convert this topic (biomolecules +bioenergetics) into a visually structured study sheet using tables ,flowchart,mindmaps,icons,and colour coded section make it easy too revise in 5 minutes

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~/biomolecules-bioenergetics/study_sheet.html

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<title>Biomolecules + Bioenergetics — 5-Minute Revision Sheet</title>
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</head>
<body>

<!-- ══════════════════════════════════════════════ HEADER ══ -->
<header>
  <h1>🧬 Biomolecules + Bioenergetics</h1>
  <p>Biochemistry Rapid Revision — Harper's & Lippincott Illustrated Reviews</p>
  <span class="badge">⚡ 5-Minute Revision Sheet</span>
</header>

<main>

<!-- ══════════════════════════════════════════════ SECTION 1: MIND MAP ══ -->
<section>
  <div class="section-title" style="color:#1a237e;border-color:#1a237e;">
    🧠 Section 1 — Big Picture Mind Map
  </div>

  <div class="mindmap">
    <div class="mm-grid">
      <!-- Top row -->
      <div class="mm-branch carb" style="color:var(--carb-h);">🍭 Carbohydrates<br/><span style="font-weight:400;font-size:10px;">Monosaccharides → Polysaccharides<br/>Energy source, cell signals</span></div>
      <div></div>
      <div class="mm-branch prot" style="color:var(--prot-h);">🧩 Proteins<br/><span style="font-weight:400;font-size:10px;">Amino acids → Polypeptides<br/>Structure, enzymes, transport</span></div>

      <!-- Lines row -->
      <div class="mm-line"></div>
      <div></div>
      <div class="mm-line"></div>

      <!-- Center row -->
      <div style="display:flex;flex-direction:column;align-items:flex-end;gap:16px;width:100%;">
        <div class="mm-branch lipid" style="color:var(--lipid-h);text-align:right;">🧈 Lipids<br/><span style="font-weight:400;font-size:10px;">FA, Triglycerides, Phospholipids<br/>Energy storage, membranes</span></div>
        <div class="mm-branch atp" style="color:var(--atp-h);text-align:right;">⚡ ATP &amp; Bioenergetics<br/><span style="font-weight:400;font-size:10px;">ΔG, Keq, Free Energy<br/>Coupled reactions</span></div>
      </div>
      <div>
        <div class="mm-center">BIOCHEMISTRY<br/>CORE</div>
      </div>
      <div style="display:flex;flex-direction:column;align-items:flex-start;gap:16px;width:100%;">
        <div class="mm-branch nucleic" style="color:var(--nucleic-h);">🔬 Nucleic Acids<br/><span style="font-weight:400;font-size:10px;">DNA &amp; RNA<br/>Purine / Pyrimidine bases</span></div>
        <div class="mm-branch etc" style="color:var(--etc-h);">🔋 ETC &amp; OXPHOS<br/><span style="font-weight:400;font-size:10px;">Complexes I–V<br/>32 ATP per glucose</span></div>
      </div>
    </div>
  </div>
</section>


<!-- ══════════════════════════════════════════════ SECTION 2: BIOMOLECULES TABLES ══ -->
<section>
  <div class="section-title" style="color:var(--carb-h);border-color:var(--carb-h);">
    🍬 Section 2 — Biomolecules at a Glance
  </div>

  <div class="grid2">

    <!-- Carbohydrates -->
    <div class="card carb">
      <div class="card-header carb-h"><span class="icon">🍭</span> Carbohydrates</div>
      <table class="tbl-carb">
        <tr><th>Type</th><th>Examples</th><th>Key Feature</th></tr>
        <tr><td><b>Monosaccharide</b></td><td>Glucose, Fructose, Galactose</td><td>Aldoses / Ketoses; reducing sugars</td></tr>
        <tr><td><b>Disaccharide</b></td><td>Sucrose, Lactose, Maltose</td><td>Glycosidic bond (α or β)</td></tr>
        <tr><td><b>Oligosaccharide</b></td><td>Raffinose, cell-surface oligosaccharides</td><td>3–10 monosaccharides</td></tr>
        <tr><td><b>Polysaccharide</b></td><td>Glycogen, Starch, Cellulose</td><td>α-1,4 (+ α-1,6 branches in glycogen)</td></tr>
      </table>
      <div class="remember r-green"><b>🟢 Remember:</b> Glucose is the primary fuel; brain is 100% glucose-dependent under normal conditions.</div>
    </div>

    <!-- Proteins -->
    <div class="card prot">
      <div class="card-header prot-h"><span class="icon">🧩</span> Proteins — Amino Acid Levels</div>
      <table class="tbl-prot">
        <tr><th>Level</th><th>Description</th><th>Forces</th></tr>
        <tr><td><b>1° (Primary)</b></td><td>AA sequence; peptide bonds</td><td>Covalent (peptide bond)</td></tr>
        <tr><td><b>2° (Secondary)</b></td><td>α-helix, β-sheet, turns</td><td>H-bonds along backbone</td></tr>
        <tr><td><b>3° (Tertiary)</b></td><td>Full 3D fold of polypeptide</td><td>H-bonds, Van der Waals, hydrophobic, disulfide</td></tr>
        <tr><td><b>4° (Quaternary)</b></td><td>Multiple subunits (e.g. Hb)</td><td>Same as 3°; no covalent bonds (mostly)</td></tr>
      </table>
      <div class="remember r-blue"><b>🔵 Key:</b> Hydrophobic AA cluster in protein interior; charged/polar AA on the surface in contact with water.</div>
    </div>

    <!-- Lipids -->
    <div class="card lipid">
      <div class="card-header lipid-h"><span class="icon">🧈</span> Lipids</div>
      <table class="tbl-lipid">
        <tr><th>Class</th><th>Components</th><th>Function</th></tr>
        <tr><td><b>Fatty Acids</b></td><td>Saturated / Unsaturated chains</td><td>Energy substrate (β-oxidation)</td></tr>
        <tr><td><b>Triglycerides</b></td><td>Glycerol + 3 FA</td><td>Long-term energy storage (adipose)</td></tr>
        <tr><td><b>Phospholipids</b></td><td>Glycerol + 2 FA + phosphate head</td><td>Membrane bilayer; amphipathic</td></tr>
        <tr><td><b>Cholesterol</b></td><td>Sterol ring</td><td>Membrane fluidity, precursor to steroids</td></tr>
        <tr><td><b>Sphingolipids</b></td><td>Sphingosine + FA</td><td>Cell signalling, myelin sheath</td></tr>
      </table>
      <div class="remember r-gold"><b>🟡 Key:</b> Phospholipids are amphipathic — hydrophilic head groups face water, hydrophobic tails cluster together.</div>
    </div>

    <!-- Nucleic Acids -->
    <div class="card nucleic">
      <div class="card-header nucleic-h"><span class="icon">🔬</span> Nucleic Acids</div>
      <table class="tbl-nuc">
        <tr><th>Feature</th><th>DNA</th><th>RNA</th></tr>
        <tr><td>Sugar</td><td>2'-Deoxyribose</td><td>Ribose</td></tr>
        <tr><td>Bases</td><td>A, T, G, C</td><td>A, U, G, C</td></tr>
        <tr><td>Structure</td><td>Double helix</td><td>Single strand</td></tr>
        <tr><td>Purines</td><td colspan="2">Adenine (A), Guanine (G) — double ring</td></tr>
        <tr><td>Pyrimidines</td><td colspan="2">Cytosine (C), Thymine/Uracil — single ring</td></tr>
        <tr><td>Bonds</td><td>A=T (2 H-bonds)</td><td>A=U (2 H-bonds)</td></tr>
        <tr><td></td><td>G≡C (3 H-bonds)</td><td>G≡C (3 H-bonds)</td></tr>
      </table>
      <div class="remember r-blue"><b>🔵 Mnemonic:</b> <b>PURe As Gold</b> = Purines: Adenine, Guanine. <b>CUT the PY</b> = Pyrimidines: Cytosine, Uracil, Thymine.</div>
    </div>

  </div><!-- end grid2 -->

  <!-- Bond energies quick reference -->
  <div style="margin-top:16px;">
    <div class="card" style="background:#fafafa;">
      <div class="card-header" style="background:#eceff1;color:#37474f;border-left:4px solid #607d8b;">
        <span class="icon">🔗</span> Covalent Bond Energies (Biological Significance)
      </div>
      <table>
        <tr><th style="background:#546e7a;color:#fff;">Bond</th><th style="background:#546e7a;color:#fff;">Energy (kcal/mol)</th><th style="background:#546e7a;color:#fff;">Bond</th><th style="background:#546e7a;color:#fff;">Energy (kcal/mol)</th><th style="background:#546e7a;color:#fff;">Biological Role</th></tr>
        <tr><td>O–O</td><td>34</td><td>C–H</td><td>99</td><td rowspan="4">Form backbone of organic molecules; peptide bond ~C–N</td></tr>
        <tr><td>S–S</td><td>51 <span class="chip chip-r">disulfide</span></td><td>C–S</td><td>108</td></tr>
        <tr><td>C–N</td><td>70</td><td>O–H</td><td>110</td></tr>
        <tr><td>N–H</td><td>94</td><td>C=O</td><td>164</td></tr>
      </table>
      <p style="font-size:11px;color:#555;margin-top:6px;">Non-covalent forces (H-bonds, Van der Waals, hydrophobic interactions) are weaker individually but collectively stabilize macromolecular structure.</p>
    </div>
  </div>
</section>


<!-- ══════════════════════════════════════════════ SECTION 3: BIOENERGETICS ══ -->
<section>
  <div class="section-title" style="color:var(--energy-h);border-color:var(--energy-h);">
    ⚡ Section 3 — Bioenergetics Core Concepts
  </div>

  <div class="grid3">

    <!-- Free energy -->
    <div class="card energy">
      <div class="card-header energy-h"><span class="icon">🌡️</span> Free Energy (ΔG)</div>
      <div class="eq-box" style="background:#f57f17;">
        ΔG = ΔH − TΔS
        <span class="eq-sub">ΔH = enthalpy change | T = temperature (K) | ΔS = entropy change</span>
      </div>
      <table class="tbl-energy" style="margin-top:8px;">
        <tr><th>ΔG Sign</th><th>Meaning</th><th>Reaction Type</th></tr>
        <tr><td><span class="chip chip-g">ΔG &lt; 0</span></td><td>Spontaneous; energy released</td><td>Exergonic ✅</td></tr>
        <tr><td><span class="chip chip-r">ΔG &gt; 0</span></td><td>Non-spontaneous; energy required</td><td>Endergonic ❌</td></tr>
        <tr><td><span class="chip chip-b">ΔG = 0</span></td><td>System at equilibrium</td><td>No net change ⚖️</td></tr>
      </table>
      <div class="remember r-gold"><b>🟡 Key:</b> ΔG° = standard free energy change at 1 mol/L, pH 7.0. ΔG° = −RT ln Keq</div>
    </div>

