Nucleic Acids Biochemistry

  1. Nucleic Acid Degradation and Repair
    1. Degradation of Nucleic Acids
      1. Nucleases
        1. Endonucleases
          1. DNase I
            1. DNase II
              1. Restriction Endonucleases
                1. RNase A
                  1. RNase H
                  2. Exonucleases
                    1. 3' to 5' Exonucleases
                      1. 5' to 3' Exonucleases
                        1. Processivity Differences
                      2. Catabolism of Purines
                        1. Pathway Overview
                          1. Adenine Catabolism
                            1. Guanine Catabolism
                              1. Hypoxanthine Formation
                              2. Key Intermediates
                                1. Inosine Formation
                                  1. Hypoxanthine Oxidation
                                    1. Xanthine Formation
                                    2. Uric Acid Formation
                                      1. Xanthine Oxidase
                                        1. Final Product
                                        2. Clinical Relevance
                                          1. Gout Pathophysiology
                                            1. Hyperuricemia
                                              1. Allopurinol Treatment
                                            2. Catabolism of Pyrimidines
                                              1. Pathway Overview
                                                1. Thymine Catabolism
                                                  1. Cytosine Catabolism
                                                    1. Uracil Catabolism
                                                    2. Key Intermediates
                                                      1. Dihydropyrimidines
                                                        1. β-Alanine Formation
                                                          1. β-Aminoisobutyrate Formation
                                                          2. End Products
                                                            1. CO2 and NH3
                                                              1. Acetyl-CoA Formation
                                                                1. Succinyl-CoA Formation
                                                            2. DNA Damage
                                                              1. Sources of Damage
                                                                1. Spontaneous Chemical Reactions
                                                                  1. Depurination
                                                                    1. Glycosidic Bond Hydrolysis
                                                                      1. AP Site Formation
                                                                        1. Frequency and Consequences
                                                                        2. Deamination
                                                                          1. Cytosine to Uracil
                                                                            1. 5-Methylcytosine to Thymine
                                                                              1. Adenine to Hypoxanthine
                                                                              2. Tautomeric Shifts
                                                                                1. Keto-Enol Tautomers
                                                                                  1. Amino-Imino Tautomers
                                                                                    1. Mispairing Consequences
                                                                                  2. Environmental Agents
                                                                                    1. Chemical Mutagens
                                                                                      1. Alkylating Agents
                                                                                        1. Base Analogs
                                                                                          1. Intercalating Agents
                                                                                          2. Ultraviolet Radiation
                                                                                            1. Pyrimidine Dimer Formation
                                                                                              1. 6-4 Photoproducts
                                                                                              2. Ionizing Radiation
                                                                                                1. Direct DNA Damage
                                                                                                  1. Indirect Radical Damage
                                                                                                    1. Double-Strand Breaks
                                                                                                  2. Replication Errors
                                                                                                    1. Polymerase Errors
                                                                                                      1. Slippage Events
                                                                                                        1. Template Switching
                                                                                                      2. Types of DNA Lesions
                                                                                                        1. Single-Strand Breaks
                                                                                                          1. Phosphodiester Bond Cleavage
                                                                                                            1. Sugar Damage
                                                                                                              1. Base Loss
                                                                                                              2. Double-Strand Breaks
                                                                                                                1. Simultaneous Breaks
                                                                                                                  1. Staggered Breaks
                                                                                                                    1. Blunt vs Cohesive Ends
                                                                                                                    2. Base Modifications
                                                                                                                      1. Oxidative Damage
                                                                                                                        1. Alkylation Products
                                                                                                                          1. Deamination Products
                                                                                                                          2. Thymine Dimers
                                                                                                                            1. Cyclobutane Dimers
                                                                                                                              1. 6-4 Photoproducts
                                                                                                                                1. Spore Photoproducts
                                                                                                                            2. DNA Repair Mechanisms
                                                                                                                              1. Direct Reversal of Damage
                                                                                                                                1. Photoreactivation
                                                                                                                                  1. DNA Photolyase
                                                                                                                                    1. Light-Dependent Repair
                                                                                                                                      1. Dimer Splitting
                                                                                                                                      2. Alkyltransferases
                                                                                                                                        1. O6-Methylguanine Repair
                                                                                                                                          1. Suicide Enzymes
                                                                                                                                            1. MGMT Function
                                                                                                                                          2. Mismatch Repair
                                                                                                                                            1. Recognition of Mismatches
                                                                                                                                              1. MutS Protein Function
                                                                                                                                                1. Mismatch Binding
                                                                                                                                                  1. Conformational Changes
                                                                                                                                                  2. Strand Discrimination
                                                                                                                                                    1. Dam Methylation
                                                                                                                                                      1. Nick-Directed Repair
                                                                                                                                                        1. Hemimethylated DNA
                                                                                                                                                        2. Excision and Resynthesis
                                                                                                                                                          1. MutL and MutH Function
                                                                                                                                                            1. Exonuclease Activity
                                                                                                                                                              1. DNA Polymerase Filling
                                                                                                                                                            2. Base Excision Repair
                                                                                                                                                              1. Glycosylases
                                                                                                                                                                1. Uracil-DNA Glycosylase
                                                                                                                                                                  1. 8-Oxoguanine Glycosylase
