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Biochemistry- First Aid > Biochemistry First Aid- Metabolism Part 1 (98-106) > Flashcards

Biochemistry First Aid- Metabolism Part 1 (98-106) Flashcards

1
Q

name four major metabolic processes that take place in the mitochondria

A

fatty acid oxidation (beta oxidation), acetyl CoA production, the TCA cycle, and oxidative phosphorylation

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2
Q

what major metabolic processes occur in the cytoplasm (try to name 6)

A

glycolysis, HMP shunt, fatty acid synthesis, protein synthesis (RER), steroid synthesis (SER), cholesterol synthesis

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3
Q

name three metabolic processes that occur both in the mitochondria and in the cytoplasm

A

heme synthesis, urea cycle, gluconeogenesis

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4
Q

define the term kinase

A

an enzyme that uses ATP to phosphorylate a substrate

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5
Q

define the term phosphorylase

A

an enzyme that phosphorylates a substrate without using ATP

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6
Q

define the term dehydrogenase

A

an enzyme that catalyzes redox reactions

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7
Q

define the term hydroxylase

A

an enzyme that adds a hydroxyl group to a substrate

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8
Q

define the term carboxylase

A

an enzyme that transfers CO2 groups with the help of biotin

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9
Q

define the term mutase

A

an enzyme that relocates a functional group within a molecule

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10
Q

what is the rate limiting step of glycolysis and what enzyme catalyzes it?

A

conversion of F6P to fructose-1,6-bisphosphanate

catalyzed by phosphofructokinase-1 (PFK-1)

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11
Q

what molecules promote or inhibit phosphofructokinase-1 activity?

A

promote: AMP and fructose-2,6-bisphosphate
inhibit: ATP and citrate

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12
Q

what enzyme catalyzes the rate-limiting step of gluconeogenesis? what is the rxn?

A

fructose-1,6,-bisphosphatase, which converts fructose-1,6,-bisphosphate to F6P

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13
Q

what molecules positively and negatively regulate fructose-1,6,-bisphosphatase?

A

positive: ATP and acetyl-CoA
negative: AMP and fructose-2,6-bisphosphate

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14
Q

what is the rate limiting reaction and enzyme of the TCA cycle?

A

conversion of isocitrate to alpha-ketoglutarate catalyzed by isocitrate dehydrogenase

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15
Q

what molecules positively and negatively regulate isocitrate dehydrogenase?

A

positive: ADP
negative: ATP and NADH

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16
Q

what is the rate limiting reaction and enzyme of glycogenesis?

A

addition of UDP-glucose to glycogen catalyzed by glycogen synthase

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17
Q

what are the negative and positive regulators of glycogen synthase

A

positive: G6P, insulin, cortisol
negative: epinephrine, glucagon

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18
Q

what is the rate limiting reaction and enzyme of glycogenolysis?

A

release of glucose-1-phosphate from glycogen catalyzed by glycogen phosphorylase

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19
Q

what are the positive and negative regulators of glycogen phosphorylase?

A

positive: epinephrine, glucagon, AMP
negative: G6P, insulin, ATP

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20
Q

what is the rate limiting reaction and enzyme of the HMP shunt?

A

conversion of G6P to 6-phosphogluconolactone catalyzed by G6PD

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21
Q

what molecules are the positive and negative regulators of G6PD?

A

positive: NADP+
negative: NADPH

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22
Q

what is the rate limiting reaction and enzyme for de novo pyrimidine synthesis

A

glutamine + CO2 conversion to carbamoyl phosphate catalyzed by carbamoyl phosphate synthetase II

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23
Q

what is the rate limiting enzyme for de novo purine synthesis

A

PRPP amidotransferase

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24
Q

what are the negative regulators of PRPP amidotransferase

A

AMP, inosine monophosphate (IMP), GMP

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25
Q

what enzyme catalyzes the rate limiting step of the urea cycle

A

carbamoyl phosphate synthetase I

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26
Q

what molecule upregulates the urea cycle

A

N-acetylcysteine

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27
Q

what enzyme catalyzes the rate limiting step in the fatty acid synthesis pathway

A

Acetyl-CoA carboxylase (ACC)

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28
Q

what molecules positively and negatively regulate fatty acid synthesis?

