lec 1: dna replication Flashcards
1
Q
is the process by which a double-stranded DNA molecule is copied to produce two identical DNA molecules
A
dna replication
2
Q
replication model of dna
A
semi-conservative
3
Q
base pairing allows each strand to serve as a template for a new strand
A
dna replication
4
Q
new strand is 1/2 parent template & 1/2 new DNA
A
semi-conservative
5
Q
types of dna replication models
A
semi-conservative
conservative
dispersive
6
Q
dNA replication occurs ____ in many locations along the very long ____ chromosomes.
A
simultaneously; eukaryotic
7
Q
an unwound and open region of a DNA helix where DNA replication occurs.
A
replication bubble
8
Q
unwinds part of DNA helix
A
DNA helicase
9
Q
the unwind strands are stabilized by
A
single-stranded binding proteins
10
Q
- builds daughter DNA strand
- adds new complementary bases
- needs a “starter” nucleotide to bond to
A
dna polymerase III
11
Q
Adding bases can only add nucleotides to ___ end of a growing DNA strand
A
3’ end
12
Q
they are synthesized by dna primase
A
rna primers
13
Q
synthesizes primers for rna transcription
A
rna primase
14
Q
makes double-stranded dna during replication
A
dna polymerase
15
Q
makes single-stranded rna during transcription
A
rna polymerase
16
Q
is an enzyme that synthesizes short RNA sequences called primers
A
dna primase
17
Q
synthesizes in the 5’ to 3’ direction
A
dna primase
18
Q
relieves additional coiling
A
topoisomerase
19
Q
dna polymerase adds to new rna primer to start new ____
A
okazaki fragment
20
Q
old rna primer is erased and replaced by
A
dna polymerase I
21
Q
nick sealing by
A
dna ligase
22
Q
what is the limit of dna polymerase III?
A
can only build unto 3’ end of an existing DNA strand
23
Q
- okazaki fragments
- joined by ligase
A
lagging strand
24
Q
spot welder enzyme
A
dna ligase
25
continuous synthesis
leading strand
26
- built by primase
- serves as starter sequence for DNA polymerase III
rna primer
27
removes sections of RNA primer and replaces with DNA nucleotides
dna polymerase I
28
but DNA polymerase I still can only build onto ____ of an existing DNA strand
3' end
29
a process by which chromosomes lose genetic material
chromosome erosion
30
all DNA polymerases can only add to 3' end of an existing DNA strand
chromosome erosion
31
loss of bases at 5' ends in every replication
chromosome erosion
32
problem with the end of the lagging strand:
progressive shortenin of chromosomal ends
33
what do you call the chromosomal ends at 3'?
3' G-strand hang
34
made of tandem repeats
telomeres
35
telomere of A. thaliana
TTTAGGG
36
telomere of human
TTAGGG
37
- repeating, non-coding sequences at the end of chromosomes (protective cap)
- limit to 50 cell divs
telomeres
38
- enzyme that extends telomeres
- can add DNA bases at 5' end
- different level of activity in different cells
- not active in all cells
telomerase
39
telomerase is the enzyme responsible for maintenance of the length of telomeres by addition of ___________
guanine-rich repetitive sequences
40
telomerase is exhibited in what cells?
gametes
stem cells
tumor cells
41
telomerase with bound rna template binds to what strand?
3' end of the parental strand
42
what is the direction of the telomere synthesis?
opposite to the direction of the dna polymerase
43
psychological stress is significantly associated with?
higher oxidative stress
lower telomerase activity
shorter telomere length
44
it takes E. coli _____ to copy its DNA
less than 1 hr
45
how many bp in its single chromosome of E. coli?
5 million bp
46
human cell copies its _____ bases & divide into daughter cells in only _______
6 billion; few hours
47
how many error in human replication?
1 error per 100 million bp
30 errors/cell cycle
48
who discovered dna polymerase III?
roger kornberg (son)
49
who discovered dna polymerase I?
