Biol 213 In-Class Problem Set 4

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Biol 213 In-Class Problem Set 4

due F 3/6/26 @ noon

1) DNA vs. mature mRNA

A geneticist isolates a eukaryotic gene that contains five exons. They then isolate the mature mRNA* transcribed from this gene. After melting the DNA so that it becomes single stranded, they mix the DNA and RNA. Some of the single-stranded DNA hybridizes (base-pairs) with the mRNA.
*mature mRNAs have completed all mRNA processing steps

What will the structure of the DNA-mRNA hybrid complex look like? To figure this out, answer the questions below.

A) Which strand of the DNA would hybridize with the mRNA, the coding or the template strand?

Here are some sequences that are found in genes or in mRNAs:
1. the promoter
2. the 5' UTR (UnTranslated Region)
3. exons
4. introns
5. the 3' UTR
6. the poly A tail
B) Fill in the chart to determine the properties of these sequences.
Tip: Answer this question before attempting Q1C, because the answers to 1B will help you answer 1C.

Which of these sequences are:
only in DNA
 only in RNA
 in both
because they are:
never transcribed
 spliced out
 added to mRNa after transcription
promotor



exons



introns



poly A tail



5'/3'UTR
un translated



The experiment (also described above):

A geneticist isolates a eukaryotic gene that contains five exons. They then isolate the mature mRNA transcribed from this gene. After melting the DNA so that it becomes single stranded, they mix the DNA and RNA. Some of the single-stranded DNA hybridizes (base-pairs) with the mRNA.

C) Do the DNA and mature mRNA molecules hybridize completely? Draw a picture of what the DNA-RNA hybrid complex would look like.

As an example, here is a drawing of two nucleic acids strands that hybridize partially but not completely:

If two strands are perfectly complimentary, the picture will look like a railroad track. If the strands are only partly complementary, there will be regions that are single stranded, either as tails hanging off the end or bubbles in middle.

D) In your drawing, label
• The DNA
• The RNA
• The 5' end of the RNA
• the part of the DNA and/or RNA that would contain the following:
1. - the promoter
2. - the 5' UTR (UnTranslated Region)
3. - exon 1
4. - intron 1
5. - exon 5
6. - the 3' UTR
7. - the poly A tail
Note that I'm only asking you to label exons 1 and 5, but other exons may be present too. 

2) Genetic diseases can be caused by mutations that affect splicing

Anemia is a disease in which red blood cells contain less hemoglobin than normal. A genetic disease called b thalassemia is an inherited form of anemia caused by a defect in splicing.

The gene for b hemoglobin codes for three exons and two introns. In b thalassemia, the b hemoglobin gene contains a single point mutation that causes the mature mRNA to be missing the second exon.

What sorts of point mutations might cause this disease? Answer the questions below to figure this out.

A) Draw three stages in a splicing reaction:
1) A precursor mRNA, before any splicing has occurred
• include two exons and one intron.
• indicate the location of all sequences required for splicing.
2) A splicing intermediate in which one end of the intron has been attached to the branch point A
• indicate the location of all sequences required for splicing
3) The final mRNA with the intron removed
• indicate the location and name of the sequences that were required for splicing
Draw the RNA at each of these stages of splicing. In each. indicate the location of any conserved sequences necessary for splicing. No need to draw any proteins!

A gene for hemoglobin codes for three exons and two introns. In the genetic disease b thalassemia, the hemoglobin gene contains a single point mutation that causes the mature mRNA to be missing the second exon.

Below is a picture of the precursor mRNA.

B) Indicate the location of all* sequences that are required for normal splicing of the WT precursor mRNA. *Hint: 3 sequences are required to splice out one intron.

Name each sequence with a unique name. Use (1) or (2) in the names to distinguish whether a sequence is required for splicing of intron 1 or intron 2. e.g. " 5' ss (1) " might mean the 5' splice site from intron 1.4

Below are pictures of the mature WT mRNA and the mature mutant mRNA
C) On both pictures, indicate the location of any sequences that were required for splicing that still remain in these RNAs. If sequences or parts of sequences are present, label them with the same names as you used in part (B) above.

D) Looking at your previous answers, name one sequence that could be mutated to in b thalassemia to cause the mature hemoglobin mRNA to be missing the second exon. (There is more than one possible answer, but you only have to name one.)

Hint: Think about which sequences in the mutant mRNA must have been still be functioning.5

3) How deleterious are different types of mutations likely to be?

Which of the types of mutations listed below would be very likely to harm an organism? Which might be benign?

For each type of mutation,
• Explain how the protein’s sequence or structure could be altered.
• Explain why this change might or might not disrupt the protein's function.
• Decide how likely it is that the change would disrupt the protein's function.
Possible answers:
a) very likely to disrupt the protein’s function
b) might or might not be so bad, depending on the exact details
c) quite possibly not harmful.

Know that these likelihood answers are not absolute. Just be sure to justify your choice.

A) Deletion of four consecutive nucleotides in the middle of the coding sequence
B) Insertion of a single nucleotide within the coding sequence but very near the 3' end.6
C) Deletion of three consecutive nucleotides in the middle of the coding sequence.
Assume the three nucleotides are part of the same codon.
D) Deletion of three consecutive nucleotides in the middle of the coding sequence.
Assume the three nucleotides are not part of the same codon.
E) Substitution of one nucleotide for another in the middle of the coding sequence8
4) tRNA-mRNA interactions
Cell-free translation systems allow scientists to experimentally manipulate translation by adding non natural components.

What do you predict would happen if you created a tRNA with an anticodon of 5′-CAA-3′ that is charged with methionine, and then added this modified tRNA to a cell-free translation system that has all the normal components required for translating RNAs?

To figure this out, answer the questions below.

A) Draw a generic* mRNA paired with a generic* tRNA (draw the tRNA as a cloverleaf structure)

On the mRNA, 

• Indicate the location of the codon.

• Label the 5' and 3' ends of the codon.
*generic means don't write any letters to specify the nucleotides in the codon.

On the tRNA, 

• Indicate the location of the anticodon.

• Label the 5' and 3' ends of the anticodon.
*in this question, don't write letters to specify the nucleotides in the anticodon.
• Label the 5' and 3' end of the entire tRNA.
• Draw a circle to indicate the location of the amino acid. 
B) What is the codon for methionine? Label the 5' and 3' ends.
C) Draw an mRNA with a WT methionine codon paired with a WT tRNA attached to a methionine amino acid.

Use the steps in A to do this, except this time:

• This time, write the nucleotide letters in both the codon and the anticodon.
(Be sure to label all 5' and 3' ends.)
• Label the amino acid with its 3-letter code.
D) What is the anticodon is in tRNA? In the box below, write the anticodon sequence, with 5' written on left (as is always done in biology). Label the 5' and 3' ends of your sequence.
Cell-free translation systems allow scientists to experimentally manipulate translation by adding non natural components.

What do you predict would happen if you created a tRNA with an anticodon of 5′-CAA-3′ that is charged with methionine, and then added this modified tRNA to a cell-free translation system that has all the normal components required for translating RNAs?

Possible answers:

1) methionine would be incorporated into proteins at some positions where glutamine should be
2) methionine would be incorporated into proteins at some positions where leucine should be
3) methionine would be incorporated into proteins at some positions where valine should be
4) translation would no longer be able to initiate
E) Draw the altered tRNA paired with an mRNA, then choose one of the answer choices above and briefly explain why you chose it.
Honor Code:

2026-03-17