PCQ's

Question 1

The affinity of a sequence-specific transcriptional regulator for a DNA sequence can increase if it dimerizes because

Answer 1

• more bases in the DNA can be bound
• more contacts can be made with the phosphodiester backbone
• the potential for cooperative binding exists

Question 2

How are eukaryotic mRNAs processed?

Answer 2

• Capped on the 5’ end
• Polyadenylated on the 3’ end
• Internal segments removed by splicing

Question 3

What parts of a gene are included in a mature mRNA?

Answer 3

• coding (translated) sequence
• exons
• noncoding (untranslated) sequence
• the poly(A) signal (AAUAAA)

Question 4

What parts of a gene are included in the lariat?

Answer 4

Introns

Question 5

CPSF

Answer 5

Binds to the poly(A) signal (AAUAAA) to help specify the 3’ end of an mRNA

Question 6

CstF

Answer 6

Binds to a GU rich signal, helps specify the 3’ end of an mRNA.

Question 7

PAP

Answer 7

adds poly(A) tail to mRNA.

Question 8

poly(A) binding protein

Answer 8

associates with poly(A) tails.

Question 9

spliceosome

Answer 9

Joins exons together.

Question 10

Alternative splicing can yield mRNAs that differ by the inclusion or exclusion of what?

Answer 10

a particular exon

Question 11

How might alternative splicing yield mRNAs that differ only in the length of a particular exon?

Answer 11

• the use of an alternative 3’ splice site.

- the use of an alternative 5’ splice site.

Question 12

Enzymes involved in degrading prokaryotic mRNAs are primarily

Answer 12

3’->5’ exonucleases

Question 13

For mRNA-specific regulation of translation and mRNA stability, regulatory proteins or non-coding RNAs bind to particular structures or sequences in target mRNAs. To translationally repress bacterial mRNAs, regulators typically bind _________

Answer 13

Shine Dalgarno sequence

Question 14

For mRNA-specific regulation of translation and mRNA stability, regulatory proteins or non-coding RNAs bind to particular structures or sequences in target mRNAs. To translationally repress eukaryotic mRNAs regulators typically bind_________

Answer 14

the 3’ or 5’ UTR

Question 15

Enzymes involved in degrading eukaryotic mRNAs are

Answer 15

• endonucleases
• 5’->3’ exonucleases
• 3’->5’ exonucleases

Question 16

Although individual mRNAs can be regulated in their translation, translation can also be controlled globally. In eukaryotes, global repression of translation involves:

Answer 16

• accumulation of eIF2 in its inactive, GDP bound form.
• increased affinity of phosphorylated eIF2 for its GEF (eIF2B).
• phosphorylation of translation initiation factor eIF2.
• prevention of eIF2B from being able to function

Question 17

MicroRNAs and siRNAs function by base-pairing with target RNAs. What can cause immediate degradation of the target mRNA?

Answer 17

Extensive base-pairing

Question 18

MicroRNAs and siRNAs function by base-pairing with target RNAs.What can cause translational repression, followed by eventual mRNA degradation

Answer 18

less extensive base-pairing

Question 19

piRNAs

Answer 19

• newly discovered class of small RNAs
• can act to silence
  transposons (mobile DNA elements that can hop and in out of genomes)

Question 20

Xist

Answer 20

a ncRNA that acts as a scoffold to repress the X chromosome in XX mammals.

Question 21

Splice site usage can be affected by:

Answer 21

• speed of RNA polymerase.
• chromatin structure.
• sequences within exons.
• sequences at the exon-intron and intron-exon boundaries.

Question 22

What catalyzes the transesterification reactions involved in pre-mRNA splicing?

Answer 22

non-coding RNAs

Question 23

Recognition of the 5’ splice site and the branch-point site during splicing involves:

Answer 23

• base-pairing by snRNAs to the pre-mRNA

- binding by sequence-specific binding proteins

Question 24

The splicing reaction proceeds as follows

Answer 24

• recognition of the branch-point sequence and 5’ splice site.
• formation of a lariat, causing separation of the upstream exon from the intron.
• joining of the upstream and downstream exons.

Question 25

How were the snRNAs discovered?

Answer 25

through immunoprecipitation of snRNPs using human autoantibodies

Question 26

Why did the normal serum of Dr. Steitz's MD/PhD student serve as a good control for the experiments that led to the discovery of snRNAs?

Answer 26

it didn't contain any antibodies against snRNPs

Question 27

What does it mean that the genetic code is a triplet code?

Answer 27

Three nucleotides specify one amino acid

Question 28

The fact that the genetic code is degenerate means that:

Answer 28

- Different tRNAs can add the same amino acids | - More than one codon specifies the same amino acid

Question 29

whats required during synthesis of a polypeptide chain in cells (ignoring requirements for the formation of aminoacyl-tRNA and translation initiation)?

Answer 29

- tRNA - ribosome - rRNA - GTP hydrolysis

Question 30

what matches the mRNA codon with the correct amino acid?

Answer 30

tRNA

Question 31

what adds an amino acid to tRNA?

Answer 31

tRNA synthetase

Question 32

what adds an amino acid to elongate a polypeptide?

Answer 32

peptidlytransferase

Question 33

whats the overall direction of ribosome movement on mRNA?

Answer 33

5' to 3'

Question 34

which site is the ribosomal site for new amino-acyl tRNA?

Answer 34

A site

Question 35

at which end of the polypeptide are new amino acids are added

Answer 35

C-teminis

Question 36

When can a new round of translation initiate?

Answer 36

after initiation of the last round

Question 37

Using the following schematic of a short eukaryotic mRNA, identify the major translation product. (5’- AGGCUUUAACCAUGGUAUGGACCUAAAUAAGUGAAUAUUG-3’)

Answer 37

MVWT