A

positive: insulin, citrate
negative: glucagon, palmitoyl-CoA

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29
Q

what enzyme catalyzes the rate limiting step of fatty acid oxidation

A

acetyl-CoA acyltransferase I

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30
Q

what molecule negatively regulates fatty acid oxidation?

A

malonyl-CoA

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31
Q

what enzyme catalyzes the rate limiting step in ketogenesis

A

HMG-CoA synthase

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32
Q

what enzyme catalyzes the rate limiting step in cholesterol synthesis

A

HMG-CoA reductase

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33
Q

what molecules upregulate and downregulate cholesterol synthesis

A

upregulate: insulin and thyroxine
downregulate: glucagon and cholesterol

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34
Q

how many net ATP molecules does aerobic metabolism produce in the heart and liver?
in the muscle?

A

in heart and liver via malate-aspartate shuttle: 32

in muscle via glycerol-3-phosphate shuttle: 30

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35
Q

how does arsenic affect energy production?

A

arsenic causes glycolysis to produce zero net ATP (also uncouples oxidative phosphorylation)

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36
Q

how many ATP molecules are produced by anaerobic glycolysis

A

2 net ATP per glucose

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37
Q

what are CoA and lipoamide carriers of

A

acyl groups

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38
Q

what general rxn does biotin carry out

A

carboxylation

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39
Q

what do tetrahydrofolates carry

A

1-carbon groups

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40
Q

what does S-adenosyl methionine (SAM) carry

A

methyl groups

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41
Q

what does thiamine pyrophosphate (TPP) carry

A

aldehydes

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42
Q

NADP+ is generally used in _________ processes while NADPH is used in _________ processes

A

NADP+ is generally used in catabolic processes (to accept reducing equivalents) while NADPH is used in anabolic processes to supply reducing equivalents

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43
Q

what major processes use NADPH

A

anabolic processes, respiratory burst, cytochrome P450, glutathione reductase

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44
Q

differentiate hexokinase from glucokinase in terms of location, affinity, Vmax and insulin induction

A

hexokinase: in most tissues, but not liver nor beta cells of pancreas, lower affinity for glucose, lower Vmax, not induced by insulin
glucokinase: in liver and beta cells, higher affinity for glucose, higher Vmax, induced by insulin

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45
Q

is hexokinase or glucokinase feedback inhibited by G6P

A

hexokinase

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46
Q

is hexokinase or glucokinase gene mutation associated with the maturity-onset diabetes of the young

A

glucokinase

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47
Q

list the reactants and products of the glycolysis net reaction

A

Glucose + 2Pi + 2ADP+ NAD –>

2 pyruvate + 2ATP + NADH + 2H+ + 2H2O

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48
Q

which steps of glycolysis require ATP

A

glucose—> G6P (catalyzed by hexo/glucokinase)

F6P—> F-1,6-BP (catalyzed by PFK-1)

49
Q

which steps of glycolysis makes ATP

A

1,3-BPG —> 3-phosphoglycerate (catalyzed by phosphoglycerate kinase)

PEP —> pyruvate (catalyzed by pyruvate kinase)

50
Q

list the the molecules in the steps of glycolysis

A

glucose—> G6P —> F6P —> F-1,6-BP —> Glyceraldehyde-3P and DHAP (DHAP gets converted to Glyceraldehyde-3P) —>
1,3-bisphosphoglycerate —> 3-phosphoglycerate —> 2-phosphoglycerate —> phosphoenolpyruvate (PEP) —> pyruvate

51
Q

what’s the relationship between FBPase-2 and phosphofructokinase-2

A

FBPase-2 and phosphofructokinase-2 are parts of the same bifunctional enzyme. Which activity the enzyme performs depends on phosphorylation by protein kinase A.

