Key points addressed correctly in your answer (5 points)

    October 7, 2022

FEEK 1 Grading Rubric: BIOL 7133
Short Answer Section (10 points each)
The short answer section is meant for you to show understanding of a few specific concepts. Answers should range from 1-2 sentences to a short paragraph.
1. Key points addressed correctly in your answer (5 points)
2. Correct terminology was used (3 points)
3. Answer was written clearly and justification made when necessary (2 points)
Medium Answer Section (20 points)
This question requires you to bring several pieces of information/concepts together to clearly describe a process. In doing so you should included concepts of DNA structure and why each molecule is necessary.
1. Process was accurately described using appropriate terminology (5 points)
2. The relationship between the structure of the DNA molecule and the process of replication was clearly connected (5 points)
3. The role of each enzyme included in the question was correctly described and the importance (“the why”) of that role was clearly explained (5 points)
4. Writing was clear and information was presented in a logical manner (5 points)
“Long Answer” Section (30 points)
This question requires you to compare and contrast processes. In addition, I would like you to challenge yourself by looking up additional resources (include your references) and include more information than what was specifically discussed in class (i.e. expand upon an area that was discussed in little detail or not discussed at all in class. The specific area of the question you choose to expand upon does not matter. You might approach this by assuming I only know exactly what we talked about it class and teach me something I don’t know.
1. Processes were accurately compared with respect to each piece of information asked for in the question (12 points)
2. The consequences of a mutant XPC gene were described in the context of the global NER pathway and Xeroderma pigmentosa. Consequences of the disease are presented in a way that relates NER to the biology of the organism (i.e. not just a list of symptoms) (8 points)
3. One area of this topic was expanded upon using appropriate resources (references included) (5 points)
4. Writing was clear and information was presented in a logical manner (5 points)
Actual Questions:
1. For each of the sequencing methods listed below, briefly describe the key concept of DNA replication/chemistry that had to be understood to develop the method allowing the sequence of nucleotides to be digitized.
Example Answer for Ion Torrent method: It was necessary to understand that when a polymerase enzyme catalyzes the reaction between a dNTP and the growing DNA strand a H is released as a by-product. By detecting this by-product we can “digitize” the sequence.
A. Sanger/dideoxy Sequencing
B. 454/Pyrosequencing
C. Illumina Sequencing
2. You have found a strain of a single celled eukaryotic species that has a different sequence at the end of its telomeres than other strains of the same species. A) Briefly discuss the structure and function of telomerase. B) In doing so, justify why the difference in the strain you found likely originated in a mutation in the telomerase itself rather than the chromosome (DNA). (Hint: use the term ribonucleoprotein or reverse transcriptase in your answer).
3. Are mutations random? In answering this question you might want to mention transition, transversions, slippage (repeat slippage), and biased gene conversion.
4. How can homologous recombination cause mismatch mutations?
5. What is a spontaneous mutation? Give an example.
Medium Answer Section (20 points)
6. Describe the process of eukaryotic DNA replication. Specifically explain:
A) The stages of initiation and the core molecules involved
B) Why leading and lagging strand replication is necessary
C) The role of the following enzymes in the process
– Helicase and the Fork Protection Complex (ORC, mcm, And1, PCNA, RPA, and polymerases discussed)
– Main DNA polymerases involved
– Topoisomerase
– Telomerse
Long Answer Section (30 points)
7. A) Compare and contrast Mismatch Repair, Global and TC-Nucleotide Excision Repair, and either Base Excision Repair or Homologous Recombination.
1. Types of mutations recognized and repaired by each and the basic causes/origins of these mutations.
2. General categories of enzymes/proteins involved in each process and their role in the repair pathway (i.e. recognition, removal or repair/resynthesis).
– Highlight similarities and differences in enzymes/proteins involved
– Highlight enzymes common to repair and replication
3. Differences and similarities in the basic processes
B) Xeroderma pigmentosa is a diseases caused by a disruption in the NER pathway. One of the most common forms is linked to a mutant version of the protein XPC. Research this disease, and briefly describe how a non-functional XPC protein would disrupt the Global NER pathway. What are the consequences for a person carrying this mutation?

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