biochem lecture 4 pt 1 Flashcards
what serves as a major energy source in organisms
glucose
what are different sources of glucose
from glycogen stores, directly from diet
how can glucose be stored
glycogen, starch, sucrose
one way glucose can be used
oxidation into ribose-5-phosphate via pentose phosphate pathway
another way glucose can be used
oxidized into pyruvate via glycolysis
what does glycolysis mean
“sweet splitting”
what cells is glucose catabolism carried out in
all cells
what is glycolysis basically
glucose catabolism
where does glycolysis take place
in cytoplasm
what is glycolysis to certain cells
only source of metabolic energy
how many reactions in glycolysis
10 reactions
is glycolysis same or different in all cells
same
what are products of glycolysis?
pyruvate, ATP, NADH
what are the three possible fates for pyruvate
aerobic oxidation, anaerobic glycolysis (lactate), anaerobic fermentation (ethanol)
what does glycolysis involve/entail
breakdown of glucose (6 C molecule) into 2 molecules of pyruvate/pyruvic acid (3 C molecule)
describe the aerobic fate for pyruvate
complete oxidation of pyruvate thru rest of cell respiration; TCA cycle, and reducing power from TCA cycle is fed into ETC, which drives ox phos or ATP synthesis
what happens to pyruvates generated at end of glycolysis in cell respiration
we produced CO2
what happens in aerobic fate of pyruvate in glycolysis
6 carbons of glycolysis will undergo complete oxidation; some in TCA cycle, some in end of cell respiration
what is anaerobic metabolism
fermentation
what happens in anaerobic metabolism
any form of oxidation where you don’t have O2 as final electron acceptor
what is the final electron acceptor in cell respiration /aerobic respiration
O2
when do organisms use anaerobic respiration
lack of oxygen, or if oxygen is toxic to them
is glycolysis well conserved
yes
what does a well conserved process imply
implies that there is a high level of utility of this pathway across species barriers
what does pyruvate produced at end of glycolysis represent
only a partial oxidation of glucose
how much energy do we generate at end of glycolysis
2 ATPs, 2 NADHs per glucose molecule
is there still more E to be extracted from pyruvate at end of glycolysis?
yes
does glycolysis generate a lot or a little energy
only a little bit
how do we generate ATP in glycolysis
substrate-level phosphorylation
where do we generate more ATP from (what other process)
complete oxidation of glucose
when is ATP production via glycolysis important
anaerobic conditions (oxygen is lacking or toxic to them)
what are the 3 main catabolic fates of pyruvate
aerobic respiration, anaerobic processes [ethanol fermentation and lactic acid fermentation]
describe aerobic process / complete oxidation of glucose
there is complete oxidation of glucose through TCA, and transfer of electrons from reduced electron carriers generated in TCA cycle to completely oxidized glucose’s carbons, through ETC and ox phos
what type of organisms go thru TCA cycle, ETC, and ox phos
aerobic
why don’t anaerobic organisms go thru TCA cycle, ETC, and ox phos
because there is no oxygen to serve as the final electron acceptor
so how do they extract E from glucose
have to find another way; via ethanol or lactic acid fermentation
who does lactic acid fermentation
humans
who does ethanol fermentation
yeast
what are the 2 end products for these 2 anaerobic pathways
ethanol and lactic acid
what is Ethanol fermentation
when we convert pyruvates into ethanol molecules
what is lactic acid fermentation
when we convert pyruvates into lactic acid molecules
what is net energy yield of glycolysis
2 ATP, 2 NADH per glucose
what is big picture of glycolysis
1 molecule of glucose (6 C) is degraded to make 2 molecules of pyruvate (3 C)
describe thermodynamics of glycolysis
irreversible & exergonic
how does ATP synthesis in glycolysis occur
strictly thru substrate-level phosphorylation
why do we invest a bit of ATP early on
to set the stage for more ATP production later
does glycolysis have input of ATP
yup; it’s like investing
is ATP synthesis exergonic or endergonic
endergonic; input of E
where does the E needed to make ATP come from
from partial oxidation of glucose into 2 pyruvates
what is delta G for conversion of glucose –> pyruvate
large and negative (exergonic)
what does this exergonic delta G do
