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Biochemistry > DNA > Flashcards

DNA Flashcards

1
Q

4 deoxyribonucleotides of DNA

A

deoxyadenylate, deoxyguanylate, deoxycytidylate, thymidylate

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2
Q

the 4 deoxyribonucleotides are combined through

A

3’ to 5’ phosphodiester bonds

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3
Q

composition of nucleotide

A

base + sugar + phosphoric acid

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4
Q

the 3’ hydroxyl of 1 sugar is combined with the _____ through a phosphate group

A

5’ hydroxyl of another sugar

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5
Q

thymidine is attached to _____ then _____ is attached to ______ through ______

A

cytidine, cytidine, adenosine, phosphodiester bonds

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6
Q

in DNA, the ______ is of paramount importance

A

base sequence

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7
Q

the deoxyribose and phosphodiester linkages are the _____ in all repeating nucleotides

A

same

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8
Q

polarity of DNA molecule

A

the base sequence is always written from the 5’ to 3’ end

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9
Q

(A, B, or Z DNA) right-handed helix

A

A & B DNA

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10
Q

(A, B, or Z DNA) left-handed heliz

A

Z DNA

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11
Q

(A, B, or Z DNA) base pairs per turn of 11

A

A DNA

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12
Q

(A, B, or Z DNA) base pairs per turn of 10.5

A

B DNA

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13
Q

(A, B, or Z DNA) base pairs per turn of 12

A

Z DNA

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14
Q

(A, B, or Z DNA) 2.6 nm helical diameter

A

A DNA

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15
Q

(A, B, or Z DNA) 2.0 nm helical diameter

A

B DNA

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16
Q

(A, B, or Z DNA) 1.8 nm helical diameter

A

Z DNA

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17
Q

(A, B, or Z DNA) 2.6 nm helical length

A

B DNA

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18
Q

(A, B, or Z DNA) 3.4 nm helical length

A

B DNA

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19
Q

(A, B, or Z DNA) 3.7 nm helical length

A

Z DNA

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20
Q

(A, B, or Z DNA) Broadest and shortest in shape

A

A DNA

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21
Q

(A, B, or Z DNA) Intermediate shape

A

B DNA

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22
Q

(A, B, or Z DNA) narrowest and longest shape

A

Z DNA

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23
Q

(A, B, or Z DNA) major grove is wide, deep

A

A DNA

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24
Q

(A, B, or Z DNA) major grove is narrow, deep

A

B DNA

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25
Q

(A, B, or Z DNA) major grove is flat

A

Z DNA

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26
Q

(A, B, or Z DNA) minor grove is narrow, shallow

A

A DNA

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27
Q

(A, B, or Z DNA) minor grove is broad, shallow

A

B DNA

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28
Q

(A, B, or Z DNA) minor grove is narrow, deep

A

Z DNA

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29
Q

the watson crick structure is referred to as the

A

B-form DNA

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30
Q

the most stable structure for a random-sequence DNA molecule under physiological conditions

A

B DNA

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31
Q

in the Watson-Crick model, right-handed double helix DNA consists of _____ chains twisted around another in a right-handed double -helix similar to a spiral staircase

A

2 polydeoxyribonucleotide chains

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32
Q

in the Watson-Crick model, what is the base-pairing rule

A

the 2 strands are complementary to each other

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33
Q

in the Watson-Crick model, what is the Chargaff’s rule

A

the no. of purines id equal to the number of pyrimidines

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34
Q

in the Watson-Crick model, the 2 strands in a DNA molecule run in a ________

A

antiparallel manner

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35
Q

alkali or heat causes strands of DNA to separate but does not break phosphodiester bonds

A

denaturation

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36
Q

this is also called as the melting of DNA

A

denaturation

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37
Q

this is when strands of DNA are separated by heat and then the temperature is slowly decreased under the appropriate conditions, base pair re-for, and a complementary strands of DNA come back together

A

renaturation/annealing

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38
Q

a single strand of DNA pairs with complementary base sequences on another strand of DNA or RNA

A

hybridization

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39
Q

in higher organisms, DNA is organized inside the

A

nucleus

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40
Q

double-stranded DNA is 1st wound over histones, and this is now called

A

nucleosomes

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41
Q

this is a loose term employed for a long stretch of DNA in association with histones

