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Author Topic:   Alleles at the amino-acid/SNP level? Any experts out there?
Tranquility Base
Inactive Member


Message 1 of 14 (13955)
07-22-2002 9:29 PM


Here is a link on the basics of alleles (as the source of biological traits) for the uninitiated: http://www.borg.com/~lubehawk/multalle.htm
Here are some questions for the experts:
------------------------------------------------
1. Does anybody out there know some examples at the SNP (single nucelotide polymorphism) and amino-acid level?
2. Something I have wanted to know for years - blue/brown eyes - what are the allele amino-acid sequences/differences/SNP(s)?
3. Do allele's differ trivially or by many amino-acids?
4. What patterns are there? Two alleles seems to be very common but is this just in the simplified dominant/recessive case?
5. Of course there are lots of SNPs which don't have a clear phenotypic trait. Are these referred to in some special way?
It relates to CvsE but I'm also just plain interested.
[This message has been edited by Tranquility Base, 07-22-2002]

Replies to this message:
 Message 2 by Fred Williams, posted 07-23-2002 1:29 AM Tranquility Base has replied
 Message 3 by Peter, posted 07-23-2002 3:35 AM Tranquility Base has replied
 Message 4 by peter borger, posted 07-23-2002 5:24 AM Tranquility Base has replied

  
Tranquility Base
Inactive Member


Message 5 of 14 (13993)
07-23-2002 7:25 AM
Reply to: Message 2 by Fred Williams
07-23-2002 1:29 AM


Thanks Fred - I'm familiar with sickle cell anemia (Val 3 I think??). Thanks for Haplotypes. I'd love to see the sequences of some real alleles. Of course the human genome did this and found lots of SNPs which form the basis of alleles. I'd love to see some classic and characteristic cases studies.

This message is a reply to:
 Message 2 by Fred Williams, posted 07-23-2002 1:29 AM Fred Williams has not replied

  
Tranquility Base
Inactive Member


Message 6 of 14 (13994)
07-23-2002 7:28 AM
Reply to: Message 3 by Peter
07-23-2002 3:35 AM


Thanks Peter - Yes, I've heard a lot of these words over the years and would love to see it reframed in the language of genomes and SNPs. (I study structural genomics and rarely think about SNPs). I wonder if the blood groups come down to three alleles (or even 3 SNPs) for example?

This message is a reply to:
 Message 3 by Peter, posted 07-23-2002 3:35 AM Peter has replied

Replies to this message:
 Message 8 by Peter, posted 07-23-2002 10:51 AM Tranquility Base has replied

  
Tranquility Base
Inactive Member


Message 7 of 14 (13995)
07-23-2002 7:35 AM
Reply to: Message 4 by peter borger
07-23-2002 5:24 AM


Thanks Peter B - Even though most traits will be governed by more than just one gene it is probably still the case that many traits can be said to be single gene at first order. I picked eye color because it is well known and is to a fairly good extent true. Anyway there are lots of approximately dominant/recessive traits that probably have only two major alleles in the population. I would love to see what their amino-acid seqeunces are! Similarly for traits governed by more than two alleles or more than one gene. But simple is easier at the start.
[This message has been edited by Tranquility Base, 07-23-2002]

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 Message 4 by peter borger, posted 07-23-2002 5:24 AM peter borger has not replied

  
Tranquility Base
Inactive Member


Message 9 of 14 (14028)
07-23-2002 9:10 PM
Reply to: Message 8 by Peter
07-23-2002 10:51 AM


