Transcription

Question 1

Creation of complementary mRNA sequences from short strands of DNA

Answer 1

Transcription

Question 2

Which strand of DNA is transcribed and in what direction

Answer 2

Template strand; 5’ to 3’

Question 3

3 major components need in transcription

Answer 3

1. a DNA template
2. Raw materials or substrates for RNA
3. Transcription apparatus consisting of enzymes to catalyze RNA synthesis

Question 4

Transcription starts when enzymes recognize the _________ and ends at the _________. In between is the ______ of the gene which is copied into an RNA molecule

Answer 4

Promoter region; Terminator region; RNA-coding region

Question 5

In terms of direction, upstream refers to the what end of the DNA

Answer 5

5’-end

Question 6

The mRNA is complementary and antiparallel to the ____ strand

Answer 6

Template

Question 7

Bacterial RNA polymerase has _ alpha, _ beta, _beta prime, and _ omega

Answer 7

2,1,1,1

Question 8

It joins and leaves the core enzymes as it is needed forming a holoenzyme. It recognizes a specific promoter region for every particular gene

Answer 8

Sigma factor

Question 9

_______ are antibiotics that target bacterial RNA polymerases. Commonly used as cures against______

Answer 9

Rifamycins; Tubercolosis

Question 9

True or False: An RNA polymerase without a sigma factor will not bind to any part of the genome

Answer 9

False

Question 10

Define the mechanistic action of rifamycin

Answer 10

Binds to the part where the RNA polymerase should bind to the DNA

Question 11

Enumerate the phases of transcription

Answer 11

1. Initiation phase
2. Elongation Phase
3. Termination Phase

Question 12

Enumerate the phases of initiation

Answer 12

-Promoter recognition
-Formation of the transcription bubble
-Creation of first bonds between rNTPs
-Escape of transcription apparatus from the promoter

Question 13

Promoters have different affinities for RNA polymerase. Give a consequence/advantage of these differences

Answer 13

These differences lead to variations on frequency and prioritization of expression of genes.

Question 14

Are short sequences of considerable similarity found in promoter regions

Answer 14

Consensus sequence

Question 15

The most common consensus sequence in prokaryotes

Answer 15

Pribnow box or -10 consensus sequence

Question 15

Give an example of a specific sequence in Pribnow box/ -10 consensus sequence

Answer 15

TATAAT

Question 16

True or False: Pribnow box is always TATAAT

Answer 16

False

Question 17

A consensus sequence in prokaryotes that control the rate of transcription

Answer 17

-35 consensus sequence

Question 18

Difference between down mutation and up mutation

Answer 18

Rate of transcription (Down= Reduce, Up=Increase)

Question 19

Unwinding of gene beings at the ___ consensus sequence and extends downstream covering ___ to ___ sites

Answer 19

-10; -12: +12

Question 20

How much nucleotides are transcribed as initial abortive attempts before proceeding to the elongation phase?

Answer 20

2-6 nucleotides

Question 21

True or False: During elongation, the sigma subunit should always be released regardless of the type of RNA

Answer 21

False; Should be either depending on the type of RNA

Question 22

During elongation phase, the leading edge is found in what direction. In what direction does the trailing edge found?

Answer 22

Downstream= Leading edge
Upstream= Trailing edge

Question 23

Which is faster, the transcription of bacteria or eukaryotes? Describe the magnitude of their difference

Answer 23

Eukaryotes are faster having 1000-2000 nucleotides per second while prokaryotes have 40 nucleotides per second

Question 24

In Elongation phase, it is around 18 nucleotides in length of unwound DNA where the mRNA is continuously synthesized

Answer 24

Transcription bubble

Question 25

Negative supercoiling is found upstream of downstream?

