DNA Replication and Repair

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DNA Replication:

• Semi-conservative and bidirectional process.

Prokaryote DNA Replication Steps:

1. DNA A protein binds origin of replication; replication bubble formed.

2. Helicase unwinds DNA.

3. SSB protects DNA from nucleases and prevents separated DNA from rejoining.

4. RNA primer synthesized by primase.

5. DNA polymerase III synthesizes DNA in 5 to 3 direction.

6. RNA primers removed by DNA polymerase I; DNA polymerase I also fills DNA gaps near from step 5.

7. DNA polymerase I and III proofread.

8. DNA ligase removes gaps between Okazaki fragments.

9. DNA gyrase (DNA topoisomerase II) rejoins the DNA.

Telomerases:

• Shorten with each cycle of replication and keep track of cell age; cancer cells have relatively large amounts of telomerase.

Quinolones and Fluoroquinolones:

• Inhibit DNA gyrase.

p53 Gene Mutation:

• Li Fraumeni syndrome, various tumors.

ATM Gene Mutation:

• Ataxia telangiectasia.

BRCA-1 Gene Mutation:

• Breast, ovarian, prostate cancer.

BRCA-2 Gene Mutation:

• Breast cancer.

Nucleotide Excision Repair:

1. Excision endonuclease (excinuclease) removes the defective oligonucleotide.

2. DNA polymerase fills in the gap by synthesizing DNA in 5 to 3 directon.

3. DNA ligase rejoins the repaired strand.

S Phase Control:

• RB and TP53 control entry into S phase.

Lynch Syndrome:

• Hereditary nonpolyposis colorectal cancer.

• Mutated hMLH2 or hMSH2.

• Colorectal cancer due to defective DNA repair mechanisms.

Additional DNA Replication and Repair Notes:

• Excinucleases: remove and thymine dimers.

• Excinucleases: decreased in patients with Xeroderma Pigmentosum.

• CFTR protein: chloride transport.

• Sickle cell anemia: hydrophilic AA to hydrophobic AA.

• Alpha-amanitin, produced by Amanita phalloides: inhibits eukaryotic polymerase II.

• Sigma factor allows core enzymes to recognize promoter.

• Mutant RNA is not repaired, it is destroyed.

• Too much tubulin in a cell signals a negative feedback, so more tubulin cannot be produced.

• Advantage of Human Genome Project: determine mutations in genes involved in a given disease.

• Most mitochondrial proteins synthesized in the cytosol.

• Thalassemias: unequal crossing-over between gene clusters.

Additional Readings:

Basic Biochemistry

1. Nucleic Acid Structure and Organization
2. DNA Replication and Repair
3. Transcription and RNA Processing
4. Genetic Code, Mutations, and Translation
5. Genetic Regulation
6. Recombinant DNA
7. Amino Acids, Proteins, Enzymes
8. Hormones
9. Vitamins
10. Energy Metabolism
11. Glycolysis and Pyruvate Dehydrogenase
12. Citric Acid Cycle and Oxidative Phosphorylation
13. Glycogen, Gluconeogenesis, and Hexose Monophosphate Shunt
14. Lipid Synthesis and Storage
15. Lipid Mobilization and Catabolism
16. Amino Acid Metabolism Disorders
17. Purine and Pyrimidine Metabolism
18. Electron Transport
19. Citric Acid Cycle and Glyoxylate Cycle
20. Glycolysis
21. Pyruvate Metabolism
22. Mitochondrial ATP formation
23. Gluconeogenesis
24. Glycogen Metabolism
25. Nitrogen Fixation (Metabolism) reactions, and Heme Metabolism
26. Amino Acid Metabolism
27. What is Medium Chain Acyl-CoA Dehydrogenase Deficiency (MCADD)?

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