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MedBiochem > quiz 3.4 mutation, oncogenes > Flashcards

quiz 3.4 mutation, oncogenes Flashcards

1
Q

kinds of point mutation

A

synonymous
missense
nonsense

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2
Q

point mutation can be caused by

A

insertion of transposon

abberant recombination

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3
Q

repreats of simple tri- di- or tetranucleotide sequences

A

DNA microsatellites

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4
Q

imino form of cytosine pairs with

A

adenine

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5
Q

enol form of thymine pairs with

A

guanine

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6
Q

imino form of adenine pairs with

A

cytosine

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7
Q

enol form of guanine pairs with

A

thymine

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8
Q

mutation of purine to purine or pyri to pyri

A

transition

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9
Q

mutation of pyri to purine or vice versa

A

transversion

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10
Q

mutation where altered codon corresponds to stop codon

A

nonsense

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11
Q

depurination leads to

A

apurinic site

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12
Q

depurination is repaired by

A

base excision repair

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13
Q

occurs when bases become spontaneously ionized

A

mispair

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14
Q

thymine analogue that has bromine at C5 instead of methyl group

A

5-bromouracil

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15
Q

causes G-C to A-T or vice versa transitions

A

5-BU

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16
Q

keto form of 5-BU pairs with

A

adenine

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17
Q

ionized form of 5-BU pairs with

A

guanine

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18
Q

base analog of adenine

A

2-aminopurine

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19
Q

protonated 2-AP can mispair with

A

C

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20
Q

rate of spontaneous mutations

A

10-6 to 10-11 per round of replication

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21
Q

in streisinger model, when template strand slips, ____ results

A

deletion

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22
Q

in streisinger model, when primer slips, ___ results

A

+1 insertion

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23
Q

steps in restriction mapping

A

restriction endonucleases
separation
visulaization

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24
Q

restriction endonucleases commonly cleave

A

palindromic segments

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25
Q

selectively cut the DNA in a sequence-specific manner

A

restriction endonuclease

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26
Q

presence of restriction endonucleaserestrict the growth of what

A

bacteriophage

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27
Q

type of RE commonly used

A

type 2

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28
Q

generated when cleavage is asymm

A

sticky/chosive/overlapping ends

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29
Q

generated when cleavage is symm

A

blunt ends

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30
Q

rest. fragments can base pair with each other if

A

sticky ends are complementary

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31
Q

two unrelated fragments can base pair with each other if

A

cleaved by same RE

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32
Q

the ends are linked by

A

DNA ligase

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33
Q

blunt ends are only linked by

A

T4 ligase

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34
Q

ligation of two DNA from differetn sources creates a

A

recombinant or chimeric DNA

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35
Q

gel for higher resolving power

A

polyacrylamide

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36
Q

more proous, resolves mixtures of larger fragments

A

agarose

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37
Q

detects specific DNA fragments among thousands of molecules

A

southern blot

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38
Q

detects RNA fragments instead of DNA

A

northern blot

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39
Q

detects proteins, used with southern blot

A

western blot

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40
Q

blotting to study protein-DNA interactions

A

southwestern blot

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41
Q

steps for souther blot

A

separate
laying of gel onto nitrocelulose
labeling
reading

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42
Q

methods for determining DNA structure and relation to gene expression

A

Maxam and Gilbert (chemical)

Sanger (manual enzymatic)

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43
Q

in Maxam and Gilbert, ssDNA is 32P-labeled where

A

5’-hydroxy end

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44
Q

Maxam and Gilbert uses what separation technique

A

PAGE

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45
Q

Maxan and Gilbert can sequence stretches of DNA containing around how many bases

A

250 bases

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46
Q

procedure of choice for DNA sequencing

A

Sanger

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47
Q

Sanger can sequence up to how many bases

A

400

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48
Q

Sanger employs what

A

controlled interruption of enzymatic replication

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49
Q

in Sanger, this required to introduce segment into host cell where complementary DNA is synthesized

A

vector

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50
Q

______ of each base is mixed with 4 dNTPs together with e. coli DNA polymerase

A

2,3-dideoxynucleotide

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51
Q

dNTP when incorporated into the growing DNA strand causes what

A

strand to stop

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52
Q

commonly used cloning vectors

A 
plasmid
bacteriophage lambda
cosmids
ssBacteriohage vector
expresson vector
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53
Q

genes within a plasmid

A

for antibiotic resistance
restriction sites (cloning sites)
origin of replication

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54
Q

double stranded, closed mini-circular extra-chromosomal DNA containing 1-200 kbp, capable of independent replication

A

plasmid

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55
Q

plasmid occurs naturally in some bacteria as

A

accessory chromosomes

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56
Q

can destroy its host or become part of its host, bacterial virus containing a double-stranded linear DNA

A

bacter lambda

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57
Q

ideal cloning vectors for DNA up to 20 kbp, usually for eukaryotic

A

bacte lambda

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58
Q

plasmids that contain DNA sequences from baceriophage with combined features of plasmids and phages

