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Biochem Take 2. > Nucleotide Metabolism. > Flashcards

Nucleotide Metabolism. Flashcards

1
Q

What 3 components do nucleotides contain?

A

A nitrogenous base.

A ribose sugar or a de-oxyribose sugar.

At least 1 phosphate.

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2
Q

How many nucleotides are required for DNA synthesis?

A

4.

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3
Q

What consequences are there if the body cannot synthesise a DNA nucleotide?

A

It will have serious consequences as DNA cannot be synthesised.

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4
Q

Drugs that target nucleotide metabolism are often used to treat what illness’?

A

Cancer and bacterial infections.

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5
Q

What are nucleotides used for?

A

The building blocks for DNA and RNA.

Carriers for activated intermediates.

Structural components of coenzyme A, FAD, NAD+ and FAD+.

High energy molecules such as ATP, GTP and UTP.

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6
Q

The nitrogenous bases that make up nucleotides are derived from what 2 families?

A

Purines and pyrimidines.

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7
Q

What is the major difference between purines and pyrimidines?

A

Purines have 2 rings and pyrimidines only have 1.

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8
Q

What purines are found in DNA and RNA?

A

Adenine.

Guanine.

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9
Q

What are the pyrimidines that are common to DNA?

A

Cytosine.

Thymine.

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10
Q

What are the pyrimidines that are common to RNA?

A

Cytosine.

Uracil.

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11
Q

What are 2 other common bases that are found in cells and are involved in the metabolism of purines?

A

Hypoxanthine.

Xanthine.

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12
Q

Where is hypoxanthine found?

A

In inosine monophosphate (IMP).

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13
Q

What is the job of inosine monophosphate (IMP)?

A

It is an intermediate in purine synthesis and degradation.

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14
Q

Where is xanthine found?

A

In xanosine monophosphate.

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15
Q

What is the job of xanthine?

A

It is an intermediate in purine synthesis and degradation..

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16
Q

What is the location of some unusual bases?

A

In tRNA and in viral DNA.

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17
Q

Unusual bases account for what % of the bases in tRNA?

A

5%.

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18
Q

Unusual bases are often found as methyl derivatives of what bases?

A

As methyl derivatives of the major bases.

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19
Q

What 2 things need to be added together to make a nucleoside?

A

The addition of a pentose sugar to the base makes a nucleoside.

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20
Q

The addition of a ribose sugar to the bases A, G, C, T and U forms what?

A

Adenosine.

Guanidine.

Cytidine.

Thymidine.

Uridine.

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21
Q

If the pentose sugar is a deoxyribose then what is produced when a base is added?

A

A deoxyribonucleoside.

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22
Q

If A, G, C, T and U are added to a deoxyribose what is produced?

A

De-oxyadenosine.

De-oxyguanidine.

De-oxycytidine.

De-oxythymidine.

De-oxyuridine.

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23
Q

What kind of sugar does DNA have?

A

Deoxyribose sugars.

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24
Q

What kind of sugar does RNA have?

A

Ribose sugars.

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25
Q

What is the major difference between a ribose and a deoxyribose?

A

The number 2 hydroxyl group on a ribose is lost and replaced with hydrogen on a deoxyribose.

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26
Q

For a nucleotide to be made from a nucleoside what must be added?

A

At least 1 phosphate group.

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27
Q

What is associated with the negative charge in DNA and RNA?

A

The phosphate groups.

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28
Q

The addition of 1, 2 or 3 phosphate groups will form what?

A

Nucleoside monophosphate (NMP).

Nucleoside diphosphate (NDP).

Nucleoside triphosphate (NTP).

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29
Q

Nucleoside triphosphates are needed for what?

A

To make nucleotides and also for high energy molecules, e.g. ATP.

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30
Q

How is the type of pentose sugar donated in the nomenclature of nucleotides?

A

In the prefix e.g.

Ribonucleotide.

Deoxyribonucleotide.

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31
Q

How is the type of attached base donated in the nomenclature of nucleotides?

A

Adenosine triphosphate (ATP).

Deoxy-adenosine triphosphate (dATP).

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32
Q

De-novo purine synthesis is accomplished by what process?

A

By constructing the purine ring in a series of reactions that add the carbon and nitrogen to a preformed ribose 5-phosphate.

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33
Q

Ribose 5-phosphate is a product of what pathway?