    <!-- ATP -->
    <div class="card atp">
      <div class="card-header atp-h"><span class="icon">⚡</span> ATP — The Energy Currency</div>
      <ul class="dot">
        <li>Adenosine + <b>3 phosphate</b> groups</li>
        <li>Hydrolysis of each terminal phosphate: <b>ΔG° ≈ −7.3 kcal/mol</b></li>
        <li>ATP → ADP + Pi (most common)</li>
        <li>ATP → AMP + PPi (adenylyl cyclase reactions)</li>
        <li>Functions as <b>Mg²⁺ complex</b> in cells</li>
        <li>NOT an energy store — turned over rapidly</li>
      </ul>
      <div class="eq-box" style="background:#880e4f;margin-top:10px;">
        2 ADP ⇌ ATP + AMP
        <span class="eq-sub">Adenylate kinase — keeps adenine nucleotide pool balanced</span>
      </div>
      <div class="remember r-red"><b>🔴 Exam trap:</b> ATP has 2 high-energy bonds (between β–γ and α–β phosphates), NOT 3!</div>
    </div>

    <!-- Coupled reactions -->
    <div class="card" style="background:#f9fbe7;">
      <div class="card-header" style="background:#f9fbe7;color:#558b2f;border-left:4px solid #558b2f;"><span class="icon">🔄</span> Coupled Reactions</div>
      <ul class="dot">
        <li>Endergonic reactions are driven by coupling to exergonic ATP hydrolysis</li>
        <li>Share a <b>common intermediate</b></li>
        <li>ΔG° values are <b>additive</b> in sequential reactions</li>
        <li>If total ΔG° is negative → overall reaction is spontaneous</li>
      </ul>
      <div style="margin-top:10px;background:#dcedc8;border-radius:8px;padding:8px 12px;font-size:12px;">
        <b>Example:</b><br/>
        Glucose + Pi → Glucose-6-P &nbsp; <span class="chip chip-r">ΔG°= +3.3</span><br/>
        ATP → ADP + Pi &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span class="chip chip-g">ΔG°= −7.3</span><br/>
        <hr style="margin:4px 0;border:1px dashed #aaa;"/>
        <b>Net:</b> Glucose + ATP → G-6-P + ADP &nbsp;<span class="chip chip-g">ΔG°= −4.0 ✅</span>
      </div>
    </div>

  </div>
</section>


<!-- ══════════════════════════════════════════════ SECTION 4: FLOWCHART — GLUCOSE METABOLISM ══ -->
<section>
  <div class="section-title" style="color:#00695c;border-color:#00695c;">
    🔀 Section 4 — Glucose → ATP Flowchart
  </div>

  <div class="card" style="background:#e8f5e9;padding:20px;">
    <div class="flow-wrap">

      <div class="flow-box" style="border-color:#2e7d32;background:#a5d6a7;color:#1b5e20;">
        🍭 <b>Glucose</b>
        <span class="flow-sub">C₆H₁₂O₆</span>
      </div>
      <div class="flow-arrow">→</div>

      <div style="text-align:center;">
        <div class="flow-box" style="border-color:#f57f17;background:#ffe082;color:#e65100;">
          <b>Glycolysis</b>
          <span class="flow-sub">Cytoplasm</span>
          <span class="flow-sub">2 ATP net</span>
          <span class="flow-sub">2 NADH</span>
        </div>
      </div>
      <div class="flow-arrow">→</div>

      <div style="text-align:center;">
        <div class="flow-box" style="border-color:#6a1b9a;background:#e1bee7;color:#4a148c;">
          <b>Pyruvate</b>
          <span class="flow-sub">Decarboxylation</span>
          <span class="flow-sub">→ Acetyl-CoA</span>
          <span class="flow-sub">2 NADH + 2 CO₂</span>
        </div>
      </div>
      <div class="flow-arrow">→</div>

      <div style="text-align:center;">
        <div class="flow-box" style="border-color:#1565c0;background:#bbdefb;color:#0d47a1;">
          <b>TCA Cycle</b>
          <span class="flow-sub">Krebs Cycle</span>
          <span class="flow-sub">Mitochondria</span>
          <span class="flow-sub">6 NADH, 2 FADH₂</span>
          <span class="flow-sub">2 GTP</span>
        </div>
      </div>
      <div class="flow-arrow">→</div>

      <div style="text-align:center;">
        <div class="flow-box" style="border-color:#006064;background:#80deea;color:#004d40;">
          <b>ETC</b>
          <span class="flow-sub">Inner mitochondrial</span>
          <span class="flow-sub">membrane</span>
          <span class="flow-sub">Complexes I–IV</span>
          <span class="flow-sub">Proton gradient</span>
        </div>
      </div>
      <div class="flow-arrow">→</div>

      <div style="text-align:center;">
        <div class="flow-box" style="border-color:#880e4f;background:#f48fb1;color:#880e4f;">
          <b>ATP Synthase</b>
          <span class="flow-sub">Complex V</span>
          <span class="flow-sub">ADP + Pi → ATP</span>
          <span class="flow-sub">~32 ATP total</span>
        </div>
      </div>
      <div class="flow-arrow">→</div>

      <div style="text-align:center;">
        <div class="flow-box" style="border-color:#37474f;background:#b0bec5;color:#212121;">
          <b>CO₂ + H₂O</b>
          <span class="flow-sub">Final products</span>
        </div>
      </div>

    </div>

    <!-- ATP Yield bar -->
    <div style="margin-top:16px;">
      <p style="font-weight:700;font-size:12.5px;margin-bottom:6px;text-align:center;">⚡ Total ATP Yield from 1 Glucose (aerobic)</p>
      <div class="yield-bar">
        <div class="yb" style="flex:2;background:#a5d6a7;color:#1b5e20;">Glycolysis<br/>2 ATP</div>
        <div class="yb" style="flex:2;background:#ffe082;color:#e65100;">Pyruvate Decarboxylation<br/>~5 ATP</div>
        <div class="yb" style="flex:4;background:#bbdefb;color:#0d47a1;">TCA Cycle<br/>~20 ATP</div>
        <div class="yb" style="flex:3;background:#ce93d8;color:#4a148c;">FADH₂ (ETC)<br/>~3 ATP</div>
        <div class="yb" style="flex:3;background:#f48fb1;color:#880e4f;">GTP/misc<br/>~2 ATP</div>
        <div class="yb" style="flex:2;background:#37474f;color:#fff;font-size:14px;font-weight:800;">≈ 32 ATP</div>
      </div>
    </div>
  </div>
</section>


<!-- ══════════════════════════════════════════════ SECTION 5: ETC COMPLEXES ══ -->
<section>
  <div class="section-title" style="color:var(--etc-h);border-color:var(--etc-h);">
    🔋 Section 5 — Electron Transport Chain (ETC) Complexes
  </div>

  <div class="etc-strip">
    <div class="etc-block c1">
      <div style="font-size:1.3rem;">Ⅰ</div>
      <b>NADH Dehydrogenase</b><br/>
      <span style="font-size:10px;">NADH → NAD⁺<br/>Pumps <b>4H⁺</b><br/>Contains FMN<br/>Fe-S clusters</span>
    </div>
    <div class="etc-arrow">▶</div>
    <div class="etc-block c2">
      <div style="font-size:1.3rem;">Ⅱ</div>
      <b>Succinate Dehydrogenase</b><br/>
      <span style="font-size:10px;">FADH₂ → FAD<br/><b>No H⁺ pump</b><br/>Links TCA to ETC<br/>Fe-S clusters</span>
    </div>
    <div class="etc-arrow">▶</div>
    <div class="etc-block c3">
      <div style="font-size:1.3rem;">Ⅲ</div>
      <b>Cytochrome bc₁</b><br/>
      <span style="font-size:10px;">CoQ → Cyt c<br/>Pumps <b>4H⁺</b><br/>Q cycle<br/>Cytochromes b, c₁</span>
    </div>
    <div class="etc-arrow">▶</div>
    <div class="etc-block c4">
      <div style="font-size:1.3rem;">Ⅳ</div>
      <b>Cytochrome c Oxidase</b><br/>
      <span style="font-size:10px;">Cyt c → O₂<br/>Pumps <b>2H⁺</b><br/>O₂ → H₂O<br/>Cu, heme a, a₃</span>
    </div>
    <div class="etc-arrow">▶</div>
    <div class="etc-block c5">
      <div style="font-size:1.3rem;">Ⅴ</div>
      <b>ATP Synthase</b><br/>
      <span style="font-size:10px;">ADP + Pi → ATP<br/>H⁺ flows back<br/>F₀ motor / F₁ head<br/>~3 ATP per NADH</span>
    </div>
  </div>

  <div class="grid2" style="margin-top:16px;">
    <div class="card etc">
      <div class="card-header etc-h"><span class="icon">🔬</span> Mobile Electron Carriers</div>
      <table class="tbl-etc">
        <tr><th>Carrier</th><th>Location</th><th>Carries</th></tr>
        <tr><td><b>CoQ (Ubiquinone)</b></td><td>Lipid bilayer (mobile)</td><td>2 electrons + 2H⁺</td></tr>
        <tr><td><b>Cytochrome c</b></td><td>Intermembrane space</td><td>1 electron only</td></tr>
        <tr><td><b>NADH</b></td><td>Matrix (from Complex I)</td><td>2 electrons (as H⁻)</td></tr>
        <tr><td><b>FADH₂</b></td><td>Bound to Complex II</td><td>2 electrons</td></tr>
      </table>
    </div>

    <div class="card atp">
      <div class="card-header atp-h"><span class="icon">🛑</span> ETC Inhibitors — High Yield</div>
      <table class="tbl-atp">
        <tr><th>Inhibitor</th><th>Target</th><th>Effect</th></tr>
        <tr><td><b>Rotenone / Amytal</b></td><td>Complex I</td><td>Blocks NADH oxidation</td></tr>
        <tr><td><b>Malonate</b></td><td>Complex II</td><td>Competitive succinate inhibitor</td></tr>
        <tr><td><b>Antimycin A</b></td><td>Complex III</td><td>Blocks Q cycle</td></tr>
        <tr><td><b>Cyanide / CO / H₂S</b></td><td>Complex IV</td><td>Bind heme a₃; block O₂ binding</td></tr>
        <tr><td><b>Oligomycin</b></td><td>Complex V (F₀)</td><td>Blocks H⁺ channel; stops ATP synthesis</td></tr>
        <tr><td><b>DNP / Thermogenin</b></td><td>Inner membrane</td><td>Uncoupler — dissipates H⁺ gradient as heat</td></tr>
      </table>
    </div>
  </div>

  <div class="remember r-red" style="margin-top:10px;font-size:12.5px;">
    <b>🔴 Exam Tip — Uncouplers vs Inhibitors:</b> Inhibitors stop both electron transport AND ATP synthesis. Uncouplers (e.g. DNP) allow electron transport to continue but dissipate the proton gradient as heat — ATP synthesis stops but O₂ consumption INCREASES.
  </div>
</section>


<!-- ══════════════════════════════════════════════ SECTION 6: COENZYME TABLE ══ -->
<section>
  <div class="section-title" style="color:#00796b;border-color:#00796b;">
    🧪 Section 6 — Key Coenzymes &amp; Vitamins
  </div>