A

cosmids

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59
Q

DNA sequences found in cosmids

60
Q

cosmids are usually used for

A

large segments of DNA

61
Q

cloning vector that does not kill its host

A

ss bacte vector

62
Q

filamentous virus 900 nm long and 9 nm wide

63
Q

vector in which the protein coded by the gene introduced by recombinant DNA technology is actually synthesized , vector with very active inducible promoter regions

A

expresson vector

64
Q

recombinant DNA molecule is basically what

A

vector with DNA insert

65
Q

process where recombinant piece is then introduced into a suitable host

A

transformation/transfection

66
Q

tranformation or transfection can be by what methods

A 
calcium chloride tx and heat shock transformation
electroporation
calcium-phosphate-mediated
protoplast fusion by PEG
microinjection
67
Q

recombinant DNA in the host cells are screened by

A

selection of antibiotic-resistant colonies (ampicillin-tetracycline)
gal-x
ID of individual phage plaques

68
Q

complete collection of genomic clones in bacterial host cells comprise a _____

A

DNA library

69
Q

process in which cloned DNA is characterized using agarose gel electrophoresis to check for the gene of interest

A

library screening

70
Q

how to acquire DNA from a library

A

lyse cells and cleave plasmids with specific RE

71
Q

in constructing recombinant DNA, the signal or spot on the autoradiogram represent the what

A

plaques or colonies that contain the gene of interest

72
Q

steps/features in recombiannt DNA construction and coning

A

vector
construction
cDNA cloning

73
Q

cDNA is synthesized from and how

A

mRNA thru rev. transcription

74
Q

enzymatic amplification of specific DNA sequences

75
Q

requiremetns for PCR

A

DNA to be amplifeid
two oligo primers complementary to the DNA strand
all four dNTPs
thermo-stable DNA polymerase (usually Taq polymerase)

76
Q

basic steps in PCR

A

mixing
strand separation
annealing
synthesis

77
Q

how is the DNA separated during PCR

A

heating to 90-95degC for 15 secs

78
Q

how is annealing done during PCR

A

abruptly cooled to 54 to 60degC

79
Q

the DNA polymerase extends the chains at around ___degC because this is the ____________

A

72degC

optimum temp for Taq polymerase

80
Q

the repeaing cycles or steps 2-4 of PCR causing the number of the target to rise to ___

A

2 raised to n, n number of cycles

81
Q

6-4 PPS are formed by

A

C6 bind covanlently to c4 of another pyrimidine

82
Q

5-6 PPs are altered by UV radiation to form

A

CPDs or 6-4 PP lesions

83
Q

CPD lesions comprise of ___ of all UV dmaage while 6-4 PP lesions comrpise _______

A

70-80%

20-30%

84
Q

Which is more mutagenic? CPD or 6-4 lesions

A

6-4 lesions

CPD more repaired efficiently

85
Q

The phosphates in the DNA backbone interact with the photolyase by forming

A

Salt bridges and hydrogen bonds

86
Q

photolyase repairs dna damage in a method called

A

Phtoreactivation

87
Q

CPD is formed when

A

66 cova bind to C5 of another pyrimidine

88
Q

CPD has 2 activities

A

Light indep and dep

89
Q

The photolyase during the light indep rxn causes what

A

CPD to flip into the active site

90
Q

The photolyase cause what during th light dep rxn

A

Fadh donates electron to CPD disrupting the 6-5 bond

91
Q

Bases altered by methylatin ir ethylating rhts are primarily what

92
Q

Mos tmutagenic methylating agent

A

06-alkylguanine

93
Q

06-alkylguanine us highly mutagenic bcoz

A

Modified base pairs with thymine

Causes GC-AT mutation

94
Q

Rapir of the methylating or ethylating damage reuqires what enzyme

A

06-alkylguanine transferase

95
Q

Action of 06-alkylguanine alkyltransferase

A

Transfers methyl or ethyl group from 06-ethylguanine or ethylguanine residue to cysteine

96
Q

Remove the damage base and repair it

A

Base excision repair

97
Q

Can BER repair minir damages

A

Yes pak diba bongga

98
Q

BER mechanism

A

Glycosylase recognize damaged, remove

AP endonuclease cleaves abasic sugarphos backbone

Exinuc, DNA polym, ligase work to conplete repair

99
Q

Damaged DAN section is excised followed by actijb of DNA polym and the ligase to regen closed duplex at the site

A

Nucleotide excision repair

100
Q

The first step in NER uses enzymes coded by

A

uvrA
uvrB
uvrC

101
Q

product of uvrD presumably used to unwind and removes excised olignucl

A

helicase II

102
Q

the second excision repair system requires what mechanism

A

DNA-N-glycosylase mechanism

103
Q

the DNA-N-glycosylase mechanism recognized 5’ thymne in a dimer and cleaves the glycosidic bond creating what

