Exam 1
Name:_____________________________
[18 points] Membrane formation /4 1a) Explain the entropy of cleaving lactose to make glucose and galactose. Explain in 1-­‐‑2 sentences, max. The entropy is increasing, since the two molecules on their own are less ordered than when combined into a single larger molecule. Grader Note: -­‐‑ 4/4 if you said entropy goes up AND gave reason (1 molecule turns into 2) -­‐‑ 2/4 if you said entropy goes up w/o reason -­‐‑ 0/4 entropy decreases /5 1b) Which structure below would be the best substitute for a phospholipid in a bilayer? Circle the single best answer, then explain your answer in 1 sentence, max. The molecule is amphipathic in that has both a predominantly polar region and a predominantly non-­‐‑polar region and will be a good replacement for the very amphipathic phospholipid. Grader Note: -­‐‑ 2 points for selecting the correct molecule (far right) -­‐‑ 3 point for an explanation of what makes for a good bilayer (amphipathic, or part hydrophobic and part hydrophilic) /4 1c) Channel proteins allow ions into the cell. In one particular species, the cell uses unique membrane motions to eventually move ions into the nucleus. Diagram the membrane motions needed to move ions into the nucleus. Two possible correct diagrams: Show a vesicle budding from the membrane with the channel protein embedded and then recombining with the nucleus. This would put the channel in the nuclear membrane. Or Show a vesicle budding from the membrane and taking ions with it. The vesicle would merge with the membrane of the nucleus, releasing the ions into the nucleus. Grader Note: -­‐‑ 4/4 if you clearly diagrammed vesicle emptying into into a membrane, even if was into the plasma membrane and not the nuclear membrane -­‐‑ 4/4 if you clearly diagrammed a vesicle transporting the membrane protein from plasma membrane to the nuclear membrane -­‐‑ 2/4 if you had ions go through the membrane protein and then magically appear in a vesicle and then enter the nucleus Total: _____
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Exam 1
Name:_____________________________
-­‐‑ 1/4 if you only show ions coming in through membrane channel or if you talk about passive diffusion -­‐‑ 0/4 else /5 1d) Two mutant versions of the channel protein exist. Mutant C has an additional charged side chain that forms an extra ionic bond that inhibits flexibility. Mutant D has a change in the 153rd codon (of 155 codons total) from 5’ UAC 3’ ! 5’ UAA 3’. Your colleague hypothesizes that Mutant C is less able to catalyze transport than Mutant D. Do you agree or disagree? Be specific, and explain why in 1-­‐‑2 sentences, max. Agree that Mutant C is less able to catalyze transport. Loss of flexibility will inhibit the overall transport function because the channel cannot shift conformations to push/pull the molecule through its structure. The premature stop mutation only changes the last 2-­‐‑3 amino acids, so it is unlikely to influence the structure of the protein nearly as much as the loss of flexibility. Grader Note: -­‐‑ 5/5 if you select mutant C (i.e. agree with your colleague) AND explain that membrane channels very much require flexibility to function AND describe that the nonsense mutation of mutant D will not affect the protein too severely because it is towards the end of the peptide chain -­‐‑ 3/5 if you if you select mutant C (i.e. agree with your colleague) AND explain that membrane channels require flexibility to function BUT didn'ʹt discuss mutant D -­‐‑ 2/5 if you select mutant D (i.e. disagree with your colleague) and give a good reason about how a shortened protein (nonsense mutation) can impact structure/function -­‐‑ 0/5 else Total: _____
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Exam 1
Name:_____________________________
[26 points] Mutations /5 2a) A free radical creates a 2-­‐‑bp insertion into a gene in the region between the +1 transcription site and the ribosome binding site of the mRNA. Predict how the mutation would impact translation. Explain why in 1-­‐‑2 sentences, max. This insertion does not change the reading frame because it happens upstream of the start codon.
This mutation is unlikely to impact translation.
(Alternatively: If there is any impact, it would be most likely to the RBS and would decrease
translation by decreasing ribosome-mRNA binding.)
