Proteins + enzymology Flashcards
enzymes
biological catalysts - make reactions happen more rapidly
regenerated and unchanged
work under mild physiological conditions
specific for reaction and substrate
enzyme reaction
forms enzyme-substrate complex
rapidly reversible process
E + S = ES -> E + P
velocity
vmax
km
v = vmax x [s]/km + [s]
v = initial velocity
vmax = maximum possible velocity
km = [s] that gives reaction velocity that is 1/2 of vmax
- approximates affinity to substrate
kcat
kcat = describes how fast it works
v = kcat x [ES]
at saturation: v = kcat x [E total]
specificity constant
kcat/km
best single measure of enzyme catalytic efficiency
ideally high
lineweaver burke plot
used to find vmax
plot 1/v by 1/s
produce a y intercept of 1/vmax
reversible and competitive inhibition
inhibitor and substrate both complementary to enzyme
cannot be at active site at same time
reduce overall speed of enzyme as distracted
with high substrate concentrations vmax unchanged
changes km as need more substrate to overcome inhibitor
inhibition velocity equation
v = vmax x [s] / km x (1 + ([i]/ki)) + [s]
kmapp = km x (1 + ([i]/ki))
kmapp = presence of inhibitor
ki = inhibitor constant
specific and irreversible inhibition
reacts with enzyme, bonds covalently to permanently block active site
cysteine in many enzymes, -SH group reacts with iodoacetate
km unchanged - enzyme takes same [s] to get to 1/2 vmax
vmax changed - rate and max rate reduced as less enzymes working
functions of proteins
defence - external coverings + immunity
structure- mechanical support, coordinated movement
catalysis- enzymes
transport- haemoglobin
amino acids
general formula:
R
NH2-C-COOH (carbonyl + amino
H
zwitterion- (coo- nh3+) more likely in physiological conditions
chiral centre- optical isomers
all have L-configuration
complex 3D structures determined entirely by amino acid sequence
amino acid side chains
R is variable side chain
glycine H
cysteine CH2SH
serine CH2OH
alanine CH3
histidine
peptide bond
COOH + NH3 = peptide bond + H2O
N has lone pair, becomes delocalised in region
partial double bond characteristics between O and N
secondary structure - alpha helix
right handed helix
good H bonding wihtin backbone
3.6 residues/turn
side chains project away from core + interact with other things
helix forming residues = more likely
helix destabilisers (eg tyrosine) = can, but if grouped become unstable
helix breaker (proline)= side chain bond with N so cannot participate in H bonding as no NH
secondary structure- beta sheet
antiparallel:
straight alligned = stronger H bond
carbonyl H bond with amino group of other chain
parallel:
H bond at more of an angle = weaker
less common as more unstable
tertiary structure
3D folded polypeptide
sidechain interactions
sequence of sidechains determine how it folds
hydrophobic: valine, leucine, phenylalanine
hydrophilic: aspartate, lysine, serine
tertiary structure - hydrophobic effect
most important determinant
phobic + phobic
philic + water
tendency of phobic side chains to cluster within inside of fold + philic on outside
water molecules form “cage”
tertiary structure - van der waal’s interactions
non covalent interactions between electrically neutral molecules
interaction between permanent dipoles
induced dipoles (london forces)
only significant when atoms very close
tertiary structure - hydrogen bonding
between side chains or backbones
-NH -OH have lone pairs
both good H bond donors + acceptors
tertiary structure - disulfide bonds
covalent
2 cysteine side chains
oxidation to form bond
-SH HS- -> S-S
tertiary structure - ion pair
salt bridge
aspartate + lysine
ionisation
domains
globular unit formed from part of a polypeptide
often associated with a particular function
eg yeast hexokinase - large domain binds ATP glucose
quaternary structure
assembly of more than one polypeptide chain
advantages- eg haemoglobin tetramer. one O2 binds increases affinity
