Exam #2

Questions on midterm 2

General Questions

• Also do you want the save file in the same format as the midterm?

  • Please use the same lastname_firstname_exam2 format from the first exam

• Would it be easier to grade if we put the question before we answered it?

  • Ideally you would put the answer on the same page as the question, but it definitely needs to be clear which answer goes with what question. As there are no regrades, you will not have a chance to point out errors if the TAs/grader cannot find your answer, even if it is correct. So make it obvious!

• Is there a way we have to format our answers (such as being under a certain length)?

  • As specified on the front page, please keep answers to 4-5 sentences.

• Is it alright to upload a Word file to Smart Site containing the numbered answers to certain questions and then upload a second or subsequent submission(s) for the remaining answers that are hand-written and/or hand drawn answers that I have scanned into the computer?

  • I would advise uploading everything together the first time. You may upload multiple files, but we would prefer to have everything uploaded as a single pdf. You can scan (or take quality photos with your smartphone) drawings or handwritten text and include those in the same pdf as your type-written answers.

• Do we need to explain our answers?

  • Only where you are asked.

Question 1

• Question 1 is impossible, there's an error, or a trick, or...

  • No, no, and no. No trick, no error, totally solvable. See questions/answers below.

• Can we still get b, c and d and correct if we don't get the correct protein sequence?

  • Technically possible, but probably pretty hard to do in practice.

• There's a trick in number 1 he's not telling us...

  • Nope. Pretty straightforward, standard stuff. You gotta know about DNA and RNA and proteins, that's all.

1A

• For #1 do we have to find out which strand is the template strand and which one is the compementary strand? How do we know which strand starts at 5' and 3' from left to right?

  • Presumably knowing which strand is which is necessary for figuring out transcription. No information on 5' or 3' is given.

• Is it reasonable to assume that the given DNA sequence can be circular?

  • No.

• For 1a, it says to write the protein sequence using the one letter abbreviations for the Amino Acid. Does that mean that we should represent phenylalanine as "F", Proline as "P" and so on and so forth when giving the final answer?

  • Yes. E.g. this site

• Can we assume the top strand is 5'-3' and bottom is 3'-5'?

  • No.

• I was wondering if for question 1 if we are supposed to use the start/stop codons we are familiar with (wikipedia says that bacteria sometimes use different ones)?

• No need to use weird start/stop codons.

• Do you mean the whole sequence is translated into amino acids, that the start and stop codons are not drawn in the sequence, or just a portion of it for us to figure out the start and stop codons within the sequence like one hw problem?

  • Everything needed is in the sequence. Start codon, stop codon, and if you look hard enough, a laser robot alien overlord.

• There is no protein coding sequence that starts with a start codon and ends with a stop codon.

  • Yes, there is.

• Are we to assume the start codon is right before the first letter or do we need to find a start codon and go from there until we hit a stop codon?

  • No assumptions need to be made. Start and stop codons that generate a short protein are in the sequence.

• Is there supposed to be a stop codon in both sequences?

  • There is only one sequence. Both strands are shown.

1B

• In question 1b, you didnt accidentally type glycine instead of glucine did you?

  • No.

• 1 part B, did the tRNA initially code for glycine and then mutate to something else, or did it initial code for something else and then mutate into coding for glycine?

  • The question is asking what would happen to the protein in 1a if the cell had a nonfunctional tRNA for glycine.

• Does 1(b) not depend on 1(a)?

  • The answer to 1b depends on 1a.

1C

• Can we pick either mRNA transcript to design a probe for or would you like us to do one specifically?

  • The DNA in part 1a makes only a single complete mRNA.

• Is the 10 bp probe supposed in RNA form?

  • You can write out either DNA or RNA sequence that would function as a probe.

1D

• In question 1 part d what exactly do you mean by region. Does this mean both strands?

  • You may circle either one or both strands. Doesn't matter.

• For question1 part d, are you referring to the protein sequence we got in part a or are you referring to the double stranded DNA sequence?

  • The question is referring to the DNA sequence in 1A.

1F

• Wait, my exam doesn't have 1F!

  • Good! Neither does the key.

Question 2

• When asking "What type of TE is this...?" Does that mean two individuals have same TE? Or actually it must be "what kind of TEs are they...?"

  • The question is asking to describe the transposable element that is actively making new copies. All the new copies are of the same original TE.

