* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Download DNA Replication and DNA Repair Study Guide Focus on the
DNA barcoding wikipedia , lookup
DNA methylation wikipedia , lookup
Nutriepigenomics wikipedia , lookup
History of RNA biology wikipedia , lookup
DNA sequencing wikipedia , lookup
Comparative genomic hybridization wikipedia , lookup
Site-specific recombinase technology wikipedia , lookup
Zinc finger nuclease wikipedia , lookup
Mitochondrial DNA wikipedia , lookup
Holliday junction wikipedia , lookup
Genomic library wikipedia , lookup
DNA profiling wikipedia , lookup
Point mutation wikipedia , lookup
No-SCAR (Scarless Cas9 Assisted Recombineering) Genome Editing wikipedia , lookup
Microevolution wikipedia , lookup
SNP genotyping wikipedia , lookup
Cancer epigenetics wikipedia , lookup
DNA vaccination wikipedia , lookup
DNA nanotechnology wikipedia , lookup
Genealogical DNA test wikipedia , lookup
Microsatellite wikipedia , lookup
Vectors in gene therapy wikipedia , lookup
Gel electrophoresis of nucleic acids wikipedia , lookup
United Kingdom National DNA Database wikipedia , lookup
Bisulfite sequencing wikipedia , lookup
Non-coding DNA wikipedia , lookup
Cell-free fetal DNA wikipedia , lookup
Molecular cloning wikipedia , lookup
Therapeutic gene modulation wikipedia , lookup
Epigenomics wikipedia , lookup
DNA damage theory of aging wikipedia , lookup
History of genetic engineering wikipedia , lookup
Artificial gene synthesis wikipedia , lookup
Extrachromosomal DNA wikipedia , lookup
Primary transcript wikipedia , lookup
DNA replication wikipedia , lookup
DNA polymerase wikipedia , lookup
Nucleic acid double helix wikipedia , lookup
Nucleic acid analogue wikipedia , lookup
DNA supercoil wikipedia , lookup
Cre-Lox recombination wikipedia , lookup
Helitron (biology) wikipedia , lookup
DNA Replication and DNA Repair Study Guide Focus on the following. 1. Meselon and Stahl experiments showing semiconservatism. a. N-15 labeled DNA is heavier than N-14 DNA. b. N-15 bacteria placed in medium (which only contains N-14 DNA). c. CsCl density gradient used to note difference between N-15 (lower in tube) and N14(higher in tube) DNA. i. Transfer of N-15 DNA to N-14 media produces an intermediate layer of ½ N-14 and ½ N-15. d. Therefore, each new DNA molecule consists of one old strand (N-14) and one new strand (N-15). i. Semiconservatism. 2. Origin and Direction of Replicatin (Replication Fork a. Origin of Replication i. Beginning point of replication ii. Prokaryotes (bacteria)- 1 origin of replication iii. Eukaryotes- 1 to 2000 origins of replication per chromosome b. Direction- two forks proceed in opposite directions c. Forks i. Replication sites ii. Proceed in one direction (one for each direction) iii. Replication can only proceed in ϱ͛ƚŽϯ͛ĚŝƌĞĐƚŝŽŶ 3. Role of RNA primers a. Short strand of RNA that is complementary to the template strand and contains a free OH group for attachment i. Can be 1 to 60 bases long. b. Leading Strand- replication is continuous i. DNA synthesized uninterrupted from 1 RNA primer c. Lagging Strand- replication occurs from multiple primers i. Synthesis is discontinuous ii. Short strand eventually joined together 1. ƌƌĂŶŐĞĚϯ͛ƚŽϱ͛;ďƵƚƉƌŽĐĞĞĚƐϱ͛ƚŽϯ͛) d. RNA Primase (RNA Polymerase in DNA) i. Lays down RNA primer during DNA replication ii. DNA polymerase needs free OH to start (which RNA primer has). 4. Okazaki Fragments. Describe Formation a. Short sections of RNA primer and DNA on a lagging strand. b. Discontinuous. i. WƌŽĐĞĞĚƐŝŶϱ͛ƚŽϯ͛ĚŝƌĞĐƚŝŽŶ;ŽŶϯ͛ƚŽϱ͛ƐƚƌĂŶĚͿ ii. Very fragmented 5. Role of helicases, topoisomerases,and single stranded binding proteins a. Helicases i. Unwind DNA ii. Require ATP 1. Hydrolyzed in order to function iii. Supercoiling-increased or decreased torsional strain put on molecule 1. Caused by the formation of multiple closed loops. b. Topoisomerases i. Relieve tension ahead of the replication fork. 1. Type I: DNA topisomerase a. Nicks (breaks) one strand b. Passes other strand through break c. NO ATP!!! 2. TyperII: Topoisomerases a. Enzyme-bridged break b. Another duplex passes through c. Takes out 2 supercoils at once d. REQUIRES ATP!!! 3. Type II: Topoisomerase II a. TARGET FOR MANY MEDICINES!!!! c. Single Strand Binding Proteins (SSB) i. Keep strands as single entities. ii. Reusable! iii. 1000x greater affinity for single strands iv. Protects against nucleases. 