A

The HMP pathway.

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34
Q

Where does purine synthesis take place?

A

In the cytoplasm of the cell.

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35
Q

What must occur before purine synthesis can take place?

A

The ribose 5-phosphate must be activated.

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36
Q

How is ribose 5-phosphate activated for purine synthesis?

A

By adding a pyrophosphate to it.

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37
Q

What does the activation of ribose 5-phosphate for purine synthesis form?

A

5-phosphoribosyl-1 pyrophosphate (PRPP).

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38
Q

What enzyme is used to activate ribose-5 phosphate in purine synthesis?

A

PRPP synthetase.

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39
Q

What is the foundation for the building of purine rings?

A

5-phosphoribosyl-1 pyrophosphate (PRPP).

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40
Q

What amino acids are used to form purine rings?

A

Glycine.

Glutamine.

Aspartate.

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41
Q

What molecule donates carbons to purine rings?

A

Tetrahydrofolate (THF).

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42
Q

What is the beginning of a purine base?

A

The activated ribose (5-PRPP) carbons, nitrogens and amino acids.

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43
Q

What is the rate limiting enzyme of purine synthesis?

A

Glutamine phosphoribosyl pyrophosphate amido transferase.

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44
Q

What is the job of glutamine phosphoribosyl pyrophosphate amido transferase?

A

To convert 5-PRPP to 5-phosphoribosylamine.

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45
Q

Where does the nitrogen for purine rings comes from?

A

From glutamine.

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46
Q

The rate of the rate limiting step of purine synthesis is controlled by?

A

The intracellular amounts of glutamine and PRPP.

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47
Q

What inhibits glutamine phosphoribosyl pyrophosphate amido transferase when in purine synthesis?

A

The purine nucleotides AMP, GMP and IMP.

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48
Q

What is the product of phosphoribosyl pyrophosphate amido transferase when in purine synthesis?

A

IMP.

GMP.

AMP.

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49
Q

How can di and triphosphates be formed from the monophosphates in purine synthesis?

A

Phosphate groups can be added by specific kinases to form the di and triphosphates.

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50
Q

What is the first purine that is always made by glutamine phosphoribosyl pyrophosphate amido transferase?

A

IMP (inosine monophosphate).

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51
Q

How can AMP and GMP be synthesised from IMP?

A

IMP can synthesise AMP and then AMP can synthesise GMP.

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52
Q

The synthesis of AMP from IMP requires what molecule to be present?

A

GTP.

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53
Q

The synthesis of GMP from AMP requires what molecule to be present?

A

ATP.

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54
Q

How many ATP molecules are required for purine synthesis?

A

4 ATP molecules.

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55
Q

What coenzyme does glutamine phosphoribosyl pyrophosphate amido transferase require?

A

Tetrahydrofolate (THF) and purines cannot be synthesised without it.

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56
Q

What part of the purine synthesis an important target site for drugs in microorganisms?

A

THF.

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57
Q

Why is THF in microorganisms a target sequence for drugs?

A

Because they require THF for purine synthesis.

58
Q

What are the family of drugs that will competitively inhibit the synthesis of THF?

A

Sulphonamides.

59
Q

How do sulphonamides inhibit the synthesis of THF in microorganisms?

A

Via competitive inhibition.

60
Q

How do sulphonamides inhibit microorganisms from growing?

A

They inhibit purine synthesis so DNA synthesis cannot take place.

61
Q

What drug will competitively inhibit THF synthesis in humans?

A

Methodextrate.

62
Q

What kind of disease is methodextrate used to fight in humans?

A

Cancer.

63
Q

How does methodextrate work?

A

By inhibiting dihydrofolate reductase which is responsible for activating folate, this stops purine synthesis in the body and prevents the cancer cells from dividing.

64
Q

How can cancer cells become resistant to methodextrate?

A

By up-regulating the gene for dihydrofolate reductase.

65
Q

What drug will inhibit THF synthesis in prokaryotes.

A

Trimethoprim.

66
Q

How do bacteria obtain folic acid?

A

They synthesise their own folic acid.

67
Q

How do mammals obtain folic acid?

A

Via the diet.

68
Q

What is the most common vitamin deficiency in the world?

A

A folate deficiency.

69
Q

What are the symptoms of folate deficiencies?

A

Megaloblastic anaemias.

