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Essential Amino Acids
Essential AAs: PVT TIM HaLL — Private TIM Hall
Essential Amino Acids
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.
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🃏 Essential Amino Acids
Essential amino acids (PVT TIM HaLL) — which nine?
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🃏 Answer
Essential AAs: PVT TIM HaLL — Private TIM Hall
PPhenylalanine
VValine
TThreonine
TTryptophan
IIsoleucine
MMethionine
HHistidine
LLeucine
LLysine
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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.
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🃏 Amino Acid Structure
Amino acid structure — the parts?
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🃏 Answer
AA structure: amine + carboxyl + R group (side chain determines properties)
Amino Acid Structure — Central alpha carbon bonded to: NH₂ (amino group), COOH (carboxyl), H, and R group (side chain). R group determines: charged, polar, nonpolar, or aromatic.
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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.
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.
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🃏 Hydrophobic Effect
Hydrophobic effect — where do nonpolar amino acids go, and why?
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🃏 Answer
Nonpolar AAs cluster in the protein interior — hydrophobic core
Hydrophobic Effect — 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.
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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.
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🃏 Isoelectric Point
Isoelectric point (pI)?
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🃏 Answer
Isoelectric point (pI): pH where amino acid has no net charge — used in gel electrophoresis
Isoelectric Point — 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.
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).
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🃏 Protein Denaturation
Protein denaturation — causes, and what survives?
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🃏 Answer
Denaturation: protein loses 3D structure due to heat, pH change, or chemicals. Primary structure intact.
Protein Denaturation — 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.
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.
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🃏 Peptide Bond Formation
Peptide bond — how does it form?
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🃏 Answer
Peptide bond: formed between carboxyl group of one AA and amino group of next. Water released (condensation).
Peptide Bond Formation — 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.
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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.
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🃏 Aromatic Amino Acids
Aromatic amino acids — which three, and what do they absorb?
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🃏 Answer
Aromatic amino acids: FWY — Phenylalanine, Tryptophan, Tyrosine. Absorb UV at 280nm.
Aromatic Amino Acids — 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.
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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.
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🃏 Collagen Structure
Collagen — structure and requirements?
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🃏 Answer
Collagen: most abundant protein in body. Triple helix. Needs glycine every 3rd position + vitamin C for synthesis.
Collagen Structure — 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.
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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.
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🃏 Enzyme Active Site
Enzyme active site?
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🃏 Answer
Enzyme active site: specific 3D pocket that binds substrate. Shape complementary to substrate (induced fit).
Enzyme Active Site — 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.