Biochemistry

  1. Genetic Information Pathways
    1. DNA Replication
      1. Basic Principles
        1. Semiconservative Replication
          1. Antiparallel Synthesis
            1. 5' to 3' Direction
            2. DNA Polymerases
              1. Prokaryotic Polymerases
                1. Pol I
                  1. Pol II
                    1. Pol III
                    2. Eukaryotic Polymerases
                      1. Pol α
                        1. Pol δ
                          1. Pol ε
                          2. Polymerase Properties
                            1. 3' to 5' Exonuclease Activity
                              1. Proofreading Function
                            2. Replication Process
                              1. Initiation
                                1. Origin of Replication
                                  1. DnaA Protein
                                    1. Helicase Loading
                                    2. Elongation
                                      1. Leading Strand Synthesis
                                        1. Lagging Strand Synthesis
                                          1. Okazaki Fragments
                                            1. Primase Function
                                              1. DNA Ligase
                                              2. Termination
                                                1. Ter Sites
                                                  1. Tus Protein
                                                2. Replication Machinery
                                                  1. Helicase
                                                    1. Single-Strand Binding Proteins
                                                      1. Topoisomerases
                                                        1. Type I
                                                          1. Type II
                                                          2. Sliding Clamp
                                                            1. Clamp Loader
                                                            2. Eukaryotic Replication
                                                              1. Multiple Origins
                                                                1. Chromatin Remodeling
                                                                  1. Telomeres
                                                                    1. End Replication Problem
                                                                      1. Telomerase
                                                                  2. DNA Repair
                                                                    1. Types of DNA Damage
                                                                      1. Spontaneous Damage
                                                                        1. Environmental Damage
                                                                          1. Replication Errors
                                                                          2. Repair Mechanisms
                                                                            1. Direct Repair
                                                                              1. Photolyase
                                                                                1. Methyltransferases
                                                                                2. Base Excision Repair
                                                                                  1. DNA Glycosylases
                                                                                    1. AP Endonuclease
                                                                                      1. Pol β
                                                                                      2. Nucleotide Excision Repair
                                                                                        1. Global Genome Repair
                                                                                          1. Transcription-Coupled Repair
                                                                                            1. UvrABC System
                                                                                            2. Mismatch Repair
                                                                                              1. MutS and MutL
                                                                                                1. Dam Methylation
                                                                                                2. Double-Strand Break Repair
                                                                                                  1. Homologous Recombination
                                                                                                    1. Non-Homologous End Joining
                                                                                                  2. Repair Defects and Disease
                                                                                                    1. Xeroderma Pigmentosum
                                                                                                      1. Lynch Syndrome
                                                                                                        1. BRCA Mutations
                                                                                                      2. DNA Recombination
                                                                                                        1. Homologous Recombination
                                                                                                          1. Holiday Junction Formation
                                                                                                            1. RecA Protein
                                                                                                              1. Branch Migration
                                                                                                                1. Resolution
                                                                                                                2. Site-Specific Recombination
                                                                                                                  1. Lambda Phage Integration
                                                                                                                    1. Cre-lox System
                                                                                                                    2. Transposition
                                                                                                                      1. DNA Transposons
                                                                                                                        1. Retrotransposons
                                                                                                                      2. Transcription
                                                                                                                        1. RNA Polymerases
                                                                                                                          1. Prokaryotic RNA Polymerase
                                                                                                                            1. Core Enzyme
                                                                                                                              1. Sigma Factors
                                                                                                                              2. Eukaryotic RNA Polymerases
                                                                                                                                1. RNA Pol I
                                                                                                                                  1. RNA Pol II
                                                                                                                                    1. RNA Pol III
                                                                                                                                  2. Transcription in Prokaryotes
                                                                                                                                    1. Promoter Recognition
                                                                                                                                      1. -10 and -35 Elements
                                                                                                                                        1. Sigma Factor Binding
                                                                                                                                        2. Initiation
                                                                                                                                          1. Closed Complex
                                                                                                                                            1. Open Complex
                                                                                                                                              1. Promoter Clearance
                                                                                                                                              2. Elongation
                                                                                                                                                1. Transcript Elongation
                                                                                                                                                  1. Pausing and Antitermination
                                                                                                                                                  2. Termination
                                                                                                                                                    1. Rho-Independent
                                                                                                                                                      1. Rho-Dependent
                                                                                                                                                    2. Transcription in Eukaryotes
                                                                                                                                                      1. Promoter Elements
                                                                                                                                                        1. TATA Box
                                                                                                                                                          1. Initiator Elements
                                                                                                                                                            1. CAAT Box
                                                                                                                                                              1. GC Box
                                                                                                                                                              2. Transcription Factors
                                                                                                                                                                1. General Transcription Factors
                                                                                                                                                                  1. Specific Transcription Factors
                                                                                                                                                                  2. Enhancers and Silencers
                                                                                                                                                                    1. Distant Regulatory Elements
                                                                                                                                                                      1. Chromatin Looping
                                                                                                                                                                      2. Chromatin Structure
                                                                                                                                                                        1. Nucleosome Positioning
                                                                                                                                                                          1. Chromatin Remodeling
                                                                                                                                                                            1. Histone Modifications
                                                                                                                                                                          2. RNA Processing
                                                                                                                                                                            1. 5' Capping
                                                                                                                                                                              1. 7-Methylguanosine Cap
                                                                                                                                                                                1. Cap-Binding Proteins
                                                                                                                                                                                2. 3' Polyadenylation
                                                                                                                                                                                  1. Polyadenylation Signals
                                                                                                                                                                                    1. Poly(A) Polymerase
                                                                                                                                                                                    2. RNA Splicing
