LEC3 and 4 - REPLICATION and TRANSCRIPTION Flashcards
1
Q
DNA double helix is approximately ___ in nm
A
2 nm
2
Q
the double stranded DNA that is intertwimed is attached to a protein called
A
histone
3
Q
how many units of histone molecules to form 1 nucleosome
A
8 histone molecule intertwined in the DNA
4
Q
it is called as “the core”
A
nucleosome
5
Q
proteins involved in epigenesis, rich in arginine and lysine
A
histone
6
Q
do prokaryotes have histone?
A
naur
7
Q
each core histone subunit will the one that has 8 histone molecules w2ill form ___ approx 10 nm in diameter
A
nucleosome filament
8
Q
the nucleosome filament will then contribute in making
A
fiber - 30 nm
9
Q
regarded as a string of pearl/ bead of string appearance
A
nucleosome filaments
10
Q
the fibers now are folded in _____
A
looped domain
11
Q
looped domain is also called as
A
solenoid
12
Q
the looped domain or solenoid can be in what shape
A
tubular, helical, coiled
13
Q
forms the backbone of the molecule
A
sugar and the phosphate
14
Q
connects the sugar and the phosphate
A
phosphodiester bonds
15
Q
what makes the double helical DNA stabilize
A
hydrogen bond
16
Q
connects the nitrogenous bases together
A
hydrogen bond
17
Q
is hyrophobic bond same with hydrogen bond?
A
yes
18
Q
The two strands of the DNA double helix are arranged in______; their chemical orientations are different.
A
antiparallel
19
Q
opposing orientation of the 2 helical strand
A
anti parallelism
20
Q
DOUBLE HELICAL MODEL always follow what model
A
semi conservative model
21
Q
a model when replication takes place, the parent cell will stay as it is and will only produce a newly si=ynthesized daughter
A
conservative replication
22
Q
parental DNA strands remained together in 1 of the daughter cell the newly synthesized DNA strands went to the other daughter cell
A
Conservative Replication
23
Q
each daughter cell received 1 parental DNA
strand and 1 newly synthesized complementary
strand parental strand was the template
A
. Semiconservative Replication
24
Q
replication of the strands always happen at ____
A
5 to 3
25
the reading of the parental strand happen in what direction
3` to 5`
26
the addition of the template happens in what direction
5` to 3`
27
bonds that connect nitrogenous bases to
pentose sugar
Glycosidic bond
28
Debunked model
o Replaced by semi-conservative
CONSERVATIVE MODEL
29
he --
demonstrated semiconservative replication
meselson-stahl experiments
30
in Meselson-Stahl Experiment, what components he use?
bacteria and nitrogen
31
o same with semi-conservative
o Here, 3rd generation will have the gene of the
parent
DISPERSIVE MODEL
32
application of heat or alkaline solution causing the strands to separate but not break the phosphodiester bonds
denaturation
33
is bidirectional and
semiconservative
REPLICATION
34
means that replication begins at
a site of origin and simultaneously moves out
in both directions from this point.
Bidirectional
35
) Prokaryotes have how many site of origin on each
chromosome.
one
36
Eukaryotes have hwo many sites of origin on each
chromosome
multiple
37
ORI C means
origin of replication
38
found in ORI C where in all the replication events will take place inside
replication bubble
39
inside ORI C, wherein it Forms a V letter shape known as
replication fork
40
a part where the helicase enzyme lyse
replication fork
41
replication is always consensus or starting with AT base pairs, why?
