A (virtual) place for BIOL335 (2008) people to ask questions, answer questions, make requests, comment, wonder, discuss, complain and rejoice.
Thursday, January 31, 2008
Questions on ORFs and cloning
Please post here alll your questions and requests regarding ORFs, cloning and related material.
6 comments:
Anonymous
said...
hi Pam, regarding ORFs and stuff answer sheet, START codons are diagonal and STOP codons are vertical lines, right? (seems like they are switched..)
and my questions are, -when there are two start codons per one stop codon, like #2, do you count it as only one ORF? -I'm not sure why you counted #3, even tho there's no stop codon..did u assume there SHOULD be stop codon beyond the 1000bp segment?
I don't think they are switched...you'll notice that I alternated the reading frames (instead of going 3 positive first, and 3 negative below).
To answer your questions: - you can count it as only one ORF because the start codon is in reality just an AUG...it may be an AUG in the protein. But you could also say that, since we don't know which one (if any) is the actual start codon, #2 would count as 2 distinct, outative ORFs. In fact, I think i like your idea better!
- I counted #3 because we are only looking at a fragment, so the stop may be right after the end of the fragment (the genome keeps going, although we don't physically have it to be analyzed), or it may be many kbs away...since we don't know, we can count #3 as a potential ORF.
You would need both a start and a stop if wou were told that the ENTIRE coding sequence for a protein of interest is within the fragment. I would have had to specify that here,we are looking for ORFs that COULD (potentially) give >10aa.
I am posting some hints and help for question 2 of the practice midterm on the "answers" page-click on the link "our answers to problem sets, practice questions...."
I am posting some hints and help for question 2 of the practice midterm on the "answers" page-click on the link "our answers to problem sets, practice questions...."
The link for the hints and help for question two on the answers page leads to the homepage of cfkeep.org. Would you be able to repost the link please? Thanks =)
Much of the material found on this blog represents creative work in a tangible form, and is therefore subject to those copyright laws that apply. Unless stated otherwise, the authors of the works posted are myself and the UBC BIOL335 (Spring 2008) students in tutorial sections T53 and T59.
6 comments:
hi Pam, regarding ORFs and stuff answer sheet, START codons are diagonal and STOP codons are vertical lines, right? (seems like they are switched..)
and my questions are,
-when there are two start codons per one stop codon, like #2, do you count it as only one ORF?
-I'm not sure why you counted #3, even tho there's no stop codon..did u assume there SHOULD be stop codon beyond the 1000bp segment?
Thanks,
I don't think they are switched...you'll notice that I alternated the reading frames (instead of going 3 positive first, and 3 negative below).
To answer your questions:
- you can count it as only one ORF because the start codon is in reality just an AUG...it may be an AUG in the protein. But you could also say that, since we don't know which one (if any) is the actual start codon, #2 would count as 2 distinct, outative ORFs.
In fact, I think i like your idea better!
- I counted #3 because we are only looking at a fragment, so the stop may be right after the end of the fragment (the genome keeps going, although we don't physically have it to be analyzed), or it may be many kbs away...since we don't know, we can count #3 as a potential ORF.
You would need both a start and a stop if wou were told that the ENTIRE coding sequence for a protein of interest is within the fragment.
I would have had to specify that here,we are looking for ORFs that COULD (potentially) give >10aa.
Good point, thanks!
Cheers
Pam
Anybody interested in going over the old exam posted on the 335 course webpage?
I am posting some hints and help for question 2 of the practice midterm on the "answers" page-click on the link "our answers to problem sets, practice questions...."
Pam
I am posting some hints and help for question 2 of the practice midterm on the "answers" page-click on the link "our answers to problem sets, practice questions...."
Pam
Hey Pam,
The link for the hints and help for question two on the answers page leads to the homepage of cfkeep.org. Would you be able to repost the link please? Thanks =)
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