• Are the individuals in problem 2 haploid?

  • They are diploid.

• I would like to know if active transposable elements mean that they are able to move around

  • Yes, active transposable elements mean that copies of the transposable element are actively being made.

• On question 2 where it says that the F1 accumulates insertions similar to one of the parents, does it mean than some F1 are like Individual 1 and some are like Individual 2?

  • No. This means that the all the F1 show active transposition. Some of the F2, however, show no additional transposition or new insertions when selfed for several generations.

Question 3

• Can we assume that the mutant alleles are dominant to the wildtype? Or are the wildtype dominant to the mutants?

  • No such assumptions are required, and knowing dominant/recessive is not necessary for answering the question.

• For question #3 the paper says they excised tourist and found no effect. Is excise equivalent to knock out?

  • Excise

Question 5

• Are you asking why you could consider recombination mutagenic, like the crossing over made a new combination of DNA so could be considered a mutation or are you asking with the recombination what errors could occur?

  • The latter.

• Can we just put the short answer or do we have to explain why?

  • The question doesn't ask why, so if you're certain of your answer, go for it. It should take only a few words to answer.

• Is 5 referring to recombinant dna?

  • No, it is referring to recombination as in crossing over.

• When it talks about recombination, is it referring to meiotic recombination or homologous recombination?

  • Either, but generally usually that means meiotic recombination.

Question 6

• When it asks what kind of gene is absent, do we have to name a particular gene or can we just say the gene codes for ___ type of proteins?

  • You do not need to name a particular gene/protein, the question is asking for what class of gene/protein is problematic.

• Do proteins fold correctly when the mouse is exposed to regular temperatures?

  • Yes. But in reality it shouldn't matter too much for answering the question.

• Do we have to specify a gene that is nonfunctional or can we specify a protein that is nonfunctional?

  • The question is not asking you to name a gene. It is asking you to name a class of genes/proteins that would likely explain the observation.

Question 7

• Given the last statement provided about Vibrio fischeri being in high density to allow for sufficient I protein levels in order to produce light, can I assume that there are functional bacteria surrounding the mutant bacteria in this question?

  • Yes

• Is Vibrio fischeri really #^@!$ awesome?

  • Yes, yes it is.

• R bind on I (gene) to activate, not protein I as described?

  • The question is correct as stated. LuxI produces an effector protein that binds to the protein produced by LuxR

• "R- mutant" in the question means gene or protein?

• The nature of the R- mutant is given in both i. and ii.

• Do the proteins A and B create luciferase when working together/combined, or do they create viable luciferase individually and having them both is just a fail safe for being able to create the end product?

  • Both proteins are needed for proper function.

7b

• Does the binding domain refer to the binding area on the already folded protein (similar to part a) or does it refer to the ability to bind to the DNA strand itself?

• The question refers to a mutation in the DNA sequence of the R locus which results in a change to the binding domain of the protein produced.

Question 8

• Do you want us to go into detail on the two techniques used to identify enhancers/promoters or should we focus on the general technique in which those two specific techniques fall under?

  • No need for horrible detail. A few sentences explaining the general technique should be sufficient.

• Is there going to be a Lynch et al "annotated" pdf posted on smartsite?

  • Should be there now.

• The paper mentions multiple enhancer sequences, do we have to explain the methods of how they found each of them?

  • The question is asking the general method Lynch et al used to identify enhancers genome-wide.

• Question 8 states that it wants us to give the methods used to identify putative enhancer and promoter sequences. Under the Material and Methods portion at the end of the paper, there is an italicized portion that reads "Identification of Transposable Element Derived Promoters and Enhancers". Do we need to be more specific than the generalized digital methods stated?

  • You need to explain the genetic method used. What's the assay/technique used to figure out what part of the DNA is an enhancer? How does that assay/technique work?

Question 10

• for 10a do you want a detailed approach or a general one if fine? for 10b do you want us to just state the method to use or have detailed steps for the method?

• A few sentences explaining the methods you would use should be sufficient.

Question 11

• In Q11, would this extra copy of the locus be considered a trans-gene?

  • Yes.

• For question 11, we are transforming a plant with only 1 copy of the locus that produces red pigmentation, correct?

  • The transformation plasmid includes only a single copy of the red pigmentation gene.