Nine essential amino acids your body cannot synthesize
Phenylalanine, Valine, Threonine, Tryptophan, Isoleucine, Methionine, Histidine, Leucine, Lysine. Must come from diet. Deficiency causes protein malnutrition.
P
Phenylalanine
V
Valine
T
Threonine
T
Tryptophan
I
Isoleucine
M
Methionine
H
Histidine
L
Leucine
L
Lysine
Amino Acid Structure
AA structure: amine + carboxyl + R group (side chain determines properties)
Amino Acid Structure
All amino acids share the same backbone — R group makes each unique
Central alpha carbon bonded to: NH₂ (amino group), COOH (carboxyl), H, and R group (side chain). R group determines: charged, polar, nonpolar, or aromatic.
Charged Amino Acids
Charged AAs: DEHKR — Asp Glu His Lys Arg
Charged Amino Acids
Five amino acids with charged side chains at physiological pH
Negatively charged (acidic): Aspartate (D), Glutamate (E). Positively charged (basic): Histidine (H), Lysine (K), Arginine (R). Hydrophilic — found on protein surfaces.
D
Aspartate — negative
E
Glutamate — negative
H
Histidine — positive
K
Lysine — positive
R
Arginine — positive
Hydrophobic Effect
Nonpolar AAs cluster in the protein interior — hydrophobic core
Water repels nonpolar side chains → they pack together in protein interior. The hydrophobic effect is the main driving force of protein folding. Disrupt it (heat, detergents) → denaturation.
Isoelectric Point
Isoelectric point (pI): pH where amino acid has no net charge — used in gel electrophoresis
Isoelectric Point
The pH at which an amino acid carries zero net charge
Below pI: amino acid is positively charged (protonated). Above pI: negatively charged (deprotonated). At pI: zwitterion with no net charge. Electrophoresis at pI → amino acid doesn't migrate. Used to separate proteins.
How amino acid sequences become functional 3D proteins
Primary: linear sequence of amino acids — determined by DNA. Secondary: local folding patterns — alpha helix (hydrogen bonds within chain), beta pleated sheet (between strands). Tertiary: overall 3D shape — hydrophobic core, disulfide bonds, ionic interactions. Quaternary: multiple polypeptide chains (hemoglobin: 4 chains).
Primary
Amino acid sequence — the blueprint
Secondary
Alpha helix and beta sheet
Tertiary
Overall 3D fold
Quaternary
Multiple polypeptide chains
Protein Denaturation
Denaturation: protein loses 3D structure due to heat, pH change, or chemicals. Primary structure intact.
Protein Denaturation
Unfolding a protein — what's lost and what remains
Denaturation disrupts secondary, tertiary, and quaternary structure — but the primary sequence (covalent peptide bonds) remains intact. Heat: disrupts hydrogen bonds and hydrophobic interactions. Strong acid/base: disrupts ionic interactions. Cooking an egg: albumin denatures irreversibly. Some proteins can renature (refold).
Six amino acids with polar but uncharged side chains
These are hydrophilic — found on protein surfaces. Serine and Threonine: hydroxyl groups — common phosphorylation sites (signaling). Tyrosine: also a phosphorylation site. Cysteine: can form disulfide bonds — important for protein stability. Asparagine and Glutamine: amide groups.
S
Serine — hydroxyl, phosphorylation
T
Threonine — hydroxyl, phosphorylation
Y
Tyrosine — hydroxyl, signaling
C
Cysteine — forms disulfide bonds
N
Asparagine — amide
Q
Glutamine — amide
Peptide Bond Formation
Peptide bond: formed between carboxyl group of one AA and amino group of next. Water released (condensation).
Peptide Bond Formation
How amino acids link together to form proteins
Condensation reaction: carboxyl (-COOH) of one amino acid + amino (-NH₂) of next → peptide bond (-CO-NH-) + water released. N-terminus: free amino group at start. C-terminus: free carboxyl at end. Peptide bonds are planar and partially double-bond character — restricts rotation.
Aromatic Amino Acids
Aromatic amino acids: FWY — Phenylalanine, Tryptophan, Tyrosine. Absorb UV at 280nm.
Aromatic Amino Acids
Three amino acids with aromatic ring side chains
Phenylalanine (F): benzene ring, nonpolar. Tryptophan (W): indole ring, nonpolar — largest amino acid. Tyrosine (Y): hydroxyl on benzene ring, polar. Proteins absorb UV light at 280nm due to these residues — used to measure protein concentration (A₂₈₀). Tryptophan is the most UV-absorbent.
Collagen Structure
Collagen: most abundant protein in body. Triple helix. Needs glycine every 3rd position + vitamin C for synthesis.
Collagen Structure
The structural protein that holds the body together
Collagen: fibrous structural protein — skin, tendons, bones, cartilage. Triple helix: three polypeptide chains wound together. Requires glycine (smallest AA) every third position — fits into helix center. Proline and hydroxyproline add rigidity. Vitamin C required for hydroxylation of proline — deficiency causes scurvy.
Enzyme Active Site
Enzyme active site: specific 3D pocket that binds substrate. Shape complementary to substrate (induced fit).
Enzyme Active Site
The specific region where substrate binds and catalysis occurs
Active site: small portion of enzyme (~3-4% of total protein). Specifically shaped to bind substrate. Amino acid side chains in active site: provide binding interactions and catalytic groups. Lock and key (Fischer): rigid complementarity. Induced fit (Koshland): active site flexes to wrap around substrate — modern accepted model.