Amino Acids, peptides, and proteins Flashcards
In neutral pH (7.4 in the body) what is the charge of an amino acid?
Zero, exists as a zwitterion, NH3 is protonated, while COOH is deprotonated to COO-
How are peptide bonds formed?
Why does C-N bond have partial double-bond character?
Condensation or dehydration reaction in which the nucleophilic amine group attacks the carbonyl carbon of a second amino acid. The OH group is lost as water and replaced with a peptide bond.
C-N bond has partial double-bond character due to resonance between carbonyl =O and lone pair on N.
What causes denaturation of proteins?
Heat, detergents like SDS that solubize proteins creating a hydrophobic core, and solutes like urea that interrupt intermolecular forces holding together structure.
What is the purpose of conjugating proteins with prosthetic groups?
Prosthetic groups are added to enzymes because they are needed for activity of the enzyme.
Direct a protein to a specific organelle including the cell membrane.
What type of amino acid side chain is needed to create a tightly-wound alpha helix?
One with very little steric hindrance.
Which amino acids have ionizable side chains?
Where might these amino acids be found and why?
+histidine, arginine, lysine (basic, N in side chains easily protonated)
-glutamate, aspartate (acidic, will lose proton easily)
Exterior of a protein, hydrophilic.
Why does adding base to a solution containing an enzyme reduce activity to zero?
Denatures enzyme.
Catalyses hydrolysis of peptide bonds that make up the enzyme.
Achiral amino acids
Glycine -CH2NH2
Non-polar, non-aromatic amino acids
Glycine(Gly) - CH2 Alanine(Ala) - CH3 Valine(Val) - C(CH3)2 Leucine(Leu) - CH2C(CH3)2 Isoleucine(ILe) - CCH3CH2CH3 Methionine(Met) - CH2CH2SCH3 Proline(Pro) - N w/5-member ring including N.
Aromatic Amino acids
Tryptophan(Trp) - N+5C ring w/cyclohexane
Phenylalanine(Phe) - cyclohexane
Tyrosine(Tyr) - Cyclohexanol.
Polar amino acids
Serine(Ser) - CH2OH Threonine(Thr) - CH(OH)CH3 Asparagine(Asn) - amide Glutamine(Gln) - (CH2)2+amide Cysteine(Cys) - CH2SH.
Acidic amino acids
Aspartic acid(Asp) - CH2COOH - ion is aspartate.
Glutamic acid(Gln) - (CH2)2COOH - ion is glutamate.
Basic amino acids
Arginine(Arg) - 3N, + delocalized over all 3.
Lysine(Lys) - terminal primary N.
Histidine(His) - ring with 2N, imidazole.
Intermolecular forces for each level of structure.
Primary - covalent peptide bonds.
Secondary - H bonding
Tertiary - van der Waals forces, H bonds, hydrophobic/hydrophilic interactions, disulfide bonds
Quaternary - van der Waals forces, H bonds, hydrophobic/hydrophilic interactions, disulfide bonds
What is a disulfide bond?
Bond formed between two cysteine chains when they become oxidized to form cystine. Create loops in proteins (tertiary structure.)
