7-enzymes C Flashcards
what kind of curve is the michaelis-menten kinetics curve
logarithmic
do allosteric enzymes follow the michaelis-menten kinetics curve
no
what kind of curve does allosteric enzymes folloe
sigmoidal curves
what kind of allostery is cooperative substrate binding
positive allostery
what are the two states called in the allostery cooperative stuff
R and T states
what does the T state mean
tense and low affinity for substrate
what does the R state mean
relaxed state and high affinity for substrate
do effects bind covalently or non-covalently to regulatory sites
non-covalently
what is homoallostery
the substrates act as effects (like oxygen on hemoglobin)
where to homoallosteric effectors bind
to active sites or regulatory sites
what is heteroallostery
when the substrates are not the effectors (like BPG on hemoglobin)
where to heteroallosteric enzymes bind
to regulatory sites
what kind of structure do many allosteric enzymes have
quaternary
where can regulatory sites be (2 options we learned)
their own subunit but they may be on catalytic subunits
what can effects do to activity
increase (positive) or decrease (negative)
what do positive effectors do to the graph
shift to the left
which state do positive effects favor
the R state
what is Km
concentration of substrate it takes to get to 50% of Vmax
what do negative effectors do to the graph
shift it to the right
which state do negative effects favor
the T state
what is a generalization of the symmetry model of allostery
that the enzyeme can either be only in R or T state, no inbetween
what kind of structures do allosteric proteins in symmetry model of allostery have
quaternary structure
what are the states that each oligomer can exist in in symmetry model of allostery
in R or T state
what causes a shift in equilibrium in T and R states in symmetry model of allostery
when ligands/substrates bind (with different addinities)
what state is the enzyme in when there is no substrate bound (in symmetry model of allostery)
almost exclusively T state
which state in symmetry model of allostery is high activity
R state
which state in symmetry model of allostery is low activity
T state
what is the sequential model of allostery
when binding of substrate causes a conformational change which makes other subunits switch to the R state
what is in the symmetry model of allostery
binding of substrate affects the probability that the enzyme is in R or T state (the entire enzyme as a whole)
what kind of structure do the enzymes in sequention model of allostery have
quaternary structure
what are the states that each subunit can exist in in symmetry model of allostery
T or R state
is it the subunit or oligomer that can be in either T or R state in sequential model of allostery
subunits
is it the subunit or oligomer that can be in either T or R state in symmetry model of allostery
oligomer (whole enzyme, not just subunits)
is symmetry maintained in the sequential model of allostery
why
no, the subunits are not necessarily in the same conformation
what happens once a ligand binds in the sequential model of allostery
1 subunit becomes R state, there is an increased affinity for substrate in the other subunits
what is ATCase (what does it stand for)
aspartate transcarboamoylase
what kind of structure does ATCase (aspartate transcarboamoylase) have
quaternary
how many catalytic subunits does ATCase (aspartate transcarboamoylase)
6
how many regulatory subunits does ATCase (aspartate transcarboamoylase)
6
what is the symmetry for ATCase (aspartate transcarboamoylase)
D3
what is the role of ATCase (aspartate transcarboamoylase)
first step in CTP synthesis
what activates ATCase (aspartate transcarboamoylase)
ATP
which model of allostery does ATCase (aspartate transcarboamoylase) follow
symmetry
what inhibits ATCase (aspartate transcarboamoylase)
and how (which mechanism)
CTP, feedback inhibited
what composes the protomers in ATCase (aspartate transcarboamoylase)
1 catalytic and 1 regulatory subunit
how many protomers in ATCase (aspartate transcarboamoylase)
6
what is feedback inhibition
when the concentration of the end product of a pathway often signals the amount of activity required in the pathway
what kind of modulation are most feedback inhibitors
allosteric (because they have little resemblance to the origional substrate)
what is the T state of ATCase (aspartate transcarboamoylase) look like
the aspartate binding domain is blocked off
what is the R state of ATCase (aspartate transcarboamoylase) look like
the aspartate binding domain is not blocked off
is CTP binding favored in the R or T state of ATCase (aspartate transcarboamoylase)
favored in T state because its the inhibitor (T is closed off and compressed)
what does PALA do to the R state in ATCase (aspartate transcarboamoylase)
why
it stabilizes it because it looks like the intermediate for ATCase
is PALA an inhibitor or potentiatory and why
inhibitor because it mimics the intermediate for ATCase so it wont allow the enzyme to work
what does ATP do to the curve (Vo vs [S]) of ATCase
shifts it to the left
what does CTP do to the curve (Vo vs [S]) of ATCase
shifts it to the right
what does CTP do to ATCase
inhibit
what kind of inhibitor is CTP and why
heterotropic