52
Q

how is F2,6-BP regulate glucose in the fasting state

A

increased glucagon –> increased cAMP –> increased PKA –> increased FBPase-2 –> decreased PFK-2, leading to less glycolysis and more gluconeogenesis

53
Q

what two metabolic pathways does pyruvate dehydrogenase complex link

A

glycolysis and TCA cycle

54
Q

what are the reactants and products in the reaction catalyzed by pyruvate dehydrogenase complex

A

pyruvate + NAD + CoA —> AcetylCoA +NADH + CO2

55
Q

what are the 5 cofactors that are needed for the pyruvate dehydrogenase complex to function

A
  1. pyrophosphate (TPP from thiamine aka B1)2. FAD (from riboflavin aka B2)3. NAD (from niacin aka B3)4. CoA (from panthenate)5. Lipoic acid
56
Q

what stimulus upregulates activity of the pyruvate dehydrogenase complex and via what molecular changes

A

exercise causes increased NAD/NADH ratio, increased ADP, and increased calcium (stimulators of pyruvate dehydrogenase complex activity)

57
Q

the pyruvate dehydrogenase complex is similar to what other enzyme

A

alpha-ketoglutarate dehydrogenase (they have the same cofactors, similar substrate and similar mechanism of action)

58
Q

what inhibits lipoic acid

A

arsenic

59
Q

what are the symptoms of arsenic poisoning

A

vomiting, rice-water stools, garlic breath

60
Q

what molecules build up as a result of pyruvate dehydrogenase complex deficiency

A

pyruvate buildup leads to shunting to lactate (via LDH) and alanine (via ALT)

61
Q

what is the clinical presentation of pyruvate dehydrogenase complex deficiency

A

neurologic defects, lactic acidosis, increased serum alanine starting in infancy

62
Q

how is pyruvate dehydrogenase complex deficiency treated

A

increased intake of ketogenic nutrients (i.e. high fat content or increased lysine and leucine, which are the only purely ketogenic amino acids)

63
Q

explain the four different ways that pyruvate can be metabolized

A
  1. into alanine catalyzed by alanine amintransferase (cofactor=B6)2. into oxaloacetate catalyzed by pyruvate carboxylase (cofactor=biotin)3. into acetyl-CoA catalyzed by pyruvate dehydrogenase (cofactors=B1,B2,B3,B5,lipoic acid)4. into lactic acid catalyzed by lactate dehydrogenase (cofactor=B3)
64
Q

what is generated as a result of the TCA cycle (per acetyl-CoA molecule)how many ATP molecules does this eventually translate into

A

3 NADH, 1 FADH2, 2 CO2, 1 GTP (per acetyl CoA molecule)==> 10 ATP (per acetyl CoA molecule)

65
Q

list the enzymes in the TCA cycle from right after entry of Acetyl-CoA until completion of a cycle

A

acetyl-CoA–> citrate–> isocitrate –> alpha-ketoglutarate –> succinyl-CoA –> succinate –> fumarate –> malate –> oxaloacetate

66
Q

name three enzymes in the TCA cycle that catalyze irreversible reactions

A

isocitrate dehydrogenase, alpha-ketoglutarate dehydrogenase, citrate synthase

67
Q

how do NADH electrons from glycolysis enter the mitochondria

A

via the malate-aspartate shuttle or via the glycerol-3-phosphate shuttle

68
Q

to what complex in the inner mitochondrial membrane are NADH electrons transferred?what about FADH2?

