Alex A. Cardenas Week 8: Difference between revisions
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==Chapter 6== | ==Chapter 6== | ||
*Working with a single protein sequence. | *Working with a single protein sequence. | ||
*Followed link www.expasy.org/tools/#primary and clicked on the ProtParam link. | |||
**Accession number was entered for gp120 sequence. N and C terminus boxes left blank in order to analyze the whole sequence. | |||
**Submitted amino acids 266-288 in order to show molecular weight, extinction coefficient, and estimated half-life. | |||
***Molecular weight - 2547.8 | |||
***Extinction coefficient - As there are no Trp, Tyr or Cys in the region considered, your protein should not be visible by UV spectrophotometry. | |||
***Estimated half-life - 100 hours. | |||
*Looking for transmembrane segments in the next sectional exercise. Followed www.expasy.org/cgi-bin/protscale.pl and entered accession number into the search box, selecting the appropriate boxes for properties and widow size. Transmembrane protein gp41 (TM) (Glycoprotein 41) (gp41). | |||
==Links== | ==Links== |
Revision as of 22:26, 25 October 2011
Chapter 2
- Retreiving protein sequences for envelope glycoprotein gp160 (pp. 42-51)
- Went to www.expasy.org/sprot/.
- Envelope glycoprotein gp160 was typed into search box and retreived. The description of envelope glycoprotein gp160 can be found [here].
- Entry Name - ENV_HV1C4
- Primary Accession Number - P05879
- FASTA format was viewed (FATSA - a sequence alignment-and-database-scanning program). New window appeared with all amino acids in the protein sequence.
- Protein sequences retrieved by advanced search methods. Clicked on advance search tab and typed in envelope glycoprotein gp160.
Chapter 4
- Reading a SWISS-PROT entry (pp. 110-123). The link can be found [here].
- Went through steps in deciphering the envelope glycoprotein gp160 swiss-prot entry. Information on entry name, primary accession number, protein name, gene name, etc., can be found in the link above.
- 8 References were found in the article.
- The Cross references - not all cross references were displayed online as they were in the book as seen below in the picture:
Chapter 5
- ORFing DNA sequence. Retrieved sequence from clicking on FASTA in UniProtKB and posted it in open reading frame finder. DNA sequence is displayd as 6 parallel horizontal. There are 6 possible translation frames: +1, +2, +3 on on reverse --> -1, -2, -3.
- ORF displayed the following
Chapter 6
- Working with a single protein sequence.
- Followed link www.expasy.org/tools/#primary and clicked on the ProtParam link.
- Accession number was entered for gp120 sequence. N and C terminus boxes left blank in order to analyze the whole sequence.
- Submitted amino acids 266-288 in order to show molecular weight, extinction coefficient, and estimated half-life.
- Molecular weight - 2547.8
- Extinction coefficient - As there are no Trp, Tyr or Cys in the region considered, your protein should not be visible by UV spectrophotometry.
- Estimated half-life - 100 hours.
- Looking for transmembrane segments in the next sectional exercise. Followed www.expasy.org/cgi-bin/protscale.pl and entered accession number into the search box, selecting the appropriate boxes for properties and widow size. Transmembrane protein gp41 (TM) (Glycoprotein 41) (gp41).
Links
- Alex A. Cardenas
- Week 8 Assignment
- Alex A. Cardenas Week 2
- Alex A. Cardenas Week 3
- Alex A. Cardenas Week 4
- Alex A. Cardenas Week 5
- Alex A. Cardenas Week 6
- Alex A. Cardenas Week 7
- Alex A. Cardenas Week 8
- Alex A. Cardenas Week 9
- Alex A. Cardenas Week 10
- Alex A. Cardenas Week 11
- BIOL368/F11:Class Journal Week 1
- BIOL368/F11:Class Journal Week 2
- BIOL368/F11:Class Journal Week 3
- BIOL368/F11:Class Journal Week 5
- BIOL368/F11:Class Journal Week 6
- BIOL368/F11:Class Journal Week 7
- BIOL368/F11:Class Journal Week 8
- BIOL368/F11:Class Journal Week 9
- BIOL368/F11:Class Journal Week 10