Biochemistry
Amino Acid Structure
Building blocks of proteins — 20 standard amino acids with diverse side chains
Amino acids are organic molecules with both an amino group (-NH₂) and carboxylic acid group (-COOH) on the same carbon. The α-carbon also has an H and an R group (side chain) — defines the specific amino acid. 20 standard amino acids in proteins. R groups vary: hydrophobic (alanine, valine), polar uncharged (serine, threonine), positively charged (lysine, arginine), negatively charged (aspartate, glutamate), aromatic (phenylalanine, tryptophan), unique (cysteine, proline). At physiological pH: zwitterion form (NH₃⁺, COO⁻). Linked by peptide bonds → proteins.
- Number standard20 amino acids in proteins
- General structureH₂N-CHR-COOH (R = side chain)
- At pH 7Zwitterion (NH₃⁺, COO⁻)
- Categories (R group)Hydrophobic, polar, charged, aromatic, unique
- Linked byPeptide bond (-NH-CO-)
- ChiralityAll natural amino acids are L (S configuration except Cys)
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Why amino acids matter
- Proteins. All proteins from amino acids.
- Enzymes. Catalytic activity from specific residues.
- Drug design. Many drugs target proteins.
- Nutrition. Essential amino acids must come from diet.
- Chirality. All natural L; pharmacological implications.
- Structural biology. Side chain interactions fold proteins.
- Cell biology. Signaling, transport, defense.
Common misconceptions
- 20 amino acids in all life. Mostly; some 21st-22nd in specific organisms.
- D-amino acids don't exist. They do; just not in proteins.
- Amino acid has 1 charged form. Zwitterion at physiological pH.
- All amino acids essential. 9 are essential; 11 can be synthesized.
- Side chain doesn't matter. Defines protein function.
- Peptide bonds easily rotate. Resonance restricts; partial double bond.
Frequently asked questions
What's an amino acid?
Molecule with both amino (-NH₂) and carboxylic acid (-COOH) groups on same carbon (α-carbon). Plus H and R (side chain). Generic structure: H₂N-CHR-COOH. R = different group for each amino acid. 20 standard ones in proteins. Each has 3-letter (Gly, Ala, Val, etc.) and 1-letter (G, A, V) codes.
What's a zwitterion?
Both + and - charges on same molecule (no net charge). At physiological pH, amino acids: NH₃⁺ (protonated amine) and COO⁻ (deprotonated acid). Zwitterion form. -NH₂ pKa ≈ 9-10; -COOH pKa ≈ 2. At pH 7: amine protonated; acid deprotonated. Net neutral.
What's the isoelectric point (pI)?
pH at which amino acid has zero net charge. For neutral side chains: pI = (pKa1 + pKa2)/2 ≈ 5-6. For acidic side chains (Asp, Glu): pI lower (~3). For basic side chains (Lys, Arg): pI higher (~10). pI useful for: separating amino acids by isoelectric focusing, determining behavior at given pH.
What's a peptide bond?
Amide bond between amino group of one amino acid and carboxylic acid of another. -NH-CO-. Forms by dehydration: -COOH + H₂N- → -CO-NH- + H₂O. Polypeptide: chain of many amino acids. Protein: large polypeptide with specific sequence + 3D structure. Peptide bond shows resonance — planar, restricts rotation; affects protein structure.
How are side chains classified?
By chemistry. (1) Nonpolar, hydrophobic: Ala, Val, Leu, Ile, Pro, Met, Phe, Trp, Cys (S-H acidic but generally hydrophobic). (2) Polar uncharged: Ser, Thr, Tyr, Asn, Gln. (3) Positively charged (basic): Lys, Arg, His. (4) Negatively charged (acidic): Asp, Glu. Categories influence: protein folding, solubility, function.
Why are all natural amino acids L?
Mystery of biological homochirality. All proteins use L-amino acids (S configuration, except Cys which is R). D-amino acids exist in nature (cell walls of bacteria, antibiotics) but not in proteins. Proposed origins: random + amplification, photosynthetic selection, meteorite-delivered. Origin of homochirality remains unsolved.
What's the genetic code connection?
DNA encodes proteins via codons (3 nucleotides = 1 amino acid). 64 codons; 20 amino acids + stop signals. Some amino acids have multiple codons (redundancy). Universal across nearly all life — strong evolutionary conservation. Translation: ribosome reads mRNA, attaches amino acids to chain via peptide bonds. Total: 20 standard amino acids in all living organisms.