DNA and Genetics

  1. Gene Expression: Transcription
    1. Transcription Overview
      1. Central Dogma Context
        1. RNA Synthesis Direction
          1. Template Strand Usage
          2. Prokaryotic Transcription
            1. RNA Polymerase Structure
              1. Core Enzyme
                1. Sigma Factors
                  1. Holoenzyme Formation
                  2. Promoter Recognition
                    1. Consensus Sequences
                      1. -10 Box (Pribnow Box)
                        1. -35 Box
                          1. Promoter Strength
                          2. Transcription Initiation
                            1. Closed Complex Formation
                              1. Open Complex Formation
                                1. Promoter Clearance
                                2. Transcription Elongation
                                  1. RNA Chain Growth
                                    1. Transcription Bubble
                                      1. Pausing and Antitermination
                                      2. Transcription Termination
                                        1. Intrinsic Termination
                                          1. Hairpin Structures
                                            1. Poly-U Sequences
                                            2. Rho-Dependent Termination
                                              1. Rho Protein Function
                                                1. Rho Utilization Sites
                                            3. Eukaryotic Transcription
                                              1. RNA Polymerases
                                                1. RNA Polymerase I
                                                  1. rRNA Transcription
                                                  2. RNA Polymerase II
                                                    1. mRNA Transcription
                                                      1. Protein-Coding Genes
                                                      2. RNA Polymerase III
                                                        1. tRNA and 5S rRNA Transcription
                                                      3. Promoter Elements
                                                        1. Core Promoter Elements
                                                          1. TATA Box
                                                            1. Initiator Elements
                                                              1. CAAT Box
                                                                1. GC Box
                                                                2. Regulatory Elements
                                                                  1. Enhancers
                                                                    1. Silencers
                                                                      1. Response Elements
                                                                    2. Transcription Factors
                                                                      1. General Transcription Factors
                                                                        1. TFIID Complex
                                                                          1. TFIIB Function
                                                                            1. TFIIF Function
                                                                            2. Specific Transcription Factors
                                                                              1. DNA-Binding Domains
                                                                                1. Activation Domains
                                                                              2. Transcription Process
                                                                                1. Pre-initiation Complex Assembly
                                                                                  1. Promoter Melting
                                                                                    1. RNA Synthesis Initiation
                                                                                      1. Promoter Escape
                                                                                        1. Elongation Complex
                                                                                          1. Transcription Termination
                                                                                        2. RNA Processing in Eukaryotes
                                                                                          1. 5' Capping
                                                                                            1. Cap Structure
                                                                                              1. Capping Enzymes
                                                                                                1. Cap Functions
                                                                                                2. 3' Polyadenylation
                                                                                                  1. Polyadenylation Signals
                                                                                                    1. Cleavage and Polyadenylation
                                                                                                      1. Poly-A Tail Functions
                                                                                                      2. RNA Splicing
                                                                                                        1. Intron and Exon Definition
                                                                                                          1. Splice Site Recognition
                                                                                                            1. Spliceosome Assembly
                                                                                                              1. U1 snRNP
                                                                                                                1. U2 snRNP
                                                                                                                  1. U4/U6•U5 tri-snRNP
                                                                                                                  2. Splicing Mechanism
                                                                                                                    1. Two-Step Transesterification
                                                                                                                      1. Lariat Intermediate
                                                                                                                      2. Alternative Splicing
                                                                                                                        1. Exon Skipping
                                                                                                                          1. Intron Retention
                                                                                                                            1. Alternative 5' and 3' Sites
                                                                                                                              1. Mutually Exclusive Exons

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                                                                                                                        4. DNA Replication

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                                                                                                                        6. Gene Expression: Translation