Difference between revisions of "KSherbina Week 2"
From LMU BioDB 2013
(Discussed which reading frame is an open reading frame.) |
(Corrected the response regarding which readings frames are open readings frames.) |
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*The 6 possible reading frame: | *The 6 possible reading frame: | ||
+1 cgu aug cua aua cca ugu ucc gcg uau aac cca gcc gcc agu ucc gcu ggc ggc auu uua | +1 cgu aug cua aua cca ugu ucc gcg uau aac cca gcc gcc agu ucc gcu ggc ggc auu uua | ||
| + | |||
+2 gua ugc uaa uac cau guu ccg cgu aua acc cag ccg cca guu ccg cug gcg gca uuu | +2 gua ugc uaa uac cau guu ccg cgu aua acc cag ccg cca guu ccg cug gcg gca uuu | ||
| + | |||
+3 uau gcu aau acc aug uuc cgc gua uaa ccc agc cgc cag uuc cgc ugg cgg cau uuu | +3 uau gcu aau acc aug uuc cgc gua uaa ccc agc cgc cag uuc cgc ugg cgg cau uuu | ||
| + | |||
-1 uaa aau gcc gcc agc gga acu ggc ggc ugg guu aua cgc gga aca ugg uau uag cau | -1 uaa aau gcc gcc agc gga acu ggc ggc ugg guu aua cgc gga aca ugg uau uag cau | ||
| + | |||
| + | '''''The correct sequence of nucleotides in the -1 reading frame:''''' | ||
| + | |||
| + | -1 uaa aau gcc gcc agc gga acu ggc ggc ugg guu aua cgc gga aca ugg uau uag cau acg | ||
| + | |||
-2 aaa aug ccg cca gcg gaa cug gcg gcu ggg uua uac gcg gaa cau ggu auu agc aua | -2 aaa aug ccg cca gcg gaa cug gcg gcu ggg uua uac gcg gaa cau ggu auu agc aua | ||
| + | |||
-3 aaa ugc cgc cag cgg aac ugg cgg cug ggu uau acg cgg aac aug gua uua gca uac | -3 aaa ugc cgc cag cgg aac ugg cgg cug ggu uau acg cgg aac aug gua uua gca uac | ||
:Corresponding amino acid sequences: | :Corresponding amino acid sequences: | ||
+1 R-M-L-I-P-C-S-A-Y-N-P-A-A-S-S-A-G-G-I-L | +1 R-M-L-I-P-C-S-A-Y-N-P-A-A-S-S-A-G-G-I-L | ||
| + | |||
+2 V-C-Stop-Y-H-V-P-R-I-T-Q-P-P-V-P-L-A-A-F | +2 V-C-Stop-Y-H-V-P-R-I-T-Q-P-P-V-P-L-A-A-F | ||
| + | |||
+3 Y-A-N-T-M-F-R-V-Stop-P-S-R-Q-F-R-W-R-H-F | +3 Y-A-N-T-M-F-R-V-Stop-P-S-R-Q-F-R-W-R-H-F | ||
| + | |||
-1 Stop-N-A-A-S-G-T-G-G-W-V-I-R-G-T-W-Y-Stop-H | -1 Stop-N-A-A-S-G-T-G-G-W-V-I-R-G-T-W-Y-Stop-H | ||
| + | |||
| + | '''''I missed the last amino acid when translating the -1 reading frame because I forgot the last codon when I was recording the nucleotide sequence of the reading frame. Below is the correct sequence of amino acids encoded by the -1 reading frame:''''' | ||
| + | -1 Stop-N-A-A-S-G-T-G-G-W-V-I-R-G-T-W-Y-Stop-H-T | ||
| + | |||
-2 K-M-P-P-A-E-L-A-A-G-L-Y-A-E-H-G-I-S-I | -2 K-M-P-P-A-E-L-A-A-G-L-Y-A-E-H-G-I-S-I | ||
| + | |||
-3 K-C-R-Q-R-N-W-R-L-G-Y-T-R-N-M-V-L-A-Y | -3 K-C-R-Q-R-N-W-R-L-G-Y-T-R-N-M-V-L-A-Y | ||
*The +1 and -2 reading frames are most likely open reading frames because they do not contain any stop codons. While it also does not contain any stop codons, the -3 reading frame is probably not an open reading frame because the only methionine that could be a start codon appears very late in the sequence. | *The +1 and -2 reading frames are most likely open reading frames because they do not contain any stop codons. While it also does not contain any stop codons, the -3 reading frame is probably not an open reading frame because the only methionine that could be a start codon appears very late in the sequence. | ||
