Download DNA extraction activity

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)