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Bioc 221 > BIOC 221 - Midterm #2 > Flashcards

BIOC 221 - Midterm #2 Flashcards

1
Q

Anaerobic Conditions: Alcohol Fermentation

A

In yeast, pyruvate first converted to acetaldehyde (∂-keto acid decarboxylation) then reduced to ethanol by NADH (regenerating NAD+ for glycolysis)

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2
Q

Alcohol Fermentation Reaction

A 
Pyruvate + H+ --> Acetaldehyde + CO2
(pyruvate decarboxylase) cofactors: Mg TPP (vit.b1)
- ∂-keto acid decarboxylation
acetaldehyde + NADH +H+  ethanol
(alcohol dehydrogenase) - reduction
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3
Q

What happens when we drink alcoholic beverages?

reactions

A

ethanol + NAD+ -> acetaldehyde + NADH +H+
(alcohol dehydrogenase)

acetaldehyde + NAD+ -> acetic acid + NADH + H+
(aldehyde dehydrogenase)

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4
Q

What happens when we drink alcoholic beverages?

what is produced

A

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)

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5
Q

Pentose Phosphate Pathway

- what for?

A

to generate NADPH and pentoses (ribose-5-phosphate)

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6
Q

(2) phases of the Pentose Phosphate Pathway

A

1) oxidative phase

2) non-oxidative phase

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7
Q

oxidative phase of PPP

A

NADPH for reductive fatty acid biosynthesis

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8
Q

non-oxidative phase of PPP

A

ribose-5-phosphate for nucleic acid synthesis

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9
Q

Non-oxidative phase of PPP is active in?

A

rapidly dividing cells (blood marrow, mucosa, tumor)

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10
Q

Which tissues is PPP dominant in?

A

liver, adipose tissues, mammary glands and adrenal cortex actively synthesize steroids and fatty acids

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11
Q

Which tissues lack PPP?

A

skeletal muscle

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12
Q

Where does PPP take place?

A

cytosol

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13
Q

Cytosolic concentrations of NADH vs NADPH

A

high [NAD+] for glycolysis

high [NADPH] for FA synthesis

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14
Q

Purpose of the phosphate group on NADPH?

A

enables NADPH to interact with only specific dehydrogenase enzymes

  • ensures NADH and NADPH aren’t interchangeable
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15
Q

Glucose 6P dehydrogenase
what does this enzyme do?
- inhibited by? stimulated by?

A

the enzyme that produces NADPH
inhibited by NADPH (product inhibition)
stimulated by NADP+

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16
Q

NADPH production is tightly coupled to?

A

its utilization

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17
Q

Oxidative phase of PPP (rxns)

A

G6P -> 6-phospho-glucono-∂-lactone -> 6-phosphogluconate -> ribulose-5-p -> ribose-5-phosphate -> nucleotide, coenzymes, DNA, RNA

(g6p and 6-phosphogluconate in cyclic form)

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18
Q

Overall Rxn of Oxidative Phase of PPP

A

g6p +2NADP+ +H2O ->ribose-5-p + CO2 + 2NADPH + 2H+

oxidative decarboxylated of G6P

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19
Q

G6P -> 6-phospho-∂-lactone

logic?

A

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

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20
Q

allosteric regulator

A

regulator that doesn’t bind to E active site

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21
Q

6-phospho-∂-lactone -> 6-phosphogluconate

A

lactone: cyclic estr
add H2O
cyclic to linear

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22
Q

6-phosphogluconate -> ribulose-5-P

A 
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
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23
Q

Logic of:

6-phosphogluconate -> ribulose-5-P

A

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+,

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24
Q

In cells that aren’t using ribose-5-P (from oxidative phase) for biosynthesis…

A

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

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25
Q

Non-oxidative pathway interconverts…

A

hexoses/pentoses

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26
Q

Ribose-5-phosphate –> Xylulose-5-P

A

isomerase -(ribulose-5-P)- epimerase

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27
Q

Non-oxidative pathway rxns

A

xylulose-5P + rib-5P -TK> sedoheptulose-7P + G3P -TA> erythrose-4P + F6P

xylulose-5P + erythrose-4P -(TK)> G3P + F6P

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28
Q

The first reaction catalyzed by transketolase

A

xylulose-5P + rib-5P -> sedoheptulose-7P + G3P

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29
Q

Reaction catalyzed by transaldolase

A

seduheptulose-7-P + G3P -> erythrose-4P + F6P

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30
Q

The second reaction catalyzed by transketolase

A

xylulose-5P + erythrose-4P -> G3P + F6P

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31
Q

NADPH formed in oxidative phase is used to ?