A

apryrimidic site

104
Q

family of dses in which one or more enzymes of the excision pathway are deficient

A

xeroderma pigmentosum

105
Q

in XP patient, ultraviolet DNA damage can be repaired by

A

intro of bifunctional glycosylase-endonuclease specified phage T4

106
Q

DNA damages can be repaired by recombination mechanism caled

A

sister-strand exchange

107
Q

protein that binds to DNA double-strand break ends and is required for nonhomologous end joining (NHEJ) pathway of DNA repair

108
Q

Ku is required in what pathway

A

nonhomologous end joining

109
Q

recBCD processes DNA to form

A

3’ ssDNA tail

110
Q

part of recBCD pathway that promotes strand invasion

111
Q

part of the recBCS pathway that catalyzes branch migration

112
Q

part of the recBCD pathwy that catalyzes Holliday junction resolution

113
Q

processes that can repair gaps

A

recombinational repair/daughter strand gap repair

SOS rpair/error prone repair

114
Q

the recombinational repair/daughter strand gap repair

SOS rpair/error prone repair are dependent on what enzyme

115
Q

two properties of recA

A

catalyzes strand pairing or assimilation

genetic regulator

116
Q

the adaptve response due to recA to metabolic stresses is called

A

SOS response

117
Q

joining of two different DNAs by homologous base pairing with each other

A

strand assimilation

118
Q

metabolic alarm system that helps the cell to save itself in the presence of potentially lethal stresses

A

bacterial SOS response

119
Q

inducers of SOS response

A

UV irradiation
thymine starvation
tx with certain DNA-modifying rgts such as cross linker mitomycin C
inactivation of genes essential to DNA replication

120
Q

SOS responses include

A

mutagenesis
filamentation
activated excision repair
activation of latent bacteriophage genoes

121
Q

small, solid supports onto which the sequences from thousands of different genes are immobilized, attached or fixed

A

DNA microarrays

122
Q

the supports are usually ___ but may be siliconchips or nylon membranes

A

glass microscope slides

123
Q

two major application of DNA microarray

A

identification of sequence
determination of expression level of genes of one sample or comparing gene transcription in two or more different kinds of cells

124
Q

recombinant dna tech can be used in production of what prtoeins

A 
somatostatin
insulin
factor 8
colony-stimulating factor
interferon
GH
EPO
tPA
IL
vacines
125
Q

detection of DNA polymorphism can be done by

A

restriction fragment length polymorphism

analysis of variable number tandem repeats by probe hybridization

126
Q

cancer cells proliferate rapidly and are unresponsive to antiproliferation because of loss of

A

contact inhibition

127
Q

group of genes which predispose to spcific forms of neoplasia

128
Q

regulate normal cell proliferation, comprise a set of related distinct normal genes that can be transformed by various factors

A

proto-oncogenes

129
Q

encode proteins that normally suppress cell growth but which are inactivated when altered by mutations

A

tumor suppressor gene

130
Q

act by causing mutation in the regulatory region of a gene, increasing the rate of production of the prto-oncogene protein

A

radiation and chemmical carcinogens

131
Q

aside from causing a mutation int eh regulatory protion of a gene, ano pa action ng radiation at chemical carcinogens

A

produce mutation in the coding protion of the oncogene that results in the synth of a protein os slightly different amino acid compos capable of transforming the cell

132
Q

characteristics of a cancer cell

A 
proliferate rapidly
diminished growth control
loss of contact i hib
invasion and metastasis
selfsufficiency
unresponsive to antiprolif
stimulate angiogenesis
evade apoptosis
133
Q

mutation in the coding region causes

A

production of hyperactive protein

134
Q

muation in the promoter region causes

A

excessive expression

135
Q

___ of proto-oncogenes allows more protein to be produced

A

amplification

136
Q

gene rearrangeent of protooncogenes may be caused by

A

transposition

translocation

137
Q

induce various cellular responses, pure signal and no metabolic purpose

A

growth hormone

138
Q

samples of GHs

A

PDGF
EGF
CSF
insulin-like growth factor`

139
Q

when may signal from growth hormone

A

when bound to receptor

140
Q

classes of growth controlling proteins

A

GH
GFR
intracell transducers
nuclear transcription factors

141
Q

classes of second messenger/intracellular transsducers

A

protein-tyrosine kinase
protein-serine/threonine kinase
ras-proteins
phospholipase C-related

142
Q

action of tyrosine kinase second messenger

A

phosphorylates tyrosine residues

143
Q

sample ng tyrosine kinases

A

src
abl
fps

144
Q

serine/theronine kinase action

A

prhosphorylates ser or thr residues

145
Q

sample ng ser/thr kinase

146
Q

guanine nucleotide proteins with GTPase activity taht binds GTP

A

ras proteins

147
Q

action of ras protein

MedBiochem (16 decks)

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