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Metabolism > phosphogluconate pathway, PDH, TCA > Flashcards

phosphogluconate pathway, PDH, TCA Flashcards

1
Q

what are the 2 phases of the phosphogluconate pathway

A

oxidative and non-oxidative

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2
Q

what is the purpose of the PPP

A
  1. reduction of NADP+ to NADPH for reductive biosynthetic rxns or to counter oxygen radicals
  2. Synthesis of ribose 5 phosphate (precursor for nucleotides, RNA,DNA, and coenzymes ATP, NADH, FADH2, coenzyme A )
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3
Q

NADPH is used for the synthesis of what

A

fatty acids and other molecules

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4
Q

what tissues have little shunt actvity

A

Tissues that produce little fat and are not actively dividing have little shunt activity (i.e. muscle)

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5
Q

what is used for nucleic acid synthesis

A

Ribose phosphate are used for nucleic acid synthesis

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6
Q

what happens to tissues only need NADPH and not any other product (such as ribose 5 phosphate)

A

In tissues requiring NADPH, ribulose-5-P is recycled to G-6-P

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7
Q

what is the general rxn that happens in the non-oxidative phase

A

six 5-carbon molecules are converted to 5

6-carbon molecules, thus regenerating glucose-6-phosphate

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8
Q

what is the first rxn of PPP

A

G-6-P + NADP+ to 6-phospho-δ-gluconolactone + NADPH

G-6-P dehydrogenase

NADP+ is reduced to NADPH

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9
Q

what kind of rxn happens in the 1st PPP rxn

A

redox: G6P oxidized and NADP+ is reduced

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10
Q

what is the 2nd rxn of PPP

A

6-phospho-δ-gluconolactone reacts with water to form 6-phosphogluconate (hydrolysis)

enzyme: lactonase
cofactor: Mg2+

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11
Q

3rd rxn in PPP

A

6-phosphogluconate + NADP+ reacts to form D-Ribulose-5-phosphate + NADPH + H+ + CO2

enzyme: 6-phosphogluconate dehydrogenase

Oxidation and decarboxylation rxn

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12
Q

4th rxn in PPP

A

D-Ribulose-5-phosphate to D-ribose 5 phosphate

phosphopentose isomerase

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13
Q

what creates superoxide radicals (*O2)

A

mitochondrial respiration, ionizing radiation, sulfa drugs, herbicides, antimalarials, divicine

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14
Q

what do superoxide radical *O2 become and what do they react with to become that.

A

they become H2O2; they react with 2 H+ and an e-

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15
Q

what does H2O2 become if not reduced

A

a hydroxyl free radical *OH

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16
Q

a hydroxyl free radical *OH cause what type of damage? What do they damage?

A

oxidative damage to lipids, proteins, DNA

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17
Q

what cells keep high levels of NADPH/NADP+ ratios to combat oxidative damage?

A

cells of lens and cornea; erythrocytes

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18
Q

how does NADPH help fight oxidative damage

A

it reduces GSSG to 2 GSH (glutathione)

enzyme: glutathione reductase

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19
Q

what does 2GSH do?

A

it reacts with H2O2 to form 2 H2O

it can (also) inhibit reactive hydroxyl radical damage to tissues

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20
Q

R-5-P recycling involves what

A

• R-5-P recycling involves a complex series of reactions involving transketolase and transaldolase

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21
Q

what intermediates are formed in R-5-P recycling

A

• 7-carbon, 4-carbon, and 3-carbon sugar phosphates are intermediates

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22
Q

what does epimerase do

A

converts between ribose 5 phoshate and xylulose 5 phosphate

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23
Q

what does transketolase do to R5P and X5P

A

makes sedoheptulose 7 phosphate and G3P

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24
Q

what does transaldolase do to sedoheptulose 7 phosphate and G3P

A

makes F6P and Erythrose 4 phoshate

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25
Q

what is F6P converted to

A

G6P

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26
Q

what is Erythrose 4 phoshate and X5P (from another origin) converted to and by what enzyme

A

F6P and G3P by transketolase

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27
Q

what can happen to G3P made from X5P

A

enter gluconeogenesis

Or react with sedoheptulose 7 phosphate to make F6P and erythrose 4 Phosphate via transaldolase rxn

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28
Q

what is made in ribose 5 phosphate recycling (generally)

A

six 5 carbon sugars make five 6 carbon sugars

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29
Q

what is a disease of the PPP: describe it

A

Wernicke-Korsakoff Syndrome:

-caused by TPP deficiency

-exarcerbated by mutation in the
transketolase gene (lowered affinity for
TPP); more sensitive to thiamine deficiency

