BIOL 442 Remote Graded Activity #5 (15 points)

Instructions:

 Submit as a word document to the designated assignment folder on the course Blackboard site no
later than 11:59 PM on April 13, 2020 (if you have any difficulty with uploading your file to
Blackboard, you can email it to me instead: laalli@wm.edu)

 The activity should only take about 50 minutes to complete, but you can take as much time as you
need, as long as you submit your worksheet by the deadline.

 The activity is “open book.” Although the activity is designed to be completed individually, you are
welcome to communicate with a group of three while you complete the worksheet, but you will still
need to each turn in a completed worksheet.

 For the multiple choice questions (1 point each), use the “Text Highlight Tool” to highlight the
correct answer.

Review Questions

1. As scientists were unraveling the mysteries associated with transcription in eukaryotes, they
discovered there was not a one-to-one correspondence between the nucleotide sequence of a gene
and the base sequence of the mature messenger RNA (mRNA) it codes for. They proposed the split
genes hypothesis. How can the split genes hypothesis be explained?

A) An intron is present in a gene and the initial RNA transcript, but it is usually removed by splicing.
B) An exon is present in a gene and the initial RNA transcript, but it is usually removed by splicing.
C) An intron is a segment of a gene that is not transcribed by RNA polymerase II.
D) An exon is a segment of a gene that is not transcribed by RNA polymerase II.

2. Eukaryotes have three nuclear RNA polymerases. The primary function of RNA polymerase II is
transcription of ________.

A) only ribosomal RNA (rRNA)-coding genes

B) only transfer RNA (tRNA)-coding genes
C) both rRNA- and tRNA-coding genes
D) protein-coding genes

3. What molecule functions as the template for 3′ poly(A) tail synthesis in eukaryotes?

A) The template strand in the DNA

B) The nontemplate strand in the DNA
C) The mRNA acts as its own template
D) No template is necessary for 3′ poly(A) tail synthesis

4. A ribozyme is ________.

A) a catalyst that uses RNA as a substrate

B) an RNA with catalytic activity
C) a special protein with catalytic activity
D) an enzyme that synthesizes RNA as part of the transcription process

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5. What molecules in the spliceosome catalyze the intron removal reactions?

A) exons
B) snRNAs
C) rRNAs
D) introns

6. Use this model of a eukaryotic transcript to answer the question below.

5′ UTR-E1 I1 E2 I2 E3 I3 E4-UTR 3′ (E = exon; I = intron; UTR = untranslated region)

Which components of the eukaryotic transcript shown above will also be found in mRNA in the
cytosol?

A) 5′-UTR I1 I2 I3 UTR-3′
B) 5′-E1 E2 E3 E4-3′
C) 5′ UTR-E1 E2 E3 E4-UTR 3′
D) 5′-I1 I2 I3-3′

7. In most cases, introns are spliced out of mature mRNA and are not a part of the final translated
protein product of a gene. Even though they are not included in the final protein, why are introns
important?

A) Introns allow for alternative splicing of exons to create multiple proteins from one gene sequence
B) Introns can generate non-coding RNAs (such as microRNAs) that influence gene expression
C) Introns are “junk” sequences and are not considered to be important
D) Both A and B

Background information for Questions 8-10: Temperature-dependent alternative splicing

The activity of CDC-like kinases (CLKs) is extremely sensitive to physiological temperature changes.
This “cellular thermometer” is based on minor structural rearrangements of a domain of the protein
called the kinase activation segment, representing a new concept in enzymology. CLKs have been
found to globally control alternative splicing and gene expression in a body temperature-dependent
manner, with wide implications ranging from circadian biology to disease conditions. In addition, this
thermometer is evolutionarily adapted to the growth temperature of diverse organisms and may be
important for reptilian temperature-dependent sex determination. What is the connection between CLK
activity and alternative splicing? Recent data suggest that the phosphorylation status of SR proteins,
which are RNA-binding proteins that play a role in regulating alternative splicing, is controlled by
CLK1/4.

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8. The figure below shows the results of an in vitro kinase assay visualized by gel electrophoresis. The
top panel labeled “activity” shows the ability of CLK to phosphorylate itself (top band) and
phosphorylate its substrate (SR protein, lower band) at different body temperatures. The bottom panel
labeled “loading” is a control to show that there was equal loading of
samples of CLK and SR Body temperature protein.

I. II.

a. Indicate at which arrow (I or II) the inactive form of CLK1/4 should be

placed in the diagram (1 point)

b. Indicate at which arrow (I or II) the active form of CLK1/4 should be

placed in the diagram (1 point)

9. At colder body temperatures, RNA-seq data show that the

hyperphosphorylated SR protein regulates an alternative splicing event in
which there is an increase in exon inclusion. Draw (or describe in words) what
the resulting mRNA would look like after splicing (3 points)

10. At warmer body temperatures RNA-seq data show that the

hypophosphorylated SR protein regulates an alternative splicing event in
which there is an increase in exon skipping. Draw (or describe in words) what
the resulting mRNA would look like after splicing (3 points).

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