Biochemistry Flashcards
Chiral
AKA stereogenic center Has four different groups attached to carbon Optically active
Nonpolar amino acids
Glycine, alanine, valine, leucine, isoleucine, methionine, proline, phenylalanine, tryptophan
Polar amino acids
Tyrosine, serine, threonine, cysteine, asparagine, glutamine
Acidic amino acids
Aspartate and glutamate
Basic amino acids
Lysine, arginine, histidine
Catalytic triad
Found in chymotrypsin The histidine residue in its active site removes a proton from the -COOH group in an aspartic acid residue, which can then deprotonate a serine residue.
Amphoteric species
Can either accept a proton or donate a proton
pKa
The pH at which, on average, half of the molecules of that species are deprotonated. [HA]=[A-] If pH < pKa then majority protonated If pH > pKa then majority deprotonated
Amino acid deprotonation
pKa1 = pKa for carboxyl group = 2 pKa2 = usually amino group = 9-10
Zwitterions
At pH 7.4, you will have zwitterion COO- and NH3+ Overall charge is neutral
Isoelectric point (pI)
The pH at which the molecule is electrically neutral.
(pka1 + pKa2)/2 = pI of neutral aa
average of two lowest pKa’s for acidic aa
average of two highest pKa’s for basic aa
Oligopeptide
A relatively small peptide, up to about 20 residues
Peptide bond
Joins residues in peptides together. Forms between the COO- of one group and the NH3+ of another. Forms through dehydration or condensation reaction. Has partial double bond character from resonance.
Hydrolytic enzymes
Catalyze hydrolysis of peptides. Trypsin and chymotrypsin. Break apart amide bond by adding a hydrogen atom to the amide nitrogen and an OH group to the carbonyl carbon.
Lactose
Sucrose
Glycogen
Starch
Cellulose
Secondary Structure
H-bonds between amino hydrogens and carboxyl oxygen atoms of backbone.
Alpha helixes and Beta sheets
Tertiary structure
Interaction of side chains (hydrophobic interactions, VDW forces, ionic bonds, and H bonds)
Competitive Inhibition
Inhibitor competes with substrate to bind to active site
Can be overcome by increasing the concentration of substrate
Vmax does not change
Km increases
Noncompetitive Inhibition
Inhibitor binds to allosteric site that causes conformational change of active site and prevents substrate from binding. Can bind to enzyme or enzyme-substrate complex.
Km does not change
Vmax decreases
Uncompetitive Inhibition
Inhibitor binds to enzyme-substrate complex (can’t bind to enzyme alone) and prevents substrate from being released. Allosteric site is opened only after substrate binds to enzyme
Km is lowered
Vmax is lowered
Acetylation
Euchromatin
DNA less tightly bound
Chromatin is more active
Methylation
heterochromatin
