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POM Molecular Biology of the Cell > Cell Metabolism > Flashcards

Cell Metabolism Flashcards

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1
Q

What are the types of reactions? (6)

A

Oxidation reduction

Ligation requiring ATP cleavage

Isomerization

Group transfer

Hydrolytic

Addition or removal of functional groups

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2
Q

What is an oxidation reduction reaction?

A

electron transfer

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3
Q

What is a ligation requiring ATP cleavage reaction?

A

Formation of covalent bonds (e.g., C-C bonds)

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4
Q

What is an isomerization reaction?

A

Rearrangement of atoms to form isomers
Usually isomerase enzyme

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5
Q

What is a group transfer reaction?

A

Transfer of a functional group from one molecule to another
Usually a kinase enzyme e.g., hexokinase

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6
Q

What is a hydrolytic reaction?

A

Cleavage of bonds by the addition of water

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7
Q

What is an addition or removal of functional groups reaction?

A

Addition of functional groups to double bonds or their removal to form double bonds

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8
Q

What does glycolysis produce?

A

2 x Pyruvate
2 x NADH
2 x Net ATP (4 made 2 used)

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9
Q

What reaction is irreversible and commits the cell to glycolysis?

A

The conversion of glucose to glucose - 6 - phosphate

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10
Q

What is the complete reaction steps of glycolysis?

A

Glucose
Glucose - 6 - Phosphate
Fructose - 6 - Phosphate
Fructose - 1,6 - Bisphosphate –> dihydroxyacetone phosphate and
Glyceraldehyde - 3 - Phosphate
1,3 - Bisphosphoglycerate
3 - Phosphoglycerate
2 - Phosphoglycerate
Phosphenolpyruvate
Pyruvate

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11
Q

How does glucose to glucose-6-phosphate?

A

Group transfer
Hexokinase
ATP-> ADP
forms H+ asw

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12
Q

How does glucose-6-phosphate go to fructose-6-phosphate?

A

Isomerisation
phosphoglucose isomerase

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13
Q

What is special about fructose?

A

It can be split into equal halves when cleaved

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14
Q

How does fructose-6-phosphate go to fructose-1,6-bisphosphate?

A

Group transfer
phosphofructokinase
ATP-> ADP

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15
Q

How does phosphofructokinase use ATP?

A

uses it to attach phosphate to fructose-6-phosphate which makes biphosphate

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16
Q

Which step of glycolysis does phosphofructokinase control?

A

The conversion of fructose - 6 - phosphate into fructose - 1,6 - bisphosphate

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17
Q

How does fructose-1,6-bisphosphate fo to glyceraldehyde-3-phosphate and dihydroxyacetone phosphate?

A

Hydrolytic reaction
Aldolase

Glyceraldehyde-3-phosphate can progress through glycolysis
Dihydroxyacetone cannot

They are both high E compounds

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18
Q

How does dihydroxyacetone phosphate go to glyceraldehyde-3-phosphate?

A

Isomerisation
Triose phosphate isomerase (TPI)

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19
Q

Why is deficiency in Triose phosphate isomerase fatal?

A

RBCs in brain would suffer most because only half of your input of ATP would be there/ consumed ATP

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20
Q

How does glyceraldehyde-3-phosphate go to 1,3-bisphosphoglycerate?

A

Redox and group transfer
Glyceraldehyde 3-phosphate dehydrogenase
NAD+ +Pi –> NADH

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21
Q

How does 1,3-bisphosphoglycerate go to 3-phosphoglycerate?

A

Group transfer
Phosphoglycerate kinase
ADP–> ATP
(remember at this stage its x2 as its split)

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22
Q

How does 3-phosphoglycerate make 2-phosphoglycerate?

A

Isomerisation
Phosphoglycerate mutase

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23
Q

How does 2-phosphoglycerate make phosphoenolpyruvate?

A

Group removal/ dehydration
Enolase

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24
Q

How does phosphoenolpyruvate make pyruvate?

A

Group transfer
Pyruvate kinase
ADP-> ATP

transfer of high E phosphate to ADP

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25
Q

What is the only glycolytic enzymopathy which is fatal?

A

Deficiency in TPI

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26
Q

Which reactions produce ATP in glycolysis?

