1. CHAPTER 14 LECTURE SLIDES
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2. DNA: The Genetic Material
Chapter 14

3. DNA Structure DNA is a nucleic acid Composed of nucleotides
5-carbon sugar called deoxyribose
Phosphate group (PO4)
Attached to 5′ carbon of sugar
Nitrogenous base
Adenine, thymine, cytosine, guanine
Free hydroxyl group (—OH)
Attached at the 3′ carbon of sugar

4. NH2 N N N CH2 O Nitrogenous Base Nitrogenous base NH2 O N C N C C N C
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Nitrogenous Base
Nitrogenous base
NH2
NH2 O 7 N 6 5 N C N C C N C N H 1 H C H C
Phosphate group 8
Purines C C 2 N C H N C
NH2 N N O N 4 N H H 9 3
Adenine
Guanine –O P O
CH2 5´ O– O
NH2 O O 1´ C C C 4´ H C N
H3C C N H H C N H H C C O H C C O H C C O 3´ 2´
OH in RNA
Pyrimidines N N N OH H H H
H in DNA
Sugar
Cytosine
(both DNA and RNA)
Thymine
(DNA only)
Uracil
(RNA only)

5. The chain of nucleotides has a 5′-to-3′ orientation
Phosphodiester bond
Bond between adjacent nucleotides
Formed between the phosphate group of one nucleotide and the 3′ —OH of the next nucleotide
The chain of nucleotides has a 5′-to-3′ orientation
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PO4
Base
CH2 O C O
Phosphodiester
bond –O P O O
Base
CH2 O OH 3´

6. Chargaff’s Rules Erwin Chargaff determined that
Amount of adenine = amount of thymine
Amount of cytosine = amount of guanine
Always an equal proportion of purines (A and G) and pyrimidines (C and T)

7. Rosalind Franklin
Performed X-ray diffraction studies to identify the 3-D structure
Discovered that DNA is helical
Using Maurice Wilkins’ DNA fibers, discovered that the molecule has a diameter of 2 nm and makes a complete turn of the helix every 3.4 nm

8. James Watson and Francis Crick – 1953
Deduced the structure of DNA using evidence from Chargaff, Franklin, and others
Did not perform a single experiment themselves related to DNA
Proposed a double helix structure

9. Double helix 2 strands are polymers of nucleotides
Phosphodiester backbone – repeating sugar and phosphate units joined by phosphodiester bonds
Wrap around 1 axis
Antiparallel
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Phosphate group P 5´ O 4´ 1´
Phosphodiester bond 3´ 2´ P 5´ O 4´ 1´ 3´ 2´ P 5´ O 4´ 1´
5-carbon sugar 3´ 2´
Nitrogenous base P 5´ O 4´ 1´ 3´ 2´ OH 3´

11. Complementarity of bases A forms 2 hydrogen bonds with T
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Hydrogen
bond H
Complementarity of bases
A forms 2 hydrogen bonds with T
G forms 3 hydrogen bonds with C
Gives consistent diameter H N O H N H N G N H N C H
Sugar N N N H
Sugar H
Hydrogen
bond H H N N H O
CH3 N A N H N T H
Sugar N N H
Sugar

12. DNA Replication Requires 3 things Something to copy
Parental DNA molecule
Something to do the copying
Enzymes
Building blocks to make copy
Nucleotide triphosphates

13. DNA replication includes
Initiation – replication begins
Elongation – new strands of DNA are synthesized by DNA polymerase
Termination – replication is terminated

15. All have several common features
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RNA polymerase makes primer
DNA polymerase extends primer
DNA polymerase
Matches existing DNA bases with complementary nucleotides and links them
All have several common features
Add new bases to 3′ end of existing strands
Synthesize in 5′-to-3′ direction
Require a primer of RNA

16. Unwinding DNA causes torsional strain
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Supercoiling
Replisomes
No Supercoiling
Replisomes
DNA gyrase
Unwinding DNA causes torsional strain
Helicases – use energy from ATP to unwind DNA
Single-strand-binding proteins (SSBs) coat strands to keep them apart
Topoisomerase prevent supercoiling
DNA gyrase is used in replication

17. Semidiscontinous DNA polymerase can synthesize only in 1 direction
Leading strand synthesized continuously from an initial primer
Lagging strand synthesized discontinuously with multiple priming events
Okazaki fragments

19. Partial opening of helix forms replication fork
DNA primase – RNA polymerase that makes RNA primer
RNA will be removed and replaced with DNA

20. Leading-strand synthesis
Single priming event
Strand extended by DNA pol III
Processivity –  subunit forms “sliding clamp” to keep it attached

21. Lagging-strand synthesis
Discontinuous synthesis
DNA pol III
RNA primer made by primase for each Okazaki fragment
All RNA primers removed and replaced by DNA
DNA pol I
Backbone sealed
DNA ligase
Termination occurs at specific site
DNA gyrase unlinks 2 copies

22. Leading strand (continuous)
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DNA ligase
Lagging strand
(discontinuous)
RNA primer
DNA polymerase I
Okazaki fragment
made by DNA
polymerase III
Primase
Leading strand
(continuous) 3´

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25. Telomeres
Specialized structures found on the ends of eukaryotic chromosomes
Protect ends of chromosomes from nucleases and maintain the integrity of linear chromosomes
Gradual shortening of chromosomes with each round of cell division
Unable to replicate last section of lagging strand

27. Telomeres composed of short repeated sequences of DNA
Telomerase – enzyme makes telomere of lagging strand using and internal RNA template (not the DNA itself)
Leading strand can be replicated to the end
Telomerase developmentally regulated
Relationship between senescence and telomere length
Cancer cells generally show activation of telomerase

29. DNA Repair Errors due to replication
DNA polymerases have proofreading ability
Mutagens – any agent that increases the number of mutations above background level
Radiation and chemicals
Importance of DNA repair is indicated by the multiplicity of repair systems that have been discovered

30. DNA Repair Falls into 2 general categories Specific repair Nonspecific
Targets a single kind of lesion in DNA and repairs only that damage
Nonspecific
Use a single mechanism to repair multiple kinds of lesions in DNA

31. Photorepair Specific repair mechanism
For one particular form of damage caused by UV light
Thymine dimers
Covalent link of adjacent thymine bases in DNA
Photolyase
Absorbs light in visible range
Uses this energy to cleave thymine dimer

33. Excision repair Nonspecific repair
Damaged region is removed and replaced by DNA synthesis
3 steps
Recognition of damage
Removal of the damaged region
Resynthesis using the information on the undamaged strand as a template