-slows down PPP

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30
Q

TTP is a cofactor what what in PPP

A

transketolase

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31
Q

what is the general names for the 2 substrates of transketolase

A

aldose acceptor and ketose donor

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32
Q

what are the 2 fates of G6P and what influences its fate

A

• G-6-P is partitioned between glycolysis and the PPP, depending on current needs of cell and on conc. of NADP+ in cytosol

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33
Q

what inhibits and what activates G6P entrance into PPP

A

-NADP+ is allosteric activator and NADPH is allosteric inhibitor

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34
Q

what is pyruvate oxidized to in respiration

A

Pyruvate produced by glycolysis is further oxidized

to H20 and C02 in an aerobic phase of catabolism

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35
Q

what are the 3 major stages of cellular respiration

A

1) Organic fuel molecules - glucose, fatty acids, some amino acids are oxidized to yield 2-carbon fragments in the form of acetyl group of acetyl-CoA
2) The acetyl groups enter the citric acid cycle, which oxidizes them to C02; energy released is conserved in reduced electron carriers NADH and FADH2
3) Reduced coenzymes are themselves oxidized, giving up H+ and electrons; electrons are transferred to 02- via the mitochondrial electron transport chain

During electron transfer, the large amount of energy
released is conserved in the form of ATP

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36
Q

what is acetyl CoA made from

A

Oxidation of fatty acids, glucose, and some amino acids yield acetyl-CoA

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37
Q

what transports pyruvate into mitochondria

A

pyruvate translocase (cotransport with H+)

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38
Q

what is the delta G of the PDH

A

-33 kj/mol

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39
Q

what are the cofactors of PDH

A

TPP, lipoate (lipoic acid), FAD+, NAD+, CoA-SH

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40
Q

what are the subtrates and products of PDH

A

pyruvate to acetyl CoA , Co2 and NADH

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41
Q

what is the rxn of PDH called

A

oxidative decarboxylation: irreversible

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42
Q

what happens to NADH formed

A

donate hydride to ETC

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43
Q

how many ATP’s per NADH and FADH2

A

2.5; 1.5

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44
Q

what happens in the first part of PDH

A

pruvate is releases CO2 and forms Hydroxyethyl TPP (HETPP)

enzyme: pyruvate dehydrogenase

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45
Q

what happens in 2nd part of PDH

A

Hydroxyethyl group is transfered to lipoic acid and is oxidized to form acetyl dihydrolipoamide

enzyme: dihydrolipoyl transacetylase

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46
Q

what happen in 3rd part of PDH

A

acetyl group is transfered to CoA

enzyme: dihydrolipoyl transacetylase

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47
Q

4th part of PDH

A

Dihydrolipoamaide is reoxidized and lipoic acid is regenerated

enzyme: dihydrolipoyl dehydrogenase

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48
Q

what does FAD stand for

A

Flavin adenine dinucleotide

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49
Q

what does TPP do?

A

Thiamine Pyrophospate(TPP): involved incleavage of bonds adjacent to carbonyl groups and transfer of activated acetaldehyde groups from one C to another

decarboxylates pyruvate

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50
Q

what does lipoic acid do

A

serves as both an electron carrier and an acyl carrier

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51
Q

what does TPP do

A

1) TPP reacts with pyruvate, which undergoes decarboxylation.
C-1 of pyruvate is released as CO2; C-2 of pyruvate, now an
aldehyde, is attached to TPP

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52
Q

what is the ring in TPP called? what is it involved in?

A

thiazolium ring: C2 of ring attaches with what was C2 of pyruvate (active acetaldehyde). C1 of pyruvate was released as CO2

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53
Q

what does lipoic acid do?

A

-contains 2 thiol groups which are found in either reduced (dithiol) or oxidized (disulfide) forms;
functions as an electron carrier or an acyl carrier

-Pyruvate dehydrogenase transfers two electrons and the acetyl
group to lipoic acid. This reduces the oxidized lipoic acid and transfer
of the acetyl group to the lipoyllysyl group to form an acetyl thioester.

54
Q

what does CoA do

A
  • Functions as an acyl carrier by forming a thiol ester bond
    between its thiol group and the acyl group

3) Transter of the acetyl group to CoA-SH, forming acetyl-CoA
4) Reoxidation of lipoic acid, transferring reducing equivalents to NAD+

55
Q

Which are co-substrates in PDH and which are prosthetic groups

A

CoA-SH and NAD+ are cosubstrates; TPP, lipoate andn FAD are prosthetic groups

56
Q

Wernicke Encephalopathy

A

Characterized by ocular
abnormalities, ataxia, and state of global
confusion. commonly (but not exclusively)
associated with chronic alcohol abuse.

