biochem lecture 2 pt 2 Flashcards
what is least oxidized/most reduced form of C
alkane
2nd least oxidized / 2nd most reduced
alcohol
what comes after alcohol
aldehyde/ketone
what comes after aldehyde/ketone
carboxylic acid
what comes after carboxylic acid
carbon dioxide
what’s the most oxidized form of carbon
carbon dioxide
when is something oxidized
when it’s bonded to oxygen, and double bonds; it withdraws electron density from the carbon, making it less negative and have less electrons, hence less reduced and more oxidized
going from lactate to pyruvate is what
oxidation
is this oxidation w/ dehydrogenase reversible
yes
what is oxidation of lactate to pyruvate catalyzed by
lactate dehydrogenase
where do electrons go when they oxidize lactate to pyruvate
transferred to NAD+ to reduce it to NADH
how do we know lactate to pyruvate is an oxidation
going from an alcohol to a ketone, so more oxidized
2 mechanisms for cleavage of C-C or C-H bond
homolytic and heterolytic cleavage
homolytic cleavage
symmetric; each product retains one electron
what does homolytic cleavage produce
radicals (whether 2 carbon radicals or 1 C and 1 H radical)
heterolytic cleavage
asymmetric retention of electrons; 1 retains both electrons, other retains nothing
what are possible products of heterolytic cleavage (remember C-C or C-H)
C- and H+ (carbanion and H proton), C+ and H- (carbocation and. hydride ion) or C+ and C- (carbocation carbanion)
isomerization
redistribution of electrons within a molecule
what is isomerization catalyzed by
isomerases
example of isomerization
glucose-6-phosphate to fructose-6-phosphate
what does isomerization lead to
isomerization, transposition of double bonds, cis-trans rearrangement
are we changing chem formula of substrate when we isomerize something
nope, just rearranging
what happens in G6P –> F6P
aldehyde in one is reduced to form alcohol, alcohol in another is oxidized to form keto group
can you have oxidations/reductions that result in isomerization
yeah
are isomerases the only enzymes that catalyze isomerizations
nope
elimination reaction
eliminates water, introduces C=C bond
group transfer reactions
phosphorylation; transfer of acyl, glycosyl, phosphoryl groups
what does group transfer reactions occur between
from one nucleotide to another
is phosphorylation example of group transfer reaction
yea
what is phosphoryl group transfer
attachment of a good leaving group to a metabolic intermediate to ‘activate’ intermediate for subsequent rxns
what makes phosphoryl group transfer rxns favorable
you have transfer of phosphate group from ATP to another substrate ike glucose
what happens w/ ATP in metabolic processes
phosphate is not just released from ATP, but transferred to another substrate in pathway
explain this process
That process, b/c if you’re hydrolyzing ATP has high E phosphate bonds, negatively charged phosphate groups that are covalently bonded, there’s a lot of bond strain bc of negative chargers so close together
When you hydrolyze/break one of these phosphate bonds, release a phosphate group, significant amount of energy being released
Some of that free energy is available to facilitate transfer of phosphate group from ATP to other substrate (in this case glucose)
extremely common type of reaction
use of ATP as a source of phosphate in phosphoryl group transfer reaction
what does energy convert glucose into
glucose to glucose-6-phosphate (adds a phosphoryl group, free energy helps do this)
free radical reactions
homolytic cleavage of covalent bonds to generate free radicals
example of free radical reactionq
methylmalonyl coA mutase mechanism
who worked out methylmalonyl coA mutase mechanism
Dorothy Crowfoot Hodgkin
describe methylmalonyl coA rxn
swapping of CoA and Hydrogen on adjacent carbons
what is generated from methylmalonyl coA
succinyl coA
what enzymes catalyzes isomerization of methylmalonyl coA to succinyl coA
enzyme involved in oxidation of odd chain length fatty acids
what does this isomerization reaction use
coenzyme b12
what does coenzyme b12 contain
cobalt
what is coenzyme b12`
modified form of vitamin b12
describe process