                                                                                                                                                                    1. Alkylpurine Glycosylase
                                                                                                                                                                    2. AP Endonuclease
                                                                                                                                                                      1. AP Site Recognition
                                                                                                                                                                        1. 5' Incision
                                                                                                                                                                          1. 3' Phosphatase Activity
                                                                                                                                                                          2. Short-Patch Repair
                                                                                                                                                                            1. Single Nucleotide Replacement
                                                                                                                                                                              1. DNA Polymerase β
                                                                                                                                                                                1. DNA Ligase III
                                                                                                                                                                                2. Long-Patch Repair
                                                                                                                                                                                  1. Multiple Nucleotide Replacement
                                                                                                                                                                                    1. PCNA Involvement
                                                                                                                                                                                      1. FEN1 Nuclease
                                                                                                                                                                                    2. Nucleotide Excision Repair
                                                                                                                                                                                      1. Damage Recognition
                                                                                                                                                                                        1. XPC-RAD23B Complex
                                                                                                                                                                                          1. Transcription-Coupled Repair
                                                                                                                                                                                            1. Global Genome Repair
                                                                                                                                                                                            2. Dual Incision
                                                                                                                                                                                              1. XPF-ERCC1 Nuclease
                                                                                                                                                                                                1. XPG Nuclease
                                                                                                                                                                                                  1. Oligonucleotide Excision
                                                                                                                                                                                                  2. DNA Synthesis and Ligation
                                                                                                                                                                                                    1. Repair Synthesis
                                                                                                                                                                                                      1. Gap Filling
                                                                                                                                                                                                        1. Nick Sealing
                                                                                                                                                                                                      2. Double-Strand Break Repair
                                                                                                                                                                                                        1. Homologous Recombination
                                                                                                                                                                                                          1. Mechanism Overview
                                                                                                                                                                                                            1. End Processing
                                                                                                                                                                                                              1. Strand Invasion
                                                                                                                                                                                                                1. Holiday Junction Formation
                                                                                                                                                                                                                  1. Resolution
                                                                                                                                                                                                                  2. RAD51 Protein Function
                                                                                                                                                                                                                    1. Nucleoprotein Filament
                                                                                                                                                                                                                      1. Strand Exchange
                                                                                                                                                                                                                      2. Role in Meiosis
                                                                                                                                                                                                                        1. Crossing Over
                                                                                                                                                                                                                          1. Chromosome Segregation
                                                                                                                                                                                                                            1. Genetic Diversity
                                                                                                                                                                                                                          2. Non-Homologous End Joining
                                                                                                                                                                                                                            1. Mechanism Overview
                                                                                                                                                                                                                              1. End Recognition
                                                                                                                                                                                                                                1. End Processing
                                                                                                                                                                                                                                  1. Ligation
                                                                                                                                                                                                                                  2. Ku Protein Function
                                                                                                                                                                                                                                    1. DNA End Binding
                                                                                                                                                                                                                                      1. DNA-PKcs Recruitment
                                                                                                                                                                                                                                        1. Synapsis Formation
                                                                                                                                                                                                                                        2. Error-Prone Nature
                                                                                                                                                                                                                                          1. Sequence Loss
                                                                                                                                                                                                                                            1. Insertions
                                                                                                                                                                                                                                              1. Chromosomal Rearrangements

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                                                                                                                                                                                                                                      6. The Genetic Code and Protein Synthesis

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                                                                                                                                                                                                                                      8. Epigenetics and Nucleic Acid Modifications