BIOC 221 - Midterm #2 Flashcards
Anaerobic Conditions: Alcohol Fermentation
In yeast, pyruvate first converted to acetaldehyde (∂-keto acid decarboxylation) then reduced to ethanol by NADH (regenerating NAD+ for glycolysis)
Alcohol Fermentation Reaction
Pyruvate + H+ --> Acetaldehyde + CO2 (pyruvate decarboxylase) cofactors: Mg TPP (vit.b1) - ∂-keto acid decarboxylation acetaldehyde + NADH +H+ ethanol (alcohol dehydrogenase) - reduction
What happens when we drink alcoholic beverages?
reactions
ethanol + NAD+ -> acetaldehyde + NADH +H+
(alcohol dehydrogenase)
acetaldehyde + NAD+ -> acetic acid + NADH + H+
(aldehyde dehydrogenase)
What happens when we drink alcoholic beverages?
what is produced
acetaldehyde is extremely toxic (hangover molecules)
- reactive with amino groups & may interact with proteins
- competes for plasma carrier of pyridoxal (vit. b6)
- vitamin deficiency
(interferes with vit. b6 transfer)
Pentose Phosphate Pathway
- what for?
to generate NADPH and pentoses (ribose-5-phosphate)
(2) phases of the Pentose Phosphate Pathway
1) oxidative phase
2) non-oxidative phase
oxidative phase of PPP
NADPH for reductive fatty acid biosynthesis
non-oxidative phase of PPP
ribose-5-phosphate for nucleic acid synthesis
Non-oxidative phase of PPP is active in?
rapidly dividing cells (blood marrow, mucosa, tumor)
Which tissues is PPP dominant in?
liver, adipose tissues, mammary glands and adrenal cortex actively synthesize steroids and fatty acids
Which tissues lack PPP?
skeletal muscle
Where does PPP take place?
cytosol
Cytosolic concentrations of NADH vs NADPH
high [NAD+] for glycolysis
high [NADPH] for FA synthesis
Purpose of the phosphate group on NADPH?
enables NADPH to interact with only specific dehydrogenase enzymes
- ensures NADH and NADPH aren’t interchangeable
Glucose 6P dehydrogenase
what does this enzyme do?
- inhibited by? stimulated by?
the enzyme that produces NADPH
inhibited by NADPH (product inhibition)
stimulated by NADP+
NADPH production is tightly coupled to?
its utilization
Oxidative phase of PPP (rxns)
G6P -> 6-phospho-glucono-∂-lactone -> 6-phosphogluconate -> ribulose-5-p -> ribose-5-phosphate -> nucleotide, coenzymes, DNA, RNA
(g6p and 6-phosphogluconate in cyclic form)
Overall Rxn of Oxidative Phase of PPP
g6p +2NADP+ +H2O ->ribose-5-p + CO2 + 2NADPH + 2H+
oxidative decarboxylated of G6P
G6P -> 6-phospho-∂-lactone
logic?
G6P dehydrogenase
NADPH produced
LOGIC: from 6C to 5C (decarbox.)?
oxidation of hemiacetal (aldehyde) C1 to an ester (acid) C
couple this ox. to red. of NADP+ to NADPH
allosteric regulator
regulator that doesn’t bind to E active site
6-phospho-∂-lactone -> 6-phosphogluconate
lactone: cyclic estr
add H2O
cyclic to linear
6-phosphogluconate -> ribulose-5-P
oxidize ß OH group to carbonyl group base takes H of OH group H on other side goes to NADP+ to form NADPH CO2 leaving group forms enol enol to keto ribulose-5-phosphate
Logic of:
6-phosphogluconate -> ribulose-5-P
decarboxylation of ß-keto acid
(ß-keto group serves as e sink during decarbox)
oxidize ß-OH to ß-keto couple with NADP+ reduc.
