lecture 4 Flashcards
4 ways enzymes can catalyze reactions
move two molecules into correct alignment to initiate reaction (oriented binding)
change charge of substrate (stabilize transition state)
recruit cofactors to help reaction
cause strain on substrate, change shape (induced fit)
site on enzyme where substrate binds
active site- usually in cleft of enzyme
two examples of proteases
chymotrypsin and trypsin
explain how chymotrypsin works
breaks peptide bonds
binds to R group of Try, Phe and Trp (rings)
member of SERINE proteases
at edge of enzyme ser has OH that will form covalent bond and break the peptide bond of polypeptide chains
explain trypsin
works by binding to + R group of Lys, Arg
has negative charged Asp that binds to + charge NH3 on side chain
enzyme that breaks down polysaccaride chains in bacteria cell walls
lysozyme
michaelis-menten kinetics
v=Vmax(S)
Km + (S)
how fast a reaction can go is determined by how much substrate an enzyme can take over the affinity of enzyme and substrate
Vmax
the max velocity at which a reaction can occur
can only add a certain amount of substrate until enzymes become full
if you add more enzyme V max goes up
Km
constant, measure of binding affinity of enzyme and substrate
(how much substrate needed to reach half of Vmax)
high Km
weak binding between enzyme and substrate
low Km
high binding between enzyme and substrate- binds really fast
two types of enzyme inhibition
irreversible- enzyme destroyed during process
reversible
three types of reversible enzyme inhibition
competitive- fight for same site (feedback reactions)
noncompetitive- inhibitor binds to different site usually changes shape of enzyme - Vmax is lowered and Km unchanged
mixed- can bind if substrate is attached or not attached. binds at different site then substrate
describe noncompetitive inhibition
inhibitor binds to different site usually changes shape of enzyme
Vmax is lowered and Km unchanged
competitive enzyme inhibitor will
not work well when the substrate concentration is high
when an enzyme reaction is inhibited by a noncompetitive inhibitor what happens to Vmax and Km
the Vmax is lowered and the Km unchanged
allosteric interactions
effector binds to “other site”
homotypic allostery
heterotypic allostery
when the effector is the same as the substrate
homotypic allostery
cooperative kinetic interactions
when the effector is different from the substrate
heterotypic allostery
delay in curve means (S curve-sigmoidal curve)
allosteric interaction
delay is from binding has to occur in one site then whole thing change shape and more binding can happen
(conformational change)
example hemoglobin
what happens to allosteric curve with a positive and negative effector
+ effector first (goes faster)
no effect normal S curve
-effector (goes slower)
Aspartate Transcarbamoylase
ATCase
(1st step in biosynthesis of pyrimidines)
homotypic and heterotypic allostery
ATP + effector goes faster
CTP - effector, goes slower, reduces affinity of enzyme with substrate- makes conformational change in the structure to inactive (tense) state
ATCase is the committing step in the synthesis of CTP. If you already have enough CTP in the cell it will inhibit ATCase (feedback inhibition)
explain how CTP affects aspartate transcarbamoylase (ATCase)
CTP inhibitor
ATCase is the committing step in the synthesis of (pyrimidine)CTP. If you already have enough CTP in the cell it will inhibit ATCase (feedback inhibition)
explain how ATP affects aspartate transcarbamoylase (ATCase)
activator
will push the reaction to go faster.
high ATP levels means the cell is in good energy change, so energy is available for the production of pyrimidines (DNA replication)(CTP is an example of a pyrimidine that is made by ATCase)
sometimes an enzyme reaction is helped by ATP because ATP transfers its ___ to the sustrate
phosphate
called phosphorylation
___ is the enzyme that transfers phosphate from ATP to OH group of protein
protein kinase
end up with ADP and phosphate attached to O of R group
enzyme to take phosphate off R group
protein phosphatase
add water, Phosphate comes off
during the cascade of enzyme reactions that occur in fight or flight. the majority of the enzyme reactions are stimulated by the attachment of ____ to the enzyme
phosphate
the initial inactive form of proteins activated by proteolysis is called
zymogen
chymotrypsin is synthesized in the pancreas as an inactive precursor___. ___ needs to happen for activation into digestive enzyme
zymogen called chymotrypsinogen
Proteolysis (cleaves parts)
___ actives chymotrypsinogen(zymogen). but trypsin is released in inactive state ____ and needs to be activated by ____
trypsin
trypsinogen
enteropeptidase
example of isozyme
fetal and adult hemoglobin
NADH functions as a coenzyme in biological ___ reactions
catabolic
sometimes an enzyme reaction is helped by ATP because ATP transfers its ___ to the substrate
phosphate
Aspartate Transcarbamoylase
ATCase
oligomeric (multi subunit) enzyme
1st step in the making of pyrimidines which are required for synthesis of DNA and RNA
type of covalent modification of proteins which is irreversible
proteolytic activation
classic example of zymogen activation is ___, but a similar mechanism is also key in
digestive enzymes
blood clotting
___ is synthesized in the pancreas as an inactive zymogen called chymptrypsinogen
chymotrysin
the single cleavage by ___ causes a conformation change which results in the formation of the ____, which chymotrypsin is specific for aromatic and bulky nonpolar R Groups
trypsin
substrate specificity site
what is the master step in the activation of pancreatic enzymes
the cleavage of trypsinogen to form trypsin which eats chymotrypsinogen into active chymotrysin
what is an isozyme
related forms of an enzyme or protein that may differ functionally
ex. y hemoglobin in utero
vs
B hemoglobin at birth
does y hemoglobin or B hemoglobin attach to oxygen better
Y hemoglobin (fetal)
what is oriented binding
when an enzyme forces substrate into a specific position to help a reaction to happen
explain induction of strain by an enzyme
enzyme will change the shape of a substrate making it more likely to do a reaction
___ assist in the chemistry of a reaction between an enzyme and a substrate
cofactor
chymotrypsin breaks what
peptide bonds in amino acid chains that make proteins
___ is a digestive enzyme, a protease that is a member of serine proteases
chymotrypsin
___ is a “natural antibiotic” enzyme that catalyzed the severing of the polysaccaride chain that form the bacterial cell wall
lysozyme
present in saliva, tears and egg whites
lysozyme is present in
saliva and tears and egg whites
____ inhibitors bind to the enzyme covalently or destroy an enzymes functional group
irreversible
___ hijack the normal enzymes reaction to destroy it
suicide inactivators
___ enzyme inhibitors are used in ____ and form the basis for many successful medicines.
irreversible
drug design
___ is a suicide inhibitor that is used to treat the pathogen trypansome by ___
ornitine decarboxylace
irreversibly blocking the life cycle of the pathogen