because they only have 2 hydrogen bonds as it is easier to separate them compared to CG
42
HOW MANY HYDROGEN BOND DOES CYTOSINE AND
GUANINE
3
43
HOW MANY HYDROGEN BOND OF ADENINE AND THYMINE
2
44
primase is the one that will form
primer (5 - 3`)
45
the leading strand runs in what direction
5` - 3 `
46
unzipping of dna is done by ___ resulting to replication form
helicase
47
marks the starting point for the construction of the DNA
primer made by primase
48
binds the primer and will make new strand of the DNA
dna polymerase
49
the polymerase will add bases one by one in a ____ strand, it will run continuously from 5` to 3`
leading strand
50
in this strand, the polymerase will add bases one by one in small chunks as it runs in opposite direction
lagging starnd
51
the small chunks made by polymerase is called as
ozaki fragments
52
each strand is started with what primer
rna primer
53
it's function is to remove all the rna primer in both strands
exonuclease
54
another ___ will fill out the gaps of the removed primar
dna polymerase
55
this enzyme will glue and seal the strands
ligase
56
BASIC REQUIREMENTS FOR DNA SYNTHE
SUBSTRATES
TEMPLATES
PRIMER
57
4 deoxynucleotide triphosphates (dNTPs)
1. deoxyadenosine triphosphate (dATP)
2. deoxyguanosine triphosphate (dGTP)
3. deoxycytidine triphosphate (dCTP)
4. deoxythymidine triphosphate (dTTP)
58
Prepares the template strand for the addition of nucleotides
PRIMER
59
usually how long is the primer
10 nucleotide long
60
direct DNA polymerase at the origin of
replication
Primer
61
always first in the replication
Primer
62
source of DNA polymerase in vitro
Taq (Thermus
aquaticus)
63
a type of protein that will initiate the replication
DNA A protein
64
it will prevent the reannealing of DNA after unwinding of helicase
single stranded binding protein
65
it creates the enzyme primase
primosome
66
primer's direction
3` to 5`
67
what type of polymerase is used by eukaryotes
type D - polymerase D
68
what type of polymerase is used by prokaryotes
polymerase 3
69
it will create the subsequent bases until it reach the fork
polymerase in lagging strand
70
new polymerase that will remove all the primer
polymerase 1 and alpha
71
polymerase Delta and 3
replication
proof read
repair
72
polymerase 1 and alpha
exonuclease, and repair
73
polymerase always happen in what direction
5` - 3`
74
proofreading or repair always happen in what direction
3` - 5`
75
direction of exonuclease
5` - 3`
76
adding of cap on the 5` untranslated end
capping
77
adding of tail on the 3` untranslated end
Polyadenylation
78
DNA POLYMERASE I (POL I)
functions
DNA replication
Repair of damaged DNA
Removes RNA primers via its 5′ → 3 exonuclease activity
Proofreading
79
molecular weight of polymerase 1
103,000 MW
80
Recognizes mismatched nucleotides →halts
polymerization → 3’ to 5’ exonuclease removes
mismatched nucleotide →polymerization
resumes.
Proofreading
81
82
DNA POLYMERASE II (POL II)
function
Some DNA repair processes
Proofreading
no replication
83
DNA POLYMERASE III (POL III)
function
catalyzes leading and lagging strand
synthesis (5′ → 3′ polymerase activity)
proofreading and reading
84
a type of dna polymerase that is
Holoenzyme
85
Holoenzyme means
have 2 subunits, alpha sub unit and epsilon subunit
86
a subunit of a holoenzyme - polymerase 3 that is responsible for polymerase activity
alpha subunit
87
a subunit of a holoenzyme - polymerase 3 that is responsible for exonuclease activity
epsilon sub unit
88
Unwinds double helix. Requires energy
(ATP)
DNA helicase
89
Binds and stabilizes ssDNA to prevent
reannealing
Single stranded DNA binding (SS-B)
Protein
90
Synthesizes 10 nucleotide primer
RNA primase
91
Binds to origin of replication and causes
dsDNA to melt into a local region of
ssDNA
Dna A protein
92
Creates a nick in the helix to relieve the
supercoils/strain imposed by DNA
unwinding
DNA topoisomerase
93
function of topoisomerase that refers to the cutting of strand
nuclease
94
function of topoisomerase that refers to the rejoining of cutted strands
ligase
95
type 1 and type 2 topoisomerase is for ___
eukaryotes
96
type 3 and type 2 topoisomerase is for ___
prokaryotes
97
type II topoisomerase in prokaryotes is called as
DNA gyrase
98
responsible for making single stranded break in a negative supercoil
type 2 topoisomerase
99
negative supercoil means
coils towards left
100
REPLICATION SEQUENCE SUMMARY
1. Initiation
2. Elongation
3. Termination
101
refers to all events happening in 1 replication bubble, wherein all the enzymes are working and replicating
replisome
102
when will be the termination happen
when 2 replisome meet
103
Eukaryotes can create _____ base pairs per second
100
104
Prokaryotes can replicate ______ base pairs per
second
1000
105
the principle helicase in e.coli is called as
dna B protein
106
type of eukaryotic polymerase
