JAGGERS EXAM 3 Flashcards
triose phosphate isomerase
converts DHAP to GAP
central core of 8 B strands surrounded by 8 a helices (aB barrel)
active site: Glu 165 and His 95, form enediol intermediate
kinetically perfect enzyme
stage 1 of glycolysis
trapping and priming of glucose
glucose > G6P > F6P > F16BP > DHAP & GAP (2 3C fragments, interconvert with TPI, worth using ATP instead of having a 2C and a 4C)
stage 2 glycolysis
GAP > 13BPG > 3PG > 2PG > phosphoenol-pyruvate > pyruvate
GAP to 13BPG
oxidation
dehydration via GAP dehydrogenase
2 rxns COUPLED to occur
formation of thioester intermediate (high energy) which captures energy released from oxidation to drive dehydration
how is redox maintained in glycolysis?
NAD+ lost from GAP > 13BPG is replenished when pyruvate is converted into ethanol
pyruvate to ethanol
1) decarboxylation of pyruvate to acetaldehyde
2) reduction of acetaldehyde to ethanol –> regenerates NAD+ for glycolysis
glucose > 2 ethanol + 2 ATP + 2 CO2
lactic acid fermentation
pyruvate is produced faster than it can be oxidized in CAC, but NAD+ must be recycled
glucose > 2 lactate + 2 ATP
fructose 1-phosphate pathway
fructose > F1P > glyceraldehyde + DHAP > GAP (enters at GAP)
1 fructose = 2 ATP
galactose processing in glycolysis
galactose > galactose 1P
galactose 1P + UDP-glucose > G1P + UDP-gal
G1P to G6P by phosphoglucomutase (enters glycolysis at G6P)
UDP-gal > UDP-glu via epimerase
regulation of glycolysis in muscle
high ATP inhibits phosphofructokinase by binding to regulatory sites
G6P inhibits hexokinase
pyruvate kinase is inhibited by ATP and activated by F16BP
fructose 2,6 BP in the liver
excess F6P forms F2,6BP via PFK2
F26BP is an activator of phosphofructokinase, accelerates glycolysis
PFK2 activity regulated by phosphorylation
glucokinase and hexokinase activity
glucokinase is an enzyme in the liver that produces G6P for glycogen synthesis
glucose has lower affinity for glucokinase than hexokinase
glucose inhibits hexokinase but not glucokinase, when glucose is abundant hexokinase is inhibited and glucokinase activity occurs
forms of pyruvate kinase
L-form in liver, M-form in muscle and brain
only L-form subject to regulation by phosphorylation
when blood glucose is low, its more urgently needed in muscle and brain
glycolysis regulation in the liver (3)
pyruvate kinase regulated by phosphorylation
glucokinase activity based on affinity of hexokinase
PFK activated by F26BP
when blood glucose levels are low, pyruvate kinase…
is mostly in M-form (muscle and brain), L-form is inhibited by glucagon
what are the major non-carb precursors?
lactate
amino acids
glycerol
gluconeogenesis
noncarb precursors (AAs, lactate, glycerol) are converted to pyruvate > glucose
pyruvate > oxaloacetate > PEP > 2 PG > 3PG > 13BPG > GAP > F16BP > F6P
lactase dehydrogenase reaction
L-lactate to pyruvate (and vice versa), promoted by low glucose and therefore low pyruvate
low glucose causes L-lactate to make pyruvate
what determines glycolysis vs glucogenesis occuring?
