mkdir -p /home/daytona/workspace/biological-oxidation-ppt && ls /home/daytona/wo…

~/biological-oxidation-ppt/create_ppt.js

const pptxgen = require("pptxgenjs");
const { execSync } = require("child_process");

const pres = new pptxgen();
pres.layout = "LAYOUT_16x9";
pres.title = "Biological Oxidation";
pres.author = "Medical Biochemistry";

// ── Color palette ──────────────────────────────────────────────
const C = {
  navy:    "0D1B4B",   // dominant dark
  teal:    "0A7E8C",   // supporting
  amber:   "E8A020",   // accent / highlight
  white:   "FFFFFF",
  offWhite:"F4F6FA",
  ltGray:  "DDE3EE",
  midGray: "6B7A99",
  darkTxt: "1A2340",
  green:   "1A8C4E",
  red:     "C0392B",
};

// ── Helper: section‑divider slide ────────────────────────────
function sectionDivider(title, subtitle) {
  const sl = pres.addSlide();
  // full‑bleed gradient rect
  sl.addShape(pres.ShapeType.rect, { x:0, y:0, w:"100%", h:"100%",
    fill:{ type:"solid", color:C.navy } });
  sl.addShape(pres.ShapeType.rect, { x:0, y:0, w:"40%", h:"100%",
    fill:{ type:"solid", color:C.teal }, transparency:60 });
  // accent bar
  sl.addShape(pres.ShapeType.rect, { x:0.5, y:2.1, w:0.12, h:1.5,
    fill:{ type:"solid", color:C.amber }, line:{ color:C.amber } });
  sl.addText(title, { x:0.8, y:2.0, w:8.5, h:1.0,
    fontSize:34, bold:true, color:C.white, fontFace:"Calibri" });
  if (subtitle) {
    sl.addText(subtitle, { x:0.8, y:3.1, w:8.5, h:0.7,
      fontSize:18, color:C.ltGray, fontFace:"Calibri" });
  }
}

// ── Helper: content slide ────────────────────────────────────
function contentSlide(title, bodyItems, opts = {}) {
  const sl = pres.addSlide();
  // header bar
  sl.addShape(pres.ShapeType.rect, { x:0, y:0, w:"100%", h:0.85,
    fill:{ type:"solid", color:C.navy } });
  sl.addShape(pres.ShapeType.rect, { x:0, y:0.85, w:"100%", h:0.06,
    fill:{ type:"solid", color:C.amber }, line:{ color:C.amber } });
  // title
  sl.addText(title, { x:0.3, y:0.1, w:9.4, h:0.65,
    fontSize:22, bold:true, color:C.white, fontFace:"Calibri", valign:"middle" });
  // body background
  sl.addShape(pres.ShapeType.rect, { x:0, y:0.91, w:"100%", h:4.72,
    fill:{ type:"solid", color:C.offWhite } });

  if (opts.twoCol) {
    // left col
    sl.addText(opts.leftItems, {
      x:0.3, y:1.05, w:4.5, h:4.4, fontSize:13, color:C.darkTxt,
      fontFace:"Calibri", valign:"top",
    });
    // divider
    sl.addShape(pres.ShapeType.line, {
      x:4.9, y:1.1, w:0, h:4.2, line:{ color:C.ltGray, width:1 }
    });
    // right col
    sl.addText(opts.rightItems, {
      x:5.1, y:1.05, w:4.5, h:4.4, fontSize:13, color:C.darkTxt,
      fontFace:"Calibri", valign:"top",
    });
  } else {
    sl.addText(bodyItems, {
      x:0.35, y:1.05, w:9.3, h:4.4, fontSize:14, color:C.darkTxt,
      fontFace:"Calibri", valign:"top",
    });
  }
  return sl;
}

// ── Helper: key‑point box ────────────────────────────────────
function keyBox(sl, text, x, y, w, h, bg = C.teal) {
  sl.addShape(pres.ShapeType.roundRect, {
    x, y, w, h, rectRadius:0.08,
    fill:{ type:"solid", color:bg }, line:{ color:bg }
  });
  sl.addText(text, { x, y, w, h,
    fontSize:12, color:C.white, bold:true, fontFace:"Calibri",
    align:"center", valign:"middle" });
}

