chapter 38

Question 1

what are the 3 ways rRNA and tRNA are modified

Answer 1

1. The final mature RNA is cleaved from a larger precursor
   molecule.
2. Many tRNA transcripts lack the CCA sequence at the 3′ end of
   the strand. These nucleotides are added post-transcriptionally.
3. The bases and riboses of tRNA and rRNA are modified, for
   instance, by the attachment of methyl groups.

Question 2

RNA polymerase I synthesizes what

Answer 2

large precursor RNA (45S)

Question 3

RNA (45S) is processed to yield what

Answer 3

18S, 28S, 5.8S rRNAs

Question 4

what does snoRNP do

Answer 4

catalyze reactions in the nucleolus that modify and alter the large precursor RNA (45S)

Question 5

RNase P removes nucleotides from what end of the precursor

Answer 5

5’

Question 6

RNase T removes nucleotides from what end of the precursor

Answer 6

3’

Question 7

CCA-adding enzyme adds nucleotides to what end of the precursor

Answer 7

3’ end

Question 8

how is the 5’ end of the pre-mRNA transcript modified

Answer 8

a 5’ cap is added

Question 9

what is the purpose of the 5’ cap

Answer 9

increases mRNA stability by protecting the 5’ end from phosphatases and nucleases

Question 10

5’ cap enhances

Answer 10

translation of mRNA

Question 11

how is the poly A tail form

Answer 11

3’ end is cleaved by a specific endonuclease and a stretch of polyadenylate is added by poly A polymerase

Question 12

3’ poly A tail is beneficial how

Answer 12

increases mRNA stability and enhances the translation

Question 13

exons are what kind of region

Answer 13

coding regions

Question 14

introns are what kind of region

Answer 14

noncoding regions

Question 15

what are the 3 common features of intron-exon junctions

Answer 15

1. The 5′ end of the junction has the sequence 5′AGGUAAGU3′, with the
   first GU from the 5′ end demarcating the beginning of the intron.
2. The 3′ end of the intron is marked by a stretch of pyrimidines
   (polypyrimidine tract) followed by any base, a C, and then the intron ends
   with AG.
3. The branch site is located 20–50 nucleotides from the 3′ end of the
   intron.

Question 16

when does RNA splicing begin

Answer 16

the cleavage of the phosphodiester linkage between
the upstream exon (exon 1) and the 5′
end of the intron

Question 17

what is the attacking group in RNA splicing

Answer 17

The attacking group
is the 2′-OH of an adenylate residue at
the branch site. This is a
transesterification reaction

Question 18

what kind of reaction is RNA splicing

Answer 18

This is a
transesterification reaction

Question 19

the transesterification reaction generates and forms what

Answer 19

generates a branch and forms a lariat intermediate

Question 20

how are the two exons joined together in RNA splicing

Answer 20

The 3′-OH of exon 1
attacks the
phosphodiester linkage
between the intron and
exon 2, joining the two
exons with another
transesterification
reaction.

Question 21

what is snRNA

Answer 21

small nuclear RNA (<300 nucleotides)

Question 22

what is snRNP

Answer 22

small nuclear ribonucleoprotein particles

snRNA with associated proteins

Question 23

spliceosomes are composed of

Answer 23

snRNPs, splicing factor, pre-mRNA being processed

Question 24

functions of the CTD include

Answer 24

1. Recruiting enzymes to
   synthesize the 5′ cap.
2. Recruiting components of the
   splicing complex.
3. Recruiting the endonuclease
   that cleaves the pre-mRNA to
   expose the site for poly(A)
   addition.

Question 25

what is CTD for dummies

Answer 25

carboxyl-terminal domain of RNA pol II

transcription and splicing coordination

Question 26

what is a ribozyme

Answer 26

some RNA that function as catalysts

Question 27

what are examples of ribozymes

Answer 27

RNaseP
snRNAs
rRNAs