Kevin Wyllie Week 2 - Revision history

Kwyllie: Edited link to my user page (used to say "see my user page for the protocol") since the protocol is now on this page instead of my user page.

2015-09-18T19:18:33Z

Edited link to my user page (used to say "see my user page for the protocol") since the protocol is now on this page instead of my user page.

Kwyllie: Pasted in my protocol (previously on user page) as instructed in class.

2015-09-18T18:52:35Z

Pasted in my protocol (previously on user page) as instructed in class.

Kwyllie: Oops, that didn't work. Fixing it now.

2015-09-15T05:49:22Z

Oops, that didn't work. Fixing it now.

Kwyllie: Linked to my user page.

2015-09-15T05:48:58Z

Linked to my user page.

Kwyllie: Another formatting change.

2015-09-15T05:16:44Z

Another formatting change.

@@ Line 1: / Line 1: @@
 === Journal Week 2 ===
-''See my protocol for this assignment on my [[User:kwyllie|user page.]]
+See my [[User:kwyllie|user page.]]
 The given DNA sequence is written in the top strand, while its complementary strand is shown below it.

← Older revision		Revision as of 18:52, 18 September 2015
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	* [[User:Kwyllie]]		* [[User:Kwyllie]]
		+
		+
		+	====Protocol====
		+
		+
		+	# First, using the given DNA strand, write out the sequence for the complementary strand. A's pair with T's, while C's pair with G's.
		+	#* Remember that although you may have written the new strand from left to right, due to DNA's antiparallel characteristic, it will be ''read'' in the reverse direction, assuming you designated that this new strand was the "bottom strand." To remind yourself of this, add the 5' and 3' notation as done for the original strand, although remember that the sides for either will be reversed.
		+	# To avoid errors when using the amino acids translation chart (discussed below), you should write out the mRNA transcript for all six of the frames.
		+	## Start by copy/pasting the original (or top) strand and grouping the nucleotides into groups of three (retaining their order, of course). This allows you to more easily visualize each codon. This first sequence is your "+1" frame.
		+	## Again, copy/paste the top strand, and group into threes, but this time start by deleting the very first nucleotide in the sequence. You'll notice that you have two nucleotides left over at the end. These can also be deleted. This is your "+2" frame.
		+	## For the "+3" frame, start by deleting the first two nucleotides and continue as normal.
		+	## For the "-1" frame, you should start by re-writing the strand in the 5' to 3' direction (remember that it is currently in the 3' to 5' direction). This may be tedious, but it can get very confusing to read the strand in reverse. After that, as before, group the nucleotides into groups of three.
		+	## Once the bottom strand has been re-written appropriately, repeat the steps used for the "+" frames to get your "-2" and "-3" frames.
		+	# Finally, translate each frame.
		+	#* Use the amino acid translator chart to convert each codon into an amino acid. [https://www.manylabs.org/file/lessonMedia/69/geneticCode.png Here's an amino acids chart from ManyLabs.org]
		+	#* If a "stop codon" is reached, the amino acid chain is terminated. No need to write "STOP." Instead, indicate the beginning and end of the chain with the "Nter" and "Cter" notation.
		+	#** "Nter," short for "N-terminus" denotes the beginning of the chain, while "C-ter" denotes the end.
		+	#* If a frame does not contain a STOP codon, then it referred to as an "open reading frame."

@@ Line 1: / Line 1: @@
 === Journal Week 2 ===
-''See my protocol for this assignment on my [[Kwyllie user page|user page.]]
+''See my protocol for this assignment on my [[User:kwyllie|user page.]]
 The given DNA sequence is written in the top strand, while its complementary strand is shown below it.

← Older revision		Revision as of 05:48, 15 September 2015
Line 1:		Line 1:
	=== Journal Week 2 ===		=== Journal Week 2 ===
		+
		+	''See my protocol for this assignment on my [[Kwyllie user page\|user page.]]

	The given DNA sequence is written in the top strand, while its complementary strand is shown below it.		The given DNA sequence is written in the top strand, while its complementary strand is shown below it.

@@ Line 7: / Line 7: @@
-Translated reading frames:
+Reading frames:
 * '''+1'''
-** 5'- cgu aug cua aua cca ugu ucc gcg uau aac cca gcc gcc agu ucc gct ggc ggc auu uua -3'
+** Transcribed: 5'- cgu aug cua aua cca ugu ucc gcg uau aac cca gcc gcc agu ucc gct ggc ggc auu uua -3'
-** Nter-R-M-L-I-P-C-S-A-Y-N-P-A-A-S-S-A-G-G-I-L-Cter '''(This is an open reading frame.)'''
+** Translated: Nter-R-M-L-I-P-C-S-A-Y-N-P-A-A-S-S-A-G-G-I-L-Cter '''(This is an open reading frame.)'''
 * '''+2'''
-** 5'- gua ugc uaa uac cat guu ccg cgu ata acc cag ccg cca guu ccg ctg gcg gca uuu -3'
+** Transcribed: 5'- gua ugc uaa uac cat guu ccg cgu ata acc cag ccg cca guu ccg ctg gcg gca uuu -3'
-**Nter-V-C-Cter
+** Translated: Nter-V-C-Cter
 * '''+3'''
-** 5'- uau gcu aau acc aug uuc cgc gua uaa ccc agc cgc cag uuc cgc ugg cgg cat uuu -3'
+** Transcribed: 5'- uau gcu aau acc aug uuc cgc gua uaa ccc agc cgc cag uuc cgc ugg cgg cat uuu -3'
-** Nter-Y-A-N-T-M-F-R-V-Cter
+** Translated: Nter-Y-A-N-T-M-F-R-V-Cter
 * '''-1'''
-** 5'- uaa aau gcc gcc agc gga acu ggc ggc ugg guu aua cgc gga aca ugg uau uag cau acg -3'
+** Transcribed: 5'- uaa aau gcc gcc agc gga acu ggc ggc ugg guu aua cgc gga aca ugg uau uag cau acg -3'
-** The first codon in this reading frame is a STOP codon, so there is no polypeptide.
+** Translated: The first codon in this reading frame is a STOP codon, so there is no polypeptide.
 * '''-2'''
-** 5'- aaa aug ccg cca gcg gaa cug gcg gcu ggg uua uac gcg gaa cau ggu auu agc aua -3'
+** Transcribed: 5'- aaa aug ccg cca gcg gaa cug gcg gcu ggg uua uac gcg gaa cau ggu auu agc aua -3'
-** Nter-K-M-P-P-A-E-L-A-A-G-L-Y-A-E-H-G-I-S-I-Cter '''(This is an open reading frame.)'''
+** Translated: Nter-K-M-P-P-A-E-L-A-A-G-L-Y-A-E-H-G-I-S-I-Cter '''(This is an open reading frame.)'''
 * '''-3'''
-** 5'- aaa ugc cgc cag cgg aac ugg cgg cug ggu uau acg cgg aac aug gua uua gca uac -3'
+** Transcribed: 5'- aaa ugc cgc cag cgg aac ugg cgg cug ggu uau acg cgg aac aug gua uua gca uac -3'
-** Nter-K-C-R-Q-R-N-W-R-L-G-Y-T-R-N-M-V-L-A-Y-Cter '''(This is an open reading frame.)'''
+** Translated: Nter-K-C-R-Q-R-N-W-R-L-G-Y-T-R-N-M-V-L-A-Y-Cter '''(This is an open reading frame.)'''