Lecture 34(ADD U1/U4 sites)

Question 1

What are the phases of transcription?

Answer 1

Initiation, elongation, and termination

Question 2

What does initiation determine?

Answer 2

It determines where transcription will begin and which gene will be transcribed

Question 3

What are promoters?

Answer 3

DNA sequences located in the 5’ region adjacent to the transcriptional start site

Question 4

What happens to DNA when RNA pol holoenzyme binds?

Answer 4

It bends and unwinds

Question 5

What is true about sigma factors?

Answer 5

They have different degrees of binding and gene expressions

Question 6

What happens when the promoter region unwound?

Answer 6

Both strands become accessible and can be used for transcription

Question 7

What is true about the strands during transcription?

Answer 7

Only one of them is used while the other isn’t

Question 8

Which one is the coding strand?

Answer 8

The DNA strand that is complementary to the template strand

Question 8

What happens to the template strand?

Answer 8

It is by the RNA pol to make an mRNA. Bases are also added to the mRNA that are complementary to the template strand

Question 8

Does transcription need a primer?

Answer 8

No because RNA pol can initiate the synthesis of a new RNA chain using the temp DNA strand

Question 9

What nucleoside does RNA Pol use to begin transcription?

Answer 9

ribonucleoside 5 triphosphate to start the chain

Question 10

What is used to continue the chain during transcription by RNA pol?

Answer 10

Triphosphate monophosphate

Question 11

What provides energy for the chain that is built during transcription by RNA Pol?

Answer 11

Energy is provided by hydrolysis of the incoming triphosphate molecule

Question 12

What is released during DNA replication?

Answer 12

Pyrophosphate is released when a new nucleotide triphosphate is added onto the 3’ hydroxyl group of the previous nucleotide

Question 13

What does pyrophosphate do?

Answer 13

It forms a phosphodiester bond and is also hydrolyzed in a exergonic way that provides energy

Question 14

What happens when the first 10 nucleotides have been added? What is promoter escape?

Answer 14

The sigma dissociates upon transition from transcription initiation to transcription elongation. This is known as promoter escape.

Question 15

What happens when the sigma dissociates?

Answer 15

The remainder of the RNA polymerase will move down the DNA transcribing mRNA

Question 16

What is rho-independent?

Answer 16

It is where the DNA-RNA forms a loop due to a GC 3’ area that binds to itself. This loop causes the RNA pol to fall off. Also happens because of weak A-U bonds.

Question 16

What is the transcription bubble?

Answer 16

It is where approx. 18 bp of DNA are unwound within the polymerase. In other words, a small portion of DNA is unwound during transcription.

Question 17

What is rho-dependent?

Answer 17

This is where the rho protein has to bind and dissociates the RNA pol and moves it off the template. This happens during C rich areas because RNA pol usually stops here. Rho unwinds it and releases it.

Question 18

What do eukaryotes use for transcription?

Answer 18

They use transcription factors(not really the greek system). They also deal with other stuff like histones and chromatin

Question 19

What is a polycistronic message?

Answer 19

It is where one RNA transcript encodes for many proteins. This is only for bacteria(prokaryotes)

Question 20

What is a monocistronic message?

Answer 20

It is where one mRNA encodes for only one protein. This is for eukaryotes.

Question 21

what is the region of the TATA box?

Answer 21

-20 to -30 upstream. This is for euka.

Question 22

What is the region of the CCAT box?

Answer 22

-75. This is for euka

Question 23

What do transcription factors do?

Answer 23

They recruit and bind polymerase to the correct location

Question 24

What are the two domains of transcription factors?

Answer 24

1. DNA enhancing domain that binds to enhancer 2. transcriptional activation domain

Question 25

What does Carboxyl Terminal Domain do?

Answer 25

This domain regulates transcription and recruits protein that cap, splice and Poly A the RNA transcript.

Question 26

What regulates CTD?

Answer 26

phosphorylation

Question 27

What do enhancers do?

Answer 27

They recruit other activator proteins, transcription activating factors that later recruit transcription factors for transcription

Question 28

How does termination happen in transcription in eukaryotes?

Answer 28

It happens until the end of the gene and makes a AAUAAA signal where the RNA pol is cut and the tail is asses.

Question 29

What is the Poly A tail needed for?

Answer 29

It helps for stabilization and transport from nucleus to cytoplasm

Question 30

How is the cap made?

Answer 30

It is made of RNA Pol 2 and is made from 5 to 5 linkage. It uses a modified G that is also methylated at the 7 N position and at the 2 OH for the following position

Question 31

What is the cap useful for?

Answer 31

Protects the 5' end from exonuclease attack and is important for initiation and translation

Question 32

What do exons do that introns don't?

Answer 32

Exons encode AA while introns do not

Question 33

What does splicing do?

Answer 33

Removes introns, linking together protein coding regions

Question 34

Why do introns need to be removed?

Answer 34

You only want the cap, tail, and exons for mature mRNA

Question 35

How do proteins recognize introns?

Answer 35

Sequences at splice sites like introns having GU(begin) and AG (end)

Question 36

What is a lariat?

Answer 36

It is a looped intron removes during splicing

Question 37

How does a lariat happen?

Answer 37

Attack of 5’ end by branch point -OH to form lariat structure. Then cleavage of 3’ occurs, release of “lariat” RNA intron, which then gets degraded

Question 38

What is transesterification? How does it happen?

Answer 38

The 2’ –OH of the A residue attacks the 5’ phosphate of the G nucleotide at the splice site

Question 39

What happens because of the transesterification?

Answer 39

Phosphodiester group is transferred from 3’ end of exon sequence to A nucleotide of intron. Also, a branchpoint

Question 40

What are spliceosomes?

Answer 40

Spliceosomes are small nuclear ribonucleoprotein particles (snRNPs) containing small nuclear RNAs (snRNAs).

Question 41

What is alternative splicing?

Answer 41

Different combination of exons from the same gene are combined together

Question 42

What is an example of alternative splicing?

Answer 42

Tropomyosin gene. Different proteins can been coded by only one gene. Can allow for tissue-specific differences

Question 43

What happens to mRNA due to alternative splicing?

Answer 43

Mature mRNA possess different coding sequences and undergo translation into different proteins. Enlarges the number of possible proteins

Question 44

How does transcription work?

Answer 44

It is catalyzed by RNA Pol and can start without a primer

Question 45

What is TFIID? What does it contain?

Answer 45

The TBP(TATA) box that bends DNA and recruits polymerase to open DNA and initiate transcription

Question 46

What does U1 do?

Answer 46

binds G site of 5’ end intron

Question 47

What does U2 do?

Answer 47

Binds sits at branchpoint

Question 48

What does U4/6/5 do?

Answer 48

Bind the 5' end mediating 5' end cleavage and transfer branch point. Then

Question 49

What do U5/6 do together?

Answer 49

mediate cleavage of 3' end of intron and ligation of the 3' end of the first exon to the 5' end of the second exon