Low haemoglobin levels.

High levels of megaloblastic cells in the bone marrow.

Large immature erythrocytes.

70
Q

What kind of cells are particularly affected by a folate deficiency?

A

Rapidly growing cells.

71
Q

What is a common symptom of a folate deficiency that is caused in babies due to the pregnant mother not taking enough folate?

A

Neural tube defects such as spina bifada.

Homocysteine-anemia is also a common symptom.

72
Q

What happens to purines that come from the normal turnover of cellular nucleic acids or are obtained from the diet?

A

They can either be degraded or salvaged.

73
Q

When IMP purines and guanine nucleotides are degraded, what intermediates do they produce?

A

Hypoxanthine and guanine.

74
Q

What intermediates do adenosine nucleotides produce when they are degraded?

A

Adenosine.

75
Q

Will hypoxanthine, guanine and adenosine be fully degraded in purine degradation?

A

No.

They can be recycled.

76
Q

The recycling of hypoxanthine and guanine in purine degradation requires what enzyme?

A

Hypoxanthine-guanine phosphoribosyltransferase (HGPRT).

77
Q

The recycling of adenosine in purine degradation requires what enzyme?

A

Adenosine phosphoribosyltransferase (APRT).

78
Q

How are the hypoxanthine, guanine and adenine intermediates recycled?

A

They still have their ring structures and HGPRT or APRT can take PRPP and attach it to the ring to recreate XMP.

79
Q

The re-attachment of PRPP to hypoxanthine creates what?

A

IMP.

80
Q

The reattachment of the PRPP to guanine creates what?

A

GMP.

81
Q

The re-attachment of PRPP to adenosine by APRT creates what?

A

AMP.

82
Q

The process of adding PRPP to a recycled purine can be thought of as adding what to what?

A

Adding of a sugar to a base.

83
Q

HGPRT + hypoxanthine = what?

A

IMP.

84
Q

HGPRT + guanine = what?

A

GMP.

85
Q

APRT + adenosine = what?

A

AMP.

86
Q

A deficiency in HGPRT will affect what?

A

The salvage of guanine and hypoxanthine from nucleotide degradation.

87
Q

What causes a deficiency in HGPRT?

A

An X linked recessive disorder called in Lesch-Nyhan syndrome.

88
Q

What is Lesch Nyhan syndrome is characterised by?

A

Increased levels of PRPP.

Decreased levels of IMP and GMP.

Increased de-novo synthesis of IMP and GMP.

89
Q

What are the symptoms of Lesch Nyhan syndrome?

A

Excessive production of uric acid.

Self mutilation.

Involuntary movements.

90
Q

What is the final product of purine degradation?

A

Uric acid.

91
Q

What is hyperuriceamia also known as?

A

Gout

92
Q

When guanine and hypoxanthine are being broken down, what will degrade them?

A

Xanthine oxidase.

93
Q

What does xanthine oxidase degrade guanine and hypoxanthine to?

A

To xanthine and then uric acid.

94
Q

What will cause hyperuricaemia?

A

Excess degradation of purine nucleotides or under excretion of uric acid.

95
Q

What drug can inhibit xanthine oxidase so that uric acid isn’t formed, relieving the symptoms of gout?

A

Allopurinol.

96
Q

How does allopurinol relieve the symptoms of gout?

A

It inhibits xanthine oxidase and leads to the accumulation of xanthine which is more soluble than uric acid and can be excreted through the kidney.

97
Q

How does pyrimidine synthesis differ from purine synthesis?

A

Pyrimidines are synthesised before attachment to ribose 5-phosphate.

98
Q

What is the rate limiting step of pyrimidine synthesis?

A

The synthesis of carbamoyl phosphate from glutamine and CO2.

99
Q

What enzyme in pyrimidine synthesis will synthesise carbamoyl phosphate from glutamine and CO2?

A

Carbamoyl phosphate synthetase II (CPSII).

100
Q

Is folic acid is required for pyrimidine synthesis?

A

No.

101
Q

What amino acids are used in pyrimidine synthesis?

A

Glutamine.

Aspartic acid.

102
Q

What is the source of the amino group in pyrimidine synthesis?

A

Glutamine.

103
Q

What is the source of the amino group in purine synthesis?

A

Ammonia.

104
Q

What substrates does CPS II require to form carbamoyl phosphate in pyrimidine synthesis?

