metabolism - staniforth Flashcards
why is NADPH used in anabolism ?
allows body to separate catabolism (NADP) and anabolism (NADPH)
when are disulphides found?
in intracellular env, reductive (mild conditions)
why is sulphur useful?
SH bond = high energy s binds Fe - redox energy store (-sh groups)
why are sulphur proteins so abundant?
early earth S was v abundant
FeS + H2S –> FeS2 +2H (reductive power)
how is cysteine made?
serine formed from glycolysis
serine activated by acetyl-coA
cysteine synthase produces cysteine from this
describe the link between the law of mass action and polymerisation
Law of mass action: (Kc = products/reactants)
by liberating water in polymerisation of sugars it increases the molar ratio of products, pushing equilibrium to the reactants
what is gluconeogenesis? where and why does it happen?
reverse glycolysis
provides sugar when glucose is scarce
occurs in mitochondrion and cytosol in liver and kidney
describe the differences in primary and secondary pathways
primary: basic housekeeping functions present in essentially all cellls largely costitutive secondary: specialised functinos present in differentiated cells inducible
whats the purpose of glycolysis? where does it happen?
ATP and NADH generation
forms intermediated for biosynthesis
happens in cytosol
whats the purpose of the PPP and where does it happen?
generated C5 sugars and NADPH for biosynthesis
breakdown route for C5 sugars
other intermediates for biosynthesis
happens in cytosol (in biosynthetic tissues)
how do cells choose between PPP or glycolysis?
PPP is for biosynthesis
glycolysis for energy
what is the purpose of the link reaction? where does it happen?
processes pyruvate for krebs
source of a-coA
NADH production
happens in mitochondrion
what is the purpose of krebs cycle? where does it happen?
NADH and GTP production
intermediates for biosynthesis
in mitochondrion
name 4 chemicals formed in krebs and what theyre used for
oxaloacetate and alpha kg - a/as
citrate - f/a’s
succ-CoA - porphyrins
why is a cycle a good design for a precursor supply system?
extraa supply of any intermediate can top up cycle
what is the purpose of OP and where does it happen
generates ATP and GTP
maintains redox balance
happens in mit IM
what is the purpose of b f/a oxidation? where does it happen?
used for extracting energy from lipid stores
generating 2-c units for biosynthesis
in mitochondrion
why do anabolic reactions require energy
creating ordered structure - entropy
why are branched pathways regulated at the enzyme that makes the first product?
this is because if latter enzymes were regulated then intermediates would still be made - waste of energy
name 3 strategies to prevent product down regulation caused by first product enzyme modulation and briefly explain them
enzyme multiplicity (isoenzymes) - several enzymes for the first step, that can be regulated by different things
cumulative control - production of metabolic products allosterically inhibit the enzyme (all products inhibit slightly but all properly inhibit)
concerted control - all products are required to allosterically inhibit enzyme (each product alone cannot inhibit)
give an example of isoenzymes
a/a biosynthesis from aspartate
3 versions of aspartokinase, each with a regulatory domain (one inhib by thr and one inhib by lysine)
therefore if there is too much threonine this domain will be regulated and threonine production will decrease, not affecting lysine/methionine production
give an example of concerted allosteric control
lysine biosynthesis
- makes 1< product, all products are required to allosterically inhibit the control enzyme
give an example of cumulative allosteric control
glutamine synthase
cumulative production of products (from control enzyme) is required to allosterically inhibit the control enzyme (however both can inhibit a little bit)
what is the distributive control hypothesis?
The flux through a pathway is a system property rather than simply a property of individual control enzymes ie enzymes work together to increase/decrease flux
define flux and flux coefficient
flux = no. of molecules being transformed per unit time
flux coefficient = (change in steady state flux/steady state flux)/(change in [enz]/[enz])
what value of C (flux coefficient) do early enzymes have in comparison to later enzymes
early enzymes have low C values
later enzymes have high C values
(high coefficient = big effect on flux)
how can we experimentally measure flux?