mutase swaps coenzyme A and H between the two Cs to generate an isomeric form of methylmalonyl coA called succinyl-coA
why is there efficient trapping of this specific 3rd hydrogen as opposed to another hydrogen
the nature of coenzyme b12 utilized in this rxn
describe formation of coenzyme b12
involves cleavage/removal of all 3 phosphates group s from aTP molecule
what does removal of all 3 phosphates result in
conjugation of this 5’ carbon (part of ATP structure) to a cobalt atom; weak covalent bond
what is the weak covalent bond between
relevant 5’ carbon (part of ATP) and cobalt atom (part of vitamin b12)
what is cobalt atom from
part of vitamin B12
what is 5’ carbon from
part of ATp
basically what results from elimination of triphosphate group from ATP
coenzyme B12
what is coenzyme b12
cofactor form of vitamin b12
what is the key
weak covalent bond b/w cobalt (from vitamin) and C-5’ carbon (from ATP)
what does the breakage of this weak bond result in
5’ adenosyl radical which helps permit the transferase reaction
what is the mutase enzyme gonna use as a coenzyme
coenzyme b12
what does breaking of weak covalent bond lead to
produces relatively unstable radical
what kind of radical is produced
5’ adenosyl radical
why do we get efficient trapping of that specific H
because we are generating a series of radical intermediates that are unstable
what does it mean if something is unstable
gonna try to stabilize, assume lowest free energy state possible
what are the steps
substrate radical, product-like radical, 5’ deoxyadenosyl free radical
what happens to the susbtrate
H and coenzyme functional group are gonna be swapped
what is the key
relatively unstable radical intermediates effectively trap the H, prevent them from being lost to surrounding environment so that there’s better retention of that H
what does enzyme do
traps H, use it in transfer rxn so that only that H will be transferred
what is the main point
it’s about trying to stabilize these radical forms (short-lived, unstable radical intermediates)
what do you end up with
swapped functional groups in the product
what is regenerated
coenzyme B12 w/ intact deoxyadenosine / bond b/w 5’C and cobalt
what is this enzyme ready for
another round of catalysis, b/c it has the weak covalent bond (that’s ready to be broken)
summarize it?
going from relatively short-lived, unstable radical intermediate forms back into coenzyme B12 form
what makes ATP useful and valuable currency of energy in the cell
high energy, negatively charged phosphate groups that are adjacent
what do these adjacent negative phosphate groups mean
charge repulsions, a lot of bond strain b/w adjacent groups
what happens when you break a bond
releases a significant amount of energy stored up in the bond (due to bond strain)
cleaving bond results in
release of inorganic phosphate, lot of resonance stabilization leads to stabilizing
is there a lot of delta G;
yes; -30.5 kJ/mol
what is the idea behind this
take this exergonic step (ATP hydrolysis) and couple it to endergonic process to help drive it
is it just ATP hydrolysis or is there more
there is more; instead of phosphate group being just released, it’s often transferred to something else
describe conversion of amino acid glutamate into glutamine
transfer of amino group to glutamate to generate glutamine, and this endergonic process is coupled w/ ATP hydrolysis
describe the steps
enzyme hydrolyzes ATP, releases phosphate, tacks it onto carboxyl group of glutamate. forms glutamyl phosphate intermediate.
what does phosphate group being attached to an intermediate do
activates it; serves as a good leaving group
what happens after intermediate is attached to phosphate group
releases phosphate group, easily accepts amino group.
what does the formation of this phospho substrate intermediate do
provides free E
what is free E from phospho substrate intermediate useful for
helping transfer or displacement reaction
what is the point
not just simple hydrolysis, but rather phospho-substrate intermediate formation
what does phospho-substrate intermediate formation do
yields more free energy available to catalyze transfer reactions, etc.
