quiz 3.4 mutation, oncogenes Flashcards
1
Q
kinds of point mutation
A
synonymous
missense
nonsense
2
Q
point mutation can be caused by
A
insertion of transposon
abberant recombination
3
Q
repreats of simple tri- di- or tetranucleotide sequences
A
DNA microsatellites
4
Q
imino form of cytosine pairs with
A
adenine
5
Q
enol form of thymine pairs with
A
guanine
6
Q
imino form of adenine pairs with
A
cytosine
7
Q
enol form of guanine pairs with
A
thymine
8
Q
mutation of purine to purine or pyri to pyri
A
transition
9
Q
mutation of pyri to purine or vice versa
A
transversion
10
Q
mutation where altered codon corresponds to stop codon
A
nonsense
11
Q
depurination leads to
A
apurinic site
12
Q
depurination is repaired by
A
base excision repair
13
Q
occurs when bases become spontaneously ionized
A
mispair
14
Q
thymine analogue that has bromine at C5 instead of methyl group
A
5-bromouracil
15
Q
causes G-C to A-T or vice versa transitions
A
5-BU
16
Q
keto form of 5-BU pairs with
A
adenine
17
Q
ionized form of 5-BU pairs with
A
guanine
18
Q
base analog of adenine
A
2-aminopurine
19
Q
protonated 2-AP can mispair with
A
C
20
Q
rate of spontaneous mutations
A
10-6 to 10-11 per round of replication
21
Q
in streisinger model, when template strand slips, ____ results
A
deletion
22
Q
in streisinger model, when primer slips, ___ results
A
+1 insertion
23
Q
steps in restriction mapping
A
restriction endonucleases
separation
visulaization
24
Q
restriction endonucleases commonly cleave
A
palindromic segments
25
selectively cut the DNA in a sequence-specific manner
restriction endonuclease
26
presence of restriction endonucleaserestrict the growth of what
bacteriophage
27
type of RE commonly used
type 2
28
generated when cleavage is asymm
sticky/chosive/overlapping ends
29
generated when cleavage is symm
blunt ends
30
rest. fragments can base pair with each other if
sticky ends are complementary
31
two unrelated fragments can base pair with each other if
cleaved by same RE
32
the ends are linked by
DNA ligase
33
blunt ends are only linked by
T4 ligase
34
ligation of two DNA from differetn sources creates a
recombinant or chimeric DNA
35
gel for higher resolving power
polyacrylamide
36
more proous, resolves mixtures of larger fragments
agarose
37
detects specific DNA fragments among thousands of molecules
southern blot
38
detects RNA fragments instead of DNA
northern blot
39
detects proteins, used with southern blot
western blot
40
blotting to study protein-DNA interactions
southwestern blot
41
steps for souther blot
separate
laying of gel onto nitrocelulose
labeling
reading
42
methods for determining DNA structure and relation to gene expression
Maxam and Gilbert (chemical)
| Sanger (manual enzymatic)
43
in Maxam and Gilbert, ssDNA is 32P-labeled where
5'-hydroxy end
44
Maxam and Gilbert uses what separation technique
PAGE
45
Maxan and Gilbert can sequence stretches of DNA containing around how many bases
250 bases
46
procedure of choice for DNA sequencing
Sanger
47
Sanger can sequence up to how many bases
400
48
Sanger employs what
controlled interruption of enzymatic replication
49
in Sanger, this required to introduce segment into host cell where complementary DNA is synthesized
vector
50
______ of each base is mixed with 4 dNTPs together with e. coli DNA polymerase
2,3-dideoxynucleotide
51
dNTP when incorporated into the growing DNA strand causes what
strand to stop
52
commonly used cloning vectors
```
plasmid
bacteriophage lambda
cosmids
ssBacteriohage vector
expresson vector
```
53
genes within a plasmid
for antibiotic resistance
restriction sites (cloning sites)
origin of replication
54
double stranded, closed mini-circular extra-chromosomal DNA containing 1-200 kbp, capable of independent replication
plasmid
55
plasmid occurs naturally in some bacteria as
accessory chromosomes
56
can destroy its host or become part of its host, bacterial virus containing a double-stranded linear DNA
bacter lambda
57
ideal cloning vectors for DNA up to 20 kbp, usually for eukaryotic
bacte lambda
58
plasmids that contain DNA sequences from baceriophage with combined features of plasmids and phages
cosmids
59
DNA sequences found in cosmids
cos site
60
cosmids are usually used for
large segments of DNA
61
cloning vector that does not kill its host
ss bacte vector
62