13C NMR
31P NMR
mass spec
define metabolome
the quantitative complement of all the low molecular weight molecules present in the cell under a given set of conditions
what is the general principle of group carriers in biosynthesis
Pi from ATP used to stick molecule B to the carrier to form an activated carrier
activated carrier sticks B onto A to form product A-B
name the C1 carrier molecule
tetrahydrofolate - C1 carried in a variety of oxidation states
eg FH4 gets C1 from serine (–> glycine)
FH4 donates methyl group (unusual) FH4–>FH2
NADPH: FH2 –> FH4
this is used to make glycine and dUMP –> tUMP
name the C1 methyl carrier molecule
s-methyladenosine
presence of S+ near CH3 leaves CH3 vulnerable to attack by accepting e- from elsewhere
name the C1 carboxyl carrier molecule
biotin (think of decarboxylation transport - key Lys res)
ATP+bicarbonate –> carboxyP —> donates COO- to biotin
name the C2 carrier molecule
acetyl CoA
its thioester bond is unstable - likes to donate CH2 group eg f/a biosynthesis
name the C3 carrier molecule
PEP (think of phosphotransferase)
P acts as energy source
electronegative elements in close proximity - advantageous to remove P
name the C5 carrier molecule
isopentenyl pyrophosphate (IPP)
mevalonic acid from 3CoA’s
IPP formed from that by loss CO2 - thermodynamic pull
IPP v reactive - releases loads of energy when Pi removed therefore adding C5 group (eg cholesterol 4*5C)
name the a/a carrier molecule
glutamine –> glutamate
ATP required for this reaction
NH2 removed - no obvious reason - this is why ATP is suggested to be used
name the S carrier molecule
cysteine
name the sugar carrier molecule
nucleosidediphosphates
name the complex (C-C-N) carrier molecule
glycine
briefly describe the 3 components of a nucleotide
purine/pyrimidine ring
ribose sugar
phosphate
in which pathway are nt’s made
PPP - when cells are in biosynthetic not catabolic ‘mode’
describe the difference in purine/pyrimidine sythesis
pyrimidine - ring assembled then ribose attached
purine - purine assembled onto the activated (2P) ribose
similar reactions, different modes of biosynthesis
what name is given to activated ribose?
5-phosphoribosyl-1-pyrophosphate
how is 5-phosphoribosyl-1-pyrophosphate made?
ribose-5-P + ATP —> 5-phosphoribosyl-1-pyrophosphate + AMP
uses by ribosephosphate pyrophosphokinase
how is the biosynthesis of 5-phosphoribosyl-1-pyrophosphate regulated?
downregulated by presence of ADP/GDP which indicates the cell is low on energy, therefore should be using glycolysis not PPP
briefly describe the first step of purine biosynthesis
we have PRPP
lose the PP’s (input of energy)
add NH2 in place of this (gln —> glu) - this required energy as not activated carrier
briefly describe the second step of purine biosynthesis
requires ATP - as no obvious source of energy from glycine
ATP activates the OH group on glycine (–> -ve) and NH attacks this C+ and attaches itself
briefly describe the third step of purine biosynthesis
C1 addition via FH4
energy comes from FH4 via NADPH
adds formyl (H-C=O) to ring
briefly describe the fourth step of purine biosynthesis
NH2 addition
- beginning of 2nd ring
glutamine NH2 donation - attacks C+ (made by ATP)
briefly describe the fifth step of purine biosynthesis
ring closure - formation of double bond between what was the formyl group and N (away from ribose)
single bond formation between ribose N and what was the formyl group
requires ATP
briefly describe the sixth step of purine biosynthesis
CO2 attaches, NH2 rearranges
CO2 - source of CO2 varies - biotin not usually used in mammals
briefly describe the seventh and eighth step of purine biosynthesis
NH2 donation via Asp (NH3 backbone used)
ATP activates C as usual
hydrolysis - release of fumarate
briefly describe the ninth and tenth step of purine biosynthesis
9) C1 (formyl) addition by FH4
10) ring closure, attack of C by NH2 - loss of H2O
forms IMP - precursor
state the core pathway and the processing reactions in purine biosynthesis
core: ribose-5-P —> PRPP —> phosphoribosylamine —> IMP
Processing: IMP —> AMP/GMP
how is IMP processed to AMP?
