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GSBS Biochem > DNA 1 and 2 > Flashcards

DNA 1 and 2 Flashcards

1
Q

RNA stands for

A

ribonucleic acid

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2
Q

DNA stands for

A

Deoxyribonucleic acid

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3
Q

what is responsible for storing and translating the information encoding each of the proteins and performing other chemistry

A

ribose-phosphate polymers

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4
Q

RNA is responsible for

A

enzymatically synthesizing all proteins

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5
Q

about how much of DNA is protein encoding

A

2%

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6
Q

how many monomers are found in each DNA set in the human cell

A

3x10^9
3 billion

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7
Q

total length of polymer of DNA in a cell

A

1 meter/cell

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8
Q

what two things contribute to errors

A

translation and transcription

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9
Q

in what organisms are mutation rates low

A

bacteria and humans

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10
Q

low mutation rate

A

1 per 1-^8or9

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11
Q

what organisms have a high mutation rate

A

viruses and cancers

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12
Q

high mutation rate

A

1 per 1000

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13
Q

why might a high mutation rate be a good thing?

A

it helps the virus evade the immune system.
makes cancer harder to treat

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14
Q

two types of bases

A

purines and pyrimidines

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15
Q

purines

A

adenine
guanine

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16
Q

pyrimidines

A

uracil
cytosine
thymine

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17
Q

how are bases linked to the ribose sugar

A

N-linked
via the nitrogen on the base

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18
Q

another name for a ribose sugar

A

furanose

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19
Q

what does ribose do in water

A

cyclizes and puckers

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20
Q

nucleoside

A

a base linked to a pentose sugar
NO PHOSPHATE

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21
Q

nucleotide

A

a base linked to a phosphate ester of a pentose
base, sugar and phosphate

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22
Q

base, nucleoside, nucleotide nomenclature for A

A

adenine
adenosine
adenylate

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23
Q

base, nucleoside, nucleotide nomenclature for G

A

guanine
guanosine
guanylate

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24
Q

base, nucleoside, nucleotide nomenclature for U

A

uracil
uridine
uridylate

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25
Q

base, nucleoside, nucleotide nomenclature for C

A

cytosine
cytidine
cytidylate

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26
Q

base, nucleoside, nucleotide nomenclature for T

A

thymine
thymidine
thymidylate

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27
Q

DNA at base pair levels form what kinds of bonds

A

hydrogen bonds

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28
Q

A and T/U form how many base pairs

A

2

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29
Q

C and G form how many base pairs

A

3

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30
Q

the hydrogen bonds between the bases make the DNA

A

flexible

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31
Q

in purines, where does the first nitrogen come from

A

aspartate

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32
Q

in purines where does the second carbon come from

A

N10-Formyl-tetrahydrofolate (THF)

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33
Q

in purines, where does the third nitrogen come from

A

glutamine

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34
Q

in purines, where does the 4th carbon come from

A

glycine

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35
Q

in purines where does the 5th carbon come from

A

glycine

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36
Q

in purines where does the 6th carbon come from

A

CO2

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37
Q

in purines where does the 7th nitrogen come from

A

glycine

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38
Q

in purines, where does the 8th carbon come from

A

N10-Formyl-tetrahydrofolate (THF)

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39
Q

in purines where does the 9th nitrogen come from

A

glutamine

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40
Q

PRPP

A

5-phosphoribosyl-1-pyrophosphate

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41
Q

what is the activated donor of the sugar unit in biosynthesis of nucleosides using a phosphoribosyl transferase

A

PRPP

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42
Q

the purine rings are synthesizes on the

A

ribophosphate

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43
Q

what amino acid is needed to start the process of turning PRPP into a purine

A

glutamine

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44
Q

what is the initial purine made from the PRPP pathway

A

Inosinate (IMP)
hypoxanthine base

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45
Q

Inosinate (IMP) can be turned into

A

Adenylate (AMP)
Guanylate (GMP)

46
Q

Free bases can be recycled and attatched directly in what is known as

A

a salvage reaction

47
Q

how is a salvage reaction done

A

using a phosphoribosyl transferase reaction

48
Q

the monophosphates are enzyme … for their own synthesis

A

inhibitors

49
Q

AMP production from IMP is inhibited by

A

AMP

50
Q

GMP production from IMP is inhibited by

A

GMP

51
Q

IMP production from PRPP is inhibited by

A

IMP, AMP, and GMP

52
Q

in pyrimidines where is the 1st nitrogen from

A

aspartate

53
Q

in pyrimidines where is the second carbon from

A

carbamoyl phosphate

54
Q

in pyrimidines where is the 3rd nitrogen from

A

carbamoyl phosphate

55
Q

in pyrimidines where is the 4th carbon from

A

aspartate

56
Q

in pyrimidines where is the 5th carbon from

A

aspartate

57
Q

in pyrimidines where is the 6th carbon from

A

aspartate

58
Q

aspartate and carbamoyl phosphate come together to make

A

orotate

59
Q

orotate is used to make the precursor pyrimidine called

A

uridylate (UMP)

