Gene Transcription & RNA modification (part 2)

Question 1

After ________ is assembled into its six subunits it binds loosely to the DNA & slides along the DNA looking for the promoter

Answer 1

RNA polymerase holoenzyme

Question 2

Once the RNA polymerase holoenzyme finds the promoter what happens?

Answer 2

The sigma factor recognizes both the -35 & -10 sequences & its helix turn - helix motif allows it to bind tightly to those sequences

Question 3

Describe the initiation process in bacterial transcription?

Answer 3

1. Holoenzyme scans DNA & sigma factor recognizes promoter & binds tightly to it
2. A close complex is formed
3. Short RNA is made in the open complex where the sigma factor is released
4. Core enzymes elongates

Question 4

The process of _________ is initiated when the sigma factor within holoenzyme binds to the promoter to form a closed complex

Answer 4

Transcription

Question 5

In the ________ the strand of DNA in the promoter region are not separated

Answer 5

Closed Complex

Question 6

So to actually begin transcription in bacteria what must happen?

Answer 6

The double-stranded DNA must be unwinded by DNA helicase to form a open complex

Question 7

Where does the unwinding of DNA begin at?

Answer 7

The TATAAT or TATA box region because its easier to break A-T bonds since it only has 2 hydrogen bonds

Question 8

Sigma binding occurs in the ________ where the DNA is still double stranded

Answer 8

Close complex

Question 9

TATA box unwinding occurs in the ________ to actually start transcription

Answer 9

Open complex

Question 10

__________RNA is made in the open complex & when the sigma factor is released initiation ends

Answer 10

Nascent RNA

Question 11

The RNA transcript is synthesized during __________ stage

Answer 11

Elongation Stage

Question 12

The mRNA is made in the ________ direction with no proof reading

Answer 12

5’ to 3’ direction

Question 13

Template strand

Answer 13

DNA strand that is used as a template for RNA synthesis (antisense strand)

Question 14

Coding Strand

Answer 14

Strand being formed by using the template strand (sense strand & uses U instead of T)

Question 15

RNA follow what base rules?

Answer 15

A-U & G-C

Question 16

The template strand is read in the 3’ to 5’ direction but mRNA is made in the __________ direction

Answer 16

5’ to 3’ direction

Question 17

The location of the template strand can affect the ______ mRNA is made where if the top strand is the template strand then it is made from right to left but if the bottom strand is use then its made from left to right ( so transcription can occur in opposite directions)

Answer 17

Direction

Question 18

Transcription is terminated by either an __________ or a ___________

Answer 18

RNA binding protein or intrinsic terminator

Question 19

Describe the elongation stage

Answer 19

1. RNA polymerase slides along the DNA creating an open complex as it moves
2. The template strands is used to make complementary copy of RNA as RNA-DNA hybrid
3. RNA polymerase moves along the template strand in a 3’-5’ direction & mRNA is made in the 5’-3’ direction

Question 20

_________ occurs when the short RNA-DNA hybrid region is forced to separate & release new mRNA & RNA polymerase

Answer 20

Termination

Question 21

_________ ends elongation

Answer 21

Termination

Question 22

What are the two different mechanism of termination in E. Coli?

Answer 22

1. p (rho)-dependent

2. p(rho)-independent

Question 23

In p(rho) dependent termination what happens?

Answer 23

The termination requires a protein to end termination

Question 24

What are the 2 sequences that p(rho) dependent termination need?

Answer 24

1. Rut Site (rho utilization site)

2. p(rho) protein

Question 25

Rut site acts as a recognition site for ________

Answer 25

rho (p) protein

Question 26

The ________ acts as a helicase & separates the RNA-DNA hybrid region

Answer 26

rho (p) protein

Question 27

Describe the rho(p) dependent termination process

Answer 27

1. p recognition site on the mRNA allows the rho (p) protein to bind to the rut site on the mRNA & move toward the 3' end 2. RNA polymerase trancribes a region that forms a stem loop & proceeds to the terminator . The stem loop cause RNA polymerase to pause 3. While its paused the rho (p) protein catches up to the open complex & separates the RNA -DNA hybrid & the complete RNA strand & RNA polymerase is released

Question 28

rho (p) independent (or intrinsic) termination

Answer 28

Doesn't require rho (p) protein

Question 29

What are the two sequences (regions) in rho (p) independent?

Answer 29

1. U rich region at 3' which has weak A-U bonds | 2. Stem loop before U rich region

Question 30

Describe rho (p) independent process

Answer 30

1. Stem loop causes RNA polymerase to pause & NusA stabilizes the pausing 2. While RNA polymerase is paused the weak bonded U rich sequences is not bale to hold the RNA-DNA hybrid together & is termination occurs by it falling apart

Question 31

Gene transcription in eukaryotes is similar to bacterial gene transcription but more _______

Answer 31

Complex

Question 32

Why is eukaryote gene transcription more complex?

Answer 32

Its larger, contain organelles & is multicellular

Question 33

What are the 3 different types of RNA polymerase used in eukaryote gene transcription?

Answer 33

1. RNA polymerase 1 2. RNA polymerase 2 3. RNA polymerase 3

Question 34

RNA polymerase 1

Answer 34

Transcribes all of the genes for ribosomal RNA (rRNA)

Question 35

RNA polymerase 2

Answer 35

Transcribe all protein-encoding genes so its responsible for the synthesis of mRNA which leads to translation

Question 36

RNA polymerase 3

Answer 36

Transcribes all the genes for tRNA (transfer RNA) & leads to translation

Question 37

RNA polymerase in prokaryotes & eukaryotes have a _______ shape

Answer 37

Hand Shape

Question 38

Eukaryotic protein encoding genes have a _________ & _________

Answer 38

Core promoter & regulatory elements

Question 39

What are the 2 features found in most promoters ?

Answer 39

1. Core promoter | 2. Regulatory sequences

Question 40

Core promoter

Answer 40

Short DNA sequence that is necessary for transcription to take place, it contains TATA box & transcriptional star site where transcription begins

Question 41

Core promoter produces what?

Answer 41

Basal transcription- produces low level of transcription & has no regulatory sequence

Question 42

Regulatory sequences

Answer 42

Short DNA sequences that affect the ability of RNA polymerase to recognize the core promoter & also where regulatory proteins bind to

Question 43

What are the two types of regulatory sequences?

Answer 43

1. Enhancer | 2. Silencer

Question 44

Enhancer

Answer 44

Are activating sequences that are need to stimulate transcription

Question 45

Silencers

Answer 45

Prevent transcription of a gene

Question 46

Regulatory sequence are found between _______ & _______

Answer 46

-100 & -50

Question 47

TATA Box, enhancers, & silencers are all _________ factors

Answer 47

Cis-acting Factors

Question 48

What are the two factors that control transcription?

Answer 48

1. Cis-acting factor | 2. Trans-acting factor

Question 49

Cis-acting factor

Answer 49

Are always on the same molecule as the gene they regulate & they regulate themselves (used for DNA sequences)

Question 50

Trans-acting factor

Answer 50

Binds to cis acting factor & regulates others, they are on a different molecule from the gene they regulate (use for proteins)

Question 51

RNA polymerase & regulatory proteins are __________

Answer 51

Trans-factors

Question 52

Transcription of eukaryotic protein encoding genes is initiated when ________ & __________ factors bind to a promoter sequence

Answer 52

RNA polymerase 2 & general transcription factors