high energy levels > glycolysis inhibited, glucogenesis promoted
in liver, determined by blood glucose level
why is acetyl CoA an activated carrier
hydrolysis is highly exergonic due to thioester linkage
pyruvate to acetyl CoA net reaction
pyruvate + CoA-SH + NAD+ –> acetyl CoA + CO2 + NADH + H+
pyruvate to acetyl CoA mechanism
TPP coenzyme becomes a carbanion (highly acidic, pKa 10)
carbanion attacks pyruvate carbonyl
joined complex decarboxylates and releases CO2, forming hydroxyethyl-TPP
hydroxyethyl-TPP and lipoamide form TPP carbanion and acetyllipoamide (thioester bond)
acetyllipoamide + CoA > acetyl CoA + dihydrolipoamide (which is then oxidized to form NADH)
transacetylase
enzyme for pyruvate to acetyl CoA
has 3 distinct active sites (E1, E2, E3)
lipoamide group in E2 extends away and can swing around
1) lipoamide collects acetyl group from E1
2) transfers acetyl to CoA to form acetyl CoA in E2
3) E3 to get reoxidized
citrate synthase reaction
acetyl CoA + oxaloacetate forms Citroyl CoA
CoA cleaved by hydrolysis, citroyl leaves
energy from thioester is used to synthesize a larger molecule
citrate synthase
catalyzes acetyl CoA and oxaloacetate to form citrate, uses induced fit
binding of oxaloacetate causes CC to form acetyl CoA active site, prevents wasteful hydrolysis because citroyl CoA is made before hydrolysis
how do amino acids enter glycolysis?
turned into oxaloacetate > PEP
how does glycerol enter glycolysis?
converted to G3P > DHAP
how does lactate enter glycolysis?
turns into pyruvate via lactase dehydrogenase reaction
what hormone activates glycolysis and inhibits gluconeogenesis?
insulin
what hormone inhibits glycolysis and activates gluconeogenesis?
glucagon
what is special about 1,3-BPG?
high energy compound
can make ADP into ATP
The formation of what intermediate allows the oxidation of GAP to 1,3-BPG, and the addition of a phosphate, to be coupled by GAP dehydrogenase?
thioester intermediate
cleavage of thioester bond provides energy needed for the formation of high phosphoryl transfer compound
What intermediate is galactose converted to in order to feed into glycolysis? What other molecule is necessary for this process?
G-6P, UDP glucose
Describe how the carbons from glucose get fed into the Citric Acid Cycle
glycolysis: glucose to pyruvate
pyruvate dehydrogenase: pyruvate to acetyl CoA
CAC: acetyl CoA + oxaloacatete > citrate
Describe the negative regulation of alpha-ketoglutarate dehydrogenase and isocitrate dehydrogenase
in the Citric Acid Cycle
both experience negative feedback
alpha-ketoglutarate dehydrogenase: inhibited by succinyl CoA and NADH
isocitrate dehydrogenase: NADH
3 enzymes for the 3 irreversible steps of glycolysis
hexokinase: glucose > G6P
phosphofructokinase: F6P > F16BP
pyruvate kinase: PEP > pyruvate
pyruvate dehydrogenase complex, 5 cofactors
converts pyruvate to acetyl CoA
3 enzyme components (E1, E2, E3)
5 cofactors: TPP, lipoamide, CoA, FAD, NAD+
CO2 released
aconitase
isomerizes citrate to isocitrate, moves hydroxyl group
isocitrate dehydrogenase
isocitrate > oxalosuccinate > a-Ketogluterate
a-ketoglutarate dehydrogenase
a-ketoglutarate > succinyl CoA
mechanistically similar to pyruvate dehydrogenase complex
pyruvate dehydrogenase - 3 enzymatic active sites
lipoamide group (E2) can swing around and interact with E1 to collect acetyl group, transfers acetyl to CoA, E3 to get reoxidized
succinyl CoA synthetase
succinyl CoA to succinate
generates GTP
only CAC step that produces a high-phosphoryl-transfer potential
citric acid cycle
CIKSSFMO
why is FAD the electron acceptor when succinate is converted to fumerate?
the free-energy change is not sufficient to reduce NAD to NADH
3 reactions of succinate to oxaloacete
oxidation, hydration, oxidation
which reaction in the CAC has a large positive free energy charge? how is it driven?
