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MODX > LEC3 and 4 - REPLICATION and TRANSCRIPTION > Flashcards

LEC3 and 4 - REPLICATION and TRANSCRIPTION Flashcards

1
Q

DNA double helix is approximately ___ in nm

A

2 nm

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2
Q

the double stranded DNA that is intertwimed is attached to a protein called

A

histone

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3
Q

how many units of histone molecules to form 1 nucleosome

A

8 histone molecule intertwined in the DNA

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4
Q

it is called as “the core”

A

nucleosome

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5
Q

proteins involved in epigenesis, rich in arginine and lysine

A

histone

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6
Q

do prokaryotes have histone?

A

naur

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7
Q

each core histone subunit will the one that has 8 histone molecules w2ill form ___ approx 10 nm in diameter

A

nucleosome filament

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8
Q

the nucleosome filament will then contribute in making

A

fiber - 30 nm

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9
Q

regarded as a string of pearl/ bead of string appearance

A

nucleosome filaments

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10
Q

the fibers now are folded in _____

A

looped domain

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11
Q

looped domain is also called as

A

solenoid

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12
Q

the looped domain or solenoid can be in what shape

A

tubular, helical, coiled

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13
Q

forms the backbone of the molecule

A

sugar and the phosphate

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14
Q

connects the sugar and the phosphate

A

phosphodiester bonds

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15
Q

what makes the double helical DNA stabilize

A

hydrogen bond

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16
Q

connects the nitrogenous bases together

A

hydrogen bond

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17
Q

is hyrophobic bond same with hydrogen bond?

A

yes

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18
Q

The two strands of the DNA double helix are arranged in______; their chemical orientations are different.

A

antiparallel

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19
Q

opposing orientation of the 2 helical strand

A

anti parallelism

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20
Q

DOUBLE HELICAL MODEL always follow what model

A

semi conservative model

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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

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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

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23
Q

each daughter cell received 1 parental DNA
strand and 1 newly synthesized complementary
strand parental strand was the template

A

. Semiconservative Replication

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24
Q

replication of the strands always happen at ____

A

5 to 3

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25
Q

the reading of the parental strand happen in what direction

A

3 to 5

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26
Q

the addition of the template happens in what direction

A

5 to 3

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27
Q

bonds that connect nitrogenous bases to
pentose sugar

A

Glycosidic bond

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28
Q

Debunked model
o Replaced by semi-conservative

A

CONSERVATIVE MODEL

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29
Q

he –
demonstrated semiconservative replication

A

meselson-stahl experiments

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30
Q

in Meselson-Stahl Experiment, what components he use?

A

bacteria and nitrogen

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31
Q

o same with semi-conservative
o Here, 3rd generation will have the gene of the
parent

A

DISPERSIVE MODEL

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32
Q

application of heat or alkaline solution causing the strands to separate but not break the phosphodiester bonds

A

denaturation

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33
Q

is bidirectional and
semiconservative

A

REPLICATION

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34
Q

means that replication begins at
a site of origin and simultaneously moves out
in both directions from this point.

A

Bidirectional

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35
Q

) Prokaryotes have how many site of origin on each
chromosome.

A

one

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36
Q

Eukaryotes have hwo many sites of origin on each
chromosome

A

multiple

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37
Q

ORI C means

A

origin of replication

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38
Q

found in ORI C where in all the replication events will take place inside

A

replication bubble

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39
Q

inside ORI C, wherein it Forms a V letter shape known as

A

replication fork

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40
Q

a part where the helicase enzyme lyse

A

replication fork

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41
Q

replication is always consensus or starting with AT base pairs, why?