  <div class="card">
    <table>
      <tr>
        <th style="background:#00695c;color:#fff;">Coenzyme</th>
        <th style="background:#00695c;color:#fff;">Vitamin Precursor</th>
        <th style="background:#00695c;color:#fff;">Oxidised Form</th>
        <th style="background:#00695c;color:#fff;">Reduced Form</th>
        <th style="background:#00695c;color:#fff;">ETC Complex</th>
        <th style="background:#00695c;color:#fff;">ATP Yield</th>
      </tr>
      <tr><td><b>NAD⁺</b></td><td>Niacin (B₃)</td><td>NAD⁺</td><td>NADH</td><td>Complex I → III → IV → V</td><td><span class="chip chip-g">~2.5 ATP</span></td></tr>
      <tr><td><b>FAD</b></td><td>Riboflavin (B₂)</td><td>FAD</td><td>FADH₂</td><td>Complex II → III → IV → V</td><td><span class="chip chip-o">~1.5 ATP</span></td></tr>
      <tr><td><b>CoA</b></td><td>Pantothenic acid (B₅)</td><td colspan="2">Acyl-CoA, Acetyl-CoA</td><td>Carries acyl groups</td><td>—</td></tr>
      <tr><td><b>TPP</b></td><td>Thiamine (B₁)</td><td colspan="2">Active form</td><td>Decarboxylation reactions</td><td>—</td></tr>
      <tr><td><b>Biotin</b></td><td>Biotin (B₇)</td><td colspan="2">Active form</td><td>CO₂ carrier (carboxylations)</td><td>—</td></tr>
      <tr><td><b>PLP</b></td><td>Pyridoxine (B₆)</td><td colspan="2">Active form</td><td>Amino acid metabolism (transamination)</td><td>—</td></tr>
    </table>
    <div class="remember r-green" style="margin-top:8px;"><b>🟢 Mnemonic:</b> <b>NAD = 2.5 ATP | FADH₂ = 1.5 ATP</b> (P/O ratios, chemiosmotic coupling)</div>
  </div>
</section>


<!-- ══════════════════════════════════════════════ SECTION 7: QUICK RECALL ══ -->
<section>
  <div class="section-title" style="color:#c62828;border-color:#c62828;">
    🎯 Section 7 — Last-Minute High-Yield Facts
  </div>

  <div class="grid4">
    <div class="card" style="background:#fff3e0;border-top:4px solid #ef6c00;">
      <div style="font-size:1.5rem;text-align:center;">🍭</div>
      <p style="font-weight:700;text-align:center;color:#e65100;">Carbs</p>
      <ul class="dot" style="font-size:11.5px;">
        <li>Reducing sugar = free anomeric –OH</li>
        <li>Glycogen = α-1,4 + α-1,6 (liver &amp; muscle)</li>
        <li>Cellulose = β-1,4 (not digestible)</li>
        <li>Glycoproteins: N-linked (Asn) &amp; O-linked (Ser/Thr)</li>
      </ul>
    </div>

    <div class="card" style="background:#e3f2fd;border-top:4px solid #1565c0;">
      <div style="font-size:1.5rem;text-align:center;">🧩</div>
      <p style="font-weight:700;text-align:center;color:#1565c0;">Proteins</p>
      <ul class="dot" style="font-size:11.5px;">
        <li>20 standard amino acids</li>
        <li>9 essential (cannot synthesize)</li>
        <li>Disulfide bonds: Cys–Cys (oxidation)</li>
        <li>Denaturation: disrupts 2°, 3°, 4° — NOT 1°</li>
        <li>Chaperones: prevent misfolding</li>
      </ul>
    </div>

    <div class="card" style="background:#fce4ec;border-top:4px solid #880e4f;">
      <div style="font-size:1.5rem;text-align:center;">⚡</div>
      <p style="font-weight:700;text-align:center;color:#880e4f;">ATP Facts</p>
      <ul class="dot" style="font-size:11.5px;">
        <li>ΔG° hydrolysis = −7.3 kcal/mol</li>
        <li>Phosphoenol pyruvate &gt; ATP &gt; AMP</li>
        <li>In cell: [ATP] &gt;&gt; [ADP] (drives reactions)</li>
        <li>High energy phosphoanhydride bonds</li>
        <li>Creatine phosphate: muscle energy reserve</li>
      </ul>
    </div>

    <div class="card" style="background:#e0f7fa;border-top:4px solid #006064;">
      <div style="font-size:1.5rem;text-align:center;">🔋</div>
      <p style="font-weight:700;text-align:center;color:#006064;">ETC Numbers</p>
      <ul class="dot" style="font-size:11.5px;">
        <li>NADH → 2.5 ATP (enters at Complex I)</li>
        <li>FADH₂ → 1.5 ATP (enters at Complex II)</li>
        <li>1 Glucose → ~32 ATP (aerobic)</li>
        <li>1 Glucose → 2 ATP (anaerobic)</li>
        <li>Cytochrome c: between III &amp; IV</li>
        <li>O₂ consumed only at Complex IV</li>
      </ul>
    </div>
  </div>

  <!-- Final comparison table -->
  <div class="card" style="margin-top:16px;">
    <div class="card-header" style="background:#eceff1;color:#37474f;border-left:4px solid #607d8b;">
      <span class="icon">📊</span> Aerobic vs Anaerobic — Side by Side
    </div>
    <table>
      <tr>
        <th style="background:#455a64;color:#fff;">Feature</th>
        <th style="background:#2e7d32;color:#fff;">🌬️ Aerobic</th>
        <th style="background:#b71c1c;color:#fff;">🚫 Anaerobic</th>
      </tr>
      <tr><td>O₂ required</td><td>✅ Yes</td><td>❌ No</td></tr>
      <tr><td>ATP yield (per glucose)</td><td>~32 ATP</td><td>2 ATP</td></tr>
      <tr><td>Final electron acceptor</td><td>O₂ (→ H₂O)</td><td>Pyruvate (→ Lactate)</td></tr>
      <tr><td>Location</td><td>Cytoplasm + Mitochondria</td><td>Cytoplasm only</td></tr>
      <tr><td>NADH fate</td><td>ETC → ATP</td><td>Regenerates NAD⁺</td></tr>
      <tr><td>End products</td><td>CO₂ + H₂O</td><td>Lactate (animals) / Ethanol (yeast)</td></tr>
    </table>
  </div>
</section>


<!-- ══════════════════════════════════════════════ FOOTER ══ -->
<footer style="text-align:center;padding:20px;color:#90a4ae;font-size:11px;margin-top:16px;">
  Sources: Harper's Illustrated Biochemistry 32e &amp; Lippincott's Biochemistry 8e &nbsp;|&nbsp; Orris Study Sheet &nbsp;|&nbsp; For revision only
</footer>

</main>
</body>
</html>

Running Command

cd /home/daytona/workspace/biomolecules-bioenergetics && wc -l study_sheet.html && echo "File exists and ready"

Your study sheet is ready! Download it here:

study sheet
HTML File · HTML

Open it in any browser - it's fully self-contained.

Here's exactly what's packed inside across 7 colour-coded sections:

🗂️ What's in the Sheet

Section	Content	Visual Type
1 — Big Picture	All 6 biomolecule + energy topics linked	🧠 Mind Map
2 — Biomolecules	Carbs, Proteins, Lipids, Nucleic Acids with bond energies	🗃️ Colour Tables
3 — Bioenergetics	ΔG, ATP structure, coupled reactions with worked example	⚡ Cards + Equations
4 — Glucose → ATP	Glycolysis → Pyruvate → TCA → ETC → ATP Synthase	🔀 Flowchart + ATP yield bar
5 — ETC Complexes	Complexes I–V, mobile carriers, inhibitors (Cyanide, DNP, etc.)	🔋 Strip diagram + tables
6 — Coenzymes	NAD⁺, FAD, CoA, TPP, Biotin, PLP — vitamins + ATP yields	🧪 Reference table
7 — High-Yield Facts	Aerobic vs Anaerobic, exam traps, mnemonics	🎯 Chip cards + comparison

⚡ Key Numbers to Burn Into Memory

1 Glucose (aerobic) = ~32 ATP
NADH → 2.5 ATP | FADH₂ → 1.5 ATP
ATP hydrolysis ΔG° = −7.3 kcal/mol
Anaerobic = only 2 ATP (cytoplasm only)
Uncouplers (DNP) = O₂ consumption ↑ but ATP ↓ (exam trap!)

Sources: Harper's Illustrated Biochemistry 32e & Lippincott's Biochemistry 8e

how to open this html file

Here are all the ways to open it:

Option 1 — Download & Open (Easiest) ✅

Click the link in my previous message: study_sheet.html
Your browser will download the file
Find it in your Downloads folder
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Option 2 — Open Directly in Browser

Open Chrome / Firefox / Edge
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Navigate to your Downloads folder
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Drag it into an open browser window
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Option 4 — Right-click Method

Right-click the .html file
Select "Open with"
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⚠️ Troubleshooting

Problem	Fix
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Link doesn't download	Try right-click → "Save link as"
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The file is completely self-contained (no internet needed once downloaded) — all colours, tables, and layouts are built into the single HTML file.

this is not open in my laptop

Reading File

Running Command

which wkhtmltopdf && wkhtmltopdf --version

Running Command

which weasyprint && weasyprint --version 2>/dev/null; which chromium-browser 2>/dev/null; which google-chrome 2>/dev/null; which chromium 2>/dev/null; python3 -c "import weasyprint; print('weasyprint ok')" 2>/dev/null; python3 -c "import pdfkit; print('pdfkit ok')" 2>/dev/null

Running Command

chromium --headless --disable-gpu --no-sandbox --print-to-pdf=/home/daytona/workspace/biomolecules-bioenergetics/study_sheet.pdf --print-to-pdf-no-header "file:///home/daytona/workspace/biomolecules-bioenergetics/study_sheet.html" 2>&1 | tail -5

Your PDF is ready! Download it here:

study sheet
PDF Document · PDF

How to open it:

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No special software needed - PDFs work on every laptop out of the box

this pdf will not open

Running Command

python3 -c "from reportlab.lib.pagesizes import A4; print('reportlab ok')"

Writing File

~/biomolecules-bioenergetics/build_pdf.py

from reportlab.lib.pagesizes import A4
from reportlab.lib import colors
from reportlab.lib.units import cm, mm
from reportlab.lib.styles import getSampleStyleSheet, ParagraphStyle
from reportlab.platypus import (SimpleDocTemplate, Paragraph, Spacer, Table,
                                 TableStyle, HRFlowable, KeepTogether)
from reportlab.lib.enums import TA_CENTER, TA_LEFT, TA_RIGHT
from reportlab.platypus.flowables import Flowable
import os

OUT = "/home/daytona/workspace/biomolecules-bioenergetics/Biomolecules_Bioenergetics_StudySheet.pdf"

