The Naked Scientists

The Naked Scientists Forum

Author Topic: protein sequencing  (Read 4634 times)

Offline vj_tu

  • Jr. Member
  • **
  • Posts: 29
    • View Profile
protein sequencing
« on: 25/12/2005 14:29:49 »
I just doubt how scientists determine the amino acid sequence of a protein of interest.In other words,how they know which amino acid is which?Then they can construct the sequence of that protein.


 

Offline DoctorBeaver

  • Naked Science Forum GOD!
  • *******
  • Posts: 12656
  • Thanked: 3 times
  • A stitch in time would have confused Einstein.
    • View Profile
Re: protein sequencing
« Reply #1 on: 25/12/2005 15:06:33 »
Chris! CHRIS!! This is 1 for you, I think

You have moved your mouse. Please re-start Windows for this change to take effect
 

another_someone

  • Guest
Re: protein sequencing
« Reply #2 on: 25/12/2005 15:22:43 »
quote:
Originally posted by vj_tu

I just doubt how scientists determine the amino acid sequence of a protein of interest.In other words,how they know which amino acid is which?Then they can construct the sequence of that protein.



Do you have a particular reason for this doubt?

Amino acids, like all chemicals, have particular characteristics (molecular weight, the reactions they are involved in, electrical properties) all of which can be measured.  I suspect all they do is chop the protein up, and see what bits come off.

As far as my limited knowledge goes, the bigger problem biochemists have is not so much working out the sequence of amino acids in a protein, but working out how the protein is folded, since that will alter which amino acids are spatially where, and which are exposed, etc.

 

Offline DoctorBeaver

  • Naked Science Forum GOD!
  • *******
  • Posts: 12656
  • Thanked: 3 times
  • A stitch in time would have confused Einstein.
    • View Profile
Re: protein sequencing
« Reply #3 on: 25/12/2005 17:23:57 »
I'm taking part in the Stanford university "Folding At Home" project. I don't really know what it's all about even though I posted about it here and got a few infomative replies.
 

another_someone

  • Guest
Re: protein sequencing
« Reply #4 on: 25/12/2005 17:46:22 »
quote:
Originally posted by DoctorBeaver

I'm taking part in the Stanford university "Folding At Home" project. I don't really know what it's all about even though I posted about it here and got a few infomative replies.



I suppose the best way to look at it is the difference between knowing how to make paper and knowing how to do origami.

By folding proteins in a particular way, you can shape them to become a key to unlock a particular biochemical lock, or to be a catalyst in a particular biochemical reaction.

http://www.hhmi.org/annual94/b130.html
quote:

What actually determines the biologically active, three-dimensional shape of a protein is the great unsolved problem of structural biology. How does the linear sequence of amino acids that constitutes a protein give rise to a three-dimensional structure? Or, put another way, how does a particular chain of amino acids "know" how to fold into a particular three-dimensional shape? Although the rules for translating sequences of DNA into sequences of amino acids have become clear, the rules that govern protein folding have not.



http://www.faseb.org/opar/protfold/protein.html
quote:

Alzheimer's disease. Cystic fibrosis. Mad Cow disease. An inherited form of emphysema. Even many cancers. Recent discoveries show that all these apparently unrelated diseases result from protein folding gone wrong. As though that weren't enough, many of the unexpected difficulties biotechnology companies encounter when trying to produce human proteins in bacteria also result from something amiss when proteins fold.



http://en.wikipedia.org/wiki/Protein_folding
quote:

Protein folding is the process by which a protein structure assumes its functional shape or conformation. All protein molecules are heterogeneous unbranched chains of amino acids. By coiling and folding into a specific three-dimensional shape they are able to perform their biological function.


quote:

Preconditions for correct folding

In certain solutions and under some conditions proteins will not fold at all. Temperatures above or below the range that cells tend to live in will cause proteins to unfold or "denature" (this is why boiling makes the white of an egg opaque). High concentrations of solutes and extremes of pH can do the same. A fully denatured protein lacks both tertiary and secondary structure, and exists as a so-called random coil. Cells sometimes protect their proteins against the denaturing influence of heat with enzymes known as chaperones or heat shock proteins, which assist other proteins both in folding and in remaining folded. Some proteins never fold in cells at all except with the assistance of chaperone molecules, that isolate individual proteins so that their folding is not interrupted by interactions with other proteins. DNA conformation is maintained by another set of enzymes: the topoisomerases.

Incorrect protein folding and neurodegenerative disease

Incorrectly folded proteins are responsible for prion related illness such as Creutzfeldt-Jakob disease and Bovine spongiform encephalopathy (mad cow disease), and amyloid related illnesses such as Alzheimer's Disease. These diseases are associated with the aggregation of misfolded proteins into insoluble plaques; it is not known whether the plaques are the cause or merely a symptom of illness.

« Last Edit: 25/12/2005 18:00:56 by another_someone »
 

Offline ukmicky

  • Moderator
  • Neilep Level Member
  • *****
  • Posts: 3011
    • View Profile
    • http://www.space-talk.com/
Re: protein sequencing
« Reply #5 on: 25/12/2005 18:13:41 »
Well that post cleared it up for me, quite an interesting subject actually.

Michael                                      
 

Offline DoctorBeaver

  • Naked Science Forum GOD!
  • *******
  • Posts: 12656
  • Thanked: 3 times
  • A stitch in time would have confused Einstein.
    • View Profile
Re: protein sequencing
« Reply #6 on: 25/12/2005 18:43:48 »
What I do know about protein folding, however, is that Jehovah's Witnesses use it as an indication that we were created by God. They claim the immense complexity of it could not have been arrived at by random chance.
 

Offline Simmer

  • Sr. Member
  • ****
  • Posts: 229
    • View Profile
Re: protein sequencing
« Reply #7 on: 29/12/2005 00:01:22 »
quote:
Originally posted by DoctorBeaver

What I do know about protein folding, however, is that Jehovah's Witnesses use it as an indication that we were created by God. They claim the immense complexity of it could not have been arrived at by random chance.


AIUI that is the Intelligent Design argument generally.  

Where I think it falls down is that they assume only this particular complexity would work, whereas I think it more likely that many different random arrangement of proteins will lead to some kind of life.
 

The Naked Scientists Forum

Re: protein sequencing
« Reply #7 on: 29/12/2005 00:01:22 »

 

SMF 2.0.10 | SMF © 2015, Simple Machines
SMFAds for Free Forums