Block 1 Flashcards
what do enzymes increase
speed of reaction
what type of molecule are most enzymes
proteins
what is an apoenzyme
enzyme without its co-factor
non functional
a cofactor that is tightly bound to the enzyme is called what
prosthetic group
cofactors that are complex organic molecules are called what
coenzymes
what are isoenzymes
same enzyme, different structure
what is a zymogen
an inactive enzyme that must be cleaved to become active
what are 2 examples of zymogens
trypsin and chymotrypsin
what are the 4 basic steps of enzyme catalyzed reactions
- binding of substrate
- formation of enzyme substrate complex
- conversion of substrate to product
- release of product from active site
the active site of an enzyme is composed of the __ site and the __ site
catalytic and substrate binding
what does the induced fit model tell
interaction of substrate with enzyme induces conformational changes so the binding is a better fit
what do enzymes reduce
activation energy
what is the transition state for enzymes
peak of energy curve where reactants convert to products
what is involved in catalysis by bond strain
rearrangement when enzyme is bound to substrate induces strain
what is involved in covalent catalysis
formation of a covalent intermediate
what is an example of a covalent intermediate in covalent catalysis
serine proteases
what amino acids make up the serine protease triad
histidine
serine
glutamate (or aspartate)
co-enzymes are often what
water soluble vitamins
increased transcription of a gene or decreased proteolysis of enzyme protein increases or decreases enzyme activity
increases
effect of temperature on enzyme activity
too high= denature
too low= slow down
pH effect on enzyme activity
too high or low= denature
what is Km
the substrate concentration at 1/2Vmax
small Km means high or low enzyme affinity for substrate
high
high enzyme affinity means high or low substrate concentration
low
what do oxido-reductases do
transfer H+ or e-
what do hydrolases do
cleave bonds by addition of water
what do transferases do
transfer a group (not hydrogen or oxygen) from one molecule to another
what do isomerases do
interconvert isomers
what do lyases do
alter bonds without addition of water
what do ligases do
link 2 molecules
what is hydrolysis
bond cleavage by addition of water
what do racemases and epimerases do
interconvert optical isomers
what do dehydrogenases do
remove H
what does the y intercept represent in lineweaver burk plots
1/Vmax
what does the x intercept represent in lineweaver burk plots
-1/Km
what are 3 classifications of reversible inhibitors
competitive
noncompetitive
uncompetitive
where does the inhibitor bind in competitive inhibition
active site
where does the inhibitor bind in noncompetitive inhibition
allosteric site (changes shape)
where does the inhibitor bind in uncompetitive inhibition
enzyme-substrate complex
what effect does competitive inhibition have on Vmax and Km
Vmax unchanged
Km increases
what is an example of a competitive inhibitor in the citric acid cycle
malonate with succinate for succinate dehydrogenase
what is an example of a drug that is a competitive inhibitor
viagra
what effect does noncompetitive inhibition have on Vmax and Km
Vmax decreases
Km unchanged
what type of reversible inhibition can be reversed by increasing substrate concentrations
competitive inhibition
what effect does uncompetitive inhibition have on Vmax and Km
both decrease
what is an example of an uncompetitive inhibitor used to treat manic depression
lithium
what effect does irreversible inhibition have on Vmax and Km
Vmax decreases
Km unchanged
*same effects as reversible noncompetitive inhibition
irreversible inhibition has the same effects on Vmax and Km as what type of reversible inhibition
noncompetitive
what is an example of a toxin that is an irreversible inhibitor
cyanide
how does cyanide act as an irreversible inhibitor
binds to cytochrome oxidase and inhibits complex IV of ETC
what is an example of an irreversible inhibitor type of drug
aspirin
how does aspirin work
inhibits cyclo-oxygenase (COX) –>decreased pain and inflammation
what is an example of a reversible inhibitor drug that acts in the same way as aspirin
ibuprofen
what is an example of an allosterically regulated protein
PFK-1
what does phosphatase do
removes phosphate
what are the usual sites for phosphate addition to proteins (3 amino acids)
serine
threonine
tyrosine
does phosphorylation of glycogen phosphorylase activate or inactivate glycogen utilization
activates
does phosphorylation of glycogen synthase inhibit or activate glycogen synthesis
inhibit
what is enthalpy
amount of heat absorbed or released
what is the symbol for enthalpy
delta H
in endothermic reactions, are reactants or products at a higher energy level