A

NADH at complex 1FADH2 at complex 2

69
Q

explain how the electron chain and oxidative phosphorylation drive ATP production (briefly summarize the pathway)

A

electrons from NADH and FADH2 are transferred to complexes 1 and 2 in the inner mitochondrial membrane leading to a build up of protons in the intermembrane space; protons rush into the mitochondrial matrix via complex 5 and this movement of H+ down its gradient is coupled to phosphorylation of ADP to make ATP

70
Q

ATP produces how many ATP per NADH?how many per FADH2?

A

2.5 ATP per NADH1.5 ATP per FADH2

71
Q

name four inhibitors of electron transport chain;how do they work?

A

rotenone, cyanide, antimycin A and CO directly inhibit electron transport leading to low proton gradient and low ATP synthesis

72
Q

what electron transport complex does rotenone inhibit and therefore what electron carrier is directly affected

A

complex 1; transfer of electrons from NADH is blocked

73
Q

what electron transport complex is blocked by antimycin A

A

Complex 3

74
Q

what molecules inhibit complex 4 of electron transport chain

A

cyanide and CO

75
Q

what molecule directly inhibits mitchondrial ATP synthase;what happens to the proton gradient across the inner mitochondrial membrane as a result

A

oligomycin;H+ gradient increases (causing electron transport to stop)

76
Q

what are some uncoupling agents and how do they work

A

2,4-dinitrophenol, aspirin, thermogenin in brown fat;they increase the permeability of the inner mitochondrial membrane leading to lower proton gradient and higher O2 consumption –> ATP synthesis stops, but electron transport continues (produces heat instead)

77
Q

what is 2,4-dinitrophenol used for

A

used illicitly for weight loss

78
Q

name the irreversible enzymes of gluconeogenesis

A

(“pathway produces fresh glucose”) pyruvate carboxylase, phosphoenolpyruvate carboxykinase, fructose-1,6-bisphosphatase, glucose-6-phosphatase

79
Q

what reaction does pyruvate carboxylase catalyze, where does it occur, and what is needed for the reaction to happen (cofactors and activators)

A

pyruvate –>oxaloacetate;occurs in mitochondria;requires biotin and ATP, activated by acetyl-CoA

80
Q

what reaction does PEP carboxykinase catalyze;where does it occur;what is required

A

oxaloacetate –> PEP;takes place in the cytosol;GTP is required

81
Q

what reaction is catalyzed by F-1,6-bisphosphatase; where does it occur;what upregulates and downregulates this reaction

A

F-1,6-BP–> F-6-P;occurs in the cytosol;upregulated by citrate, downregulated by F-2,6-BP

82
Q

what reaction does G-6-phosphatase catalyze;where does it occur

A

G-6-P;occurs in the ER

83
Q

where does gluconeogenesis predominantly occur and why

A

in the liver; to maintain euglycemia in states of fasting

84
Q

besides the liver where else are enzymes of gluconeogensis found

A

kidney and intestinal epithelium

85
Q

why can’t the muscle do gluconeogenesis

A

it lacks G-6-phosphatase

86
Q

how can odd chain fatty acids get converted to glucose

A

odd chain fatty acids yield 1 proprionyl-CoA during metabolism which enters the TCA cycle as succinyl-CoA –> oxaloacetate and undergoes gluconeogenesis

87
Q

why can’t even-chain fatty acids yield new glucose

A

even-chain fatty acids get metabolized to acetyl-CoA, which cannot enter the pathway for gluconeogenesis

88
Q

what is the purpose of the HMP (hexose monophosphate) shunt

A

to use G-6-P to generate NADPH (used as a reducing agent i.e. for glutathione, fatty acid synthesis and cholesterol synthesis)

89
Q

what are the end products of the HMP shunt

A

NADPH, ribose (can be used for DNA synthesis or glycolytic intermediates)

90
Q

where does the HMP shunt take place (what cellular location)

A

in the cytoplasm

91
Q

how much ATP does the HMP shunt use?how much ATP does the HMP shunt produce?

A

trick question!: none and none!

