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Biochemistry > Nucleotides > Flashcards

Nucleotides Flashcards

1
Q

Define nucleoside.

A

composed of ribose and a heterocyclic base

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2
Q

Define nucleotide.

A

composed of ribose, heterocyclic base, and 1 or more phosphates

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3
Q

Define deoxynucleotide.

A

nucleotide lacking a 2’-hydroxyl group on ribose ring, replaced by a hydrogen

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4
Q

How many rings do purines have?

A

2 fused heterocyclic rings

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5
Q

How many rings do pyrimidines have?

A

one heterocyclic ring

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6
Q

True or false genes are DNA.

A

True

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7
Q

What does DNA stand for?

A

deoxyribonucleic acid

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8
Q

Where does DNA come from?

A

nucleotides

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9
Q

What is the process going from DNA to RNA?

A

transcription

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10
Q

What is the process going from RNA to DNA, and what utilizes this process?

A

reverse transcription; viruses

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11
Q

What is the process going from RNA to proteins?

A

translation

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12
Q

What are the repeating units of DNA?

A

nucleotides, sugar, bases

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13
Q

What is the difference between RNA and DNA?

A

OH group on sugars, T in DNA, U in RNA

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14
Q

What is the molecule of heredity in all prokaryotic and eukaryotic organisms?

A

DNA

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15
Q

True or false, viruses can contain RNA or DNA.

A

True

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16
Q

All cellular DNA consists of ____ very long ____ polynucleotide strands _____ around a common ____.

A

2; helical; coiled; axis

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17
Q

What is the DNA backbone and how is it oriented?

A

sugar-phosphate; to the outside

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18
Q

How are the bases oriented?

A

to the inside

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19
Q

What forces stabilize the bases?

A

stacking

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20
Q

How are the bases connected?

A

Hydrogen bonding

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21
Q

How do the 2 strands run compared to each other?

A

in opposite directions

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22
Q

True or false, the 2 strands of the double helix of DNA compliment each other.

A

True

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23
Q

Adenine is paired with ____ and they form ___ H-bonds.

A

thymine; 2

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24
Q

Cytosine is paired with ____ and they form ___ H-bonds.

A

guanine; 3

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25
Q

List the forms of DNA and their handedness.

A

Z (L), A (R), B (R)

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26
Q

What are the effects of super coiling of DNA?

A

compacts the DNA

Makes DNA more accessible for interactions with other biomolecules

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27
Q

_____ give rise to ____ _____ _____ regions in complicated ____ structures of single stranded nucleic acids (___).

A

hairpin turns; extensive double helical; 3-D; RNA

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28
Q

Describe semi-conservative replication.

A
  • strands of helix separate
  • new strand complimentary to each original strand is synthesized
  • 2 new helices are generated with 1 original and 1 new strand each
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29
Q

True or false the sequence of bases in one strand determines the sequence of bases in the other strand of DNA.

A

True

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30
Q

Define melting.

A

heating a solution of double helical DNA to separate the strands

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31
Q

Define cooling.

A

lowering the temperature of the melted/heated strands so they can reanneal and reform the double helix

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32
Q

True or false, in the cell special proteins temporarily separate the strands in replication.

A

True

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33
Q

True or false pyrimidine is first assembled and then linked to they ribose phosphate to form a pyrimidine nucleotide.

A

True

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34
Q

What is the donor of the ribose phosphate moiety?

A

5-phosphoribosyl-1-pyrophosphate

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35
Q

What is the salvage pathway of pyrimidine synthesis?

A

thymine to thymidine to TMP

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36
Q

From what precursors is the purine ring assembled?

A

glutamine, glycine, aspartate, , N10-THF, CO2

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37
Q

True or false the purine ring is synthesized directly on the ribose phosphate.

A

True

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38
Q

What is the committed step in purine ring synthesis?

A

formation of 5-phophoribosylamine from PRPP & glutamine

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39
Q

What is the salvage pathway of purine synthesis?

