Difference between revisions of "Msamdars Week 2"
Jump to navigation
Jump to search
(→Tasks A & B: vh doesn't work) |
(→Electronic Lab Notebook: Finish Task A) |
||
| Line 6: | Line 6: | ||
====Task A==== | ====Task A==== | ||
# Loaded each allele in to Aipotu | # Loaded each allele in to Aipotu | ||
| + | # Created pure-breeding species by continuously self-breeding each initial flower in the Genetics tab. | ||
| + | # Created hybrids between each pure-breeding flower and a pure-breeding white flower | ||
| + | # Compared each of these hybrids's DNA seq by using built in compare tool, shown in a screenshot below. | ||
| + | # Compared each of the amino acid sequences by hand, copying the sequence over from the Molecular Bio screen into the table in the Results section. | ||
====Task B==== | ====Task B==== | ||
| Line 27: | Line 31: | ||
|R | |R | ||
|Red | |Red | ||
| − | |<code> | + | |<code>CAGCTATAACCGAGATTGATGTCTAGTGCGATAAGCCCCAAAGATCGGCACATTTTGTGCGCTATACAAAGGTTAGTG<u style="color: red">'''T'''</u>TCTGTCGGCAGTAGTAGGGGGCGT</code> |
| − | |<code>N- | + | |<code>N-MetSerAsnArgHisIleLeuLeuVal<u style="color: red">'''Phe'''</u>CysArgGln-C</code> |
|- | |- | ||
|G | |G | ||
|Green | |Green | ||
| − | |<code> | + | |<code>CAGCTATAACCGAGATTGATGTCTAGTGCGATAAGCCCCAAAGATCGGCACATTTTGTGCGCTATACAAAGGTTAGTG<u style="color: red">'''TA'''</u>CTG<u style="color: red">'''G'''</u>CGGCAGTAGTAGGGGGCGT</code> |
| − | |<code>N- | + | |<code>N-MetSerAsnArgHisIleLeuLeuVal<u style="color: red">'''TyrTrp'''</u>ArgGln-C</code> |
|- | |- | ||
|Y | |Y | ||
|Yellow | |Yellow | ||
|<code>CAGCTATAACCGAGATTGATGTCTAGTGCGATAAGCCCCAAAGATCGGCACATTTTGTGCGCTATACAAAGGTTAGTGTGGTGTCGGCAGTAGTAGGGGGCGT</code> | |<code>CAGCTATAACCGAGATTGATGTCTAGTGCGATAAGCCCCAAAGATCGGCACATTTTGTGCGCTATACAAAGGTTAGTGTGGTGTCGGCAGTAGTAGGGGGCGT</code> | ||
| − | |<code>N- | + | |<code>N-MetSerAsnArgHisIleLeuLeuVal<u style="color: red">'''Trp'''</u>CysArgGln-C</code> |
|- | |- | ||
|W | |W | ||
Revision as of 21:09, 10 September 2019
Contents
Electronic Lab Notebook
Purpose
The purpose of this experiment is to learn about models and modeling, as well as the central dogma of molecular biology by utilizing the software Aipotu. We will use this software to learn about the real computational work that systems biologists do and emulate that work with hypothetical organisms as a control.
Methods
Task A
- Loaded each allele in to Aipotu
- Created pure-breeding species by continuously self-breeding each initial flower in the Genetics tab.
- Created hybrids between each pure-breeding flower and a pure-breeding white flower
- Compared each of these hybrids's DNA seq by using built in compare tool, shown in a screenshot below.
- Compared each of the amino acid sequences by hand, copying the sequence over from the Molecular Bio screen into the table in the Results section.
Task B
- Loaded sample by double-clicking on White alleles (as pictured).
- Compared sequence using compare tool
Results
Changes from white allele are highlighted.
Tasks A & B
| Allele | Color | Change(s) in Amino Acid Sequence | Change(s) in DNA Sequence |
|---|---|---|---|
| B | Blue | CAGCTATAACCGAGATTGATGTCTAGTGCGATAAGCCCCAAAGATCGGCACATTTTGTGCGCTATACAAAGGTTAGTGTACTGTCGGCAGTAGTAGGGGGCGT
|
N-MetSerAsnArgHisIleLeuLeuValTyrCysArgGln-C
|
| R | Red | CAGCTATAACCGAGATTGATGTCTAGTGCGATAAGCCCCAAAGATCGGCACATTTTGTGCGCTATACAAAGGTTAGTGTTCTGTCGGCAGTAGTAGGGGGCGT
|
N-MetSerAsnArgHisIleLeuLeuValPheCysArgGln-C
|
| G | Green | CAGCTATAACCGAGATTGATGTCTAGTGCGATAAGCCCCAAAGATCGGCACATTTTGTGCGCTATACAAAGGTTAGTGTACTGGCGGCAGTAGTAGGGGGCGT
|
N-MetSerAsnArgHisIleLeuLeuValTyrTrpArgGln-C
|
| Y | Yellow | CAGCTATAACCGAGATTGATGTCTAGTGCGATAAGCCCCAAAGATCGGCACATTTTGTGCGCTATACAAAGGTTAGTGTGGTGTCGGCAGTAGTAGGGGGCGT
|
N-MetSerAsnArgHisIleLeuLeuValTrpCysArgGln-C
|
| W | White | CAGCTATAACCGAGATTGATGTCTAGTGCGATAAGCCCCAAAGATCGGCACATTTTGTGCGCTATACAAAGGTTAGTGGTCTGTCGGCAGTAGTAGGGGGCGT
|
N-MetSerAsnArgHisIleLeuLeuValValCysArgGln-C |
Task C
Given the screenshot on the right, there were no differences in the white alleles.
Task D
Tyrosine Phenylalanine Tryptophan added make purple. Because both the
Task E
Task F
Conclusion
Other Links
| Links | ||
|---|---|---|
| Mihir Samdarshi User Page | ||
| Assignment Pages | Personal Journal Entries | Shared Journal Entries |
| Week 1 | Journal Week 1 | Class Journal Week 1 |
| Week 2 | Journal Week 2 | Class Journal Week 2 |
| Week 3 | FAS2/YPL231W Week 3 | Class Journal Week 3 |
| Week 4 | Journal Week 4 | Class Journal Week 4 |
| Week 5 | Database - AmtDB | Class Journal Week 5 |
| Week 6 | Journal Week 6 | Class Journal Week 6 |
| Week 7 | Journal Week 7 | Class Journal Week 7 |
| Week 8 | Journal Week 8 | Class Journal Week 8 |
| Week 9 | Journal Week 9 | Class Journal Week 9 |
| Assignment Pages | Personal Journal Entries | |
| Week 10 | Journal Week 10 | |
| Week 11 | Journal Week 11 | |
| Week 12/13 | Journal Week 12/13 | |
| Team Project Links | ||
| Skinny Genes Team Page | ||
Acknowledgement
This week my partner was John Nimmers-Minor. Except for what is noted above, this individual journal entry was completed by me and not copied from another source.
References
LMU BioDB 2019. (2019). Week 2. Retrieved September 11, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_2 MediaWiki (2019). Category: Help. Retrieved September 11, 2019, from https://www.mediawiki.org/wiki/Category:Help