92
Q

in what tissues of the body use the HMP shunt

A

lactating mammary glands, liver, adrenal cortex, RBC’s

93
Q

what are the two phases of the HMP shunt and which phase is reversible

A

two phases: oxidative and nonoxidativethe nonoxidative phase is reversible

94
Q

what are the reactants and products of the oxidative branch of the HMP shunt

A

G-6-P —–> CO2 + 2NADPH + ribulose-5-P

95
Q

what enzyme catalyzes the rate limiting step of the oxidative branch of the HMP shunt

A

G-6-P dehydrogenase

96
Q

what are the reactants and products of the nonoxidative branch of the HMP shunt

A

ribulose-5-P ——> ribose-5-P + G3P and F6P

97
Q

explain the respiratory burst (steps)

A

within the phagolysosome of (neutrophils and monocytes) NADPH reduces oxygen; superoxide dismutase then converts radical oxygen to hydrogen peroxide; which gets combined with chloride to generate HOCl radical (hyperchlorite aka bleach) or gets shunted over to the HMP shunt to regenerate more NADPH

98
Q

what is the purpose of respiratory burst

A

rapid release of ROS for immune response

99
Q

what defect causes chronic granulomatous disease

A

NADPH oxidase deficiency

100
Q

why are patients with chronic granulomatous disease at increased risk for infection by catalse positive species (i.e. S. aureus and aspergillus)

A

patients with CGD can use the hydrogen peroxide produced by pathogens (since they can’t generate their own), but when pathogens invade that can neutralize their own H2O2 (using catalase) there is no H2O2 for the patient’s immune system to utilize against infection

101
Q

what molecule allows P. aeruginosa to kill competing microbes

A

pyocyanin

102
Q

when lactoferrin is secreted how does it inhibit microbial growth

A

iron chelation

103
Q

explain why NADPH is important

A

generates glutathione used by RBCs and other cells to detoxify free radicals

104
Q

what are the two main categories of triggers for NADPH deficiency patients

A

drugs (i.e. sulfa drugs, primaquine, antimycobacterials, fava beans)infection (immune response triggers free radical release)

105
Q

what is the inheritance of GDPD deficiency

A

X-linked

106
Q

what benefit does G6PD deficiency confer

A

increased malaria resistance

107
Q

what is seen on histology for G6PD deficiency

A

Heinz bodies (oxidized hemoglobin)Bite cells (partially consumed cells that escaped splenic macrophage destruction)

108
Q

what defect causes essential fructosuria

A

defect in fructokinase

109
Q

what is the inheritance of essential fructosuria

A

autosomal recessive

110
Q

what are the symptoms of essential fructosuria like

A

essential fructosuria is a benign condition; generally asymptomaticalthough, fructose appears in the blood and urine

111
Q

are defects in fructose or galactose metabolism more injurious

A

galactose metabolism(fructose metabolism defects are fairly benign)

112
Q

what defect causes fructose intolerance

A

hereditary deficiency of aldolase B

113
Q

what is the inheritance pattern of fructose intolerance

A

autosomal recessive

114
Q

what causes the injurious effects seen in fructose intolerance

A

F-1-P accumulates leading to a decrease in available phosphate, leading to decreases in glycogenolysis and gluconeogenesis

115
Q

when do symptoms of fructose intolerance present

A

after eating fruit, honey, juice (anything with fructose)

116
Q

what will the urine dipstick show in a patient with fructose intolerance

A

negative result; it only tests for glucose

117
Q

what can you detect in the urine of a patient with fructose intolerance

A

reducing sugars (test for inborn errors of carbohydrate metabolism)

118
Q

what are the symptoms of fructose intolerance

A

hypoglycemia, jaundice, cirrhosis, vomitting

119
Q

what is the treatment for fructose intolerance

A

decrease intake of fructose and sucrose (glucose + fructose)

Biochemistry- First Aid (6 decks)

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