malate to oxaloacetate, driven bc NADH is consumed and it is produced from the reaction
CAC net reaction
Acetyl CoA + 3 NAD+ + FAD + ADP + Pi + 2 H20 > 2 CO2 + 3 NADH + FADH2 + ATP + 3 H+ + CoA—SH
regulation of pyruvate dehydrogenase complex (PDH)
(1) feedback inhibition: inhibited by pyruvate and acetyl CoA (accumulation)
(2) covalent modification of E1: phosphatase turns PDH on in response to insulin/muscle contractions/epinephrine, kinase turns PDH off
Isocitrate dehydrogenase regulation
stimulated by ADP, inhibited by ATP and NADH
a-ketoglutarate dehydrogenase
inhibited by energy charge (ATP, NADH) and reaction products (succinyl CoA and NADH)
If oxaloacetate is pulled from the cycle by a cell’s demand for
biosynthesis, how is it replenished so that energy demand is also accommodated?
Oxaloacetate can be synthesized directly from pyruvate
complex I of ETC
Goal: transfer e- from NADH (from CAC) to CoQ
NADH reduces FMN > FMNH2 > [Fe-S] > Q > QH2 leaves to Q pool
4 H+ pumped from matrix to IM space
1 NADH + 5H(matrix) + Q = QH2 + 4H(IM space)
where do the protons to reduce Q to QH2 come from?
FADH2 from CAC in matrix (complex II) or NADH + H+ (complex I)
NADH-Q oxidoreductase
transfer electrons in NADH to CoQ
complex II of ETC
Goal: feed the Q pool
feeds the Q pool (H+), FADH2 from CAC reduces Q to QH2
complex III of ETC
Goal: Q cycle
1) QH2 enters complex III and gives 2 e-: 1 to cyt c, other to distal Q > semiquinone
2) another QH2 enters complex II and gives 2 e-: 1 to cyt c, other to complete reduction of semiquinone > QH2
during reduction of distal Q, H+ pulled from matrix
how many net cyt c reduced per QH2
2 reduced cyt c per QH2
how does the Q cycle contribute to the proton gradient?
they become reduced (Q>QH2) via protons from the matrix, and release into IM space during oxidation
complex IV of ETC
CuA/CuA > Heme a > Heme a3 > CuB
1) 2 cyt c transfer e- to heme a3 and CuB
2) reduced CuB and Fe in Heme a3 bind O2 to form peroxide bridge
3) 2 H(matrix) and 2e- cleaves bridge
4) another 2H(matrix) releases water
4 H(matrix) end up in water
where does glycolysis take place?
cytoplasm
where does CAC take place?
mitochondrial matrix
where does ETC/ox phosphorylation take place?
inner membrane of mitochondria, protons are pumped from matrix to IM space to create gradient
what is needed to reduce molecular oxygen?
2 NADH = 4 cyt c = 4 e-
2 main units of ATP synthase
F0: sits in membrane, forms proton channel
10-14 c subunits form a c ring
F1: catalytic activity, protrudes in matrix
why can O2 as an electron acceptor have adverse consequences? how is it prevented?