A

reduce glutathione GSSG

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32
Q

Entry of glucose 6-phosphate either into glycolysis or into the pentose phosphate pathway is largely determined by …

A

the relative concentrations of NADP

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33
Q

Where does G6P go? Glycolysis or PPP?

A

the cell decides depending on its relative needs for biosynthesis (PPP) or energy (glycolysis)

relative activities of PFK (glycolysis) and G6PDH (PPP)

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34
Q

Both Ribose-5-P and NADPH needed?

A

Oxidative Pathway of PPP

G6P + 2NADP + H2O -> Rib5P + CO2 + 2NADH + 2H+

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35
Q

More Ribose-5-P than NADPH needed?

A

Non-oxidative PPP

2F6P + G3P -> 3 ribose-5-P

(net: 5 G6P + ATP -> 6 Rib5P + ADP + H+)

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36
Q

More NADPH than Ribose-5-P needed?

A

Ribose-5P is recycled to form glycolytic intermediates

ultimately 6CO2

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37
Q

Both ATP and NADPH needed BUT not Ribose-5-P?

A

Ribose-5-P recycled to produce glycolytic intermediates (Glu-6-P, Gal-3-P) which then go on to glycolysis

(forming pyruvate and ATP)

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38
Q

Often Anabolic and Catabolic pathways use the same…. but…

A

same reversible reactions BUT at least 1 reaction differs

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39
Q

Anabolic and Catabolic output is defined by?

A

metabolic needs

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40
Q

Anabolic and Catabolic pathways are controlled by…

A

one or more reactions unique to that pathway at an early step

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41
Q

Why are Anabolic and Catabolic pathways controlled by 1 or more reactions at an EARLY step?

A

so nutrients are wasted and so regulation is reciprocal (anabolism is on while catabolism is off and vice versa)

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42
Q

Biosynthetic (anabolic) processes are coupled to… so?

A

ATP hydrolysis so overall process is irreversible in vivo when required and process is favourable even when [reactant] are low

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43
Q

Gluconeogenesis

A

glucose synthesis from non-carb precursors

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44
Q

Gluconeogenesis

what for? in mammals

A

in mammals some tissues depend almost completely on glucose for energy

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45
Q

Which tissues in mammals depend almost completely on glucose for energy?

A

brain, neurone, RBC, testes

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46
Q

Brain requires how much glucose?

A

120g/day

1/2 of all glucose stored as glycogen in muscle and liver

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47
Q

Where does Gluconeogenesis take place?

A

cytosol

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48
Q

In animals, what are important precursors for Gluconeogenesis?

A

3C compounds of lactate, pyruvate, glycerol and some amino acids

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49
Q

Gluconeogenesis is mostly in?

A

liver (and kidney)

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50
Q

Cori Cycle

A

lactate form muscle -> glucose in liver -> back to muscle

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51
Q

Both glycolysis and gluconeogenesis occur in?

A

cytosol

52
Q

How many reactions do Glycolysis and Gluconeogenesis share?

A

7/10

53
Q

Which enzymes must be bypassed in Gluconeogenesis?

A

hexokinase (step1), PFK-1 ( step 3), pyruvate kinase (step 10/last) are irreversible & must be bypassed

54
Q

Bypass 1

A

Pyruvate Kinase

PEP synthesized by either pyruvate or lactate (glycogenic precursor)

55
Q

(2) ways for Bypass 1

A

a) via OAA

b) via lactate

56
Q

Bypass 1

a) via OAAA

A

OAA pathway borrows an anapletoric reaction in TCA cycle

57
Q

Anapletoric reactions

A

form metabolic intermediates for replenishment

58
Q

via OAA

step 1

A

transport to mitochondria

59
Q

via OAA

step 2

A

pyruvate carboxylase
pyruvate + bicarbonate + ATP -> OAA + ADP + Pi

cofactor: biotin

60
Q

Logic of: pyruvate -> OAA

A

carboxylation allows enolate O anion to serve as Nu in next phosphorylated rxn

61
Q

via OAA

step 3

A

mitochondria has no OAA transporter so
mitochondrial malate DH :

OAA + NADH + H+ L-malate + NAD+

62
Q

via OAA

step 4

A

malate-α-ketoglutarate transporter in the inner mitochondria membrane (IMM) :
transport of malate to the cytosol

63
Q

via OAA

step 5

A

cytosolic malate DH

L-malate + NAD+ -> OAA + NADH + H+

64
Q

via OAA

step 6

A

PEP carboxylase (Mg2+ and GTP dependant)

OAA + GTP -> PEP + CO2 + GDP

65
Q

Chemical Logic of carbox/decarbox:

A

represents a way of “activating” pyruvate

the decarboxylation of OAA facilitates PEP formation.

