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Biology

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1. RNA processing. 6 points total 
A.    Which of the following is true of tRNA processing? Select all that apply. If the option is true of some tRNAs, include it in your answer. 3 points. 
a.    precursors are spliced 
b.    precursors are cleaved 
c.    precursors undergo base modification 
d.    a precursor encodes more than one tRNA 
e.    none of these 
Answer(s):  _____________________ 
 
B.    Which of the following is true of rRNA processing? Select all that apply. If the option is true of some rRNAs, include it in your answer. 3 points. 
a.    precursors are spliced 
b.    precursors are cleaved 
c.    precursors undergo base modification 
d.    a precursor encodes more than one rRNA 
e.    none of these 
Answer(s):  _____________________ 
 
2. Central Dogma. 6 points total 
For each of the following comparisons, use a <, >, or = symbol and fill in the box to show which one has a greater impact on the cell. Assume the non-functional protein has some consequence. 
 
A.    One-time error in transcription that  one-time error in translation leading to a 
encodes a non-functional protein           non-functional protein 
 
B.    One-time error in transcription that     one-time error in aminoacylation that misencodes a non-functional protein                 codes to make a non-functional protein 
 
Explain your answers below. Recommended word limit: 50 words.  
3. ORFs and translation. 28 points total. The mRNA sequence diagrammed below was analyzed by a program that finds open reading frames. ORFs that begin with a start codon are shown in red boxes below and are labeled ORF1-6. The following set of questions (A-G) refer to this mRNA. 
 
A.    Which of the following is true of an ORF? Select all that apply. 4 points 
a.    it must be made of a multiple of 3 nucleotides 
b.    it must be made of a multiple of 2 nucleotides c, it must begin with AUG d. it must end with UAA 
e.    it must end with CCA 
f.    there must be at least two per mRNA 
g.    none of the above are true 
 
Answer(s):  _____________________ 
 
B.    Which ORF (1-6 in the diagram above) is most likely translated by the ribosome? Select one answer and explain. 5 points 
 
ORF ____________ 
Explain your choice. Recommended word limit: 40 words 
 
 
 
 
 
 
 
 
3 continued C. Describe two different things that could change your answer and lead to translation of a different ORF.  Assume no errors in the DNA or RNA sequence in your answers. Your answer should be something other than the presence of UPF proteins, which is described in part E. 6 points 
I.   
 
 II.  
 
 
 
 
D.    Initiation factors are important for the beginning of translation. What is the role of eIF4? 
Select all that apply. 3 points 
a.    base pairs with the start codon 
b.    binds near the 5’ end of the mRNA 
c.    responds to the concentration of amino acids in the cell 
d.    binds to bot the small and large subunit to assemble the 80S ribosome 
e.    translocates the ribosome toward the 3’ end of the mRNA 
 
Answer(s):  ______________________ 
E.    Researchers studying the mRNA diagrammed above found that translation of the various ORFs changed based on the presence or absence of UPF proteins. What role do UPF proteins play in determining which ORFs are translated (and which are not)? Your answer should include a description of how they perform their function. Recommended word limit: 50 words. 4 points 
 . 3 continued F. How would the absence of UPF proteins likely impact translation of these ORFs? Fill in the blanks in the sentence below to indicate your answer. Answer options for each blank are shown in parentheses before the blank and are blue. 4 points 
 
The absence of UPF proteins would (increase or decrease)  _______________  nonsense mediated decay and lead to (more or less)  ________________ uORF translation compared to wild-type samples with functional UPF proteins. 
 
G. Briefly explain: your answer to part F. Recommended word limit:.40 words. 2 points. 
 
 
 
      
 
4. tRNA charging and SILAC 29 points total 
Arginine amino acids are attached to tRNAs by the Arg-RS enzyme. 
A.    tRNAs with which of the following anticodons are bound by Arg-RS? Select all that apply. 
Anticodons are written 5’ to 3’. 4 points. 
a.    CGI     e. GCU 
b.    GCI     f. ACG 
c.    UCU     g. ICG 
d.    CUC     h. CCU  
      
Answer(s):  ______________________  
 
 
B.    Arg-encoding tRNAs are synthesized in the nucleolus. For each statement below, write whether it is true or false. 2 points each. 
The nucleolus is a membrane-bound subcompartment within the nucleus. _____________ 
 
The nucleolus is also the site of rRNA transcription.   _____________ 
 
The nucleolus is also the site of rRNA translation.   _____________ 
 
tRNAs have many sites that can be covalently modified. One Adenosine (A) base on the right loop can be methylated by a methyltransferase enzyme and demethylated by a demethylase enzyme. Researchers found that demethylated (left) tRNAs are more likely to be found in the nucleus and methylated (right) are more likely to be found in the cytoplasm. This has been suggested as a way that cells regulate translation. 
 