partial reduction yields peroxide / ROS (reactive oxygen species) which cause oxidative damage
complex IV holds it tightly until fully reduced, but sometimes ROS released
If ROS released, there are defense systems - Super Oxide Dismutase
5 subunits of F1 ATP synthase
α3, β3, γ, δ, ε
α and β subunits arranged alternately in hexameric ring
γ and ε form the central stock
γ makes different contacts with each β unit (different conformational states)
3 conformational states of β-subunit
L: loose, binds ADP and Pi loosely
T: tight, forms ATP from bound ADP + Pi
O: open, ATP is released and new ADP + Pi can enter
rotation of c-subunit
aspartic acid residue in c subunit can be -/0 if deprot/prot
1) IM channel is H+ rich so Asp protonated
2) protonation causes entire ring to turn so Asp is in hydrophobic environment
3) another c subunit is positioned next to matrix half channel (H+ poor) and deprotonated
malate dehydrogenase
oxaloacetate to malate, reduces malate (can then act as an electron carrier in malate shuttle)
malate-aspartate shuttle
1) in cytoplasm: oxaoloacetate to malate via malate dehydrogenase, malate carries electrons
2) malate shuttle moves across inner m membrane
3) malate reoxidized to oxaloacetate by malate dehydrogenase, mitrochondrial NAD is reduced to NADH + H
4) oxaloacetate converted to aspartate, which can cross back to cytoplasm
5) aspartate converted back to oxaloacetate
glycerol 3-phosphate shuttle
DHAP to Glycerol 3P, glycerol 3P takes electrons from NADH
glycerol 3P donates e- to E-FAD on inner mitochondrial membrane
E-FADH2 used to oxidize Q
ATP-ADP translocase
allows a 1:1 exchange of ADP for ATP
ADP from cytoplasm to matrix, ATP from matrix to cytoplasm
energetically expensive, dampens membrane potential
complete oxidation of 1 glucose molecule yields how much ATP?
30-32 depending on transport system from cytoplasm
(30 for glycerol, 32 for malate)
net ATP / NADH in glycolysis
2 ATP, 2 NADH (cytoplasmic)
(2 ATP used then 4 ATP made)
how do electrons enter ETC via glycerol 3P shuttle?
electrons transferred to FAD which are then transferred to Q, bypassing complex I
how do electrons enter ETC via malate aspartate shuttle?
e- transferred to NAD which transfers e- to complex I
what energy is produced from pyruvate dehydrogenase?
2 NADH (mitochondrial)
(per glucose)
how many protons are pumped per 1NADH in ETC?
complex I, III, IV: 4, 4, 2 = 10 protons/NADH
what energy carriers are produced in the CAC (1 glucose = 2 cycles)
2 GTP = 2 ATP, 6 NADH, 2 FADH2
how many protons per ATP produced in ATP synthase?
4 H+ / ATP
About 3 H+ per ATP in oxidative phosphorylation, plus calculating for offsetting the dampening of membrane potential
1 NADH yields how much ATP?
2.5
10 H+ / 4 used per ATP
hibernation & ETC
electron transport can be uncoupled from ATP production, no H+ gradient, energy released as heat, keeps animal warm
how many protons are pumped per 1 FADH2 in ETC?
complex III, IV: 4, 2 = 6 H+/FADH2
bypasses complex I
how does low [ADP] affect the CAC?
less NADH is consumed > NAD+ levels drop > slows CAC
porphyrins
central N binds metal ion - Fe in heme, Mg in chlorophyll a
planar and aromatic - absorbs visible light
light rxn in photosynthetic bacterium
photoexcitation in special pair (P960)
electron transferred to BPh
BPh transferred to QA
QA transfers to QB to form semiquinone intermediate
after 2nd cycle, fully reduced to QBH2
QBH2 > QB > cyt bc1 > cyt c2 > P960
electrons from QBH2 contribute to proton motive force
PSII goal & electron flow
P680, catalyzes transfer of e- from water to plastoquinone
reduction of Q + water splitting help establish H+ gradient
H2O → photoexcitation in P680 → Ph → QA → QB → QBH2 → cyt bf → plastocyanin (Pc)
how does plastocyanin contribute to the proton gradient
via electron carrier QBH2, protons are transferred from stroma to thylakoid lumen
how does electron transfer from water to P680 work?
coordinated by manganese (Mn) center of PSII
how many electrons are needed for 1 oxygen acceptor? how many water molecules?
4e- from 2 H2O = 2QH2 = 1 O2
how many protons are moved into the thylakoid space from 2 H2O?
4H+ from 2H2O, 8H+ from stroma via Q cycle = 12H+
PSI
P700, uses high energy e- to produce reducing power in the form of NADPH
e- transfer through a series of intermediates to ferredoxin
ferredoxin-NADP+ reductase
uses 1 FAD to collect 2 e- from 2 ferredoxin and catalyzes transfer of NADP+ > NADPH
how much ATP is produced as a result of oxidizing 2 water molecules
in photosynthesis?
