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BIS101-01, Fall 2022

Midterm Exam II

The exam has 60 questions and is worth a total of 120 points. It is to be done individually with no assistance from others. The only resource allowed are your own notes with no hyperlinks.

The test is split into distinct sections. The total number of questions is 60 and they are sequential across all the sections.

In each section it is stated if there are more than one possible answers and if you need to fill in more than one bubble to answer a question. Please pay attention to this.

The online form is on Canvas to allow you to enter your answers to the 60 questions on Midterm I. It will be available until 11:59 PM on Tuesday November 8th.

For the entire exam, the questions have been replicated in the quiz to allow you to enter your answer there and make sure that you are providing the answer you wish to provide. Remember that some sections may have multiple correct answers and these are clearly marked.

You will only be able to enter your answers once on the quiz form. So it is best to do the whole exam offline and have your answers ready once you begin entering them. It would also be advisable to try to make sure your internet is as stable as possible when you begin answering the questions online.

The points are set to 0 and the quiz will not give you feedback of any value to ascertain the grade. This is because we have a complex partial credit rubric that is nearly impossible to do in Canvas so we will port your answers out of Canvas to another system. The grades will then be re-entered in a day or two under Midterm II.

For the midterm, you are only allowed to use your own notes without any video or external links. This is to maximize the uptake of the material.

Please remember that this exam has a lot more memorization material on it so the wording in the question can be very important. Make sure to double check what a question is asking.

Section I. Complete the following Table, assuming that the DNA is written with the top left being a 5’ end and that the columns represent transcriptional and translational alignments. For DNA, use ACTG or N where N represents any possible nucleotide. The RNA is drawn in the direction that it is read from the DNA. Use the filled in table to answer the questions on the following page. There can be more than one correct answer per question in this section. Assume that the ribosome initiates transcription outside of this sequence and reads through it.

1. Which row in the chart is the coding strand of the DNA?

A. First Row

B. Second Row

C. Third Row
D. Fourth Row

E. Fifth row

2. Fill in the following sentence by selecting the words below that would fit in these blanks “A stop codon occurs when a _________ is not present for a specific codon and this allows the __________ into the ribosome to stop translation”? (Don’t worry about the order, simply chose the two appropriate terms)

A. tRNA

B. Initiation factor
C. Release Factor
D. Ribosomal Protein

E. Ef-G

3. What is the most N terminal amino acid of this protein?

A. CYS

B. TRP
C. TYR
D.MET

E. SER

4. What is the typical first codon read by a ribosome in starting translation?

A. UGU

B. ATG
C. CGU
D. UGC

E. AUG

5. What is the mRNA sequence of the first codon in this mRNA as the ribosome would read it?

A. AUG

B. UGG
C. ACC
D. UAC

E.  ACG

6. What is the last amino acid that is encoded in this peptide sequence?

A.  PRO

B.  TRP
C.  TYR
D.  MET

E. CYS

7. What is the DNA sequence in 5’ to 3’ direction of the template strand for the second codon with respect to what the ribosome would read?

A. ATG

B. CCA
C. ACG
D. TGG

E. ATG

8. What is the most correct statement about tRNAs?

A. They enter the ribosome with or without an amino acid attached

B. They spontaneously bind the amino acid that is linked to their anti-codon
C.  They can only enter the ribosome after having an amino acid attached.
D. They are small RNAs that bind amino acids.

E.  An Ef-Tu protein checks them to see if they have an amino acid attached and then guides the tRNA into the Ribosome.

9. What is the point of starting translation with a formyl-methionine?

A. The formyl group creates the potential for bidirectional translation

B. The formyl group allows the tRNA to read a different codon.
C. The formyl group inhibits bond formation in the wrong direction.
D. The formyl group provides more energy to create a peptide bond.

E. You want translation to be precise so the more formal the better.

Section 2. Answer the following questions about DNA structure, function and replication. Make sure to fill in all circles that are appropriate as there may be more than one correct answer in this section. Use the picture below to answer questions that refer to the DNA replication picture. Assume that A and B refer to the region covered by the brackets while C, D and E refer to the individual DNA strand being pointed at.

10.   Which part(s) of this diagram represent the lagging strand in its entirety?
A. A
B. B
C. C
D. D
E. E

11.  What part(s) of the replication diagram have RNA?
A. A
B. B
C. C
D. D
E. E

12.  Why does an Okazaki Fragment happen?
A. Because DNA synthesis only goes 5’ to 3’
B. Because DNA replication only goes 5’ to 3’
C. Because DNA replication is bidirectional
D. Because you need primase to make DNA
E. Because there is only one origin of replication

13. DNA Polymerase III, a key enzyme for synthesizing DNA has which of these biochemical function(s)?

A.  5’ to 3’ DNA polymerase

B.  3’ to 5’ DNA polymerase
C.  5’ to 3’ exonuclease
D.  5’ to 3’ RNA primase

E.  3’ to 5’ exonuclease

14. Of these enzymes, which are involved in DNA synthesis, which makes a nick in one strand  of double stranded DNA to relieve tension on the DNA?