A

because they only have 2 hydrogen bonds as it is easier to separate them compared to CG

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42
Q

HOW MANY HYDROGEN BOND DOES CYTOSINE AND
GUANINE

A

3

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43
Q

HOW MANY HYDROGEN BOND OF ADENINE AND THYMINE

A

2

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44
Q

primase is the one that will form

A

primer (5 - 3`)

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45
Q

the leading strand runs in what direction

A

5 - 3

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46
Q

unzipping of dna is done by ___ resulting to replication form

A

helicase

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47
Q

marks the starting point for the construction of the DNA

A

primer made by primase

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48
Q

binds the primer and will make new strand of the DNA

A

dna polymerase

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49
Q

the polymerase will add bases one by one in a ____ strand, it will run continuously from 5 to 3

A

leading strand

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50
Q

in this strand, the polymerase will add bases one by one in small chunks as it runs in opposite direction

A

lagging starnd

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51
Q

the small chunks made by polymerase is called as

A

ozaki fragments

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52
Q

each strand is started with what primer

A

rna primer

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53
Q

it’s function is to remove all the rna primer in both strands

A

exonuclease

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54
Q

another ___ will fill out the gaps of the removed primar

A

dna polymerase

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55
Q

this enzyme will glue and seal the strands

A

ligase

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56
Q

BASIC REQUIREMENTS FOR DNA SYNTHE

A

SUBSTRATES
TEMPLATES
PRIMER

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57
Q

4 deoxynucleotide triphosphates (dNTPs)

A
  1. deoxyadenosine triphosphate (dATP)
  2. deoxyguanosine triphosphate (dGTP)
  3. deoxycytidine triphosphate (dCTP)
  4. deoxythymidine triphosphate (dTTP)
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58
Q

Prepares the template strand for the addition of nucleotides

A

PRIMER

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59
Q

usually how long is the primer

A

10 nucleotide long

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60
Q

direct DNA polymerase at the origin of
replication

A

Primer

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61
Q

always first in the replication

A

Primer

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62
Q

source of DNA polymerase in vitro

A

Taq (Thermus
aquaticus)

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63
Q

a type of protein that will initiate the replication

A

DNA A protein

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64
Q

it will prevent the reannealing of DNA after unwinding of helicase

A

single stranded binding protein

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65
Q

it creates the enzyme primase

A

primosome

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66
Q

primer’s direction

A

3 to 5

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67
Q

what type of polymerase is used by eukaryotes

A

type D - polymerase D

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68
Q

what type of polymerase is used by prokaryotes

A

polymerase 3

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69
Q

it will create the subsequent bases until it reach the fork

A

polymerase in lagging strand

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70
Q

new polymerase that will remove all the primer

A

polymerase 1 and alpha

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71
Q

polymerase Delta and 3

A

replication
proof read
repair

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72
Q

polymerase 1 and alpha

A

exonuclease, and repair

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73
Q

polymerase always happen in what direction

A

5 - 3

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74
Q

proofreading or repair always happen in what direction

A

3 - 5

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75
Q

direction of exonuclease

A

5 - 3

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76
Q

adding of cap on the 5` untranslated end

A

capping

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77
Q

adding of tail on the 3` untranslated end

A

Polyadenylation

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78
Q

DNA POLYMERASE I (POL I)

functions

A

DNA replication
Repair of damaged DNA
Removes RNA primers via its 5′ → 3 exonuclease activity
Proofreading

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79
Q

molecular weight of polymerase 1

A

103,000 MW

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80
Q

Recognizes mismatched nucleotides →halts
polymerization → 3’ to 5’ exonuclease removes
mismatched nucleotide →polymerization
resumes.

A

Proofreading

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81
Q
A
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82
Q

DNA POLYMERASE II (POL II)

function

A

Some DNA repair processes
Proofreading

no replication

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83
Q

DNA POLYMERASE III (POL III)

function

A

catalyzes leading and lagging strand
synthesis (5′ → 3′ polymerase activity)

proofreading and reading

84
Q

a type of dna polymerase that is

A

Holoenzyme

85
Q

Holoenzyme means

A

have 2 subunits, alpha sub unit and epsilon subunit

86
Q

a subunit of a holoenzyme - polymerase 3 that is responsible for polymerase activity

A

alpha subunit

87
Q

a subunit of a holoenzyme - polymerase 3 that is responsible for exonuclease activity

