BIO1140 Final Exam W2021 Student PDF

Preview

Summary

Download BIO1140 Final Exam W2021 Student PDF

Description

Name: ______________________________

Student #: ___________________________________

BIO1140 - Introduction to Cell Biology – Final Exam Professor: Dr. Alexandra Pettit

Due – April 22nd 12:30pm

General Instructions: 1. This exam is worth 30% of your final mark. 2. This exam is open book. I encourage you to use any of the materials I have given you for the class (videos, articles, molecular animations, etc…) and the notes you have created while working with this material. All answers eligible for full marks can be developed from an understanding of these materials. 3. This is an individual exam, you are not to complete it in groups. Should there be evidence of collaboration or plagiarism on your submitted exam, you will face allegations of academic fraud. 4. You should expect to complete the exam in ~ 3 hours; you should NOT spend copious amounts of time reading and researching to complete the exam. Should you choose to consult any sources beyond the course materials, they must be referenced as part of your answer. 5. You can answer this exam in any way you choose/are able. This includes but is not limited to:  Printing the exam, filling it in by hand, then scanning/photographing it.  Answering each question by hand on a blank paper, then scanning/photographing it. *You do not need to recopy the questions to your sheet of paper but be sure to clearly indicate which question you are answering and if you must copy sequences/images/etc… to your sheet, do so very carefully to avoid making errors.  Handwriting your answers digitally. (e.g. with a stylus capable of writing in e-ink)  Typing your responses directly into the file. 6. You may ask questions via email. Question which can be answered (e.g. – the question is relevant, makes sense, and does not require disclosing the answer), will be posted along with the answer to the ‘final exam questions’ discussion board on Brightspace for all students to see. Only questions of a technical nature (i.e. – submission issues) will be answered in the final 30 minutes of the exam. 7. Name the digital file (use .pdf format ONLY) containing your completed exam student#_1140_finalexam_surname.pdf (e.x - I would name my completed exam – 12345678_1140_finalexam_Pettit.pdf). 8. You must submit your completed exam by 12:30pm on April 22nd .  Upload a single pdf file with the entire completed exam to the "BIO1140_Final Exam" on Brightspace by 12:30pm on April 22nd .  You will receive an email confirmation of the receipt of your submission. I do, recognize that last minute issues are at times unavoidable and I will navigate these with you on a case-by-case basis.

If you find yourself unable to submit your file due to technical issues (e.g. – computer crash, poor internet connectivity, etc…) you should do the following if at all possible: 

avoid re-opening your exam file after the deadline



contact me as soon as you are aware an issue has arisen



if possible (i.e – using your data plan or an alternative internet connection), send me your exam file via email

Name: ______________________________

Student #: ___________________________________

Helpful Hints and Tips: 



If completing the exam digitally, it is recommended that before beginning to write, that you name and save the document and also activate any automatic save function that your software may have. If scanning/photographing your exam to digitize a handwritten file, you may find it helpful to use a free app/program such as clear scanner (for android or iPhone) or pdf merge (web based) to compile multiple pages into a single file.

Academic Integrity Statement Please complete the section below and submit it with your exam. If completing the exam by hand on blank paper, you do not need to re-copy the academic integrity statement, but you must sign your document.  

I have completed this exam independently. I will keep the contents of this examination confidential.

_______ (initial here) _______ (initial here)

By signing this statement, I am attesting to the fact that I have reviewed the entirety of my submitted work and that this assessment meets all of the rules in uOttawa’s Academic Regulations about Academic Integrity. I confirm that I did not act in any way that would constitute cheating, misrepresentation, or unfairness, including but not limited to, using unauthorized aids and assistance, impersonating another person, or providing unauthorized assistance to someone else. Signature: _________________________________________ Date: ________________________ Name (print/type):___________________________________ Student # : ____________________

Exam Questions (5 questions – 65 marks total) The questions on the following pages ask you to consider a novel cell biology scenario. Throughout the exam, you will find pertinent background information about this specific scenario. You are expected to use the provided information AND apply the knowledge you have acquired thus far in BIO1140 to answer the questions posed. You must answer all of the questions below. Answer each question as concisely as possible, unless otherwise specified, limit yourself to no more than 2-3 sentences per response. Do not simply put all related information about a topic down to answer a question. If a question, asks you to provide a specified number of answers (e.g. – 2 reasons why something occurs) only the first X entries you include in your answer will be graded. Answers in point form and/or those accompanied by drawings will be accepted so long as they are complete.

Name: ______________________________

Student #: ___________________________________

In many mammalian species, including humans, there is a hormone (H) that acts as a key regulator of hexose (6 carbon sugar, e.g - glucose) metabolism, cell cycle progression, and ultimately cell survival. Hormone H regulates these effects via its receptors which are found at both the cell surface (csRH) and within the cell (icRH). The signalling pathways that become activated in the presence of hormone H are depicted and described below.