3 ATP
For PSI cyclical electron transport, 4 photons absorbed by PSI leads to the release of ____ protons into the
thylakoid lumen, yielding ____ ATP by ATP synthase (____ photon/ATP)
For PSI cyclical electron transport, 4 photons absorbed by PSI leads to the release of 8 protons into the
thylakoid lumen, yielding 2 ATP by ATP synthase (2 photon/ATP)
accessory pigments
ex. carotenoids
capture remaining light, transfer energy to reaction center (special pair)
where does the calvin cycle take place?
stroma
stage 1 of calvin cycle: CO2 fixation
rate-limiting step in hexose synthesis
ribulose 1,5 bisphosphate > + CO2 > (2) 3PG
catalyzed by rubisco
what is the purpose of the calvin cycle?
ATP and NADPH from LRS are used to reduce CO2 into carbon fuel
rubisco
catalyzes first step of calvin cycle
8 small regulatory subunits, 8 large catalytic subunits
required Mg2+ ion for activity
carbamate formation required to bind Mg2+ ion in enzyme active site
How can the wasteful reaction product of rubisco be repurposed?
oxygenase activity forms phosphoglyolate
phosphoglycolate salvage pathway: save 3 of 4 carbon molecules by producing serine and glutamine. Wasteful because organic carbon is converted into CO2 without the production of ATP, NADPH, or another energy-rich metabolite
stage 2 calvin cycle: reduction
(2) 3PG > (2) 1,3 BPG > (2) GAP > (1) F6P
stage 3 calvin cycle: regeneration
GAP > F6P
F6P + 2 GAP + DHAP + 3 ATP > (3) RuBP
how many turns of calvin cycle to make a hexose sugar?
6 turns
C4 pathway
for tropical plants at high risk of oxygenase activity (increases w temp)
1) high CO2 exposure in mesophyll (air exposed) - malate moves CO2 to bundle sheath cells
2) malate decarboxylated to pyruvate, releasing CO2
3) pyruvate returns to mesophyll
2 ATP to transport 1 CO2
How many ATP are needed to make 1 glucose using the Calvin Cycle? How many are needed to make 1 glucose in a C4 plant?
18 ATP/ glucose in the Calvin Cycle (3 ATP/CO2)
30 ATP/glucose in C4 plant (need an additional 2 ATP/CO2 to move CO2)
why is rubisco more active during the day?
the stroma is more alkaline due to the light reactions, so Mg2+ is released from the thylakoid space into the stroma to compensate for increased H+ in thylakoid space
carbamate formation is favored at alkaline conditions and Mg2+ is needed to form active site
pentose phosphate pathway
G6P + 2NADP+ > ribose-5P + 2 NADPH
NADPH: reducing power for biosynthesis
ribose 5P: dNTP, RNA, DNA, ATP, NADH synthesis
how do plants make NADPH? how do organisms without photosynthesis make NADPH?
plants use PPP and photosynthesis
other organisms use PPP
where does reduced ferredoxin transfer its electrons?
thioredoxin
during the day, stromal ferredoxin is…
reduced due to PSI
thioredoxin
activates many enzymes like rubisco
where does pentose phosphate pathway occur?
cytoplasm
phosphopentose isomerase
isomerizes between ribulose 5P (R5P) and ribose 5P and xylulose 5P (X5P)
phase 1 PPP
produces NADPH and ribulose-5P
G6P > ribulose 5P
phase 2 PPP
conversion of ribulose-5P into many different sugars, produces F6P and GAP via transketolase and transaldolase
transketolase and transaldolase
ketose donor and aldose acceptor
transketolase moves 2C, transaldolase moves 3C
how is phase 1 PPP controlled?