A

epsilon sub unit

88
Q

Unwinds double helix. Requires energy
(ATP)

A

DNA helicase

89
Q

Binds and stabilizes ssDNA to prevent
reannealing

A

Single stranded DNA binding (SS-B)
Protein

90
Q

Synthesizes 10 nucleotide primer

A

RNA primase

91
Q

Binds to origin of replication and causes
dsDNA to melt into a local region of
ssDNA

A

Dna A protein

92
Q

Creates a nick in the helix to relieve the
supercoils/strain imposed by DNA
unwinding

A

DNA topoisomerase

93
Q

function of topoisomerase that refers to the cutting of strand

A

nuclease

94
Q

function of topoisomerase that refers to the rejoining of cutted strands

A

ligase

95
Q

type 1 and type 2 topoisomerase is for ___

A

eukaryotes

96
Q

type 3 and type 2 topoisomerase is for ___

A

prokaryotes

97
Q

type II topoisomerase in prokaryotes is called as

A

DNA gyrase

98
Q

responsible for making single stranded break in a negative supercoil

A

type 2 topoisomerase

99
Q

negative supercoil means

A

coils towards left

100
Q

REPLICATION SEQUENCE SUMMARY

A
  1. Initiation
  2. Elongation
  3. Termination
101
Q

refers to all events happening in 1 replication bubble, wherein all the enzymes are working and replicating

A

replisome

102
Q

when will be the termination happen

A

when 2 replisome meet

103
Q

Eukaryotes can create _____ base pairs per second

A

100

104
Q

Prokaryotes can replicate ______ base pairs per
second

A

1000

105
Q

the principle helicase in e.coli is called as

A

dna B protein

106
Q

type of eukaryotic polymerase

A

alpha - minor same with type 1
major - major same with type 3
beta and epsilon - repair
gamma - replication of mitochondrial DNA

107
Q

Activities of Type I DNA
Topoisomerases

A

 Nuclease (strand-cutting)
 Ligase (strand-resealing)

108
Q

relax only negatively supercoiled DNA

A

Type IA Topoisomerases

109
Q

relax negative and positive supercoils by a
controlled rotation mechanism in eukaryotic cells

A

Type IB Topoisomerases

110
Q

type of topoisomerase that has energy involvement

A

type 2 and 3

111
Q

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)

A

Type II DNA Topoisomerases

112
Q

bp16

A

Etoposide/Tenoposide

113
Q

nhibit Top 2 and
cancer cells (Eukaryote

A

Etoposide/Tenoposide

114
Q

class of antibiotic that inhibits UTI

A

Fluoroquinolones

115
Q

example of Fluoroquinolones is

A

ciprofloxaciin

116
Q

Eukaryotic chromosomes end in
distinctive sequences called
______that help preserve the
integrity and stability of the
chromosome

A

telomeres

117
Q

Telomeres
don’t code
for any RNA

true or false

A

true

118
Q

enzyme contained by cells that do not age (Ex. Germ Line
Cells and Cancer Cell

A

Telomerase

119
Q

-replaces the lost ends

A

Telomerase

120
Q

special kind ofreverse transcriptase

A

telomerase

121
Q

act as template primer at the extreme ends of the
chromosomes → protects against telomere shortening

A

Telomerase

122
Q

carries its own RNA molecule

A

Telomerase

123
Q

have longer telomeres than their terminally differentiated
daughters

A

. Stem Cells

124
Q

-have great therapeutic potential

A

Stem Cells

125
Q

● A genetic mutation in the LMNA
gene causes .

A

progeria

126
Q

The LMNA gene is responsible for
making a protein called

A

lamin A.

127
Q

_____is an important part of the
structural scaffolding that holds
the nucleus of each cell in your
body together.

A

Lamin A

128
Q

Progeria -Progeria gets its name from the Greek
word “___,” which means, “old age.”

A

geras

129
Q

●-premature ageing syndrome
●-cells have extremely short telomeres

A

Progeria

130
Q

In RNA do we need a primer?