A. Helicase

B.  DNA Polymerase III
C.  Primase
D.  Topoisomerase

E.   Telomerase

15. Complete the following sentence in the most accurate form “A direct terminator sequence …”

A. is a specific DNA sequence that binds itself as RNA

B. is a specific DNA sequence that binds RNA
C.  is a specific DNA sequence that is bound by protein as an RNA sequence
D.  exists to terminate transcription

E.  exists to terminate replication

16. All of these are enzymes involved in DNA synthesis, which one(s) have the capacity to create new strands of ribonucleic acid?

A. DNA Polymerase I

B.  Topoisomerase I
C. DNA Polymerase III
D. Helicase

E. Primase

17. Which one of these is completely made of RNA and only RNA when it does its intended function?

A. tRNA

B.  Ribosome
C.  Okazaki Fragment
D.  Shine Delgarno Sequence

E.   Release Factor

18. What does a nucleosome do?

A. Enucleates DNA crystallization in water.

B. Bind RNA to help with DNA replication.
C. Helps with packaging of DNA.
D. Provides information to initiate translation.

E.  Helps in the control of transcription from DNA.

19. All of these are enzymes involved in DNA synthesis, which one functions in the absence of ATP, CTP, GTP, UTP or TTP?

A. DNA Polymerase I

B. Telomerase
C. Primase
D.  Ligase

E.  DNA Polymerase III

Section 3. Answer the following questions on cloning DNA into vectors and libraries using the information you gleaned from the lectures. There can be only one answer per question in this section. Partial credit will be applied and incorrect answers will be penalized such that there is a minimum possible score of 0 per question. Use the labeled picture below to answer some of the following questions.

20. This section of the plasmid is required to identify/find E. coli that have been transformed with a plasmid that contains an insert in the correct location?

A. AmpR

B. LacZ
C. MCS
D. Ori

E. Unused plasmid DNA

21. This section of the plasmid determines how big a piece of DNA can be insterted into the plasmid?

A. AmpR

B. LacZ
C. MCS
D. Ori

E. PCR Primers

22. If you wanted to find the promoter for the gene for the major photosynthetic protein Rubisco protein in corn plants, what type of Donor DNA would you use for a library? Remember that Rubisco is needed for photosynthesis.

A. Genomic DNA

B. Genomic DNA isolated from a corn leaf.
C. cDNA made from all the transcripts in a human body
D. cDNA made from RNA extracted from corn roots.

E.  cDNA made from RNA extracted from corn leaves.

Section 4. Answer the following questions assuming that gene Z is regulated by the following regulatory network. Presume that B, C and D are proteins each with their own gene and that the interactions are showing how the proteins regulate the specific promoters. Assume that stimulus A is a metabolite and the arrow shows how its binding to protein B influences that protein’s DNA binding activity. Assume that the organism is haploid. There is only one correct answer per question in this section.

23. Which of these statements is completely true about the WT situation above?

A. Gene Z is expressed in the presence of Stimulus A and blocked in the absence of A

B. Gene Z is blocked in the presence of Stimulus A and expressed in the absence of A
C. Gene Z is blocked in the presence of Stimulus A and blocked in the absence of A
D. Gene Z is expressed in the presence of A and expressed in the absence of A

E. None of the above

24. Which of these statements is completely true if C is a dominant mutant that is insensitive to B?

A. Gene Z is expressed in the presence of Stimulus A and blocked in the absence of A

B. Gene Z is blocked in the presence of Stimulus A and expressed in the absence of A
C. Gene Z is blocked in the presence of Stimulus A and blocked in the absence of A
D. Gene Z is expressed in the presence of A and expressed in the absence of A

E. None of the above

25. Which of these statements is completely true if B is a mutant like the i^s mutant?

A. Gene Z is expressed in the presence of Stimulus A and blocked in the absence of A

B. Gene Z is blocked in the presence of Stimulus A and expressed in the absence of A
C. Gene Z is blocked in the presence of Stimulus A and blocked in the absence of A
D. Gene Z is expressed in the presence of A and expressed in the absence of A

E.  None of the above

26. Which of these statements is completely true if D is similar to the i- mutant?

A. Gene Z is expressed in the presence of Stimulus A and blocked in the absence of A

B. Gene Z is blocked in the presence of Stimulus A and expressed in the absence of A
C. Gene Z is blocked in the presence of Stimulus A and blocked in the absence of A
D. Gene Z is expressed in the presence of A and expressed in the absence of A

E. None of the above

27. What is directly controlling C in trans?

A. A

B. B
C. C
D. D

E. Z

Section 5. In each strain shown below, determine whether or not there would be expression of B-gal or permease from the lac operon. The following questions will ask about your answers for each of these cells with two copies of the Lac operon in the same order as the table below with YES meaning expressed versus NO meaning not expressed at the level of enzyme activity. (Assume glucose is not present.) There is only one correct answer per question for this section unless explicitly noted in the question.

