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BIS101-01, Fall 2021

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 9th.

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 I.

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.

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. What type of gene(s) would you synthesize on a computer and insert into an organism to remove an existing stop codon?

A. tRNA gene

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

E. tRNA synthetase gene

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 third codon in this mRNA as the ribosome would read it?

A. AUG

B. UAC
C. UGC
D. AGU

E.  AAG

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

A.  THR

B.  TRP
C.  TYR
D.  MET

E. ILE

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

A. GCA

B. ATG
C. ACG
D. AGT

E. ATG

8. What is the benefit of some tRNAs having the ability to conduct wobble binding?

A. Wobble saves energy for translation

B. Wobble decreases the number of tRNAs needed for translation
C.  Wobble confers proof-reading ability for translation
D. Wobble allows post-transcriptional regulation of gene expression

E.  Wobble increases the number of codons necessary to specify an individual Amino Acid

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 parts of this diagram has one or more pieces of DNA with a free 5’Phosphate?
A. A
B. B
C. C
D. D
E. E

11.  What part(s) of the replication diagram do not 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 I, 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 allows two pieces of double stranded DNA circles to disentangle from each other?

A. DNA Polymerase I

B.  DNA Polymerase III
C.  Primase
D.  Topoisomerase

E.   Telomerase

15. Complete the following sentence in the most accurate form “A rho 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 no capacity to create new strands of nucleic acid?

A. DNA Polymerase I

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

E. Primase

17. Topoisomerase is a family of enzymes in replication that do what (Use all correct answers)?

A. Unwinds DNA by separating the two strands

B.  Relieves pressure on DNA caused by too much winding
C.  Can function by cutting both strands of the DNA
D.  Can function by cutting one strand of the DNA

E.   Functions without cutting DNA strands

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. A DNA Polymerase removes deoxyribonucleic acids during the process of replication, which activity(ies) are responsible for this?

A. 5’ to 3’ DNA polymerase

B. 3’ to 5’ endonuclease
C. 5’ to 3’ exonuclease
D.  3’ to 5’ DNA polymerase

E.  3’ to 5’ exonuclease

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 E. coli that have been transformed with a plasmid?

A. AmpR

B. LacZ
C. MCS
D. Ori

E. Unused plasmid DNA

21. This section of the plasmid allows the plasmid to have your favorite DNA easily inserted?

A. AmpR

B. LacZ
C. MCS
D. Ori

E. PCR Primers

22. If you wanted to find 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 D 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.

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 elements function as RNA in cis?
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^- 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.

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.

35.  Where could translated tryptophan codons be located?

A. A

B. B
C. C
D. D

E. E

36. Where is the DNA sequence encoding the Shine-Dalgarno sequence?

A. A

B. B
C. C
D. D

E. E

37.  Where can a RNA sequence encoding a stop codon be located?

A. A

B. B
C. C
D. D

E. E

38.  If the protein is 200 amino acids long, which is the minimal length of RNA that could fully function to encode the functional RNA in parts B through D?

A. 600 bases

B. 602 bases
C. 603 bases
D. 604 bases

E. >620 bases

39. If two genes use the same strand of DNA as their coding strand, where could this second gene be located in this diagram?

A. A

B. B
C. C and D
D. E

E. Not in this diagram as there can only be one gene per piece of DNA.

40.  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. Prokaryotic transcripts have multiple ribosomes on them
C. Eukaryotic transcripts have a cap structure that is 3’ OH – G – 5’ – PPP – 5’ N
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 introns.

41. 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.

Section 7. We have discussed the three major sites of a ribosome, the E, P and A sites. Use the following diagram of a ribosome to answer the following questions about translation. Make sure to answer with all of the appropriate sites for each question as there can be more than one correct answer. Please notice that in this diagram, the E site is indicated by choice B, for the following questions. The start and end of the RNA are marked by A and E.

42. Which site(s) is empty when the EF-Tu protein catalyzes GTP to GDP to indicate that the proper tRNA has entered the ribosome?

A. A

B. B
C. C
D. D

E.E

43. At which site(s) will the tRNA with the polypeptide chain be when the release factor enters the ribosome to stop translation?

A. A

B. B
C. C
D. D

E.E

44.  At the initiation of translation, at which site(s) is the tRNA containing an amino acid chain located on this diagram?