A

The conversion of 1,3-Bisphosphoglycerate into 3-phosphglycerate and phosphenolpyruvate into pyruvate

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27
Q

What do kinases do?

A

Transfer phosphate groups to molecules

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28
Q

Which step in glycolysis needs NAD+?

A

Glyceraldehyde - 3 - phosphate into 1,3 - bisphosphoglycerate

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29
Q

Which steps of glycolysis require ATP?

A

Glucose -> glucose - 6 - phosphate
Fructose - 6 - phosphate -> Fructose - 1,6 - bisphosphate

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30
Q

Does glycolysis need oxygen to occur?

A

No - it is anaerobic

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31
Q

Where does glycolysis occur?

A

In the cytoplasm

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32
Q

Why are high energy phosphate groups added to some of the substrates involved in glycolysis?

A

Adding the phosphate groups makes them easier to split as they are more reactive

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33
Q

What are the three fates of pyruvate?

A
  1. Lactate generation
  2. Acetyl CoA Production
  3. Alcohol fermentation
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34
Q

What enzyme is needed to generate Acetyl CoA from pyruvate?

A

Pyruvate dehydrogenase complex

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35
Q

What occurs during alcohol fermentation?

A

Pyruvate->acetaldehyde (via pyruvate decarboxylase H+-> CO2)

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

This is a characteristic of yeasts and can occur under anaerobic conditions

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36
Q

What does pyruvate dehydrogenase complex needed as a cofactor?

A

Thiamine pyrophosphate
It readily loses a proton and resulting carbanion attacks pyruvate

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37
Q

What does a deficiency in thiamine result in?

A

Beri - Beri
This is a condition which leads to muscle weakness
impaired dehydrogenation of pyruvate

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38
Q

What are the symptoms of beri-beri syndrome?

A

damage to PNS, weakness of the musculature and decreased cardiac output
The brain is particularly vulnerable as it relies heavily on glucose metabolism

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39
Q

How is pyruvate converted into lactate?

A

Using lactate dehydrogenase complex

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40
Q

What is lactate generation?

A

Anaerobic and is a characteristic of mammalian muscle during intense activity when O2 is a limiting factor.

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41
Q

What does the fermentation of alcohol and lactate production both regenerate?

A

NAD+ - this is needed for glycolysis to continue occurring (by NADH + H+-> NAD+)
In condition of oxygen deprivation

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42
Q

How long does ATP work in muscles?

A

The amount of ATP needed during exercise is only enough to sustain contraction for around 1 second

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43
Q

What is the role of creatine phosphate?

A

It is a large reservoir of creatine phosphate and buffers the demands for phosphate (25mM creatine phosphate c.f. 4mM ATP in resting muscle)

Reservoir of phosphate groups to make ATP

creatine phosphate –> <– creatine + ATP (via creatine kinase)

buffers ATP concentrations

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44
Q

How pyruvate make acetyl CoA?

A

pyruvate + HS-CoA–> acetyl CoA + CO2
via pyruvate dehydrogenase complex
NAD+ –> NADH

This is a series of reactions in the mitochondria of the cell. The acetyl CoA thus formed is committed to entry into the TCA cycle.

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45
Q

What is special about Acetyl CoA?

A

Has a high E bond (ester linkage) between C-S
Acetyl CoA can enter TCA CYCLE

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46
Q

What happens to the Acetyl CoA that is produced?

A

It enters into the Krebs Cycle

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47
Q

What are the stages of the Krebs Cycle?

A

Acetyl CoA combines with oxaloacetate to make Citrate
Then Alpha - keto glutarate
Succinyl CoA
Succinate
Fumerate
Malate

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48
Q

What does one turn of the Krebs cycle produce?

A

2 x CO2
1 x GTP
3 x NADH
1 x FADH

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49
Q

Are the kreb’s cycle enzymes soluble?

A

Yes, except 1
they are located in the mitochondrial matrix space

50
Q

When is the bulk of ATP generated?

A

when the reduced coenzymes are re-oxidised with the help of oxygen (aka oxidative phosphorylation)

51
Q

What reaction in the Krebs cycle produces FADH2?