| + | :'''''Correction: Since the presence or absence of a start codon is not being considered, the -3 reading frame is also an open reading frame because it does not contain a stop codon.''''' | ||
| + | |||
| + | [[User:Ksherbina|Ksherbina]] ([[User talk:Ksherbina|talk]]) 23:42, 5 September 2013 (PDT) | ||
[[Category:Journal Entry]] | [[Category:Journal Entry]] | ||
Latest revision as of 05:03, 12 September 2013
| Assignment Description | Week 1 | Week 2 | Week 3 | Week 4 | Week 5 | Week 6 | Week 7 | Week 8 | Week 9 | Week 10 | Week 11 | Week 12 | Week 13 | Week 15 |
| Class Journal | Week 1 | Week 2 | Week 3 | Week 4 | Week 5 | Week 6 | Week 7 | Week 8 | Week 9 | |||||
| Individual Journal | Week 2 | Week 3 | Week 4 | Week 5 | Week 6 | Week 7 | Week 8 | Week 9 | Week 10 | Week 11 |
| Other | Week 5: Database Wiki |
| Final Project | Team H(oo)KD Project Page | Journal Club Presentation | Project Individual Journal |
[edit] Week 2 Individual Journal Assignment
- Given strand of DNA (top strand):
5'-cgtatgctaataccatgttccgcgtataacccagccgccagttccgctggcggcatttta-3'
- Complementary strand of DNA (bottom strand):
3'-gcatacgattatggtacaaggcgcatattgggtcggcggtcaaggcgaccgccgtaaaat-5'
- The 6 possible reading frame:
+1 cgu aug cua aua cca ugu ucc gcg uau aac cca gcc gcc agu ucc gcu ggc ggc auu uua
+2 gua ugc uaa uac cau guu ccg cgu aua acc cag ccg cca guu ccg cug gcg gca uuu
+3 uau gcu aau acc aug uuc cgc gua uaa ccc agc cgc cag uuc cgc ugg cgg cau uuu
-1 uaa aau gcc gcc agc gga acu ggc ggc ugg guu aua cgc gga aca ugg uau uag cau
The correct sequence of nucleotides in the -1 reading frame:
-1 uaa aau gcc gcc agc gga acu ggc ggc ugg guu aua cgc gga aca ugg uau uag cau acg
-2 aaa aug ccg cca gcg gaa cug gcg gcu ggg uua uac gcg gaa cau ggu auu agc aua
-3 aaa ugc cgc cag cgg aac ugg cgg cug ggu uau acg cgg aac aug gua uua gca uac
- Corresponding amino acid sequences:
+1 R-M-L-I-P-C-S-A-Y-N-P-A-A-S-S-A-G-G-I-L
+2 V-C-Stop-Y-H-V-P-R-I-T-Q-P-P-V-P-L-A-A-F
+3 Y-A-N-T-M-F-R-V-Stop-P-S-R-Q-F-R-W-R-H-F
-1 Stop-N-A-A-S-G-T-G-G-W-V-I-R-G-T-W-Y-Stop-H
I missed the last amino acid when translating the -1 reading frame because I forgot the last codon when I was recording the nucleotide sequence of the reading frame. Below is the correct sequence of amino acids encoded by the -1 reading frame:
-1 Stop-N-A-A-S-G-T-G-G-W-V-I-R-G-T-W-Y-Stop-H-T
-2 K-M-P-P-A-E-L-A-A-G-L-Y-A-E-H-G-I-S-I
-3 K-C-R-Q-R-N-W-R-L-G-Y-T-R-N-M-V-L-A-Y
- The +1 and -2 reading frames are most likely open reading frames because they do not contain any stop codons. While it also does not contain any stop codons, the -3 reading frame is probably not an open reading frame because the only methionine that could be a start codon appears very late in the sequence.
- Correction: Since the presence or absence of a start codon is not being considered, the -3 reading frame is also an open reading frame because it does not contain a stop codon.