A

chromatin

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42
Q

chromatin is then further and further condensed to form

A

chromosomes

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43
Q

these are proteins containing unusually high concentrations of basic amino acids

A

histones

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44
Q

the 5 classes of histones

A

H1, H2A, H2B, H3, H4

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45
Q

the ___ histone is loosely attached to the DNA

A

H1

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46
Q

the other histones other than H1 are called

A

core histones

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47
Q

core histones form the

A

nucleosome

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48
Q

amino-terminal 1/3 region of ____ and _____ are lysine rich

A

H2A, H2B

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49
Q

H3, H4 histones are

A

arginine histones

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50
Q

[cell cycle of eukaryotic cells] synthesis at DNA (replication) occurs

A

S1 (synthesis phase)

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51
Q

[cell cycle of eukaryotic cells] cells prepare to duplicate their chromosomes

A

G1/first gap

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52
Q

[cell cycle of eukaryotic cells] cells prepare to divide

A

G2/2nd gap

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53
Q

[cell cycle of eukaryotic cells] cell division occurs

A

mitosis

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54
Q

[cell cycle of eukaryotic cells] can _____ the cell cycle many times

A

traverse

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55
Q

[cell cycle of eukaryotic cells] cells can also leave the cycle ____ to divide again

A

never

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56
Q

[cell cycle of eukaryotic cells] phase that cells enter in which they remain for extended periods

A

G0

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57
Q

[cell cycle of eukaryotic cells] in response to _____, cells reenter the cell cycle and divide again

A

appropriate stimulus

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58
Q

During cell division, each daughter cell gets
an exact copy of the genetic information of
the mother cell. This process of copying the
DNA is known as

A

DNA replication

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59
Q

what model of DNA replication is characterized by the two parental strands separate and each makes a
copy of itself. After one round of replication, the two daughter molecules each comprise one old and one new strand. Note that after two rounds, two of the DNA molecules consist only of new material, while the other two contain one old and one new strand.

A

semi-conservative model

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60
Q

what model of DNA replication is characterized by the parental molecule directs the synthesis of an entirely new double-stranded molecule, such that after one round of replication, one molecule is conserved as two old strands. This is repeated in the second round

A

conservative model

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61
Q

This model is only theoretical, this does not actually take place

A

conservative

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62
Q

[Stages of DNA replication] 3 stages of DNA replication

A

initiation, elongation, termination

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63
Q

[Stages of DNA replication] in initiation, DNA synthesis is initiated at particular points within the DNA strand known as

A

origins

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64
Q

[Stages of DNA replication] these are specific coding regions

A

origins

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65
Q

[Stages of DNA replication] the specific coding regions are targeted by

A

initiator proteins

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66
Q

[Stages of DNA replication] initiator proteins go on to recruit more proteins that help aid the replication process, forming a ________ around the DNA origin

A

replication complex

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67
Q

[Stages of DNA replication] There are multiple origin sites, and when replication of DNA begins, these sites are referred to as

A

replication forks

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68
Q

[Stages of DNA replication] Within the replication complex is the enzyme

A

DNA Helicase

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69
Q

[Stages of DNA replication] the action of DNA helicase is

A

unwinding the double helix to expose each of the 2 strands so that they can be used as template for replication

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70
Q

[Stages of DNA replication] the DNA helicase used to ______ that form the bonds between the nucleobases, therefore breaking the bond holding the two strands together

A

hydrolyzes ATP

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71
Q

[Stages of DNA replication] this synthesizes a small RNA primer, which acts as a ‘kick-starter’ for DNA
Polymerase

A

DNA primase

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72
Q

[Stages of DNA replication] this is the enzyme that is ultimately responsible for the creation and expansion of new strands of DNA

A

DNA polymerase

73
Q

[Stages of DNA replication] DNA polymerase is only able to extend the primer by adding free nucleotides to the

A

3’ end

74
Q

[Stages of DNA replication] Polymerization of the new strand of DNA is taking place from

A

5’ to 3’ direction

75
Q

[Stages of DNA replication] the template is read in the

A

3’ to 5’ direction

76
Q

[Stages of DNA replication] in elongation, the 3rd hydroxyl of the last deoxynucleotide is joined with the _______, Thus, the 3’ end of the last nucleotide is free

A

5th phosphate of the newly
entering nucleotide

77
Q

[Stages of DNA replication] One newly formed strand is referred to as the

A

leading strand

78
Q

[Stages of DNA replication] along the leading strand, DNA Primase only needs to synthesize an _____ once,
at the beginning, to initiate DNA Polymerase

