PREVIEW: You have six choices, all different from each other. The three "virtual" lab choices involve doing computer tasks to solve problems; the three "wimp" lab choices involve more reading and demonstrating that you understand the reading. Pick one of the six.. The "create a virtual protein" choice is recommended.

"VIRTUAL LABS"

1. CREATE A VIRTUAL PROTEIN version 1:

   • Practice by copying this code ("block-mark" it and then "control"C works in almost any software):  aug aug aug aug aug aug uga uau gag ucu uga gau aga uga ugu cac gcc aau aac uga aug aug aug 
     (for this software you can use "U" or "T" but the first few codons seem to turn out strange no matter what you do)
     • Beam up to  http://www.ncbi.nlm.nih.gov/gorf/gorf.html  and paste ("control"V) your code in the box that looks like this:  

     • Enter GI or ACCESSION   or sequence in FASTA format (paste your code here. Then click the OrfFind button above left.) FROM: TO:

     • 
       on the next page, click the "sixframes" button at right on the part that looks like this:
       1 GenBank 50 100 300
       
       then (on that page that looks like this) change "2 Fasta nucleotide" to

       2 Fasta nucleotide 3 Fasta protein

     • "3 Fasta protein."  And click the "View" button on the left (not here, but on that page that looks like this).

       2 Fasta nucleotide 3 Fasta protein

   • When it works, you should get this:
            >Sequence 1 Frame +0
              FLMMMM*YES*DR*CHANN*MMM
     
   • Now create your own codon message and save it.  Repeat the steps above with your own secret message and see if it prints something clever.  Experiment. You can't hurt anything. If you need help, check with Dr. Jann.
   • When you get your codon message to work (to print out a sequence of letters representing the one-letter symbols for the primary structure of the designer protein), then e-mail your codon sequence (not the amino acid sequence) to jannr@queens.edu. You can paste it directly onto your e-mail "send form" (the same "Control C" /"control V" sequence). If it works before the deadline for turning it in, your grade is 50, unless your protein is almost like somebody else's protein. If your protein is particularly clever or funny or beautiful, you get extra credit bonus *'s.  Here's an example by Jonathon Keitt three years ago:  ATG AGA AAA GAT AAT CAT CCT TGG ACT GGT ATG TGT TTT CTT GTT ATT TGA.  Can you figure out why he got extra credit?
   • You  get another 50 points if your e-mail explains exactly why two of the amino acids in your protein are very different in polarity.   [Hint:  Use your textbook amino acid chart to examine each amino acid's R-group (side chain)].   To get all 50 points for this part, you will have to describe how the R-group atoms interact with each other and with water.
   • To understand the relevance of this information, review this tutorial:  http://www.clunet.edu/BioDev/omm/chymo/chymo.htm ). 
   • Reminder:  the second part of this grade requires evidence that you understand the differences in bonding of the atoms of R-groups.
     
     

2. CREATE A VIRTUAL PROTEIN version 2:

   • Start with the DNA codons (like mRNA with T's instead of U's). It must contain start and stop codons to work. Type them into a computer file which you can edit and copy ("Control C" after you block mark it is one technique).
     Example:
     ATG TTT TTC TTA TTG CTT CTC CTA CTG ATA ATT GTT GTG GTC GTG GCG GTA GGG GTG GGA GGT GAG GAG GAG CAT CAT CAT TGA
   • Then beam up to http://darwin.bio.geneseo.edu/~yin/WebGene/Protein.html. Follow instructions there. (If you don't have another way to enter the DNA you invented, "Control V" once your cursor is in the box for DNA code.)   (if website doesn't work, try http://www.ncbi.nlm.nih.gov/gorf/gorf.html (version 1 above) but you don't get colors)
   • Set the virtual lab for "0 BP." 
   • When you get to the next page, go to the bottom of the window on the left, and put a dot in the O for the first ORF. 
   • Then push the "submit" button. 
   • Experiment. You can't hurt anything. If you need help, check with Dr. Jann.
   • When you get your DNA to work (to print out a colorful sequence of letters representing the one-letter symbols for the primary structure of the designer protein), then e-mail your DNA sequence to jannr@queens.edu. You can copy it directly onto your e-mail "send form" (the same "Control C" /"control V" sequence). If it works before the deadline for turning it in, your grade is 50, unless your protein is almost like somebody else's protein. If your protein is particularly clever or funny or beautiful, you get extra credit bonus *'s.  Here's an example by Jonathon Keitt three years ago:  ATG AGA AAA GAT AAT CAT CCT TGG ACT GGT ATG TGT TTT CTT GTT ATT TGA.  Can you figure out why he got extra credit?
   • You  get another 50 points if your e-mail explains exactly why two of the amino acids in your protein are different colors. (Hint:  Use your textbook amino acid chart or click on the amino acid name at the virtual site to examine each amino acid's R-group (side chain).   To get all 50 points for this part, you will have to describe how the R-group atoms interact with each other and with water.
   • To understand the relevance of this information, review this tutorial:  http://www.clunet.edu/BioDev/omm/chymo/chymo.htm ). 
   •  

