PPT 1

Protein chemistry

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🧬 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:

Hydrolyze protein in 6 M HCl
Label amino groups fluorescently
Separate chromatographically
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

Primary — sequence
Secondary — helices, sheets
Tertiary — 3D fold
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.

Quiz

Score: 0/29 (0%)

Q0. Why do proteins have vastly greater chemical and functional diversity than DNA?

Proteins are longer than DNA molecules

Proteins are composed of 20 chemically distinct amino acids

Proteins are always folded into 3D structures

Proteins are synthesized faster than DNA

Q1. At physiological pH, amino acids in solution are best described as:

Fully protonated cations

Fully deprotonated anions

Neutral molecules without charge

Zwitterions containing both positive and negative charges

Q2. Which amino acid is NOT chiral at the Cα position?

Alanine

Valine

Glycine

Threonine

Q3. What does the CORN rule determine?

Whether an amino acid is acidic or basic

Whether an amino acid is hydrophobic or polar

Whether an amino acid is in the L or D configuration

Whether an amino acid is aromatic

Q4. Which two amino acids contain two chiral centers?

Valine and leucine

Isoleucine and threonine

Serine and cysteine

Phenylalanine and tyrosine

Q5. Which side-chain category contains amino acids that can form disulfide bonds?

Hydroxyl-containing

Aromatic

Sulfur-containing

Amide-containing

Q6. Why are aromatic amino acids important for protein UV absorbance measurements?

They fluoresce strongly in the visible range

They contain charged side chains

They absorb ultraviolet light due to conjugated ring systems

They are always exposed on protein surfaces

Q7. What does a pKa value represent on an amino-acid titration curve?

The net charge of the amino acid

The pH where the amino acid is neutral

The pH at which a protonatable group is 50% protonated

The maximum buffering capacity of the amino acid

Q8. Why does cysteine have a special role in enzyme active sites?

Its side chain is always negatively charged

Its thiolate form is highly nucleophilic

It is the most abundant amino acid

It has two chiral centers

Q9. Which amino acid side chain has a pKa closest to physiological pH, making it sensitive to small pH changes?

Aspartate

Lysine

Histidine

Tyrosine

Q10. What is the defining structural feature of the peptide bond?

It freely rotates around the C-N bond

It is planar due to partial double-bond character

It forms ionic interactions between residues

It always adopts the cis conformation

Q11. Which dihedral angles define the protein backbone conformation?

α and β

φ (phi) and ψ (psi)

θ and ω

χ1 and χ2

Q12. What information does a Ramachandran plot provide?

Amino-acid abundance in proteins

Allowed and disallowed backbone conformations

Protein molecular weight distributions

Hydrophobicity of amino acids

Q13. What characterizes a right-handed α-helix?

2.2 residues per turn

Hydrogen bonds between adjacent residues

3.6 residues per turn with i to i+4 hydrogen bonds

Parallel hydrogen bonds between strands

Q14. Why does proline often disrupt α-helices?

It is too hydrophobic

It lacks a backbone amide hydrogen

It is negatively charged

It forms disulfide bonds

Q15. Proteins are composed of only 20 amino acids.

True

False

Q16. At pH values above its pKa, an acidic side chain will predominantly be protonated.

True

False

Q17. Hydrophobic amino acids have titration curves dominated by only two pKa values.

True

False

Q18. The isoelectric point (pI) corresponds to the pH at which the net charge of an amino acid is zero.

True

False

Q19. Histidine is classified as a basic amino acid because it is always positively charged at physiological pH.

True

False

Q20. Disulfide bonds contribute to the tertiary structure of proteins.

True

False

Q21. The peptide bond most commonly adopts the trans conformation.

True

False

Q22. β-strands are more extended per residue than α-helices.

True

False

Q23. The helical wheel projection is used to visualize amphipathic α-helices.

True

False

Q24. Glycine is restricted to a narrow region of the Ramachandran plot due to steric hindrance.

True

False

Q25. Environmental factors within a protein can shift the pKa of an amino-acid side chain.

True

False

Q26. Aromatic amino acids generally have higher hydrophobicity than charged amino acids.

True

False

Q27. A peptide is defined as a naturally occurring polypeptide with a fixed three-dimensional structure.

True

False

Q28. Sequence databases like UniProt provide both manually reviewed and automatically annotated protein entries.

True

False