1. A T C G
Isn’t this a great illustration!?

2. Macromolecules: Nucleic Acids
Examples:
RNA (ribonucleic acid)
single helix
DNA (deoxyribonucleic acid)
double helix
Structure:
monomers = nucleotides
DNA
RNA

3. Nucleotides 3 parts nitrogen base (C-N ring) pentose sugar (5C)
ribose in RNA
deoxyribose in DNA
phosphate (PO4) group
Nitrogen base I’m the A,T,C,G or U part!
Are nucleic acids charged molecules?
DNA & RNA are negatively charged:
Don’t cross membranes.
Contain DNA within nucleus
Need help transporting mRNA across nuclear envelope.
Also use this property in gel electrophoresis.

4. Types of nucleotides 2 types of nucleotides different nitrogen bases
Purine = AG
Pure silver!
2 types of nucleotides
different nitrogen bases
purines
double ring N base
adenine (A)
guanine (G)
pyrimidines
single ring N base
cytosine (C)
thymine (T)
uracil (U)

5. Dangling bases? Why is this important?
Nucleic polymer
Backbone
sugar to PO4 bond
phosphodiester bond
new base added to sugar of previous base
polymer grows in one direction
N bases hang off the sugar-phosphate backbone
Dangling bases? Why is this important?

6. Pairing of nucleotides
Nucleotides bond between DNA strands
H bonds
purine :: pyrimidine
A :: T
2 H bonds
G :: C
3 H bonds
The 2 strands are complementary.
One becomes the template of the other & each can be a template to recreate the whole molecule.
Matching bases? Why is this important?

7. H bonds? Why is this important?
DNA molecule
Double helix
H bonds between bases join the 2 strands
A :: T
C :: G
H bonds = biology’s weak bond
• easy to unzip double helix for replication and then re-zip for storage
• easy to unzip to “read” gene and then re-zip for storage
H bonds? Why is this important?

8. Matching halves? Why is this a good system?
Copying DNA
Replication
2 strands of DNA helix are complementary
have one, can build other
have one, can rebuild the whole
when cells divide, they must duplicate DNA exactly for the new “daughter” cells
Why is this a good system?
Matching halves? Why is this a good system?

9. When does a cell copy DNA?
When in the life of a cell does DNA have to be copied?
cell reproduction
mitosis
gamete production
meiosis
when cells divide, they must duplicate DNA exactly for the new “daughter” cells
Why is this a good system?

10. But how is DNA copied? Replication of DNA
base pairing suggests that it will allow each side to serve as a template for a new strand

11. Models of DNA Replication
Can you design a nifty experiment to verify?
Models of DNA Replication
Alternative models
become experimental predictions
conservative
semiconservative
dispersive P 1 2

12. Replication forks
In eukaryotes, the linear DNA has many replication forks

14. Learning Check
Break the toothpicks at the center of your models and replicate your DNA strand
You should end up with 2 complete strands of DNA
Keep in mind Chargaff’s rules and Meselson & Stahl’s semi-conservative model
Animation

15. Replication- Create a diagram that shows how the following components interact with each other (15 min)
Replication fork
RNA primer
Leading strand
DNA ligase
RNA primase
Okazaki fragments
Lagging strand
Helicase
DNA polymerase
Single stranded binding protein
Topoisomerase

16. DNA Replication Issues
1. DNA strands must be unwound during replication
DNA helicase
unwinds the strands
Single stranded binding proteins (SSB)
prevent immediate reformation of the double helix
Topoisomerases
“untying” the knots that form

17. Replication Issues
2. A new DNA strand can only elongate in the 5’  3’ direction
DNA polymerase can add only at the 3’ end
Replication is continuous on one strand
Leading Strand
discontinuous on the other
Lagging strand
Okazaki fragments

18. Okazaki fragments Synthesis of the leading strand is continuous
The lagging strand (discontinuous) is synthesized in pieces called Okazaki fragments

20. Replication Issues
3. DNA polymerase cannot initiate synthesis because it can only add nucleotides to end of an existing chain
Requires a “primer” to get the chain started
RNA Primase
can start an RNA chain from a single template strand
DNA polymerase can begin its chain after a few RNA nucleotides have been added

22. Summary
At the replication fork, the leading strand is copied continuously into the fork from a single primer
Lagging strand is copied away from the fork in short okazaki fragments, each requiring a new primer

24. Learning Check What is the purpose of DNA replication?
How is the new strand ensured to be identical to the original strand?
How is replication on one side of the strand different from the other side?

25. Replication Issues
4. Presence of RNA primer on the 5’ ends of daughter DNA leading strand leaves a gap of uncopied DNA
Repeated rounds of replication produce shorter and shorter DNA molecules
Telomeres
protect genes from being eroded through multiple rounds of DNA replication

26. Telomeres
Ends of eukaryotic chromosomes, the telomeres, have special nucleotide sequences
Humans - this sequence is typically TTAGGG, repeated ,000 times
Telomerase adds a short molecule of RNA as a template to extend the 3’ end
Room for primase & DNA pol to extend 5’ end

27. Summary
Explain how the cell overcomes each of the following issues in DNA replication
DNA strands must be unwound during replication
A new DNA strand can only elongate in the 5’  3’ direction
DNA polymerase cannot initiate synthesis and can only add nucleotides to end of an existing chain
Presence of RNA primer on the 5’ ends of daughter DNA leading strand leaves a gap of uncopied DNA