8) Start codon issues - Revision history

Karicheson: /* Alternative Start Codon Issues */

2009-09-09T22:24:03Z

‎Alternative Start Codon Issues

Karicheson: /* Alternative Start Codon Issues */

2009-09-09T22:21:58Z

‎Alternative Start Codon Issues

Karicheson: /* Alternative Start Codon Issues */

2009-09-09T22:10:37Z

‎Alternative Start Codon Issues

Karicheson: /* Alternative Start Codon Issues */

2009-09-09T22:06:51Z

‎Alternative Start Codon Issues

Karicheson: /* Alternative Start Codon Issues */

2009-09-09T22:06:20Z

‎Alternative Start Codon Issues

Karicheson: /* Alternative Start Codon Issues */

2009-09-09T21:51:06Z

‎Alternative Start Codon Issues

Karicheson: /* Alternative Start Codon Issues */

2009-09-09T21:50:51Z

‎Alternative Start Codon Issues

Karicheson: /* Alternative Start Codon Issues */

2009-09-09T21:50:39Z

‎Alternative Start Codon Issues

Karicheson: /* Alternative Start Codon Issues */

2009-09-09T21:48:40Z

‎Alternative Start Codon Issues

Karicheson at 21:44, 9 September 2009

2009-09-09T21:44:26Z

New page

== Alternative Start Codon Issues==

Possible start codons AUG (most common in archaea), GUG and UUG [1].

Olivia came across a very interesting condundrum because she checked and tried to verify a lot of the computer's work.

Good Articles to Reference:

1. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TD0-3TDR71X-D&_user=2665120&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_searchStrId=1006327537&_rerunOrigin=scholar.google&_acct=C000058476&_version=1&_urlVersion=0&_userid=2665120&md5=84e8a1e982ec7f0b9c7d17c9573c26c0 Transcription and translation in Archaea: a mosaic of eukaryal and bacterial features.]

@@ Line 13: / Line 13: @@
 There is not much published research I could find on this  issue but the articles/links below are summarized:
-). Yokobori, et al establishes that ". . . potential start codons ATR (Met), ATT (Ile), TTG (Leu), and GTG (Val) . . . " do not all encode Met.  I unfortunately only received references to this article through other articles, but I will continue searching for the following article (which may hold some answers).
+). Yokobori, et al establishes that ". . . potential start codons ATR (Met), ATT (Ile), TTG (Leu), and GTG (Val) . . . " [5] do not all encode Met.  I unfortunately only received references to this article through other articles, but I will continue searching for the following article (which may hold some answers).
@@ Line 24: / Line 22: @@
-" It is generally thought that the first amino acid incorporated into the polypeptide chain is methionine. However, in some cases where an initiator tRNA is altered, the non-AUG start codon can initiate protein synthesis with amino acids other than methionine" [4].
+). " It is generally thought that the first amino acid incorporated into the polypeptide chain is methionine. However, in some cases where an initiator tRNA is altered, the non-AUG start codon can initiate protein synthesis with amino acids other than methionine" [4].
@@ Line 36: / Line 34: @@
 . [http://www3.interscience.wiley.com/cgi-bin/fulltext/104551612/HTMLSTART  Non-AUG translation initiation of mRNA encoding acidic ribosomal P2A protein in Candida albicans]

@@ Line 22: / Line 22: @@
 ). [http://en.wikipedia.org/wiki/Codon#cite_note-3  Wikipedia] also asserts that , "Alternative start codons (depending on the organism), include "GUG" or "UUG", which normally code for valine or leucine. However, when used as a start codon, these alternative start codons are translated as methionine or formylmethionine" [3].
@@ Line 30: / Line 33: @@
 . [http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi The Genetic Codes]
-. Touriol C, Bornes S, Bonnal S, et al. (2003). "Generation of protein isoform diversity by alternative initiation of translation at non-AUG codons". Biology of the cell / under the auspices of the European Cell Biology Organization 95 (3-4): 169–78. PMID 12867081. (I could not find a hard copy of this yet)
+. Touriol C, Bornes S, Bonnal S, et al. (2003). "Generation of protein isoform diversity by alternative initiation of translation at non-AUG codons". Biology of the cell / under the auspices of the European Cell Biology Organization 95 (3-4): 169–78. PMID 12867081. (I could not find a hard copy of this yet).