// ══════════════════════════════════════════════════════════════
// SLIDE 1 – TITLE
// ══════════════════════════════════════════════════════════════
{
  const sl = pres.addSlide();
  // navy background
  sl.addShape(pres.ShapeType.rect, { x:0, y:0, w:"100%", h:"100%",
    fill:{ type:"solid", color:C.navy } });
  // teal accent panel right
  sl.addShape(pres.ShapeType.rect, { x:7.0, y:0, w:3.0, h:"100%",
    fill:{ type:"solid", color:C.teal }, transparency:50 });
  // amber top strip
  sl.addShape(pres.ShapeType.rect, { x:0, y:0, w:"100%", h:0.12,
    fill:{ type:"solid", color:C.amber }, line:{ color:C.amber } });
  // amber bottom strip
  sl.addShape(pres.ShapeType.rect, { x:0, y:5.5, w:"100%", h:0.12,
    fill:{ type:"solid", color:C.amber }, line:{ color:C.amber } });

  sl.addText("BIOLOGICAL OXIDATION", {
    x:0.5, y:0.8, w:9.0, h:1.3,
    fontSize:44, bold:true, color:C.white, fontFace:"Calibri",
    align:"left", charSpacing:3
  });
  sl.addText("Bioenergetics  ·  Electron Transport Chain  ·  Oxidative Phosphorylation", {
    x:0.5, y:2.1, w:9.0, h:0.6,
    fontSize:17, color:C.amber, fontFace:"Calibri", align:"left"
  });
  sl.addShape(pres.ShapeType.line, {
    x:0.5, y:2.8, w:6.0, h:0, line:{ color:C.ltGray, width:1 }
  });
  sl.addText("First Year MBBS  |  Biochemistry", {
    x:0.5, y:3.0, w:6, h:0.5,
    fontSize:14, color:C.ltGray, fontFace:"Calibri"
  });
  sl.addText("Based on Lippincott Illustrated Reviews & Basic Medical Biochemistry", {
    x:0.5, y:4.9, w:9.0, h:0.5,
    fontSize:11, color:C.midGray, fontFace:"Calibri", italic:true
  });
}

// ══════════════════════════════════════════════════════════════
// SLIDE 2 – LEARNING OBJECTIVES
// ══════════════════════════════════════════════════════════════
{
  const sl = pres.addSlide();
  sl.addShape(pres.ShapeType.rect, { x:0, y:0, w:"100%", h:"100%",
    fill:{ type:"solid", color:C.offWhite } });
  sl.addShape(pres.ShapeType.rect, { x:0, y:0, w:0.18, h:"100%",
    fill:{ type:"solid", color:C.navy } });
  sl.addText("LEARNING OBJECTIVES", {
    x:0.35, y:0.3, w:9.0, h:0.6,
    fontSize:26, bold:true, color:C.navy, fontFace:"Calibri"
  });
  sl.addShape(pres.ShapeType.line, {
    x:0.35, y:0.96, w:9.0, h:0, line:{ color:C.amber, width:2 }
  });

  const objs = [
    "1.  Define bioenergetics and explain the concept of free energy (ΔG)",
    "2.  Understand standard free energy change (ΔG⁰') and its significance",
    "3.  Describe the structure and function of the mitochondrion",
    "4.  Identify the four complexes of the Electron Transport Chain (ETC)",
    "5.  Explain the chemiosmotic theory of ATP synthesis",
    "6.  Calculate ATP yield from NADH and FADH₂ oxidation",
    "7.  Describe inhibitors and uncouplers of oxidative phosphorylation",
    "8.  Relate defects in biological oxidation to clinical conditions",
  ];
  sl.addText(objs.map((t, i) => ({
    text: t + (i < objs.length-1 ? "\n" : ""),
    options: { color: i % 2 === 0 ? C.darkTxt : C.teal, fontSize:14, fontFace:"Calibri" }
  })), { x:0.5, y:1.1, w:9.2, h:4.2, valign:"top" });
}

// ══════════════════════════════════════════════════════════════
// SECTION 1 DIVIDER
// ══════════════════════════════════════════════════════════════
sectionDivider("Section 1: Bioenergetics & Free Energy",
               "The thermodynamic basis of biological reactions");