A

The conversion of succinate to fumerate

52
Q

When is NADH + H+ formed in the Krebs cycle?

A

isocitrate -> alpha-ketoglutarate (also makes CO2)

alpha-ketoglutarate -> succinyl CoA (also makes CO2)

malate-> oxaloacetate

53
Q

When is GTP formed in the krebs cycle?

A

succinyl CoA to succinate

54
Q

Where does the krebs cycle occur?

A

The mitochondrial matrix

55
Q

What is the order of the Krebs cycle? 8 steps…

A

Acetyl CoA (2C) enters the krebs cycle and reacts with oxaloacetate (4C) to from citrate (6C)

Citrate (6C)
Isocitrate (6C)
alpha-ketoglutarate (5C)
Succinyl CoA (4C)
Succinate (4C)
Fumerate (4C)
Malate (4C)
Oxaloacetate (4C)

56
Q

What is a transamination reaction?

A

the process of removing an amine group from one amino acid and transferring it to a ketoacid, producing another ketoacid and amino acid

57
Q

What are the seven things which can be produced from transamination reactions?/ What are the only 7 molecules that can be made by the degradation of all 20 AA?

A

Pyruvate
Succinyl CoA
Acetoacetyl CoA
Acetyl CoA
Oxaloacetate
Alpha Keto Glutarate
Fumerate

58
Q

What is the general strategy of AA degradation?

A

remove the AA group (which is excreted as urea) whilst the carbon skeleton is either funnelled into the production of glucose or fed into the TCA cycle

59
Q

Why is it essential that NAD+ is regenerated?

A

Needed for dehydrogenation of glyceraldehyde-3-phosphate to produce ATP

Allows glycolysis to occur anaerobically

60
Q

What is the Warburg effect?

A

Mutations in TCA genes of Fumerase, Succinate Dehydrogenase, Isocitrate Dehydrogenase, decreases Kreb’s Cycle activity which enhances anaerobic glycolysis

  • the preferential generation of lactate from glucose even under conditions of ample O2
61
Q

What are glucogenic amino acids?

A

Ones whose carbon skeletons are used to make glucose

62
Q

What are ketogenic amino acids?

A

Amino acids which when they are broken down, form ketone body precursors like Acetyl CoA

63
Q

What are the glucogenic AA and what do they make?

A

Alanine, Cysteine, Glycine, Serine, Threonine, Tryptophan= pyruvate

Asparagine, Aspartate= oxaloacetate

Aspartate, Phenylalanine, Tyrosine= Fumarate

Isoleucine, Methionine, Threonine, Valine= succinyl CoA

Arginine, Glutamate, Glutamine, Histidine, Proline= alpha-ketoglutarate

64
Q

How does alanine form pyruvate?

A

Alanine metabolism

Alanine undergoes transamination by the action of the enzyme alanine aminotransferase

alanine + alpha-ketoglutarate-> pyruvate + glutamate

65
Q

How is glutamate re-converted to alpha-ketoglutarate?

A

via glutamate dehydrogenase
this generates NH4+ which is ultimately converted to urea

66
Q

During fasting, which type of metabolism dominates?

A

fat metabolism, resulting in the production of ketone bodies

67
Q

What happens when the levels of Acetyl CoA is not equal to Oxaloacetate?

A

The excess Acetyl CoA is used to make ketone bodies

68
Q

What are the names of the three ketone bodies?

A

Acetone, Acetoacetate and 3 - Beta - Hydroxy Butyrate

69
Q

Why can ketone bodies be utilised by the brain but fatty acids cannot?

A

Fatty acids can’t cross the blood brain barrier

70
Q

What is the purpose of the Glycerol Phosphate Shuttle

A

To carry electrons from NADH across the matrix - this is because the mitochondrial matrix is impermeable to NADH

71
Q

Where in the body is the Glycerol-Phosphate Shuttle used?

A

brain and skeletal muscle

72
Q

Explain how the Glycerol-Phosphate Shuttle works

A

Cytosolic glycerol-3-phosphate dehydrogenase transfers electrons from NADH to DHAP to generate Glycerol-3-Phosphate

A membrane bound form of the same enzyme transfers the electrons to FAD

The FADH2 electrons are then passed onto coenzyme Q which is in the electron transport chain

73
Q

Where in the body is the Malate-Aspartate Shuttle used?