57
Q

Beriberi:

A

manifestations include fatigue, irritability,
sleep disturbance, abdominal pain, anorexia,
leading to swelling, pain, paralysis, and death

58
Q

Pyruvate Dehydrogenase Complex Deficiency:

A 
manifested in infancy or later childhood
by progressive neural symptoms, including
intermittent ataxia, poor muscle tone,
abnormal eye movements, or seizure.
Patient manifests elevated blood lactate
59
Q

what do wernicke encephalopathy, beriberi and PDH deficiency have in common?

A

thiamine deficiency?

60
Q

overview of TPP

A

1) Thiamine Pyrophospate (TPP): contains thiamine (vitamin B1)
and a pyrophosphate group. Lack of vitamin B1 in the diet
leads to beriberi, a condition characterized by accumulation of
body fluids, pain, paralysis, loss of neural function and death.
The brain usually obtains all its energy from aerobic oxidation
of glucose and therefore sensitive to thiamine deficiency.
Beriberi occurs in populations that consume polished white rice
(lacks hulls in which thiamine is found) and in alcoholics.

61
Q

overview of FAD

A

2) Flavin Adenine Dinucleotide (FAD) consists of riboflavin (vitamin
B2) and adenine dinucleotide; accepts 2 H atoms (2 electrons
and two protons) to form its reduced form FADH2

62
Q

overview of NAD+

A

3) NAD+ consists of niacin (a vitamin) and adenine dinucleotide;
accepts a hydride (2 electrons and 1 proton) to form its
reduced form NADH

63
Q

overview of CoA

A 
4) Coenzyme A (CoA-SH) consists of a phosphoadenine dinucleotide,
pantothenic acid (a vitamin) and β-mercaptoethylamine;
functions as acyl carrier by forming thiol ester bond
64
Q

lipoic acid overview

A

5) Lipoic Acid: contains 2 thiol groups which are found in either
reduced (dithiol) or oxidized (disulfide) forms; functions as an
electron carrier or an acyl carrier

65
Q

about E1 of PDH

A

1) Pyruvate dehydrogenase, E1
PDC has 12 copies of E1, each
with two identical subunits;
contains bound TPP

66
Q

about E2 of PDH

A 
2) Dihydrolipoyl transacetylase,E2
core of the PDC has 60 copies
of E2; lipoate is covalently
attached to lysine groups in E2
lipollysyl groups provide long
flexible arms to deliver attached
acyl groups from one active site to
another
67
Q

about E3 of PDH

A

3) Dihydrolipoyl dehydrogenase,E3
PDC has 6 copies of E3, each
with two identical subunits;
contains bound FAD

68
Q

generally what are the rxn steps of PDH and what enzyme catalyzes each step

A

Pyruvate dehydrogenase, E1:
1) Oxidative decarboxylation of pyruvate occurs after reaction with TPP; C-1
of pyruvate released as CO2; C-2, now an aldehyde, is attached to TPP
Dihydrolipoyl transacetylase, E2:
2) Hydroxyethyl group is oxidized to carboxylic acid (acetate); 2 e- now
reduce disulfide bonds in lipoyl group on E2 to 2 thiol groups; acetate is
transferred to one of thiol groups on E2
3) Acetate is transesterified to CoA to yield acetyl-CoA
Dihydrolipoyl dehydrogenase, E3:
4) Thiol moieties of lipoate are oxidized to regenerate the disulfide bond;
2 H atoms reduce FAD (associated with E3); Hydride ion is transferred
from FADH2 to NAD+ to form NADH

69
Q

how is PDH regulated

A

PDC is regulated both allosterically and by chemical
modification:
Inhibited by: ATP, acetyl-CoA, NADH, fatty acids,
phosphorylation of serine on E1
Activated by: AMP, CoA-SH, NAD+, Ca2+ (signal for
muscle contraction and increased demand for ATP)

FIND better diagram

70
Q

what are 4 general features of TCA

A

1) Four steps that generate NADH or
FADH2

2) One step that generates ATP/GTP

3) Oxidation dependent on availability of
oxaloacetate

4) Entry of 2 carbonfrom acetyl-CoA
…two mol.of C02 leave
-one mol of OAA used
…one mol. of OAA is regenerated,
Thus no net change
71
Q

What is the purpose of having

a circular pathway?