what is a homotropic modulator
substrate for its target enzyme, as well as a regulatory molecule of the enzyme’s activity
what is a heterotropic modulator
regulatory molecule that is not the enzyme’s substrate
what kind of modulator is CTP to ATCase (2)
heterotropic inhibitor
what kind of modulator is ATP to ATCase (2)
heterotropic activator
what kind of modulator is aspartate to ATCase (2)
homotropic activator
why does CTP shift the ATCase graph to the right
because it makes it stay in the T state a little longer
why does ATP shift the ATCase graph to the left
because it makes it stay in the R state a little longer
is the catalytic and regulatory part on the same subunit in ATCase
no
is the catalytic and regulatory part on the same subunit in phosphofructokinase
yes
what kind of enzyme class is phosphofructokinase
transferase
what kind of symmetry does phosphofructokinase have
D2
what does each subunit in phosphofructokinase contain
an active AND a regulatory site
what is a homotretramer
protein complex made up of four identical subunits
what kind of protein is PFK (what are the subunits like and how many)
homotetramer
what happens to phosphofructokinase activity without AMP
why
it stays in the T state for longer
AMP is its activator
what happens to phosphofructokinase activity with AMP present
why
it goes into the R state faster because AMP is its activator
what happens to phosphofructokinase activity without ATP
why
there is high activity
ATP inhibits PFK
what happens to phosphofructokinase activity with ATP
why
it makes an inverted U shape curve because ATP starts to decrease activity (it is a negative regulator)
what kind of molecule is ATP to PFK
homotropic inhibitor
what kind of molecule is fructose-6-phosphate to PFK
homotropic activator
what kind of graph relationship does fructose-6-phosphate have to PFK
a sigmoidal relationship
where does fructose-6-phosphate bind to PFK
active site
where does ATP bind to PFK
it has 2 binding sites, active site and regulatory site
what kind of molecule is AMP to PFK
heterotropic activator
where does AMP bind to PFK
the same regulatory site as ATP
what kind of molecule is PEP to PFK
heterotropic inhibitor
what state does PFK shift to when AMP binds
why
to the R state
because its an activator
what is the nucleophile in the PFK reaction
fructose-6-phosphate towards the phosphate
what is the most common type of reversible covalent modification
phosphorylation
where can phosphorylation occur (which residues)
Ser, Thr, Tyr, His
what is the general formula for phosphorylation
Enzyme + ATP –> Enzyme-P + ADP
what are 2 types of reversible covalent modification
phosphorylation and adenylylation
which residues can get adenylylation
Tyr
what is the general formula for adenylylation
Enzyme + ATP –> Enzyme-AMP + PPi (pyrophosphate)
-it takes the adenosine
is adenylylation or phosphorylation a bigger physical change
adenylylation because thats taking an adenosineMP instead of just a phosphate
what are 2 conditions for the target sequence to act as a substrate for kinase
sequence must match the kinase active site and be available on protein surface
can some proteins have multiple targets/ protein kinases
yes
what do multiple targets/ protein kinases allow for in protein kinases
finer control of activity
what is the role of glycogen synthase
catalyzes glycogen synthesis (anabolic process)
does glycogen synthesis only get phosphorylated at phosphorylate 1 site
no it can be phosphorylated at multiple sites
what activates glycogen phosphorylase
phosphorylated by a kinase (it becomes phosphorylated to be active)
which state of glycogen phosphorylase is active (is it phosphorylated or not)
phosphorylated is the active state
what happens with phosphorylation of glycogen synthase
it becomes less active
what does multiple phosphorylations of glycogen synthase do
act in concert to reduce its activity
overall, how does phosphorylation effect glycogen synthase vs glycogen phosphorylase
reduction in glycogen synthase activity
increase in glycogen phosphorylase activity
what is irreversible covalent modification
a covalent change in PRIMARY structure
what are zymogen
unaltered inactive enzymes
what activates zymogen
modifications by other enzymes, like a proteinase
how do you turn off an activated zymogen
you need to destroy it or inactivate it
what happens when you phosphorylate isocitrate dehydrogenase and why
it is inactive because the phosphase (negative) interacts at the same site as the substrate (negative)
what activates trypsinogen
enteropeptidase
what is the active form of trypsinogen
trypsin
what does trypsin do
activates chymotrypsinogen into pi-chymotryipsin
what does pi-chymotryipsin di
cleaves and activates itself to become alpha-chymotryipsin
what kind of enzyme is enteropeptidase
proteinase
what kind of enzyme is trypsinogen
zymogen
what kind of enzyme is trypsin
proteinase
what kind of enzyme is chymotripsinogen
zymogen
what kind of enzyme is pi-chymotrypsin
proteinase
what kind of enzyme is alpha-chymotrypsin
proteinase
what happens in chymotrypsin maturation
trypsin cleaves it, exposes +ve N terminal which pulls back into an Asp group which stabilizes the negative charge
can aa far in 1ary structure be close in 3D space
yes