A

Liver, kidney and the heart

74
Q

Outline the processes in the Malate-Aspartate Shuttle

A
75
Q

What reactions are happening in the malate-aspartate shuttle?

A

REDOX and transamination

76
Q

What are the transamination reactions in the malate-aspartate shuttle?

A

glutamate + oxaloacetate–> alpha-ketoglutarate + aspartate

77
Q

How many ATP do you get from NADH and FADH2?

A

3 ATP from NADH
2 ATP from FADH

From their re-oxidation of the reduced cofactors by the process of oxidative phosphorylation

78
Q

What are the two main concepts of glycolysis?

A

The formation of a high energy compound, and the splitting of this compound

79
Q

Why is the generation of NADH useful?

A

NADH is generated here which can be later used to generate yet more ATP within the mitochondria in a process known as oxidative phosphorylation

80
Q

How is creatine used by athletes?

A

As a dietary supplement

81
Q

How is Acetyl CoA able to donate the acetate group (2C) to other molecules?

A

The thioester linkage which it contains is a high energy linkage so is readily hydrolysed

82
Q

Mutations in which TCA genes have been shown to decrease TCA activity and enhance aerobic glycolysis?

A

Isocitrate dehydrogenase
Succinate dehydrogenase
Fumerase

83
Q

How many ATP does the TCA cycle give?

A

12= 3xNADH + 1xFADH + 1xGTP

84
Q

What is the name of the process of fatty acid metabolism?

A

Beta oxidation

85
Q

How much of your body’s energy needs come from? (including liver, not the brain)

A

fatty acid oxidation (enhanced over long periods of fasting)

86
Q

where does beta oxidation occur?

A

In the mitochondria

87
Q

What is the general formula of beta-oxidation of fatty acids?

A
88
Q

How are fatty acids converted into an Acyl CoA Species?

A

Using Acyl CoA synthetase

89
Q

Where does the generation of Acyl CoA occur?

A

In the outer mitochondrial membrane

90
Q

What is the name of the shuttle used to transport Acyl CoA species into the matrix?

A

Carnitine shuttle

91
Q

Describe how the carnitine shuttle works?

A

Acyl CoA is coupled to the molecule carnitine to form acyl carnitine - this is done using an enzyme carnitine acyltransferase 1

The acyl carnitine is then shuttle across the membrane via translocase

The acyl Carnitine is then converted back into carnitine and Acyl CoA via carnitine acyltransferase II

92
Q

What is used as a supplement when you have primary carnitine deficiency?

A

Carnitor / levocarnitine

93
Q

What type of deficiency is primary carnitine deficiency?

A

Autosomal recessive disorder

94
Q

What are some symptoms of primary carnitine deficiency?

A

encephalopathies, cardiomyopathies, muscle weakness; and hypoglycaemia
symptoms appear during infancy or early childhood

95
Q

Describe the mutations involved in primary carnitine deficiency?

A

Mutations in a gene known as SLC22A5 which encodes a carnitine transporter result in reduced ability of cells to take up carnitine, needed for the β-oxidation of fatty acids.

96
Q

What are the four reactions in Beta-oxidation?

A

oxidation, hydration, oxidation and thiolysis

97
Q

What does one cycle of beta oxidation result in?

A

The production of Acetyl CoA and an Acyl CoA species which is 2 carbons shorter than the original

98
Q

Write the overall equation for the Beta-Oxidation of palmitoyl CoA?

A

palmitoyl CoA + 7 FAD + 7 NAD+ + 7 H2O + 7 CoA —-> 8 acetyl CoA + 7 FADH2 + 7 NADH

(the b oxidation reactions continue to consecutively remove 2C units from the acyl CoA thereby producing acetyl CoA)

On the final cycle (4C fatty acyl CoA intermediate), 2 acetyl CoA molecules are formed

From just 7 b-oxidation reactions, the 16 carbon palmitoyl CoA molecule produces 8 molecules of acetyl CoA

During each cycle one FADH2 and one NADH are produced

99
Q

What happens to the acetyl CoA generated through beta-oxidation?