decarbox of ß leto to lose 1C unit as CO2
(OH to carbonyl for e sink and reduction of NADP+,
In cells that aren’t using ribose-5-P (from oxidative phase) for biosynthesis…
the non-oxidative pathway recycles 6 of the pentose into 5 hexose g6p allowing continued production of NADPH and converting g6p (in 6 cycles) to CO2
Non-oxidative pathway interconverts…
hexoses/pentoses
Ribose-5-phosphate –> Xylulose-5-P
isomerase -(ribulose-5-P)- epimerase
Non-oxidative pathway rxns
xylulose-5P + rib-5P -TK> sedoheptulose-7P + G3P -TA> erythrose-4P + F6P
xylulose-5P + erythrose-4P -(TK)> G3P + F6P
The first reaction catalyzed by transketolase
xylulose-5P + rib-5P -> sedoheptulose-7P + G3P
Reaction catalyzed by transaldolase
seduheptulose-7-P + G3P -> erythrose-4P + F6P
The second reaction catalyzed by transketolase
xylulose-5P + erythrose-4P -> G3P + F6P
NADPH formed in oxidative phase is used to ?
reduce glutathione GSSG
Entry of glucose 6-phosphate either into glycolysis or into the pentose phosphate pathway is largely determined by …
the relative concentrations of NADP
Where does G6P go? Glycolysis or PPP?
the cell decides depending on its relative needs for biosynthesis (PPP) or energy (glycolysis)
relative activities of PFK (glycolysis) and G6PDH (PPP)
Both Ribose-5-P and NADPH needed?
Oxidative Pathway of PPP
G6P + 2NADP + H2O -> Rib5P + CO2 + 2NADH + 2H+
More Ribose-5-P than NADPH needed?
Non-oxidative PPP
2F6P + G3P -> 3 ribose-5-P
(net: 5 G6P + ATP -> 6 Rib5P + ADP + H+)
More NADPH than Ribose-5-P needed?
Ribose-5P is recycled to form glycolytic intermediates
ultimately 6CO2
Both ATP and NADPH needed BUT not Ribose-5-P?
Ribose-5-P recycled to produce glycolytic intermediates (Glu-6-P, Gal-3-P) which then go on to glycolysis
(forming pyruvate and ATP)
Often Anabolic and Catabolic pathways use the same…. but…
same reversible reactions BUT at least 1 reaction differs
Anabolic and Catabolic output is defined by?
metabolic needs
Anabolic and Catabolic pathways are controlled by…
one or more reactions unique to that pathway at an early step
Why are Anabolic and Catabolic pathways controlled by 1 or more reactions at an EARLY step?
so nutrients are wasted and so regulation is reciprocal (anabolism is on while catabolism is off and vice versa)
Biosynthetic (anabolic) processes are coupled to… so?
ATP hydrolysis so overall process is irreversible in vivo when required and process is favourable even when [reactant] are low
Gluconeogenesis
glucose synthesis from non-carb precursors
Gluconeogenesis
what for? in mammals
in mammals some tissues depend almost completely on glucose for energy
Which tissues in mammals depend almost completely on glucose for energy?
brain, neurone, RBC, testes
Brain requires how much glucose?
120g/day
1/2 of all glucose stored as glycogen in muscle and liver
Where does Gluconeogenesis take place?
cytosol
In animals, what are important precursors for Gluconeogenesis?
3C compounds of lactate, pyruvate, glycerol and some amino acids
Gluconeogenesis is mostly in?
liver (and kidney)
Cori Cycle
lactate form muscle -> glucose in liver -> back to muscle
Both glycolysis and gluconeogenesis occur in?
cytosol
How many reactions do Glycolysis and Gluconeogenesis share?
7/10
Which enzymes must be bypassed in Gluconeogenesis?
hexokinase (step1), PFK-1 ( step 3), pyruvate kinase (step 10/last) are irreversible & must be bypassed
Bypass 1
Pyruvate Kinase
PEP synthesized by either pyruvate or lactate (glycogenic precursor)
(2) ways for Bypass 1
a) via OAA
b) via lactate
Bypass 1
a) via OAAA
OAA pathway borrows an anapletoric reaction in TCA cycle
Anapletoric reactions
form metabolic intermediates for replenishment
via OAA
step 1
transport to mitochondria
via OAA
step 2
pyruvate carboxylase
pyruvate + bicarbonate + ATP -> OAA + ADP + Pi
cofactor: biotin
Logic of: pyruvate -> OAA
carboxylation allows enolate O anion to serve as Nu in next phosphorylated rxn
via OAA
step 3
mitochondria has no OAA transporter so
mitochondrial malate DH :
OAA + NADH + H+ L-malate + NAD+
via OAA
step 4
malate-α-ketoglutarate transporter in the inner mitochondria membrane (IMM) :
transport of malate to the cytosol
via OAA
step 5
cytosolic malate DH
L-malate + NAD+ -> OAA + NADH + H+
via OAA
step 6
PEP carboxylase (Mg2+ and GTP dependant)
OAA + GTP -> PEP + CO2 + GDP
Chemical Logic of carbox/decarbox:
represents a way of “activating” pyruvate
the decarboxylation of OAA facilitates PEP formation.