# ── Colour palette ──────────────────────────────────────────────────────────
C_NAVY    = colors.HexColor("#1a237e")
C_CARB    = colors.HexColor("#2e7d32")
C_CARB_BG = colors.HexColor("#e8f5e9")
C_PROT    = colors.HexColor("#1565c0")
C_PROT_BG = colors.HexColor("#e3f2fd")
C_LIPID   = colors.HexColor("#e65100")
C_LIPID_BG= colors.HexColor("#fff3e0")
C_NUC     = colors.HexColor("#6a1b9a")
C_NUC_BG  = colors.HexColor("#f3e5f5")
C_ATP     = colors.HexColor("#880e4f")
C_ATP_BG  = colors.HexColor("#fce4ec")
C_ETC     = colors.HexColor("#006064")
C_ETC_BG  = colors.HexColor("#e0f7fa")
C_ENERGY  = colors.HexColor("#f57f17")
C_ENERGY_BG=colors.HexColor("#fff8e1")
C_GRAY    = colors.HexColor("#546e7a")
C_LGRAY   = colors.HexColor("#eceff1")
C_WHITE   = colors.white
C_YELLOW  = colors.HexColor("#fffde7")
C_YEL_BOR = colors.HexColor("#fdd835")
C_GREEN_L = colors.HexColor("#f1f8e9")
C_RED_L   = colors.HexColor("#ffebee")
C_BLUE_L  = colors.HexColor("#e3f2fd")

doc = SimpleDocTemplate(
    OUT, pagesize=A4,
    topMargin=1.2*cm, bottomMargin=1.2*cm,
    leftMargin=1.4*cm, rightMargin=1.4*cm,
    title="Biomolecules + Bioenergetics Study Sheet"
)
W, H = A4
CW = W - 2.8*cm   # content width

styles = getSampleStyleSheet()

def S(name, **kw):
    """Quick paragraph style factory."""
    base = styles["Normal"]
    return ParagraphStyle(name, parent=base, **kw)

# ── Reusable styles ──────────────────────────────────────────────────────────
sNormal  = S("sNormal", fontSize=8, leading=11)
sBold    = S("sBold",   fontSize=8, leading=11, fontName="Helvetica-Bold")
sSmall   = S("sSmall",  fontSize=7, leading=10)
sCenter  = S("sCenter", fontSize=8, leading=11, alignment=TA_CENTER)
sCenterB = S("sCenterB",fontSize=8, leading=11, alignment=TA_CENTER, fontName="Helvetica-Bold")
sTinyC   = S("sTinyC",  fontSize=6.5, leading=9, alignment=TA_CENTER)

def sec_title(text, color=C_NAVY):
    return Paragraph(f"<font color='#{color.hexval()[2:]}' size='12'><b>{text}</b></font>",
                     S("st", fontSize=12, fontName="Helvetica-Bold", spaceAfter=4,
                       borderPadding=(0,0,3,0)))

def card_hdr(text, bg, fg=C_WHITE):
    tbl = Table([[Paragraph(f"<b>{text}</b>",
                            S("ch", fontSize=9, fontName="Helvetica-Bold",
                              textColor=fg))]],
                colWidths=[CW], rowHeights=[18])
    tbl.setStyle(TableStyle([
        ("BACKGROUND", (0,0), (-1,-1), bg),
        ("LEFTPADDING",  (0,0), (-1,-1), 8),
        ("RIGHTPADDING", (0,0), (-1,-1), 8),
        ("TOPPADDING",   (0,0), (-1,-1), 3),
        ("BOTTOMPADDING",(0,0), (-1,-1), 3),
        ("ROUNDEDCORNERS", [5]),
    ]))
    return tbl

def remember_box(text, bg, border_color):
    tbl = Table([[Paragraph(text, S("rb", fontSize=7.5, leading=10))]],
                colWidths=[CW-4])
    tbl.setStyle(TableStyle([
        ("BACKGROUND",   (0,0),(-1,-1), bg),
        ("LEFTPADDING",  (0,0),(-1,-1), 8),
        ("RIGHTPADDING", (0,0),(-1,-1), 6),
        ("TOPPADDING",   (0,0),(-1,-1), 5),
        ("BOTTOMPADDING",(0,0),(-1,-1), 5),
        ("LINEBEFOREBOX",(0,0),(-1,-1), 4, border_color),
        ("BOX",          (0,0),(-1,-1), 0.5, border_color),
    ]))
    return tbl

def hr(color=C_NAVY, thickness=1.5):
    return HRFlowable(width="100%", thickness=thickness, color=color, spaceAfter=4, spaceBefore=2)

def sp(h=6):
    return Spacer(1, h)

# ────────────────────────────────────────────────────────────────────────────
story = []

# ══════════════ HEADER ══════════════════════════════════════════════════════
hdr_data = [[
    Paragraph("<font color='white' size='18'><b>🧬 Biomolecules + Bioenergetics</b></font>",
              S("h1", fontSize=18, fontName="Helvetica-Bold", alignment=TA_CENTER, textColor=C_WHITE)),
],[
    Paragraph("<font color='white' size='9'>Biochemistry Rapid Revision  |  Harper's 32e &amp; Lippincott's 8e</font>",
              S("h2", fontSize=9, alignment=TA_CENTER, textColor=C_WHITE)),
],[
    Paragraph("<font color='#212121' size='8'><b>⚡ 5-Minute Revision Sheet</b></font>",
              S("badge", fontSize=8, fontName="Helvetica-Bold", alignment=TA_CENTER)),
]]
hdr = Table(hdr_data, colWidths=[CW])
hdr.setStyle(TableStyle([
    ("BACKGROUND",   (0,0),(0,1), C_NAVY),
    ("BACKGROUND",   (0,2),(0,2), colors.HexColor("#ffeb3b")),
    ("TOPPADDING",   (0,0),(-1,-1), 8),
    ("BOTTOMPADDING",(0,0),(-1,-1), 6),
    ("ALIGN",        (0,0),(-1,-1), "CENTER"),
    ("ROUNDEDCORNERS", [8]),
]))
story += [hdr, sp(10)]

# ══════════════ SECTION 1 — MIND MAP (as a colour grid) ═════════════════════
story += [sec_title("🧠  Section 1 — Big Picture Mind Map", C_NAVY), hr(C_NAVY)]

mm_data = [
    [
        Paragraph("<b>🍭 Carbohydrates</b><br/><font size='7'>Monosaccharides→Polysaccharides<br/>Energy source, cell signals</font>",
                  S("mm", fontSize=8, leading=11, alignment=TA_CENTER)),
        Paragraph("<b>🧩 Proteins</b><br/><font size='7'>Amino acids→Polypeptides<br/>Structure, enzymes, transport</font>",
                  S("mm2", fontSize=8, leading=11, alignment=TA_CENTER)),
        Paragraph("<b>🧈 Lipids</b><br/><font size='7'>FA, Triglycerides, Phospholipids<br/>Energy storage, membranes</font>",
                  S("mm3", fontSize=8, leading=11, alignment=TA_CENTER)),
    ],
    [
        Paragraph("<b>🔬 Nucleic Acids</b><br/><font size='7'>DNA &amp; RNA<br/>Purine/Pyrimidine bases</font>",
                  S("mm4", fontSize=8, leading=11, alignment=TA_CENTER)),
        Paragraph("<font color='white' size='9'><b>BIOCHEMISTRY\nCORE</b></font>",
                  S("mmc", fontSize=9, fontName="Helvetica-Bold", alignment=TA_CENTER, textColor=C_WHITE, leading=14)),
        Paragraph("<b>⚡ ATP &amp; Bioenergetics</b><br/><font size='7'>ΔG, Keq, Free Energy<br/>Coupled reactions</font>",
                  S("mm5", fontSize=8, leading=11, alignment=TA_CENTER)),
    ],
    [
        Paragraph("<b>🔋 ETC &amp; OXPHOS</b><br/><font size='7'>Complexes I–V<br/>32 ATP per glucose</font>",
                  S("mm6", fontSize=8, leading=11, alignment=TA_CENTER)),
        Paragraph("<font size='7'>All pathways converge<br/>on ATP production</font>",
                  S("mm7", fontSize=7, leading=10, alignment=TA_CENTER)),
        Paragraph("<b>🧪 Coenzymes</b><br/><font size='7'>NAD+, FAD, CoA<br/>Vitamin-derived carriers</font>",
                  S("mm8", fontSize=8, leading=11, alignment=TA_CENTER)),
    ],
]
col_w = CW / 3
mm_tbl = Table(mm_data, colWidths=[col_w]*3, rowHeights=[38, 45, 38])
mm_tbl.setStyle(TableStyle([
    # row 0
    ("BACKGROUND", (0,0),(0,0), C_CARB_BG),
    ("BACKGROUND", (1,0),(1,0), C_PROT_BG),
    ("BACKGROUND", (2,0),(2,0), C_LIPID_BG),
    # row 1
    ("BACKGROUND", (0,1),(0,1), C_NUC_BG),
    ("BACKGROUND", (1,1),(1,1), C_NAVY),
    ("BACKGROUND", (2,1),(2,1), C_ATP_BG),
    # row 2
    ("BACKGROUND", (0,2),(0,2), C_ETC_BG),
    ("BACKGROUND", (1,2),(1,2), C_LGRAY),
    ("BACKGROUND", (2,2),(2,2), C_ENERGY_BG),
    ("ALIGN",      (0,0),(-1,-1), "CENTER"),
    ("VALIGN",     (0,0),(-1,-1), "MIDDLE"),
    ("GRID",       (0,0),(-1,-1), 0.5, C_WHITE),
    ("TOPPADDING", (0,0),(-1,-1), 5),
    ("BOTTOMPADDING",(0,0),(-1,-1), 5),
    ("ROUNDEDCORNERS", [6]),
]))
story += [mm_tbl, sp(12)]

# ══════════════ SECTION 2 — BIOMOLECULES ════════════════════════════════════
story += [sec_title("🍬  Section 2 — Biomolecules at a Glance", C_CARB), hr(C_CARB)]

# ── Carbohydrates ────────────────────────────────────────────────────────────
story += [card_hdr("🍭  Carbohydrates", C_CARB), sp(2)]
carb_data = [
    ["Type", "Examples", "Key Feature"],
    ["Monosaccharide", "Glucose, Fructose, Galactose", "Aldoses/Ketoses; reducing sugars"],
    ["Disaccharide",   "Sucrose, Lactose, Maltose",    "Glycosidic bond (α or β)"],
    ["Oligosaccharide","Raffinose, cell-surface", "3–10 monosaccharides"],
    ["Polysaccharide", "Glycogen, Starch, Cellulose",  "α-1,4 (+ α-1,6 branches in glycogen)"],
]
carb_tbl = Table(carb_data, colWidths=[CW*0.22, CW*0.38, CW*0.40])
carb_tbl.setStyle(TableStyle([
    ("BACKGROUND",   (0,0),(-1,0), C_CARB),
    ("TEXTCOLOR",    (0,0),(-1,0), C_WHITE),
    ("FONTNAME",     (0,0),(-1,0), "Helvetica-Bold"),
    ("FONTSIZE",     (0,0),(-1,-1), 7.5),
    ("ROWBACKGROUNDS",(0,1),(-1,-1), [C_CARB_BG, C_WHITE]),
    ("GRID",         (0,0),(-1,-1), 0.3, colors.HexColor("#c8e6c9")),
    ("TOPPADDING",   (0,0),(-1,-1), 4),
    ("BOTTOMPADDING",(0,0),(-1,-1), 4),
    ("LEFTPADDING",  (0,0),(-1,-1), 6),
]))
story += [carb_tbl, sp(3)]
story += [remember_box("<b>Remember:</b> Glycogen = α-1,4 backbone + α-1,6 branch points (liver & muscle). "
                       "Cellulose = β-1,4 (not digestible). Brain is 100% glucose-dependent normally.",
                       C_GREEN_L, C_CARB), sp(8)]

