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Transcription Flashcards

1
Q

RNA is a polymer of _____ and ____ nucleotides linked by

A

purine and pyrimidine
phosphodiester bonds

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2
Q

Distribution of RNA in different cellular locations:

A

Distribution of RNA in different cellular locations:
50% in ribosomes and endoplasmic reticulum
25% in cytoplasm
15% in mitochondria
10% in nucleus

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3
Q

DNA replication occurs only during _____
Transcription occurs continuously, all the time.

A

cell division.

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4
Q

Genetic information of DNA is transcribed (copied) to

A

mRNA

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5
Q

During transcription, the message from the DNA is copied in the language of nucleotides (4-letter language).

A
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6
Q

The mRNA then reaches the _____ where it is translated into functional proteins.

A

cytoplasm

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7
Q

During translation, the nucleotide sequence is translated to the language of amino acid sequence (20-letter language).

A
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8
Q

during the process of DNA replication, not the entire DNA molecule is copied. Instead, only specific regions or segments of the DNA, which are located on the sense strand of the double-stranded DNA molecule, are replicated or copied.

A
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9
Q

RNA synthesis is carried out by large enzymes called .

A

RNA polymerases
This process is common to all living organisms

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10
Q

Rna polymerase search for specific sites on the DNA called

A

promoters, which mark the beginning of a gene. In E. coli bacteria, there are about 2000 promoter sites in their DNA.

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11
Q

How do RNA polymerases locate initiation sites or promoters on DNA?

A

RNA polymerases locate initiation sites or promoters on DNA by searching for specific sequences that mark the beginning of a gene. In the case of E. coli bacteria, there are approximately 2000 promoter sites in their DNA

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12
Q

How does RNA polymerase unwind DNA during transcription?

A

RNA polymerase unwinds DNA during transcription by separating the two strands of the double helix in a localized region, creating a single-stranded DNA template that can be used as a blueprint for RNA synthesis

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13
Q

What is the function of ribonucleoside triphosphates in transcription?

A

Ribonucleoside triphosphates are the building blocks of RNA. They provide the necessary nucleotide units that are added to the growing RNA chain during transcription.

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14
Q

How does RNA polymerase catalyze the formation of a phosphodiester bond?

A

RNA polymerase catalyzes the formation of a phosphodiester bond during transcription. The 3’-hydroxyl group of the last nucleotide in the RNA chain attacks the α-phosphoryl group of the incoming ribonucleoside triphosphate, resulting in the formation of a bond between them.

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15
Q

What is the processivity of RNA polymerase?

A

Processivity refers to the ability of RNA polymerase to synthesize the entire RNA strand in one continuous process without falling off the DNA template.

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16
Q

How does RNA polymerase identify termination signals?

A

RNA polymerase identifies termination signals that specify where the transcript should end. These signals can be specific DNA sequences or structural features that cause the RNA polymerase to stop transcription and release the completed RNA molecule.

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17
Q

How do activator and repressor proteins affect transcription initiation?

A

Activator and repressor proteins interact with RNA polymerase and modulate the rate of transcription initiation. Activator proteins enhance transcription, while repressor proteins suppress or inhibit transcription.

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18
Q

gene expression controlled at the level of

A

Transcription

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19
Q

What’s the main goal of RNA synthesis

A

is the formation of a phosphodiester bond. This reaction involves the 3’-hydroxyl group of the last nucleotide in the RNA chain attacking the α-phosphoryl group of the incoming ribonucleoside triphosphate, resulting in the formation of a bond between them

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20
Q

What is the significance of the two metal ions in RNA polymerases?

A

The catalytic sites of RNA polymerases contain two metal ions, typically magnesium ions. These metal ions assist in facilitating the chemical reactions involved in transcription.

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21
Q

What happens to the pyrophosphate molecule during RNA synthesis?

A
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22
Q

Why is the formation of a phosphodiester bond

A

The formation of a phosphodiester bond is thermodynamically favorable because it releases energy and results in the production of a more stable molecule (RNA) compared to the individual reactants.

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23
Q

What happens to the pyrophosphate molecule during RNA synthesis?

