DNA METABOLISM Flashcards
1
Q
the tendency of an organism to
possess the characteristics of its
parent(s)
A
Heredity
2
Q
- the elements/units carrying and
transferring inherited characteristics from parent to offspring - contained within the nuclei of cells in association with the chromosomes
A
genes
3
Q
must be very Blank so that genetic info can be stored in it and transmitted countless times to subsequent generations
A
stable
4
Q
must be capable of precise copying or Blank so that its info is not lost or altered
A
replication
5
Q
although stable, must also be subject to change in order to account for the appearance of Blank (short term) and for Blank (long term)
A
mutant forms, evolution
6
Q
the material of heredity
A
DNA
7
Q
- 2 identical copies of the
original DNA - strand separation
- copying of each strand
- each separated strand
acts as a template for
the synthesis of a new
complementary strand
A
DNA replication
8
Q
one completely
new DNA duplex
& the original
DNA duplex
A
Conservative
9
Q
one parental
strand & one
new strand
A
Semiconservative
10
Q
each of the 4 strands
contains both newly
synthesized segments &
segments from the
parental strands
A
Dispersive
11
Q
replication of DNA molecules begins at one or more specific regions called the Blank
A
origin(s) of replication
12
Q
excepting certain Blank and Blank, proceeds in both directions from this origin
A
bacteriophage chromosomes and plasmids
13
Q
replication of E. coli DNA begins at
Blank, a unique 245-bp chromosomal site that contains Blank tetranucleotide sequences along its length
A
oriC, 11 GATC
14
Q
- involves two replication forks that move in opposite directions
- predicts that, if radioactively labeled nucleotides are provided as substrates for new DNA synthesis, both replication forks will become radioactively labeled
A
bidirectional replication
15
Q
- the enzyme that carries out DNA
replication - uses single-stranded DNA (ssDNA) as a template and makes a complementary strand by polymerizing deoxynucleotides in the order specified by their pairing with bases in the template
A
DNA polymerase
16
Q
synthesize DNA only in a Blank
direction, reading the antiparallel
template strand in a Blank sense
A
5’→3’, 3’→5’
17
Q
How does DNA polymerase copy the parent strand that runs in the 5’→3’ direction at the replication fork?
A
DNA polymerase copies the parent strand running in the 5’→3’ direction by synthesizing the new strand in short fragments, called Okazaki fragments, in the opposite 5’→3’ direction. These fragments are later joined by DNA ligase to form a continuous strand.
18
Q
because DNA polymerase must read the template
strand in the 3’→ 5’ direction, the 5’→ 3’ parental strand must wrap around in Blank
A
trombone fashion
19
Q
chain growth is in the Blank & Blank to the template strand
A
5’→ 3’ direction, antiparallel
20
Q
require a primer Blank w/ a free Blank to initiate DNA synthesis
A
oligonucleotide, 3’-OH
21
Q
Why primer is essential?
A
A primer is essential because DNA polymerase cannot start DNA synthesis on its own; it can only add nucleotides to an existing strand. The primer, a short piece of RNA or DNA, provides the necessary starting point with a free 3’-OH group for DNA polymerase to begin replication.
22
Q
Biochemical Characterization of DNA polymerases can catalyze the synthesis of DNA if provided with
A
- all 4 dNTPs
- a template DNA strand to copy
- a primer
23
Q
the primer must possess a free 3’-OH end to which an incoming Blank is added
A
deoxynucleoside monophosphate
24
Q
in vivo, a short Blank is invariably the primer, synthesized by a DNA dependent RNA polymerase activity
A
RNA strand
25
* the degree to which a particular DNA polymerase remains associated with the template
processivity
26
are extraordinarily processive
replicative DNA polymerases
27
some DNA polymerases (DNA repair) are only modestly processive, synthesizing a DNA strand only Blank to Blank bases long before falling off
3 to 200
28
The Blank (DNA polymerase III
holoenzyme) can replicate an entire strand of the E. coli chromosome (4.6 mega bases) without falling off
E. coli replicative DNA
polymerase
29
DNA duplex is unwound by the action of DNA Blank and Blank
gyrase and helicase
30
periodically primes synthesis on the lagging strand
primase
31
the single strands are coated with Blank
SSB (ssDNA-binding protein)
32
each half of the dimeric replicative polymerase is a core polymerase bound to its template strand by a Blank
β-subunit sliding clamp
33
*act downstream on the lagging
strand to remove RNA primers, replace them with DNA, and ligate the Okazaki fragments
DNA polymerase I and DNA ligase
34
the polymerase active site is a Blank, and the 3’-exonuclease activity is an Blank
proofreader, editor
35
* located diametrically opposite from oriC on the E. coli circular
chromosome
* where the oppositely moving
replication forks meet and
replication is terminated
terminus region (Ter or t) locus
36
* act as terminators
Ter sequences
37
clusters of Blank or Blank Ter sequences are organized into 2 sets inversely
oriented with respect to one
another
3 or 4
38
termination requires binding of a
specific replication termination
protein, Blank, Blank
Tus protein, to Ter
39
* a contrahelicase
* prevents the DNA duplex from
unwinding by blocking progression
of the replication fork
* inhibit the ATP dependent DnaB
helicase activity
Tus protein
40
is organized into
chromosomes that are
compartmentalized within the
nucleus
eukaryotic DNA
41
in a dividing human cell, a carefully choreographed replication of Blank of DNA distributed among 46 chromosomes occurs
6 billion bp
42
* the events associated with cell
growth and division in eukaryotic
cells
cell cycle
43
* longest part of the cell cycle
* characterized by rapid growth
and metabolic activity
G1 (gap)
44
* cells that are quiescent, that is,
not growing and dividing (such
as neurons)
G0
45
* time of DNA synthesis
S phase
46
* a relatively short period of
growth when the cell prepares
for cell division
G2
47
How are the ends of chromosomes replicated?