# ── Proteins ─────────────────────────────────────────────────────────────────
story += [card_hdr("🧩  Proteins — Structural Levels", C_PROT), sp(2)]
prot_data = [
    ["Level", "Description", "Stabilising Forces"],
    ["1° Primary",   "AA sequence; peptide bonds",            "Covalent (peptide bond)"],
    ["2° Secondary", "α-helix, β-sheet, turns",               "H-bonds along backbone"],
    ["3° Tertiary",  "Full 3D fold of polypeptide",           "H-bonds, Van der Waals, hydrophobic, disulfide"],
    ["4° Quaternary","Multiple subunits (e.g. Haemoglobin)",  "Same as 3° (mostly non-covalent)"],
]
prot_tbl = Table(prot_data, colWidths=[CW*0.18, CW*0.35, CW*0.47])
prot_tbl.setStyle(TableStyle([
    ("BACKGROUND",   (0,0),(-1,0), C_PROT),
    ("TEXTCOLOR",    (0,0),(-1,0), C_WHITE),
    ("FONTNAME",     (0,0),(-1,0), "Helvetica-Bold"),
    ("FONTSIZE",     (0,0),(-1,-1), 7.5),
    ("ROWBACKGROUNDS",(0,1),(-1,-1), [C_PROT_BG, C_WHITE]),
    ("GRID",         (0,0),(-1,-1), 0.3, colors.HexColor("#bbdefb")),
    ("TOPPADDING",   (0,0),(-1,-1), 4),
    ("BOTTOMPADDING",(0,0),(-1,-1), 4),
    ("LEFTPADDING",  (0,0),(-1,-1), 6),
]))
story += [prot_tbl, sp(3)]
story += [remember_box("<b>Key:</b> Hydrophobic AA cluster in protein interior; charged/polar AA on surface. "
                       "Denaturation disrupts 2°/3°/4° — NOT primary structure (peptide bonds remain).",
                       C_BLUE_L, C_PROT), sp(8)]

# ── Lipids + Nucleic acids side by side ──────────────────────────────────────
story += [card_hdr("🧈  Lipids", C_LIPID), sp(2)]
lipid_data = [
    ["Class", "Components", "Function"],
    ["Fatty Acids",    "Saturated/Unsaturated chains", "Energy substrate (β-oxidation)"],
    ["Triglycerides",  "Glycerol + 3 FA",              "Long-term energy storage (adipose)"],
    ["Phospholipids",  "Glycerol + 2 FA + phosphate",  "Membrane bilayer; amphipathic"],
    ["Cholesterol",    "Sterol ring",                   "Membrane fluidity; steroid precursor"],
    ["Sphingolipids",  "Sphingosine + FA",              "Cell signalling; myelin sheath"],
]
lipid_tbl = Table(lipid_data, colWidths=[CW*0.22, CW*0.38, CW*0.40])
lipid_tbl.setStyle(TableStyle([
    ("BACKGROUND",   (0,0),(-1,0), C_LIPID),
    ("TEXTCOLOR",    (0,0),(-1,0), C_WHITE),
    ("FONTNAME",     (0,0),(-1,0), "Helvetica-Bold"),
    ("FONTSIZE",     (0,0),(-1,-1), 7.5),
    ("ROWBACKGROUNDS",(0,1),(-1,-1), [C_LIPID_BG, C_WHITE]),
    ("GRID",         (0,0),(-1,-1), 0.3, colors.HexColor("#ffe0b2")),
    ("TOPPADDING",   (0,0),(-1,-1), 4),
    ("BOTTOMPADDING",(0,0),(-1,-1), 4),
    ("LEFTPADDING",  (0,0),(-1,-1), 6),
]))
story += [lipid_tbl, sp(3)]
story += [remember_box("<b>Key:</b> Phospholipids are amphipathic — hydrophilic head groups face water, "
                       "hydrophobic fatty acyl tails cluster together (bilayer).",
                       C_YELLOW, C_YEL_BOR), sp(8)]

story += [card_hdr("🔬  Nucleic Acids — DNA vs RNA", C_NUC), sp(2)]
nuc_data = [
    ["Feature",     "DNA",                          "RNA"],
    ["Sugar",       "2'-Deoxyribose",               "Ribose"],
    ["Bases",       "A, T, G, C",                   "A, U, G, C"],
    ["Structure",   "Double helix (B-form)",        "Single strand (mostly)"],
    ["Purines",     "Adenine (A), Guanine (G)",      "Same — double ring"],
    ["Pyrimidines", "Cytosine (C), Thymine (T)",     "Cytosine (C), Uracil (U) — single ring"],
    ["H-bonds",     "A=T (2 bonds), G≡C (3 bonds)", "A=U (2), G≡C (3)"],
]
nuc_tbl = Table(nuc_data, colWidths=[CW*0.22, CW*0.39, CW*0.39])
nuc_tbl.setStyle(TableStyle([
    ("BACKGROUND",   (0,0),(-1,0), C_NUC),
    ("TEXTCOLOR",    (0,0),(-1,0), C_WHITE),
    ("FONTNAME",     (0,0),(-1,0), "Helvetica-Bold"),
    ("FONTSIZE",     (0,0),(-1,-1), 7.5),
    ("ROWBACKGROUNDS",(0,1),(-1,-1), [C_NUC_BG, C_WHITE]),
    ("GRID",         (0,0),(-1,-1), 0.3, colors.HexColor("#e1bee7")),
    ("TOPPADDING",   (0,0),(-1,-1), 4),
    ("BOTTOMPADDING",(0,0),(-1,-1), 4),
    ("LEFTPADDING",  (0,0),(-1,-1), 6),
]))
story += [nuc_tbl, sp(3)]
story += [remember_box("<b>Mnemonic:</b>  PURe As Gold = Purines: Adenine, Guanine (double ring).  "
                       "CUT the PY = Pyrimidines: Cytosine, Uracil, Thymine (single ring).",
                       C_BLUE_L, C_NUC), sp(10)]

# ══════════════ SECTION 3 — BIOENERGETICS ═══════════════════════════════════
story += [sec_title("⚡  Section 3 — Bioenergetics Core Concepts", C_ENERGY), hr(C_ENERGY)]

# Free energy table
story += [card_hdr("🌡️  Free Energy (ΔG)  —  ΔG = ΔH − TΔS", C_ENERGY, fg=colors.HexColor("#212121")), sp(2)]
dg_data = [
    ["ΔG Sign", "Meaning", "Reaction Type", "Spontaneous?"],
    ["ΔG < 0",  "Energy released",           "Exergonic",  "YES ✓"],
    ["ΔG > 0",  "Energy required",           "Endergonic", "NO  ✗"],
    ["ΔG = 0",  "System at equilibrium",     "Equilibrium","No net change"],
]
dg_tbl = Table(dg_data, colWidths=[CW*0.18, CW*0.35, CW*0.25, CW*0.22])
dg_tbl.setStyle(TableStyle([
    ("BACKGROUND",   (0,0),(-1,0), C_ENERGY),
    ("TEXTCOLOR",    (0,0),(-1,0), colors.HexColor("#212121")),
    ("FONTNAME",     (0,0),(-1,0), "Helvetica-Bold"),
    ("BACKGROUND",   (0,1),(-1,1), colors.HexColor("#c8e6c9")),
    ("BACKGROUND",   (0,2),(-1,2), colors.HexColor("#ffcdd2")),
    ("BACKGROUND",   (0,3),(-1,3), colors.HexColor("#bbdefb")),
    ("FONTSIZE",     (0,0),(-1,-1), 7.5),
    ("GRID",         (0,0),(-1,-1), 0.3, C_LGRAY),
    ("TOPPADDING",   (0,0),(-1,-1), 4),
    ("BOTTOMPADDING",(0,0),(-1,-1), 4),
    ("LEFTPADDING",  (0,0),(-1,-1), 6),
    ("FONTNAME",     (0,1),(0,-1), "Helvetica-Bold"),
]))
story += [dg_tbl, sp(3)]
story += [remember_box("<b>Key equations:</b>  ΔG° = −RT ln Keq  |  ΔG = ΔG° + RT ln [products]/[reactants]  |  "
                       "ΔG° values are ADDITIVE in sequential reactions.",
                       C_YELLOW, C_YEL_BOR), sp(8)]

# ATP card
story += [card_hdr("⚡  ATP — The Energy Currency", C_ATP), sp(2)]
atp_data = [
    ["ATP Property",                        "Detail"],
    ["Structure",                           "Adenosine + 3 phosphate groups"],
    ["ΔG° of hydrolysis (ATP→ADP+Pi)",      "−7.3 kcal/mol"],
    ["ΔG° of hydrolysis (ATP→AMP+PPi)",     "−7.3 kcal/mol (+ PPi→2Pi adds ~−4 more)"],
    ["High-energy bonds",                   "2 phosphoanhydride bonds (β–γ and α–β)"],
    ["In-cell form",                        "Mg²⁺ complex (Mg-ATP)"],
    ["Adenylate kinase rxn",                "2 ADP ⇌ ATP + AMP (keeps pool balanced)"],
    ["NOT used as",                         "Long-term energy store (turned over rapidly)"],
]
atp_tbl = Table(atp_data, colWidths=[CW*0.42, CW*0.58])
atp_tbl.setStyle(TableStyle([
    ("BACKGROUND",   (0,0),(-1,0), C_ATP),
    ("TEXTCOLOR",    (0,0),(-1,0), C_WHITE),
    ("FONTNAME",     (0,0),(-1,0), "Helvetica-Bold"),
    ("FONTSIZE",     (0,0),(-1,-1), 7.5),
    ("ROWBACKGROUNDS",(0,1),(-1,-1), [C_ATP_BG, C_WHITE]),
    ("GRID",         (0,0),(-1,-1), 0.3, colors.HexColor("#f8bbd0")),
    ("TOPPADDING",   (0,0),(-1,-1), 4),
    ("BOTTOMPADDING",(0,0),(-1,-1), 4),
    ("LEFTPADDING",  (0,0),(-1,-1), 6),
    ("FONTNAME",     (0,1),(0,-1), "Helvetica-Bold"),
]))
story += [atp_tbl, sp(3)]
story += [remember_box("<b>EXAM TRAP:</b> ATP has 2 high-energy bonds (β–γ and α–β phosphoanhydride), NOT 3! "
                       "The α-phosphate bond to ribose is NOT high-energy.",
                       C_RED_L, colors.HexColor("#e53935")), sp(10)]