A

Enters the TCA cycle only if Beta oxidation and carbohydrate metabolism are balanced, as oxaloacetate is needed for entry. Hence the saying “fat burns in the flame of carbohydrate”

100
Q

What does Acetyl CoA form during fasting/ when fat breakdown predominates?

A

D-3-hydroxybutyrate, Acetone and Acetoatcetate (collectively known as ketone bodies)

101
Q

What is fatty acid biosynthesis known as?

A

Lipogenesis

102
Q

What are the two enzymes involved in fatty acid biosynthesis/ lipogenesis?

A

Acetyl CoA Carboxylase and fatty acid synthase

103
Q

Following each round of elongation, what occurs to the fatty acid in lipid biosynthesis?

A

undergoes reduction and dehydration by the sequential action of ketoreductase (KR), dehydratase (DH) and enol reductase (ER) activity

104
Q

What are the key difference between fatty acid synthesis and degradation? (carriers, reducing power, locations)

A

Degradation: CoA is carrier, FAD/ NAD+ is reducing power, in mitochondrial matrix

Synthesis: Acyl carrier protein, NADPH, Cytoplasm

105
Q

During lipogenesis, what is the growing fatty acid group linked to?

A

An Acyl carrier protein

106
Q

What is the overall reaction of lipogenesis, to form Palmitate?

A

Acetyl CoA (C2) + 7 Malonyl CoA (C3) + 14 NADPH +14 H+
—-> Palmitate (C16) + 7 CO2+ 6 H2O + 8 CoA-SH + 14 NADP+

107
Q

Elongation of the acyl group to make fatty acids longer than 16C occur where?

A

Occurs separately from palmitate synthesis in the mitochondria and endoplasmic reticulum (ER)

108
Q

What does the desaturation of fatty acids required?

A

the action of fatty acyl-CoA desaturases

109
Q

What is the enzyme that creates oleic acid and palmitoleic acid from stearate and palmitate, respectively called?

A

∆-9 desaturase
As it generates a double bond nine carbons from the terminal carboxyl group

110
Q

In adults where is de novo Faty acid biosynthesis restricted to?

A

The liver, adipose tissue and lactating breasts

111
Q

Can reactivation of fatty acid synthesis occur in certain cancer cells, and give an example of inhibition of this.

A

Yes, evidence suggests it can
Leads to Q of “can we selectively target FA synthetase in cancer?”
Inhibition of FASN by cerulenin shown to reduce tumour growth of ovarian cancer cells

112
Q

What is meant by Acyl-CoA-dehydrogenase specificity?

A

Each acyl-CoA-dehydrogenase can bind a fatty acid chain of varying lengths

113
Q

What are the families of acyl-CoA-dehydrogenases?

A

Short chain acyl-Co enzyme A dehydrogenase (<6C)

Medium chain acyl-Co enzyme A dehydrogenase (C6-C12)

Long chain acyl-Co enzyme A dehydrogenase (C13-C21)

Very long chain acyl-Co enzyme A dehydrogenase (>22C)

114
Q

What is MCADD?

A

Medium chain Acyl CoA dehydrogenase deficiency
- disorder of fatty acid metabolism, can be treated with lifestyle
- if undiagnosed can be fatal
- autosomal recessive

115
Q

What are the lifestyle adaptations of MCADD?

A
  • A high carbohydrate diet
  • Never go without food for longer than 10-12 hours (typical overnight fast)
116
Q

What must patients with MCADD need it their illness manifests as apetite loss or severe vomiting?

A

i.v glucose to make sure their body is not dependant on fatty acids for energy

117
Q

How are fats stored in the adipocytes?

A

As triglycerides

118
Q

What are triglycerides broken down into?

A

glycerol and fatty acids using lipase

119
Q

How many ATP does the generation of the Fatty Acyl CoA need?

A

2

120
Q

What is the net gain of ATP per molecules of palmitoyl?

A

129 ATP

121
Q

How much ATP is formed overall by glucose metabolism?

A

8 from glycolysis
6 from TCA/ krebs cycle
24 from oxidative phosphorylation

122
Q

How many NADH and FADH2 does beta oxidation produce?

A

1 of each

POM Molecular Biology of the Cell (15 decks)

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