A

The pyrophosphate molecule, which is released during the formation of a phosphodiester bond, is further degraded to orthophosphate. This breakdown helps drive the reaction in the direction of RNA synthesis.

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24
Q

What is the role of orthophosphate in RNA synthesis?

A

Orthophosphate, which is produced from the degradation of pyrophosphate, helps lock the reaction in the direction of RNA synthesis and further contributes to the overall stability of the RNA molecule.

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25
Q

The template strand transcribed to give mRNA is called

A

(-), antisense strand
It has complementary sequence to mRNA ie opposite

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26
Q

The opposite strand has the same sequence as the mRNA, and is called

A

coding strand or antitemplate strand or nontemplate or (+) or sense strand.

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27
Q

What’s RNA transcription signals

A

RNA transcription signals are specific areas on DNA that act as starting signals for the initiation process of making RNA copies.

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28
Q

______specific spot on the DNA where a molecule called RNAP attaches.
RNA polymerase

A

Promoter

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29
Q

Human DNA has approximately transcription initiation sites.

A

105

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30
Q

Bacterial DNA has a specific sequence called ____’, and _____located about ___ & _____base pairs upstream of the transcription start site.

A

5’-TGTTGACA-3 and 5’-TATAAT-3(known as the TATA box or Pribnow box)
35 & 10

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31
Q

In mammals, the TATA box sequence is slightly different it’s ____ and is called the
The TATA box is located at position ____ to ____and serves as a signal for the start region of transcription.

A

(TATAAA)
Golberg-Hogness box.
-25 to -30

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32
Q

Further upstream, between positions ___&____ there is another sequence called , known as the CAAT box.

A

-70 and -80,
GGCCAATCT

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33
Q

These recognition signals are cis-acting, meaning

A

they are located near the gene they regulate.

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34
Q

Enhancers increase the rate of transcription, while silencers decrease the rate.

A
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35
Q

Other regulatory signals for transcription include

A

hormone response elements (HRE), repressors, inducers, and derepressors.

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36
Q

The starting point of transcription in bacteria is the
The nucleotide next to the downstream of the starting point is numbered

A

5’ nucleotide of the DNA, designated as +1.
as -1.

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37
Q

RNA polymerase (RNAP) binds to the ______ site on DNA with the help of a _________, forming the pre-initiation complex (PIC). Prokaryotes

A

RNA polymerase (RNAP) binds to the promoter site on DNA with the help of a sigma factor, forming the pre-initiation complex (PIC).

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38
Q

The first nucleotide of the mRNA attaches to the initiation site on the RNAP when it reaches the appropriate site on the gene. This nucleotide becomes the _____’ end of the mRNA and is complementary to the DNA base at that site.

A

5

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39
Q

Transcription begins with the initiation of the mRNA, and______ is usually the first unit in the mRNA.

A

a purine ribonucleotide

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40
Q

After about 10-20 nucleotides are polymerized, the RNAP undergoes a conformational change and moves away from the promoter region. This is called _____ and the sigma factor is released.

A

promoter clearance,

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41
Q

Eukaryote

A
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42
Q

In eukaryotes, the transcription process is more complex. It involves at least ___ transcription factors collectively referred to as ___.

A

7
Tf-II

43
Q

The TATA box, a specific DNA sequence, is recognized by a protein called TBP (TATA binding protein) in prokayotes. In eukaryotes, a different factor called ___ ensures that the RNAP can locate the start point.

A

SL1

44
Q

In humans, there are approximately 105 transcription initiation sites available
.The human TATA box binds to a multi-subunit protein called __, and other proteins called ___ bind to TBP to form a complex called .

A

TBP
TAFs

TFIID

45
Q

______ is the first step in the transcription process in eukaryotes.

A

Binding of the TFIID complex to the TATA box

46
Q

mammals, there are general transcription factors (GTFs) that help with promoter-specific binding to form the pre-initiation complex

A
47
Q

______ classes of transcription factors are involved in the transcription of mammalian genes namelt

A

Three
: basal components (e.g., TBP, TFIIA, B, E, F, and H), co-regulators (e.g., TAFs, TFIID, Meds, chromatin modifiers), and activators (e.g., SP1, ATF, AP1).

