In your research, you are comparing the transcriptome and the proteome for two related species. One gene in species B has a similar transcript but a much smaller protein than in species A, and the protein seems to be nonfunctional. What do you predict about this gene? (Select all that apply)

Question

_____  It is a pseudogene.
_____  It will have an increased number of persistant mutations in species B.
_____  It probably has a STOP codon early in the coding region.
_____  It probably has a defect in the enhancer region.
_____  It probably is not methylated correctly.

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 pseudogenes?
  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

__X__  It is a pseudogene.
__X__  It will have an increased number of persistant mutations in species B.
__X__  It probably has a STOP codon early in the coding region.
_____  It probably has a defect in the enhancer region.
_____  It probably is not methylated correctly.


Clarify Question
· What is the key concept addressed by the question?
        o This question addresses pseudogenes.
· 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 The transcriptome is the set of all transcripts in a cell (ie, mRNAs and other RNAs).
        o The proteome is the set of all proteins in a cell.
  Gather Content
· What do you already know about pseudogenes?
        o Pseudogenes are genes that have recently in evolution become nonfunctional, often due to a frameshift or nonsense mutation that create an early STOP.
  Consider Possibilities
· Consider the different answer options. Which can you rule out?
        o Can you predict that this gene has a defect in the enhancer region? No, because it is being transcribed normally – only the protein is wrong.
        o Can you predict that this gene is not methylated correctly? No, because that would affect its transcriptional expression, but that aspect is normal.
  Choose Answer
· Given what you now know, what information and/or problem solving approach is most likely to produce the correct answer?
        o Can you predict that this gene is a pseudogene? Yes, it fits the description of a pseudogene.
        o Can you predict that this gene will have an increased number of persistant mutations in species B? Yes, because there is no selection against mutations in a nonfunctional gene.
        o Can you predict that this gene probably has a STOP codon early in the coding region? Yes, that would explain why the protein is smaller and nonfunctional.
  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 you would predict about a nonfunctional gene.
        o The question required you to take what you already know and apply it to this unfamiliar situation.
        o Did you recognize that this scenario describes a pseudogene?