RNA

Question 1

How is RNA hydrolyzed?

Answer 1

RNA is far more easily hydrolyzed than DNA due to nucelophilic attach by 2’ OH on the phosphodiester bond.

Question 2

What are the three classes of RNA in the human cell?

Answer 2

Structural RNA, Regulatory RNA and Information-Containing RNA

Question 3

How does puromycin mimic amino-acyl tRNA to terminate translation?

Answer 3

Puromycine is a nucleotide analog that mimics the tRNA acceptor region, targeting the acceptor stem loop, and binding to the ribosome as it elongates the polypeptide chain to terminate translation.

Question 4

Transcription Unit

Answer 4

The segment of DNA which gets transcribed into RNA

Question 5

Gene

Answer 5

Transcription unit flanked non-transcribed “regulatory” DNA seqeunces

Question 6

The first base pair where transcription initiates is designated __________

Answer 6

+1

Question 7

Downstream, bases are assigned ________ numbers

Answer 7

Positive

Question 8

Upstream, bases are assigned ___________ numbers

Answer 8

Negative

Question 9

RNA pol II makes ___________

Answer 9

mRNA

Question 10

RNA transcript is read from the __________ and mimics the ___________

Answer 10

DNA template strand; DNA nontemplate (coding) strand

Question 11

Enhancers

Answer 11

Enhance promoters; can be upstream or downstream; can also be an intron

Question 12

Transcription always begins on ___________

Answer 12

Exon 1

Question 13

DNA binding domain

Answer 13

Segment in a protein which recognizes the correct DNA sequence (promotor)

Question 14

Activation domain

Answer 14

Facilitates protein-protein contact with general transcription factors

Question 15

RNA synthesis is __________ and ___________, meaning it can only grow from one end.

Answer 15

Unidirectional; processive

Question 16

Explain the five steps in the transcription cycle common to bacterial and eukaryotic polymerases.

Answer 16

1. RNA polymerase sits on the promoter sequence, upstream of the transcription start site
2. The double-stranded DNA is opened, creating a transcription bubble and exposing the template strand
3. RNA nuceloside triphosphates come and lay themselves down after polymerase creates the phosphodiester linkage of two initial rNTP’s
4. Reaches the end of a gene and gets signal to terminate transcription
5. RNA polymerase lets go of template (DNA) and RNA product

Question 17

Promoter escape

Answer 17

Point where RNA polymerase begins moving

Question 18

When is the moment of initiation?

Answer 18

When the polymerase catalyzes the phosphodiester linkage of two initial rNTP’s

Question 19

When does regulation of transcription occur?

Answer 19

Regulation of transcription occurs during initiation and elongation

Question 20

Function of RNA polymerase I

Answer 20

Make rRNA

Question 21

Where are polymerase I-III located?

Answer 21

Nucleus

Question 22

Polymerase I-III are in the same family as _________

Answer 22

bacterial RNA polymerase

Question 23

Function of polymerase II

Answer 23

Makes mRNA, snRNA, miRNA, incRNA

Question 24

Where is polymerase IV located?

Answer 24

In the mitochondria

Question 25

What is a promoter?

Answer 25

Promoters direct RNA polymerase to the start of genes; control the direction and frequency of transcription

Question 26

Binding of the ________ to the_______ helps direct assembly of the pre-initiation complex at the promoter.

Answer 26

TATA box binding protein; TATA box

Question 27

Where is the TATA box located?

Answer 27

In the minor groove

Question 28

What is the promoter recognition factor in RNA polymerase II?

Answer 28

TFIID

Question 29

Alpha-AMantin, from the death cap mushroom Amnita phalloides is a ___________ inhibitor of RNA pol II. It binds to the _______ and blocks RNA chain elongation by preventing translocation.

Answer 29

non-competative inhibitor; bridge helix

Question 30

Rifampin is an __________ which binds to bacterial RNA polymerase and blocks the ________

Answer 30

Antibiotic, RNA exit channel

Question 31

What is TFIID transcription factor's role in the pre-initiation complex

Answer 31

Recognizes the TATA box

Question 32

What is TFIIB transcription factor's role in the pre-initiation complex?

Answer 32

Positions RNA polymerase at the start site of transcription.

Question 33

What is TFIIF transcription factor's role in the pre-initiation complex?

Answer 33

Stabilizes RNA polymerase interaction and attracts TFIIE and TFIIH

Question 34

What is TFIIH transcription factor's role in the pre-initiation complex?

Answer 34

Unwinds DNA at transcription start point, phosphorylates Ser3 of the RNA polymerase CTD, releases RNA polymerase from the promotor

Question 35

TFIIH is a _________ and a ___________

Answer 35

Transcription factor; DNA repair factor

Question 36

What is the function of XPB helicase of the TFIIH transcription factor?

Answer 36

XPB helicase opens DNA at the promoter to permit initiation of transcription

Question 37

What are the three diseases associated with TFIIH mutation?

Answer 37

Xeroderma pigmentosum, Cockaynes syndrome and trichothiodystrophy

Question 38

What the three benefits in the addition of the Poly-A tail?

Answer 38

1. Binds to the poly A binding protein 2. Protection from degradation on the 3' end 3. Enhanced translation

Question 39

What the three major ways in which most pre-RNA's are processed?

Answer 39

1. Capping 2. Splicing 3. Cleavage/polyadenylation

Question 40

During capping of the _________ end, the first base is replaced by a cap, Which is a _________ structure that is added backwards.

Answer 40

5'; Guanine

Question 41

What are the three main function of the 5' cap of the mRNA?

Answer 41

1. Protects the 5' end from exonucleases 1. Provides a recognition site 3. Decapping is the initiation of degradation of mRNA

Question 42

What is elF4E?

Answer 42

elF4E is a cap-binding protein and a critical stimulator of translation on ribosomes

Question 43

What are the three enzymatic reactions required to add a 5' cap to pre-mRNA?

Answer 43

1. Triphosphatase removes a phosphate 2. Guanyltransferase adds a GMP backwards 3. Guanine 7 methyl transferase methylates the N7 position on Guanine

Question 44

What is the sequence at the 5' splice site?

Answer 44

GU/GT

Question 45

What is conserved within every branch point?

Answer 45

'A' residue

Question 46

What is the sequence at the 3' splice site?

Answer 46

AG

Question 47

What is the consensus sequence at the poly-A tail?

Answer 47

AATAA/ AAUAA

Question 48

What is the Spliceosome?

Answer 48

Ribonucleoprotein complex composed of multiple small nuclear ribonuceloprotins (snRNPs)

Question 49

What is Marfan's Syndrome?

Answer 49

A dominant autosomal disease caused by a mutation that disrupts splicing of the fibrullin gene transcript (connective tissue)

Question 50

What is the function of U1 snRNA?

Answer 50

The 5' splice site is recognized by base-pairing to the U1 snRNA

Question 51

What is the function of U2 snRNA?

Answer 51

The branch point is recognized by base pairing to the U2 snRNA

Question 52

What are the two reaction that make the mature 3'end of RNA?

Answer 52

1. Cleavage 2. Polyadenlyation

Question 53

________ fails to _________ without the Poly A tail.

Answer 53

RNA polymerase; terminate