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.
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🎓 Common Exam Questions
Q: What does PVT TIM HaLL stand for and why are these amino acids essential?
A: PVT TIM HaLL = Phenylalanine, Valine, Threonine, Tryptophan, Isoleucine, Methionine, Histidine, Leucine, Lysine. These 9 amino acids are called essential because the human body cannot synthesize them in sufficient quantities and they must be obtained from dietary protein. Complete proteins (meat, fish, eggs, dairy, soy) contain all 9 essential amino acids. Incomplete proteins (most plant proteins) lack one or more. Kwashiorkor is severe protein malnutrition caused by essential amino acid deficiency — particularly common in children. Branched-chain amino acids (BCAAs) are Valine, Leucine, and Isoleucine — all essential, metabolized in muscle rather than liver, important in exercise nutrition. Histidine was once considered non-essential for adults but is now classified as essential for all age groups.
Q: Describe the four levels of protein structure and the forces stabilizing each level.
A: Primary structure: the linear sequence of amino acids linked by covalent peptide bonds. Determined by DNA sequence. All higher levels of structure arise from this sequence. Secondary structure: local folding into alpha helices (hydrogen bonds between C=O and N-H groups within the same chain, every 4th residue) or beta pleated sheets (hydrogen bonds between adjacent strands running parallel or antiparallel). Tertiary structure: overall 3D shape of a single polypeptide chain, stabilized by: hydrophobic interactions (nonpolar residues cluster in interior), disulfide bonds (covalent S-S bonds between cysteine residues), ionic interactions (salt bridges between charged residues), hydrogen bonds, and van der Waals forces. Quaternary structure: assembly of two or more polypeptide chains (subunits) held together by the same noncovalent forces as tertiary. Example: hemoglobin has 4 subunits (2 alpha + 2 beta chains). Denaturation disrupts secondary, tertiary, and quaternary structure but leaves primary sequence intact.
Q: What is the isoelectric point (pI) and how is it used in protein separation?
A: The isoelectric point (pI) is the pH at which an amino acid or protein has zero net charge — it exists as a zwitterion (has both positive and negative charges that cancel). Below the pI: the molecule is net positive (more protonated). Above the pI: net negative (more deprotonated). Applications: Isoelectric focusing (IEF): proteins migrate through a pH gradient gel until they reach their pI and stop moving. Used in 2D gel electrophoresis (first dimension = pI, second = molecular weight). Precipitation: proteins are least soluble at their pI — adding ammonium sulfate at the pI precipitates them selectively. Column chromatography: ion exchange resins bind proteins depending on pH relative to pI. Amino acid pI values: Glycine pI = 5.97. Acidic amino acids (Asp, Glu) have low pI (~3). Basic amino acids (Lys, Arg, His) have high pI (~10). Most proteins have pI between 4 and 7.
Q: What is STYCNQ and what do these amino acids have in common?
A: STYCNQ = Serine, Threonine, Tyrosine, Cysteine, Asparagine, Glutamine — the six polar uncharged amino acids. They are hydrophilic (water-loving) but carry no net charge at physiological pH. Common features: all contain polar functional groups capable of hydrogen bonding. Serine (S) and Threonine (T): hydroxyl (-OH) groups — the most commonly phosphorylated amino acids in cell signaling. Kinases add phosphate; phosphatases remove it. Tyrosine (Y): also phosphorylated by tyrosine kinases — important in receptor signaling (EGF receptor, insulin receptor). Cysteine (C): thiol (-SH) group that can form disulfide bonds (-S-S-) with other cysteines — key for protein stability (insulin has 3 disulfide bonds) and in the active sites of many enzymes. Asparagine (N): N-linked glycosylation site — sugar chains attach here on secreted and membrane proteins. Glutamine (Q): primary nitrogen carrier in blood; donor for nucleotide synthesis.
Q: What is collagen structure and why does vitamin C deficiency cause scurvy?
A: Collagen is the most abundant protein in the human body (~30% of total protein), found in skin, tendons, ligaments, bones, and cartilage. Structure: triple helix of three polypeptide chains (alpha chains) wound around each other. Critical requirement: glycine must occupy every third position in the sequence (Gly-X-Y repeating pattern) because glycine is the only amino acid small enough to fit in the center of the triple helix. Proline and hydroxyproline in the X and Y positions add rigidity through ring structures. Synthesis and vitamin C connection: proline and lysine residues must be hydroxylated (hydroxylproline, hydroxylysine) for collagen to form stable triple helices and cross-link properly. The enzyme prolyl hydroxylase requires vitamin C (ascorbic acid) as a cofactor. Vitamin C deficiency → prolyl hydroxylase cannot function → defective collagen → scurvy. Symptoms of scurvy: bleeding gums, poor wound healing, weakened blood vessels, joint pain, bruising — all tissues requiring strong collagen are affected. Historical significance: scurvy killed thousands of sailors until James Lind demonstrated citrus prevented it in 1747.