Lecture 4: RNA Synthesis

Question 1

True or false: RNA (and DNA) chains can form double strands?

Answer 1

True.

Question 2

What are the two strands of DNA?

Answer 2

The coding strand (+) and the template strand (-).

Question 3

Which strand of DNA is RNA complimentary to?

Answer 3

The template strand (-).

Question 4

What is the role of RNA Pol I?

Answer 4

Transcription of nucleolar RNA (rRNA).

Question 5

What is the role of RNA Pol II?

Answer 5

Transcription of heterogenous nuclear RNA.

Question 6

What is the role of RNA Pol III?

Answer 6

Transcription of tRNA, 5s rRNA, and other small RNA.

Question 7

What two RNA polymerases are sensitive to a-amanitin?

Answer 7

RNA Pol II and RNA Pol III.

Question 8

What RNA polymerase is resistant to a-amanitin?

Answer 8

RNA Pol I.

Question 9

What RNA components make up the 60s subunit of a ribosome?

Answer 9

1. 28S (RNA Pol I)
2. 5.8S (RNA Pol I)
3. 5S (RNA Pol III)

Question 10

What RNA component makes up the 40S subunit of a ribosome?

Answer 10

1. 18S (RNA Pol I)

Question 11

The 40S subunit and the 60S subunit of a ribosome together make a ribosome that is…

Answer 11

…80S.

Question 12

True or false?

An rRNA transcription unit contains all RNA for the subunit.

Answer 12

True. Once processed (by cleavage) you have the separated final RNA strands. There is only one regulatory region.

Question 13

Factor B

Answer 13

“Binding.” Helps RNA Pol I bind.

Question 14

Factor S

Answer 14

“Stimulating.” Helps to stimulate Factor B and subsequent RNA Pol I binding and activity.

Question 15

What are the three steps of tRNA (and other small RNA) transcription?

Answer 15

1. Binding of TFIIIA and TFIIIC to promoters within the gene itself.
2. TFIIIB binding to the promoter near TFIIIA and TFIIIC.
3. Binding of RNA Pol III.
4. Transcription.

Question 16

What are the major steps of rRNA transcription?

Answer 16

1. Binding of Factor B to the upstream element.
2. Binding of Factor S to Factor B.
3. Binding of RNA Pol I to the Factor B-Factor S complex.
4. Cleavage of rRNA precursor to rRNA segments: 18S, 5.8S, and 28S.

Question 17

What helps initiate mRNA transcription?

Answer 17

Synthesis and subsequent binding of PDX-1 to other transcription factors on DNA.

Question 18

Name the four major steps needed to initiate RNA Pol II transcription.

Answer 18

1. Binding of TFIID to the TATA box.
2. Binding of other transcription factors to the TATA box.
3. Binding of RNA Pol II to the TATA box-TF complex.
4. Phosphorylation of RNA Pol II by a kinase.
5. Transcription.

Question 19

What are the major steps required to process immature RNA into mature RNA?

Answer 19

1. Adding a 5’ cap made of 7-methyl guanosine.
2. Polyadenylation with PolyA Polymerase (PAP) in a template-dependent “stuttering” mechanism on the 3’ end.
3. Splicing of introns at the 5’ end of the intron-exon junction with simultaneous lariat formation.
4. Mature RNA is transported to the cytosol for translation.

Question 20

Promoter

Answer 20

Regions of DNA crucial to accuracy and rate of transcription; immediately upstream from the gene.

Question 21

Enhancer

Answer 21

Sequences of DNA that can up-regulate

transcription of neighboring genes.

Question 22

What are some unique characteristics of enhancers?

Answer 22

• They act over long distances.
• They function in either orientation.
• They can be located upstream, downstream, or within a gene.

Question 23

CPSF

Answer 23

Cleavage and poly-adenylation specificity factor. Recruits poly(A) polymerase to add AAA tail.

Question 24

Intron

Answer 24

Part of primary transcript, but not found in mature RNA.

Question 25

Exon

Answer 25

Part of RNA that will ultimately be spliced into mature RNA and code for protein.

Question 26

Spliceosome

Answer 26

Large ribonucleotide proteins whose role is to splice RNA.

Question 27

What is the relationship between the calculated number of proteins in our body and alternative splicing?

Answer 27

Although our genome only encodes for about 25,000 proteins, this is greatly amplified by alternative splicing, which creates different, but related proteins.

Question 28

What is an example of a functional outcome of alternative splicing?

Answer 28

The creation of an antibody that is meant to be membrane-bound (integral motif included) or its alternative, meant for secretion (no integral motif).

Question 29

What is rifampicin?

Answer 29

An antibiotic that works by blocking bacterial RNA synthesis.

Question 30

What is actinomycin D?

Answer 30

Binds to double-helical DNA, blocking it from being transcribed.

Question 31

cDNA

Answer 31

A DNA template of mature RNA (that has no introns, has already been processed).

Contrast with genomic DNA library.

Question 32

Once a vector/plasmid is incorporated into a bacterial cell, how can one separate that cell from the cells that did not take it up?

Answer 32

Usually the plasmid contains an antibiotic-resistance gene as well. Therefore, one can treat the colony with antibiotic and be left with only the cells with the vector/plasmid.