60
Q

How is RNA reduced to DNA

A

by a ribonucleotide reductase known as ribonucleoside diphosphate reductase

61
Q

DNA bases are aromatic and therefore

A

stack well

62
Q

what provides specific pairing and form specific structed in salt water in reguards to DNA

A

hydrogen bonds

63
Q

what do the major and minor groove in DNA do

A

hold water, ions, and provide many recognition sites for other molecules including proteins

64
Q

duplex (ds) DNA is often characterized as

A

a nearly rigid charged rod

65
Q

duplex DNA has a persistance length (P) of

A

500 A

66
Q

single stranded DNA (or RNA) had a persistance length (P) of

A

less than 10 A

66
Q

two ways to measure persistance length (P)

A

FRET and FCS

67
Q

what packs the DNA in phages

A

ATP consuming motor

68
Q

many of the common cofactors are also

A

nucleotides

69
Q

three common cofactors

A

coenzyme A
NAD+
FAD

70
Q

how many phosphates can be added onto a nucleoside

A

1, 2, or 3

71
Q

synthesis and degradation of the bases are very

A

material and energy intensive reactions

72
Q

de novo synthesis molecule for pyrimidines

A

UMP

73
Q

end products for pyrimidine degredation

A

B-alanine and B-aminoisobutyric acid

74
Q

B-aminoisobutyric acid smells like

A

old tennis shoes

75
Q

de novo synthesis molecule of purines

A

IMP

76
Q

end/waste product of purine degredation

A

uric acid

77
Q

the synthesis cycles are dependent on

A

energy molecules

78
Q

AMP synthesis depends on

A

GTP

79
Q

GMP synthesis depends on

A

ATP

80
Q

essentially any -OH on the furanose ring could be substituted with

A

phosphates

81
Q

3’ and 5’ OH substitutions on the furanose ring are for

A

the backbone

82
Q

2’ and 3’ OH substitutions on the same furanose ring make

A

a Cyclic NMP molecule used in secondary messenger pathways

83
Q

given the number of rotatable bonds, the number of conformations per base is

A

large meaning there is lots of flexibility

84
Q

the glycosidic linkage at the base is called the

A

X dihedral
flagpole

85
Q

syn

A

the base is turned toward the furanose ring

86
Q

anti-

A

the base is turned away from the furanose ring

87
Q

examples of less common bases

A

5-methylcytidine
N6-methyladenosine
N2-methylguanosine
5-hydroxymethylcytidine
inosine
pseudouridine
7-methylguanosine
4-thiouridine

88
Q

the bases pair up specifically with H-bonds and yeild similar

A

C-1’ to C-1’ distances

89
Q

differences between RNA and DNA

A

the OH in the backbone and the change of T for U

90
Q

A problem with RNA stability

A

can be easily hydrolized on the 2’OH by water or OH

91
Q

each base has a unique UV absorption spectrum due to

A

the electronic differences in the rings and substitutions

92
Q

the bases have several titratable groups and as a result

A

several resonance tautomers exist
so pH plays a role

93
Q

guanine tautomers

A

keto and enol

94
Q

adenine tautomers

A

amine and imine

95
Q

tautomers for pyrimidines

A

lactam, lactim and double lactim

96
Q

tautomers cause what

A

mutations during replication and repair

97
Q

different resonance states are allowed due to

A

the number of hetero atoms in conjuction in the rings

98
Q

the absorption spectrum of the nucleic acids depends on

A

pH

99
Q

nucleotide availability via synthesis is crucial to

A

dividing cells where a new copy of the chromosome is needed

100
Q

nucleotide synthesis is a good candidate for

A

chemo therapeutics

101
Q

an example of nucleotide synthesis for a target

A

dihydro-foliate reductase
folic acid
p-aminobenzoic acid

102
Q

attractive forces in DNA

A

base pair hydrogen bonds
base pi stacking

103
Q

repulsive forces in DNA

A

excluded volume
phosphate-phosphate repulsions

104
Q

two charges q1 and q2 interact with each other by

A

coulomb’s law

105
Q

The interaction between two charges can be changes by the presence of

A

excess salt (debye and Huckel)

106
Q

dipoles align to oppose the

A

external field in dielectric screening

107
Q

all biochemistry requires

A

salt water or buffers

108
Q

liquid state order: solvation shells

A

when the molecules are tumbling in solution and there is salt, the system is not crystalline the distribution has structure but is not periodic like a lattice.

109
Q

The electric fild around DNA changes the probability of finding

A

salt and other DNA

110
Q

counter ions pile up near

A

a helix or between two helices

111
Q

counter ions increase

A

the ionic strength and screening locally

GSBS Biochem (10 decks)

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