A

2 ATP molecules.

A CO2.

A glutamine.

105
Q

Where is CPS II located?

A

In the cytoplasm.

106
Q

What will activate CPS II in pyrimidine synthesis?

A

ATP.

107
Q

What is the final product of CPS II in pyrimidine synthesis?

A

UTP.

108
Q

What will inhibit CPS II in pyrimidine synthesis?

A

UTP.

109
Q

After carbamoyl phosphate has been formed, a few more steps occur until what ring structure is formed?

A

Orotate.

110
Q

What 2 steps are required to form UTP from orotate?

A

Orotate + Orotate phosphoribosyl transferase + PRPP gives oritidine 5-monophosphate (OMP).

This is when the sugar group is added in pyrimidine synthesis.

Oritidine 5-monophosphate + OMP decarboxylase gives uridine monophosphate (UMP).

111
Q

What is always synthesised 1st in pyrimidine synthesis?

A

UMP.

112
Q

How is UMP converted to UDP?

A

By nucleoside monophosphate kinase.

113
Q

How is UDP converted to UTP?

A

By UTP nucleoside diphosphate kinase.

114
Q

How is UTP converted to CTP?

A

By CTP synthase where glutamine is the nitrogen donor.

115
Q

What is the product of CPS II?

A

Carbamoyl phosphate.

116
Q

What is the substrate of CPS II?

A

CO2, glutamine and ATP.

117
Q

What process is CPS 1 involved in?

A

Urea synthesis.

118
Q

What process is CPS II involved in?

A

Pyrimidine synthesis.

119
Q

What is the source of nitrogen for CPS I?

A

Free ammonia.

120
Q

What is the source of nitrogen for CPS II?

A

Glutamine.

121
Q

What is the cellular location of CPS-1?

A

Mitochondria.

122
Q

What is the cellular location of CPS-II?

A

Cytoplasm.

123
Q

What is CPS-I activated by?

A

N-acetylgluatamate.

124
Q

What is CPS-II inhibited by?

A

UTP or UDP.

125
Q

A deficiency in OMP decarboxylase or in orotate phosphoribosyl transferase results in what?

A

Orotic adicuria and UMP cannot be synthesised.

126
Q

What are the symptoms of orotic adicuria?

A

Slow growth.

Megaloblastic anaemia.

The secretion of a lot of orotate (orotic acid) in the urine.

127
Q

What nucleotides are used in DNA synthesis?

A

Deoxyribonucleotides.

128
Q

What catalyses the formation of deoxyribonucleotides from ribonucleotides?

A

Ribonucleotide diphosphate reductase.

129
Q

Ribonucleotide diphosphate reductase catalyses the formation of what from ADP, CDP, GDP and UDP?

A

ADP - dADP.

CDP - dCDP.

GDP - dGDP.

UDP - dUDP.

130
Q

What are 2 important inhibitors of ribonucleotide diphosphate reductase?

A

dATP and hydroxyurea.

131
Q

What anticancer drug will target ribonucleotide diphosphate reductase?

A

Hydroxyurea.

132
Q

Why is hydroxyurea used as an anti cancer drug?

A

To prevent the synthesis of DNA which stops cellular growth, inhibiting tumour growth.

133
Q

dThymidine MP is synthesised from what molecule?

A

dUMP.

134
Q

What enzyme is responsible for synthesising dThymidine MP from dUMP?

A

Thymidilate synthase.

135
Q

What coenzymes does thymidilate synthase use when it synthesises dthymidine MP from dUMP?

A

THF.

136
Q

What inhibits thymidilate synthase when it synthesises dthymidine MP from dUMP?

A

MTX.

137
Q

How is 5-fluouracil an inhibitor of thymidate synthase?

A

5-fluorouracil is converted to 5-FdUMP which is a very strong inhibitor of thymidate synthase and is often used as an anticancer drug.

138
Q

Why is 5-fluouracil a good anticancer drug?

A

Because it prevents the synthesis of a single nucleotide (d thymidine) meaning that cancer tumours are inhibited from growing.

139
Q

How does methotrexate inhibit the synthesis of dthymidine?

A

By inhibiting thymidate synthase by blocking the availability of THF.

140
Q

What kind of disease is methotextrate used to fight?

A

Cancer.

Biochem Take 2. (24 decks)

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