DNA Replication Flashcards
1
Q
What composes a DNA polymer?
A
nucleotide monomers
2
Q
Describe the structure of a DNA nucleotide
A
a 5-carbon sugar (deoxyribose)
one of four nitrogenous bases (A, G, C, T)
up to 3 phosphate groups
3
Q
What is the sugar in DNA nucleotides?
A
deoxyribose
4
Q
How many sugars does the deoxyribose have?
A
5
5
Q
What is bonded to the 1’ carbon of the deoxyribose?
A
a nucleotide base
6
Q
What is bonded to the 3’ carbon of the deoxyribose?
A
a hydroxyl group
7
Q
What is bonded to the 5’ carbon of the deoxyribose?
A
1-3 phosphates
8
Q
What are the 2 types of DNA bases?
A
pyrimidines
purines
9
Q
Describe the structure of pyrimidine
A
a single ring
10
Q
Describe the structure of purines
A
a double ring
11
Q
Which nitrogenous bases are pyrimidines?
A
C and T
12
Q
Which nitrogenous bases are purines?
A
A and G
13
Q
What assembles nucleotides into a polymer?
A
DNA polymerase
14
Q
How does DNAP assemble a polymer?
A
DNAP catalyzes the formation of covalent bonds between the 3’ OH and 5’ phosphate group
15
Q
What is the name of the covalent bond that forms between the 3’ OH and 5’ phosphates?
A
phosphodiester bonds
16
Q
What type of backbone does each polynucleotide chain have?
A
a sugar-phosphate backbone
17
Q
T or F: the two polynucleotide chains are complementary
A
True
18
Q
T or F: the two polynucleotide chains are antiparallel
A
True
19
Q
Which nitrogenous bases pair together in complementary pairing?
A
C - G
A - T
20
Q
What are 3 attributes of DNA replication?
A
- each strand of the parental DNA molecule remains intact during replication
- each parental strand serves as a template for formation of a daughter strand
- result = formation of 2 identical daughter duplexes composed of one parental and one daughter strand
21
Q
T or F: the covalent bonds holding monomers together are broken during replication
A
FALSE they’re never broken
22
Q
T or F: each strand of the parental DNA molecule is altered during replication
A
false, they remain intact
23
Q
What do the parental strands serve during replication?
A
as a template for a daughter strand
24
Q
Describe a daughter DNA strand
A
produced by DNA replication of the parental DNA and is complementary and antiparallel
25
When does DNA replication occur (in the cell cycle)?
In S phase (DNA synthesis)
26
Which 6 macromolecules are involved in DNA replication?
```
helicase
single strand binding protein
DNAPIII
Primase
DNAPI
Ligase
```
27
Where does DNA replication start?
the origins of replication (ori)
28
How does replication start?
proteins recognize ori DNA sequences and separate DNA strands to form a replication bubble
29
How does a replication bubble form?
When proteins recognize the ori DNA sequences and separate the DNA strands
30
What direction does DNA replication occur in relation to the origin?
bi-directionally (both ways)
31
What direction are strands always replicated? And what end are all nucleotides added to?
5' - 3'
nucleotides always added at 3'
32
What occurs at each end of a replication bubble?
replication forks
33
What enzyme functions at the replication forks? What does it do?
helicase unwinds and separates DNA strands
34
What holds the DNA strands apart after they are separated and until they are replicated?
Single Stranded Binding Proteins (SSBPs)
35
What happens once a single stranded DNA template forms?
Primase synthesizes a short RNA primer
36
What is the function of primase?
it synthesizes a short RNA primer after a single stranded DNA template forms
37
What is the main enzyme of DNA replication?
DNAPIII
38
What does DNAPIII require to add nucleotides?
a primer
39
What is the function of DNAPIII?
catalyzes synthesis by elongating RNA primers by adding nucleotides complementary to template strand
40
What direction does DNAPIII catalyze synthesis?
5' - 3'
41
What kind of nuclease activity does DNAPIII have?
3' - 5' exonuclease
42
What direction does DNAPIII have exonuclease activity?
3' to 5'
43
What is the purpose of the 3' - 5' exonuclease activity of DNAPIII?
it allows it to remove mismatched bases
44
What is the function of DNAPI?
it removes RNA primers and fills in the resulting gap with DNA
45
What type of nuclease activity does DNAPI have?
5' - 3' exonuclease activity
THIS IS UNCLEAR IN SLIDES?
46
What direction does DNAPI catalyze chain growth?
5' - 3'
47
What occurs after DNAPI removes the RNA primer and fills in the gap with DNA?
DNA ligase links the DNA fragments together by catalyzing the formation of phosphodiester bonds
48
Which enzyme links DNA fragments together after DNAPI adds the DNA?
DNA Ligase
49
As the DNA strands unwind, how many template strands are there?
2
50
Describe the leading strand
one of the template strands that is elongated in the same direction of the unwinding DNA
(5' to 3')
51
Describe the lagging strand
one of the template strands that elongates away from the replication fork (3'- 5')
52
How is the leading strand synthesized?
continuously
53
How many RNA primers does the synthesis of the leading strand require?
one RNA primer
54
How is the lagging strand synthesized?
discontinuously
55
How many RNA primers does the synthesis of the lagging strand require?
many RNA primers
56
Describe Okazaki fragments
the short fragments synthesized on lagging strand
57
How are Okazaki fragments linked together?
by Ligase
58
How many origin of replications do prokaryotes have?
1
59
Describe prokaryotic chromosomes
they have only one small circular chromosome
60
Describe eukaryotic chromosomes
they have long linear chromosomes
61
How many origins or replication does each eukaryotic chromosome have?
many
62
What happens if DNAPI is not properly functioning and the DNA cannot be filled in after the primer is removed from the leading strand?
chromosomes are shortened = loss of DNA sequences at the end of chromosomesc
63
How can loss of DNA sequences at the end of chromosomes be prevented?
by adding multiple copies of simple noncoding sequences to DNA at the chromosome ends
64
Describe telomerase
an enzyme that adds multiple copies of simple noncoding sequences to 3' ends of DNA molecules
65
Which end of DNA molecules does telomerase add copies of noncoding sequences?
3' end
66
Describe telomeres
The regions on a DNA molecule that form when telomerase adds multiple copies of noncoding sequences to the 3' ends
67
Which cells is telomerase functional in?
germ line cells
68
What would happen to somatic cells each time they divide if telomerase wasn't present?
their chromosomes would shorten with each division
69
How do telomeres preserve chromosome integrity?
they associate with proteins to form protective caps that prevent the degradation of linear chromosomes
70
What are the 5 essential characteristics known about DNA before it was identified as the hereditary molecule?
1. localized to the nucleus and a component of chromosomes
2. present in stable form in cells
3. complex and contains info needed for structure, function, development and reproduction of an organism
4. ability to accurately replicate itself so that daughter cell contains same information as parent cells
5. mutable - undergoes a low rate of mutants that introduce genetic variation which is the basis for evolutionary change
71
Where is DNA localized? What is it a component of?
to the nucleus
component of chromosomes
72
In what form is DNA present in cells?
stable form
73
what information does DNA contain?
info for structure, function, development and reproduction of an organism
74
T or F: DNA can accurately replicate itself so that the daughter cells have the same info as the parent cells
true
75
What is the basis for evolutionary change?
the low rate of mutations of DNA that introduce genetic variation
76
What did Griffith's experiment discover?
the process of transformation
77
Describe transformation
the genetic alteration of a cell by the uptake of isolated pieces of external DNA
DNA in environment is taken into bacterial cell and incorporated into its genome
78
What organisms did Griffith use in his 1928 experiment?
Pneumococcal bacteria and mice
79
What two strains of Pneumococcal bacteria did Griffith identify in his 1928 experiment?
S (smooth) strain
R (rough) strain
80
In Griffith's experiment, what did the two Pneumococcal bacterial strains cause in the mice?
smooth (S) = caused pneumonia in mice
rough (R) = did not cause pneumonia in mice
81
What was Griffith's experiment?
he infected mice with Pneumococcal bacteria to determine whether the mice could take up the bacterial DNA and get pneumonia
82
What happened to the mice that were infected with Pneumococcal strain S?
they got pneumonia and died
83
What happened to the mice that were infected with Pneumococcal live strain R OR heat-killed strain S?
they survived
84
What happened to the mice infected with heat-killed strain S AND live strain R?