A

RNA primase

79
Q

[Stages of DNA replication] fragments in the lagging strand are called

A

Okazaki fragments

80
Q

[Stages of DNA replication] the stage where 2 replication forks meet or no more DNA template is left to replicate

A

termination

81
Q

[Stages of DNA replication] The meeting of two replication forks is not _______ along the course of the chromosome

A

regulated and happens randomly

82
Q

[Stages of DNA replication] Once DNA synthesis has finished, it is important that the newly synthesized strands are

A

bound and stabilized

83
Q

[Stages of DNA replication] in the lagging strand in the termination phase, ______ removes the RNA primer that is at the beginning of each Okazaki
fragment

A

RNAase H

84
Q

[Stages of DNA replication] in the lagging strand in the termination phase, _______ joins fragments together to create one complete strand

A

DNA ligase

85
Q

[mechanism of replication] replication is

A

bidirectional and semiconservative

86
Q

[mechanism of replication] this means that replication begins at a site of origin and simultaneously moves out in both directions from this point

A

bidirectional

87
Q

[mechanism of replication] Prokaryotes have ____ site of origin on each chromosome

A

1

88
Q

[mechanism of replication] ______ have multiple sites of origin on each chromosome

A

eukaryotes

89
Q

[mechanism of replication] this means , following replication, each daughter molecule of DNA contains one intact parental strand and one newly synthesized strand joined by base pairs

A

semiconservative

90
Q

[mechanism of replication] __________ are the sites at which DNA synthesis is occurring

A

replication forks

91
Q

[mechanism of replication] Helicases unwind the helix, and _______ hold it in a single-stranded conformation.

A

single-strand binding proteins

92
Q

[mechanism of replication] _______ act to prevent the extreme supercoiling of the parental helix that would result as a consequence of unwinding at a replication fork

A

Topoisomerases

93
Q

[mechanism of replication] _____ a topoisomerase inhibited by the quinolone family of antibiotics, is found only in
prokaryotes

A

DNA gyrase

94
Q

[mechanism of replication] _______ catalyze the synthesis of DNA

A

DNA polymerases

95
Q

[mechanism of replication] Prokaryotes have _____ DNA polymerases

A

3

96
Q

[mechanism of replication] the polymerases of prokaryotes

A

pol I, pol II, pol III

97
Q

[mechanism of replication] the polymerase of prokaryotes that is the replicative enzyme

A

pol III

98
Q

[mechanism of replication] the polymerase of prokaryotes that is involved in repair and synthesis on the lagging strand

A

pol I

99
Q

[mechanism of replication] eukaryotic polymerase for replication (in a complex with primase and aids in starting the primer, and is also for DNA repair

A

pol alpha

100
Q

[mechanism of replication] eukaryotic polymerase for DNA repair exclusively

A

pol beta

101
Q

[mechanism of replication] eukaryotic polymerase for DNA replication in mitochondria

A

pol gamma

102
Q

[mechanism of replication] eukaryotic polymerase for replication on lagging strand, and for DNA repair

A

pol delta

103
Q

[mechanism of replication] eukaryotic polymerase for replication on leading strand, and for DNA repair

A

pol epsilon

104
Q

[mechanism of replication] DNA polymerases can only copy a DNA template in the ______ direction and produce the newly synthesized
strand in the ______

A

3’ to 5’; 5’ to 3’ direction

105
Q

[mechanism of replication] Deoxyribonucleoside triphosphates which include _______ are the precursors for DNA synthesis

A

dATP, dGTP, dTTP, and dCTP

106
Q

this refers to injuries to DNA that introduce deviations from its normal, intact structure and which may if left unrepaired, results in a mutation or a block of NDA replication

A

DNA damage

107
Q

this refers to permanent alteration of the nucleotide sequence of the genome of an organism, virus, or extrachromosomal DNA or other genetic elements