// ══════════════════════════════════════════════════════════════
// SLIDE 3 – WHAT IS BIOENERGETICS
// ══════════════════════════════════════════════════════════════
{
  const sl = contentSlide("What is Bioenergetics?", []);

  // 3 concept boxes
  const boxes = [
    { label:"Bioenergetics", body:"Study of energy transfer\nand utilization in\nbiological systems", bg:C.navy },
    { label:"Thermodynamics", body:"Predicts feasibility &\ndirection of reactions\n(not the rate)", bg:C.teal },
    { label:"Kinetics", body:"Measures the RATE\nof a reaction\n(separate from ΔG)", bg:C.amber },
  ];
  boxes.forEach((b, i) => {
    const x = 0.4 + i * 3.2;
    sl.addShape(pres.ShapeType.roundRect, { x, y:1.2, w:2.9, h:1.0,
      rectRadius:0.08, fill:{ type:"solid", color:b.bg }, line:{ color:b.bg } });
    sl.addText(b.label, { x, y:1.2, w:2.9, h:0.45,
      fontSize:15, bold:true, color:C.white, fontFace:"Calibri", align:"center", valign:"middle" });
    sl.addShape(pres.ShapeType.rect, { x, y:2.2, w:2.9, h:1.8,
      fill:{ type:"solid", color:"F0F4FA" }, line:{ color:C.ltGray, width:1 } });
    sl.addText(b.body, { x, y:2.2, w:2.9, h:1.8,
      fontSize:13, color:C.darkTxt, fontFace:"Calibri", align:"center", valign:"middle" });
  });

  sl.addText([
    { text:"Key Insight: ", options:{ bold:true, color:C.navy } },
    { text:"ΔG predicts IF a reaction can occur; enzymes control HOW FAST it occurs.", options:{ color:C.darkTxt } }
  ], { x:0.4, y:4.2, w:9.2, h:0.6, fontSize:13, fontFace:"Calibri",
    fill:{ type:"solid", color:C.ltGray }, margin:8 });
}

// ══════════════════════════════════════════════════════════════
// SLIDE 4 – FREE ENERGY (ΔG)
// ══════════════════════════════════════════════════════════════
{
  const sl = contentSlide("Free Energy (ΔG) — Gibbs Free Energy", []);

  // Equation box
  sl.addShape(pres.ShapeType.roundRect, { x:2.5, y:1.15, w:5.0, h:0.9,
    rectRadius:0.1, fill:{ type:"solid", color:C.navy }, line:{ color:C.navy } });
  sl.addText("ΔG = ΔH – T·ΔS", { x:2.5, y:1.15, w:5.0, h:0.9,
    fontSize:26, bold:true, color:C.amber, fontFace:"Calibri", align:"center", valign:"middle" });

  const items = [
    ["ΔH", "Change in enthalpy (heat content of reactants & products)"],
    ["ΔS", "Change in entropy (degree of disorder / randomness)"],
    ["T",  "Absolute temperature in Kelvin (K = °C + 273)"],
  ];
  items.forEach(([sym, def], i) => {
    const y = 2.3 + i * 0.75;
    sl.addShape(pres.ShapeType.roundRect, { x:0.4, y, w:1.0, h:0.55,
      rectRadius:0.06, fill:{ type:"solid", color:C.teal }, line:{ color:C.teal } });
    sl.addText(sym, { x:0.4, y, w:1.0, h:0.55,
      fontSize:18, bold:true, color:C.white, fontFace:"Calibri", align:"center", valign:"middle" });
    sl.addText(def, { x:1.6, y, w:8.0, h:0.55,
      fontSize:13, color:C.darkTxt, fontFace:"Calibri", valign:"middle" });
  });

  // Decision table
  const rows = [
    [{ text:"ΔG Sign", options:{bold:true,color:C.white,fill:{type:"solid",color:C.navy}} },
     { text:"Reaction Type", options:{bold:true,color:C.white,fill:{type:"solid",color:C.navy}} },
     { text:"Spontaneous?", options:{bold:true,color:C.white,fill:{type:"solid",color:C.navy}} }],
    ["ΔG < 0 (negative)", "Exergonic", "✓ YES – proceeds spontaneously"],
    ["ΔG > 0 (positive)", "Endergonic", "✗ NO – requires energy input"],
    ["ΔG = 0", "Equilibrium", "— No net change"],
  ];
  sl.addTable(rows, {
    x:0.4, y:4.55, w:9.2, h:0.9,
    fontSize:12, fontFace:"Calibri",
    border:{ type:"solid", color:C.ltGray },
    fill:C.offWhite,
    colW:[3.0, 3.0, 3.2],
  });
}

// ══════════════════════════════════════════════════════════════
// SLIDE 5 – ΔG⁰' and ATP
// ══════════════════════════════════════════════════════════════
{
  const sl = contentSlide("Standard Free Energy Change (ΔG⁰') & ATP", []);

  // Two columns
  // Left: ΔG⁰' explanation
  sl.addShape(pres.ShapeType.rect, { x:0.3, y:1.1, w:4.5, h:3.8,
    fill:{ type:"solid", color:"EAF2FB" }, line:{ color:C.ltGray, width:1 } });
  sl.addText("ΔG⁰' — Standard Free Energy", { x:0.3, y:1.1, w:4.5, h:0.5,
    fontSize:14, bold:true, color:C.navy, fontFace:"Calibri",
    fill:{ type:"solid", color:C.teal }, align:"center" });
  sl.addText([
    { text:"• Measured at pH 7.0, 25°C, [reactants] = [products] = 1 mol/L\n", options:{} },
    { text:"• Constant value for any given reaction\n", options:{} },
    { text:"• Useful for comparing reactions\n", options:{} },
    { text:"• Determined from the equilibrium constant (Keq)\n\n", options:{} },
    { text:"ΔG⁰' = –RT ln Keq\n\n", options:{ bold:true, color:C.teal, fontSize:15 } },
    { text:"where R = 1.987 cal/mol·K", options:{ italic:true, fontSize:12 } },
  ], { x:0.4, y:1.7, w:4.3, h:3.0, fontSize:13, color:C.darkTxt, fontFace:"Calibri", valign:"top" });

  // Right: ATP box
  sl.addShape(pres.ShapeType.rect, { x:5.2, y:1.1, w:4.5, h:3.8,
    fill:{ type:"solid", color:"FFF8EC" }, line:{ color:C.ltGray, width:1 } });
  sl.addText("ATP — The Energy Currency", { x:5.2, y:1.1, w:4.5, h:0.5,
    fontSize:14, bold:true, color:C.white, fontFace:"Calibri",
    fill:{ type:"solid", color:C.amber }, align:"center" });
  sl.addText([
    { text:"ATP hydrolysis:\n", options:{ bold:true, color:C.navy, fontSize:14 } },
    { text:"ATP + H₂O → ADP + Pᵢ\nΔG⁰' = –7.3 kcal/mol\n\n", options:{} },
    { text:"Why ATP is special:\n", options:{ bold:true, color:C.navy } },
    { text:"• Intermediate position in phosphate transfer potential\n", options:{} },
    { text:"• Electrostatic repulsion in ATP molecule\n", options:{} },
    { text:"• Resonance stabilization of products\n", options:{} },
    { text:"• Hydration of products\n", options:{} },
  ], { x:5.3, y:1.7, w:4.3, h:3.0, fontSize:13, color:C.darkTxt, fontFace:"Calibri", valign:"top" });
}

// ══════════════════════════════════════════════════════════════
// SECTION 2 DIVIDER
// ══════════════════════════════════════════════════════════════
sectionDivider("Section 2: Mitochondria — The Powerhouse",
               "Structure underpins function in oxidative phosphorylation");

// ══════════════════════════════════════════════════════════════
// SLIDE 6 – MITOCHONDRIAL STRUCTURE
// ══════════════════════════════════════════════════════════════
{
  const sl = contentSlide("Mitochondrial Structure & Function", []);

  const comps = [
    { name:"Outer Membrane", color:C.teal, body:"Contains porins (VDAC)\nFreely permeable to ions\nand small molecules (<5 kDa)" },
    { name:"Intermembrane Space", color:C.midGray, body:"H⁺ accumulates here\nduring electron transport\n(site of proton gradient)" },
    { name:"Inner Membrane", color:C.navy, body:"Impermeable to most ions\nRich in cardiolipin\nForms cristae (↑ surface area)\nContains ETC complexes" },
    { name:"Matrix", color:C.green, body:"TCA cycle enzymes\nβ-oxidation of fatty acids\nPyruvate dehydrogenase\nmtDNA + ribosomes" },
  ];

