1. DNA STRUCTURE AND REPLICATION
DNA bursts forth from this treated bacterial cell. Illustrating just how much DNA is found in a single cell.
Chapter 12

2. A. DNA Structure
DNA is a nucleic acid composed of nucleotide monomers.
DNA nucleotide consists of:
one phosphate group
one deoxyribose sugar (5 carbon sugar)
one nitrogenous base (G, A, C or T)
Purines are two-ringed structures (one 6C ring & one 5C ring). Guanine & adenine are purines.
Pyrimidines have a single 6C ring. Cytosine & thymine are pyrimidines.
Phosphate is attached to the 5lC of deoxyribose.
Nitrogenous base is attached to the 1lC of deoxyribose.

3. DNA is a double-stranded helix (Watson & Crick 1953).
Sides of ladder make up sugar-phosphate “backbone”.
Rungs of ladder composed of base pairs joined by hydrogen bonds.
Double helix - appears like a ladder that has been twisted vertically.
If we untwist a section of DNA helix observe that sides of ladder are composed of repeating sugar-phosphates, while rungs of ladder are base pairs joined by hydrogen bonds.

4. Pyrimidines (T & C) form hydrogen bonds with purines (A & G).
Thymine pairs with Adenine, forming 2 hydrogen bonds.
Cytosine pairs with Guanine, forming 3 hydrogen bonds.

5. DNA strands are antiparallel.
Numbering of strands is based on position of deoxyribose sugars.
Antiparallel - strands run in opposite directions.
Chemists assign numbers to differently positioned carbons in organic molecules. The 5 carbons of deoxyribose are numbered 1’-5’. Bases are attached to the 1’C, while the phosphate groups are attached to the 5’C.
Notice that the 5’C is uppermost on the left strand, and the 3’C is uppermost on the right strand.
5’ to 3’ strand
3’ to 5’ strand

6. DNA is highly condensed.
DNA is wrapped tightly around proteins & folded.
DNA must unwind for replication to occur.
As seen in the figure opening this chapter, DNA molecules are exceedingly long molecules, yet they fit inside very tiny cells.
In eukaryotic cells, DNA is wrapped twice around histone proteins, forming nucleosomes. A continuous thread of DNA connects nulceosomes like a string of pearls. These strings of pearls are wound to form chromatin fibers that in turn fold into more compact structures.
DNA in bacteria & archaea wrap around non-histone proteins.

7. B. DNA Replication Process by which DNA is duplicated.
occurs during the S phase of Interphase
is semiconservative (Meselson & Stahl) 
Semiconservative replication - two parental DNA strands separate & each constructs a new, complementary strand. Thus a newly replicated DNA molecule consists of 1 parental strand & 1 new strand.

8. Overview of DNA Replication:
Unreplicated DNA.
Strands “unzip” at several points creating replication forks.
Each strand serves as template for complementary nucleotides to H-bond.
New nucleotides of each daughter strand are linked.

9. Steps in DNA Replication:
Helicase breaks hydrogen bonds.
Binding proteins stabilize strands; prevent them from rejoining.
Primase makes an RNA primer.
RNA primer is a short segment of RNA that functions to attract an enzyme called DNA polymerase.

10. DNA polymerase “proofreads” new strand (replaces incorrect bases).
Free nucleotides move in & H-bond; DNA polymerase links nucleotides to each other starting at primer & working in the 5’ to 3’ direction.
DNA polymerase “proofreads” new strand (replaces incorrect bases).
DNA polymerase works directionally. It can add new nucleotides only to the 3’ end of a growing strand. Thus, DNA polymerase moves along parental strands in opposite directions.

11. DNA replication is continuous on one strand.
DNA replication is discontinuous on other strand, producing Okazaki fragments.

12. Repair enzymes remove RNA primers; Ligase connects Okazaki fragments.
Keep in mind that DNA replicates at hundreds of points along a chromosome, and then the newly made pieces merge (hooked together by ligase) to make one complete DNA molecule from each parent strand.

13. Determine the base sequence of daughter DNA replicated from the following parental DNA strand.
parental DNA C T A G G T A C T
daughter DNA G A T C C A T G A

14. C. DNA Repair
UV radiation damages DNA by causing thymine dimers to form.
Thymine dimer - adjacent thymines on the same strand covalently bond together.
DNA damage can be repaired by photoreactivation or excision repair.

15. 1. Photoreactivation – photolyase (enzyme) uses light energy to split dimer.
2. Excision repair - repair enzyme cuts out damaged area; DNA polymerase inserts replacement sequence & ligase seals backbone.

16. 3. Mismatch repair - enzymes proofread newly replicated DNA for base mispairing & correct the error.
Faulty DNA repair results in chromosome breaks & an increased susceptibility to cancer.
Ex. Xeroderma pigmentosum
Xeroderma pigmentosum is caused by a defect in excision repair mechanism.
Individuals with xeroderma pigmentosum must avoid all exposure to sunlight. Just a ray of sunlight causes painful blisters, eventually leading to skin cancer.