products
are endothermic reactions anabolic or catabolic
anabolic
what does bioenergetics describe
transfer and utilization of energy
do catabolic or anabolic reactions release heat
catabolic
what is the standard free energy for each of the 2 terminal phosphates that ATP can release
-7.3 for each
what is Gibbs free energy
energy available to do work
what do negative delta G^0’ tell
it is an exergonic reaction proceeding to the right (to lower energy state)
spontaneous
what do positive delta G^0’ tell
it is an endergonic reaction proceeding to the left (to lower energy state), nonspontaneous
phosphorylation of glucose by ATP is catalyzed by what 2 enzymes
hexokinase and glucokinase
what is involved in reaction coupling
product of one reaction is the reactant of another
what is the common intermediate compound in coupled reaction in living cells
ATP
how can all sugars be activated
by adding a nucleotide
what is reduction potential a measurement of
the tendency for a substrate (reactant) to accept electrons
how can the proportions of NAD+ and NADH in a solution be determined
UV absorption spectra
a high value at 340nm in UV absorption tells us there is high or low NADH content
high
how is UV spectrophotometry used for lactate dehydrogenase
pyruvate–>lactate, NADH is consumed= decrease in absorbance at 340nm
lactate–>pyruvate, NADH is produced= increase in absorbance at 340nm
why is ATP called a high energy phosphate compound
it has a large negative standard free energy value (-7.3 for each of the 2 terminal phosphates)
what are the 3 main sources of phosphate for ATP
- oxidative phosphorylation
- glycolysis (phosphoglycerate kinase and pyruvate kinase)
- citric acid cycle (succinate thiokinase)
what 2 processes does oxidative phosphorylation couple
respiration and generation of ATP
how does the inner mitochondrial membrane differ from the outer
outer is permeable
inner is impermeable
what is needed due to the impermeability of the inner mitochondrial membrane
transporters
what is the function of cristae of the inner mitochondria membrane
increase SA
where does the electron transport chain occur in the cell
inner mitochondrial membrane
what is the role of the respiratory chain of the mitochondria
conversion of food energy to ATP
what is the basis of the ETC
high energy molecules (ex: glucose) are metabolized by redox reactions to yield CO2 and water
what do the metabolic intermediates of ETC reactions donate electrons to
NAD+ and FAD to form NADH and FADH2
as electrons are passed down the ETC, do they gain or lose free energy
lose
what is the energy lost by electrons as they are passed down the ETC used for
creating a proton gradient
what processes does oxidative phosphorylation couple
electron transport with ATP synthesis
what is the remainder of the free energy not trapped as ATP in the ETC used to drive
calcium transport into mitochondria
generate heat
how many complexes make up the inner mitochondrial membrane
5
what complexes of the inner mitochondrial membrane are used in the ETC
1-4
what are the 2 mobile electron carriers used in the ETC
co-enzyme Q
cytochrome c
what is the final e- acceptor of the ETC
molecular O2
what process accounts for the body’s use of the greatest amount of oxygen
ETC
what is complex 5 of the inner mitochondrial membrane also called
ATP synthase
what complex of the inner mitochondrial membrane catalyzes ATP synthesis
5
what complexes of the inner mitochondrial membrane do e- pass through
1, 3, and 4
what is complex 1 of the inner mitochondrial membrane also called
NADH-Q oxidoreductase
what occurs in complex 1 of the inner mitochondrial membrane
e- are transferred from NADH to CoQ
what is CoQ also referred to as
ubiquinone
what is CoQH2 also known as
ubiquinol
what is complex 3 of the inner mitochondrial membrane also called
Q-cytochrome c oxidoreductase
what does complex 3 of the inner mitochondrial membrane do
pass e- from CoQ to cytochrome c
what is complex 4 of the inner mitochondrial membrane also called
cytochrome c oxidase
what does complex 4 of the inner mitochondrial membrane do
pass e- to O2, causing it to be reduced to H2O
what is complex 2 of the inner mitochondrial membrane also called
succinate-Q reductase
why are e- passed to Q through complex 2 instead of 1
the substrate (succinate) has a greater redox potential then NAD+/NADH
NADH carries a free protein. In the ETC, where is this proton transferred to
NADH dehydrogenase in complex 1
what complexes of the ETC contain iron-sulfur proteins
1, 2, 3
all members of the ETC are proteins with the exception of __ which is a __
coenzyme Q
lipid
coenzyme Q in the ETC accepts e- from what 2 complexes
1 and 2
coenzyme Q can accept e- from what enzyme in glycolysis