6. Activity of DNA polymerase III a. Read over how it was discovered. b. Extends growing DNA i. ^ƚŽƉƐĂƚϱ͛ŶƵĐůĞŽƚŝĚĞŽĨZEƉƌŝŵĞƌ ii. CAN GO NO FURTHER!!! 1. Think of the nun ĨƌŽŵ͞dŚĞĂsŝŶĐŝŽĚĞ͊͟ iii. Once bound to template, it never dissociates. iv. 2 at each replication fork (4 in the bubble) 7. Activities of DNA polymerase I, including proof reading and error repair a. 3 Functions i. džŽŶƵĐůĞĂƐĞϱ͛ƚŽϯ͛ĂĐƚŝǀŝƚLJ 1. Cuts out primer ii. Fills in spot with dNTP that matches exposed template iii. džŽŶƵĐůĞĂƐĞϯ͛ƚŽϱ͛ĂĐƚŝǀŝƚLJ 1. Proofreads 2. ůĞĂǀĞƐϯ͛ƚĞƌŵŝŶĂůĞŶĚƐ͘ iv. DNA Ligase (extra) 1. Seals in nicks between fragments a. Uses DNA b. Also links with phosphodiester bond b. ATP necessary for replication and repair!!!! 8. Mechanism of Replisome a. Helicase separates into leading and lagging strands i. SSBS maintain stability of single strands ii. Primase lays down RNA primers for DNA polymerase III iii. DNA polymerase III lays down nucleotides for leading and lagging strand iv. DNA polymerase I replaces RNA primers with DNA v. DNA ligase links fragments in lagging strand 9. Eukaryotic DNA Polymerases a. Alpha i. Location-nucleus ii. Function-synthesis and priming of lagging strand 1. RNA primers and DNA synthesis b. Beta i. Location-nucleus ii. Function-DNA repair c. Gamma i. Location-Mitochondria ii. Function-replicates mit. DNA d. Delta i. Location- nucleus ii. Function-synthesis of leading strand (DNA synthesis) 10. Dissociation of histones from DNA and cooperative mechanism of nucleosome synthesis a. Histones i. At initiation sites ii. Weakened by acetylation and phosphorylation iii. Allows replication to begin b. Nucleosome i. Increased synthesis of histones required for new nucleosomes. ii. Occurs with DNA replication iii. Distributed only to 1 daughter strand 11. DNA damage: Thymine Dimers and Deamination a. Physical Agentsi. High temperatures ii. Radiation at different wavelengths 1. 240-300nm most effective iii. X-rays b. Chemical Agents i. Methylating agents ii. Nitrous acid iii. Nitrosamines iv. Acridine dyes, etc c. Types of Damage i. Thymine Dimer 1. Covalent linkage of two adjacent thymines in the same strand 2. H-bonding disrupted 3. Inhibits replication forks ii. Deamination 1. Loss of amino group 2. Results in conversion a. C to U b. A to hypoxanthine 12. Nucleotide excision repair mechanism a. Removal of the following i. Bulky chemical modifications of DNA ii. Pyrimidine (thymine) dimmers b. Recognition of problem by protein complex c. Endonuclease i. EŝĐŬŝŶŐŽĨEĂƚϱ͛ĂŶĚϯ͛ĞŶĚƐ d. DNA Polymerase epsilon i. Fills in gap e. DNA Ligase i. Forms phosphodiester bonds. f. In summary i. Endonuclease-cutting ii. Polymerase-replacement of damaged DNA iii. Ligase-seals 13. Base Excision Repair: Uracil DNA glycosylase ; SOS Repair a. Uracil DNA glycosylase i. Hydrolyzes the bond between uracil and deoxyribose 1. Results in the removal of uracil from DNA 2. Apyrimidine formed ii. Nicked by endonuclease iii. Repaired by DNA polymerase and ligase b. SOS Repair i. Not very well understood ii. Found in eukaryotes iii. Many enzymes are induced in response to high DNA damage iv. SOS-SAVE OUR SUBUNITS!!!!! 14. Xeroderma pigmentosum and other repair defects, lethality of DNA damage a. Xeroderma pigementosum i. Increased sensitivity to light 1. More prone to skin cancer 2. Due to defects in repair of UV problems ii. Autosomal recessive inheritance 1. Mutation on 1 gene iii. Defect in excision repair system 1. XP variants a. Symptoms but normal excision repair system b. Polymerase problem b. Other Repair Defects-See chart in notes c. Lethality of DNA Damage i. D37 (only 37 % survive) 1. Damaging agent that kills 63% of cells in culture 2. Average Damage per cell a. Ionizing Radiation- Single strand breaks-1000 per cell b. Ionizing Radiation- Double strand breaks- 40 per cell c. Ultraviolet Radiation- Thymine dimmers-400,000 per cell REMEMBER, THE FORCE WILL BE WITH YOU. ALWAYS!