1. DO Now Identify the circled structure.
What type of interaction is occurring between the bases of the two nucleotides at the bottom of the diagram?
What parts of two different nucleotides covalently bonded together?
Are the two strands complementary?
What two parts of the nucleotide are bonded to the 5’ carbon?

2. Why is one end 3’ and the other 5’?
Look at the 3’ end. Notice the black line which represents a bond. What functional group belongs here?
Look at the 5’ end. What functional group is bonded to the 5’ carbon?

3. DNA is antiparallel
Antiparallel means that the two strands run in opposite direction.
One strand runs in the 3’ to 5’ direction and opposite strand runs in the 5’ to 3’ direction.
Diagrams to right illustrate antiparallel…look at the arrows.

4. Biotech Lab#2 DNA Scissors
Extract DNA from cell
Magnify a portion of DNA & it looks like this: Double Helix
Magnify a portion of Double Helix & it looks like this:
*This is a sequence of nucleotides.
a. How many nucleotides?
b. How many bases?
c. How many base pairs?
*Segments of DNA can be considered to have s specific function. This segment represents a gene. Can you define the word gene?

5. The Many Definitions of the Gene:
A gene is a segment of DNA with a specific sequence of nucleotides.
The sequence of nucleotides or bases has a specific location within the mass of DNA found in the nucleus of a cell.
A gene is a sequence of nucleotides that codes for a specific protein.
A gene’s sequence provides the information to code for a specific protein. For example, a specific sequence of DNA (gene) to make the protein lactase or insulin. Insulin is a signal protein in the human body. It tells the cell to remove extra glucose from the blood.
A gene is the unit of heredity.
DNA Sequence  polypeptide chain
TACCGTAAATAA  amino acid 1- amino acid 2- amino acid 3- amino acid 4- etc.
Insulin gene  insulin (signal protein)
If the body were to make a part of the insulin protein, would the DNA
sequence be the same as the insulin sequence? Explain.

6. Relationship between chromosome, gene and DNA….

7. Here is a more complex picture
Note: The red DNA matches up with the red protein. Gene codes for protein.

8. Review: Types of Proteins
Transport – hemoglobin, Sodium/Potassium pump
Receptor - membrane protein
Storage - albumin
Signal - insulin, estrogen, testosterone
Contractile - actin, myosin
Enzyme - catalase, lactase
Structural - collagen
This is insulin….

9. Molecular Biologists will
Want to be able to remove the gene from the extracted DNA
Want to take the removed gene and put it in another area of the DNA or in another organism’s DNA
Restriction enzymes can
Cut DNA at a specific location by recognizing the restriction site (sequence that will be cut)
Cut DNA in a specific way
In the illustration to the right, red
DNA is now bonded with blue DNA. Let’s look at the lab to find out how to do this….

10. Restriction Enzymes
Enzymes that catalyze a reaction that will cut the DNA at a specific location
The location on the DNA is called the restriction site
A restriction site has a specific sequence of nucleotides called a palindrome. This is an example below is a palindrome: “RACECAR”
Bacteria synthesize restriction enzymes to protect their genomic DNA from foreign DNA which enters their cells.
Eukaryotic cells have restriction endonucleases which are used to repair DNA when it did not replicate accurately.

11. What kind of cuts are made?
Sticky ends
Blunt ends
How Restriction Enzyme Works

12. DNA Scissors
This lab is about restriction enzymes which cut DNA into smaller fragments.
This lab explains where restriction enzymes are found in nature.
This lab will have you simulate the action of specific RE’s on DNA.
This lab will have you identify which type of cut is best for recombining DNA.

13. The picture shows the (4) strips of DNA that will be used to simulate the action of a restriction enzyme.
Pieces of DNA

14. Now do the lab…….. Read each step carefully.
Answer questions located in specific steps on the lined paper neatly and clearly.
Upon completion, tape DNA strips to a piece of colored paper.
Each person will complete the activity and simulate the restriction enzyme.
You may help each other.
Return all materials to proper location

15. Review What you Learned in the Lab…
Practice Questions

16. Answer these three questions:
Question Set #1
Answer these three questions:
What type of cut is #1? #2?
Identify an enzyme that can make a cut like cut#1.
Which cut only breaks phosphodieser bonds?
Which cut involves a chemical reaction and a weakening of an intermolecular force?

17. Question Set #2
1. Why does the restriction enzyme select the location shown on diagram 2? 2. What enzyme would be needed to put the pieces back together? 3. If you wanted to join an unknown piece of DNA to the segment on the right in picture 3, what color for the nucleotides could not be used? Why?

18. Thinking ahead…
Now that you know how to put DNA from different sources
Together. What is meant by when molecular biologists use the term
recombinant DNA?

19. Can you write a story about how a little red plasmid became no more?