A

mutation

108
Q

a structural change in DNA

A

DNA damage

109
Q

an alteration of the nucleotide sequence in DNA

A

mutation

110
Q

most damages are repaired by cellular mechanisms

A

DNA damage

111
Q

permanent changes in DNA

A

mutation

112
Q

unrepaired DNA damages become ____ in replication cells

A

mutations

113
Q

this is caused by compounds released during metabolism and environmental factors

A

DNA damage

114
Q

caused by errors in DNA replication and recombination

A

mutation

115
Q

3 types of DNA damage

A

changes of nitrogenous bases, missing bases, breaks in DNA strands

116
Q

three types of mutations

A

substitutions, deletions, insertions

117
Q

prevents the proceeding of DNA replication

A

DNA damage

118
Q

change the genetic information encoded by DNA

A

mutation

119
Q

this can be passed over generations

A

mutation

120
Q

2 types of DNA damage

A

endogenous, exogenous

121
Q

type of DNA damage such as attack by reactive oxygen species produced from normal metabolic byproducts

A

endogenous damage

122
Q

type of DNA damage caused by external agents such as UV (200-400), other radiation frequencies, certain plant toxins, and viruses

A

exogenous damage

123
Q

3 types of mutations

A

base substitutions, deletions, insertions

124
Q

2 types of base substitutions

A

transition, transversion

125
Q

[types of mutations] Single base substitutions are called

A

point mutations

126
Q

[types of mutations] the most common type of mutation

A

point mutations/single base substitutions

127
Q

[types of mutations] example of single base mutations

A

sickle cell anemia

128
Q

[types of mutations] type of point mutation that occurs when a purine is substituted with another purine or when a pyrimidine is substituted with another pyrimidine

A

transition

129
Q

[types of mutations] type of point mutation occurs when a purine is substituted for a pyrimidine or a pyrimidine replaces a purine

A

transversion

130
Q

[types of mutations] results when one or more base pairs are lost from the DNA that further leads to a frameshift

A

deletion

131
Q

[types of mutations] an example of deletion mutation

A

cystic fibrosis

132
Q

[types of mutations] additional base pairs may lead to frameshifts

A

insertion

133
Q

[types of mutations] Diseases caused by insertional mutations include

A

Fragile X Syndrome. Huntington’s Disease. Myotonic dystrophy

134
Q

involves the removal of the segment of DNA that contains a damaged region or mismatched bases

A

DNA repair

135
Q

[DNA repair] filling in the gap by action of a ________ that uses the ______ strand as a template, and _______ of the newly synthesized segment to the remainder of the chain

A

DNA polymerase, undamaged sister, ligation

136
Q

[DNA repair] types of single strand repair

A

nucleotide excision repair (NER), base excision repair (BER), DNA mismatch repair (MMR)

137
Q

[DNA repair] type of single strand repair which is a particularly important excision mechanism that removes DNA damage
induced by ultraviolet light (UV)

A

nucleotide excision repair

138
Q

[DNA repair] UV DNA damage results in

A

bulky DNA adducts

139
Q

[DNA repair] bulky DNA adducts are usually

A

pyrimidine dimers

140
Q

[DNA repair] in NER, Recognition of the damage leads to removal of a ______ that contains the lesion

A

short single-stranded DNA segment

141
Q

[DNA repair] type of single strand repair that is a cellular mechanism for removing damaged bases that could otherwise
cause mutations by mispairing or lead to breaks in DNA during replication

A

base excision repair (BER)

142
Q

[DNA repair] BER is initiated by

A

DNA glycosylases

143
Q

[DNA repair] DNA glycosylases recognize and remove specific damaged or inappropriate bases, forming

A

AP (apurinic/apyrimidic) sites

144
Q

[DNA repair] AP sites are cleaved by

A

AP endonuclease

145
Q

[DNA repair] The resulting single-strand break can then be processed by either:

A

short patch or long patch BER

146
Q

[DNA repair] short patch BER is where a

A

single nucleotide is replaced

147
Q

[DNA repair] long patch BER is where

A

2–10 new nucleotides are synthesized

148
Q

[DNA repair] is a system for recognizing and repairing erroneous insertion, deletion, and mis-incorporation of bases that can arise during DNA

A

DNA mismatch repair (MMR)

149
Q

[DNA repair] During DNA
synthesis the _______________. In order
to begin repair, the mismatch repair
machinery distinguishes the newly
synthesized strand from the template
(parental)

A

newly synthesized (daughter)
strand will commonly include errors

150
Q

[DNA repair] In gram-negative bacteria,
____________ distinguishes the strands

A

transient hemi-methylation

151
Q

[DNA repair] in gram-negative bacteria, (the parental is ______ and daughter is not)

A

methylated

152
Q

[DNA repair] in eukaryotes, the damage is repaired by _____, _____ and excising the wrongly incorporated base and replacing it with the correct nucleotide