they developed pneumonia and died
85
What was recovered from the mice that were injected with heat killed strain S AND live strain R?
live type S bacteria
86
What can be concluded from the Griffith's experiment?
the hereditary molecule (DNA) in mice 'transformed' the live R strain bacteria into live S strain bacterial
87
Describe the experiment by Avery, MacLeod, and McCarty
they infected mice with extracts from heat-killed S bacteria and live R bacteria
88
What was the purpose of the extract from heat-killed S bacteria? (Avery, MacLeod, McCarty)
it was divided into aliquots and treated to destroy either DNA, RNA, proteins, lipids, polysaccharides
89
In Avery et al., study, what was injected into the mice?
one of the aliquots with treated heat-killed S bacteria and live R bacteria
90
What were the results of the Avery et al. study?
all aliquots killed the mice except the one with destroyed DNA
91
What was the significance of the experiment by Avery, MacLeod and McCarty?
they identified DNA as the most likely hereditary molecule
92
What did Hershey and Chase's experiment show?
that DNA is responsible for bacteriophage infection of bacterial cells
93
What are bacteriophages?
viruses that infect bacteria
94
What was unique about the bacteriophages used in Hershey and Chase's experiment?
the phages had a protein shell with a tail segment that attaches to the host cell and a head that contains DNA
95
Describe the phages used in the Hershey and Chase experiment
the phages have a protein shell with a tail segment that attaches to the host cell
and a head that contains DNA
96
How do phages reproduce?
by infecting bacterial hosts
97
When does phage infection begin in bacteria?
when the phage injects DNA into the bacterial cell and leaves its protein shell on the surface
98
What happens after the phage has injected DNA into the bacterial cell and leaves its protein shell?
the phage DNA replicates in the bacterium and produces proteins that are assembled into progeny phage
99
How are progeny phage produced?
the phage DNA replicates in the bacterium and produces proteins
these proteins are assembled into the progeny phage
100
How are progeny phage released from the host cell?
lysis of the host cell
101
What does protein contain large amounts of?
sulfur
102
What does protein contain almost nothing of?
phosphorous
103
What does DNA contain large amounts of?
phosphorous
104
What does DNA contain none of?
sulfur
105
How did Hershey and Chase collect the results for their experiment?
they labelled phage protein with 35^S or phage DNA with 32^P and traced them during the course of infection
106
How did Hershey and Chase separate the empty phage particles from the injected bacteria?
infection agitation by using a blender
107
What was detected by Hershey and Chase in the protein labelling experiment?
radioactivity in the empty phage particles
108
What was detected by Hershey and Chase in the DNA labelling experiment?
radioactivity in the infected bacteria
109
Who identified the secondary helical structure of DNA?
Franklin
110
Who modelled the secondary helical structure of DNA?
Watson and Crick
111
Describe the structure of DNA
composed of four kinds of nucleotides joined by covalent phosphodiester bonds with 2 polynucleotide chains that come together to form a double helix
112
What is the type of bond that joins nucleotides to make a DNA polymer?
covalent phosphodiester bonds
113
How many competing models of DNA replication are there?
3
114
What is common across the 3 competing models of DNA replication?
the idea that the original strands of the duplex act as templates for the daughter strand synthesis
115
What are the 3 models of DNA replication?
semiconservative
conservative
dispersive
116
Describe semiconservative DNA replication
each daughter duplex contains one parental and one daughter strand
117
Describe conservative DNA replication
one daughter duplex contains both parental strands and the other daughter duplex contains both daughter strands
118
Describe dispersive DNA replication
each daughter duplex contains interspersed parental and daughter segments
119
Describe the Meselson-Stahl experiment
they used cesium chloride centrifugation to separate molecules with different weights to test the models of DNA replication
120
What organism did Meselson-Stahl use? What did they grow it in?
they grew E. coli in a medium containing heavy nitrogen
121
What did Meselson-Stahl do after all the E.coli had DNA containing heavy nitrogen only?
they transferred it to Nitrogen-14 and allowed one round of replication
122
After replication of E.coli cells, what did Meselson and Stahl do?
they isolated the DNA of a small amount of cells and centrifuged it to determine its density
123
What were the results of the Meselson-Stahl experiment?
after 1 replication: DNA molecules had the densities expected
after 2 rounds: half the molecules had expected densities
