GTCAATC...etc.etc. Old School vs. New School

 DNA SEQUENCING

A couple weeks ago we started looking at DNA. And how it is sequenced. We learned about this in a couple different ways. First we did an activity with some nice old fashioned paper and pencil (It's wonderful to get back to the basics haha) This first activity was a simulation of a DNA sequencing gel. We had to read the DNA sequences for each patient. Then find the protein sequences. We would then compare those sequences to the sequences of the normal control. This would helps us to determine if a disease state was present in one of the patients. Abby, Bob and Carol were our three patients. And "Norm" was the normal DNA sequence we were looking at.

Sample of a DNA sequence.

 We first read the normal sequence and used a handy little chart to record the sequences. Norms read: ATG  GTG CAC CTG ACT CCT GAG GAG AAG TCT GCC.  

Next we took a look at Abby's DNA sequence. Abby's read: ATG GTG CAC CTG ACT CCT GTG GAG AAG TCT GCC. 

Bob was next. His DNA Sequence read: ATG GTG CAC CTG ACT CCT GAG GAG TAG TCT GCC. 

Last was Carol's Sequence. Hers read: ATG GTG CAC CTG ACC CTG AGG AGA AGT CTG CCC.

Okay so I took advantage of the technological ability to change the text color to show you the differences between the Normal sequence and the sequences of the three patients. The normal sequence is in all red. Where the other sequences matched the normal sequence I kept in red. The blue parts are where the sequence differs from the normal sequence. As you can see the Abby and Bob's sequences stayed pretty much the same with the normal sequence. Only differing in one part. Carol's sequence on the other hand is pretty different. Carol is missing a base. A T to be exact. This is called a Frame Shift Mutation. The sequence is off by that one T. There is a C where the T was. But it isn't because the T was traded out for a C. The T is completely missing, causing the "shift".

Codon Usage Table

The next step was to find the protein sequences. We used the sequences I showed above in red and blue and this table to find the Protein Sequences.
 For example Norms Protein Sequence: MET VAL HIS VAL SER SER GLU GLU LYS SER ALA.
After we found the DNA and Protein sequences for Norm and the three patients we could see if and what mutations were present. Abby's sequence showed a point mutation. And there was truncation mutation in Bob's protein sequence. It traded out a Lysine for a Stop in the sequence. The sequence was three amino acids short. And Carol's sequence as mentioned before had a Frame Shift Mutation present.

Graph showing the similarity between Norm and the three patients.

 So after we finished up our "old-school" DNA sequencing, Mr. Ludwig had us take a look at a website that did a virtual lab of DNA sequencing. The new-school way! We basically set up a whole experiment to find the DNA sequence of a patient and see if they had a disease present. The website for this experiment is:
http://www.hhmi.org/biointeractive/vlabs/bacterial_id/index.html

I personally like doing the "old-school" way better. In the virtual experiment version it was cool to watch and make it happen but I really did enjoy looking at the sequences and writing it all out. Then again, I only did about three inches worth of a DNA sequence...it would probably get old after a while. So feel free to take a look at the "new-school" way of DNA sequencing. And see what you think. NEW SCHOOL or OLD SCHOOL?

Protein Code Chart found at : http://www.nbii.gov/portal/server.pt/community/basic_genetics___cell_biology/401/genetic_blueprints/559

DNA Sequencing Sample found at: http://www.biology.fourcroy.org/chapters/09dna/handouts/dna_seq_activity.htm