48
* specialized structures at the ends of chromosomes
telomeres
49
consist of short (5–8 bp), tandemly
repeated, GC-rich nucleotide
sequences that form protective caps Blank to Blank at the ends of chromosomal DNA
1 to 12 kbp long
50
aid in chromosome maintenance
and stability by protecting against
Blank or Blank
DNA degradation or rearrangement
51
lagging strand synthesis at the 3’
ends of chromosomes is primed by
Blank to form Blank, but these RNA primers
are subsequently removed, resulting
in gaps in the progeny 5’-terminal
strands at each end of the
chromosome after each round of
replication (primer gap)
RNA primase, Okazaki
fragments
52
* an RNA-dependent DNA
polymerase which adds telomeres
to the ends of chromosomal DNA
* maintains chromosome length by
restoring telomeres at the 3’-ends
of chromosomes
telomerase
53
a specialized reverse transcriptase
containing a catalytic subunit
✓ TERT (TElomerase Reverse
Transcriptase)
54
RT, for
RNA Template
55
TER, for
TEmplate
containing telomerase RNA
56
a Blank is created at the 3’-end of each DNA strand
G-rich region
57
a Blank is created at the 5’-end of each DNA strand
C-rich region
58
the Blank serves as the template for the DNA polymerase activity of telomerase
ribonucleic acid of human telomerase
59
in replication of the lagging strand, short RNA
primers are added (pink) and extended by Blank
DNA polymerase
60
the result is a Blank at the 5’-end of each
strand (only one end of a
chromosome)
gap (primer gap)
61
indicate sequences at the
3’-end that cannot be copied by
conventional DNA replication
asterisks
62
* the G-rich ends of telomeres can
arrange into four-stranded Blank
G quadruplex structures
63
the single-stranded 3’-overhangs at
the telomeric ends of chromosomes
are a hazard because they resemble
Blank
Damaged DNA
64
* a protein complex with 6 distinct
subunits
* telomere end-protection protein
shelterin
65
How are RNA Genomes Replicated?
66
* noted that inhibitors of DNA
synthesis prevented infection of
cells in culture by RNA tumor
viruses such as avian sarcoma virus
* noted that inhibitors of DNA synthesis
prevented infection of cells in culture
by RNA tumor viruses such as avian
sarcoma virus
* proposed that DNA is an intermediate
in the replication of such viruses
* an RNA tumor virus can use viral RNA
as the template for DNA synthesis
Howard Temin (1964)
67
* independently discovered a viral
enzyme capable of mediating such a
process
Temin and David Baltimore (1970)
68
* an RNA-directed DNA polymerase
* synthesizes polynucleotides in the
5’→ 3’ direction
* requires a primer
reverse transcriptase
69
the primer is a specific Blank
molecule captured by the virion
from the host cell in which it was
produced
tRNA
70
the 3’-end of the tRNA is base
paired with the Blank at the site where DNA synthesis initiates
viral RNA template
71
reverse transcriptase then
transcribes the RNA template into a
complementary DNA (cDNA) strand
to form a Blank
double-stranded DNA:RNA hybrid
72
all RNA tumor viruses contain
reverse transcriptase within their
Blank
virions (viral particles)
73
* RNA viruses that replicate their
RNA genomes via a DNA
intermediate
retroviruses
74
* this enzymatic activity creates a ss
stranded DNA copy of the RNA
genome of the virus
RNA-directed DNA polymerase
activity
75
* a nuclease that specifically
degrades RNA chains in DNA:RNA
hybrids
* an exonuclease activity that
degrades the template genomic
RNA
* removes the priming tRNA after
DNA synthesis is completed
RNase H activity
76
* replicates the ssDNA remaining after
RNase H degradation of the viral
genome, yielding a DNA duplex
DNA-directed DNA polymerase
activity
77
this DNA duplex directs the
remainder of the viral infection
process or becomes integrated into
the host chromosome, where it can lie
dormant for many years as a Blank
provirus
78
Blank is of great clinical interest because it is the
enzyme for replication of the AIDS virus
HIV reverse transcriptase
79
DNA synthesis by HIV reverse
transcriptase is blocked by
dideoxynucleoside analogs such as
Blank and Blank
AZT and 3TC
80
HIV reverse transcriptase
incorporates these analogs into
growing DNA chains in place of
Blank or Blank
dTMP (in the case of AZT) or dCMP
(in the case of 3TC)
81
HIV reverse transcriptase is error
prone: It incorporates the wrong base at a frequency of 1 per Blank to Blank
nucleotides polymerized
2000 to
4000
82
How is the Genetic Information
Rearranged by Genetic
Recombination?