		Lactose Present		Lactose Absent
Cell Genotype		LacZ	LacY	LacZ	LacY
i+ p+ o+ z- y+	i- p+ oc z+ y-	YES	YES	YES	NO
i- p+ o+ z- y+	i+ p+ oc z- y-	NO	YES	NO	NO
i+ p+ o+ z- y+	is p+ o+ z+y+	NO	NO	NO	NO
i+ p+ oc z+ y-	is p+ o+ z-y-	YES	NO	YES	NO

28. What is the expression of LacZ and Lac Y in the presence and absence of lactose for the first genotype above (the genotype in the first line). Answer in the same order as the table above.

A. YES YES YES NO

B. YES NO NO NO
C. YES YES NO NO
D. YES YES NO YES

E. NO NO NO NO

29. What is the expression of LacZ and Lac Y in the presence and absence of lactose for the second genotype above (the genotype in the second line). Answer in the same order as the table above.

A. YES YES YES YES

B. NO YES NO NO
C. YES YES YES NO
D. YES NO YES NO

E. NO YES NO YES

30. What is the expression of LacZ and Lac Y in the presence and absence of lactose for the third genotype above (the genotype in the third line). Answer in the same order as the table above.

A. NO NO NO NO

B. YES NO YES NO
C. NO YES NO YES
D. YES YES YES YES

E. YES NO YES YES

31. What is the expression of LacZ and Lac Y in the presence and absence of lactose for the fourth genotype above (the genotype in the fourth line). Answer in the same order as the table above.

A. YES YES YES YES

B. YES YES NO NO
C. YES NO YES NO
D. NO NO NO NO

E. NO YES NO YES

32.  Take another look at the genotype in the second line and what would be your best answer if there was glucose added in the media of both conditions?

A. YES YES YES YES

B. YES YES NO NO
C. YES NO YES NO
D. NO NO NO NO

E. NO YES NO YES

33.  In the TRP operon, which of these regulatory components of the operon functions in the opposite manner to the lacI (i) in the lac operon which ends up changing the entire pattern of regulation?
A. TRP tRNA
B. TRP Operator
C. TRP Attenuator
D. R Repressor
E. Tryptophan

34. What would be the result on tryptophan regulation of a trp repressor allele that affected the protein similar to the way that the i^s allele affects the i protein?

A.  The TRP operon would be expressed in the presence and absence of Tryptophan.

B.  The TRP operon would not be expressed in the presence and absence of Tryptophan.
C. The TRP operon would be regulated by lactose.
D. The TRP repressor would bind the lac operator and inhibit Lac operon expression.

E. The TRP repressor would require CAP-cAMP to function.

35. What is the proper dominance relationship for the three different alleles of i?

A. i⁺ > i^- > i^S

B. i⁺ > i^S > i^-
C. i^S > i⁺ > i^-
D. i⁺ > i^- = i^S

E. i^S = i⁺ > i^-

36. Study of the lac operon by Jacob and Monod had to involve which genetic processes?
A. Epistasis
B. Dominance
C. Mapping
D. Mutation
E. Meiosis

Section 6. We have discussed numerous components of a gene that must be present in DNA to allow for transcription and translation to occur. Assume that the vertical line is exactly at the base being indicated. For instance the line between D and E would be at the last base of the stop codon (so this stop codon would be in section D). Below is a diagram of a bacterial single gene operon that has been separated into sections as labeled. Make sure to use all of the appropriate sections to answer the following questions if there are multiple regions that are appropriate.

37.  Where could sequences that represent un-translated tryptophan codons be located?

A. A

B. B
C. C
D. D

E. E

38. Where is the RNA sequence encoding the Shine-Dalgarno sequence?

A. A

B. B
C. C
D. D

E. E

39.  If this is a prokaryote, where can sequences that function solely as DNA for this specific gene be located?

A. A

B. B
C. C
D. D

E. E

40.  Where will the E site of the ribosome be located when translation terminates?

A. A

B. B
C. C
D. D

E. E

41. Where can elements that regulate the level of transcription be located if this is a eukaryotic gene?

A. A

B. B
C. C and D
D. E

E. There are no elements in this diagram as transcription factors function in trans and would be on a different piece of DNA

42.  Which of the following is true about how eukaryotic transcription is different from prokaryotic transcription?

A. Eukaryotic transcripts must be capped, poly-A tailed and spliced

B. Introns in eukaryotic transcripts are marked by sequences at the 5’ and 3’ ends of the introns.
C. Eukaryotic transcripts have a poly U tail on them to provide stability.
D. Prokaryotic promoter sequences are less frequent per kilobasepair than Eukaryotic

E. Introns in eukaryotic transcripts are marked by sequences at the 5’ and 3’ ends of the exons.

43. What did the lac and trp operons tell us about gene regulation?

A. Induction of a gene can be the result of negative regulation.

B. Repression of a gene can be the result of positive regulation.
C. Single proteins can have multiple functions.
D. Translation can influence transcriptional regulation.

E. Proteins can be regulated post-transcriptionally.