A

1) Citric acid cycle intermediates are
starting materials in anabolic pathways,
and they are endproducts of catabolic pathways such as degradation of glucogenic amino
acids

2) the oxidation of acetyl units would be coordinated with other pathways such as the synthesis of
glucose

72
Q

step 1 of TCA

A

Acetyl CoA + OAA + H20–> citrate + CoA-SH

enzyme: citrate synthase

73
Q

describe step 1 of TCA

-what is delta G

A
  • Citrate is formed by the condensation of acetyl-CoA with oxaloacetate; CoA is released
  • Irreversible reaction - large negative free energy of reaction (-32,2 kj/mol) is necessary to drive reaction because oxaloacetate is present in very low concentration in cells
74
Q

structure of citrate synthase

A 
Structure of citrate
synthase:
Subunits undergo
conformational change
from open (a) to closed
(b) form on binding
oxaloacetate creating
a binding site
for acetyl-CoA
75
Q

what makes citrate rxn highly exergonic

A 
Hydrolysis of
high energy
thioester
intermediate
(citroyl-CoA)
makes forward
rxn highly
exergonic
76
Q

what is the only step in TCA cycle that involves formation of C-C bond

A

citrate synthase rxn

77
Q

what is the intermediate in citrate synthase intermediate

A

citryl -CoA

78
Q

conformational change of citrate synthase

A

Subunits undergo conformational change from open to
closed form on binding oxaloacetate creating a binding site
for acetyl-CoA; forms transient citroyl-CoA that rapidly
undergoes hydrolysis to CoA and citrate

79
Q

step 2 of TCA

A

citrate –> cis-aconitate –> isocitrate

aconitase in both reactions

80
Q

what is delta G of step 2 of TCA

A

13.3 kj/mol reversible

81
Q

what types of rxn happen in each step in aconitase rxns

A

Isocitrate is formed by 2-step mechanism involving dehydration
and hydration via the intermediate cis-aconitate

82
Q

what kind of center does aconitase have? what attaches to it?

A

iron sulfur center

3 Cys residues of enzyme bind 3 Fe atoms; 4th Fe is bound to
one of the carboxyl groups of citrate and interacts noncovalently
with a hydroxyl group of citrate

83
Q

step 3 of TCA

A

isocitrate + NAD+ –> oxalosuccinate + NADH and H+–> CO2 + intermediate –> alpha ketogluterate

Oxidation of Isocitrate

(Isocitrate dehydrogenase)

84
Q

what are byproducts of isocitrate dehydrogenase rxn

A

CO2 and NADH

85
Q

isocitrate dehydrogenase rxn is the first in what 2 categories in the TCA

A

first oxidation, generating NADH

first rxn where carbon unit is lost

86
Q

step 4 of TCA

A

Oxidation of a-ketoglutarate + CoA-SH and NAD+ to succinyl-CoA and CO2 with generation of NADH

enzyme: alpha ketogluterate dehydrogenase complex

87
Q

delta G of step 4 of TCA

A

-33.5; irreversible

88
Q

compare alpha ketogluterate dehydrogenase complex to PDH

A

virtually identical rxn to PDH

89
Q

step 5 of TCA

A

Succinyl-CoA is converted to succinate + CoA-SH with generation of GTP

succinate CoA synthetase

90
Q

delta G of step 5 of TCA

A

-2.9; reversible

91
Q

what is conserved in Succinyl CoA synthetase rxn?

what do the 2 isozymes yield?

A

The energy of the thioester bond is conserved by phosphorylation
of GDP or ADP to GTP or ATP; two isozymes, one specific for
GDP and the other for ADP

92
Q

step 6 of TCA

A

Succinate is oxidized to fumarate with the generation of FADH2 from FAD

succinate dehydrogenase

93
Q

enzymatic activity

A

in Complex II of ETC

94
Q

what happens to reducing equivalents in succinate dehydrogenase rxn

A

Reducing equivalents are transferred via FAD and iron-sulfur

centers to ubiquinone

95
Q

what is delta G knot of step 6 of TCA

A

0; reversible

96
Q

succinate dehydrogenase inhibited by

A

malonate (similar structure)

97
Q

step 7 of TCA

A

fumarate + OH- –> carbanion transition state + H+ (from outside)–> Malate

enzyme: fumarase

98
Q

delta G of step 7 of TCA

A

-3.8

99
Q

step 8 of TCA

A

L-Malate + NAD+ –> NADH + Oxaloacetate

malate dehydrogenase

100
Q

delta G of step 8 of TCA

A

29.7 reversible

101
Q

malate dehydrogenase rxn has high positive delta G: how does it proceed

A

Although this reaction has a high positive G’o, the reaction
proceeds from left to right since oxaloacetate is present at very
low concentrations (<1 μM)