offsets the positive (endergonic) delta G for synthesis ATP
what is glycolysis overall
exergonic, but there are endergonic reactions embedded
how do we do ATP synthesis in glycolysis
substrate level phosphorylation
what kind of intermediates do we have
high energy intermediates
what are two phases of glycolysis
preparatory phase and payoff phase
what happens in prep phase
phosphorylation of glucose & conversion to glyceraldehyde - 3 phosphate (basically glucose –> GAP)
how many steps in prep phase
4 (5 if you count DHAP –> GAP)
what does prep phase do/convert
converts 6 C sugar to 2 3C sugars
how much ATP used in prep phase
2 ATP
what is prep phase
investment phase (we use ATP)
what is payoff phase
oxidative conversion of GAP to pyruvate, and coupled formation of ATP and NADH
how many steps in payoff phase
6 (or 5)
what is converted in payoff phase
converts two 3C sugars to 2 pyruvates
how much ATP is made in payoff phase
4 ATP (2 from each 3 C sugars)
what do we do after step 5
we multiply everything by 2, because DHAP –> GAP means 2 GAPs
what is yielded in payoff phase
the energy invested in the two priming rxns in prep phase yield our 2 examples of high E intermediates
what are 1,3-BPG and PEP
high E intermediates
what does it mean when we see these high E intermediates
something important is gonna happen (high E compounds are gonna be used in substrate-level phosphorylation)
where is ATP generated (what steps)
7 and 10
when are priming reactions
prep phase
what happens when we see a high E intermediate
ATP production
what is step 1
phosphorylation of glucose to glucose-6-phosphate
what enzyme catalyzes step 1
hexokinase
what is our first priming rxn
step 1
where do we invest our first ATP
step 1
what is kinase
enzyme that utilizes ATP as phosphate donor; transfers phosphate group from ATP to a substrate (in this case glucose)
what is the point of phosphorylating glucose in step 1
we trap glucose in the cell; glucose will remain in cell, used in glycolysis
what do you do to G6P when you have lot of ATP and don’t need to do glycolysis
G6P can be redirected to glycogen synthesis or hexose phosphate pathway
step 2
conversion of glucose-6-P to fructose-6-P
what kinda reaction is in step 2
isomerization reaction
what enzyme catalyzes step 2
phosphohexose isomerase
ddscribe delta G
positive but very small –> reversible rxn
is step 2 reversible or irreversible
reversible
what is step 3
phosphorylation of fructose-6-p to fructose-1,6-bisphosphate (f6p to f-1,6-bp)
when is. second priming reaction
step 3
what is first committed step of glycolysis
step 3
describe step 3
second priming reaction, first committed step of glycolysis
what enzyme is in step 3
phosphofructokinase-1 (PFK-1)
why do we call step 3 first committed step
fructose-1,6-bisphosphate is only targeted for glycolysis; its dedicated to glycolysis and is gonna be directed thru glycolysis exclusively at this point
describe step 3s delta G
negative; allows rxn to occur
what kinda reaction is step 3
phosphate group transfer reaction involving ATP
how is PFK activity regulated and influenced
by ATP levels
describe PFK activity when [ATP] is low
activity is high
describe PFK activity when [ATP] is high
activity is low
what does a lot of ATP mean
energy state is high, things are good
what does high ATP serve as an inhibitor of
PFK-1 activity
describe the inhibitor effect on PFK in presence of little ATP
not as pronounced effect; steeper slope
what happened to graph when we add ATP
activity curve shifts to the right
what does it mean when we see a rightward shift in activity curve
indicates something is reducing activity of that enzyme
what does ATP do to enzyme
lowers/reduces activity of enzyme
how does ATP reduce activity of PFK-1
ATP binds to an allosteric site on PFK-1, lowering the activity
describe curve with ATP mixed with a bit of AMP
curve shifts back to the left partially
what is ATP indicator of
high E state in the cell
what does AMP an indicator of
low E state in the cell
why is AMP an indicator of low E state
more AMP means less ATP, so less E
what does adding AMP with ATP do
shifts the curve a little bit; we don’t have as high activity as we would w/ no inhibitor, but we’ve reinstated a significant level of activity in presence of AMP
what does AMP does to the effect of ATP
antagonizes the effect of ATP
what is allosteric regulator of PFK-1
ATP (AMP?)