A

naur

131
Q

RNA polymerase can initiate the synthesis of new chains.

true or false

A

true

132
Q

In RNA polymerase, The DNA template is copied in the____ direction,

A

3’ to 5’

133
Q

The DNA template is copied in the 3’ to 5’ direction, and the RNA
chain grows in the ___direction.

A

5’ to 3’

134
Q

In RNA, we only need __ to initiate the synthesis of new chain

A

regions -

135
Q

what are the regions needed for RNA synthesis

A

■ Promoter region
■ Coding region
■ Termination region/silencer/enhancer

136
Q

In transcription, what region is the only one needed

A

promoter region

137
Q

Once the RNA polymerase found the promoter region,
initially transcription starts and is helped by a
transcription factor

which factor is it?

A

transcription factor II D (TFIID)

138
Q

RIBONUCLEATIDE TRIPHOSPHATE OF RNA

A

adenosine triphosphate,
Guanosine triphosphate
uridine triphosphate
and cytidine triphosphate

139
Q
A
140
Q

structural formula for RNA polymerase of bacteria

A

2 alpha
1 beta
1 beta prime
1 small omega

141
Q

6th subunit of RNA polymerase is the

A

sigma factor

142
Q

purpose of the 6th subunit

A

sigma factor is the one that will bind to the promotor region guided by the transcription factor II D

143
Q

RNA polymerases are holoenzyme because they contain how many units

A

2 units

144
Q

before the initiation takes place, there are ___ that are waiting for the RNA polymerase

A

transcription factors

145
Q

what are the example of transcription factors

A

transcription factors II B
transcription factors II E
transcription factors II H

146
Q

which transcription factors is responsible for the unwinding of the double helix sytructure

A

transcription factors II H

147
Q

they form the pre-initiations complex

A

transcription factors II B
transcription factors II E
transcription factors II H

148
Q

2 promoted sequences

A

TATAAT (PRIBNOW or TATA box )
TTGACA (a second consensus sequence )

149
Q

TATAAT (PRIBNOW or TATA box ) has bases upstream

A

10 bases upstream

150
Q

TTGACA (a second consensus sequence )

how many bases upstream

A

35 bases upstream

151
Q

the strand that is formed after unwinding and the strand that the RNA polymerase will attached is called as

A

non coding strand/antisense strand/template strand

152
Q

this strand will serves as the initial site for the RNA polymerase location

A

anti sense strand

153
Q

the other strand formed aside from the anti sense strand and what its characteristics

A

sense strand and the same with mRNA

154
Q

two types of termination

A

RHO dependent termination and intrinsic termination

155
Q

a type of termination wherein there’s a formation of hairpin loop due to the weak binding of adenine and thymine

A

Intrinsic termination

156
Q

type of termination that depends on a protein that will bind to the RNA polymerase removing it on the antisense strand

A

Protein dependent termination

157
Q

in Protein dependent termination, what is the protein being talked about?

A

RHO protein

158
Q

mRNA is considered as a ____ as it can code to different proteins

A

polycistronic

159
Q

proteins produced in polycistronic mRNA is called as

A

polysomes

160
Q

____is often produces as a polycistronic transcript that is translated as it is being transcribed

A

mRNA

161
Q

do prokaryotic mRNA need post transcriptional modification?

A

no, they dont have cap or something

162
Q

coding sequences of prokaryotic mRNA

A

cystron

163
Q

space between cystron is called as

A

interspacers

164
Q

___ is produced as a large transcript that is cleaved during the 16s rRNA that appears in the 30s ribosomal subunit

A

rRNA

165
Q

what is the precursor RNA

A

45s rRNA

166
Q

Precursor RNA–45S rRNA (undergoes cleavage to
produce two subunit:

A

the large and small ribosomal
subunit)

167
Q

the precursor RNA - 45S rRNA

the large ribosomal unit of the precursor RNA consists of

A

5s rRNA and 23s rRNA

168
Q

the precursor RNA - 45S rRNA

the small ribosomal unit of the precursor RNA consists of

A

16s rRNA

169
Q

a component of small ribosomal sub unit of precursor RNA that can detect the bacterial specie

A

16s rRNA

170
Q

do we have 16s rRNA?