3. Another virtual choiceRestriction enzyme analysis:  http://darwin.bio.geneseo.edu/~yin/WebGene/RE.html: DESIGN YOUR OWN LAB. For example, copy a long DNA sequence and analyze it using one of these sites; then take the same sequence and "mutate" it by changing or adding or deleting some bases; then do a virtual analysis of it. Describe or print out your results along with a paragraph summary of your experience.

4. Another virtual choice  Do the MIT PROBLEM SET for analyzing blots. Just hand in the same answers they have to hand in at MIT for one type of blot (Southern, Northern, or Western): http://web.mit.edu/esgbio/www/rdna/solvingblots.html

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SUBSTITUTES FOR VIRTUAL WIMPS

1. PLASMIDS & THEIR USES: http://www.accessexcellence.org/AB/WYW/cohen/index.html (click on the right-aiming arrows to go all the way through, including all the biographical information. You'll know you're through when it comes back to the title page).  Choose either of these:

   • write at least 3 short summaries of experiments described in this presentation (You should make sure you review chapter 13 before you finish this project.)

   • outline in detail how these discoveries were like the "Race for the Double Helix" video and how they were different.
     
     

2. Another wimpy substitute DNA on the WITNESS STAND:

   • STUDY http://www.accessexcellence.org/AB/WYW/lander/lander_1.html (go all the way through until it comes back to the title page.  Lander won a Nobel Prize a couple of years ago, by the way.)

   • and also find some recent news on forensic DNA technology http://science.bio.org/ or some other source

   • List the examples of forensic use of DNA technology. Be sure you make it clear that you understand the details of the procedures and exactly what "evidence" results from the procedures. You should make sure you master chapter 13  and DNA medical applications before you finish this project.

   • Make another list of the possible dangers or potentials for mis-use or abuse of the technology.
     

3. Another wimpy substitute DIAGNOSIS of CHROMOSOME DISORDERS

   • STUDY
     http://www.pathology.washington.edu:80/Cytogallery/ (Go through the whole "gallery" live, not via print-outs.   Click on any terms you don't understand, and review the basic points until you think your instructor would consider you well-trained in cytogenetic diagnosis and disorders.)

   • DRAW a series of cartoons or sketches which show

     • the diffference between constitutional and acquired disorders

     • how to diagnose a disorder with FISH 

     • the "diagnostic" part of a karyotype or ideotype for examples of disorders caused by each of these:

       1. aneuploidy

       2. translocation

       3. deletion

       4. any other chromosomal disorder of your choice

     • Include brief descriptions of the symptoms of these four disorders.

• You will need to be able to
  1. predict the primary structure and other characteristics of proteins, given the DNA base sequence of their genes,
  2. analyze and interpret news reports (like http://science.bio.org/ and other research news),
  3. analyze and interpret results of experiments, like in the Virtual Fly labs
  4. suggest specific experimental tools or procedures which could provide evidence for hypotheses or 
     • for diagnoses of genetic disorders 
     • or for legal cases 
     • or for dealing with anthrax or other bioterrorism situations,
  5. display sophisticated understanding of replication and transcription and translation and nucleic acid hybridization all their connections with evolution and genetics and technology,
  6. weigh ethical considerations, like in the ethics lab.
• Any of the choices for this lab should help you with at least one of these objectives. For the others, you'll have to rely on the textbook and study guides for 

  • DNA basics

  • Codons and RNA

  • DNA tech

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