Grader Notes:
- 5/5 if you say that the mutation will have NO effect on translation AND describe why (because the
mutation is upstream of the RBS)
- 2/5 if you say that this mutation will affect the ribosome's ability to bind to the mRNA which will
decrease translation frequency (the prompt states that this mutation occurs before the RBS)
- 1/5 if you say that this is a frameshift mutation and describe how a frameshift will negatively affect
translation
- 0.5 else
/5 2b) A 1-­‐‑bp deletion in the 4th codon (of 246 codons) of the gene that encodes the release factor. Mark all correct answers: __X_ Some/all translated proteins would be too long. ____ Different stop codons would be used. ____ Translated protein length would be unchanged. ____ The cell would survive well. ____ A few translated proteins would be too short. _X__ The cell would have major problems. Grader Notes: -­‐‑ 5 points for BOTH correct answers together -­‐‑ 2 points each correct answer on its own is only worth 2 points -­‐‑ [-­‐‑1] point for each wrong answer (except the bottom left is [-­‐‑2] if selected) -­‐‑ Scores can'ʹt go below 0/5 /5 2c) A very small protein acts as a competitive inhibitor of the ribosome active site. The gene encoding this protein has a change in a single codon from 5’-­‐‑CAC-­‐‑3’ to 5’-­‐‑CAG-­‐‑3’. Explain the effects of this mutation in 1-­‐‑2 sentences, max. This single replacement of one amino acid might change the protein primary structure and the overall shape of the very small protein. If it cannot bind to the ribosome with this new shape, then translation will increase. Alternatively: If you decide that the single change does not influence protein structure, you’d need to discuss the relatively small difference between the His and Gln amino acid side chains. Grader Notes: -­‐‑ 5/5 for saying that this mutation will change primary/secondary/tertiary protein structure AND realizing that this is a small protein so even one amino acid change can have a big effect AND saying that this will (most likely) negatively affect this protein'ʹs function as a competitive inhibitor AND saying that without this inhibition, translation activity will increase -­‐‑ 4/5 for saying the above but not including that translation will increase (just saying that inhibition will decrease is not enough) Total: _____
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Exam 1
Name:_____________________________
-­‐‑ 2/5 For only talking about the change in protein structure without talking about the change in it'ʹs function, or visa versa -­‐‑ 0/5 for saying there would be effects of this mutation /5 2d) All anticodons on Lysine-­‐‑charged tRNAs now bind to Arginine-­‐‑coding codons. Mark all correct answers: ____ New proteins will have no Lysine. __X__ New proteins will have no Arginine. __X_ Protein secondary structures may be lost. __X__ Protein tertiary structures may be lost. ____ All proteins will be changed. Grader Notes: -­‐‑ 5 points for BOTH correct answers together -­‐‑ 2 points each correct answer on its own is only worth 2 points -­‐‑ [-­‐‑1] point for each wrong answer (except the bottom left is [-­‐‑2] if selected) -­‐‑ Scores can'ʹt go below 0/5 /6 4a) Fill in the following chart. Answer each in a few words. Molecular Structure Example: Primarily hydrophobic What kind of biomolecule? Monomer or polymer? or primarily hydrophilic? (protein, carbohydrates, etc) hydrophobic lipid monomer hydrophilic carbohydrate polymer hydrophilic nucleic acid monomer Grader Notes:
- 1 point for each box
- commonly missed point (this is an NMP, not a NTP)
Total: _____
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Exam 1
Name:_____________________________
[20 points] Transcription and Translation
/8 5a) Draw a diagram of the part of transcription in which the mRNA is polymerized from 10 to 20 bases long. Be sure to label all RNA, DNA, and proteins involved. Include the location of the promoter. Make your diagram as clear as possible. →
Grader Notes: Not indicating which direction RNA polymerase was going -­‐‑1pt Required parts (2pts each): DNA, mRNA, RNA Poly, Promoter Region -­‐‑ 1-­‐‑3 points for clarity issues Answers that just had translated sequences (like question 5b) were marked incorrect Below is a portion of double stranded DNA from a bacterial chromosome.
The promoter region and the +1 base pair are indicated, as well as the polarity of the two DNA strands.
+1
-10
-35
...3’..GGTAGGATTCCGACGTACGCCCATACGTATGGGAGGGATACGTATTCATCAGAT..5’....
...5’..CCATGCTAAGGCTGCATGCGGGTATGCATACCCTCCCTATGCATAAGTAGTCTA..3’....
/5 5b) What is the translated protein sequence from this gene? Be sure to include the N- and C-termini. You can
abbreviate amino acids using the 3-letter code. N-­‐‑Met-­‐‑Gln-­‐‑Pro-­‐‑C Grader Notes: Added a stop codon -­‐‑2pts /4 5c) Which promoter would be stronger, and why? Promoter X: The -­‐‑10 and -­‐‑35 binding sequences have each switched a TA bp to a GC bp. Promoter Y: The -­‐‑10 and -­‐‑35 binding sequences are unchanged, but 21 bp are inserted between. Explain your reasoning in 1-­‐‑2 sentences, max. The importance of the promoter is in how well it binds to the sigma protein to bring in the RNA polymerase. While the X promoter changes will change binding, the huge increase in distance between the binding regions in Y will make it much less strong of a binding partner for sigma. Grader Notes: No points were given for answers about hydrogen bonds. No points if the correct promoter was selected but the explanation was incorrect. Total: _____
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Exam 1
Name:_____________________________