G6P + 2NADP+ > ribulose5P + 2NADPH
only occurs if [NADPH] is low
how are dNTP, RNA, DNA, ATP, NADH synthesized
via PPP, G6P > ribulose 5P, isomerized to ribose 5P. ribose 5P is used for synthesis
[NADPH] is adequate
glycolysis is favored over PPP
[R5P] low
[NADPH] adequate
G6P converted to F6P and GAP by glycolysis. transaldolase and transketolase convert these products to ribose 5P (needed for synthesis)
NADPH and R5P balanced
PPP favored since it produces both
[NADPH] low
[R5P] adequate
3 separate reaction schemes
1) PPP Phase 1: G6P to ribose 5P and NADPH
2) ribose 5P to F6P and GAP by transketolase/transaldolase
3) G6P is synthesized from F6P and GAP by gluconeogenesis pathway
glucose 6-phosphate + 12 NADP+ + 7 H2O 12 NADPH + 12H+ + 6 CO2 +Pi
NADPH and ATP are needed
PPP phase 1 (produce NADPH)
R5P to glycolysis (produce ATP)
glycogen linkages
a-1,4 linkages lends helical structure
a-1,6 linkages allow for branching
many non-reducing ends for quick degredation
cellulose linkages
B-1,4 linkages
glycogen phosphorylase
catalyzes the phosphorolytic cleavage of glycogen (a 1,4 linkages)nto release glucose 1-P
how is glycogen remodeled for cleavage?
a 1,4 linkages cannot be cleaved within 4 residues of branching
transferase transfers 3 glucose units between branches
a-1,6-glucosidase removes final glucose from branch (a 1,6 linkage)
glycogen metabolism (3 steps)
1) a-1,4-linkage cleavage
2) remodel for cleavage
3) phosphorylation
phosphorylation of glucose after glycogen metabolism
phosphoglucomutase: G1P to G6P
hexokinase: phosphorylates free glucose to G6P for glycolysis
phosphoglucomutase
G1P to G6P
how is G6P released from the liver?
glucose-6-phosphomutase converts G6P to glucose to be released into the bloodstream
glycogen phosphorylase forms
a form: usually active R state, phosphorylated, liver
b form: usually inactive T state, not phosphorylated, muscle
can interconvert by serine phosphorylation
how is Phosphorylase b regulated?
regulated allosterically by the cell’s energy charge (inhibited by ATP)
resting muscle = high ATP = ATP binding = inhibited T state
stimulated muscle = increasing AMP, decreasing ATP = AMP binding = R state
phosphorylase kinase converts to a form
how is Phosphorylase a regulated?
glucose binding converts R state to T state (no glycogen metabolism needed if glucose is present)
how is glycogen branching helpful?
increase solubility, compact the structure, increase the number of non-reducing ends available for glycogen breakdown (faster metabolism)
biosynthesis of glycogen
glucose > G6P > G1P > UDP glucose
UDP glucose adds to existing glycogen primer at non-reducing end
Branching enzymes transfer 6-7 residue terminal chains to a hydroxyl group at 6-position, forming a 1,6 linkage and adding a new nonreducing end
why is most energy stored as fat instead of glycogen?
fatty acids are more reduced = more energy
less hydrated because they are hydrophobic = lighter in weight
bile acids
secreted as bile salts by gallbladder, insert into TG droplets to make them more accessible to digestion by lipases
lipases
secreted by pancreas
convert TGs into 2 fatty acids and monoacylglycerol
chylomicrons
lipoprotein aggregates that have a hydrophilic surface and hydrophobic interior
transports triacylglycerols through the body for storage and breakdown
hydrolysis of TGs
glycerol (taken up mostly by liver for glucogenesis > GAP and DHAP) + fatty acids (enter bloodstream, binds to serum albumin, taken up by tissues)
What fuel is used by the brain during starvation?
ketone bodies (formed from excess acetyl CoA, can’t be processed by TCA)
diabetic ketoacidosis
no insulin > glucose cannot enter cells > all energy from fats > production of acetyl CoA, builds up > ketone bodies