filamentous virus 900 nm long and 9 nm wide
M13 phage
63
vector in which the protein coded by the gene introduced by recombinant DNA technology is actually synthesized , vector with very active inducible promoter regions
expresson vector
64
recombinant DNA molecule is basically what
vector with DNA insert
65
process where recombinant piece is then introduced into a suitable host
transformation/transfection
66
tranformation or transfection can be by what methods
```
calcium chloride tx and heat shock transformation
electroporation
calcium-phosphate-mediated
protoplast fusion by PEG
microinjection
```
67
recombinant DNA in the host cells are screened by
selection of antibiotic-resistant colonies (ampicillin-tetracycline)
gal-x
ID of individual phage plaques
68
complete collection of genomic clones in bacterial host cells comprise a _____
DNA library
69
process in which cloned DNA is characterized using agarose gel electrophoresis to check for the gene of interest
library screening
70
how to acquire DNA from a library
lyse cells and cleave plasmids with specific RE
71
in constructing recombinant DNA, the signal or spot on the autoradiogram represent the what
plaques or colonies that contain the gene of interest
72
steps/features in recombiannt DNA construction and coning
vector
construction
cDNA cloning
73
cDNA is synthesized from and how
mRNA thru rev. transcription
74
enzymatic amplification of specific DNA sequences
PCR
75
requiremetns for PCR
DNA to be amplifeid
two oligo primers complementary to the DNA strand
all four dNTPs
thermo-stable DNA polymerase (usually Taq polymerase)
76
basic steps in PCR
mixing
strand separation
annealing
synthesis
77
how is the DNA separated during PCR
heating to 90-95degC for 15 secs
78
how is annealing done during PCR
abruptly cooled to 54 to 60degC
79
the DNA polymerase extends the chains at around ___degC because this is the ____________
72degC
| optimum temp for Taq polymerase
80
the repeaing cycles or steps 2-4 of PCR causing the number of the target to rise to ___
2 raised to n, n number of cycles
81
6-4 PPS are formed by
C6 bind covanlently to c4 of another pyrimidine
82
5-6 PPs are altered by UV radiation to form
CPDs or 6-4 PP lesions
83
CPD lesions comprise of ___ of all UV dmaage while 6-4 PP lesions comrpise _______
70-80%
| 20-30%
84
Which is more mutagenic? CPD or 6-4 lesions
6-4 lesions
CPD more repaired efficiently
85
The phosphates in the DNA backbone interact with the photolyase by forming
Salt bridges and hydrogen bonds
86
photolyase repairs dna damage in a method called
Phtoreactivation
87
CPD is formed when
66 cova bind to C5 of another pyrimidine
88
CPD has 2 activities
Light indep and dep
89
The photolyase during the light indep rxn causes what
CPD to flip into the active site
90
The photolyase cause what during th light dep rxn
Fadh donates electron to CPD disrupting the 6-5 bond
91
Bases altered by methylatin ir ethylating rhts are primarily what
Purine
92
Mos tmutagenic methylating agent
06-alkylguanine
93
06-alkylguanine us highly mutagenic bcoz
Modified base pairs with thymine
Causes GC-AT mutation
94
Rapir of the methylating or ethylating damage reuqires what enzyme
06-alkylguanine transferase
95
Action of 06-alkylguanine alkyltransferase
Transfers methyl or ethyl group from 06-ethylguanine or ethylguanine residue to cysteine
96
Remove the damage base and repair it
Base excision repair
97
Can BER repair minir damages
Yes pak diba bongga
98
BER mechanism
Glycosylase recognize damaged, remove
AP endonuclease cleaves abasic sugarphos backbone
Exinuc, DNA polym, ligase work to conplete repair
99
Damaged DAN section is excised followed by actijb of DNA polym and the ligase to regen closed duplex at the site
Nucleotide excision repair
100
The first step in NER uses enzymes coded by
uvrA
uvrB
uvrC
101
product of uvrD presumably used to unwind and removes excised olignucl
helicase II
102
the second excision repair system requires what mechanism
DNA-N-glycosylase mechanism
103
the DNA-N-glycosylase mechanism recognized 5' thymne in a dimer and cleaves the glycosidic bond creating what
apryrimidic site
104
family of dses in which one or more enzymes of the excision pathway are deficient
xeroderma pigmentosum
105
in XP patient, ultraviolet DNA damage can be repaired by