# ══════════════ SECTION 4 — FLOWCHART ════════════════════════════════════════
story += [sec_title("🔀  Section 4 — Glucose → ATP Flowchart", colors.HexColor("#00695c")), hr(colors.HexColor("#00695c"))]

flow_data = [[
    Paragraph("<b>🍭 Glucose</b>\nC₆H₁₂O₆", sTinyC),
    Paragraph("→", sCenterB),
    Paragraph("<b>Glycolysis</b>\nCytoplasm\n2 ATP net\n2 NADH", sTinyC),
    Paragraph("→", sCenterB),
    Paragraph("<b>Pyruvate\nDecarboxylation</b>\n→ Acetyl-CoA\n2 NADH+2CO₂", sTinyC),
    Paragraph("→", sCenterB),
    Paragraph("<b>TCA Cycle</b>\n(Krebs)\nMitochondria\n6NADH,2FADH₂\n2 GTP", sTinyC),
    Paragraph("→", sCenterB),
    Paragraph("<b>ETC</b>\nComplexes I–IV\nInner mito.\nmembrane\nH⁺ gradient", sTinyC),
    Paragraph("→", sCenterB),
    Paragraph("<b>ATP Synthase</b>\nComplex V\nADP+Pi→ATP\n~32 ATP total", sTinyC),
]]
flow_tbl = Table(flow_data,
                 colWidths=[CW*0.10, CW*0.04, CW*0.12, CW*0.04,
                             CW*0.14, CW*0.04, CW*0.14, CW*0.04,
                             CW*0.14, CW*0.04, CW*0.12])
flow_tbl.setStyle(TableStyle([
    ("BACKGROUND",  (0,0),(0,0),  colors.HexColor("#a5d6a7")),
    ("BACKGROUND",  (2,0),(2,0),  colors.HexColor("#ffe082")),
    ("BACKGROUND",  (4,0),(4,0),  colors.HexColor("#e1bee7")),
    ("BACKGROUND",  (6,0),(6,0),  colors.HexColor("#bbdefb")),
    ("BACKGROUND",  (8,0),(8,0),  colors.HexColor("#80deea")),
    ("BACKGROUND",  (10,0),(10,0),colors.HexColor("#f48fb1")),
    ("BACKGROUND",  (1,0),(1,0),  C_LGRAY),
    ("BACKGROUND",  (3,0),(3,0),  C_LGRAY),
    ("BACKGROUND",  (5,0),(5,0),  C_LGRAY),
    ("BACKGROUND",  (7,0),(7,0),  C_LGRAY),
    ("BACKGROUND",  (9,0),(9,0),  C_LGRAY),
    ("ALIGN",       (0,0),(-1,-1),"CENTER"),
    ("VALIGN",      (0,0),(-1,-1),"MIDDLE"),
    ("TOPPADDING",  (0,0),(-1,-1), 6),
    ("BOTTOMPADDING",(0,0),(-1,-1),6),
    ("FONTSIZE",    (0,0),(-1,-1), 6.5),
    ("GRID",        (0,0),(-1,-1), 0.3, C_WHITE),
    ("ROUNDEDCORNERS", [4]),
]))
story += [flow_tbl, sp(6)]

# ATP Yield bar
yield_data = [[
    Paragraph("<b>Glycolysis</b>\n2 ATP", sTinyC),
    Paragraph("<b>Pyruvate\nDecarb.</b>\n~5 ATP", sTinyC),
    Paragraph("<b>TCA Cycle\n(NADH)</b>\n~20 ATP", sTinyC),
    Paragraph("<b>FADH₂\n(ETC)</b>\n~3 ATP", sTinyC),
    Paragraph("<b>GTP /\nmisc</b>\n~2 ATP", sTinyC),
    Paragraph("<font color='white'><b>TOTAL\n≈32 ATP</b></font>", sTinyC),
]]
yield_tbl = Table(yield_data, colWidths=[CW*0.13, CW*0.13, CW*0.22, CW*0.13, CW*0.13, CW*0.13],
                  rowHeights=[32])
yield_tbl.setStyle(TableStyle([
    ("BACKGROUND", (0,0),(0,0), colors.HexColor("#a5d6a7")),
    ("BACKGROUND", (1,0),(1,0), colors.HexColor("#ffe082")),
    ("BACKGROUND", (2,0),(2,0), colors.HexColor("#bbdefb")),
    ("BACKGROUND", (3,0),(3,0), colors.HexColor("#ce93d8")),
    ("BACKGROUND", (4,0),(4,0), colors.HexColor("#f48fb1")),
    ("BACKGROUND", (5,0),(5,0), colors.HexColor("#37474f")),
    ("ALIGN",      (0,0),(-1,-1),"CENTER"),
    ("VALIGN",     (0,0),(-1,-1),"MIDDLE"),
    ("FONTSIZE",   (0,0),(-1,-1), 7),
    ("FONTNAME",   (5,0),(5,0), "Helvetica-Bold"),
    ("GRID",       (0,0),(-1,-1), 0.5, C_WHITE),
    ("ROUNDEDCORNERS", [4]),
]))
story += [yield_tbl, sp(10)]

# ══════════════ SECTION 5 — ETC ══════════════════════════════════════════════
story += [sec_title("🔋  Section 5 — Electron Transport Chain Complexes", C_ETC), hr(C_ETC)]

etc_data = [[
    Paragraph("<b>Complex I</b>\nNADH\nDehydrogenase\nNADH→NAD⁺\nPumps 4H⁺\nContains FMN", sTinyC),
    Paragraph("→", sCenterB),
    Paragraph("<b>Complex II</b>\nSuccinate\nDehydrogenase\nFADH₂→FAD\nNO H⁺ pump!\nLinks TCA→ETC", sTinyC),
    Paragraph("→", sCenterB),
    Paragraph("<b>Complex III</b>\nCytochrome bc₁\nCoQ→Cyt c\nPumps 4H⁺\nQ cycle", sTinyC),
    Paragraph("→", sCenterB),
    Paragraph("<b>Complex IV</b>\nCyt c Oxidase\nCyt c→O₂\nPumps 2H⁺\nO₂→H₂O\nCu,heme a,a₃", sTinyC),
    Paragraph("→", sCenterB),
    Paragraph("<b>Complex V</b>\nATP Synthase\nADP+Pi→ATP\nH⁺ flows back\nF₀ motor/F₁\n~3 ATP/NADH", sTinyC),
]]
etc_tbl = Table(etc_data,
                colWidths=[CW*0.18, CW*0.04, CW*0.18, CW*0.04,
                            CW*0.15, CW*0.04, CW*0.18, CW*0.04, CW*0.15],
                rowHeights=[62])
etc_tbl.setStyle(TableStyle([
    ("BACKGROUND", (0,0),(0,0), colors.HexColor("#ef9a9a")),
    ("BACKGROUND", (2,0),(2,0), colors.HexColor("#ffcc80")),
    ("BACKGROUND", (4,0),(4,0), colors.HexColor("#a5d6a7")),
    ("BACKGROUND", (6,0),(6,0), colors.HexColor("#90caf9")),
    ("BACKGROUND", (8,0),(8,0), colors.HexColor("#ce93d8")),
    ("BACKGROUND", (1,0),(1,0), C_LGRAY),
    ("BACKGROUND", (3,0),(3,0), C_LGRAY),
    ("BACKGROUND", (5,0),(5,0), C_LGRAY),
    ("BACKGROUND", (7,0),(7,0), C_LGRAY),
    ("ALIGN",      (0,0),(-1,-1), "CENTER"),
    ("VALIGN",     (0,0),(-1,-1), "MIDDLE"),
    ("FONTSIZE",   (0,0),(-1,-1), 6.5),
    ("GRID",       (0,0),(-1,-1), 0.4, C_WHITE),
    ("ROUNDEDCORNERS", [4]),
]))
story += [etc_tbl, sp(6)]

# ETC Inhibitors
story += [card_hdr("🛑  ETC Inhibitors — High Yield", C_ATP), sp(2)]
inh_data = [
    ["Inhibitor",              "Target",      "Mechanism"],
    ["Rotenone / Amytal",      "Complex I",   "Blocks NADH oxidation"],
    ["Malonate",               "Complex II",  "Competitive inhibitor of succinate"],
    ["Antimycin A",            "Complex III", "Blocks Q cycle (Cyt b → Cyt c₁)"],
    ["Cyanide / CO / H₂S",     "Complex IV",  "Bind heme a₃; block O₂ binding → DEATH"],
    ["Oligomycin",             "Complex V (F₀)", "Blocks H⁺ channel; stops ATP synthesis"],
    ["DNP / Thermogenin (UCP-1)","Inner membrane","Uncoupler: dissipates H⁺ gradient as heat"],
]
inh_tbl = Table(inh_data, colWidths=[CW*0.30, CW*0.22, CW*0.48])
inh_tbl.setStyle(TableStyle([
    ("BACKGROUND",   (0,0),(-1,0), C_ATP),
    ("TEXTCOLOR",    (0,0),(-1,0), C_WHITE),
    ("FONTNAME",     (0,0),(-1,0), "Helvetica-Bold"),
    ("FONTSIZE",     (0,0),(-1,-1), 7.5),
    ("ROWBACKGROUNDS",(0,1),(-1,-1), [C_ATP_BG, C_WHITE]),
    ("BACKGROUND",   (0,6),(-1,6), colors.HexColor("#fff9c4")),
    ("GRID",         (0,0),(-1,-1), 0.3, colors.HexColor("#f8bbd0")),
    ("TOPPADDING",   (0,0),(-1,-1), 4),
    ("BOTTOMPADDING",(0,0),(-1,-1), 4),
    ("LEFTPADDING",  (0,0),(-1,-1), 6),
    ("FONTNAME",     (0,1),(0,-1), "Helvetica-Bold"),
]))
story += [inh_tbl, sp(3)]
story += [remember_box("<b>EXAM TRAP — Uncouplers vs Inhibitors:</b>  Inhibitors stop BOTH electron transport "
                       "AND ATP synthesis.  Uncouplers (DNP, Thermogenin) allow electron transport to continue "
                       "but dissipate the proton gradient as heat — ATP synthesis stops but O₂ consumption INCREASES.",
                       C_RED_L, colors.HexColor("#e53935")), sp(10)]

# ══════════════ SECTION 6 — COENZYMES ════════════════════════════════════════
story += [sec_title("🧪  Section 6 — Key Coenzymes & Vitamins", colors.HexColor("#00796b")), hr(colors.HexColor("#00796b"))]

coen_data = [
    ["Coenzyme", "Vitamin Precursor", "Oxidised Form", "Reduced Form", "ETC Entry", "ATP Yield"],
    ["NAD⁺",  "Niacin (B₃)",        "NAD⁺",   "NADH",    "Complex I",  "~2.5 ATP"],
    ["FAD",   "Riboflavin (B₂)",    "FAD",    "FADH₂",   "Complex II", "~1.5 ATP"],
    ["CoA",   "Pantothenic acid (B₅)","Active","Acyl-CoA","Acyl carrier","—"],
    ["TPP",   "Thiamine (B₁)",      "Active", "Active",  "Decarboxylations","—"],
    ["Biotin","Biotin (B₇)",        "Active", "Active",  "CO₂ carrier", "—"],
    ["PLP",   "Pyridoxine (B₆)",    "Active", "Active",  "Transamination","—"],
]
coen_tbl = Table(coen_data,
                 colWidths=[CW*0.10, CW*0.22, CW*0.13, CW*0.13, CW*0.25, CW*0.17])
coen_tbl.setStyle(TableStyle([
    ("BACKGROUND",   (0,0),(-1,0), colors.HexColor("#00695c")),
    ("TEXTCOLOR",    (0,0),(-1,0), C_WHITE),
    ("FONTNAME",     (0,0),(-1,0), "Helvetica-Bold"),
    ("FONTSIZE",     (0,0),(-1,-1), 7.5),
    ("ROWBACKGROUNDS",(0,1),(-1,-1), [C_ETC_BG, C_WHITE]),
    ("BACKGROUND",   (0,1),(-1,1), colors.HexColor("#b2dfdb")),
    ("BACKGROUND",   (0,2),(-1,2), colors.HexColor("#e0f2f1")),
    ("GRID",         (0,0),(-1,-1), 0.3, colors.HexColor("#b2dfdb")),
    ("TOPPADDING",   (0,0),(-1,-1), 4),
    ("BOTTOMPADDING",(0,0),(-1,-1), 4),
    ("LEFTPADDING",  (0,0),(-1,-1), 6),
    ("FONTNAME",     (0,1),(0,-1), "Helvetica-Bold"),
]))
story += [coen_tbl, sp(3)]
story += [remember_box("<b>Numbers to burn in:</b>  NADH → 2.5 ATP  |  FADH₂ → 1.5 ATP  |  "
                       "P/O ratio reflects chemiosmotic coupling efficiency (Mitchell hypothesis).",
                       C_GREEN_L, colors.HexColor("#43a047")), sp(10)]

# ══════════════ SECTION 7 — HIGH YIELD + COMPARISON ═════════════════════════
story += [sec_title("🎯  Section 7 — Last-Minute High-Yield Facts", colors.HexColor("#c62828")), hr(colors.HexColor("#c62828"))]

# 4-column quick facts
qf_data = [[
    Paragraph("<b>🍭 Carbs</b>\n\n"
              "• Reducing sugar =\n  free anomeric -OH\n"
              "• Glycogen: liver+\n  muscle\n"
              "• Cellulose: β-1,4\n  (not digestible)\n"
              "• Glycoproteins:\n  N-linked (Asn)\n  O-linked (Ser/Thr)", sSmall),
    Paragraph("<b>🧩 Proteins</b>\n\n"
              "• 20 standard AAs\n"
              "• 9 are essential\n  (cannot synthesise)\n"
              "• Disulfide bonds:\n  Cys-Cys (oxidation)\n"
              "• Chaperones prevent\n  misfolding\n"
              "• Zymogen = inactive\n  enzyme precursor", sSmall),
    Paragraph("<b>⚡ ATP Facts</b>\n\n"
              "• ΔG°= -7.3 kcal/mol\n"
              "• PEP > ATP > AMP\n  (energy hierarchy)\n"
              "• Creatine phosphate:\n  muscle energy reserve\n"
              "• [ATP]>>[ADP] in cell\n  drives reactions\n"
              "• Substrate-level vs\n  oxidative phosphorylation", sSmall),
    Paragraph("<b>🔋 ETC Numbers</b>\n\n"
              "• NADH → 2.5 ATP\n"
              "• FADH₂ → 1.5 ATP\n"
              "• 1 Glucose → ~32 ATP\n  (aerobic)\n"
              "• 1 Glucose → 2 ATP\n  (anaerobic)\n"
              "• O₂ consumed only\n  at Complex IV\n"
              "• Cyt c: between III & IV", sSmall),
]]
qf_tbl = Table(qf_data, colWidths=[CW/4]*4, rowHeights=[130])
qf_tbl.setStyle(TableStyle([
    ("BACKGROUND", (0,0),(0,0), colors.HexColor("#fff3e0")),
    ("BACKGROUND", (1,0),(1,0), colors.HexColor("#e3f2fd")),
    ("BACKGROUND", (2,0),(2,0), colors.HexColor("#fce4ec")),
    ("BACKGROUND", (3,0),(3,0), colors.HexColor("#e0f7fa")),
    ("LINEABOVE",  (0,0),(0,0), 4, C_LIPID),
    ("LINEABOVE",  (1,0),(1,0), 4, C_PROT),
    ("LINEABOVE",  (2,0),(2,0), 4, C_ATP),
    ("LINEABOVE",  (3,0),(3,0), 4, C_ETC),
    ("VALIGN",     (0,0),(-1,-1), "TOP"),
    ("TOPPADDING", (0,0),(-1,-1), 8),
    ("LEFTPADDING",(0,0),(-1,-1), 8),
    ("FONTSIZE",   (0,0),(-1,-1), 7.5),
    ("GRID",       (0,0),(-1,-1), 0.5, C_WHITE),
    ("ROUNDEDCORNERS", [4]),
]))
story += [qf_tbl, sp(8)]

# Aerobic vs Anaerobic
story += [card_hdr("📊  Aerobic vs Anaerobic — Side by Side", C_GRAY), sp(2)]
vs_data = [
    ["Feature",               "AEROBIC",               "ANAEROBIC"],
    ["O₂ required",           "Yes",                   "No"],
    ["ATP yield (per glucose)","~32 ATP",               "2 ATP"],
    ["Final electron acceptor","O₂ (→ H₂O)",           "Pyruvate (→ Lactate)"],
    ["Location",              "Cytoplasm + Mitochondria","Cytoplasm only"],
    ["NADH fate",             "ETC → ATP synthesis",   "Regenerates NAD⁺"],
    ["End products",          "CO₂ + H₂O",             "Lactate (animals) / Ethanol (yeast)"],
    ["Speed",                 "Slow but efficient",    "Fast but inefficient"],
]
vs_tbl = Table(vs_data, colWidths=[CW*0.32, CW*0.34, CW*0.34])
vs_tbl.setStyle(TableStyle([
    ("BACKGROUND",   (0,0),(0,0), colors.HexColor("#455a64")),
    ("BACKGROUND",   (1,0),(1,0), colors.HexColor("#2e7d32")),
    ("BACKGROUND",   (2,0),(2,0), colors.HexColor("#b71c1c")),
    ("TEXTCOLOR",    (0,0),(-1,0), C_WHITE),
    ("FONTNAME",     (0,0),(-1,0), "Helvetica-Bold"),
    ("FONTSIZE",     (0,0),(-1,-1), 7.5),
    ("ROWBACKGROUNDS",(0,1),(-1,-1), [C_LGRAY, C_WHITE]),
    ("GRID",         (0,0),(-1,-1), 0.3, colors.HexColor("#cfd8dc")),
    ("TOPPADDING",   (0,0),(-1,-1), 4),
    ("BOTTOMPADDING",(0,0),(-1,-1), 4),
    ("LEFTPADDING",  (0,0),(-1,-1), 6),
    ("FONTNAME",     (0,1),(0,-1), "Helvetica-Bold"),
]))
story += [vs_tbl, sp(8)]

# ══════════════ FOOTER ═══════════════════════════════════════════════════════
story += [
    hr(C_LGRAY, 0.5),
    Paragraph("<font color='#90a4ae' size='7'>Sources: Harper's Illustrated Biochemistry 32e &amp; "
              "Lippincott's Biochemistry 8e  |  Orris Study Sheet  |  For revision purposes only</font>",
              S("footer", fontSize=7, alignment=TA_CENTER, textColor=colors.HexColor("#90a4ae"))),
]

# ══════════════ BUILD ════════════════════════════════════════════════════════
doc.build(story)
print(f"PDF written to: {OUT}")
print(f"File size: {os.path.getsize(OUT):,} bytes")

Running Command

python3 /home/daytona/workspace/biomolecules-bioenergetics/build_pdf.py 2>&1

Your PDF is rebuilt from scratch using Python — no browser involved. Download it here:

Biomolecules Bioenergetics StudySheet
PDF Document · PDF

This PDF contains all 7 sections:

🧠 Mind Map grid (colour-coded)
🍬 Carbs, Proteins, Lipids, Nucleic Acids tables
⚡ Free Energy (ΔG) + ATP tables
🔀 Glucose → ATP flowchart with ATP yield bar
🔋 ETC complexes I–V strip + inhibitors table
🧪 Coenzymes & vitamins table
🎯 High-yield facts + Aerobic vs Anaerobic comparison

It should open on any laptop, phone, or tablet with a standard PDF viewer. Just click the link above to download.

Give me all interface in chat section

Here is the complete study sheet rendered directly in chat — all 7 sections:

🧬 Biomolecules + Bioenergetics

⚡ 5-Minute Rapid Revision Sheet | Harper's 32e & Lippincott's 8e

🧠 Section 1 — Big Picture Mind Map

                    🍭 CARBOHYDRATES              🧩 PROTEINS
                  Monosaccharides→Polysaccharides  AA→Polypeptides
                  Energy source, cell signals      Structure, enzymes
                           \                           /
                            \                         /
        🧈 LIPIDS ————————— [ BIOCHEMISTRY CORE ] ————————— 🔬 NUCLEIC ACIDS
        FA, TG, Phospholipids       ⬆⬇            DNA & RNA, Purines/Pyrimidines
        Energy storage, membranes  /   \
                                  /     \
                   ⚡ ATP & BIOENERGETICS   🔋 ETC & OXPHOS
                   ΔG, Keq, Coupled rxns   Complexes I–V, 32 ATP

🍬 Section 2 — Biomolecules at a Glance

🍭 Carbohydrates

Type	Examples	Key Feature
Monosaccharide	Glucose, Fructose, Galactose	Aldoses/Ketoses; reducing sugars
Disaccharide	Sucrose, Lactose, Maltose	Glycosidic bond (α or β)
Oligosaccharide	Raffinose, cell-surface oligosaccharides	3–10 monosaccharides
Polysaccharide	Glycogen, Starch, Cellulose	α-1,4 (+ α-1,6 branch in Glycogen)

🟢 Remember: Glycogen = α-1,4 backbone + α-1,6 branch points (liver & muscle). Cellulose = β-1,4 (NOT digestible). Brain = 100% glucose-dependent normally.

🧩 Proteins — Structural Levels

Level	Description	Stabilising Forces
1° Primary	AA sequence; peptide bonds	Covalent (peptide bond)
2° Secondary	α-helix, β-sheet, turns	H-bonds along backbone
3° Tertiary	Full 3D fold of polypeptide	H-bonds, Van der Waals, hydrophobic, disulfide
4° Quaternary	Multiple subunits (e.g. Hb)	Same as 3° (mostly non-covalent)

🔵 Key: Hydrophobic AA cluster inside the protein; charged/polar AA on the surface. Denaturation disrupts 2°/3°/4° — NOT 1° (peptide bonds remain intact).

🧈 Lipids

Class	Components	Function
Fatty Acids	Saturated / Unsaturated chains	Energy substrate (β-oxidation)
Triglycerides	Glycerol + 3 FA	Long-term energy storage (adipose)
Phospholipids	Glycerol + 2 FA + phosphate head	Membrane bilayer; amphipathic
Cholesterol	Sterol ring	Membrane fluidity; steroid precursor
Sphingolipids	Sphingosine + FA	Cell signalling; myelin sheath

🟡 Key: Phospholipids are amphipathic — hydrophilic heads face water, hydrophobic tails cluster together to form the bilayer.