Signalling via the cell surface receptor  Hormone H mediates its cell cycle stimulatory and pro-survival effects by binding to and activating the cell surface hormone H receptor (csRH).

Name: ______________________________

Student #: ___________________________________



The activated csRH activates Lyn, which activates RAS and ultimately the Raf/MEK/ERK kinase cascade.



Active ERK: o

phosphorylates and inactivates GSK-3. Inhibition of GSK-3 promotes cell survival.

o

inhibits p27, preventing it from inhibiting cell cycle progression.

o

activates Fos, a transcription factor which promotes cell cycle progression by triggering Cyclin A expression.

Signalling via the intracellular receptor 

Hormone H also binds to and activates the intracellular hormone H receptor (icRH).



The activated icRH translocates to the nucleus where it acts as a transcription factor binding to a specific sequence called a hormone H response element (HRE) found within promoters on the DNA.



icRH – HRE binding upregulates the transcription of the hexose kinase gene, which is required for hexose metabolism and ultimately cell survival.

Below is a list of mutations commonly found in different components of the hormone-signaling pathways.  Mutant #1: The icRH undergoes a loss-of-function mutation.  Mutant #2: GSK-3B can no longer be phosphorylated.  Mutant #3: ERK is constitutively active.  Mutant #4: Lyn undergoes a gain-of function mutation.  Mutant #5: The cyclin A gene’s DNA is highly compacted and inaccessible.

1a. Mutations in the signalling pathways depicted above have been associated with an increased incidence of several types of cancer. Which of the above mutations (#1-5) could potentially cause cancer in an individual? Be sure to explain why. (3 marks)

1b. Individuals with these cancers may be treated with one of the following chemotherapeutic drugs. Complete the table below about their mechanisms of action. (8 marks) Dru g

Drug’s mechanism of action

Which process is targeted first by this drug?

In which cellular compartment/structure/organelle does this process occur?

(replication, mitosis, transcription, translation, or none

If more than 1 location, be sure to specify ALL relevant locations.

Name: ______________________________

Student #: ___________________________________ of the above)? 1 mark each 1 mark each

A

Inhibits microtubule disassembly

B

Inhibits elongation by RNA polymerase Inhibits eukaryotic ribosomal function

C D

1c. Referring to the signalling diagrams above, complete the table below. Consider how cell signalling will proceed in a cell exposed to hormone H with each of the following homozygous mutations. (9 marks) Mutant (# refers to the mutant s listed above) #2 #3 #1 + #5

csRH active ?

HK expressed?

(yes/no)

(yes/no)

Cyclin A expressed ?

cell cycle progression?

cell survival compared with wildtype.

(yes/no)

(same, more, less)

(yes/no) 0.5 marks/box

1d. The csRH mRNA and protein are represented in the diagram below.

1 mark/box

Name: ______________________________

Student #: ___________________________________

i. In the boxes on the image, label the N and C termini of the csRH protein. (1 mark) ii. The ______________________ of the csRH protein must be cleaved off before it can be trafficked along the __________________________________ to the cell membrane. (2 marks) iii. On the schematic above, draw the csRH protein as you would find it at the plasma membrane. Be sure to label the N and C termini of the protein you draw to indicate its orientation. (1 mark) iv. Which protein domains would you NOT expect to find as part of the intracellular hormone H receptor protein icRH? (2 marks)

1e. In the above signalling diagram, hormone H binds to both an intracellular and a cell surface receptor. Initially you assume that hormone H must therefore be a small hydrophobic molecule. However, further analysis revealed that it is a large hydrophilic molecule. Knowing this, what would you need to add to this diagram to accurately reflect how these signalling events are possible and why? (2 mark)

The beginning of the hexose kinase gene’s sequence can be found below, the +1 nucleotide is underlined and bolded. It also contains an origin of replication (ORI) which is found at position 30.

Name: ______________________________

Student #: ___________________________________

2a. Assume that replication has been initiated at that ORI. Provide the sequence of the primer that is complementary to the DNA in each of the following positions. (2 marks) Site A - binding to the top strand of the DNA at position 20 – 30 5’ __ __ __ __ __ __ __ __ __ __ 3’

Site B - binding to the top strand of the DNA at position 31 – 41 5’ __ __ __ __ __ __ __ __ __ __ 3’

2b. Replication is occurring normally in these cells; would you expect to find a primer in both positions? Why or why not? (3 marks)

Using a computer algorithm that searches for sequence similarities in other organisms, you discover that hexose kinase is a highly conserved gene that is expressed by many species, both prokaryotic and eukaryotic. The most closely related prokaryotic homolog of hexose kinase has a protein sequence in which 90% of the amino acids are identical to those of the human version of the gene. 3. To learn more about their similarity at the DNA level, you obtain segments of the genomic DNA coding for the hexose kinase gene in both humans and this prokaryotic species. After combining both DNA samples, you heat them to denature the DNA strands and then allow them to cool and reanneal. Finally, you examine the DNA hybrids you obtain under the electron microscope. 3a. Your analysis reveals that there are three different DNA hybrids in this sample, these can be seen below. You reason that one must belong to the prokaryotic species, one to the humans and the third arose when one strand from each species base paired. Identify the origin of the DNA in each one of the observed structures by circling the correct answers below (2 marks).