logic of pyruvate transported into mitoc. forming OAA then to malate then out of mitochondria and back to OAA
more NADH in mitochondria
more NAD+ in cytosol
- transport of malate from mitoc. to cytosol and its reconversion there to oxaloacetate effectively moves reducing equivalents to the cytosol, where they are scarce.
this path from pyruvate to PEP provides important balance b/w NADH produced and consumed in cytosol
Energetics of bypass 1 via OAA
ATP consumed to make C-C bond in OAA from pyruvate that energy (plus GTP) used to build high E PEP
Metabolic logic for Bypass 1 via OAA?
steal NADH from mitochondria
bypass 1 via OAA provides balance for..
NADH produced (stolen) and consumed in the cytosol during glucose synthesis
What determines whether OAA goes through either pathway?
[NADH] in cytosol
1) low [NADH] - lactate
2) high [NADH]- OAA
Byapass 1 via lactate
lactate -> pyruvate produces NADH so export of NADH from mitochondria to cytosol is unneccessary
via Lactate
step 1
lactate dehydrogenase
Lactate–> pyruvate
reduces NAD+ to NADH in cytosol
via Lactate
step 2
pyruvate transport into mitochondria
via Lactate
step 3
pyruvate carboxylate
pyruvate -> OAA
via Lactate
step 4
mitochondrial PEP carboxykinase
OAA -> PEP
via Lactate
step 5
PEP transport to cytosol
Bypass 2
of Phosphofructokinase-1
F16BP -> F6P
fructose 1.6 biphosphatase
kinases vs phosphatases
kinase: adds phosphoryl group
phosphatase: takes phosphoryl group off
Bypass 2:
F16BP -> F6P
Mg2+ dependant FBPase-1 catalyes irreversible hydrolysis of C1 phosphate
(adds H20) (Pi leaves)
Bypass 3
of Hexokinase
G6P -> Glucose
G6Pase
Bypass 3 : Glucose-6-phosphatase
G6P -> glucose
catalyzes irreversible hydrolysis
found in liver and kidney but not in other tissue
on lumenal side of ER to keep enzyme away form glycolysis in cytosol
Regulation by compartmentalization: G6Pase
on lumenal side of ER to keep enzyme away form glycolysis in cytosol
In the liver, when bolod glucose drops?
g6p transporter transports G6P into Er lumen and G6Pase converts G6P to glucose and glucose is released into blood through glucose transporters
Sum of Gluconeogenesis
2 Pyruvate + 4ATP + 2GTP + 2NADH + 2H+ + 4H2O -> glucose + 4ADP +2GDP + 6Pi + 2NAD+
irreversible
Sum of Glycolysis
Glucose + 2ADP + 2Pi + 2NAD+ -> 2pyruvate + 2ATP + 2NADH + 2H+ + 2H2O
When is Gluconeogenesis active (2)?
1) high lactate levels from muscle activity (product of anaerobic metabolism)
2) starvation (due to lack of glucose not of food or ATP)
What is the result if both catabolic and anabolic enzyme reactions happen at the same time?
net reaction would be zero
How does the cell prevent the waste of energy?
through regulation
How does the cell prevent the waste of energy through regulation? (4)
1) Concentration
2) Reciprocal Regulation
3) Compartmentalization
Regulation: 1) Concentration
[S], intermediate, enzyme and regulator
- can control metabolic rate by mass action and enzymatic rate
Regulation: 2) Reciprocal Regulation
(one on, one off)
at least 1 favourable (irreversible) step of anabolism and catabolism are catalyzed by dif enzymes -> sites of regulation
Regulation: 3) Compartmentalization
cell can keep [intermediates] and [enzymes] at dif levels in each compartment
(ex. cytosol vs mitochondria)
Factors affecting activity of enzymes (3)
altering:
1) # of enzyme molecules in cell
2) effective activity in subcellular compartment
3) modulating activity of existing molecules
Regulation
processes to mediate metabolite homeostasis
Homeostasis
stable, relatively constant concentration of metabolites
Why regulation of metabolic pathways?
in steady state, intermediates are formed and consumed at equal rates
How does the system return to steady state after a transient perturbation that alters rate of formation/consumption of a metabolite?
compensating changes in enzyme activities
Why does regulation of glycolysis occur at more than 1 point?
because glycolytic intermediates feed into several other pathways and this allows regulation of several pathways to be coordinated
glycolytic intermediates are used in the synthesis of what other cellular constituents?
amino acids
lipids
nucleotides
(2) levels that we regulate flux of metabolic pathways?
