Nucleic Acids Biochemistry

  1. The Genetic Code and Protein Synthesis
    1. The Genetic Code
      1. Codons: The Triplet Code
        1. Three-Nucleotide Units
          1. Reading Frame Concept
            1. Codon Table Organization
            2. Characteristics of the Code
              1. Specificity
                1. One Codon, One Amino Acid
                  1. Unambiguous Assignment
                    1. Fidelity Mechanisms
                    2. Degeneracy
                      1. Multiple Codons per Amino Acid
                        1. Wobble Base Pairing
                          1. Silent Mutations
                          2. Universality
                            1. Conservation Across Species
                              1. Mitochondrial Variations
                                1. Chloroplast Variations
                                2. Non-overlapping Nature
                                  1. Sequential Codon Reading
                                    1. Frame Maintenance
                                      1. Mutation Effects
                                      2. Commaless Nature
                                        1. No Punctuation Between Codons
                                          1. Continuous Reading
                                            1. Frame Shift Consequences
                                          2. Start Codon
                                            1. AUG Initiation
                                              1. Alternative Start Codons
                                                1. Ribosome Binding
                                                2. Stop Codons
                                                  1. UAG Amber
                                                    1. UAA Ochre
                                                      1. UGA Opal
                                                        1. Nonsense Suppression
                                                        2. Reading Frame
                                                          1. Open Reading Frames
                                                            1. ORF Identification
                                                              1. Start-Stop Boundaries
                                                                1. Coding Potential
                                                                2. Frame Shift Mutations
                                                                  1. Insertion Effects
                                                                    1. Deletion Effects
                                                                      1. Compensatory Mutations
                                                                  2. Translation: RNA-Directed Polypeptide Synthesis
                                                                    1. The Ribosome
                                                                      1. Structure of Prokaryotic Ribosomes
                                                                        1. 70S Ribosome Composition
                                                                          1. 30S Small Subunit
                                                                            1. 50S Large Subunit
                                                                              1. rRNA and Protein Components
                                                                              2. Structure of Eukaryotic Ribosomes
                                                                                1. 80S Ribosome Composition
                                                                                  1. 40S Small Subunit
                                                                                    1. 60S Large Subunit
                                                                                      1. rRNA and Protein Components
                                                                                      2. Functional Sites
                                                                                        1. A Site Function
                                                                                          1. P Site Function
                                                                                            1. E Site Function
                                                                                              1. Peptidyl Transferase Center
                                                                                            2. The Role of tRNA in Translation
                                                                                              1. Aminoacyl-tRNA Synthetases
                                                                                                1. Class I Synthetases
                                                                                                  1. Class II Synthetases
                                                                                                    1. Specificity Mechanisms
                                                                                                      1. Amino Acid Recognition
                                                                                                        1. tRNA Recognition
                                                                                                          1. Proofreading Activity
                                                                                                        2. Wobble Hypothesis
                                                                                                          1. Third Position Flexibility
                                                                                                            1. Base Pairing Rules
                                                                                                              1. Inosine Pairing
                                                                                                                1. Modified Base Effects
                                                                                                              2. The Process of Translation
                                                                                                                1. Initiation Process
                                                                                                                  1. Initiation Factors
                                                                                                                    1. eIF1 and eIF1A
                                                                                                                      1. eIF2 and GTP
                                                                                                                        1. eIF3 Function
                                                                                                                          1. eIF4F Complex
                                                                                                                          2. Assembly of Initiation Complex
                                                                                                                            1. 40S Subunit Binding
                                                                                                                              1. mRNA Recruitment
                                                                                                                                1. Start Codon Recognition
                                                                                                                                  1. 60S Subunit Joining
                                                                                                                                  2. Shine-Dalgarno Sequence
                                                                                                                                    1. Ribosome Binding Site
                                                                                                                                      1. 16S rRNA Complementarity
                                                                                                                                        1. Translation Efficiency
                                                                                                                                        2. Kozak Sequence
                                                                                                                                          1. Start Codon Context
                                                                                                                                            1. Scanning Mechanism
                                                                                                                                              1. Translation Efficiency
                                                                                                                                            2. Elongation Process
                                                                                                                                              1. Elongation Factors
                                                                                                                                                1. eEF1A Function
                                                                                                                                                  1. eEF2 Function
                                                                                                                                                    1. GTP Hydrolysis
                                                                                                                                                    2. Aminoacyl-tRNA Delivery
                                                                                                                                                      1. A Site Binding
                                                                                                                                                        1. Proofreading Steps
                                                                                                                                                          1. Accommodation
                                                                                                                                                          2. Peptide Bond Formation
                                                                                                                                                            1. Peptidyl Transferase Reaction
                                                                                                                                                              1. Ribosomal RNA Catalysis
                                                                                                                                                                1. Transition State
                                                                                                                                                                2. Translocation
                                                                                                                                                                  1. tRNA Movement
                                                                                                                                                                    1. mRNA Advancement
                                                                                                                                                                      1. Conformational Changes
                                                                                                                                                                    2. Termination Process
                                                                                                                                                                      1. Stop Codon Recognition
                                                                                                                                                                        1. Release Factor Binding
                                                                                                                                                                          1. Codon-Anticodon Mimicry
                                                                                                                                                                          2. Release Factors
                                                                                                                                                                            1. eRF1 Function
                                                                                                                                                                              1. eRF3 Function
                                                                                                                                                                                1. GTP Hydrolysis
                                                                                                                                                                                2. Peptide Release
                                                                                                                                                                                  1. Hydrolysis Reaction
                                                                                                                                                                                    1. Ribosome Recycling
                                                                                                                                                                                    2. Ribosome Disassembly
                                                                                                                                                                                      1. Subunit Dissociation
                                                                                                                                                                                        1. Factor Release
                                                                                                                                                                                    3. Post-Translational Modifications
                                                                                                                                                                                      1. Proteolytic Processing
                                                                                                                                                                                        1. Signal Peptide Removal
                                                                                                                                                                                          1. Propeptide Cleavage
                                                                                                                                                                                            1. Protein Maturation
                                                                                                                                                                                            2. Chemical Modifications
                                                                                                                                                                                              1. Phosphorylation
                                                                                                                                                                                                1. Methylation
                                                                                                                                                                                                  1. Acetylation
                                                                                                                                                                                                    1. Ubiquitination
                                                                                                                                                                                                    2. Protein Folding
                                                                                                                                                                                                      1. Chaperone Assistance
                                                                                                                                                                                                        1. Disulfide Bond Formation
                                                                                                                                                                                                          1. Quality Control

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                                                                                                                                                                                                    5. Nucleic Acid Metabolism: Biosynthesis

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                                                                                                                                                                                                    7. Nucleic Acid Degradation and Repair