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Biochemistry (material for exam II) > Nucleotide Structure, Function and Metabolism > Flashcards

Nucleotide Structure, Function and Metabolism Flashcards

1
Q

Nucleosides are what

A

bases bonded to sugars only

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2
Q

How are nucleosides named

A

by naming base with -sine or -dine added

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3
Q

What is the structure of nucleotides

A

sugar, phosphate, and base

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4
Q

how are nucleotides named

A

by adding -ylate

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5
Q

Why does thyamine not have to have deoxy added to it

A

because it is not found in RNA

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6
Q

What kind of linkages attach the base to the sugar backbone

A

Beta-glycosidic linkage

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7
Q

The C-1’ of a sugar is attached by a beta-glycosidic linkage to a ____ of a purine

A

N-9

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8
Q

The C-1’ of a sugar is attached by a beta-glycosidic linkage to a ____ of a purine

A

N-1

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9
Q

What is the portion of DNA that codes for a protein

A

Gene

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10
Q

The phosphodiester bridge has what kind of charge

A

negative

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11
Q

What is the most common site of phosphate esterification

A

C-5’

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12
Q

Addition of beta and gamma phosphates are added via

A

anhydride bonds to each other

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13
Q

In DNA what carbon of the ribose is deoxygenated

A

The C-2

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14
Q

What affect does the absence of oxygen at C-2’ have

A

it makes the DNA more resistant to hydrolytic attack, therefore increasing stability

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15
Q

DNA is written and read in what direction

A

5’-3’

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16
Q

How many hydrogen bonds are between A-T

A

2

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17
Q

How many hydrogen bonds are between C-G

A

3

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18
Q

The stacking of bases contributes to the stability of DNA in two ways what are they

A

Hydrophobic effect
- The hydrophobic bases cluster into the interior whereas the polar backbone faces the exterior
Van der Waals “stacking” forces
- The stacked base attract one antoher
- Although individually are weak when summed together they are strong

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19
Q

DNA exists in 3 forms

A

A form
B form
Z form

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20
Q

What is the A form of DNA

A

shorter and wider than B form
base pairs are tilted to the axis and in right handed spiral
only occurs in non-physiological conditions

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21
Q

What is the B form of DNA

A

Is the most common form b/c it is hydrated like living cellular environments
is longer and narrower than A form
right handed spiral w/base pairs perpendicular to the axis

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22
Q

What is the Z form of DNA

A

Occurs in segments of DNA that have been methylated

turn about the helical axis in a left handed spiral and the phosphate backbone zigzagged

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23
Q

____ + ____= chromatin

A

Protien + Nuclear DNA

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24
Q

how many nucleotides are in out genome

A

3 billion

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25
Q

an incredible amount of ____ is needed to package DNA

A

condensation

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26
Q

Mitotic chromosomes are condensed _____ times compared to interphase DNA

A

500 times

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27
Q

DNA binding proteins involved in forming chromosomes are

A

histones and non-histone chromosomal proteins

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28
Q

Polynucleotides are called

A

Nucleic acids

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29
Q

Nucleotids contain

A

a base, a sugar, and a phosphate

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30
Q

Nucleotides are _____ esters of nucleosides

A

phosphate esters

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31
Q

nucleosides consist of

A

a base and a sugar

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32
Q

Sugars are attached to a base via a ________

A

N-glycosidic linkage (in DNA it is a beta-glycosidic linkage because it is above the plane)

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33
Q

The C-1 of a sugar is attached by beta-linkage to what location of a purine

A

N-9

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34
Q

The C-1 of a sugar is attached by beta-linkage to what location of a pyrimidine

A

N-1

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35
Q

What is the purpose of the phosphodiester bridge having a negative charge

A

it repels nucleophilic species (like hydroxide ions) thus makes them less susceptible to hydrolytic attack than other esters

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36
Q

What is the most common site of phosphate esterification

A

C-5’

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37
Q

Phosphates are attached to a sugar via a

A

ester bond

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38
Q

phosphates are attached to each other via a

A

anhydride bond

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39
Q

DNA is deoxygenated at what carbon

A

C-2’

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40
Q

What is the purpose of the deoxygenation of DNA at C-2’

A

it makes DNA more resistant to hydrolytic attack and thus more stable

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41
Q

What direction is DNA written

A

5’-3’

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42
Q

how far apart are adjacent bases on DNA double helix

A

3.4 angstroms

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43
Q

The bases on DNA double helix are located

A

nearly perpendicular to the helix axis

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44
Q

The helical structure of DNA repeats every

A

10 bases or 34 angstroms

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45
Q

each base of the DNA alpha helix contributes ____ degrees of turn, so ____ bases per turn