66
Q

logic of pyruvate transported into mitoc. forming OAA then to malate then out of mitochondria and back to OAA

A

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

67
Q

Energetics of bypass 1 via OAA

A 
ATP consumed to make C-C bond in OAA from pyruvate 
that energy (plus GTP) used to build high E PEP
68
Q

Metabolic logic for Bypass 1 via OAA?

A

steal NADH from mitochondria

69
Q

bypass 1 via OAA provides balance for..

A

NADH produced (stolen) and consumed in the cytosol during glucose synthesis

70
Q

What determines whether OAA goes through either pathway?

A

[NADH] in cytosol

1) low [NADH] - lactate
2) high [NADH]- OAA

71
Q

Byapass 1 via lactate

A

lactate -> pyruvate produces NADH so export of NADH from mitochondria to cytosol is unneccessary

72
Q

via Lactate

step 1

A

lactate dehydrogenase

Lactate–> pyruvate

reduces NAD+ to NADH in cytosol

73
Q

via Lactate

step 2

A

pyruvate transport into mitochondria

74
Q

via Lactate

step 3

A

pyruvate carboxylate

pyruvate -> OAA

75
Q

via Lactate

step 4

A

mitochondrial PEP carboxykinase

OAA -> PEP

76
Q

via Lactate

step 5

A

PEP transport to cytosol

77
Q

Bypass 2

A

of Phosphofructokinase-1

F16BP -> F6P
fructose 1.6 biphosphatase

78
Q

kinases vs phosphatases

A

kinase: adds phosphoryl group
phosphatase: takes phosphoryl group off

79
Q

Bypass 2:

F16BP -> F6P

A

Mg2+ dependant FBPase-1 catalyes irreversible hydrolysis of C1 phosphate

(adds H20) (Pi leaves)

80
Q

Bypass 3

A

of Hexokinase

G6P -> Glucose
G6Pase

81
Q

Bypass 3 : Glucose-6-phosphatase

G6P -> glucose

A

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

82
Q

Regulation by compartmentalization: G6Pase

A

on lumenal side of ER to keep enzyme away form glycolysis in cytosol

83
Q

In the liver, when bolod glucose drops?

A

g6p transporter transports G6P into Er lumen and G6Pase converts G6P to glucose and glucose is released into blood through glucose transporters

84
Q

Sum of Gluconeogenesis

A

2 Pyruvate + 4ATP + 2GTP + 2NADH + 2H+ + 4H2O -> glucose + 4ADP +2GDP + 6Pi + 2NAD+

irreversible

85
Q

Sum of Glycolysis

A

Glucose + 2ADP + 2Pi + 2NAD+ -> 2pyruvate + 2ATP + 2NADH + 2H+ + 2H2O

86
Q

When is Gluconeogenesis active (2)?

A

1) high lactate levels from muscle activity (product of anaerobic metabolism)
2) starvation (due to lack of glucose not of food or ATP)

87
Q

What is the result if both catabolic and anabolic enzyme reactions happen at the same time?

A

net reaction would be zero

88
Q

How does the cell prevent the waste of energy?

A

through regulation

89
Q

How does the cell prevent the waste of energy through regulation? (4)

A

1) Concentration
2) Reciprocal Regulation
3) Compartmentalization

90
Q

Regulation: 1) Concentration

A

[S], intermediate, enzyme and regulator

- can control metabolic rate by mass action and enzymatic rate

91
Q

Regulation: 2) Reciprocal Regulation

A

(one on, one off)
at least 1 favourable (irreversible) step of anabolism and catabolism are catalyzed by dif enzymes -> sites of regulation

92
Q

Regulation: 3) Compartmentalization

A

cell can keep [intermediates] and [enzymes] at dif levels in each compartment

(ex. cytosol vs mitochondria)

93
Q

Factors affecting activity of enzymes (3)

A

altering:

1) # of enzyme molecules in cell
2) effective activity in subcellular compartment
3) modulating activity of existing molecules

94
Q

Regulation

A

processes to mediate metabolite homeostasis

95
Q

Homeostasis

A

stable, relatively constant concentration of metabolites

96
Q

Why regulation of metabolic pathways?

