PPT 1

🧬 Page 1 — Why study proteins?

Proteins are central to life and biology:

• They act as scaffolds, machines, signals, transporters, and catalysts
• Understanding structure ↔ function is key to medicine, biotechnology, and biology
• Proteins are much more complex than DNA:
  • 20 amino acids vs 4 nucleotides
• The combinatorial explosion is enormous:
  • A 37-AA protein → 20³⁷ ≈ 1.37 x 10⁴⁸ possible sequences
  • One copy of each would weigh 1.5x Earth's mass
• Average human protein length: ~373 amino acids

🧠 Key idea: proteins are chemically diverse, structurally complex, and biologically powerful

🧪 Page 2 — What this lecture covers

Overview of core protein chemistry:

• Amino acids as building blocks
• Zwitterions & charge behavior
• Chirality
• Structures & naming conventions
• Amino-acid similarities & abundance
• Charge, pI, pH
• Protein structural hierarchy
• Secondary structure elements
• Databases & tools

⚖️ Page 3 — Amino acids as zwitterions

In water at physiological pH:

• Amino acids exist as zwitterions
  • NH₃⁺ (positive) and COO⁻ (negative) simultaneously
• pH controls protonation state:
  • Low pH → fully protonated
  • Neutral pH → zwitterion
  • High pH → deprotonated
• The graph shows species distribution vs pH

🧠 Key idea: amino acids are never “neutral” in solution

🔄 Page 4 — Chirality & the CORN rule

• All amino acids except glycine are chiral at Cα
• Nature uses only L-amino acids
• CORN rule:
  • View from H → Cα
  • Read CO → R → N
  • Clockwise = L-isomer
• Isoleucine & threonine have two chiral centers

🔢 Page 5 — Carbon naming (α, β, γ…)

• Side-chain carbons are named:
  • α, β, γ, δ, ε, ζ, η
• Example: lysine
  • Long aliphatic chain ending in ε-NH₃⁺
• Important for mechanisms, mutations, PTMs

🧱 Page 6 — Aliphatic amino acids

Nonpolar, hydrophobic side chains:

• Glycine (0 carbons)
• Alanine (1)
• Valine (3)
• Leucine (4)
• Isoleucine (4, branched)

🧠 Key idea: increasing carbon count → increased hydrophobicity

🌸 Page 7 — Aromatic & imino acids

Aromatic amino acids:

• Phenylalanine
• Tyrosine
• Tryptophan (largest, absorbs UV strongly)

Proline:

• Imino acid (side chain bonds back to backbone N)
• Rigid → disrupts helices

⚡ Page 8 — Charged side chains

Basic (positively charged):

• Lysine
• Arginine
• Histidine (aromatic + titratable near pH 7)

Acidic (negatively charged):

• Aspartate
• Glutamate

💧 Page 9 — Hydroxyl side chains

• Serine
• Threonine
• Tyrosine Contain -OH groups:
• Hydrogen bonding
• Phosphorylation sites (Ser, Thr, Tyr)

🔗 Page 10 — Amide & sulfur side chains

Amide:

• Asparagine
• Glutamine

Sulfur-containing:

• Methionine (thioether)
• Cysteine (thiol → disulfide bonds)

✏️ Page 11 — Drawing amino acids (exercise)

• Practice drawing amino acids from memory
• Reinforces:
  • Backbone
  • Side-chain diversity
  • Chirality awareness

🧬 Page 12 — Genetic code organization

• Codons encoding similar amino acids cluster together
• Stop codons can be repurposed for special amino acids

📊 Page 13 — PAM matrices

PAM = Point Accepted Mutations

• Measures evolutionary substitution probability
• Example:
  • Tyr ↔ Phe appears 6.6x more often than random
• Used in sequence alignment

🌟 Page 14 — The 22 amino acids

Beyond the standard 20:

• Selenocysteine (U) — encoded by UGA
• Pyrrolysine (O) — encoded by UAG Used in specific organisms and enzymes

🔠 Page 15 — One-letter codes

Rules:

• First letter used unless conflict
• Smallest amino acid gets priority Special codes:
• X = any amino acid
• B = Asn/Asp
• Z = Gln/Glu
• J = Leu/Ile

🌊 Page 16 — Hydrophobicity

Hydrophobicity measured as:

• ΔG of transferring AA from membrane interior → water
• High positive ΔG = hydrophobic
• Charged AAs strongly unfavorable in membranes

⚖️ Page 17 — Ionization of glycine

• Two pKa values:
  • pK₁ (COOH) ≈ 2.3
  • pK₂ (NH₃⁺) ≈ 9.6
• pI ≈ 6.0
• Titration curve shows charge transitions:
  • +1 → 0 → -1

📉 Pages 18-20 — Titration of all amino acids

• Side chains add extra pKa values
• Basic AAs can reach +2
• Acidic AAs can reach -2
• Histidine is special (pKa ≈ 6)

🧮 Page 19 — Henderson-Hasselbalch

Used to calculate:

• Fraction protonated vs deprotonated
• Example: Cys-S⁻ at different pH Formula:

pH = pKa + log(base / acid)

🌍 Pages 21-22 — Environmental effects on pKa

pKa depends on environment:

• Nearby charges shift pKa
• Hydrophobic environments favor neutral states
• Proteins tune pKa to enable catalysis

🧠 Key insight: pKa is not fixed inside proteins

👁️ Page 23 — Protein visualization & light

• Aromatic AAs absorb UV
• Choice of wavelength (λ) matters for detection

🧪 Page 24 — Amino acid analysis (AAA)

Process:

1. Hydrolyze protein in 6 M HCl
2. Label amino groups fluorescently
3. Separate chromatographically
4. Quantify peaks Limitations:

• Asn, Gln, Trp destroyed or lost

📈 Page 25 — Amino acid abundance

Based on:

• 207,132 protein sequences
• 75 million amino acids Shows natural AA frequency biases

📚 Page 26 — Amino-acid properties

Derived from large-scale sequence alignments Used to infer conservation and function

🏗️ Page 27 — Protein structure hierarchy

1. Primary — sequence
2. Secondary — helices, sheets
3. Tertiary — 3D fold
4. Quaternary — subunit assembly

🔗 Page 28 — Peptides vs proteins

• Peptide: short, flexible
• Polypeptide: longer chain
• Protein: folded, functional Residue mass = AA - H₂O

➡️ Page 29 — Peptide orientation

• N-terminus → C-terminus
• Backbone direction matters

🔄 Page 30 — Peptide bond geometry

• Planar due to partial double bond
• Two conformations:
  • Trans (favored)
  • Cis (rare; more common with Pro)

📐 Pages 31-32 — φ and ψ angles

• Backbone flexibility defined by φ (phi) and ψ (psi)
• Rotations determine folding possibilities

📊 Page 33 — Ramachandran plot

• Shows allowed/disallowed φ-ψ combinations
• Glycine more flexible
• Proline more restricted

🌀 Pages 34-35 — α-helices

• Right-handed 3.6₁₃ helix
• 3.6 residues/turn
• H-bond: n → n+4
• Helical wheel reveals amphipathic nature

🧵 Pages 36-37 — β-sheets

• Parallel vs antiparallel
• H-bond geometry differs
• Side chains alternate up/down
• Turns often i → i+3

📏 Page 38 — Structural distances

• α-helix: 1.5 Å/residue
• β-strand: 3.5 Å/residue

🧬 Page 40 — Collagen triple helix

• Special case
• Rich in Gly-Pro-Hyp
• Left-handed helices assemble into right-handed triple helix

🔍 Page 41 — Protein databases & tools

• UniProtKB (Swiss-Prot & TrEMBL)
• NCBI Protein
• ExPASy ProtParam
• ProtPi
• Structures: RCSB PDB

🧠 Final takeaway

Proteins are:

• Chemically diverse
• Structurally hierarchical
• Environment-dependent
• Evolutionarily optimized

Mastering amino acids → bonds → angles → structures is the foundation of protein science.