You are studying a novel protein. To learn more about it, you performed a screen in yeast to identify proteins that could interact with it. From the screen you got a clone for a second gene. You had the clone sequenced, and you translated the gene sequence on your computer. What is the next logical step to learn more about the function of these two proteins?

Question

A.  Run a BLAST search.
B.  Identify the intron/exon organization.
C.  Localize the gene to a specific chromosomal region.
D.  Search the human genome sequence for your clone.

Clarify Question

· What is the key concept addressed by the question?
· What type of thinking is required?
· What key words does the question contain and what do they mean?

  Gather Content

· What do you already know about sequence analysis?

  Consider Possibilities

· Consider the different answer options. Which can you rule out?

  Choose Answer

· Given what you now know, what information and/or problem solving approach is most likely to produce the correct answer?

  Reflect on Process

· Did your problem-solving process lead you to the correct answer? If not, where did the process break down or lead you astray? How can you revise your approach to produce a more desirable result?

Answer 1

A.  Run a BLAST search.

Clarify Question

· What is the key concept addressed by the question?
        o This question addresses sequence analysis.
· What type of thinking is required?
        o This question is asking you to take what you already know and apply it to this unfamiliar situation.
· What key words does the question contain and what do they mean?
        o A novel protein is one that has not yet been well-studied, so we don’t know much about it.
        o A screen is a way of picking out relevant genes from a large number of candidates.
        o Having a clone sequenced means to have the DNA “read”; the sequence is sent to you in an email.
        o Translating a sequence on the computer means to use software to read the codons of the DNA into the amino acid sequence.

  Gather Content

· What do you already know about sequence analysis?
        o Usually we have DNA sequenced. Even if we want to learn about a protein, it is easier to have a gene sequenced and infer the protein sequence from the codons.

  Consider Possibilities

· Consider the different answer options. Which can you rule out?
        o After sequencing and translating the clone, you have a protein sequence. What next? Your goal is to learn what kind of cellular process or pathway the protein is involved in.
        o Would it be helpful to identify the intron/exon organization? Not particularly. That won’t tell you anything about the cellular function of the proteins.
        o Would it be helpful to localize the gene to a specific chromosomal region? Not really. Again, that won’t tell you anything about the cellular function of the proteins. Different chromosomes carry genes with all kinds of functions.
        o Would it be helpful to search the human genome sequence for your clone? No, your clone was from yeast, so the exact same sequence won’t be there.

  Choose Answer

· Given what you now know, what information and/or problem solving approach is most likely to produce the correct answer?
        o Would it be helpful to run a BLAST search? Yes! In just a few moments, you will be able to find the proteins – whether in yeast or other species – with the most similar sequence. Some of these will likely have research articles describing their functional role.
        o The BLAST search will also reveal special protein domains that may be important to function, such as a DNA-binding motif.
        o Remember, the BLAST search is for the second protein. But since the two proteins
interact – that is, bind each other – it is likely that they work together in the same cellular process.

  Reflect on Process

· Did your problem-solving process lead you to the correct answer? If not, where did the process break down or lead you astray? How can you revise your approach to produce a more desirable result?
        o This question asked what step should come next after sequencing a clone.
        o The question required you to take what you already know and apply it to this unfamiliar situation.
        o Did you recognize that the protein sequence could reveal the function of the protein, but only if you compared it to a database of other known proteins?