83
* the natural process by which
genetic information is rearranged to
form new associations.
* genetic recombination is the
exchange (or incorporation) of one
DNA sequence with (or into)
another (molecular level)
Genetic recombination
84
* recombination which involves
reaction between very similar
sequences (homologous) of DNA
homologous recombination
85
* incorporation of a DNA segment
whose sequence differs greatly from
the DNA at the point of insertion
nonhomologous recombination
86
* is generally used to fix the DNA so that
information is not lost
homologous recombination
87
* reported the results of her studies on
an activator gene in corn (Zea mays)
that was recognizable principally by its
ability to cause mutations in other
genes
Barbara McClintock(1950)
88
were an internal source of mutation
activator genes
89
* found in all kingdoms of life and
constitute a significant portion of
genomes
transposons
90
in humans, Blank of the genome is
transposon DNA
54%
91
transposons range in size from several hundred
base pairs to more than Blank
8 kbp
92
* enzyme responsible for transposon
mobility
* binds to the end of a transposon
transposase
93
catalyzes a cut-and-paste
mechanism that inserts the
transposon into a chromosome or
remobilizes the transposon to a
different location in the genome →
Blank
transposition events
94
* the smallest transposons
* insert apparently at random in the
genome
insertion sequences (Iss)
95
is a major force in
evolution because transposition
events can move genes to new
places or lead to the duplication of
existing genes
transposition
96
are susceptible to chemical alterations
that arise from environmental
damage or errors during synthesis
biological macromolecules
97
for RNAs, proteins, or other cellular
molecules, most consequences of
such damage are avoided by
replacement of these molecules
through Blank
normal turnover (synthesis
and degradation)
98
is vital to cell
survival and reproduction.
* its information content must be
protected over the life span of the cell
and preserved from generation to
generation
the integrity of DNA
99
1. high-fidelity replication systems
2. repair systems that correct DNA
damage that might alter its information
content
Safe guards
100
* the nucleotide sequence in one
strand is directly related to the
sequence in the other
DNA damage may arise from Blank and Blank
* endogenous processes
* exogenous processes
101
* chemical reactions (oxidation,
alkylation, or deamination of bases)
* loss of bases due to cleavage of N
glycosidic bonds
Endogenous processes
102
What are the examples of exogenous agents?
* UV light
* ionizing radiation
* mutagenic chemicals
103
Ways in which exogenous agents can
damage DNA
-UV-induced free-radical generation
and crosslinking of adjacent
Blank
pyrimidines
104
breakage of the polynucleotide
backbone by Blank
ionizing radiation
105
base modifications through
chemical reactions
106
* the human genome has Blank or so
genes associated with DNA repair
150
107
to remove methyl groups from chemically
modified bases
methyltransferases
108
, which repairs thymine
dimers
photolyase
109
single-strand damage repair relies
on the intact Blank
to guide repair
complementary strand
110
Systems repairing this sort of DNA
damage include
* mismatch repair (MMR)
* base excision repair (BER)
* nucleotide excision repair (NER)
111
* the most dangerous form of DNA
damage
Double-Strand DNA Breaks (DSBs)
112
can always provide a
homologous dsDNA, but so can haploid
cells such as bacteria, if the break
occurs when such cells are transiently
diploid, as they are during replication
diploid cells
113
DSBs are common in eukaryotic
cells; estimates suggest a frequency
of Blank DSBs per cell per day
10
114
2 most prominent pathways of DSB
repair are
* nonhomologous DNA end-joining
(NHEJ)
* homologous recombination (HR)
115
* the broken ends at the break site
are rejoined
* the lack of a proper DNA template
means that NHEJ is error-prone
NHEJ
116
DSBs that arise as the cell progresses from S into G2 during
the cell cycle can be repaired through Blank
homologous recombination
117
human DNA replication has an error rate of about Blank mistakes during
copying of the 6 billion base pairs in
the diploid human genome
3 bp
118
about Blank (mostly purines) are
lost per cell per day from spontaneous
breakdown in human DNA
104 bases
119
* corrects errors introduced when
DNA is replicated
* scans newly synthesized DNA for
mispaired bases, excises the