102
Q

what is the net yield of TCA per acetyl CoA

A

3 NADH, 1 FADH2, 1 GTP (ATP), and
2 CO2 (not same carbons that entered
the cycle as acetyl group)

103
Q

what is the number of total ATPs that result from TCA

A

10 per acetyl CoA

104
Q

ATP’s per glucose molecule

A

30-32

105
Q

Role of Citric Acid Cycle

In Anabolism

A

The TCA cycle provides precursors for other
biosynthetic pathways:

1) a-ketoglutarate is
a precursor of
amino acids and
nucleotides

2) Oxaloacetate is
a precursor of
a) amino acids
and can also be
b) converted to
glucose via PEP
3) Succinyl-CoA is
an intermediate
in synthesis of
porphyrin ring
of heme
106
Q

what are 3 fates of PEP

A

Glucose

AA (serine, glycine, cysteine, phenylalanine, tyrosine, tryptophan)

OAA (via PEP carboxylase)

107
Q

pyruvate can become

A

acetyl CoA

OAA ( via pyruvate carboxylase (followed by PEP carboxykinase??))

malate ( via malic enzyme)

108
Q

citrate can also become

A

FAs, sterols

109
Q

alphaketogluterate can also become

A

glutamate

  • glutamate can then become purines or AA’s ( glutamine, proline or arginine)
110
Q

succinyl CoA can become

A

porphyrins, heme

111
Q

OAA can become

A

aspartate or asparigine

  • which can then become pyrimidines
112
Q

what enzyme catlyzes the carboxylation of pyruvate to form OAA? any cofactors?

A

pyruvate carboxylate

cofactor: biotin

113
Q

what is the role of biotin in carboxylase

A

Role of biotin:

Biotin is attached
to enzyme via
amide bond with
the amino group of
a Lysine, forming a
biotinyl-enzyme
Biotin acts as a
carrier to
transport the CO2
from one active
site to another on
the same enzyme
114
Q

how is TCA cycle regulated

A

1) Availability of substrates (limits flux)
2) Allosteric regulation at its three exergonic steps.

1) Inhibited if:
high ratios of
[ATP/ADP],
[NADH/NAD],
[acetylCoA/CoA]
=energy
sufficient
metabolic state

2) Also inhibited
by succinyl-CoA,
citrate, ATP

3) Activated by:
ADP, Ca2+

115
Q

PDH is inhibited/ activated by what

A

inhibited by ATP, Acetyl CoA, NADH and fatty acids

activated by AMP, CoA, NAD+, Ca2+

116
Q

citrate synthase inhibition/activation

A

inhibitied by NADH, Succinyl CoA, citrate, ATP

activated by: ADP

117
Q

isocitrate dehydrogenase inhibition/activation

A

inhibited by : ATP

activated by Ca2+ and ADP

118
Q

alpha ketogluterate dehydrogenase complex regulation

A

inhibited by: succinyl CoA, NADH

activated by Ca2+

119
Q

what carbon of G6P is released as CO2 in PPP

A

C1

120
Q

TPP is what

A

Thiamine pyrophosphate

121
Q

where are all enzymes of TCA located

A

all except for succinate dehydrogenase are in matrix. Succinate dehydrogenase is in inner mitochondrial membrane

122
Q

malonate is a competitive inhibitor of what

A

succinate dehydrogenase

123
Q

what are 2 key regulatory enzymes of TCA

what are some compounds they inhibited by

A

citrate synthase and isocitrate dehydrogenase

ATP and/or NADH

124
Q

what is required for conversion of succinate to fumarate in TCA

A

FAD

125
Q

For the rxn :

L-Malate + NAD+ ? oxaloacetate + NADH + H+, ?G’° = 29.7 kJ/mol. The reaction as written:

can it occur?

A

yes, may occur in cells at certain concentrations of substrate and product.

126
Q

The two moles of CO2 produced in the first turn of the citric acid cycle have their origin in the

A

two carboxyl groups derived from oxaloacetate.

127
Q

what fraction of OAA carbons are used in each cycle of TCA

A

half

128
Q

The oxidation of 3 mol of glucose by the pentose phosphate pathway may result in the production of

A

3 mol of pentose, 6 mol of NADPH, and 3 mol of CO2

129
Q

The pentose phosphate pathway represents an oxidation/reduction. What is the most reduced and Oxidized product of this pathway

A

NADPH and Carbon dioxide respectively.

130
Q

The pentose phosphate pathway involves:

A

trioses, pentoses, hexoses, heptoses

131
Q

What enzyme converts GTP formed in TCA to ATP?

A

Nucleotide diphosphate kinase

Metabolism (8 decks)

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