L4- RNA Synthesis

Question 1

List three differences between RNA and DNA.

Answer 1

1. The pentose sugar in RNA is ribose rather than deoxyribose, 2. RNA has Uracil (U) instead of Thymine (T), and 3. DNA normally exists as a double helix whereas RNA exists as a single strand.

Question 2

True or False. mRNA typically exists as a single-stranded molecule.

Answer 2

True.

Question 3

The sequence of RNA transcripts is similar to that of which DNA strand?

Answer 3

The coding strand (also called the (+) strand). The other strand is called the template or (-) strand.

Question 4

In which direction is RNA synthesized?

Answer 4

5’ to 3’.

Question 5

Name the three eukaryotic polymerases involved in RNA synthesis.

Answer 5

RNA polymerase I, II and III.

Question 6

What is the cellular location and function of RNA polymerase I?

Answer 6

It is found in the nucleolus and transcribes 28S, 18S and 5.8S ribosomal RNAs (rRNA).

Question 7

What is the cellular location and function of RNA polymerase II?

Answer 7

It is found in the nucleus and transcribes pre-mRNA.

Question 8

What is the cellular location and function of RNA polymerase III?

Answer 8

It is found in the nucleus and transcribes tRNA, 5S rRNA and other small RNAs.

Question 9

What are the two subunits of eukaryotic ribosomes?

Answer 9

60S and 40S. Each of these is composed of multiple rRNA and protein subunits.

Question 10

Which two transcription factors are required for RNA polymerase I to bind to and transcribe DNA?

Answer 10

Transcription factors B and S (B for binding, S for stimulating).

Question 11

What marks the termination site of RNA poly I?

Answer 11

A string of T residues.

Question 12

What transcription factors are required to recruit and activate RNA poly III?

Answer 12

TFIIIA, TFIIIB and TFIIIC (note that the Roman numeral in the name of the transcription factor tells you which polymerase it is associated with).

Question 13

What conserved sequence in the promoter region directs Poly II binding? What protein binds this sequence?

Answer 13

The TATA box. The most common sequence is TATAAA. This is bound by the TATA-binding protein (TBP) which is part of TFIID.

Question 14

What is the purpose of an enhancer sequence?

Answer 14

Enhancers increase the transcription of neighboring genes. They can be located either upstream or downstream of the gene that is to be transcribed.

Question 15

Which set of transcriptions factors are required for the initiation of transcription?

Answer 15

Basal Transcription Factors.

Question 16

A methylguanylate (m7G) cap is placed at which end of a nascent RNA strand?

Answer 16

The 5’ end. Note that the m7G residue is linked to the RNA via a 5’ to 5’ triphosphate bond.

Question 17

Cleavage and polyadenylation occur at which end of a pre-mRNA strand?

Answer 17

The 3’ end.

Question 18

Which sequence element signals for cleavage of hnRNA and addition of the poly(A) tail?

Answer 18

The AAUAA sequence. This is located approximately 15 nucleotides upstream of the site of cleavage and subsequent polyadenylation.

Question 19

True or False. Poly A tails are encoded within genes.

Answer 19

False. The tails are added by poly(A) polymerase, a polymerase that does not utilize a template.

Question 20

What transcription factor reads the AAUAA sequence on pre-mRNA?

Answer 20

Cleavage and polyadenylation specificity factor (CPSF).

Question 21

What is RNA splicing?

Answer 21

The process by which introns are removed from the pre-mRNA molecule.

Question 22

What is the spliceosome and what is its function?

Answer 22

The spliceosome is a large ribonucleotide protein complex akin to the ribosome. Spliceosomes contain smaller nuclear snRNPs (U1, U2, U4,U5 and U6). This complex removes introns from pre-mRNA molecules.

Question 23

What is alternative splicing?

Answer 23

A single pre-mRNA can be spliced in different ways, yielding different mature mRNAs. Thus, a single gene can code for a series of related, but non-identical proteins.

Question 24

Which rRNAs make up the 40S subunit of eukaryotic ribosomes?

Answer 24

18S rRNA (and proteins).

Question 25

Which rRNAs make up the 60S subunit of eukaryotic ribosomes?

Answer 25

28S, 5.8S and 5S rRNAs (and proteins).

Question 26

Which rRNA is synthesized outside of the nucleolus?

Answer 26

5S rRNA (it is synthesized by RNA poly III).

Question 27

Which RNA polymerase is inhibited by the drug actinomycin D?

Answer 27

Mammalian RNA polymerase I.

Question 28

Which RNA polymerase is inhibited by the drug alpha-amanitin?

Answer 28

Mammalian RNA polymerases II and III.

Question 29

Which RNA polymerase is inhibited by the drug rifampicin?

Answer 29

Bacterial RNA polymerase.

Question 30

True or False. The activation region for the 5S rRNA gene is found within the gene itself.

Answer 30

True.

Question 31

True or False. Genes that are constitutively expressed contain a TATA box as a promoter.

Answer 31

False. They generally contain a GC-rich region instead.

Question 32

What is the only basal RNA polymerase II transcription factor that directly binds to DNA?

Answer 32

TFIID.

Question 33

What is the function of the RNA Gppp cap?

Answer 33

It is believed to protect against the degradation of nascent RNA.

Question 34

True or False. All RNAs acquire a poly(A) tail following transcription.

Answer 34

False. Only those RNAs that are to become mRNAs acquire a poly(A) tail.

Question 35

Introns in pre-mRNA typically have ___ residues at their 5’ end and ___ residues at the 3’ end.

Answer 35

GU, AG.

Question 36

What is the first step of RNA splicing?

Answer 36

Cleavage of the 5’ exon-intron junction by the spliceosome.

Question 37

What is an intron lariat?

Answer 37

It is an intron that has been circularized with a specific branch point between a 5’ G residue and a 3’ splice-site A residue linked in a 5’ to 2’ bond.

Question 38

Which small nuclear ribonuclearprotein (snRNP) binds to the 5’ exon-intron junction?

Answer 38

U1.

Question 39

Which small nuclear ribonuclearprotein (snRNP) binds to the branch point of an intron lariat?

Answer 39

U2.

Question 40

Which small nuclear ribonuclearprotein (snRNP) binds upstream to the 3’ intron-exon junction?

Answer 40

U5.