A

36 degrees, so 10 bases per turn

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46
Q

The sugar backbone is located on the _____ of the DNA double helix

A

outside

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47
Q

The bases are located on the _____ side of the DNA double helix

A

inside

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48
Q

The ratio of purines and pyrimidines is

A

1:1

49
Q

The ratio of what varies considerably form species

A

A-G

50
Q

DNA with high ___ content is more stable

A

GC

51
Q

what does ribonucleotide reductase due to a nucleotide diphosphate (note that NADPH is required)

A

It makes 2’- deoxynucleotide diphosphate

52
Q

ATP does what to ribonucleotide reductase

A

activates it

53
Q

dATP does what to ribonucleotide reductase

A

it inhibits it

54
Q

What converts long strand RNA to short RNA

A

Ribonucleases

55
Q

What converts long DNA chain to DNA oligomer or short chain DNA

A

Deoxyribonucleases

56
Q

What does cleaves the phosphodiester bond of DNA and RNA oligomers to form monophosphates

A

Phosphodiesterase

57
Q

What cleaves the phosphate off a nucleotide to form a nucleoside

A

Nucleotidase

58
Q

what cleaves the base of a nucleoside to form a base and separate ribose/deoxyribose

A

nucleosidase

59
Q

Allopurinol inhibits what specific enzyme

A

Xanthine oxidase

60
Q

allopurinaol inhibits xanthine oxidase and therefore does not allow ____ to be converted to ____ and ____ to be converted to _____

A

hypoxanthine to be converted to xanthine and xanthine to uric acid

61
Q

What does urate oxidase do

A

it is an enzyme not present in humans that converts uric acid to a more water soluble form Allantoin

62
Q

Plays an important role in adenosine homeostasis and modulates signaling by extracellular adenosine and so contributes indirectly to signaling

A

Adenosine Deaminase (ADA)

63
Q

The overproduction of Adenosine Deaminase (ADA) in erythrocytes causes

A

hemolytic anemia. It is rare.

increased degradation of adenosine depletes adenine nucleotide pool and triggers premature destruction of RBCs.

64
Q

What is the final product of purine catabolism

A

Uric Acid

65
Q

Underproduction of Adenosine Deaminase ADA is associated with

A

The second most common form of severe combined immunodeficiency (SCID)

66
Q

What catalyzes the oxidation of hypoxanthine to xanthine and xanthine to uric acid

A

Xanthine Oxidase

67
Q

The inhibition of what enzyme by allopurinol is a major target for the treatment of Gout

A

Xanthine oxidase

68
Q

What is the structure of xanthine oxidase

A

2 Flavin adenine dinucleotides (FADs), 2 Mo atoms, and 8 Fe atoms per molecule of enzyme

69
Q

Deficiency of ADA leads to

A

SCID, high amounts of adenosine which is then converted into dATP, high levels of which block the synthesis of all other dNDPs and dNTPs,
Impaired DNA synthesis and compromised immune system

70
Q

What is the most commonly affected area for GOUT

A

Big toe (metatarsal pharangeal joint)

71
Q

High uric acid levels in the blood, leading to sodium urate crystals precipitate in the synovial fluid joints

A

Gout

72
Q

What is primary hyperuricemia

A

overproduction of uric acid

73
Q

What is secondary hyperuricemia

A

under-excretion of uric acid

74
Q

What is the level for hyperuricemia

A

uric acid concentrations exceed plasma solubility (about 7 mg/dL)

75
Q

What kind of diet increases the risk of gout

A

Rich in Purines (beans, lentils, spinach) together with meat, seafood, and alcohol

76
Q

What are some treatments for GOUT

A

colchicine- decrease movement of granulocytes to the affected area
Allopurinol- inhibits xanthine oxidase to form the more soluble hypoxanthine
urate oxidase- catalyzes uric acid to allantoin, which is more water soluble