A

preformed bases reacts directly with PRPP

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40
Q

What is the basic DNA structure?

A

sugar-phosphate backbone with bases attached

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41
Q

True or false, a DNA strand is read 5’ to 3’.

A

true

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42
Q

How is a DNA strand synthesized?

A

each new group is added to the phosphate of the 3’C on the chain (5’ to 3’)

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43
Q

What are the two types of grooves of the double helix of DNA?

A

major, minor

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44
Q

How condensed are mitotic DNA compared to interphase DNA?

A

500 times

45
Q

How many nucleotides are in our geonome?

A

300 billion

46
Q

What distance could our stretched out genome cover?

A

to the moon and back

47
Q

Explain what is the dynamic situation of our genome.

A

must allow rapid localized access to DNA for gene expression

48
Q

What DNA binding proteins are involved in forming chromosomes?

A

histones and non-histone chromosomal proteins

49
Q

What is chromatin?

A

protein + nuclear DNA

50
Q

Nucleotides are the ____ ____ of nucleosides.

A

phosphate esters

51
Q

What do nucleotides contain?

A

base, sugar, phosphate

52
Q

base sugar = ?

A

nucleoside

53
Q

base + sugar + phosphate = ?

A

nucleotide

54
Q

nucleoside + phosphate = ?

A

nucleotide

55
Q

nucleotide - phosphate = ?

A

nucleoside

56
Q

connected nucleotides

A

polynucleotides = nucleic acids = DNA or RNA

57
Q

List the purines.

A

Adenine & guannin

58
Q

List the pyrimidines.

A

cytosine, uracil, & thymine

59
Q

What is the structure of Adenosine triphosphate (ATP)?

A

Adenine + ribose + 3 phosphates

60
Q

List the hydrolysis reactions.

A

ATP to ADP + Pi

ATP to AMP + PPi

PPi to Pi + Pi

61
Q

Of the hydrolysis reactions which yields the highest energy?

A

ATP to AMP + PPi

-10.9 kcal/mol

62
Q

Of the hydrolysis reactions which yields the second highest energy?

A

ATP to ADP + Pi

-7.3 kcal/mol

63
Q

Of the hydrolysis reactions which yields the lowest energy?

A

PPi to Pi + Pi

-4.0 kcal/mol

64
Q

What is the universal currency of free energy in biological systems?

A

ATP

65
Q

What are some specific roles of nucleotides?

A

Coenzyme A, NAD+, FAD

66
Q

How many angstroms is a turn in a DNA helix?

A

34

67
Q

How many base pairs per turn?

A

~10

68
Q

What is the most common form of DNA?

A

B DNA

69
Q

What is the limiting factor in DNA synthesis?

A

cytosine

70
Q

What do ribonucleases do for RNA?

A

breaks up long chain RNA into short RNA segments

71
Q

What do deoxyribonucleases do for RNA?

A

breaks up long chain DNA into short DNA segments

72
Q

What do phosphodiesterase do?

A

Cuts the phosphodiester bond between nucleotides

creates NMPs and dNMPs

73
Q

What do nucleotidase do?

A

cleaves phosphate off nucleotides = nucleosides

74
Q

What do nucleosidase do?

A

cleaves the base off nucleosides = purines and pyrimidines

75
Q

Describe xanthine oxidase

A

Catalyzes the oxidation of hypoxanthine to xanthine and xanthine to uric acid

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

Drug target for the treatment of gout

76
Q

What is the latin word for gout?

A

gutta (drop of discharge)

77
Q

What is gout historically regarded as and why?

A

disease of the wealthy (excess wine, food, and sex)

78
Q

What is the most commonly affected area for gout?

A

the big toe (metatarsal pharangeal joint)

79
Q

Define gout.

