🌍 Why Study Proteins?

Proteins are not just chains of amino acids—they are functional 3D machines.

• They act as enzymes, signal transducers, transporters, and structural scaffolds (e.g. antibodies).
• A single scaffold can support many functions → structure–function relationship is key.
• Understanding proteins enables:
  • Drug design 💊
  • Enzyme engineering 🧪
  • Sustainable technologies 🌱

Why proteins are hard:

• DNA has 4 building blocks → proteins have 20 amino acids
• Even a 37-residue protein has ~10⁴⁸ possible sequences
• Proteins are 3D, not linear → chemistry + physics + geometry

🧱 Amino Acids: The Building Blocks

General Structure

All amino acids share:

• Cα (alpha carbon)
• Amino group (–NH₃⁺)
• Carboxyl group (–COO⁻)
• Hydrogen
• Side chain (R group) → determines properties

They are zwitterions (carry both + and − charges at physiological pH).

⚡ Amino Acids and pH: Protonation States

pH-Dependent Charges

• Low pH (acidic): fully protonated → net positive
• Physiological pH (~7.4): zwitterionic → net 0
• High pH (basic): deprotonated → net negative

This applies before considering side chains.

🔑 Key idea: Charge is not fixed—it depends on pH relative to pKa.

⚖️ pKa and Isoelectric Point (pI)

• pKa: pH at which a group is 50% protonated
• pI: pH where the amino acid has net charge = 0

Side chains with ionizable groups shift the pI dramatically (e.g. Asp vs Lys).

🧬 Chirality and Stereochemistry

• Most amino acids are chiral → L and D forms
• Biological proteins use only L-amino acids
• Exception:
  • Glycine → achiral (side chain = H)
• Extra chiral centers:
  • Isoleucine
  • Threonine

Why life chose L-amino acids is still unknown.

🧪 Naming Side-Chain Atoms

Starting from Cα:

• β, γ, δ, ε … (moving outward)
• Important for:
  • Structural biology
  • Enzyme mechanisms
  • Mutational analysis

🧊 Classification of Amino Acids

1️⃣ Nonpolar (Hydrophobic)

• Glycine, Alanine, Valine, Leucine, Isoleucine
• Side chains = hydrocarbons
• Avoid water → buried inside proteins

🔹 Reactivity: very low 🔹 Function: structural packing, hydrophobic cores

2️⃣ Aromatic Amino Acids

• Phenylalanine (Phe)
• Tyrosine (Tyr)
• Tryptophan (Trp)

📡 Spectroscopy relevance

• Trp absorbs strongly at 280 nm → used to measure protein concentration
• Tyr absorbs moderately
• Phe weakly absorbs UV

🔹 Reactivity:

• Phe: low
• Tyr: moderate (–OH can be modified)
• Trp: chemically sensitive, fluorescence reporter

3️⃣ Proline – The Structural Disruptor

• Side chain forms a ring with backbone
• Technically an imino acid
• Severely restricts backbone flexibility

🔹 Reactivity: low 🔹 Structural role: breaks α-helices, induces turns

4️⃣ Basic (Positively Charged) Amino Acids

• Lysine (Lys) → + charged at physiological pH
• Arginine (Arg) → always + charged
• Histidine (His) → pKa ≈ 6 → can switch charge state

🔹 Reactivity:

• Lys: reactive (modifications, cross-linking)
• Arg: strong electrostatics, less chemically reactive
• His: highly reactive → acid/base catalysis

🧠 Histidine is special: perfect for enzyme active sites

5️⃣ Acidic (Negatively Charged) Amino Acids

• Aspartate (Asp)
• Glutamate (Glu)

🔹 Charge: −1 at physiological pH 🔹 Reactivity: moderate 🔹 Roles: catalysis, salt bridges, metal binding

6️⃣ Polar Uncharged (Hydroxyl-Containing)

• Serine (Ser)
• Threonine (Thr)
• Tyrosine (Tyr)

🔹 Reactive residues

• –OH group enables:
  • Phosphorylation
  • Hydrogen bonding
  • Nucleophilic catalysis (Ser!)

7️⃣ Amide Side Chains (Polar, Non-Reactive)

• Asparagine (Asn)
• Glutamine (Gln)

🔹 Charge: neutral 🔹 Reactivity: low

• Amide group is resonance-stabilized
• Excellent for hydrogen bonding
• Structural, not catalytic

8️⃣ Sulfur-Containing Amino Acids

Methionine (Met)

• Hydrophobic
• Initiates protein synthesis
• Sulfur is chemically inert

Cysteine (Cys)

• Contains thiol (–SH)
• Can form disulfide bonds
• Highly reactive

🔥 Most reactive amino acid

• Redox chemistry
• Catalysis
• Structural stabilization

🧠 Reactive vs Non-Reactive Amino Acids (Big Picture)

Highly Reactive

• Cysteine → redox, disulfides
• Histidine → acid/base catalysis
• Serine → nucleophile
• Tyrosine → phosphorylation

Moderately Reactive

• Aspartate, Glutamate
• Lysine

Largely Non-Reactive

• Glycine, Alanine, Valine, Leucine, Isoleucine
• Asparagine, Glutamine
• Methionine
• Phenylalanine

🔑 Rule of thumb: Reactivity comes from ionizable or nucleophilic side chains, not size.

🎯 Core Takeaways

• Amino acids are zwitterionic, chiral, and pH-dependent
• Side chains determine:
  • Charge
  • Reactivity
  • Structure
  • Function
• Only a subset of amino acids drive catalysis
• Protein chemistry = controlled diversity