peptide bond (covalent)
  • Much stronger than hydrogen bonds.
  • Analogy: peptide ≈ super-glue; hydrogen ≈ Velcro.
• Bacterial cell wall (peptidoglycan)
  • Carbohydrate “mesh” cross-linked by peptide bonds ➜ structural rigidity.
  • β-lactam antibiotics (e.g.
    penicillin) inhibit enzymes that make those peptide cross-links.
• Denaturation
  • Heat, pH, salt, or osmotic stress disrupt non-covalent interactions ➜ protein unfolds or misfolds.
  • Peptide backbone usually survives; tertiary/quaternary architecture is what collapses.

Four Hierarchical Levels of Protein Structure

• Primary (1°)
  • Linear amino-acid sequence (“beads on a string”).
  • 20 amino acids give ≈ 10^{10} possible short sequences.
  • Side-chains (R-groups) encode chemical personality (acidic, basic, polar, non-polar, sulfur-containing).
• Secondary (2°)
  • Local folding caused by backbone hydrogen bonds (C=O•••H-N).
  • Two canonical motifs:
  • α-helix (coiled spring)
  • β-pleated sheet (zig-zag “waffle”)—parallel or anti-parallel.
  • Tight description: H-bonds occur every 4 residues in α-helix, or between adjacent strands in β-sheet.
• Tertiary (3°)
  • Overall 3-D conformation of a single polypeptide.
  • Driving forces / stabilizers:
  • Hydrophobic collapse (non-polar residues tuck inward, away from water).
  • Hydrophilic & ionic side-chains face solvent.
  • Additional H-bonds between side-chains.
  • Disulfide bridges (-S-S-) between cysteines ➜ strong, “molecular safety-pins.”
  • Van der Waals attractions.
• Quaternary (4°)
  • Assembly of ≥2 tertiary subunits into a multimeric complex.
  • Terminology
  • Dimer (2); trimer (3); tetramer (4) …
  • Homodimer = identical subunits; heterodimer = different subunits.
  • Example hierarchy
  • Ribosome = rRNA core + ≈50 proteins (massive quaternary machine).
  • Hemoglobin = heterotetramer (α1, α2, β1, β2).

Case Study – Hemoglobin & Sickle-Cell Anemia

• Normal red blood cell (RBC)
  • Disk-shaped with central concave area; no nucleus (unique to mammalian RBCs) ➜ maximal surface/volume for O$_2$ transport.
• Mutation: single residue swap Glu➜Val in β-chain (primary-level change!)
  • Creates hydrophobic patch ➜ hemoglobin polymerizes when deoxygenated.
  • RBCs distort into rigid “sickles,” stick together ➜ vaso-occlusion, anemia, pain crises.
• Evolutionary link: Heterozygotes (one sickle allele) resist Plasmodium malaria infection ➜ high allele frequency in regions with endemic malaria (sub-Saharan Africa, Mediterranean).

Bond Strength Recap (contextual)

• Covalent (peptide, disulfide, glycosidic, phosphodiester, ester) > Ionic > Hydrogen ≈ Van der Waals.
• Rule of thumb: strong bonds build polymers; weak bonds fine-tune shape or transient interactions.

Carbohydrates vs. Lipids vs. Proteins vs. Nucleic Acids (Polymer Status)

• True polymers = carbohydrates (polysaccharides), proteins (polypeptides), nucleic acids (polynucleotides).
• Lipids NOT true polymers: triglyceride = glycerol backbone + 3 fatty acids via ester linkages (components not repetitive monomers).
• Carbohydrate monomers joined by glycosidic linkages; lipids use ester bonds; proteins use peptide; nucleic acids use phosphodiester.

Nucleic Acid Fundamentals

Monomer = Nucleotide

• Three parts
  1. Phosphate group (-PO$_4^{2-}$) ➜ negatively charged, “spring-loaded.”
  2. 5-carbon sugar (pentose)
  • Ribose in RNA (has 2′-OH)
  • Deoxyribose in DNA (lacks 2′-O ➜ DNA is "de-oxy")
  1. Nitrogenous base (information unit)
  • Pyrimidines: cytosine (C), uracil (U, RNA only), thymine (T) → mnemonic “CUT the Py.”
  • Purines: adenine (A), guanine (G).

Polymerization

• Condensation reaction between 3′-OH of one nucleotide & 5′-phosphate of next ➜ phosphodiester linkage.
• Generates directional backbone: 5′ ➜ 3′.

ATP – The Charged Nucleotide Example

• Adenosine triphosphate = adenine + ribose + 3 phosphates.
• Adding successive phosphates stores potential energy (electrostatic repulsion like “spring snake in a can”).
• Hydrolysis ATP + H2O \rightarrow ADP + Pi + \text{energy} releases usable free energy (no new energy created; it is liberated).

Double-Helical DNA Architecture

• Two antiparallel strands (one 5′➜3′, other 3′➜5′).
• Complementary base-pairing rules (Chargaff’s observations):
  • A pairs T via 2 H-bonds.
  • C pairs G via 3 H-bonds.
• X-ray crystallography (Rosalind Franklin) → helix parameters; Watson & Crick integrated data to model.
• Helix exhibits major & minor grooves → binding sites for proteins (transcription factors, repair enzymes, etc.).

DNA Tertiary Packing

• Supercoiling: twisting of double helix upon itself to relieve torsional stress.
• Histone proteins: positively charged "beads"; DNA wraps ≈1.65 turns ≈146 bp around each → nucleosome.
• Higher-order folding yields chromatin fibers, loops, and ultimately visible metaphase chromosomes.

Semiconservative DNA Replication (conceptual)

1. Helicase unzips parental helix (breaks H-bonds).
2. Each single strand acts as template.
3. DNA polymerase adds complementary nucleotides 5′➜3′.
4. Outcome: 2 identical daughter molecules, each = 1 old + 1 new strand ("semi-conservative").

Real-World & Cross-Lecture Connections

• Antibiotics exploit peptide bond strength in bacteria vs. human cells.
• Structural hierarchy mirrors other biopolymers: primary order dictates higher forms.
• Mutation at primary level can cascade to phenotypic disease (sickle cell) yet confer ecological advantage (malaria resistance) → illustration of natural selection.
• Energy logic of ATP applies to metabolic pathways (glycolysis, ETC) to be covered later.

Quick Reference Equations & Numbers

• Theoretical short peptide diversity ≈ 20^n; for n ≈ 10, diversity ≈ 10^{13} (lecture cited 10^{10} for illustrative subset).
• Peptide bond formation = condensation: \text{COOH} + \text{NH}2 \rightarrow \text{CONH} + H2O.
• Phosphodiester linkage: \text{(3′-OH) – sugar} + \text{PO}4^{2-} – \text{(5′)} \rightarrow \text{backbone} + H2O.
• ATP hydrolysis free energy ~ \Delta G^°’ \approx -30\,\text{kJ mol}^{-1} (context for future metabolism topics).