48
Q

Whats the base pairing rule.

A

The base pairing rule states that A in DNA is transcribed to U in mRNA, T to A, G to C, and C to G.

49
Q

The polarity of mRNA synthesis is analogous to the polarity in DNA synthesis meaning?

A
50
Q

As the RNAP moves on the DNA template, the DNA helix unwinds ____ and rewinds _____.

A

downstream
upstream

51
Q

The RNAP has the property of unwinding the DNA, but topo-isomerase also assists in the unwinding process

A
52
Q

A transcription bubble is formed, which includes ____,____&___. The transcription bubble is about _____ base pairs in length

A

RNAP, DNA, and the nascent RNA molecule
20

53
Q

RNAP does not have nuclease activity, which means ____

A

there is no proofreading mechanism during transcription.

54
Q

The fidelity of mRNA transcription is lower compared to DNA replication, with a mistake rate approximately _____

A

10^4 to 10^5 times higher.

55
Q

However, the mistakes in mRNA transcription are not transmitted to daughter cells or the next generation, making them less significant.

A
56
Q

____ type of RNAP is responsible for mRNA rrna and trna

A

Type 2
Type 1
Type 3

57
Q

What’s the base paring for rna

A

Thus A in DNA is transcribed to U in mRNA; T to A; G to C and C to G

58
Q

RNAP has no nuclease activity; so there is no proof reading
But it is less serious, since these mistakes are not transmitted to the daughter cells or to the next
generation.

A
59
Q

Function of RNAP

A

Stabilize
Unwinds
Read and synthsize

60
Q

TERMINATION

A
61
Q

Types of termination

A

Role dependent termination
Rho proteins causes rnaP to break away from the DNA

Rho independent termination
Inverted repeat causes a hair pin loop due to its attraction releasing cleavage enzymes that stops it CCGG

Eukaryotic cells
A sequence of DNA AAUAAA a polyadenylation signal which activates enzymes to come cleavethe DNA anway from rnaP

62
Q

RnaP reads the _____strand

A

Template

63
Q

Rho independent termination is also described.
In humans, the termination signals exist far downstream of the coding sequence, usually ____to_____bases away.

A

1000 to
2000 bases away

64
Q

There are _____ different types of RNAPS in higher organisms and all are DNA dependent.
Mammalian rnaP

A

3

65
Q

 They have molecular weight of
Mammalian rnaP

A

500 to 600 kDa

66
Q

RNAP type ____is the main enzyme synthesizing mRNAs. It is inhibited by

Mammalian rnaP

A

II or B
alpha amanitin, a toxin from the mushroom Amanita phalloides

67
Q

How does amanitin block rnaP
Mammalian rnaP

A

Amanitin blocks the translocation of RNAP during mRNA synthesis.

68
Q

____&_____ are also synthesized by the same RNAP B. Mammalian rnaP

A

SnRNA and miRNA

69
Q

RNAP has ____ large and ___ smaller subunits, it is Activated by ____
Mammalian rnaP

A

2 and 12
phosphorylation

70
Q

RNAP type I or A is responsible for synthesis of rRNA (ribosomal); it is not inhibited by
amanitin.Mammalian rnaP

A
71
Q

RNAP type III or C is responsible for production of tRNA; it is moderately sensitive to amanitin
Mammalian rnaP

A
72
Q

Bacterial RNAP:
The enzyme contains ____&____subunits
____ subunit, ____factor and _____ molecules

A

two alpha, two beta
one omega subunit and one sigma factor and two zinc molecules

73
Q

Function of them beta and sigma factor

A

Beta subunit fixes at the initiation site.
Sigma factor recognises the promoter site and increases the affinity of the holo-enzyme to the promoter site

74
Q

Types of rna and it’s% of rna

A

Mrna- DNA is transcribed into mRNA
Constitutes 2-5% of total rna
Degraded quickly

rRNA- constitutes about 80% of all RNA in the cell… They are involved in the protein biosynthesis and they are very stable

tRNA- constitute about 15% of the total RNA… They are very stable

Small RNA.- constitute about 1-2% of total RNA in the cell. There are about 30 different varities