Answer 25

Upstream

Question 26

Enzyme that relieves the stress associated with unwinding and rewinding of DNA

Answer 26

Topoisomerase

Question 27

True or False. Termination phase is an abrupt stop

Answer 27

False

Question 28

Enumerate the process of termination phase

Answer 28

-RNA polymerase stops synthesizing RNA -RNA molecules is released from RNA polymerase -Newly made RNA dissociates from the DNA -The RNA polymerase detaches from DNA

Question 29

Enumerate the process of Rho-dependent termination

Answer 29

-Rho protein binds to the binding site of the unstructured RNA and moves toward its 3'-end -Rho protein has helicase activity that unwinds RNA-DNA hybrid in the transcription bubble The RNA polymerase pauses when it encounters the terminator site, then the rho protein to catches up

Question 30

Type of terminators in prokaryotes that contains inverted repeats that form hairpins when transcribed into mRNA

Answer 30

Rho-independent terminators

Question 31

Explain the process of Rho-independent terminators

Answer 31

-Inverted repeats are followed by 7-9 A positions that convert to a string of U -The hairpins serve as blocks to destabilize the DNA-RNA pairings -The weak A-U string pairing facilitates the separation of DNA and RNA

Question 32

Polycistronic mRNA is common in _____ while monocistronic is common in _______

Answer 32

Prokaryotes; Eukaryotes

Question 33

Define the functions of the following bacterial RNA polymerase: -RNA Polymerase I -RNA Polymerase II -RNA Polymerase III -RNA polymerase IV and V

Answer 33

-For RNA transcription -For transcribing pre-mRNAs, snoRNAs, some miRNAs, and some snRNAs -Transcribing other small RNA molecules (tRNAs, small rRNA, and some miRNAs and snRNAs) -Transcribe RNAs that play roles in DNA methylation and chromatic structure in plants

Question 34

In Eukaryote Transcription, they assemble near the start site of a gene to initiate minimal levels of transcription together with the RNA polymerase

Answer 34

General Transcription Factors

Question 35

This is the combination of general transcription factor and RNA polymerase in eukaryote transcription

Answer 35

Transcriptional Activator Apparatus

Question 36

In eukaryote transcription, this stimulates formation of the basal transcription apparatus at the start site of a gene

Answer 36

Transcriptional Activator Proteins

Question 37

In eukaryote transcription, this is where the basal transcription apparatus binds and located upstream of the gene

Answer 37

Core promoter

Question 38

In eukaryote transcription, it is composed of TATAAA and is found -25 to -30bp upstream of the start site

Answer 38

TATA box

Question 39

in eukaryote transcription, these are located immediately upstream to core promoters and where transcriptional activator proteins binds. These mostly affect rate of transcription

Answer 39

Regulatory Promoters

Question 40

More distant upstream sequences in eukaryote transcription; These sites often loop out so that these can directly connect to the basal activator protein at the core promoter

Answer 40

Enhancers

Question 41

Where do the protein complex attach? Basal Transcription Apparatus: Transcriptional Activator Proteins:

Answer 41

Basal Transcription Apparatus: Core promoters Transcriptional Activator Proteins: Regulatory promoters and Enhancers

Question 42

Sigma factor of prokaryotes is what of eukaryotes?

Answer 42

Transcription factors

Question 43

What trasncription factor recognizes the TATA box with its TATA-binding protein?

Answer 43

TFIID

Question 44

In eukaryote transcription, this is formed when the single-stranded DNA is positioned within the active site of the RNA polymerase

Answer 44

Open complex

Question 45

Elongation starts at ___bp from the start site when the transcription factors separate for re-use in other transcription events

Answer 45

30bp

Question 46

True or False. RNA Polymerase I in Eukaryote Transcription is similar to rho-dependent termination in Bacteria

Answer 46

True

Question 47

In RNA polymerase I termination, it requires a _________ but it binds to a sequence ________ of the stop site

Answer 47

Termination Factor; Downstream

Question 48

True or False. RNA Polymerase III termination is similar to the Rho-dependent termination in bacteria

Answer 48

False

Question 49

Difference between RNA polymerase III and the Rho-independent termination of Bacteria

Answer 49

Lack of hairpin structure after string of U

Question 50

Describe the series of event in RNA polymerase II termination

Answer 50

-Transcription continues well beyond the termination site producing a pre-mRNA -The pre-mRNA is cleaved at a consensus site which separates from the excess non-coding part by the Rat1 -Rat 1 proceeds to degrade until it reaches the transcription machinery

Question 51

Archaea RNA polymerase recognizes TATA-box using what transcription factor?

Answer 51

TFIIB