IMP + GTP + aspartate(NH2) —> fumarate + GDP + AMP
how is ribose processed to deoxyribose?
ribose + NADPH —> NADP+ + deoxyribose
ribonucleotide reductase
how is the purine biosynthetic pathway controlled?
overall enzymatic: glutamine phosphoribosyl amidotransferase
PRPP –> phosphoribosylamine
this step reg by IMP/AMP/GMP cumulative/concerted control
IMP —> AMP/GMP
balancing mechanism exists
why is GTP used in IMP —> AMP
as IMP also processes to AMP (to ADP to ATP) the level of GTP is a good regulatory step
this is also present in processing IMP to GMP (to GDP to GTP) in which ATP is required.
this is the balancing mechanism, it stops ATP being produced if there is not enough GTP and stops GTP being produced if there is not enough ATP
name 2 balancing reactions (not incl. AMP/GMP) which enzyme is involved in these mechanisms?
ribonucleotide vs deoxyribonucleotide
purine vs pyrimidine
carried out by ribonucleotide reductase
describe the structure of ribonucleotide reductase and what they do
1 site controls catalytic activity dATP acts -vely ATP acts +vely 1 site controls substrate specificity high purine biosynthesis dATP binds - swaps to pyrimidine biosynthesis
how does a NTP turn into a dNTP
NADPH –> NADP+
give 2 anticancer drugs and the reaction they inhibit
fluorouracil: inhibits thymidylate synthase (suicide inhibitor - kills enzyme) dUMP —> dTMP
methotrexate: inhibits dihydrofolate reductase (competitive inhibitor - less drastic impact) NADPH—>NADP+ which is involved in FH2—->FH4
would fluorouracil work on purines?
no, only on pyrimidine as fluorouracil creates a fluorinated analog of dUMP which is the actual inhibitor
which cells does methotrexate kill?
all rapidly dividing cells eg bone marrow/hair follicles
how is the chirality of the alpha carbon in an a/a established? which enzyme is involved in this?
the placement of the NH2 group - transamination reaction using pyridoxal phosphate
how is NH3/NH4+ brought into a/a biosynthesis
alpha ketoglutarate is aminated to form glutamate
how is glutamate synthesised?
alpha-kg + NH3 + NAD(P)H --> NAD(P)+ + glutamate glutamate dehydrogenase (mitochondrial)
how is a schiff base formed?
-NH2 + -CHO = R1,R2-C=N-H
how does a schiff base ensure that an l-a/a is formed?
double bond = no rotation and fixed geometry
the schiff base is an intermediate, therefore when the intermediate is reduced by NAD(P)H’s H- ion the L-form is created (with help of glutamate dehydrogenase)
name the 3 general stages of a/a biosynthesis
intermediate of glycolysis/PPP/TCA
required side chain assembled on alpha-keto acid
-NH2 group added by transamination
in transamination, where does the -NH2 group come from? explain why
another a/a - this allows levels of types of a/a to be regulated
transaminase aminotransferase
in transamination, where does the -NH2 group come from? explain why
another a/a - this allows levels of types of a/a to be regulated Keq = ~1/freely reversible
transaminase aminotransferase
which (3) keto acid molecules can be turned into their corresponding a/a without R side chain synthesis?
pyruvate —> alanine
oxaloacetate —> aspartate
alpha-kg —> glutamate
what is the key cofactor involved in transamination and name a key functional group it contains
pyridoxal phosphate
aldehyde group - key for catalysis
how does PLP bind transaminase reductase?
enzyme contains lys residue that can interact with the aldehyde on PLP to form a schiff base (-/+H2O) - remember reversible nature of schiff base
new a/a then swaps with the enzyme to form a PLP-a/a structure
hydrolysis of PLP-a/a with N from schiff base going to PLP
reformation of schiff base with PLP but this time the a/a gets the NH2
lysine then binds PLP - essentially starting the process again
glutamate is a transamination ‘partner’ - what does this mean?
when an alpha-keto acid becomes an a/a it needs to undergo transamination - with an a/a donating its amine group
glutamate is the a/a that usually does this - hence being transamination partner
how does the biosynthesis of serine differ from normal a/a biosynthesis?
transamination reaction not last
3-PG from glycolysis forms 3-phosphohydroxypyruvate which undergoes transamination to form phosphoserine, H2O replaces the P to form serine