^ Nice Peter. You win the prize!
I'll have to read those sites.
Unfortunately we can't be sure that these DNA segments are 'in frame' becasue for a start they aren't multiples of three. Being a protein person (which is the business end of gene function) I want to translate those sequences into amino-acids.
Summary
CGTGGTGACCCCTT Antigen A
CGTCGTCACCGCTA Antigen B
CGTGGT-ACCCCTT Antigen O
I'll try and find out if these are exonic. O is a frame shift and obvioulsy causes the protein fragment to not translate or not fold.
I don't want to sidetrack too much away from the fascinating basic science here, but, from a creationist POV I would like to suggest that these SNPs are easy to imagine occurring in a short time even if there was only one initial allele. I would also suggest that the protein fold would be unchanged (the full gene would be probably be thousands of bases long) except for O where it is either unexpressed or doesn't fold. From a genomic/structural biology POV alleles are just varieties of a protein and as such, if still functional, wold be expected to have the same protein fold.
Does anybody know what phenotype OO people have? This gene may be semi-redundant but it's conservation suggests it is not completely redundant.
Note that O is essentially identical to A but with a frameshift causing lack of expression or folding. So blood type can be thought of as having 2 functional alleles and 1 non-functional.
PS - if they are in frame, and exonic, then the amino acid sequences of the first 12 bases is:
RGDP A
RRHR B
RGTP O (with the rest frameshifted including the stop codon)
The seqeunce of B is quite different from A. R =Arginine is very diff to G=Glycine. D=Aspartic Acid is charged as is H=Histidine. P=Proline is very diff to R=Arginine.
Note that the remaining hundreds of amino-acids of A and B will be identical and hence the proteins almost definietely have the same fold. The functions of A and B would have near identical functions and the primary difference is probably in immunological reactions due to antibody binding to these proteins.
[This message has been edited by Tranquility Base, 07-23-2002]

This message is a reply to:
 Message 8 by Peter, posted 07-23-2002 10:51 AM Peter has replied

Replies to this message:
 Message 10 by Peter, posted 07-25-2002 4:30 AM Tranquility Base has replied

  
Tranquility Base
Inactive Member


Message 11 of 14 (14347)
07-28-2002 11:15 PM
Reply to: Message 10 by Peter
07-25-2002 4:30 AM


Peter
Since (from the source you or someone posted) we discovered that O 'produces no antigen' then that would be the reason to suspect that O is due to a deletion. A single insertion wont make an active gene from random DNA. DNA coding for a functional and folded protein far more easily will yieled non-functional alleles by deletions. I'm not trying to argue as a creaitonist here - this is standard Mol/Struc Biol.
The key point is that A and B are probably active functioning enzymes or something. Life is not ust a series of letters - the genes code for functioning enzymes and structural proteins. I'm not trying to kid anyone here.
I would love to know the details of waht protien A and B code for.
So OO is type O blood (like me) so it can't be overly important (if our fact that O is inactive is true)!
I agre dominant/recessive model is a simplification but in some cases it will be a warranted one.
In principle deterministic mutaitonl baises would make parallel evolution more likely - I agree. But it is truly imposible to imagine a scenario where this could take us from random DNA to DNA that codes for folded proteins that have just the right functions! I can imagine a functional gene in chimps and man mutating to the same thing due to either (i) a codon bias or (ii) something that is tolerated (or even advantagesou) in both species.
I look forward to finding time to read your web links.
[This message has been edited by Tranquility Base, 07-28-2002]

This message is a reply to:
 Message 10 by Peter, posted 07-25-2002 4:30 AM Peter has replied

Replies to this message:
 Message 12 by Peter, posted 07-29-2002 3:41 AM Tranquility Base has replied

  
Tranquility Base
Inactive Member


Message 13 of 14 (14368)
07-29-2002 4:03 AM
Reply to: Message 12 by Peter
07-29-2002 3:41 AM


^ American billion (10^9). The Brit one got redefined to the American one (and they abolished milliard) I'm pretty sure. I've never heard of Brit's talking about milliard-year old universes (thankfully)!
PS - thanks for the info. The OO being universal makes sense from a folding/expression POV - if it isn't folded or expressed it wont generate an immune response whereas A or B in us will.
[This message has been edited by Tranquility Base, 07-29-2002]

This message is a reply to:
 Message 12 by Peter, posted 07-29-2002 3:41 AM Peter has replied

Replies to this message:
 Message 14 by Peter, posted 07-29-2002 5:07 AM Tranquility Base has not replied

  
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