arthur kornberg (father)
50
– 1000 bases/second
– main DNA builder
dna polymerase III
51
– 20 bases/second
– editing, repair & primer removal
dna polymerase I
52
a method for amplifying DNA segments using cycles of denaturation, annealing to primers, and DNA polymerase-directed DNA synthesis
polymerase chain reaction (PCR)
53
give the pcr components you need
dna sample/template
primers
nucleotides
taq dna polymerase
mix buffer
pcr tube
54
equipment used for pcr
thermal cycler
55
give the PCR steps and its corresponding temperature
denaturation (95)
annealing (55)
extension (72)
56
PCR step where strands separate
denaturating
57
PCR step where primers bind template
annealing
58
PCR step where new strand is synthesized
extension
59
DNA is heated to break the _____ between the two polynucleotide strands
two single-stranded DNA molecules serve as _____
hydrogen bonds
templates
60
short nucleotide sequences or _____ are mixed with the DNA and bind to complementary regions on single-stranded DNA
primers
61
this pcr step takes place at lower temperature
annealing
62
______ 20-30 nucleotides long, synthesized in the laboratory
primers
63
this is added to synthesize a complementary DNA strand
taq polymerase
64
Taq is a DNA polymerase from a bacterium found in hot springs
Thermus aquaticus
65
grouping of microorganisms or viruses based on their cell surface antigens
serovar
66
what is the gene that they amplified in Salmonella
invA gene
67
give 5 pcr applications
forensic practices
detection of mutations
pathogen presence test
detecting genetic disorders with heredity
cloning cDNA and nucleotide sequencing
68
process wherein a cell recognize and rectify damage to the DNA molecules
dna repair mechanism
69
give the two sources of dna damage, also give samples each
endogenous (ROS, replication errors, metabolism)
exogenous (UV, cig smoke, chemicals, ionizing radiation)
70
give the dna damage responses:
checkpoint activation
dna repair
apoptosis
71
replication stress
base mismatch
72
oxygen radicals
ionizing radiation
chemotherapeutics
single-strand break
73
ionizing radiation
chemotherapeutics
double-strand break
interstrand crosslinks
74
uv light
polycyclic aromatic hydrocarbons
bulky adducts
intrastrand crosslinks
75
give the spontaneous alterations or mutations that require dna repair
oxidation
hydrolysis
methylation
76
release of adenine or guanine bases
depurination
77
pre-dominant under acidic conditions and thermal fluctuations
depurination
78
– proofreads & corrects typos
– repairs mismatched bases
– removes abnormal bases
– repairs damage throughout life
– reduces error rate from 1 in 10,000 to 1 in 100 million bases
dna polymerase I
79
structure that forms when two adjacent pyrimidine nucleotides in a dna strand are covalently bonded together
dimer
80
what repair is needed for single-strand break and single-base damage?
base excision repair
81
what repair is needed for bulky lesions and crosslinks?
nucleotide excision repair
82
what repair is needed for base mismatch?
mismatch mediated repair
83
what repair is needed for double-strand break?
homologous recombination
non-homologous end-joining
84
repairs damage to a single base caused by what mutations?
base excision repair
deamination
alkylation
hydrolysis
oxidation
85
in BER, the damaged base is removed by what?
DNA glycosylase (an endonuclease)
86
the "missing tooth" is then recognized by an enzyme called __________
AP endonuclease
87
enzyme that cuts the phosphodiester bond
phosphodiesterase
88
they remove sugar phosphate
AP endonuclease and phosphodiesterase
89
recognizes bulky, cross- linking, helix-distorting lesions such as ______ and _____
nucleotide excision repair
pyrimidine dimers
6,4 photoproducts
90
this repair involves DNA helicase
nucleotide excision repair
91
skin cancer
xeroderma pigmentosum
92
xerdoerma pigmentosum is an autosomal ____ genetic disorder of DNA repair in which the ability to repair damage caused by ______ is deficient
recessive
ultraviolet (UV) light
93
xeroderma pigmentosum is due to failure in ___________ mechanism
nucleotide excision repair
94
corrects errors of DNA replication and recombination that result in mispaired (but undamaged) nucleotides
mismatch repair
95
mismatch repair corrects errors of _______ and __________ that result in mispaired (but _________) nucleotides
DNA replication and recombination
undamaged
96
give the 3 steps in mismatch repair
recognition (mismatches)
degradation of error (exonucleases)
synthesis (correct sequence)
97
highly conserved ____ and _____ homologs operate as protein dimers in mismatch repair (MMR)
MutS and MutL
98
inherited disorder that increases the risk of developing colorectal cancer, endometrial cancer, ovarian cancer, etc
due to mutations in MMR genes
lynch syndrome
hereditary non-polyposis colorectal cancer
99
repairs oxidative damage, abasic sites, or errors of DNA topoisomerase
single-strand break repair
100
what does single-strand break repair?
dna topoisomerase error
abasic site
oxidative damage
101
to protect the single-strand break repair, ____________ proteins coat the single strand and acts a shield
PARP1 (Poly (ADP-ribose) pol 1)
102
two types of repair for double-strand break
homologous recombination
non-homologous end-joining
103
precise repair pathway that requires a matching DNA sequence as a template
homologous recombination
104
it primarily uses the sister chromatid, a copy of the damaged DNA, for repair
homologous recombination
105
homologous recombination is active during what phases of cell division?
S
G2
M
106
simple and widely used mechanism
non-homologous end-joining
107
directly seals the broken ends of DNA without the need for a homologous DNA template
non-homologous end-joining
108
significance of DNA repair
preservation of genetic info
response to environmental stress
evolution and adaptation
prevention of diseases
protect against aging
contribution to immune system