glycerophosphate dehydrogenase
coenzyme Q can accept e- from what enzyme in fatty acid oxidation
acyl CoA dehydrogenase
cytochromes contain a __ group with iron in a +__ (2 or 3) state
heme
3+
what complex of the ETC contains copper
4
what is the importance of copper in complex 4
required for splitting of O2
complex 4 contains how many heme and how many copper groups
2 heme
2 copper (CuA and CuB)
how many protons are pumped in complex 1 of the ETC
4
how many protons are pumped in complex 2 of the ETC
none
with the proton gradient of the ETC, the matrix side of the mitochondrial becomes positive or negative
negative
what does the chemiosmotic theory explain
free energy generated by the transport of electrons in ETC is used to produce ATP from ADP+Pi
what complexes of the ETC pump electrons
1, 3, 4
what drives the mechanism of ATP synthetase
proton motive force by electrochemical potential difference due to impermeability of inner mitochondrial membrane
what complexes act as a proton pump, creating a proton gradient across the membrane
I, III, IV
what does ATP synthase convert
ADP+Pi–>ATP
is ATP synthase embedded in the inner mitochondrial membrane or mobile
embedded
what are the 2 components of ATP synthase structure
F0
F1
where is F0 of ATP synthase located
inner mitochondrial membrane
where is F1 of ATP synthase located
mitochondrial matrix
what are the subunits of F1 of ATP synthase
3 alpha, 3 beta
what subunit of F1, alpha or beta, does ADP attach to
beta
what subunit of F1, alpha or beta, does ATP attach to
alpha
one rotation of ATP synthase produces how many ATP
3 (due to having 3 beta subunits)
what makes up the F0 subunit of ATP synthase
C protein subunits
what subunit is attached to the C protein subunits of ATP synthase directly
gamma
what subunit of ATP synthase, alpha beta or gamma, rotates
gamma
what does ATP synthase produce
ATP and heat
what is the function of heat produced by ATP synthase
maintain body temperature
what is the purpose of the ATP/ADP antiporter
as soon as ADP enters and produces ATP, ATP exits
what controls the rate of respiration (ETC/oxidative phosphorylation)
availability of ADP
what are 2 examples of substrate level phosphorylation
glycolytic reactions
citric acid cycle
for each mole of substrate oxidized by complexes I, III, and IV in respiratory chain (ETC) via NADH, how many moles of ATP are produced
2.5
for each mole of substrate oxidized by complexes II, III, and IV in respiratory chain (ETC) via FADH2, how many moles of ATP are produced
1.5
what allows molecular oxygen (O2) to act as an efficient final e- acceptor
high electronegativity
does each step of the ETC have a positive or negative delta G
negative
why is having a -delta G in each step of the ETC important
free energy is created and made available to to work and movement of protons
what do uncouplers do to the ETC
increase permeability of the membrane to ions/create a channel, interfering with the proton gradient as H+ is allowed to pass without going through ATP synthase (no ATP synthesis)
what is the main result of uncouplers of the ETC
energy is released as heat (excess of body heat)
what type of protein does thermogenin act as
uncoupling
is thermogenin a physiological or pathological uncoupler
physiological
where is thermogenin found
brown fat, especially in newborns
what is the function of themogenin
production of body heat
is 2,4-dinitrophenol a physiological or pathological uncoupler
pathological
what class does 2,4-dinitrophenol belong to
uncouplers
how does 2,4-dinitrophenol act
reduces electrochemical potential and short-circuits ATP synthase, causing energy to be released as heat rather than used to synthesize ATP
what is the result of 2,4-dinitrophenol in regards to heat production
hyperthermia
what class of proteins does high dose asprin and other salicylates act as in the ETC
uncouplers
oxidative phosphorylation uncoupling agents __ (increase or decrease) proton gradient and produce heat
decrease
electron transport inhibitors __ (increase or decrease) proton gradient
decrease
ATP synthase inhibitors __ (increase or decrease) proton gradient
increase
what class of antibiotic is oligomycin
macrolide
what is the effect of oligomycin
binds to F0 of ATP synthase, closing the H+ channel and preventing re-entry of protons
e- transport is stopped so no ATP or heat is produced
do uncoupling agents act on a specific complex
no
what complex do Rotenone and metformin act on
I
what complex do antimycin A and dimercaprol (BAL) act on
III
what complex does H2S, Azide, Cyanide, and CO act on
IV
what complex does oligomycin act on
ATP synthase (complex V)
what is Rotenone, which acts on complex I, also referred to as
fish poison
insecticide
what complex do barbiturates (Amytal) act on
I