1) cellular
2) organismal
(4) ways to regulate flux of metabolic pathways at CELLULAR level?
1) [enzymes]
2) reversible allosteric regulation
3) covalent mod of enzymes
4) substrate availability
time for:
1) [enzymes]
2) reversible allosteric regulation
3) covalent mod of enzymes
1) gene expression - HOURS
2) MILLISECONDS
3) SECONDS
How does substrate availability regulate flux through metabolic pathway?
if intracellular [S] < Km, enzyme is below Vmax & rate is determined by [S]
(1) way to regulate flux of metabolic pathways at ORGANISMAL level?
Hormone and second messenger signaling
Hormone and second messenger signaling
metabolism of entire being is regulated & integrated by growth factors and hormones that act from inside cell
- modify activity of existing enzymes or enzyme synthesis/degradation
Where are regulatory enzymes found? (2)
1) at metabolic branch points (commited steps)
2) enzymes that catalyze irreversible rxns
Why are regulatory enzymes found at metabolic branch points (commited steps)?
to avoid unintended regulation of other metabolic branches
Why are regulatory enzymes the enzymes that catalyze irreversible rxns?
these essentially irreversible steps (large (-) delta G) drive the entire pathway so their activity determines overall activity of entire pathway
Flux
net rate of conversion in a pathway
For irreversible reactions: Flux = ?
reaction rate
For near equilbrium eactions: Flux = ?
forward rate - reverse rate
A pathway at steady state has what flux for each step?
same flux for each step
Why does a pathway at steady state have the same flux for each step?
otherwise intermediates would build up or be depleted
If activity at irreversible step changes, what happens to flux of other steps and overall flux?
flux of the rest of the steps will adjust accordingly so overall flux will match flux of irreversible step
If activity at reversible step changes, what happens to flux of other steps and overall flux?
both forward and reverse reactions change and it wont have same reducing effect on pathway as long as flux at irreversible step remains the same
Why can pathways only be controlled at irreversible reactions?
no way to reduce/increase rate of forward/reverse rxn selectively in reversibe rxns
Which enzymes are good candidates for glycolytic regulation?
hexokinase
phosphofructokinase-1
pyruvate kinase
How does an allosteric inhibitor?
binds to enzyme changing its conformation (shape) which changes its substrate affinity (Km)
Allosteric Regulation of Hexokinases
1) (muscle, brain)
2) liver, pancrease cells
1) Hexokinase-1
2) Hexokinase-IV (glucokinase)
Hexokinase 1 - Allosteric Regulation
low Km - high affinity for glucose allows glycolysis even at low [glucose] in blood
- allosteric inhibition by G6P (product inhibition)
Glucokinase (HK-IV) - Allosteric Regulation
regulated by blood [glucose] since it has higher Km (10mM) than normal blood [glucose] (~5mM)
NOT inhibited by G6P - excess glucose diverted to fat biosynthesis in liver and GLYCOGEN
Liver cells have an ___ for hexokinase
isozyme - enzymes that differ in amino acid sequence but catalyze same chemical rxn
(usually differ in kinetic parameters or regulatory properties)
What are primarily used by liver cells for energy?
alpha-keto acids - pyruvate & alpha-ketoglutarate
Allosteric Regulation of PFK-1
regulated by E charge of cell
INHIBITED by: ATP & Citrate
(Km increases) (citrate signals that biosyn. precursors (ac-CoA) are abundant)
ACTIVATED by: ADP, AMP, F26BP
- E required
Allosteric Regulation of Pyruvate Kinase
INHIBITED by: ATP
ACTIVATED by: ADP , F16BP
How does ATP inhibit pyruvate kinase?
high [ATP] - reduces S (PEP) affinity for enzyme
How does F16BP activate Pyruvate Kinase?
feedforward activation
- ensures that enzymes act in concert to overall goal of E production