E. How does the location of tRNAs relate to their function(s)? Please include the function you’re discussing and its location. 4 points. Recommended word limit: 40 words.  
 
 
 
 
 
4 continued. Arginine is positively charged at physiological pH. The active site of Arg-RS contains negatively-charged residues so that the charge-charge interaction favors binding of Arg in the active site. 
F.    What else is found in the active site of Arg-RS? Select the best answer. 3 points a. the 5’ end of the tRNA 
b.    the anticodon of the tRNA 
c.    the 3’ end of the tRNA 
                    Answer:  ______________________ 
 
G.    What properties would you expect of the editing site of the Arg-RS? Select all that apply.  
4 points  
a.    positively charged residues 
b.    negatively-charged residues 
c.    a binding pocket large enough to fit Arg inside 
d.    a binding pocket smaller than Arg 
e.    none of these 
               Answer(s):  ______________________ 
Briefly explain your answer:  
 
 
 
 
 
The Arg-RS can also bind 13C-containing “heavy” Arginine.  
H. What is the logic behind using “heavy” Arginine (or other amino acids) during comparative proteomics techniques like SILAC? Recommended word limit: 40 words 4 points 
 
 
      
4 continued. I. What else can SILAC tell you about proteins in the labeled vs. unlabeled samples? Select all that apply. 4 points 
a.    predicted post-translational modifications of proteins 
b.    subcellular localization of proteins 
c.    translation rate of proteins 
d.    protein function or activity 
e.    non-covalent binding interactions between proteins 
f.    none of these 
 
 
Answer(s):  ______________________ 
 
Briefly explain your choice. Recommended word limit: 40 words  
 
 
 
 
      
 
5. Ribosome function. 10 points total  The grid below shows diagrams of the ribosome. 
  
List the order in which the diagrams in order during translation. Include only those that occur. There may be steps missing between the options provided above. Assume the mRNA is longer on the 3’ end than is shown. 7 points 
 
Answer:   __________________________________  
 
B. Choose one of the images above (a-i) that you did NOT include in part A and describe what is wrong with it. Recommended word limit: 30 words 3 points 
      
 
      
6. Proteomics 21 points total. Researchers studying changes in human cells during viral infections have observed differences in phosphorylation patterns of many different proteins. One hypothesis is that the infection causes changes to kinases including Kinase 1.  
A.    What type of modification is the phosphorylation of target proteins by Kinase 1? Select the best answer. 3 points. 
a.    post-translational 
b.    post-transcriptional 
c.    base modification 
d.    none of these 
 
Answer:  ___________________ 
 
Because more proteins are phosphorylated during virus infection, the hypothesis is that Kinase 1 is more active during viral infection than in uninfected cells. RNA sequencing shows that the mRNA encoding Kinase 1 is not different in uninfected and infected cells (same abundance, length, and sequence).  
There are multiple experimental approaches you could use to investigate the cause of the increased Kinase 1 activity in infected cells. Some of them are shown below. For each, describe the result and explain how it could lead to high levels of Kinase 1 activity. Note that these are independent hypothetical results and should not be combined to create a cohesive theory of Kinase 1 regulation. Recommended word limit for each part: 30 words  
 
B.    A SILAC experiment in which the infected cells have a higher peak representing Kinase 1 than the uninfected cells. 6 points. 
 
Interpretation of this result:  
 
 
 
Explanation of how it leads to activation of Kinase 1:  
 
 
 
 
C.    A SILAC experiment in which the infected cells show a peak separated from the peak representing uninfected cells: 
6 points. 
Interpretation of this result:  
 
 
 
Explanation of how it leads to activation of Kinase 1:  
 
 
 
 
D. A Ribo-Seq/ribosome profiling experiment with the result below:     6 points 

 
Interpretation of this result 
 
 
 
 
 
Explanation of how it leads to activation of Kinase 1: 
 
 
 
      
If there are any clarifications or longer explanations you would like to add, please do so below: