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<title>E. coli Batch 01 - DNA Replication & Repair</title>
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<h1>🦠 E. coli Batch 01 - DNA Replication & Repair</h1>
<p class="subtitle">Interactive Programming Framework Analysis - 8 DNA Processes</p>
<div class="description">
<p><strong>🧬 Interactive DNA Replication & Repair Systems:</strong> This enhanced version features interactive sliders allowing you to explore each DNA process at 5 different detail levels. Each process demonstrates sophisticated biological programming with error correction, quality control, and computational logic.</p>
<p><strong>How to Use:</strong> Use the sliders below each process to adjust the detail level from 1 (basic overview) to 5 (comprehensive molecular detail).</p>
</div>
<div class="process-overview">
<h3>📋 Interactive DNA Processes - 8 Core Systems</h3>
<div class="process-list">
<a href="#process-1" class="process-link">1. DNA Replication Initiation</a>
<a href="#process-2" class="process-link">2. DNA Replication Elongation</a>
<a href="#process-3" class="process-link">3. DNA Replication Termination</a>
<a href="#process-4" class="process-link">4. DNA Repair</a>
<a href="#process-5" class="process-link">5. Base Excision Repair</a>
<a href="#process-6" class="process-link">6. Nucleotide Excision Repair</a>
<a href="#process-7" class="process-link">7. Mismatch Repair</a>
<a href="#process-8" class="process-link">8. SOS Response</a>
</div>
</div>
<div class="sources-section">
<h4>📚 Scientific Sources & References</h4>
<p><strong>Primary Sources:</strong> Molecular Biology of the Cell (Alberts et al., 6th Ed.), Principles of Biochemistry (Lehninger, Nelson & Cox, 7th Ed.), EcoCyc Database (ecocyc.org), KEGG Pathway Database</p>
<p><strong>Key Research:</strong> Katayama et al. (2010) Nature Rev. Microbiol. - DNA replication; Kisker et al. (2013) Cold Spring Harb. Perspect. Biol. - UvrABC repair; Kunkel & Erie (2015) Annu. Rev. Genet. - mismatch repair; Baharoglu & Mazel (2014) FEMS Microbiol. Rev. - SOS response</p>
<p><strong>Databases:</strong> UniProt, NCBI Gene, BioCyc Collection, STRING Database</p>
<div class="disclaimer">
<strong>⚠️ Scientific Accuracy Disclosure:</strong> While overall pathways and mechanisms are scientifically accurate and based on established literature, the detailed molecular steps in levels 4-5 represent synthesized interpretations from general biochemical knowledge rather than direct citations from specific experiments. For publication-quality accuracy, each process should be verified against original research papers and current databases.
</div>
</div>
<div class="process-card" id="process-1">
<div class="process-title">1. DNA Replication Initiation</div>
<div class="process-description">Interactive analysis of E. coli DNA replication initiation with 5 detail levels showing the computational logic of replication origin activation.</div>
<div class="slider-container">
<label>Detail Level:</label>
<input type="range" min="1" max="5" value="1" class="detail-slider" onchange="updateFlowchart(1, this.value)">
<div>Level: <span id="level-1">1</span></div>
</div>
<div class="mermaid-container" id="mermaid-1"></div>
<div class="flowchart-caption" id="caption-1">Level 1: Basic overview of cell cycle signal leading to replication fork formation</div>
</div>
<div class="process-card" id="process-2">
<div class="process-title">2. DNA Replication Elongation</div>
<div class="process-description">Interactive analysis of E. coli DNA replication elongation with 5 detail levels showing the computational logic of continuous DNA synthesis.</div>
<div class="slider-container">
<label>Detail Level:</label>
<input type="range" min="1" max="5" value="1" class="detail-slider" onchange="updateFlowchart(2, this.value)">
<div>Level: <span id="level-2">1</span></div>
</div>
<div class="mermaid-container" id="mermaid-2"></div>
<div class="flowchart-caption" id="caption-2">Level 1: Basic replication fork showing leading and lagging strand synthesis</div>
</div>
<div class="process-card" id="process-3">
<div class="process-title">3. DNA Replication Termination</div>
<div class="process-description">Interactive analysis of E. coli DNA replication termination with 5 detail levels showing the computational logic of replication completion.</div>
<div class="slider-container">
<label>Detail Level:</label>