A

recognition of the deformity caused by the mismatch, determining the template and non-template strand

153
Q

[DNA repair] types of double strand repair

A

Non-homologous end joining (NHEJ), Homology directed repair (HDR), Microhomology-mediated end joining (MMEJ)

154
Q

[DNA repair] type of double strand repair where it is a pathway that repairs double-strand breaks (DSB) in DNA

A

Non-homologous end joining (NHEJ)

155
Q

[DNA repair] in Non-homologous end joining (NHEJ), break ends are directly ligated without the need for a

A

homologous template

156
Q

[DNA repair] type of double strand repair where it requires s a homologous sequence to guide repair

A

Homology directed repair (HDR)

157
Q

[DNA repair] HDR is highly accurate and uses
the _______ as a template for accurate repair of the DSB

A

sister chromatid

158
Q

[DNA repair] type of double strand repair where . DSB breaks are sealed by microhomology (MH)-mediated base-pairing of DNA single strands

A

Microhomology-mediated end joining (MMEJ)

159
Q

[DNA repair] in Microhomology-mediated end joining (MMEJ), when the DSB breaks are sealed, this is followed by _____, _____ , and _____

A

nucleolytic trimming of DNA flaps, DNA gap filling, and DNA ligation

160
Q

[effects of DNA damage] _____ is the process in which a cell decides to kill itself

A

apoptosis

161
Q

[effects of DNA damage] is an irreversible arrest of cell proliferation while the cell maintains metabolic function (often
associated with cellular aging). State of dormancy. Cell does not divide anymore

A

senescence

162
Q

[effects of DNA damage] can cause cancer

A

unregulated cell division

163
Q

[clinical corelates] Cancer is a group of diseases in which cells are not responsive to the

A

normal restraints of growth

164
Q

[clinical corelates] The major causes of cancer are

A

radiation, chemicals, and viruses

165
Q

[clinical correlates] Radiation and chemicals cause damage to DNA, which, if not repaired rapidly, produces

A

mutations that can result in cancer

166
Q

[clinical correlates] Burning organic material (e.g., cigarettes) produces chemicals such as

A

benzopyrene

167
Q

[clinical correlates] benzopyrene that _____bind to the bases in DNA, producing mutations that lead to lung cancer

A

covalently

168
Q

[clinical correlates] Ultraviolet (UV) light, including that from the sun, produces _____ in DNA that lead to skin cancer.

A

pyrimidine dimers

169
Q

[clinical correlates] UV light leading to skin cancer, is a condition is particularly pronounced in people with _______ because their DNA repair system does not function normally

A

xeroderma pigmentosum (XP)

170
Q

[examples of mutations in other DNA repair systems] mismatch repair is defective in this disease

A

Hereditary nonpolyposis colorectal cancer (HNPCC)

171
Q

[examples of mutations in other DNA repair systems] a defect in a helicase necessary to unwind the DNA strands during replication

A

Bloom syndrome

172
Q

[examples of mutations in other DNA repair systems] a defect in repairing single- and double-strand breaks in DNA

A

Breast cancer

173
Q

[treatment of cancer] ____ prevents the conversion of dUMP to dTMP, reducing the level of thymine nucleotides required for DNA synthesis

A

5-fluorouracil (5-FU)

174
Q

[treatment of cancer] ____ prevents tile formation of tetrahydrofolate from its more oxidized precursors. As a result, the formation of both thymine for DNA synthesis and the purines for DNA and RNA syntheses is inhibited

A

Methotrexate

175
Q

[treatment of cancer] 5-fluorouracil (5-FU) prevents the conversion of _____, reducing the level of thymine nucleotides required for DNA synthesis.

A

dUMP to dTMP

176
Q

[treatment of cancer] 5-fluorouracil (5-FU) prevents the conversion of dUMP to dTMP, reducing the level of ______ required for DNA synthesis

A

thymine nucleotides

177
Q

[treatment of cancer] Methotrexate prevents tile formation of ______ from its more oxidized precursors. As a result, the formation of both thymine for DNA synthesis and the purines for DNA and RNA syntheses is
inhibited

A

tetrahydrofolate

178
Q

[treatment of cancer] Methotrexate prevents tile formation of tetrahydrofolate from its more oxidized precursors. What formations are inhibited?

A

thymine, purines

Biochemistry (5 decks)

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