alpha - minor same with type 1
major - major same with type 3
beta and epsilon - repair
gamma - replication of mitochondrial DNA
107
Activities of Type I DNA
Topoisomerases
Nuclease (strand-cutting)
Ligase (strand-resealing)
108
relax only negatively supercoiled DNA
Type IA Topoisomerases
109
relax negative and positive supercoils by a
controlled rotation mechanism in eukaryotic cells
Type IB Topoisomerases
110
type of topoisomerase that has energy involvement
type 2 and 3
111
Make transient breaks in both strands → allow a
2nd stretch of DNA double-helix to pass through
the break →reseal transient break → relief of
negative and positive supercoils (ATPdependent)
Type II DNA Topoisomerases
112
bp16
Etoposide/Tenoposide
113
nhibit Top 2 and
cancer cells (Eukaryote
Etoposide/Tenoposide
114
class of antibiotic that inhibits UTI
Fluoroquinolones
115
example of Fluoroquinolones is
ciprofloxaciin
116
Eukaryotic chromosomes end in
distinctive sequences called
______that help preserve the
integrity and stability of the
chromosome
telomeres
117
Telomeres
don’t code
for any RNA
true or false
true
118
enzyme contained by cells that do not age (Ex. Germ Line
Cells and Cancer Cell
Telomerase
119
-replaces the lost ends
Telomerase
120
special kind ofreverse transcriptase
telomerase
121
act as template primer at the extreme ends of the
chromosomes → protects against telomere shortening
Telomerase
122
carries its own RNA molecule
Telomerase
123
have longer telomeres than their terminally differentiated
daughters
. Stem Cells
124
-have great therapeutic potential
Stem Cells
125
● A genetic mutation in the LMNA
gene causes .
progeria
126
The LMNA gene is responsible for
making a protein called
lamin A.
127
_____is an important part of the
structural scaffolding that holds
the nucleus of each cell in your
body together.
Lamin A
128
Progeria -Progeria gets its name from the Greek
word “___,” which means, “old age.”
geras
129
●-premature ageing syndrome
●-cells have extremely short telomeres
Progeria
130
In RNA do we need a primer?
naur
131
RNA polymerase can initiate the synthesis of new chains.
true or false
true
132
In RNA polymerase, The DNA template is copied in the____ direction,
3’ to 5’
133
The DNA template is copied in the 3’ to 5’ direction, and the RNA
chain grows in the ___direction.
5’ to 3’
134
In RNA, we only need __ to initiate the synthesis of new chain
regions -
135
what are the regions needed for RNA synthesis
■ Promoter region
■ Coding region
■ Termination region/silencer/enhancer
136
In transcription, what region is the only one needed
promoter region
137
Once the RNA polymerase found the promoter region,
initially transcription starts and is helped by a
transcription factor
which factor is it?
transcription factor II D (TFIID)
138
RIBONUCLEATIDE TRIPHOSPHATE OF RNA
adenosine triphosphate,
Guanosine triphosphate
uridine triphosphate
and cytidine triphosphate
139
140
structural formula for RNA polymerase of bacteria
2 alpha
1 beta
1 beta prime
1 small omega
141
6th subunit of RNA polymerase is the
sigma factor
142
purpose of the 6th subunit
sigma factor is the one that will bind to the promotor region guided by the transcription factor II D
143
RNA polymerases are holoenzyme because they contain how many units
2 units
144
before the initiation takes place, there are ___ that are waiting for the RNA polymerase
transcription factors
145
what are the example of transcription factors
transcription factors II B
transcription factors II E
transcription factors II H
146
which transcription factors is responsible for the unwinding of the double helix sytructure
transcription factors II H
147
they form the pre-initiations complex
transcription factors II B
transcription factors II E
transcription factors II H
148
2 promoted sequences
TATAAT (PRIBNOW or TATA box )
TTGACA (a second consensus sequence )
149
TATAAT (PRIBNOW or TATA box ) has bases upstream
10 bases upstream
150
TTGACA (a second consensus sequence )
how many bases upstream
35 bases upstream
151
the strand that is formed after unwinding and the strand that the RNA polymerase will attached is called as
non coding strand/antisense strand/template strand
152
this strand will serves as the initial site for the RNA polymerase location
anti sense strand
153
the other strand formed aside from the anti sense strand and what its characteristics
sense strand and the same with mRNA
154
two types of termination
RHO dependent termination and intrinsic termination
155
a type of termination wherein there's a formation of hairpin loop due to the weak binding of adenine and thymine
Intrinsic termination
156
type of termination that depends on a protein that will bind to the RNA polymerase removing it on the antisense strand
Protein dependent termination
157
in Protein dependent termination, what is the protein being talked about?