@@ Line 20: / Line 20: @@
 ). [http://en.wikipedia.org/wiki/Start_codon  Wikipedia] and other basic Encylopedia's claim the following.  "Interestingly when an alternative start codon is used, it gets translated as methionine - even if the codon might normally encode a different amino acid. This is because a separate [tRNA] is used for initiation."
 ).
@@ Line 28: / Line 29: @@
 . [http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi The Genetic Codes]

@@ Line 13: / Line 13: @@
 There is not much published research I could find on this  issue but the articles/links below are summarized:
-Yokobori, et al establishes that ". . . potential start codons ATR (Met), ATT (Ile), TTG (Leu), and GTG (Val) . . . " do not all encode Met.  I unfortunately only received references to this article through other articles, but I will continue searching for the following article (which may hold some answers).
+). Yokobori, et al establishes that ". . . potential start codons ATR (Met), ATT (Ile), TTG (Leu), and GTG (Val) . . . " do not all encode Met.  I unfortunately only received references to this article through other articles, but I will continue searching for the following article (which may hold some answers).
 Yokobori, S., Ueda, T., Feldmaier-Fuchs, G., Paabo, S., Ueshima, R., Kondow, A., Nishikawa, K., and Watanabe, K. 1999. Complete DNA sequence of the mitochondrial genome of the ascidian Halocynthia roretzi (Chordata, Urochordata). Genetics 153: 1851–1862. [PubMed]

@@ Line 13: / Line 13: @@
 There is not much published research I could find on this  issue but the articles/links below are summarized:
+[http://en.wikipedia.org/wiki/Start_codon  Wikipedia] and other basic Encylopedia's claim the following.  "Interestingly when an alternative start codon is used, it gets translated as methionine - even if the codon might normally encode a different amino acid. This is because a separate [tRNA] is used for initiation."
@@ Line 23: / Line 25: @@
 . [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TD0-3TDR71X-D&_user=2665120&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_searchStrId=1006327537&_rerunOrigin=scholar.google&_acct=C000058476&_version=1&_urlVersion=0&_userid=2665120&md5=84e8a1e982ec7f0b9c7d17c9573c26c0  Transcription and translation in Archaea: a mosaic of eukaryal and bacterial features.]

@@ Line 3: / Line 3: @@
 Possible start codons AUG (most common in archaea), GUG and UUG [1].
-Olivia came across a very interesting conundrum because she checked and tried to verify a lot of the computer's work.
 When the start codon is not AUG, is the first amino acid in the protein's primary sequence a Met or the correct amino acid for that codon triplet?
 I think it would be an interesting side study but it may require wet lab work to decipher whether or not the first amino acid is really Met when an alternative start codon is used.  It may also be interesting to look for a trend in the genes that begin with an alternative start codon.
 There is not much published research I could find on this  issue but the articles/links below are summarized:

← Older revision		Revision as of 21:50, 9 September 2009
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	When the start codon is not AUG, is the first amino acid in the protein's primary sequence a Met or the correct amino acid for that codon triplet?		When the start codon is not AUG, is the first amino acid in the protein's primary sequence a Met or the correct amino acid for that codon triplet?

−	~~Here is what I have found on this issue.~~ I think it would be an interesting side study but it may require wet lab work to decipher whether or not the first amino acid is really Met when an alternative start codon is used. It may also be interesting to look for a trend in the genes that begin with an alternative start codon.	+	I think it would be an interesting side study but it may require wet lab work to decipher whether or not the first amino acid is really Met when an alternative start codon is used. It may also be interesting to look for a trend in the genes that begin with an alternative start codon.
		+
		+	There is not much published research I could find on this issue but the articles/links below are summarized:

← Older revision		Revision as of 21:48, 9 September 2009
Line 3:		Line 3:
	Possible start codons AUG (most common in archaea), GUG and UUG [1].		Possible start codons AUG (most common in archaea), GUG and UUG [1].

−	Olivia came across a very interesting ~~condundrum~~ because she checked and tried to verify a lot of the computer's work.	+	Olivia came across a very interesting conundrum because she checked and tried to verify a lot of the computer's work.
		+
		+	When the start codon is not AUG, is the first amino acid in the protein's primary sequence a Met or the correct amino acid for that codon triplet?
		+
		+	Here is what I have found on this issue. I think it would be an interesting side study but it may require wet lab work to decipher whether or not the first amino acid is really Met when an alternative start codon is used. It may also be interesting to look for a trend in the genes that begin with an alternative start codon.
		+
		+