🔬 Nucleic Acids — DNA vs RNA

Feature	DNA	RNA
Sugar	2'-Deoxyribose	Ribose
Bases	A, T, G, C	A, U, G, C
Structure	Double helix	Single strand
Purines	Adenine (A), Guanine (G) — double ring	Same
Pyrimidines	Cytosine (C), Thymine (T) — single ring	Cytosine (C), Uracil (U)
H-bonds	A=T (2 bonds), G≡C (3 bonds)	A=U (2), G≡C (3)

🟣 Mnemonic: PURe As Gold = Purines: Adenine, Guanine. CUT the PY = Pyrimidines: Cytosine, Uracil, Thymine.

🔗 Covalent Bond Energies (Quick Reference)

Bond	Energy (kcal/mol)	Bond	Energy (kcal/mol)
O–O	34	C–H	99
S–S (disulfide)	51	C–S	108
C–N	70	O–H	110
N–H	94	C=O	164

⚡ Section 3 — Bioenergetics Core Concepts

🌡️ Free Energy

        ΔG  =  ΔH  −  T·ΔS
        │       │       │
        │    Enthalpy  Entropy × Temp (K)
     Free energy change

ΔG Sign	Meaning	Reaction Type	Spontaneous?
ΔG < 0 ✅	Energy released	Exergonic	YES
ΔG > 0 ❌	Energy required	Endergonic	NO
ΔG = 0 ⚖️	Equilibrium	No net change	—

Key equations:

ΔG° = −RT ln Keq
ΔG = ΔG° + RT ln [Products]/[Reactants]
ΔG° values are additive in sequential reactions
Standard conditions: 1 mol/L, pH 7.0, 25°C

🟡 Key: ΔG° = −RT ln Keq. If Keq > 1 → ΔG° < 0 (favourable). If Keq < 1 → ΔG° > 0 (unfavourable).

⚡ ATP — The Energy Currency

ATP Property	Detail
Structure	Adenosine + 3 phosphate groups
ΔG° of hydrolysis (ATP→ADP+Pi)	−7.3 kcal/mol
High-energy bonds	2 phosphoanhydride bonds (β–γ and α–β)
In-cell form	Mg²⁺ complex (Mg-ATP)
Adenylate kinase	2 ADP ⇌ ATP + AMP
NOT used as	Long-term energy store (turned over rapidly)
Creatine phosphate	Muscle energy reserve (ΔG° = −10.3 kcal/mol)

🔴 EXAM TRAP: ATP has 2 high-energy bonds (β–γ and α–β phosphoanhydride), NOT 3! The α–ribose bond is NOT high-energy.

🔄 Coupled Reactions (Worked Example)

Glucose + Pi → Glucose-6-P       ΔG° = +3.3 kcal/mol  ❌ (unfavourable)
ATP → ADP + Pi                   ΔG° = −7.3 kcal/mol  ✅ (favourable)
─────────────────────────────────────────────────────────
NET: Glucose + ATP → G-6-P + ADP ΔG° = −4.0 kcal/mol  ✅ SPONTANEOUS

Endergonic reactions are driven by coupling to ATP hydrolysis
Share a common intermediate
Overall ΔG° = sum of individual ΔG° values

🔀 Section 4 — Glucose → ATP Flowchart

🍭 GLUCOSE
    │
    ▼ ─────────────────────────────────────────
   GLYCOLYSIS (Cytoplasm)
   • 2 ATP net (substrate-level phosphorylation)
   • 2 NADH produced
   • Glucose (C6) → 2 Pyruvate (C3)
    │
    ▼ ─────────────────────────────────────────
   PYRUVATE DECARBOXYLATION (Mitochondrial matrix)
   • Pyruvate → Acetyl-CoA
   • 2 NADH + 2 CO₂ released
   • Enzyme: Pyruvate dehydrogenase complex (needs B₁/TPP)
    │
    ▼ ─────────────────────────────────────────
   TCA CYCLE / KREBS CYCLE (Mitochondrial matrix)
   • Per glucose: 6 NADH, 2 FADH₂, 2 GTP
   • Produces: 4 CO₂
   • Key intermediates: Citrate → Isocitrate → α-KG
     → Succinyl-CoA → Succinate → Fumarate → Malate → OAA
    │
    ▼ ─────────────────────────────────────────
   ELECTRON TRANSPORT CHAIN (Inner mitochondrial membrane)
   • NADH & FADH₂ donate electrons to Complexes I–IV
   • Creates H⁺ gradient across inner membrane
    │
    ▼ ─────────────────────────────────────────
   ATP SYNTHASE — Complex V
   • H⁺ flows back through F₀F₁ ATPase
   • ADP + Pi → ATP
    │
    ▼ ─────────────────────────────────────────
   CO₂ + H₂O  +  ~32 ATP  🎉

⚡ ATP Yield Summary

Stage	NADH	FADH₂	Direct ATP	ATP Equivalent
Glycolysis	2	—	2	~7
Pyruvate decarboxylation	2	—	—	~5
TCA Cycle	6	2	2 (GTP)	~20
TOTAL	10	2	4	~32 ATP

NADH = 2.5 ATP each | FADH₂ = 1.5 ATP each

🔋 Section 5 — Electron Transport Chain

Complex Strip

Complex	Name	Substrate	H⁺ Pumped	Key Components
I	NADH Dehydrogenase	NADH → NAD⁺	4 H⁺	FMN, Fe-S clusters
II	Succinate Dehydrogenase	FADH₂ → FAD	0 H⁺ ⚠️	Fe-S, FAD; links TCA→ETC
III	Cytochrome bc₁	CoQ → Cyt c	4 H⁺	Q cycle, Cyt b, c₁
IV	Cytochrome c Oxidase	Cyt c → O₂	2 H⁺	Cu, heme a, a₃; O₂→H₂O
V	ATP Synthase	H⁺ gradient → ATP	(H⁺ re-enters)	F₀ motor, F₁ head

Mobile Carriers

Carrier	Location	Carries
CoQ (Ubiquinone)	Lipid bilayer (mobile)	2 electrons + 2H⁺
Cytochrome c	Intermembrane space	1 electron only

🛑 ETC Inhibitors — High Yield Table

Inhibitor	Target	Mechanism	Effect
Rotenone / Amytal	Complex I	Blocks NADH oxidation	↓ ATP, ↓ O₂ use
Malonate	Complex II	Competitive vs succinate	↓ FADH₂ oxidation
Antimycin A	Complex III	Blocks Q cycle	↓ ATP, ↓ O₂ use
Cyanide / CO / H₂S	Complex IV	Binds heme a₃; blocks O₂	FATAL — stops ETC
Oligomycin	Complex V (F₀)	Blocks H⁺ channel	↓ ATP, ↓ O₂ use
DNP / Thermogenin	Inner membrane	Dissipates H⁺ gradient	ATP↓, O₂ use INCREASES

🔴 EXAM TRAP: Uncouplers (DNP, Thermogenin/UCP-1) = ETC keeps running + O₂ consumption INCREASES, but ATP synthesis STOPS — energy released as heat. Inhibitors stop both.

🧪 Section 6 — Key Coenzymes & Vitamins

Coenzyme	Vitamin Precursor	Reduced Form	Role	ATP Yield
NAD⁺	Niacin (B₃)	NADH	Electron carrier → Complex I	~2.5 ATP
FAD	Riboflavin (B₂)	FADH₂	Electron carrier → Complex II	~1.5 ATP
CoA	Pantothenic acid (B₅)	Acyl-CoA	Acyl group carrier	—
TPP	Thiamine (B₁)	Active form	Decarboxylation reactions	—
Biotin	Biotin (B₇)	Carboxybiotin	CO₂ carrier (carboxylations)	—
PLP	Pyridoxine (B₆)	Active form	Transamination (AA metabolism)	—
Lipoamide	Lipoic acid	Dihydrolipoamide	PDH & α-KG dehydrogenase	—

🟢 Mnemonic for B-vitamins in metabolism: The Ripe Nectarine Provides Body's Life = Thiamine(B₁), Riboflavin(B₂), Niacin(B₃), Pantothenic(B₅), Biotin(B₇), Lipoic acid

🎯 Section 7 — Last-Minute High-Yield Facts

Quick Recall Cards

🍭 Carbs	🧩 Proteins	⚡ ATP	🔋 ETC
Reducing sugar = free anomeric –OH	20 standard AAs	ΔG° = −7.3 kcal/mol	NADH → 2.5 ATP
Glycogen: α-1,4 + α-1,6	9 are essential	PEP > ATP > AMP (energy)	FADH₂ → 1.5 ATP
Cellulose: β-1,4 (indigestible)	Disulfide = Cys-Cys	Mg²⁺ complex in cells	1 Glucose → ~32 ATP
Starch: amylose + amylopectin	Chaperones prevent misfolding	Creatine-P = muscle reserve	O₂ only at Complex IV
N-glycan → Asn; O-glycan → Ser/Thr	Zymogen = inactive precursor	2 ADP ⇌ ATP + AMP	Cyt c between III & IV

📊 Aerobic vs Anaerobic — Final Comparison

Feature	🌬️ AEROBIC	🚫 ANAEROBIC
O₂ required	Yes	No
ATP yield	~32 ATP	2 ATP
Final e⁻ acceptor	O₂ → H₂O	Pyruvate → Lactate
Location	Cytoplasm + Mitochondria	Cytoplasm only
NADH fate	ETC → ATP	Regenerates NAD⁺
End products	CO₂ + H₂O	Lactate (humans) / Ethanol (yeast)
Speed	Slow but efficient	Fast but inefficient
When used	Rest / aerobic exercise	Sprinting, hypoxia, RBCs

🧠 Top 10 One-Liners to Memorise

ΔG < 0 = spontaneous = exergonic (energy OUT)
ΔG = 0 = equilibrium (no net reaction)
ATP has 2 high-energy bonds, NOT 3
Complex II does NOT pump protons
Cyanide kills at Complex IV (blocks O₂ binding)
DNP = uncoupler → O₂ use ↑, ATP ↓, heat ↑
NADH enters at Complex I → 2.5 ATP
FADH₂ enters at Complex II → 1.5 ATP
Cellulose = β-1,4 → humans cannot digest it
G≡C has 3 H-bonds; A=T/A=U has 2 H-bonds

Sources: Harper's Illustrated Biochemistry 32e & Lippincott's Biochemistry 8e

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    return (nadh * 2.5) + (fadh2 * 1.5)

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Glucose → Pyruvate → Acetyl-CoA → TCA → ETC → ATP

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const delta_g = (dH, T, dS) => dH - T * dS;

python3 build_pdf.py

{ "molecule": "ATP", "bonds": 2, "dG": -7.3 }

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┌─────────┐     ┌─────────┐     ┌─────────┐
│ Glucose │────▶│Glycolysis│────▶│ Pyruvate│
└─────────┘     └─────────┘     └─────────┘
                                      │
                                      ▼
                               ┌─────────────┐
                               │  Acetyl-CoA  │
                               └─────────────┘

        [Topic]
       /   |   \
      /    |    \
  [A]    [B]    [C]
   |      |      |
  [a1]  [b1]   [c1]

📊 Progress / Bar Charts (ASCII)

ATP Yield:
Glycolysis  ██░░░░░░░░  2 ATP
Pyruvate    ████░░░░░░  5 ATP
TCA Cycle   ████████░░  20 ATP
TOTAL       ██████████  32 ATP

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Footnotes

Source: Harper's Illustrated Biochemistry 32e ↩

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