A

in steady state, intermediates are formed and consumed at equal rates

97
Q

How does the system return to steady state after a transient perturbation that alters rate of formation/consumption of a metabolite?

A

compensating changes in enzyme activities

98
Q

Why does regulation of glycolysis occur at more than 1 point?

A

because glycolytic intermediates feed into several other pathways and this allows regulation of several pathways to be coordinated

99
Q

glycolytic intermediates are used in the synthesis of what other cellular constituents?

A

amino acids
lipids
nucleotides

100
Q

(2) levels that we regulate flux of metabolic pathways?

A

1) cellular

2) organismal

101
Q

(4) ways to regulate flux of metabolic pathways at CELLULAR level?

A

1) [enzymes]
2) reversible allosteric regulation
3) covalent mod of enzymes
4) substrate availability

102
Q

time for:

1) [enzymes]
2) reversible allosteric regulation
3) covalent mod of enzymes

A

1) gene expression - HOURS
2) MILLISECONDS
3) SECONDS

103
Q

How does substrate availability regulate flux through metabolic pathway?

A

if intracellular [S] < Km, enzyme is below Vmax & rate is determined by [S]

104
Q

(1) way to regulate flux of metabolic pathways at ORGANISMAL level?

A

Hormone and second messenger signaling

105
Q

Hormone and second messenger signaling

A

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
106
Q

Where are regulatory enzymes found? (2)

A

1) at metabolic branch points (commited steps)

2) enzymes that catalyze irreversible rxns

107
Q

Why are regulatory enzymes found at metabolic branch points (commited steps)?

A

to avoid unintended regulation of other metabolic branches

108
Q

Why are regulatory enzymes the enzymes that catalyze irreversible rxns?

A

these essentially irreversible steps (large (-) delta G) drive the entire pathway so their activity determines overall activity of entire pathway

109
Q

Flux

A

net rate of conversion in a pathway

110
Q

For irreversible reactions: Flux = ?

A

reaction rate

111
Q

For near equilbrium eactions: Flux = ?

A

forward rate - reverse rate

112
Q

A pathway at steady state has what flux for each step?

A

same flux for each step

113
Q

Why does a pathway at steady state have the same flux for each step?

A

otherwise intermediates would build up or be depleted

114
Q

If activity at irreversible step changes, what happens to flux of other steps and overall flux?

A

flux of the rest of the steps will adjust accordingly so overall flux will match flux of irreversible step

115
Q

If activity at reversible step changes, what happens to flux of other steps and overall flux?

A

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

116
Q

Why can pathways only be controlled at irreversible reactions?

A

no way to reduce/increase rate of forward/reverse rxn selectively in reversibe rxns

117
Q

Which enzymes are good candidates for glycolytic regulation?

A

hexokinase
phosphofructokinase-1
pyruvate kinase

118
Q

How does an allosteric inhibitor?

A

binds to enzyme changing its conformation (shape) which changes its substrate affinity (Km)

119
Q

Allosteric Regulation of Hexokinases

1) (muscle, brain)
2) liver, pancrease cells

A

1) Hexokinase-1

2) Hexokinase-IV (glucokinase)

120
Q

Hexokinase 1 - Allosteric Regulation

A

low Km - high affinity for glucose allows glycolysis even at low [glucose] in blood

  • allosteric inhibition by G6P (product inhibition)
121
Q

Glucokinase (HK-IV) - Allosteric Regulation

A

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

122
Q

Liver cells have an ___ for hexokinase

A

isozyme - enzymes that differ in amino acid sequence but catalyze same chemical rxn
(usually differ in kinetic parameters or regulatory properties)

123
Q

What are primarily used by liver cells for energy?

A

alpha-keto acids - pyruvate & alpha-ketoglutarate

124
Q

Allosteric Regulation of PFK-1

A

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

125
Q

Allosteric Regulation of Pyruvate Kinase

A

INHIBITED by: ATP

ACTIVATED by: ADP , F16BP

126
Q

How does ATP inhibit pyruvate kinase?

A

high [ATP] - reduces S (PEP) affinity for enzyme

127
Q

How does F16BP activate Pyruvate Kinase?

A

feedforward activation

- ensures that enzymes act in concert to overall goal of E production

Bioc 221 (4 decks)

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