75
Q

What are the major variety of rrna

A

28S, 18S and 5S are the major varieties

76
Q

_____ are a subgroup of small RNA

A

Small Nuclear RNAs (SnRNAs)

77
Q

Some important species of SnRNAs are

A

U1 (165 nucleotides), U2 (188 nucleotides), U3 (216),U4 (139), U5 (118), U6 (106)

78
Q

SnRNA sizes ranges from ____to____

A

size ranges from 90-300 nucleotides

79
Q

 They are named as U1, U2, U4, U5, U6 and U7
SnRNA
The U stands for

A

Uracil rich nature of SnRNA

80
Q

SnRNA takes part in the formation of ____
And they are all located at

A

spliceosomes
The nucleus

81
Q

It is pronounced as “Snurps”. Production of autoantibodies against “Snurps” cause a fatal autoimmune disease called

A

systemic lupus
erythematosis (SLE),

82
Q

SnRNA are involved in DNA splicing*

A
83
Q

miRNA alter the function of mRNA and ____ly stable

A

Moderately

84
Q

Heterogeneous mRNA is also called

A

Immature mrna

85
Q

The 5 prime end has_____ and 3____

A

Phosphate group has a triphosohate
OH

86
Q

After tri phosphatase cleaves one phosphatate from the tri phosphate _____ is added to the remaining 2 by___

A

A gmp(guanocynene monophaphate) molecule is added by guanayly transferase

87
Q

After gmp is added ___ is later added by____ what

A

Methyl group is added by methyltransferase

88
Q

After adding all that it forms the 7 methyl guanosine group and the entire process is called capping
And the function of capping is?

A

Helps interact with ribosome and undergo translation
Helps prevent degradation by nucleases

89
Q

What aids methyltransferase in adding the methyl group to the 5 phosphate site

A

S Adenosyl methionine SAM

90
Q

On the 3 OH side the polyadenylation signal is located______adds AAAAAAA groups to it forming the ______

A

Poly A Polymerase
Poly A tail

91
Q

Function of Poly A tail

A

Helps interact with ribosome and undergo translation
Helps prevent degradation by nucleases
Helps in transportating immature mrna

92
Q

In the premature hnrna ____ codes for amino acids
____ doesn’t code for AA

A

Hexons
Introns

93
Q

____ helps cleave the intron and adds the hexons together forming a functional mRNA

A

SNRPS
small nucleus rna and proteins

94
Q

Retrovirus particles contain _____

A

two copies of a single-stranded RNA molecule.

95
Q

Retroviruses are a type of virus that have two copies of a single-stranded RNA molecule. When they enter a host cell, one copy of the RNA serves as a template for an unusual enzyme called

A

reverse transcriptase

96
Q

Function of reverse transcriptase

A

This enzyme makes a new DNA strand based on the RNA template.

97
Q

The resulting double-stranded DNA version of the viral genome becomes a part of the host cell’s chromosomal DNA and is replicated along with the cell’s own DNA. This means that the viral genetic material is integrated into the host cell’s DNA.

A
98
Q

To complete this process, the RNA part of the RNA-DNA hybrid is broken down by a specific enzyme called .

A

RNAse-H

99
Q

Transcription inhibitor
Some of them are of natural origin e.g.
And others are

A

from fungus such as streptomyces which produces Rifamycin and Mitomycin
Systemic & semi systemic

100
Q

What drugs are used as anticancer drugs & how? And they are from

A

Actinomycin D (antibiotics from streptomyces) by inserting phenoxazone ring between 2 G-C bp of DNA

and Mitomycin intercalate with DNA strands, thus blocking transcription hence are
used as anticancer drugs.

101
Q

____ drug is used to treat tuberculosis and leprosy
P from ____
How?

A

Rigampicin
Synthetic derivative of ryfamicin
Binds to neta subunit of RNAP which is inactivated

102
Q

Alpha manitin
A toxin from mushroom
Inactivates RNAP2

A
103
Q

3 deoxy adenosine
Synthetic analog
Causes incorrect entry into chain causing chain termination

A

BCH (16 decks)

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