77
Q

What is the normal serum uric acid level in adult males

A

4-8.6 mg/dL

78
Q

What is the normal serum uric acid level in adult females

A

3.0-5.9 mg/dL

79
Q

Serum urate levels greater than

A

> 9 mg/dL means an increased risk of gout

80
Q

Thymine derivatives final product (s) of catabolism

A

MethylmalonylCoA and Succinyl CoA

Both are glucogenic

81
Q

Cytosine and Uracil derivatives after catabolism

A

Malonyl CoA, which is ketogenic

82
Q

Malonyl CoA, Methylmalonyl CoA, and succinyl CoA are all ____ soluble

A

water soluble

83
Q

What is the source of rings atoms for Purine bases

A

CO2, Gln, Gly, Asp, N^10-formyl THF

84
Q

What is the source of the rings atoms for prymidine bases

A

HCO3-, Gln, Asp, N^5, N^10- methylene THF

85
Q

What is the committed step in the purine synthesis

A

formation of the phosphoribosyl amine (PRA)

86
Q

How many phases are there to De Novo synthesis

A

4

87
Q

Where does the alpha-D- ribose 5-phosphate from phase I of De novo purine synthesis come from

A

Pentose phosphate pathway

88
Q

What is phase I of the De Novo synthesis of purines

A

Ribose-5P activation

89
Q

What is the activated form of Ribose-5P

A

5-phospho-alpha-D-ribosyl-1- pyrophosphate (PRPP)

note that it has 3 phosphates attached, 1 at C5’ and 2 at C1’

90
Q

What is phase II of De Novo Purine synthesis

A

conversion of PRPP to PRA (phosphoribosylamine) (note that this is the converted step)

91
Q

Methotrexate blocks what phase of de novo purine synthesis

A

Phase III: construct IMP ring

92
Q

How many steps is phase III of de novo purine synthesis

A

9 steps

93
Q

What is phase IV of de novo purine synthesis

A

Convert IMP to adenosine and guanosine (deoxy) nucleotides

94
Q

Ribonuclease reductase is an enzyme that catalyzes

A

a ribose to a deoxyribose

95
Q

GMP and AMP inhibit what phases of de novo purine synthesis

A

Phase I,II, IV

96
Q

IMP inhibits what phases of de novo purine synthesis

A

Phase I and II

97
Q

Phosphates promote what phase of de novo purine synthesis

A

Phase I

98
Q

PRPP promotes what phase of de novo purine synthesis

A

Phase II

99
Q

Hypoxanthine ribose phosphate is the same thing as

A

Inosine monophosphate (IMP)

100
Q

What is the product of phase III of de novo purine synthesis

A

Inosine monophosphate (IMP)

101
Q

what are the two salvage enzymes of purine biosynthesis

A

Hypoxanthine guanine phosphoribosyl transferase

Adenine phosphoribosyl transferase

102
Q

what is the specific target of methotrexate

A

dihydrofolate reductase that converts in the liver

103
Q

methotrexate binds dihydrofolate ___ times more tighlty than the forming IMP

A

100

104
Q

AMP synthesis is stimulated by

A

GTP

105
Q

GMP synthesis is stimulated by

A

ATP

106
Q

how many phases is the de novo synthesis of pyrimidine nucleotides

A

3

107
Q

What is phase I of pyrimidine synthesis

A

fabrication of orotate ring

108
Q

What is phase II of De Novo synthesis of Pyrimidines

A

Attach PRPP to form UMP

109
Q

What is phase III of de novo synthesis of pyrimidines

A

Convert UMP to uridine, cytosine and thymine (deoxy) nucleotides

110
Q

The pyrimidine ring is sythesized from carbamoyl phosphate and aspartate by

A

aspartate-transcarbamoylase

111
Q

What is the function of carbamoyl phosphate synthetase II in pyrymidine synthesis

A

it catalyzes the formation of carbamoyl phosphate from Gln, bicarbonate, and 2ATP

112
Q

Why is uridine phosphorylase said to be versatile

A

It is able to convert Uridine/deoxyuridine and Deoxythymidine to uracil and thymine respectively

113
Q

In purine de novo synthesis Methotrexate inhibits what

A

it inhibits dihydrofolate reductase that converts in the liver that converts dihydrofolate to tetrahydrofolate, which is then used to form the ring and thus IMP

114
Q

What does 5-fluorouracil inhibit

A

it inhibits thymidylate synthase, which with Tetrahydrofolate converts dUMP to dTMP

115
Q

Orotic aciduria is a deficiency in what enzyme

A

UMP synthase

116
Q

What is orotic aciduria treated with

A

oral uridine

117
Q

The deoxyribonucleotides are formed from the ribonucleotides by the reduction of the

A

ribonucleoside diphosphates

118
Q

What is the immediate hydrogen donor for the reduction of ribonucleoside diphosphate is reduced

A

thioredoxin or glutaredoxin

Biochemistry (material for exam II) (10 decks)

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