RHO protein
158
mRNA is considered as a ____ as it can code to different proteins
polycistronic
159
proteins produced in polycistronic mRNA is called as
polysomes
160
____is often produces as a polycistronic transcript that is translated as it is being transcribed
mRNA
161
do prokaryotic mRNA need post transcriptional modification?
no, they dont have cap or something
162
coding sequences of prokaryotic mRNA
cystron
163
space between cystron is called as
interspacers
164
___ is produced as a large transcript that is cleaved during the 16s rRNA that appears in the 30s ribosomal subunit
rRNA
165
what is the precursor RNA
45s rRNA
166
Precursor RNA–45S rRNA (undergoes cleavage to
produce two subunit:
the large and small ribosomal
subunit)
167
the precursor RNA - 45S rRNA
the large ribosomal unit of the precursor RNA consists of
5s rRNA and 23s rRNA
168
the precursor RNA - 45S rRNA
the small ribosomal unit of the precursor RNA consists of
16s rRNA
169
a component of small ribosomal sub unit of precursor RNA that can detect the bacterial specie
16s rRNA
170
do we have 16s rRNA?
naur
171
the precursor RNA - 45S rRNA
the large ribosomal unit of the precursor RNA (______S)
50
172
the precursor RNA - 45S rRNA
the small ribosomal unit of the precursor RNA (______S)
30
173
if the ribosomal subunit is combined (large and small) bacteria will have ____ ribosomal unit
70S
174
why is it not 80 s if the large and small ribosomal subunit of bacteria is added (70s )
they aren't supposed to be added, the subunit is based on the shape and particle weight
175
is usually produced from larger transcripts that are cleaved
tRNA
176
cleaving enzyme of mRNA
snRNA (spliceosomes)
177
cleaving enzyme of rRNA
ribozyme
178
cleaving enzyme of tRNA
RNAse P
179
antituberculosis drug (for M.
tuberculosis)
rifampin
180
antibiotic and anticancer in pediatric populations (used to treat neuroblastoma, wilms's tumor and sarcoma)
actinomycin D
181
3 types of RNA polymerase of eukaryotes
RNA POLYMERASE I
RNA POLYMERASEII
RNA POLYMERASEIII
182
responsible of RNA POLYMERASE I
catalyzes the production of rRNA
183
where does the rRNA created
created in the darkly staining areas if the nucleus called nucleolus
184
responsible of RNA POLYMERASE II
responsible for the creation of mRNA
185
responsible of RNA POLYMERASE III
for the creation of tRNA
186
responsible of RNA POLYMERASE III
aside from the creation of tRNA
CREATES 5S rRNA
187
what makes the 5S RNA unique
only rRNA created by polymerase III
and the only rRNA synthesized in the nucleus
188
concensus region in promoter region in mRNA
TATA (hogness)
CAAT
Guanine rich area
189
TATA (hogness)
CAAT
Guanine rich area
base pairs upstream
TATA (hogness) - 25
CAAT - 70
Guanine rich area - 10 and 110
190
a region that enhances the transcription
enhances
191
a region that stops the transcriptions
silencers
192
precursor mRNA
hnRNA
193
the process of maturing hnRNA to mRNA is called as
post transcriptional modification
194
is responsible for the protection of nascent mRNA against degradation
CAP
195
CAP is responsible for the protection of nascent mRNA against degradation
aside from this?
initiates the translation and helps in exporting to cytoplasm and reach the ribosome
196
mRNA carries codon, however, it must enter the ____ and exit to enter the ribosome for protein synthesis
NUCLEUS
197
if the CAP initates translation, which tail we can fid the stoppage of initiation
poly A tail
198
problems with the cutting of introns is associated to
thalassemia
199
a toxin that can give us the death cap
MUSHROOM - alpha amanita
200
DEATH CAP symptoms
can cause, gastroenteritis, nausea, vomiting, death
201
starting and ending site of introns
AGGT
202
__is clover leaf in structure
tRNA
203
3 modified nucleoside in tRNA
dihydrouridine
ribothymidine
pseudouridine
204
dihydrouridine
ribothymidine
pseudouridine
forms what arms
dihydrouridine - D arm
ribothymidine - T arm
pseudouridine - T arm
205
holds the amino acid and the acceptor stem
covalent bonds
206
catalyzes the addition of amino acid on the 3`end
nucleotidyl transferase
207