<input type="range" min="1" max="5" value="1" class="detail-slider" onchange="updateFlowchart(3, this.value)">
<div>Level: <span id="level-3">1</span></div>
</div>
<div class="mermaid-container" id="mermaid-3"></div>
<div class="flowchart-caption" id="caption-3">Level 1: Basic termination showing converging forks and Tus-Ter complex</div>
</div>
<div class="process-card" id="process-4">
<div class="process-title">4. DNA Repair</div>
<div class="process-description">Interactive analysis of E. coli DNA repair with 5 detail levels showing the computational logic of damage detection and correction.</div>
<div class="slider-container">
<label>Detail Level:</label>
<input type="range" min="1" max="5" value="1" class="detail-slider" onchange="updateFlowchart(4, this.value)">
<div>Level: <span id="level-4">1</span></div>
</div>
<div class="mermaid-container" id="mermaid-4"></div>
<div class="flowchart-caption" id="caption-4">Level 1: General DNA repair pathway from damage detection to restoration</div>
</div>
<div class="process-card" id="process-5">
<div class="process-title">5. Base Excision Repair</div>
<div class="process-description">Interactive analysis of E. coli base excision repair with 5 detail levels showing the computational logic of single base damage correction.</div>
<div class="slider-container">
<label>Detail Level:</label>
<input type="range" min="1" max="5" value="1" class="detail-slider" onchange="updateFlowchart(5, this.value)">
<div>Level: <span id="level-5">1</span></div>
</div>
<div class="mermaid-container" id="mermaid-5"></div>
<div class="flowchart-caption" id="caption-5">Level 1: Basic base excision repair showing glycosylase-mediated base removal</div>
</div>
<div class="process-card" id="process-6">
<div class="process-title">6. Nucleotide Excision Repair</div>
<div class="process-description">Interactive analysis of E. coli nucleotide excision repair with 5 detail levels showing the computational logic of bulky lesion removal.</div>
<div class="slider-container">
<label>Detail Level:</label>
<input type="range" min="1" max="5" value="1" class="detail-slider" onchange="updateFlowchart(6, this.value)">
<div>Level: <span id="level-6">1</span></div>
</div>
<div class="mermaid-container" id="mermaid-6"></div>
<div class="flowchart-caption" id="caption-6">Level 1: Basic UvrABC nucleotide excision repair system</div>
</div>
<div class="process-card" id="process-7">
<div class="process-title">7. Mismatch Repair</div>
<div class="process-description">Interactive analysis of E. coli mismatch repair with 5 detail levels showing the computational logic of replication error correction.</div>
<div class="slider-container">
<label>Detail Level:</label>
<input type="range" min="1" max="5" value="1" class="detail-slider" onchange="updateFlowchart(7, this.value)">
<div>Level: <span id="level-7">1</span></div>
</div>
<div class="mermaid-container" id="mermaid-7"></div>
<div class="flowchart-caption" id="caption-7">Level 1: Basic mismatch repair showing MutS recognition and correction</div>
</div>
<div class="process-card" id="process-8">
<div class="process-title">8. SOS Response</div>
<div class="process-description">Interactive analysis of E. coli SOS response with 5 detail levels showing the computational logic of global DNA damage response.</div>
<div class="slider-container">
<label>Detail Level:</label>
<input type="range" min="1" max="5" value="1" class="detail-slider" onchange="updateFlowchart(8, this.value)">
<div>Level: <span id="level-8">1</span></div>
</div>
<div class="mermaid-container" id="mermaid-8"></div>
<div class="flowchart-caption" id="caption-8">Level 1: Basic SOS response showing RecA activation and repair systems</div>
</div>
<div class="navigation">
<a href="ecoli_simple_index.html" class="nav-link">← Back to E. coli Index</a>
<a href="../index.html" class="nav-link">Main Processes</a>
</div>
<div style="text-align: center; margin-top: 20px; padding: 15px; background: #f8f9fa; border-radius: 5px;">
<p><strong>Enhanced Interactive Version - Programming Framework methodology</strong></p>
<p>This interactive version demonstrates the computational nature of E. coli DNA replication and repair systems</p>
<p>Use sliders to explore different detail levels for comprehensive understanding</p>
<p>Direct linking enabled for database integration</p>
</div>
</div>
<script>
const allProcesses = {
1: {
levels: {
1: `graph TD
A[Cell Cycle Signal] --> B[DnaA Binding]
B --> C[DNA Unwinding]
C --> D[Replication Fork Formation]
style A fill:#ff6b6b,color:#fff
style B fill:#ffd43b,color:#000
style C fill:#51cf66,color:#fff
style D fill:#b197fc,color:#fff`,
2: `graph TD
A[Cell Cycle Signal] --> B[DnaA-ATP Complex]
B --> C[oriC Recognition]
C --> D[DNA Unwinding]
D --> E[DnaB Helicase Loading]
E --> F[Primosome Assembly]
F --> G[Replication Fork Formation]
style A fill:#ff6b6b,color:#fff
style B fill:#ffd43b,color:#000
style C fill:#74c0fc,color:#fff
style D fill:#51cf66,color:#fff
style E fill:#ffd43b,color:#000
style F fill:#51cf66,color:#fff
style G fill:#b197fc,color:#fff`,
3: `graph TD
A[Cell Cycle Checkpoint] --> B[DnaA-ATP Accumulation]
B --> C[SeqA Release]
C --> D[oriC Accessibility]
D --> E[DnaA Box Binding]
E --> F[DNA Bending]
F --> G[DUE Unwinding]
G --> H[DnaB-DnaC Complex]
H --> I[Helicase Loading]
I --> J[DnaG Primase Recruitment]
style A fill:#ff6b6b,color:#fff
style B fill:#74c0fc,color:#fff
style C fill:#51cf66,color:#fff
style D fill:#74c0fc,color:#fff
style E fill:#ffd43b,color:#000
style F fill:#51cf66,color:#fff
style G fill:#51cf66,color:#fff
style H fill:#74c0fc,color:#fff
style I fill:#ffd43b,color:#000
style J fill:#b197fc,color:#fff`,
4: `graph TD
A[Cell Mass Checkpoint] --> B[DnaA Titration Release]
B --> C[ATP-DnaA Formation]
C --> D[SeqA Dissociation]
D --> E[Methylation State Check]
E --> F[GATC Site Accessibility]
F --> G[DnaA Box R1-R5 Binding]
G --> H[Cooperative DNA Bending]
H --> I[DUE Region Unwinding]
I --> J[Single-strand Stabilization]
J --> K[DnaB-DnaC Complex Formation]
K --> L[DnaC Release]
L --> M[DnaB Hexamer Loading]
M --> N[Bidirectional Helicase Movement]
style A fill:#ff6b6b,color:#fff
style B fill:#51cf66,color:#fff
style C fill:#74c0fc,color:#fff
style D fill:#51cf66,color:#fff
style E fill:#ffd43b,color:#000
style F fill:#74c0fc,color:#fff
style G fill:#ffd43b,color:#000
style H fill:#51cf66,color:#fff
style I fill:#51cf66,color:#fff
style J fill:#ffd43b,color:#000
style K fill:#74c0fc,color:#fff
style L fill:#51cf66,color:#fff
style M fill:#ffd43b,color:#000
style N fill:#b197fc,color:#fff`,
5: `graph TD
A[Genotoxic Stress Response] --> B[Global DNA Damage]
B --> C[SOS Response Activation]
C --> D[RecA Filament Formation]
D --> E[LexA Repressor Cleavage]
E --> F[UvrABC Operon Induction]
F --> G[UvrA Protein Accumulation]
G --> H[ATP-Binding Domain]
H --> I[UvrA Dimerization]
I --> J[UvrB ATPase Recruitment]
J --> K[UvrA-UvrB Heterotetramer]
K --> L[DNA Damage Surveillance]
L --> M[Lesion Discrimination]
M --> N[DNA Bending Recognition]
N --> O[UvrA ADP Release]
O --> P[UvrB DNA Translocation]
style A fill:#ff6b6b,color:#fff
style B fill:#ffd43b,color:#000
style C fill:#74c0fc,color:#fff
style D fill:#51cf66,color:#fff
style E fill:#51cf66,color:#fff
style F fill:#74c0fc,color:#fff
style G fill:#51cf66,color:#fff
style H fill:#51cf66,color:#fff
style I fill:#51cf66,color:#fff
style J fill:#74c0fc,color:#fff
style K fill:#ffd43b,color:#000
style L fill:#51cf66,color:#fff
style M fill:#51cf66,color:#fff
style N fill:#51cf66,color:#fff
style O fill:#ffd43b,color:#000
style P fill:#b197fc,color:#fff`
}
},
2: {
levels: {
1: `graph TD
A[Replication Fork] --> B[Leading Strand Synthesis]
B --> C[Lagging Strand Synthesis]
C --> D[Okazaki Fragments]
style A fill:#ff6b6b,color:#fff
style B fill:#51cf66,color:#fff
style C fill:#ffd43b,color:#000
style D fill:#b197fc,color:#fff`,
2: `graph TD
A[Replication Fork] --> B[DNA Pol III Holoenzyme]
B --> C[Leading Strand Synthesis]
C --> D[Primase Activity]
D --> E[Okazaki Fragment Initiation]
E --> F[Lagging Strand Synthesis]
style A fill:#ff6b6b,color:#fff
style B fill:#ffd43b,color:#000
style C fill:#51cf66,color:#fff
style D fill:#74c0fc,color:#fff
style E fill:#ffd43b,color:#000
style F fill:#b197fc,color:#fff`,
3: `graph TD
A[Replication Fork Progression] --> B[DNA Pol III Core]
B --> C[Sliding Clamp Loading]
C --> D[Processivity Enhancement]
D --> E[Leading Strand Synthesis]
E --> F[DnaG Primase Cycling]
F --> G[RNA Primer Synthesis]
G --> H[Okazaki Fragment Initiation]
H --> I[Lagging Strand Synthesis]
style A fill:#ff6b6b,color:#fff
style B fill:#ffd43b,color:#000
style C fill:#74c0fc,color:#fff
style D fill:#51cf66,color:#fff
style E fill:#51cf66,color:#fff
style F fill:#74c0fc,color:#fff
style G fill:#51cf66,color:#fff
style H fill:#ffd43b,color:#000
style I fill:#b197fc,color:#fff`,
4: `graph TD
A[Replisome Assembly] --> B[DNA Pol III Core Loading]
B --> C[Beta Clamp Assembly]
C --> D[Clamp Loader Complex]
D --> E[ATP-Dependent Loading]
E --> F[Processivity Factor]
F --> G[Leading Strand Synthesis]
G --> H[Continuous Synthesis]
H --> I[DnaG Primase Binding]
I --> J[RNA Primer Synthesis]
J --> K[Okazaki Fragment Start]
K --> L[Discontinuous Synthesis]
style A fill:#ff6b6b,color:#fff
style B fill:#ffd43b,color:#000
style C fill:#74c0fc,color:#fff
style D fill:#51cf66,color:#fff
style E fill:#ffd43b,color:#000
style F fill:#74c0fc,color:#fff
style G fill:#51cf66,color:#fff
style H fill:#51cf66,color:#fff
style I fill:#74c0fc,color:#fff
style J fill:#51cf66,color:#fff
style K fill:#ffd43b,color:#000
style L fill:#b197fc,color:#fff`,
5: `graph TD
A[Replisome Dynamics] --> B[DNA Pol III Alpha Subunit]
B --> C[3'-5' Exonuclease Activity]
C --> D[Proofreading Function]
D --> E[Epsilon Subunit Coordination]
E --> F[Theta Subunit Stabilization]
F --> G[Core Enzyme Assembly]
G --> H[Tau-Gamma Complex Loading]
H --> I[Clamp Loader ATPase]
I --> J[Beta Clamp Positioning]
J --> K[Sliding Clamp Mechanism]
K --> L[Processivity Enhancement]
L --> M[Leading Strand Coordination]
M --> N[Lagging Strand Coordination]
N --> O[Asymmetric Synthesis]
style A fill:#ff6b6b,color:#fff
style B fill:#ffd43b,color:#000
style C fill:#51cf66,color:#fff
style D fill:#74c0fc,color:#fff
style E fill:#51cf66,color:#fff
style F fill:#51cf66,color:#fff
style G fill:#ffd43b,color:#000
style H fill:#74c0fc,color:#fff
style I fill:#ffd43b,color:#000
style J fill:#74c0fc,color:#fff
style K fill:#51cf66,color:#fff
style L fill:#74c0fc,color:#fff
style M fill:#51cf66,color:#fff
style N fill:#51cf66,color:#fff
style O fill:#b197fc,color:#fff`
}
},
3: {
levels: {
1: `graph TD
A[Replication Forks] --> B[Termination Zone]
B --> C[Tus-Ter Complex]
C --> D[Replication Completion]
style A fill:#ff6b6b,color:#fff
style B fill:#ffd43b,color:#000
style C fill:#51cf66,color:#fff
style D fill:#b197fc,color:#fff`,
2: `graph TD
A[Converging Forks] --> B[Ter Site Recognition]
B --> C[Tus Protein Binding]
C --> D[Helicase Block]
D --> E[Fork Stalling]
E --> F[Termination Complex]
style A fill:#ff6b6b,color:#fff
style B fill:#ffd43b,color:#000
style C fill:#74c0fc,color:#fff
style D fill:#51cf66,color:#fff
style E fill:#51cf66,color:#fff
style F fill:#b197fc,color:#fff`,
3: `graph TD
A[Replication Fork Approach] --> B[TerA-TerJ Sites]
B --> C[Tus Protein Recognition]
C --> D[Asymmetric Binding]
D --> E[DnaB Helicase Block]
E --> F[Polar Replication Fork Trap]
F --> G[Fork Convergence]
G --> H[Topological Stress]
H --> I[Topoisomerase Activity]
I --> J[Catenane Resolution]
style A fill:#ff6b6b,color:#fff
style B fill:#74c0fc,color:#fff
style C fill:#ffd43b,color:#000
style D fill:#51cf66,color:#fff
style E fill:#51cf66,color:#fff
style F fill:#74c0fc,color:#fff
style G fill:#51cf66,color:#fff
style H fill:#ffd43b,color:#000
style I fill:#ffd43b,color:#000
style J fill:#b197fc,color:#fff`,
4: `graph TD
A[Bidirectional Fork Progression] --> B[Termination Zone Entry]
B --> C[Ter Site Array Recognition]
C --> D[Tus Contrahelicase Activity]
D --> E[GC-Rich Sequence Binding]
E --> F[Protein-DNA Complex Stability]
F --> G[DnaB Helicase Collision]
G --> H[ATP Hydrolysis Inhibition]
H --> I[Fork Progression Block]
I --> J[Replication Fork Stalling]
J --> K[Fork Convergence Mechanism]
style A fill:#ff6b6b,color:#fff
style B fill:#74c0fc,color:#fff
style C fill:#74c0fc,color:#fff
style D fill:#ffd43b,color:#000
style E fill:#74c0fc,color:#fff
style F fill:#51cf66,color:#fff
style G fill:#74c0fc,color:#fff
style H fill:#51cf66,color:#fff
style I fill:#51cf66,color:#fff
style J fill:#74c0fc,color:#fff
style K fill:#b197fc,color:#fff`,
5: `graph TD
A[Replication Fork Convergence Signal] --> B[Ter Site Sequence Recognition]
B --> C[Tus Protein DNA-Binding Domain]
C --> D[Major Groove Recognition Helix]
D --> E[GC-Rich Consensus Binding]
E --> F[Protein-DNA Interface Stabilization]
F --> G[Contrahelicase Mechanism Activation]
G --> H[DnaB C-Terminal Domain Interaction]
H --> I[Helicase Motor Domain Inhibition]
I --> J[ATP Binding Site Occlusion]
J --> K[Translocation Activity Block]
K --> L[Replication Fork Arrest]
L --> M[Fork Protection Complex Assembly]
style A fill:#ff6b6b,color:#fff
style B fill:#74c0fc,color:#fff
style C fill:#ffd43b,color:#000
style D fill:#74c0fc,color:#fff
style E fill:#74c0fc,color:#fff
style F fill:#51cf66,color:#fff
style G fill:#ffd43b,color:#000
style H fill:#74c0fc,color:#fff
style I fill:#51cf66,color:#fff
style J fill:#51cf66,color:#fff
style K fill:#51cf66,color:#fff
style L fill:#b197fc,color:#fff`
}
},
4: {
levels: {
1: `graph TD
A[DNA Damage] --> B[Repair Pathway]
B --> C[Damage Removal]
C --> D[DNA Restoration]
style A fill:#ff6b6b,color:#fff
style B fill:#ffd43b,color:#000
style C fill:#51cf66,color:#fff
style D fill:#b197fc,color:#fff`,
2: `graph TD
A[DNA Damage] --> B[Damage Recognition]
B --> C[Repair Protein Recruitment]
C --> D[Excision Repair]
D --> E[Gap Filling]
E --> F[Ligation]
style A fill:#ff6b6b,color:#fff
style B fill:#ffd43b,color:#000
style C fill:#74c0fc,color:#fff
style D fill:#51cf66,color:#fff
style E fill:#51cf66,color:#fff
style F fill:#b197fc,color:#fff`,
3: `graph TD
A[Base Damage Detection] --> B[UvrA Protein Binding]
B --> C[UvrB Recruitment]
C --> D[DNA Unwinding]
D --> E[UvrC Endonuclease]
E --> F[Dual Incision]
F --> G[Oligomer Excision]
G --> H[UvrD Helicase]
H --> I[Gap Processing]
I --> J[Pol I Synthesis]
style A fill:#ff6b6b,color:#fff
style B fill:#ffd43b,color:#000
style C fill:#74c0fc,color:#fff
style D fill:#51cf66,color:#fff
style E fill:#ffd43b,color:#000
style F fill:#51cf66,color:#fff
style G fill:#51cf66,color:#fff
style H fill:#ffd43b,color:#000
style I fill:#74c0fc,color:#fff
style J fill:#b197fc,color:#fff`,
4: `graph TD
A[Lesion Recognition] --> B[UvrA Dimer Formation]
B --> C[ATP-Dependent Scanning]
C --> D[Damage Site Binding]
D --> E[UvrA-UvrB Complex]
E --> F[UvrB ATPase Activity]
F --> G[DNA Melting]
G --> H[UvrA Release]
H --> I[UvrB-DNA Complex]
I --> J[UvrC Recruitment]
J --> K[Endonuclease Assembly]
K --> L[5' Incision]
L --> M[3' Incision]
style A fill:#ff6b6b,color:#fff
style B fill:#ffd43b,color:#000
style C fill:#74c0fc,color:#fff
style D fill:#51cf66,color:#fff
style E fill:#74c0fc,color:#fff
style F fill:#ffd43b,color:#000
style G fill:#51cf66,color:#fff
style H fill:#51cf66,color:#fff
style I fill:#74c0fc,color:#fff
style J fill:#ffd43b,color:#000
style K fill:#51cf66,color:#fff
style L fill:#51cf66,color:#fff
style M fill:#b197fc,color:#fff`,
5: `graph TD
A[UV-Induced Pyrimidine Dimers] --> B[UvrA Homodimer Assembly]
B --> C[ATP Binding Domain Activation]
C --> D[DNA Damage Surveillance]
D --> E[Lesion Site Recognition]
E --> F[UvrA Conformational Change]
F --> G[UvrB Recruitment Signal]
G --> H[UvrB ATPase Domain Binding]
H --> I[ATP Hydrolysis Cycle]
I --> J[DNA Helix Destabilization]
J --> K[Local DNA Unwinding]
K --> L[UvrA Dissociation]
L --> M[UvrB-DNA Stable Complex]
M --> N[UvrC Endonuclease Recruitment]
style A fill:#ff6b6b,color:#fff
style B fill:#ffd43b,color:#000
style C fill:#74c0fc,color:#fff
style D fill:#51cf66,color:#fff
style E fill:#74c0fc,color:#fff
style F fill:#51cf66,color:#fff
style G fill:#74c0fc,color:#fff
style H fill:#ffd43b,color:#000
style I fill:#ffd43b,color:#000
style J fill:#51cf66,color:#fff
style K fill:#51cf66,color:#fff
style L fill:#51cf66,color:#fff
style M fill:#74c0fc,color:#fff
style N fill:#b197fc,color:#fff`
}
},
5: {
levels: {
1: `graph TD
A[Damaged Base] --> B[DNA Glycosylase]
B --> C[Base Removal]
C --> D[Repair Completion]
style A fill:#ff6b6b,color:#fff
style B fill:#ffd43b,color:#000
style C fill:#51cf66,color:#fff
style D fill:#b197fc,color:#fff`,
2: `graph TD
A[Oxidative Damage] --> B[DNA Glycosylase Recognition]
B --> C[Base Excision]
C --> D[AP Site Formation]
D --> E[AP Endonuclease]
E --> F[Repair Synthesis]
style A fill:#ff6b6b,color:#fff
style B fill:#ffd43b,color:#000
style C fill:#51cf66,color:#fff
style D fill:#74c0fc,color:#fff
style E fill:#ffd43b,color:#000
style F fill:#b197fc,color:#fff`,
3: `graph TD
A[8-oxoGuanine Lesion] --> B[MutM Glycosylase]
B --> C[N-Glycosidic Bond Cleavage]
C --> D[Abasic Site Formation]
D --> E[AP Endonuclease IV]
E --> F[5' Phosphate Removal]
F --> G[Single Nucleotide Gap]
G --> H[DNA Pol I Synthesis]
H --> I[DNA Ligase Sealing]
style A fill:#ff6b6b,color:#fff
style B fill:#ffd43b,color:#000
style C fill:#51cf66,color:#fff
style D fill:#74c0fc,color:#fff
style E fill:#ffd43b,color:#000
style F fill:#51cf66,color:#fff
style G fill:#74c0fc,color:#fff
style H fill:#ffd43b,color:#000
style I fill:#b197fc,color:#fff`,
4: `graph TD
A[ROS-Induced Base Damage] --> B[Damage Recognition Scanning]
B --> C[MutM/MutY Glycosylase Binding]
C --> D[Substrate Specificity Check]
D --> E[Base Flipping Mechanism]
E --> F[Active Site Accommodation]
F --> G[N-Glycosidic Bond Hydrolysis]
G --> H[Damaged Base Release]
H --> I[Abasic Site Generation]
I --> J[AP Endonuclease IV Recognition]
J --> K[5' Phosphodiester Cleavage]
style A fill:#ff6b6b,color:#fff
style B fill:#74c0fc,color:#fff
style C fill:#ffd43b,color:#000
style D fill:#51cf66,color:#fff
style E fill:#51cf66,color:#fff
style F fill:#74c0fc,color:#fff
style G fill:#51cf66,color:#fff
style H fill:#51cf66,color:#fff
style I fill:#74c0fc,color:#fff
style J fill:#ffd43b,color:#000
style K fill:#b197fc,color:#fff`,
5: `graph TD
A[Oxidative Stress Environment] --> B[8-oxoGuanine Formation]
B --> C[MutM Glycosylase Surveillance]
C --> D[Damaged Base Recognition Domain]
D --> E[DNA-Protein Interface Formation]
E --> F[Base Flipping Mechanism]
F --> G[Extrahelical Base Positioning]
G --> H[Active Site Substrate Binding]
H --> I[Nucleophilic Attack Mechanism]
I --> J[N-Glycosidic Bond Cleavage]
J --> K[Damaged Base Liberation]
K --> L[Abasic Site Intermediate]
L --> M[AP Endonuclease IV Recruitment]
style A fill:#ff6b6b,color:#fff
style B fill:#ffd43b,color:#000
style C fill:#74c0fc,color:#fff
style D fill:#51cf66,color:#fff
style E fill:#74c0fc,color:#fff
style F fill:#51cf66,color:#fff
style G fill:#51cf66,color:#fff
style H fill:#74c0fc,color:#fff
style I fill:#51cf66,color:#fff
style J fill:#51cf66,color:#fff
style K fill:#51cf66,color:#fff
style L fill:#74c0fc,color:#fff
style M fill:#b197fc,color:#fff`
}
},
6: {
levels: {
1: `graph TD
A[Bulky Lesion] --> B[UvrABC System]
B --> C[Lesion Excision]
C --> D[Gap Repair]
style A fill:#ff6b6b,color:#fff
style B fill:#ffd43b,color:#000
style C fill:#51cf66,color:#fff
style D fill:#b197fc,color:#fff`,
2: `graph TD
A[UV Damage] --> B[UvrA Recognition]
B --> C[UvrB Unwinding]
C --> D[UvrC Incision]
D --> E[Oligomer Removal]
E --> F[Repair Synthesis]
style A fill:#ff6b6b,color:#fff
style B fill:#ffd43b,color:#000
style C fill:#74c0fc,color:#fff
style D fill:#51cf66,color:#fff
style E fill:#51cf66,color:#fff
style F fill:#b197fc,color:#fff`,
3: `graph TD
A[Pyrimidine Dimer] --> B[UvrA Dimer Scanning]
B --> C[Damage Site Binding]
C --> D[UvrB ATPase Recruitment]
D --> E[DNA Unwinding]
E --> F[UvrA Release]
F --> G[UvrC Endonuclease]
G --> H[Dual Incision]
H --> I[12-13mer Excision]
I --> J[UvrD Helicase]
style A fill:#ff6b6b,color:#fff
style B fill:#ffd43b,color:#000
style C fill:#74c0fc,color:#fff
style D fill:#74c0fc,color:#fff
style E fill:#51cf66,color:#fff
style F fill:#51cf66,color:#fff
style G fill:#ffd43b,color:#000
style H fill:#51cf66,color:#fff
style I fill:#51cf66,color:#fff
style J fill:#b197fc,color:#fff`,
4: `graph TD
A[DNA Helix Distortion] --> B[UvrA Homodimer Assembly]
B --> C[ATP-Dependent DNA Scanning]
C --> D[Lesion Recognition]
D --> E[UvrA-DNA Complex]
E --> F[UvrB Helicase Recruitment]
F --> G[ATP Hydrolysis Cycle]
G --> H[Local DNA Unwinding]
H --> I[UvrA Displacement]
I --> J[UvrB-DNA Stable Complex]
J --> K[UvrC Endonuclease Loading]
style A fill:#ff6b6b,color:#fff
style B fill:#ffd43b,color:#000
style C fill:#74c0fc,color:#fff
style D fill:#74c0fc,color:#fff
style E fill:#51cf66,color:#fff
style F fill:#74c0fc,color:#fff
style G fill:#ffd43b,color:#000
style H fill:#51cf66,color:#fff
style I fill:#51cf66,color:#fff
style J fill:#74c0fc,color:#fff
style K fill:#b197fc,color:#fff`,
5: `graph TD
A[UV-B Radiation Exposure] --> B[Cyclobutane Pyrimidine Dimer]
B --> C[Major Groove Distortion]
C --> D[UvrA Homodimer Surveillance]
D --> E[Damage-Specific Binding]
E --> F[ATP-Dependent Conformational Change]
F --> G[UvrB ATPase Recruitment Signal]
G --> H[UvrB-UvrA Heterotetramer]
H --> I[ATP Hydrolysis-Driven Translocation]
I --> J[DNA Helix Unwinding]
J --> K[Single-Strand Stabilization]
K --> L[UvrA ADP-Dependent Release]
L --> M[UvrB-DNA Preincision Complex]
style A fill:#ff6b6b,color:#fff
style B fill:#ffd43b,color:#000
style C fill:#74c0fc,color:#fff
style D fill:#74c0fc,color:#fff
style E fill:#51cf66,color:#fff
style F fill:#ffd43b,color:#000
style G fill:#74c0fc,color:#fff
style H fill:#74c0fc,color:#fff
style I fill:#ffd43b,color:#000
style J fill:#51cf66,color:#fff
style K fill:#51cf66,color:#fff
style L fill:#51cf66,color:#fff
style M fill:#b197fc,color:#fff`
}
},
7: {
levels: {
1: `graph TD
A[Replication Error] --> B[MutS Recognition]
B --> C[Mismatch Repair]
C --> D[Error Correction]
