Amino Acids, Peptides, and Proteins

• Contain amino group and carboxyl group
• α-carbon + R chain
• Don’t need both groups bonded to same carbon
  • Example: GABA has amino group on γ-carbon
• Ornithine in nitrogen cycle is not made by codon
• Lysine converted to pyrroline
• 20 common amino acids are proteinogenic amino acids

Structure

• Most are chiral → optically active
• Glycine has H as R group → achiral → optically inactive
• All L-amino acids in eukaryotes
  • Amino group on Fischer projection is on the left
  • S configuration
• Threonine and isoleucine are only AAs with chiral carbon in side chain
• But cystine has R because SH group priority over COOH
• Methionine is nonpolar because methyl with S
• Proline is cyclic amino acid
  • Amino nitrogen is part of side chain

Aromatic

• Tryptophan, phenylalanine, tyrosine

Amide side chains

• Asparagine and glutamine have amide side chains
• Amide nitrogens don’t gain or lose protons with pH changes
• Don’t become charged

Cysteine

• Has thiol (SH) group
• Prone to oxidation

Negative

• Aspartic acid and glutamic acid
• Contain COO⁻ group
• Deprotonated form of aspartic acid is aspartate

Positive

• Lysine, arginine, histidine
• Histidine has aromatic ring with 2 N atoms (imidazole)
  • At pH 7.4, one N protonated and the other isn’t
  • In acidic conditions, second N protonated → positive charge

Khan Academy links

Introduction to proteins and amino acids

Amino acid structure and classifications

Orders of protein structure

Classification of amino acids

Special cases: Histidine, proline, glycine, cysteine

• Amphoteric → can accept or donate a proton
• Ionizable groups gain/lose protons depending on pH
• $pK_a$ is where half are protonated and half are deprotonated
• Different $pK_a$ values:
  • First for COOH ~2
  • Second for amino group ~9–10
• Zwitterion (hybrid): has + and − charges but overall neutral

Titrations

• Amino acids are good candidates because of acid–base properties
• When pH close to $pK_a$, solution is a buffer and titration curve is flat

Isoelectric point (pI)

• pI = pH where molecule is neutral

Calculating isoelectric point (pI)

• Neutral amino acids: average of 2 $pK_a$ values for amino and carboxyl groups
  • Neutral: $pI = \dfrac{pK_a(\text{NH}_3) + pK_a(\text{COOH})}{2}$
  • Example: glycine $pI = \dfrac{2.34 + 9.6}{2} = 5.97$
• Acidic amino acids:
  • $pI = \dfrac{pK_a(R) + pK_a(\text{COOH})}{2}$
  • Lower than neutral
  • USE LOWEST PI’S TO CALCULATE
• Basic amino acids:
  • $pI = \dfrac{pK_a(\text{NH}_3) + pK_a(R)}{2}$
  • Higher than neutral

Khan Academy links

Isoelectric point and zwitterions

• Dipeptides have 2 amino acids, tripeptides have 2
• Oligopeptides are <20, polypeptides are more
• Amino acids joined by peptide bonds

Peptide bonds

• Condensation reaction
  • Removes H₂O
• Acyl substitution reaction
  • Electrophile carbonyl carbon attacked by nucleophilic amino group on second AA
  • Hydroxyl group of carboxylic acid is kicked off
  • Forms peptide amide bond
• Resonance:
  • Double-bond character between O and N
  • Lack of rotation around amide bond → rigid

Hydrolysis

• Bases can catalyze peptide bond hydrolysis
• Hydrolytic enzymes catalyze peptide hydrolysis

Protease specificity

• Trypsin and chymotrypsin are specific
• Trypsin cleaves at carboxyl end of R and L
• Chymotrypsin cleaves at carboxyl end of F, W, and tyrosine (y)
• End in -inidase

Khan Academy links

Orders of protein structure

Primary structure

• Arrangement of amino acids
• Other levels of structure are energetically favorable
• Determined by sequencing
• Determined by DNA that codes for protein

Secondary structure

• Local structure from neighboring amino acids
• Due to hydrogen bonding between nearby AAs
• Most common: α-helices and β-pleated sheets

Alpha helices

• Rod-like structure
• Peptide rotates CCW around central axis
• H bond between carbonyl O and amide H 4 residues down
• Important in keratin structure

Beta pleated sheets

• Peptide chains lie alongside each other
• Pleated/rippled shape to maximize H bonding
• Fibroin (silk component) is made of β-sheets

Proline

• Kinks peptide chain in α-helix due to cyclic structure
• Rare in α-helices except in helices across cell membrane
• Common in turns between β-sheet chains or at start of α-helix

Tertiary structure

• 3D shape from interactions between R groups
• Two cysteine molecules form disulfide bond
  • Oxidized → cystine
• Disulfides create loops, affect curly hair
• Secondary structures form first, then collapse into 3D structure
• Molten globules are intermediate states
• Folding is quick
• Loss of tertiary structure = denaturation

Folding and solvation layer

• Solute dissolving in solvent forms solvation layer
• Hydrophobic residues in water cause water to rearrange
  • Negative change in entropy → nonspontaneous
• Hydrophilic molecules make water “chill” in positioning
  • Increases entropy

Quaternary structure

• Only for proteins with >1 polypeptide chain
• Aggregate of subunits (e.g., hemoglobin)
• Hemoglobin has 4 distinct subunits
• Immunoglobulin (IgG) has 4 subunits too
• Quaternary structure can:
  • Increase stability
  • Reduce DNA needed to encode protein
  • Bring catalytic sites closer
  • Create allosteric effects
    • One subunit changes → affects others

Conjugated proteins

• Function depends on covalently attached prosthetic groups
  • Organic molecules or metal ions
• Examples: lipoproteins, glycoproteins, nucleoproteins
• Used to:
  • Direct delivery to cell membrane/organelle
  • Add cofactors needed for activity
• Heme carries oxygen
  • Without heme, Hb is inactive

Khan Academy links

Protein folding and denaturation

Amino acid structure

Peptide bonds: Formation and cleavage

Four levels of protein structure

Conformational stability: Protein folding and denaturation