A

Characterized by intensely painful and inflamed joints

Characterized by high levels of uric acid levels in blood resulting from over production of uric acid (primary hyperuricemia)
or under secretion of uric acid (secondary hyperuricemia)

Sodium urate crystals precipitate in synovial fluid of joints
deposits are very painful
in the kidneys can cause kidney damage

phagocytic cells engulf crystals and release factors that initiate acute inflammatory response

80
Q

What type of diet may trigger episodes of gout?

A

rich in purines (beans, lentils, spinach) with meat, seafood, and alcohol

81
Q

What is the treatment for gout?

A

colchicine (decreases movement of granulocutes to the affected area)

allopurinol (inhibits xanthine oxidase to form the more soluble hypoxanthine)

82
Q

What are the normal serum uric acid levels for adult males and females?

A

males = 4-8.6 mg/dL

females = 3.0-5.9 mg/dL

83
Q

Serum urate levels >9mg/dL increase ____ of ___.

A

risk, gout

84
Q

What are normal urinary urate levels?

A
85
Q

True or false, urinary urate levels vary day to day.

A

True

86
Q

Dietary pyrimidines are readily converted to what in pyrimidine catabolism.

A

metabolized ketogenic or glucogenic water soluble compounds such as malonyl CoA, methyl malonyl CoA and succinyl CoA

87
Q

What are the sources for ring atoms in purine synthesis?

A

CO2, Gln, Gly, Asp, N10-formylTHF

88
Q

What are the sources for ring atoms in pyrimidine synthesis?

A

HCO32-, Gln, Asp, N5N10-methyleneTHF

89
Q

True or false, inosinate monophosphate is not commonly found in DNA or RNA.

A

True

90
Q

What is inosinate monophosphate converted into?

A

guanosin monophosphate (GMP) or adenosine monophosphate (AMP)

91
Q

What are the 2 salvage enzymes for purine biosynthesis?

A

hypoxanthine guanine phosphoribosyl transferase

adenine phosphoribosyl transferase

92
Q

What is a central constituent of nucleotide metabolism?

A

PRPP = phosphoribosyl pyrophosphate

93
Q

What is PRPP synthesized from?

A

ribose phosphate and ATP

94
Q

What does tetrahydrofolate do in purine synthesis?

A

closes the ring, makes IMP

95
Q

Describe the role of methotrexate.

A

Antineoplastic agent

inhibits dihydrofolate reductase which disrupts DNA replication in rapidly dividing cells (cancer)

efficacy depends on selective drug uptake by cancer cells versus normal cells

96
Q

How much more tightly does methotrexate bind dihydrofolate reductase?

A

100 fold

97
Q

What controls the synthesis of purine nucleotides?

A

feedback regulation at several sites to balance the production

98
Q

List the checkpoints of purine synthesis.

A

PRPP and PR-amine

AMP and GMP from IMP

99
Q

AMP synthesis is stimulated by what?

A

GTP

100
Q

GMP synthesis is stimulated by what?

A

ATP

101
Q

True or false, nucleoside phosphates can be interconverted.

A

true

102
Q

What is the committed step in pyrimidine synthesis?

A

formation of n-carbamoyl aspartate

103
Q

How is orotic aciduria treated?

A

with oral uridine

104
Q

What is the human hereditary disorder involving the synthesis of the pyrimidine nucleotides?

A

orotic aciduria

105
Q

How are deoxyribonucleotides formed?

A

from the ribonucleotides by the reduction of ribonucleoside diphosphates

106
Q

What is the hydrogen donor for the reduction of ribonucleoside diphosphates?

A

reduced thioredoxin or glutaredoxin

107
Q

Where are the 2 major control points of pyrimidine biosynthesis?

A
  1. Carbamoyl phosphate synthetase is inhibited by UMP, purines, and stimulated PRPP
  2. Aspartate transcarbamoylase is feedback inhibited by CTP
108
Q

What type of regulation are the control points of pyrimidine biosynthesis?

A

allosteric regulation

109
Q

What is the limiting factor for DNA synthesis?

A

dTTP

Biochemistry (13 decks)

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