/3 5d) What are the binding surfaces on the enzyme that creates charged tRNAs ? You do not need specific names, but describe each surface with a few general words or a phrase, each. i) a surface that binds specifically to the correct amino acid ii) a surface that binds specifically to the correct anticodon on the tRNA iii) a surface that binds to ATP Alternatively: could be a surface that binds non-­‐‑specifically to any of the 40-­‐‑or-­‐‑so tRNAs Grader Notes: Each correct answer was worth 1 pt, they just had to provide three of the four options (amino acid, anticodon, tRNA, or ATP) [21 points] Cellular architecture and new life forms /4 6a) The Smooth ER contains special molecular components. Describe one of these components and explain why locating it in this organelle is advantageous for the cell. Explain in 1-­‐‑2 sentences, max. Possibilities: transport proteins to the Golgi, enzymes that build or modify lipids, enzymes or molecules that maintain a primarily hydrophobic environment, lipids that are destined for roles around the cell. Why? Concentration helps to speed reactions, to create a microenvironment specifically tailored to building lipids, or to keep enzymes from modifying all lipids in the cell. Grader Notes: 1pt for knowing what the smooth ER does 1 pt for knowing why organelles are used in the cell 2 points for making some claim about why organelles, and in this case the smooth ER, is beneficial for cellular activity. Many people made the common mistake of explaining why lipids are important for the cell, not why it is important for the cell to sequester the lipid creating machinery in the smooth ER. /4 6c) Imagine a bacterial cell that prevents its own destruction by poisoning the crawling white blood cells. It does this by releasing a tiny molecule that allosterically stops the enzyme that depolymerizes actin polymers. Mark all correct answers: _____ The cell is likely to continue moving but in a random direction. _____ The cell is likely to stop completely. __X__ The cell is likely to move more slowly than before. __X__ The cell is likely to create pseudopodia. _____ The cell is likely to move more quickly than before. Polymerization still occurs, so pseudopodia can be formed. Motion stops, though, because the filaments cannot be depolymerized efficiently and it cannot drag in its own rear end. Grader Notes: 2pts for each correct 'ʹX'ʹ, -­‐‑1pt for each additional incorrect 'ʹX'ʹ they added. Ex: 1 correct 'ʹX'ʹ and 1 incorrect 'ʹX'ʹ, they got 1 point (2-­‐‑1=1) Total: _____
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Exam 1
Name:_____________________________
/5 6d) You made a slide to observe a moving cellular organism with a microscope. Instead, you see a motionless blob. In a few words each, give four different options that you might try. A few possibilities: use a depression slide, start from the end of the focus range, adopt diopter, lay the coverslip onto the slide more carefully /4 3a) A new life form is reported from samples of asteroids. This life form is primarily made of argon and bromine, and it lives in a fluid of uranium phosphate. Which of the following two pairs of molecules is a reasonable structure for hydrogen bonds found in this life form? Circle one. UPO4
H-Br
UPO4
Br-Br
UPO4
H-H
/4 3c) These new cells occasionally use up all of the phosphate in the cell. What is the most efficient
transport scheme for the new life form to slightly increase the concentration of phosphate?
Mark the single best answer: _____ Active Transport _____ Passive Diffusion __X__ Facilitated Diffusion The cell only needs to allow in phosphate from the external high concentration. This doesn’t require the
pumping of active transport, but a ‘door’ is necessary because phosphate is unlikely to move across a
hydrophobic membrane on its own.
Total: _____
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Exam 1
Name:_____________________________
[15 points] This take home portion should be completed before the exam and turned in at the start of the exam. Neatness
and clarity are important. Course staff (TAs, Liz, or Ben) will politely refuse to answer questions that directly relate to
this take-home portion. You can remove the instructions on this sheet if you want more room on your version to turn in.
Creativity will help, though artistic talent is unnecessary for full points.
6) Design a protein.
The protein should be an enzyme that is useful to a cell in some way. The protein should not be more than
50 amino-acids in length, and all amino acids used should be common. Your diagram should be more
complete and better presented than the simple diagrams in the textbook.
•
•
•
Proteins will be graded on the following rubric:
3 points: Use diagrams to show how the semi-flexibility of the protein allows it to help the cell. Be specific!
• 3 points: Show some key features of the protein that explain how it holds a useful structure.
• 3 points: Use your diagram to show your knowledge of enzymes. Again, be specific in relating this
knowledge to your particular enzyme.
2 points: Include the N- and C-termini, the chemical structure of at least one entire amino-acid including sidechain, and somehow clearly indicate 1 °, 2 °, 3 °, and any 4° structure.
4 points: After completing your protein, diagram two different specific mutations. Explain how one mutation
increases enzyme rate and the other decreases enzyme rate.
The average score on this question was ~11.3, with a very few 15/15 grades given. Extra points above the mean
were most commonly given for examples that:
• synthesized the information into fewer diagrams rather than showing many small diagrams with one
piece of information each • gave specific and realistic mutations that showed understanding of the impacts from genotype to
phenotype • included some understanding or appreciation for the three dimensional structure of proteins (within
the confines of the two dimensional paper medium). A few anonymized examples are shown here. Total: _____
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Exam 1
13.5 out of 15:
Name:_____________________________
15 out of 15
Total: _____
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Exam 1
Total: _____
Name:_____________________________
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Exam 1
14 out of 15
Total: _____
Name:_____________________________
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Exam 1
14.5 out of 15
Total: _____
Name:_____________________________
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