what are 3 main high energy intermediates
phosphoenol pyruvate (PEP), 1,3-bisphosphoglycerate (1,3-BPG), phosphocreatine
what are high energy compounds/intermediates
phosphorylated compounds with a high energy phosphate bond
what do transition state intermediates represent
phosphorylated compounds that have a high E phosphate bond
what does it mean when you have a high E intermediate in a pathway
something important is gonna happen
substrate level phosphorylation
transfer of phosphate group from some intermediate in a pathway –> to a molecule of ADP
what happens to PEP or 1,3BPG in glycolysis
transfer of phosphate groups from high energy intermediates to ADP
what are high energy intermediates and substrate-level phosphorylation in
formation of ATP
describe ATP formation
exergonic
what are rxns involving a phosphate group transfer form high E intermediate to ADP molecule
favorable process, because you are coupling
why is it a favorable process
you are coupling a HIGHLY exergonic process (release of phosphate, -61.9 or -49 delta G) to an endergonic process, ATP formation (+30 kJ). adds up and is still negative, meaning favorable,
what makes PEP and 1,3-BPG high energy intermediates
the phosphate group attached to part of the molecule
what does this phosphate group attached to a compound do
activates it biochemically
basically what happens to phosphate group
not jsut released, but also transferred to ADP to make ATP
what is necessary to provide E to generate ATP
high energy intermediates
where is phosphocreatine often seen
in muscle; reservoir of high E intermediates in tissue and muscle
what does this reservoir of phosphorylated high E intermediate do
used to transfer phosphate group to ADP in order to keep ATP levels high in muscle
what does intermediate do
helps keep ATP levels high in muscle (by transferring p to ADP)
what makes this a high E intermediate
formation of high E phosphate bond and resonance stabilization can occur upon release of phosphate group and transfer of phosphate to ADP
is a high E intermediate always phosphorylated
not always
example of another high E intermediate
acetyl coA
is acetyl coA phosphorylated
nope
what defines a high E intermediate
tendency of it to be involved in phosphate group transfer reaction
are all phosphorylated compounds gonna serve as high E intermediates
nope
what is the only high E intermediate w/o a high E phosphate bond
acetyl coA
what is important in high E intermediates
the amount of free E released as a result is enough to lead to formation of ATP via substrate level phosphorylation
what kind of high energy bond is in acetyl coA
thioester linkage
what is acetyl coA
common intermediate
what happens when you attach 2 C fragments, acetyl units to a molecule of coenzyme A
exists in a reduced form CoASH
what does this attachment form
thioester bond
what happens when a thioester bond is hydrolyzed
results in significant release of energy and resonance stabilization
what happens when something is linked to coenzyme A (kinda like when attached to phosphate)
it’s biochemically activated, able to participate in reaction
what is the chemical link b/w catabolic and anabolic processes
ATP
what is conversion of ATP to ADP and pi
exergonic (releases energy)
what is this exergonic process coupled to
many endergonic rxns
what does direct ATP hydrolysis do
provides E for conformational changes in proteins
is direct ATP hydrolysis the way energy release is coupled to endergonic metabolic processes
nope
what does coupling to endergonic reactions involve
TRANSFER of phosphate group from ATP to a substrate or enzyme
what is this susbtrate
high energy intermediate
what does this group transfer rxn do
provides E for anabolic rxns, etc. etc
what do PEP, 1,3-BPG, phosphocreatine, and acetyl coA have
large negative free energy (delta G) values
what does inorganic polyphosphate serve as
reservoir of phosphoryl groups w/ high group transfer potential
where is inorganic polyphosphate present
in all cells
basically
can transfer phosphate group from high E intermediate to ADP to make ATP, or when hydrolyzing ATP, can transfer that phosphate onto high E intermediate.
do these standard values always reflect what goes on in the cell
nope
does delta G reflect what goes on in the cell overall
nope
what is delta G useful for
comparing diff steps in a pathway, not the whole thing
point of glycolysis and TCA cycle
to make lots of NADH and FADH
what is the point of making lots of NADH and FADH2
act as electron carriers, help provide proton motive force to drive ATP synthesis