mismatched region, and then
replaces it by DNA polymerase
mediated local replication
mismatch repair system
120
, often an identifying
and characteristic feature of a
prokaryote’s DNA, occurs just after DNA
replication
DNA methylation
121
when the methyl-directed
mismatch repair system encounters
a mismatched base pair, it searches
along the DNA until it finds a Blank
methylated base
122
mismatch repair does this by using
an Blank to cut the new,
unmethylated strand and an
Blank to remove the
mismatched bases, creating a gap in
the newly synthesized strand
endonuclease, exonuclease
123
Blank
then fills in the gap, using the
methylated strand as template
DNA polymerase III holoenzyme
124
Blank reseals the strand
DNA ligase
125
the bases in DNA are Blank
electron-rich
126
absorption of UV light can lead to formation of Blank if 2 T residues are next to one another
thymine dimers
127
these dimers disrupt the information transfer reactions
implicit to Blank and
Blank
transcription, translation
128
promotes the
formation of covalent bonds between adjacent thymine residues
in a DNA strand, creating a
Blank
UV irradiation, cyclobutyl ring
129
a FAD-dependent enzyme, binds at the
dimer and uses the energy of visible light
to break the cyclobutyl ring, restoring
the pyrimidines to their original form
photolyase (photoreactivating enzyme),
130
* acts on single bases that have been
damaged through oxidation or other
chemical modifications during normal
cellular processes
base excision repair
131
* recognizes and repairs larger regions of damaged DNA
nucleotide excision repair (NER)
132
* consists of more than 30 proteins
engaged in DNA damage verification,
excision, gap filling, and ligation
NER pathway in humans
133
an oligonucleotide stretch Blank to blank units long is removed
27 to 29
134
the resultant gap is then filled in using
DNA polymerase (DNA polymerase I in
prokaryotes or DNA polymerase d or e
and PCNA plus RFC in eukaryotes), and
the sugar–phosphate backbone is co
valently closed by Blank
DNA ligase
134
such lesions are recognized by Blank, an inherited human syndrome whose
victims suffer serious skin lesions if
exposed to sun light
XPA
protein (xeroderma pigmentosum)
135
* a DNA-binding dimer of 31-kDa
subunits
* verifies that DNA damage has
occurred
* serves as a platform for recruitment
of other NER factors to the damaged
strand through protein–protein
interactions
XPA
136
What is the Molecular Basis of Mutation?
137
* substitution of one base pair for
another
* when a base pairs with an
inappropriate partner
* introduction of base analogs into DNA
* chemical mutagens
point mutations
138
* insertion or deletion of one or
more base pairs
insertions and deletions
139
* one purine (or pyrimidine) is
replaced by another
transitions
140
* a purine is substituted for a
pyrimidine, or vice versa
* proofreading mechanisms
operating during DNA replication
catch most mispairings
transversions
141
the frequency of spontaneous
mutation in prokaryotes and
eukaryotes (including humans) is
about Blank base pair per generation
10-8 per
142
* become incorporated into DNA and
induce mutations through changes
in base-pairing possibilities
* 5-bromouracil (5-BU)
* 2-aminopurine (2-AP)
base analogs
143
* a thymine analog
* becomes inserted into DNA at sites
normally occupied by T
5-bromouracil
144
less often, 5-BU is inserted into
DNA at Blank, not T sites
cytosine sites
145
* an adenine analog that arises in situ
in DNA through oxidative deamination
of A
* base pairs with cytosine, creating an
A–T to G–C transition
hypoxanthine
145
* agents that chemically modify
bases so that their base-pairing
characteristics are altered
chemical mutagens
145
causes the oxidative
deamination of primary amine
groups in adenine and cytosine
HNO2
146
* alkylation of reactive sites on the
bases to add methyl or ethyl groups
alters their H bonding and hence
base pairing
alkylating agents
147
nitrosoamines are mutagenic in 2 ways
* they can react to yield Blank
* they can act as Blank
HNO2, alkylating agents
148
is a very potent mutagen used in
laboratories to induce mutations in experimental
organisms such as Drosophila melanogaster
nitrosoguanidine, N-methyl-N’-nitro-N
nitrosoguanidine
149
* the addition or removal of one or
more base pairs leads to insertion or
deletion mutations, respectively
Insertions and Deletions
150
* misincorporation of all subsequent
AA in the protein encoded by the
gene
frameshift mutations
