Replies to post #67068 on DNAprint Genomics (DNAG)

[nyrome]

"junk DNA' is a term that means, "we really have no idea what goes on in here". Agreed.

As soon as something is discovered in an area of "junk DNA" that area is immediately relabeled as something else. Agreed.

your attempt to portray a 'regulatory binding site' as something outside of the protein coding process Never did. I stated, quite clearly, that the regulatory regions are essential to the process. They are not, however, coding regions.

The process of creating a protein from DNA sequences is very much like the process of transferring an e-mail message over the internet. There is the text of the message itself which is akin to the CODE,. Now you're getting it...All in all there is a great deal of information, not limited to the text itself, even though that is the main component. Nevertheless ALL OF IT is part of the coding process. BINGO. The CODE is the "text" in your analogy and the other regions are essential for the "delivery, formating, etc.." of that text, but are NOT the code. Now you've got it. (I was startin gto worry).

Yes/No questions this time.
Does the SNP in your example (1608 bases upstream of the transcription start site) play a part in the successful 'CODING' of the protein? Yes or No. No. The protein is made with or without the 5A/6A polymorphism. The amount is varied as a result (one aspect of its regulation). If the SNP variation is present, does the protein CODE the same as if it were absent? Yes or No. Yes. You see, the CODE is unaffected by this change, (although the normal "wobble" of the genetic code would also allow for SNP within the CODE to result in the same protein as well.)

[johnnyfiber]

please stop embarrassing yourself...

The impact of nucleotide differences is variable and elusive, but is clearly dependent upon the location of the polymorphism in the genome. Although the majority of SNPs are likely to occur outside of actual gene encoding regions,
polymorphisms located within the context of a gene (Figure 2) need not be involved in protein encoding to result in a functional change. Nucleotide differences in regions upstream of the protein-encoding gene regions may influence the binding of promotors or repressors, resulting in differential regulation of transcription. Polymorphisms at intron/exon boundaries may effect exonic or intronic splicing enhancer or silencer positions, or especially conserved GT donor or AC acceptor positions, modifying the resulting polypeptide. There is even demonstrated potential for phenotypic effects from non-coding or synonymous SNPs through alteration of RNA secondary structure (3). Similarly, untranslated distal 3' differences may have additional effects, including interruption of poly-adenylation, which would alter the template effectiveness.

http://www.dartmouth.edu/~brenner/gene144-05/gleim.html

[nyrome]

sciguy
Nice to see you back again. What's with all the aliases?

I just got it. You think I'm some guy called 'sciguy'.

I thought you were being sarcastic, calling me a 'science guy'. Like 'tough guy' or 'smart guy'.

Sorry, you got the 'wrongguy'

[nyrome]

By the way, if I really wanted to nail your cloaca to the wall, I would point out additional, provincial terminology, which further demonstrates your rather pedestrian understanding of the topic at hand. For example: If the SNP variation is present, does the protein CODE the same as if it were absent? First of all, the term SNP variation is meaningless, without the context of a reference point. Or simply stated, WHICH VARIATION (the 5A,6A,5T or 6T) are you referring to? And, the phrase "does the protein CODE the same" is meaningless. Proteins don't CODE anything. They are the products of the process. I guess I instantly translated what you wrote into what would make sense in this discussion; namely, "is it the same protein?"

But, I don't want to do that.

[johnnyfiber]

Yeah!!!! IT'S JUST LIKE THE INTERNET!!!!!LOL What's the matter? You didn't want to addess this? lol I've noticed you like to wait for the 50 post page to change...whenever your true colors have been exposed. sad...and funny...lol You're an amusing individual. lol

FROG STATED:

Furthermore your attempt to portray a 'regulatory binding site' as something outside of the protein coding process, says more about your aversion to reality than mine.

Without that site, without all other regulatory factors that are a part of the protein coding process, there would be no protein, period.

The process of creating a protein from DNA sequences is very much like the process of transferring an e-mail message over the internet. (yeah...it's just like the internet!...lol) There is the text of the message itself which is akin to the CODE, there is the Header and Footer information within the tranferred serial packets, Introns and Exons. There is formatting information hidden from the screen but essential for the correct display of the message when it reaches its target. All in all there is a great deal of information, not limited to the text itself, even though that is the main component. Nevertheless ALL OF IT is part of the coding process.

realy?....not very informed...

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I posted:


please stop embarrassing yourself...

The impact of nucleotide differences is variable and elusive, but is clearly dependent upon the location of the polymorphism in the genome. Although the majority of SNPs are likely to occur outside of actual gene encoding regions,
polymorphisms located within the context of a gene (Figure 2) need not be involved in protein encoding to result in a functional change. Nucleotide differences in regions upstream of the protein-encoding gene regions may influence the binding of promotors or repressors, resulting in differential regulation of transcription. Polymorphisms at intron/exon boundaries may effect exonic or intronic splicing enhancer or silencer positions, or especially conserved GT donor or AC acceptor positions, modifying the resulting polypeptide. There is even demonstrated potential for phenotypic effects from non-coding or synonymous SNPs through alteration of RNA secondary structure (3). Similarly, untranslated distal 3' differences may have additional effects, including interruption of poly-adenylation, which would alter the template effectiveness.

http://www.dartmouth.edu/~brenner/gene144-05/gleim.html