Adapted from: http://www.people.cornell.edu/pages/jl265/education.pdf
To instructor: Prepare beforehand Put rubbing alcohol in freezer Prepare ice cubes and cooler to hold alcohol during lab, if possible Print out these slides full size to place on lab table
DNA and Bananas… To extract DNA: Expose cells to chemicals
So mash banana up and shake in the chemical solution
Sodium (or ammonium) lauryl sulfate is a good chemical It is commonly found in shampoo It helps dissolve the lipid-rich cell membranes This releases the nuclei which contain DNA It also helps dissolve proteins surrounding the DNA A protein jacket and DNA inside is a “chromosome” We have 46 in each cell Baking soda neutralizes acidity which is bad for DNA Salt preserves the helical shape of the DNA
Make chemical for extracting DNA In a cup, put: ½ cup water (bottled best) 1 teaspoon shampoo
Get out of spoon with a fingertip Wipe finger on paper towel
1 teaspoon baking soda ¼ teaspoon salt (uniodized best)
Stir until all is dissolved (use e.g. a dull table knife)
Extract DNA from banana Cut off a 1-inch banana slice Peel it Put it on plate With knife and fork, mash until fairly smooth & gooey Put 1 scant tablespoon of banana mush into jar Add 2 tablespoons of extraction chemical Screw on cap, go outside class,
hold jar securely with finger on cap, and count to 120 while shaking vigorously
Separate DNA solution from junk Pour out cup into trash can Put coffee filter in cup Wrap top edge of filter over top edge of cup to secure
(Depending on how big the filter is)
Open jar and slowly pour mixture into filter Let solution collect in bottom of cup Throw away filter with junk in it Look carefully at your DNA solution Not that impressive, is it!
Precipitate out dissolved DNA The DNA is dissolved and invisible Pour in approximately equal volume of: Cold 91% rubbing alcohol (e.g. from freezer) Swirl gently DNA precipitates out It is a bubbly, cloudy, stringy-looking substance Fish some out with a toothpick or your fork (lick banana off fork first) Feel it between thumb and finger… DNA !! Wait a few minutes – DNA may get even more visible
… cleanup … Put in pile for reuse next semester: Plastic Cups Jars and lids Silverware, plates, measuring stuff Toss in trash can Filters, toothpicks, banana peels, banana goo…
Recall the “Central Dogma” This is what makes organisms tick It also makes bioinformatics tick DNA hangs out in the nuclei of cells It contains genes Copies of genes go out of the nuclei
Copies are made of RNA (“transcription”) RNA is like DNA Like cheddar is like Swiss
Each gene copy makes a protein (“translation”) Proteins are the bricks and mortar of organisms
Our bodies need that, so we’re built to like eating proteins
“Central Dogma” (concise version) DNA makes RNA (“Transcription”) RNA makes proteins (“Translation”) “Information flow is DNARNAprotein”
3 DNA ‘letters’ code for 1 protein ‘letter’ DNA and RNA are similar DNA is transcribed to RNA RNA is translated to protein DNA has 4 “letters” Adenine, cytosine, guanine, & thymine RNA has 4 “letters” Adenine, cytosine, guanine, & uracil The codon table describes which? DNA triplets -> amino acid “letters” for protein RNA triplets -> amino acid “letters” for protein
Source: http://en.wikipedia.org/wiki/Genetic_code
Codon Table, DNA, and RNA DNA and RNA are similar DNA is transcribed to RNA RNA is translated to protein DNA has 4 “letters” Adenine, cytosine, guanine, & thymine RNA has 4 “letters” Adenine, cytosine, guanine, & uracil The codon table describes which? DNA triplets -> amino acid “letters” for protein RNA triplets -> amino acid “letters” for protein
3-D Codon Tables They exist See “soccer ball” table (Made in Pakistan, just like a lot of real soccer balls!) This table can also be in the shape of a dodecahedron “do-” = 2 “dec-” = 10 Dodecahedron: a twelve-sided solid
Source: http://en.wikipedia.org/wiki/Dodecahedron
Making a “Rafikihedron” The inventor calls it the Rafiki model (After the wise Rafiki in “The Lion King” story) I call it a “Rafikihedron” We will make one now! But, how do you read it? Pick a triangle of 3 nucleotides (A, C, G, & U) Starting from one, move to another of the 2 left You pass through a region labeled by an amino acid
(Recall the 20 amino acids are the “letters” for proteins) List the starting, 2nd, and remaining nucleotides That is the codon for the amino acid!
Rafikihedron Template Tabs added to figure from paper by J. & S. Berleant (many people feel no tabs works better – try it both ways and decide for yourself!)
Making a “Rafikihedron” The inventor of this “table” calls it the Rafiki model (After the wise Rafiki in “The Lion King” story) I call his “table” a “Rafikihedron” We will make one now! But, how do you read it? Pick a triangle of 3 nucleotides (A, C, G, & U) Starting from one, move to another of the other 2 You pass through a region labeled by an amino acid
(Recall the 20 amino acids are the “letters” for proteins) List the starting, 2nd, and remaining nucleotides That is the codon for the amino acid!
Another Template (from Mark White)
Another Template Got a color printer? (from Mark White)