Name: ______________________________

Student #: ___________________________________

Hybrid B is double stranded DNA from

PROKARYOTE or

HUMAN

Hybrid C is double stranded DNA from

PROKARYOTE or

HUMAN

The hybrid A top strand is DNA from

PROKARYOTE or

HUMAN

The hybrid A bottom strand is DNA from

PROKARYOTE or

HUMAN

3b. In hybrid A what are the large loops seen on the top strand of DNA? What are the smaller loops seen on both strands of DNA? Explain your reasoning. (3 marks)

You continue to study the expression of the hexose kinase gene and capture the following electron micrograph of the gene being expressed.

Name: ______________________________

Student #: ___________________________________

4a. Was this micrograph taken of a sample prepared from human cells or prokaryotic cells? How do you know? (2 marks)

4b. What is the sequence of the first 10 nucleotides of the transcript of this gene? (1 mark) 5’ ___ ___ ___ ___ ___ ___ ___ ___ ___ ___ 3’

4c. What are the first 5 amino acids encoded by this gene? (1 mark) Note - there is a codon table available at the beginning of this exam. N’ _____ _____ _____ _____ _____ C’

4d. Will translation stop at the UAA which begins at position 41? Explain your logic. ( 2 marks)

4e. You also study the expression of 3 different mutants for this gene. For each mutant answer the following:  Does this mutation change the sequence of the protein produced? Why or why not? o If it does change the sequence of protein be sure to write out the new sequence. o If it does not change the protein sequence, what effect (if any) would you expect it to have on expression of the gene?

i. Mutant A has a single base pair substitution with the T/A being replaced with C/G base pair at position 35 (position denoted by the * in the sequence above). (2 marks)

Name: ______________________________

Student #: ___________________________________

ii. Mutant B has a 2 G/C pairs inserted between position 19 and 20 (position denoted by the ^ in the sequence above). (3 marks)

iii. Mutant C has had the first 5 base pairs deleted (position 1-5). Does this mutation change the sequence of the protein produced? Why or why not? If it does change the sequence of protein be sure to write out the new sequence. If it does not change the protein sequence, what effect (if any) would you expect it to have on expression of the gene? (3 marks)

Remember that hexose kinase is an enzyme required for hexose metabolism, a process that takes a 6-carbon sugar and breaks it down into 2 pyruvate molecules. 5a. What specific metabolic process have we studied in which hexose metabolism occurs? (1 mark)

5b. How many steps does this pathway consist of? (1 mark) ______ steps 5c. Overall, this metabolic process (hexose  2 pyruvate) is exergonic. However, if you look at the individual reactions that makeup this process, they are a mix of endergonic and exergonic reactions. Is the preceding statement true or false? ________________ (1 mark) If you selected true, describe the contribution of endergonic reactions to the overall exergonic process. If false, explain why. (2 marks)

You discover that rather than being hormonally regulated (as seen above in humans), hexose kinase is part of an operon in prokaryotic organisms. This operon is known as the “hexose operon” and it regulates expression of the complete set of enzymes needed to convert a hexose sugar into 2 pyruvate molecules.

Name: ______________________________

Student #: ___________________________________

5d. Remembering that hexose metabolism is a highly conserved process among all branches of life, how many genes do you expect to find in this operon? Explain your logic. (1 mark)

Like the lac operon, the hexose operon is controlled by a separate regulatory protein under the control of its own promoter (see the schematic of the operon below). The hexose regulatory protein is sensitive to fatty acyl CoA levels. When all hexose fuel sources are depleted, the bacteria switch to lipid metabolism and fatty acyl CoA levels increase. This turns expression of the hexose operon off.

5e. The regulatory protein that controls expression of the hexose operons is a transcriptional ACTIVTOR or REPRESSOR (circle one). (1 mark)

5f. Complete the diagrams below to reflect the proteins and any relevant cofactors (e.g. inducer/repressor molecules) that you would expect to be occupying this operon’s regulatory region in the presence of low vs high fatty acyl CoA levels. (3 marks) ↑ [hexose], [fatty acyl CoA] = negligible

[hexose] = negligible, ↑[ fatty acyl CoA]

5g. A mutation has occurred rendering the regulatory protein unable to recognize the operator sequence. What effect would this have on the expression of this operon? How would this impact the energetic demands on the cell? Justify your answer. (3 marks)

Name: ______________________________

Student #: ___________________________________...