what else is PFK/AMP an example of
feedback inhibition
what is step 4
cleavage of fructose 1,6 BP into DHAP and GAP
what enzyme is for step 4
aldolase
why is it called aldolase
cuz it carries out an aldol condensation reaction
what kinda reaction is step 4
cleavage reaction
what are DHAP and GAP to each other
isomers
where do carbons in DHAP come fro
first 3 Cs in glucose (C1 to C3)
what do carbons 4-6 correspond to
GAP
what happens to DHAp
dead end compound, can’t continue for rest of glycolysis
what do we need in order for all the PE stored in glucose to be utilized
DHAP has to be isomerized to GAP
how did we figure out what Cs in DHAP and what in GAP
radioactive labeling
what is step 5
conversion of DHAP to GAP
why do we need to convert DHAP to GAP
only GAP can be directly degraded to pyruvate
what enzyme in step 5
triose phosphate isomerase
specifically what does triose phosphate isomerase do
takes ketone form of DHAP and isomerizes it into an aldehyde and we get GAP
what happens from this point on
2 molecules of GAP, so multiply everything w/ 2
summarize phase one/prep phase
4/5 steps, converts one 6C sugar into 2 3C sugars, uses 2 ATPw
what kinda reactions are in prep phase
the 2 priming rxns
what do priming reactions involve
investment of ATP at each step AND phosphoryl group transfer reactions
what other rxns in prep phase
isomerization reaction, cleavage reactions, another isomerization reaction that generates 2 molecules of GAP
what is step 6
oxidation of gAP to 1,3-bisphosphoglycerate (1,3-BPG)
what is produced in step 5
a high energy intermediate (1,3BPG)
what else is made in step 6
NADH
basically what 2 things are done in step 6
generate NADH, and our first high E intermediate 1,3-BPG
what enzyme does step 6
glyceraldehyde 3-phosphate dehydrogenase
what is a dehydrogenase
involved in redox reactions
what’s being reduced in step 6
NAD+ to NADh
what is NADH
money in the bank, can be used in ETC, other stuff
how do we produce our first high E intermediate 1,3- BPG
dehydrogenase uses inorganic phosphate
do we invest more ATP to make 1,3-BPG?
no, doesn’t make sense to use ATP to eventually get an ATp
describe the availability of the inorganic phosphate
readily available in the cell
basically what are we doing in step 6
using a non-ATP phosphate source (inorganic phosphate) to generate ATP in the next step (step 7) thru substrate level phosphorylation
basically
we’re using inorganic phosphate to produce ATP in the next step
what is step 7
phosphoryl transfer from 1,3-BPG to ADP (to make ATP), and we make 3-PG (3-phosphoglycerate)
where does the phosphate group go
is transferred from 1,3-BPG to ADP to make ATP, and we’re left with 3-PG
what enzyme for step 7
phosphoglycerate kinase
why is it a kinase in step 7
because of its ability to catalyze the reverse reaction (to phosphorylate 3-phosphoglycerate and make 1,3-BPG) in gluconeogenesis
when is our first substrate level phosphorylation reactoin
step 7 (1,3-BPG converted to 3-PG)
what makes 1,3BPG a high E compound
how readily the phosphate group can be transferred from 1,3-BPG to a molecule of ADP
if we have something involved in substrate level phosphorylation, what is necessary
group transfer rxn potential of that high E compound has to be higher than ATP
what would happen if ATP’s rxn potential was higher than high E intermediate
reverse rxn occurs, with ATP transferring its phosphate to 3-PG to make 1,3-BPG
describe delta G values in step 7
higher and more negative for 1,3-BPG and PEP compared to ATP hydrolysis (basically phosphoryl group transfer potential of 1,3-BPG is higher than ATP) –> rxn is favored
what steps are coupled
6 and 7
describe free E change in step 6
conversion of GAP to 1,3-BPG is endergonic
how do we make step 6 go
couple it to step 7, exergonic
how are steps 6 and 8 coupled
thru a common intermediate: a thioester bond formed b/w a cysteine in GAP dehydrogenase enzyme and GAP
what does GAP DH have in its active site
a catalytically relevant cysteine and histidine
what happens to enzyme GAP DH first
will form a covalent complex w/ substrate in form of a thioester bond
what kinda bond is a thioester bond
