1. The Structure of DNA and Restriction Enzymes

2. I. DNA Is A Nucleic Acid A. Nucleic Acid = polymer of nucleotides
1. nucleotide = molecule made up of…
a. a pentose (5 carbon) sugar called Deoxyribose
b. a phosphate group attached to the 5 ´ carbon of the pentose
c. one of four nitrogenous bases is attached to the 1´ carbon of the pentose - the four DNA nitrogenous bases are Adenine, Guanine, Cytosine, and Thymine
B. DNA is a double helix
1. two individual polymers of nucleotides bond to one another
a. this process causes the two strands to coil into a “double helix”
b. this bonding forces the nitrogenous bases to the inside of the helix, while the deoxyribose and phosphate groups get forced to the outside (referred to as the sugar-phosphate backbone)

3. II. Molecular Structure Of A Nucleotide
5 ´ Carbon
1 ´ Carbon
pg. 83
the “prime” numbering system is used to distinguish between carbon atoms in deoxyribose and carbon atoms in the nitrogenous bases

4. III. Internal Bonding of DNA
A. Hydrogen Bonding - Hydrogen covalently bonded to one electronegative atom while being attracted to another electronegative atom.
1. this bonding is due to partial (+) and ( -) charges (polarity) within the molecules in question
2. Occurs primarily with F, O, and N
Hydrogen bonding between the two strands of the DNA molecule creates
1. triple bonds (H) between Guanine and Cytosine
2. double bonds (H) between Adenine and Thymine
fig pg. 292

5. 1. forces the sugar-phosphate backbone to the outside
C. Hydrogen bonding takes place between the complementary nitrogenous bases between either nitrogen and/or oxygen
1. forces the sugar-phosphate backbone to the outside
2. leaving the nitrogenous bases on the inside
3. ten base pairs make up one turn in the dbl helix
similar to fig. 16.5a pg 291
fig. 16.5b pg 291

6. IV. Antiparallel Configuration
A. The two strands of the DNA molecule are antiparallel
1. the sugar phosphate backbones run in opposite directions
2. each terminal phosphate group is attached to a 5 ´ carbon, while the terminal OH groups are attached to 3 ´ carbons.
3. as a result the complementary strand must run in the opposite direction
fig pg. 291

7. V. Restriction Enzymes
All enzymes are proteins, made up of chains of amino acids.
B. Restriction Enzymes digest DNA by “cutting” DNA between specific nucleotides (a disruption of the bond between a phosphate group and the next sugar molecule), at locations identified as recognition sequences which are approximately 6 base pairs long and enzyme specific!
In a mixture of DNA and restriction enzymes, each enzyme causes the disruption of the DNA backbone within each of the recognition sequences that occur in that particular strand of DNA.

8. D. Restriction enzymes have a dual active site
D. Restriction enzymes have a dual active site. One region of the active site bonds to its recognition sequence, while another region of the active site disrupts the DNA between two specific bases within the recognition sequence.

9. An Example of a Restriction Enzyme “Cutting” DNA
Recognition
Sequence
A - T - A - C - C - G - G - T - A - A - G
T - A - T - G - G - C - C - A - T - T - C
Restriction
Enzyme
DNA Fragment One
DNA Fragment Two
A - T - A - C C - G - G - T - A - A - G
T - A - T - G - G - C C - A - T - T - C

10. The End
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