A

naur

171
Q

the precursor RNA - 45S rRNA

the large ribosomal unit of the precursor RNA (______S)

A

50

172
Q

the precursor RNA - 45S rRNA

the small ribosomal unit of the precursor RNA (______S)

A

30

173
Q

if the ribosomal subunit is combined (large and small) bacteria will have ____ ribosomal unit

A

70S

174
Q

why is it not 80 s if the large and small ribosomal subunit of bacteria is added (70s )

A

they aren’t supposed to be added, the subunit is based on the shape and particle weight

175
Q

is usually produced from larger transcripts that are cleaved

A

tRNA

176
Q

cleaving enzyme of mRNA

A

snRNA (spliceosomes)

177
Q

cleaving enzyme of rRNA

A

ribozyme

178
Q

cleaving enzyme of tRNA

A

RNAse P

179
Q

antituberculosis drug (for M.
tuberculosis)

A

rifampin

180
Q

antibiotic and anticancer in pediatric populations (used to treat neuroblastoma, wilms’s tumor and sarcoma)

A

actinomycin D

181
Q

3 types of RNA polymerase of eukaryotes

A

RNA POLYMERASE I
RNA POLYMERASEII
RNA POLYMERASEIII

182
Q

responsible of RNA POLYMERASE I

A

catalyzes the production of rRNA

183
Q

where does the rRNA created

A

created in the darkly staining areas if the nucleus called nucleolus

184
Q

responsible of RNA POLYMERASE II

A

responsible for the creation of mRNA

185
Q

responsible of RNA POLYMERASE III

A

for the creation of tRNA

186
Q

responsible of RNA POLYMERASE III

aside from the creation of tRNA

A

CREATES 5S rRNA

187
Q

what makes the 5S RNA unique

A

only rRNA created by polymerase III
and the only rRNA synthesized in the nucleus

188
Q

concensus region in promoter region in mRNA

A

TATA (hogness)
CAAT
Guanine rich area

189
Q

TATA (hogness)
CAAT
Guanine rich area

base pairs upstream

A

TATA (hogness) - 25
CAAT - 70
Guanine rich area - 10 and 110

190
Q

a region that enhances the transcription

A

enhances

191
Q

a region that stops the transcriptions

A

silencers

192
Q

precursor mRNA

A

hnRNA

193
Q

the process of maturing hnRNA to mRNA is called as

A

post transcriptional modification

194
Q

is responsible for the protection of nascent mRNA against degradation

A

CAP

195
Q

CAP is responsible for the protection of nascent mRNA against degradation

aside from this?

A

initiates the translation and helps in exporting to cytoplasm and reach the ribosome

196
Q

mRNA carries codon, however, it must enter the ____ and exit to enter the ribosome for protein synthesis

A

NUCLEUS

197
Q

if the CAP initates translation, which tail we can fid the stoppage of initiation

A

poly A tail

198
Q

problems with the cutting of introns is associated to

A

thalassemia

199
Q

a toxin that can give us the death cap

A

MUSHROOM - alpha amanita

200
Q

DEATH CAP symptoms

A

can cause, gastroenteritis, nausea, vomiting, death

201
Q

starting and ending site of introns

A

AGGT

202
Q

__is clover leaf in structure

A

tRNA

203
Q

3 modified nucleoside in tRNA

A

dihydrouridine
ribothymidine
pseudouridine

204
Q

dihydrouridine
ribothymidine
pseudouridine

forms what arms

A

dihydrouridine - D arm
ribothymidine - T arm
pseudouridine - T arm

205
Q

holds the amino acid and the acceptor stem

A

covalent bonds

206
Q

catalyzes the addition of amino acid on the 3`end

A

nucleotidyl transferase

207
Q
A

MODX (5 decks)

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