tag:blogger.com,1999:blog-37148773.post8122707083715090311..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: The Chemical Structure of Double-Stranded DNALarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger7125tag:blogger.com,1999:blog-37148773.post-90405631638856783412007-07-24T13:20:00.000-04:002007-07-24T13:20:00.000-04:00You can often recognize incorrect amino acid seque...You can often recognize incorrect amino acid sequences because they contain odd combinations of amino acids and unusual compositions. Look for sequences that have lots of prolines and tryptophans.Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-38419802978872130292007-07-24T11:45:00.000-04:002007-07-24T11:45:00.000-04:00Sir, How can one tell if an amino acid sequence is...Sir, How can one tell if an amino acid sequence is correct or not??Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-54060879805213121082007-07-21T12:46:00.000-04:002007-07-21T12:46:00.000-04:00This comment has been removed by the author.A. Vargashttps://www.blogger.com/profile/04876504431768677209noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-48582368753128162672007-07-20T05:42:00.000-04:002007-07-20T05:42:00.000-04:00With two open reading frames you can almost always...With two open reading frames you can almost always tell which one is correct by looking at the amino acid sequence. It only takes a little knowledge of proteins to see that some amino acid sequences are very unlikely. <BR/><BR/>I'm not sure how you can write a sequence without identifying the 5' and 3' ends since the convention is that the 5' end of a sequence is always on the left. This would be the top strand of double-stranded DNA, by convention.Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-6638515795093483702007-07-19T21:27:00.000-04:002007-07-19T21:27:00.000-04:00Yes, if it is a question about open reading frame ...Yes, if it is a question about open reading frame or if you specified which was the coding strand. <BR/><BR/>But if there are two open reading frames then you don't get a unique solution, and it has much harder to come up with a DNA sequence that can lead to two good folding configurations (i.e. ones you can solve without a computer) as opposed to just one. <BR/><BR/>I suppose you could design a sequence so that there is only one open reading from even if you look at both strands, but that would be a long problem, checking for six open reading frames. If you wanted to be really evil you could leave out the 5' and 3' labels, making them check 12 open reading frames. But that is getting downright cruel not to mention unfeasibly long if you combine it with determining the proper folding configuration and the free energy change. If you add counting the number of conformational states and the free energy change from a point mutation that changes a residue from a long hydrophobic to short hydrophilic (or vice versus) you could have a whole molecular biology midterm with just one question.Unknownhttps://www.blogger.com/profile/17053845016489256894noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-24254988179862033502007-07-19T20:02:00.000-04:002007-07-19T20:02:00.000-04:00When I ask those questions I usually add that it's...When I ask those questions I usually add that it's a DNA sequence from the <I>middle</I> of a coding region and there's usually at least two open reading frames. :-)Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-55927274754038972132007-07-19T18:04:00.000-04:002007-07-19T18:04:00.000-04:00Bah, anti-parallel questions are easy. It is when...Bah, anti-parallel questions are easy. It is when they start combining parallel and anti-parallel, coding and non-coding strands, mRNA, open reading frame, and translation in one question that things start getting a bit crazy. For instance "here is a single strand of DNA from the beginning of a protein, write down the mRNA sequence and the amino acid sequence". You have to find the start codon (which may or may not be on the strand given), find the open reading frame, then get direction correct, then convert it to an amino acid sequence using that reading frame.<BR/><BR/>If you are in a particularly sadistic mood you can then make them figure out the most likely conformation for the polypeptide and the free energy loss from forming that conformation.Unknownhttps://www.blogger.com/profile/17053845016489256894noreply@blogger.com