a high energy bond
what happens when you break a thioester bond / high E bond
release E
basically how do you drive the otherwise endergonic step of GAP being converted to 1,3-BPG
formation of a thioester linked enzyme substrate intermediate
what can happen to thioester linkage
can be hydrolyzed, some of that free E released as a result of hydrolysis is gonna be enough E to generate a high E compound 1,3-BPG
what is steps 6 and 7 an example of
energy coupling; basically taking PE stored in thioester bond to form the first high E intermediate
what happens with the dehydrogenase enzyme
forms a high E intermediate form of the substrate within the cysteine residue within the active site of the enzyme
what does the dehydrogenase enzyme have
a thiol group (SH)
what is SH gonna be a part of
the thioester linked enzyme-substrate intermediate
what happens when the thioester linkage is cleaved
the free E that’s released will be enough to transfer this inorganic phosphate group from GAP to 1,3-BPG
what happens to free E if there is no thioester intermediate
large activation E
what happens to E with thioester intermediate (enzyme substrate thioester linked intermediate)
lower activation E barrier to overcome, easier
what makes this reaction of GAP to 1,3-BPG
formation of thioester intermediate
what is step 8
conversion of 3PG to 2PG
what happens after step 7, after substrate-level phosphorylation
we are left with ATP and 3PG (de-phosphorylated compound)
what happens in step 8
isomerize 3PG to 2PG
what enzyme in step 8
phosphoglycerate mutase
are mutase same or different from isomerase
different catalytic mechanism
what’s interesting about phosphoglycerate mutase
it has catalytically important histidine residue in its active site
what’s up w/ phosphoglycerate mutase
one nitrogen on the imidazole ring of histidine undergoes phosphorylation
what is phosphorylation of N on imidazole ring of histidine important for
isomerization of 3PG to 2PG
what is a mutase
catalyze transfer of a functional group from one position to another on a molecule (in this case phosphoryl from C3 to C2)
what does phosphoglycerate mutase have
unique phosphorylated HIstidine in its active site
what is step 9
dehydration of 2PG to PEP
what enzyme in step 9
enolase
what does enolase do in this step
catalyzes conversion of 2PG to PEP via elimination
what does enolase do basically
rearranges 2PG to form (PEP) from which more E can be released
why do we dehydrate 2PG to PEP
to create a high E compound capable of driving synthesis of ATP
what is free E for hydrolysis of 2PG
too low to make ATP; so we need to convert to a high E intermediate
what is step 10
phosphoryl transfer from PEP to ADP, to make pyruvate and ATP
what kinda rxn is step 10
substrate level phosphorylation
what is made in step 10
2nd ATP and pyruvate
what enzyme in step 10
pyruvate kinase
why is enzyme name pyruvate kinase confusing
b/c it’s named for the reverse reaction that we see in gluconeogenesis (pyruvate to PEP)
how many ATPs do we make
2 x 2 is 4, but we use 2 so net gain is 2
summarize payoff phase or phase 2
5 steps, converts GAP to pyruvate, makes 2 ATP and 1 NADH (per gap)
how many net NADH produced
2 NADH (1 per gap)
can we extract more E from pyruvate
yes
when do we oxidize the rest of E from pyruvate
in TCA cycle when oxidize pyruvate to CO2 and make more reducing power
what else do we make in TCA cycle
more reducing power
where does reducing power we make in cell respiration come from
TCA cycle
what is net gain in glycolysis
2 ATP, 2 NADH, 2 pyruvates
what happens as glucose is oxidized
2 NAD+ are reduced to NADH
how many fates for pyruvate at end of glycolysis
3 fates, divided in anaerobic and aerobic
what’s up w/ pyruvate and NADH in aerobic conditions
NADH is reoxidized in ETC and makes ATP in ox-phos. pyruvate enters TCA
what’s up w/ pyruvate and NADH in anaerobic conditions
NADH reoxidized to NAD+, provides more NAD+ for more glycolysis. pyruvate converted to lactate (muscles) or ethanol (yeast)
describe pyruvate conversion to lactate
lactic acid fermentation, in muscles
describe pyruvate conversion to ethanol
ethanol fermentation, in yeast