                                                                                                                                                                                      1. Spliceosome Assembly
                                                                                                                                                                                        1. snRNPs
                                                                                                                                                                                          1. Splicing Mechanism
                                                                                                                                                                                            1. Alternative Splicing
                                                                                                                                                                                            2. RNA Editing
                                                                                                                                                                                              1. C-to-U Editing
                                                                                                                                                                                                1. A-to-I Editing
                                                                                                                                                                                            3. Translation
                                                                                                                                                                                              1. The Genetic Code
                                                                                                                                                                                                1. Codon-Anticodon Pairing
                                                                                                                                                                                                  1. Degeneracy
                                                                                                                                                                                                    1. Wobble Base Pairing
                                                                                                                                                                                                      1. Start and Stop Codons
                                                                                                                                                                                                        1. Universal vs Variant Codes
                                                                                                                                                                                                        2. Transfer RNA
                                                                                                                                                                                                          1. tRNA Structure
                                                                                                                                                                                                            1. Cloverleaf Structure
                                                                                                                                                                                                              1. L-Shaped 3D Structure
                                                                                                                                                                                                              2. tRNA Modifications
                                                                                                                                                                                                                1. Base Modifications
                                                                                                                                                                                                                  1. Functional Importance
                                                                                                                                                                                                                  2. Aminoacyl-tRNA Synthetases
                                                                                                                                                                                                                    1. Class I and Class II
                                                                                                                                                                                                                      1. Proofreading Mechanisms
                                                                                                                                                                                                                    2. Ribosomes
                                                                                                                                                                                                                      1. Ribosome Structure
                                                                                                                                                                                                                        1. Large and Small Subunits
                                                                                                                                                                                                                          1. rRNA and Proteins
                                                                                                                                                                                                                          2. Ribosomal Sites
                                                                                                                                                                                                                            1. A Site
                                                                                                                                                                                                                              1. P Site
                                                                                                                                                                                                                                1. E Site
                                                                                                                                                                                                                                2. Ribosome Assembly
                                                                                                                                                                                                                                  1. Subunit Association
                                                                                                                                                                                                                                3. Translation Process
                                                                                                                                                                                                                                  1. Initiation
                                                                                                                                                                                                                                    1. Initiation Factors
                                                                                                                                                                                                                                      1. Start Codon Recognition
                                                                                                                                                                                                                                        1. Ribosome Assembly
                                                                                                                                                                                                                                        2. Elongation
                                                                                                                                                                                                                                          1. Elongation Factors
                                                                                                                                                                                                                                            1. Peptidyl Transfer
                                                                                                                                                                                                                                              1. Translocation
                                                                                                                                                                                                                                              2. Termination
                                                                                                                                                                                                                                                1. Stop Codon Recognition
                                                                                                                                                                                                                                                  1. Release Factors
                                                                                                                                                                                                                                                    1. Ribosome Recycling
                                                                                                                                                                                                                                                  2. Prokaryotic vs Eukaryotic Translation
                                                                                                                                                                                                                                                    1. Coupled Transcription-Translation
                                                                                                                                                                                                                                                      1. Polyribosomes
                                                                                                                                                                                                                                                        1. Kozak Sequence
                                                                                                                                                                                                                                                        2. Post-translational Modifications
                                                                                                                                                                                                                                                          1. Proteolytic Processing
                                                                                                                                                                                                                                                            1. Chemical Modifications
                                                                                                                                                                                                                                                              1. Phosphorylation
                                                                                                                                                                                                                                                                1. Glycosylation
                                                                                                                                                                                                                                                                  1. Acetylation
                                                                                                                                                                                                                                                                    1. Methylation
                                                                                                                                                                                                                                                                    2. Protein Targeting
                                                                                                                                                                                                                                                                      1. Signal Sequences
                                                                                                                                                                                                                                                                        1. Protein Sorting

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                                                                                                                                                                                                                                                                  6. Integration and Regulation of Metabolism