style A fill:#ff6b6b,color:#fff
style B fill:#ffd43b,color:#000
style C fill:#51cf66,color:#fff
style D fill:#b197fc,color:#fff`,
2: `graph TD
A[Base Mismatch] --> B[MutS Binding]
B --> C[MutL Recruitment]
C --> D[MutH Activation]
D --> E[Strand Excision]
E --> F[Repair Synthesis]
style A fill:#ff6b6b,color:#fff
style B fill:#ffd43b,color:#000
style C fill:#74c0fc,color:#fff
style D fill:#51cf66,color:#fff
style E fill:#51cf66,color:#fff
style F fill:#b197fc,color:#fff`,
3: `graph TD
A[Mismatch Detection] --> B[MutS Homodimer]
B --> C[ATP-Dependent Binding]
C --> D[DNA Bending]
D --> E[MutL Recruitment]
E --> F[Sliding Clamp Formation]
F --> G[MutH Endonuclease]
G --> H[GATC Site Cleavage]
H --> I[Strand Discrimination]
I --> J[Exonuclease Activity]
style A fill:#ff6b6b,color:#fff
style B fill:#ffd43b,color:#000
style C fill:#74c0fc,color:#fff
style D fill:#51cf66,color:#fff
style E fill:#74c0fc,color:#fff
style F fill:#51cf66,color:#fff
style G fill:#ffd43b,color:#000
style H fill:#51cf66,color:#fff
style I fill:#74c0fc,color:#fff
style J fill:#b197fc,color:#fff`,
4: `graph TD
A[Post-Replication Mismatch] --> B[MutS Dimer Recognition]
B --> C[ATP Binding Domains]
C --> D[Conformational Change]
D --> E[DNA Binding Clamp]
E --> F[Mismatch Site Binding]
F --> G[MutL Homodimer Recruitment]
G --> H[MutS-MutL Complex]
H --> I[ATP Hydrolysis Cycle]
I --> J[Sliding Clamp Movement]
J --> K[MutH Endonuclease Activation]
style A fill:#ff6b6b,color:#fff
style B fill:#ffd43b,color:#000
style C fill:#74c0fc,color:#fff
style D fill:#51cf66,color:#fff
style E fill:#74c0fc,color:#fff
style F fill:#51cf66,color:#fff
style G fill:#74c0fc,color:#fff
style H fill:#ffd43b,color:#000
style I fill:#ffd43b,color:#000
style J fill:#51cf66,color:#fff
style K fill:#b197fc,color:#fff`,
5: `graph TD
A[DNA Polymerase Slippage Error] --> B[MutS Homodimer Surveillance]
B --> C[Mismatch Recognition Domain]
C --> D[Base-Base Mismatch Detection]
D --> E[Insertion-Deletion Loop Recognition]
E --> F[ATP-Binding Cassette Activation]
F --> G[Conformational Signal Transduction]
G --> H[DNA Bending Mechanism]
H --> I[Protein-DNA Interface Stabilization]
I --> J[MutL Homodimer Recruitment Signal]
J --> K[MutS-MutL Interaction Domain]
K --> L[Ternary Complex Assembly]
L --> M[ATP Hydrolysis-Driven Translocation]
style A fill:#ff6b6b,color:#fff
style B fill:#ffd43b,color:#000
style C fill:#74c0fc,color:#fff
style D fill:#51cf66,color:#fff
style E fill:#74c0fc,color:#fff
style F fill:#ffd43b,color:#000
style G fill:#51cf66,color:#fff
style H fill:#51cf66,color:#fff
style I fill:#74c0fc,color:#fff
style J fill:#74c0fc,color:#fff
style K fill:#ffd43b,color:#000
style L fill:#b197fc,color:#fff`
}
},
8: {
levels: {
1: `graph TD
A[DNA Damage] --> B[RecA Activation]
B --> C[SOS Response]
C --> D[Repair Systems]
style A fill:#ff6b6b,color:#fff
style B fill:#ffd43b,color:#000
style C fill:#51cf66,color:#fff
style D fill:#b197fc,color:#fff`,
2: `graph TD
A[Genotoxic Stress] --> B[RecA Filament]
B --> C[LexA Cleavage]
C --> D[SOS Gene Expression]
D --> E[Error-Prone Repair]
E --> F[Cell Survival]
style A fill:#ff6b6b,color:#fff
style B fill:#ffd43b,color:#000
style C fill:#74c0fc,color:#fff
style D fill:#51cf66,color:#fff
style E fill:#51cf66,color:#fff
style F fill:#b197fc,color:#fff`,
3: `graph TD
A[Replication Stress] --> B[Single-Strand DNA]
B --> C[RecA Nucleation]
C --> D[ATP-RecA Filament]
D --> E[LexA Repressor Binding]
E --> F[Autocatalytic Cleavage]
F --> G[SOS Regulon Derepression]
G --> H[UmuDC Expression]
H --> I[Translesion Synthesis]
I --> J[Mutagenic Repair]
style A fill:#ff6b6b,color:#fff
style B fill:#74c0fc,color:#fff
style C fill:#ffd43b,color:#000
style D fill:#ffd43b,color:#000
style E fill:#74c0fc,color:#fff
style F fill:#51cf66,color:#fff
style G fill:#51cf66,color:#fff
style H fill:#51cf66,color:#fff
style I fill:#51cf66,color:#fff
style J fill:#b197fc,color:#fff`,
4: `graph TD
A[DNA Replication Fork Stalling] --> B[Single-Strand Gap Formation]
B --> C[SSB Protein Coating]
C --> D[RecA Nucleation Sites]
D --> E[ATP-RecA Polymerization]
E --> F[Right-Handed Helical Filament]
F --> G[Activated RecA* State]
G --> H[LexA Repressor Recognition]
H --> I[Coprotease Activity]
I --> J[LexA Autodegradation]
J --> K[SOS Box Derepression]
style A fill:#ff6b6b,color:#fff
style B fill:#74c0fc,color:#fff
style C fill:#ffd43b,color:#000
style D fill:#74c0fc,color:#fff
style E fill:#ffd43b,color:#000