intro of bifunctional glycosylase-endonuclease specified phage T4
106
DNA damages can be repaired by recombination mechanism caled
sister-strand exchange
107
protein that binds to DNA double-strand break ends and is required for nonhomologous end joining (NHEJ) pathway of DNA repair
Ku
108
Ku is required in what pathway
nonhomologous end joining
109
recBCD processes DNA to form
3' ssDNA tail
110
part of recBCD pathway that promotes strand invasion
recA
111
part of the recBCS pathway that catalyzes branch migration
ruvAB
112
part of the recBCD pathwy that catalyzes Holliday junction resolution
ruvC
113
processes that can repair gaps
recombinational repair/daughter strand gap repair
| SOS rpair/error prone repair
114
the recombinational repair/daughter strand gap repair
| SOS rpair/error prone repair are dependent on what enzyme
recA
115
two properties of recA
catalyzes strand pairing or assimilation
| genetic regulator
116
the adaptve response due to recA to metabolic stresses is called
SOS response
117
joining of two different DNAs by homologous base pairing with each other
strand assimilation
118
metabolic alarm system that helps the cell to save itself in the presence of potentially lethal stresses
bacterial SOS response
119
inducers of SOS response
UV irradiation
thymine starvation
tx with certain DNA-modifying rgts such as cross linker mitomycin C
inactivation of genes essential to DNA replication
120
SOS responses include
mutagenesis
filamentation
activated excision repair
activation of latent bacteriophage genoes
121
small, solid supports onto which the sequences from thousands of different genes are immobilized, attached or fixed
DNA microarrays
122
the supports are usually ___ but may be siliconchips or nylon membranes
glass microscope slides
123
two major application of DNA microarray
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
recombinant dna tech can be used in production of what prtoeins
```
somatostatin
insulin
factor 8
colony-stimulating factor
interferon
GH
EPO
tPA
IL
vacines
```
125
detection of DNA polymorphism can be done by
restriction fragment length polymorphism
| analysis of variable number tandem repeats by probe hybridization
126
cancer cells proliferate rapidly and are unresponsive to antiproliferation because of loss of
contact inhibition
127
group of genes which predispose to spcific forms of neoplasia
oncogenes
128
regulate normal cell proliferation, comprise a set of related distinct normal genes that can be transformed by various factors
proto-oncogenes
129
encode proteins that normally suppress cell growth but which are inactivated when altered by mutations
tumor suppressor gene
130
act by causing mutation in the regulatory region of a gene, increasing the rate of production of the prto-oncogene protein
radiation and chemmical carcinogens
131
aside from causing a mutation int eh regulatory protion of a gene, ano pa action ng radiation at chemical carcinogens
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
characteristics of a cancer cell
```
proliferate rapidly
diminished growth control
loss of contact i hib
invasion and metastasis
selfsufficiency
unresponsive to antiprolif
stimulate angiogenesis
evade apoptosis
```
133
mutation in the coding region causes
production of hyperactive protein
134
muation in the promoter region causes
excessive expression
135
___ of proto-oncogenes allows more protein to be produced
amplification
136
gene rearrangeent of protooncogenes may be caused by
transposition
| translocation
137
induce various cellular responses, pure signal and no metabolic purpose
growth hormone
138
samples of GHs
PDGF
EGF
CSF
insulin-like growth factor`
139
when may signal from growth hormone
when bound to receptor
140
classes of growth controlling proteins
GH
GFR
intracell transducers
nuclear transcription factors
141
classes of second messenger/intracellular transsducers
protein-tyrosine kinase
protein-serine/threonine kinase
ras-proteins
phospholipase C-related
142
action of tyrosine kinase second messenger
phosphorylates tyrosine residues
143
sample ng tyrosine kinases
src
abl
fps
144
serine/theronine kinase action
prhosphorylates ser or thr residues
145
sample ng ser/thr kinase
mos
146
guanine nucleotide proteins with GTPase activity taht binds GTP
ras proteins
147
action of ras protein
binds GTP