A. A

B. B
C. C
D. D

E. E

45. At which site(s) will any tRNA be located in the ribosome on the mRNA during translation?

A. A

B. B
C. C
D. D

E. E

46. What is required to allow the ribosome to translate codons in the mRNA to specific amino acids during elongation of the polypeptide?
A. tRNA synthetase
B. Release factor protein
C. RNA primer.
D. tRNA
E. CAT box

47. What are the proper connection(s) of nucleic acid to protein?
A. Protein N (nitrogen) terminus is from  3’ end of the RNA sequence
B. Protein N terminus is from the 5’ end of the RNA sequence
C. Protein N terminus is from the 5’ end of the DNA coding sequence
D. Protein C (carboxy) terminus is from the 3’ end of the DNA template sequence
E. Protein C (carboxy) terminus is from the 5’ end of the DNA coding sequence

48. What is used by the ribosomal EF proteins to provide energy for translation?

A. ATP

B. TTP
C. CTP
D. GTP

E. Pyrophosphatase

Section 8. Synthesis questions. In this section are some semi-tough questions that span the topics and may require a bit of extra time. Make sure to finish the rest of the test before working on these questions. There is only one correct answer per question in this section.

49. What would happen to DNA replication if pyrophosphatase didn’t exist?
A. Nothing as there is no pyrophosphate in DNA replication
B. DNA replication would be faster as there would be one less protein to involve
C. DNA replication would be severely inhibited because of the build-up of products
D. DNA replication isn’t an enzymatic process so precursor/product levels don’t matter.
E. DNA replication would be severely inhibited because pyrophosphatase would clip off a diphosphate from all NTPs (ATP, CTP, GTP, TTP) and remove the energy for the reaction.

50. Which one of the following types of regulation would you expect a cell to use to take a tiny stimulus like the presence of a small pathogen cell to mount a large defense response?

A. Activation of an EF Ligase/ubiquitin that targets enzyme A for degradation

B. miRNA against an activator transcription factor(TF)  that controls gene A transcription
C. miRNA that targets enzyme As transcript for degradation.
D. positive feed forward regulation.

E. negative feed back regulation.

51. Imagine that you take the TRP operon and swap the Trp operator for the lac operator and transformed this into a cell with a i^s genotype?
A. The lac operon would now be regulated like the trp operon.
B. The tryptophan operon would be controlled by lactose but not glucose.
C. The tryptophan operon would no longer be regulated by any form of tryptophan.
D. The tryptophan operon would always be off.
E. The lactose operon would be regulated by tryptophan

Section 9. Below is a summary of most of the regulatory concepts that we discussed in the class. Fill in the blank for the summary with the appropriate term from the list on the ensuing page. An answer can only be used once and each question has only one best answer. The blanks are numbered in order. There are 9 questions to be answered in this section as listed by (52) through (60).

Although all cells in an organism have the same DNA, there are ways that the expression of the DNA can be regulated to allow cells to have different functions. Some regulation happens before transcription even begins. For example, ___(52.)___ is a form of covalent modification of a deoxyribonucleic acid. This modification can lead to ___(53.)___, a state of DNA in which histones become tightly packed and physically limit the accessibility of the packaged DNA. Modifications can also occur on histones themselves causing the histones to unwrap DNA, making it more available for groups of proteins called ___(54.)___ to bind to the DNA and regulate the initiation and transcription of genes. If these proteins positively regulate transcription they are called _______(55.)_____.

After transcription, the unprocessed RNA contains _____(56.)____ and introns. The cell can create multiple different protein products from the same unprocessed RNA via __(57.)___.  Mature RNA’s may also be targeted by __(58.) ____, which uses a miRNA as a guide to enable the destruction of RNAs.

After translation, protein products are still further regulated. One example is ___(59.)___, which is a reversible covalent modification of a protein that is catalyzed by a kinase. Another regulator of proteins is ___(60.) ____, which is a very common type of small protein tag that signals a protein is destined for the proteasome.

A. Activators (55)

B. Histone methylation

C. RNA polymerase

D. siRNA

E. Ubiquitin (60)

F. Ligand

G. Transcription factors (54)

H. Antibodies

I. Enhancers

J. Euchromatin

K. Silencers

L. RISC proteins (58)

M. Introns

N. Exons (56)

O. Cytosine methylation (52)

P. Proteasomes

Q. Promoter

R. Heterochromatin (53)

S. Phosphorous

T. Cytosine Acetylation

U. Alternative splicing (57)

V. Repressors

W. Phosphorylation (59)

X. Intron Retention

Y. Cistrons