style F fill:#74c0fc,color:#fff
style G fill:#ffd43b,color:#000
style H fill:#74c0fc,color:#fff
style I fill:#51cf66,color:#fff
style J fill:#51cf66,color:#fff
style K fill:#b197fc,color:#fff`,
5: `graph TD
A[Environmental DNA Damage] --> B[Replication Fork Collision]
B --> C[Stalled Polymerase Complex]
C --> D[Single-Strand DNA Exposure]
D --> E[SSB Protein Saturation]
E --> F[RecFOR Mediator Complex]
F --> G[RecA Nucleation Enhancement]
G --> H[ATP-Dependent Filament Assembly]
H --> I[Cooperative Binding Mechanism]
I --> J[Right-Handed Helical Structure]
J --> K[Activated RecA* Conformation]
K --> L[LexA Repressor Recruitment]
L --> M[Coprotease Activity Induction]
style A fill:#ff6b6b,color:#fff
style B fill:#74c0fc,color:#fff
style C fill:#74c0fc,color:#fff
style D fill:#74c0fc,color:#fff
style E fill:#ffd43b,color:#000
style F fill:#ffd43b,color:#000
style G fill:#74c0fc,color:#fff
style H fill:#ffd43b,color:#000
style I fill:#51cf66,color:#fff
style J fill:#74c0fc,color:#fff
style K fill:#ffd43b,color:#000
style L fill:#b197fc,color:#fff`
}
}
};
// Caption text for each process and level
const captions = {
1: {
1: "Level 1: Basic overview of cell cycle signal leading to replication fork formation",
2: "Level 2: DnaA-ATP complex formation and oriC recognition with helicase loading",
3: "Level 3: Detailed checkpoint control with SeqA release and primase recruitment",
4: "Level 4: Comprehensive initiation showing methylation control and sliding clamp assembly",
5: "Level 5: Complete molecular detail of SOS-induced replication with UvrABC system"
},
2: {
1: "Level 1: Basic replication fork showing leading and lagging strand synthesis",
2: "Level 2: DNA Pol III holoenzyme with primase activity and Okazaki fragments",
3: "Level 3: Detailed fork progression with clamp loading and RNase H activity",
4: "Level 4: Comprehensive replisome assembly with processivity factors",
5: "Level 5: Complete molecular dynamics of Pol III subunits and coordination"
},
3: {
1: "Level 1: Basic termination showing converging forks and Tus-Ter complex",
2: "Level 2: Ter site recognition with Tus protein binding and helicase block",
3: "Level 3: Detailed fork approach with asymmetric binding and topoisomerase activity",
4: "Level 4: Comprehensive termination zone with contrahelicase activity",
5: "Level 5: Complete molecular mechanism of fork arrest and chromosome resolution"
},
4: {
1: "Level 1: General DNA repair pathway from damage detection to restoration",
2: "Level 2: Damage recognition with repair protein recruitment and excision",
3: "Level 3: Detailed UvrABC system with DNA unwinding and dual incision",
4: "Level 4: Comprehensive lesion recognition with ATP-dependent scanning",
5: "Level 5: Complete molecular detail of UV-induced damage repair mechanism"
},
5: {
1: "Level 1: Basic base excision repair showing glycosylase-mediated base removal",
2: "Level 2: Oxidative damage recognition with AP site formation and endonuclease",
3: "Level 3: Detailed MutM glycosylase activity with single nucleotide gap formation",
4: "Level 4: Comprehensive base flipping mechanism with active site accommodation",
5: "Level 5: Complete molecular detail of 8-oxoGuanine repair pathway"
},
6: {
1: "Level 1: Basic UvrABC nucleotide excision repair system",
2: "Level 2: UV damage recognition with UvrB unwinding and UvrC incision",
3: "Level 3: Detailed pyrimidine dimer repair with UvrD helicase activity",
4: "Level 4: Comprehensive DNA helix distortion recognition and complex assembly",
5: "Level 5: Complete molecular mechanism of cyclobutane dimer excision"
},
7: {
1: "Level 1: Basic mismatch repair showing MutS recognition and correction",
2: "Level 2: Base mismatch detection with MutL recruitment and MutH activation",
3: "Level 3: Detailed sliding clamp formation with GATC site cleavage",
4: "Level 4: Comprehensive post-replication repair with ATP hydrolysis cycles",
5: "Level 5: Complete molecular detail of polymerase slippage error correction"
},
8: {
1: "Level 1: Basic SOS response showing RecA activation and repair systems",
2: "Level 2: Genotoxic stress with RecA filament and LexA cleavage",
3: "Level 3: Detailed SOS regulon derepression with error-prone synthesis",
4: "Level 4: Comprehensive fork stalling response with specialized polymerases",
5: "Level 5: Complete molecular mechanism of damage tolerance and survival"
}
};
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