  comps.forEach((c, i) => {
    const x = 0.3 + (i % 2) * 4.85;
    const y = 1.15 + Math.floor(i / 2) * 2.1;
    sl.addShape(pres.ShapeType.roundRect, { x, y, w:4.5, h:1.85,
      rectRadius:0.08, fill:{ type:"solid", color:"F5F8FF" }, line:{ color:c.color, width:2 } });
    sl.addShape(pres.ShapeType.rect, { x, y, w:4.5, h:0.45,
      fill:{ type:"solid", color:c.color }, line:{ color:c.color } });
    sl.addText(c.name, { x, y, w:4.5, h:0.45,
      fontSize:13, bold:true, color:C.white, fontFace:"Calibri", align:"center", valign:"middle" });
    sl.addText(c.body, { x, y:y+0.5, w:4.5, h:1.3,
      fontSize:12, color:C.darkTxt, fontFace:"Calibri", align:"center", valign:"top" });
  });
}

// ══════════════════════════════════════════════════════════════
// SECTION 3 DIVIDER
// ══════════════════════════════════════════════════════════════
sectionDivider("Section 3: Electron Transport Chain (ETC)",
               "The four complexes that transfer electrons to oxygen");

// ══════════════════════════════════════════════════════════════
// SLIDE 7 – ETC OVERVIEW
// ══════════════════════════════════════════════════════════════
{
  const sl = contentSlide("Electron Transport Chain — Overview", []);

  sl.addText([
    { text:"Electrons from NADH and FADH₂ flow through four protein complexes embedded in the inner mitochondrial membrane, ultimately reducing O₂ to H₂O. " +
      "As electrons pass through the complexes, protons (H⁺) are pumped from the matrix to the intermembrane space, generating a proton gradient used to synthesize ATP.",
      options:{ color:C.darkTxt, fontSize:13 }
    }
  ], { x:0.4, y:1.1, w:9.2, h:0.9, fontFace:"Calibri" });

  // Flow diagram: NADH → C I → CoQ → C III → Cyt c → C IV → O₂
  const flow = [
    { lbl:"NADH\nFADH₂", color:C.teal },
    { lbl:"Complex I\n(NADH\nDehydrogenase)", color:C.navy },
    { lbl:"CoQ\n(Ubiquinone)", color:C.amber },
    { lbl:"Complex III\n(Cytochrome\nbc₁)", color:C.navy },
    { lbl:"Cyt c", color:C.teal },
    { lbl:"Complex IV\n(Cytochrome\nc Oxidase)", color:C.navy },
    { lbl:"H₂O\n(O₂ reduced)", color:C.green },
  ];
  const boxW = 1.25, boxH = 1.5, startX = 0.15, y = 2.1;
  flow.forEach((f, i) => {
    const x = startX + i * 1.42;
    sl.addShape(pres.ShapeType.roundRect, { x, y, w:boxW, h:boxH,
      rectRadius:0.07, fill:{ type:"solid", color:f.color }, line:{ color:f.color } });
    sl.addText(f.lbl, { x, y, w:boxW, h:boxH,
      fontSize:10, bold:true, color:C.white, fontFace:"Calibri", align:"center", valign:"middle" });
    if (i < flow.length - 1) {
      sl.addShape(pres.ShapeType.line, { x:x+boxW, y:y+boxH/2, w:0.17, h:0,
        line:{ color:C.amber, width:2 } });
    }
  });

  // FADH2 arrow to CoQ
  sl.addText("FADH₂ → Complex II → CoQ", { x:0.3, y:3.75, w:9.2, h:0.4,
    fontSize:12, italic:true, color:C.midGray, fontFace:"Calibri", align:"center" });

  // H+ pumping note
  sl.addShape(pres.ShapeType.roundRect, { x:0.3, y:4.2, w:9.4, h:0.55,
    rectRadius:0.07, fill:{ type:"solid", color:"EAF7F0" }, line:{ color:C.green, width:1 } });
  sl.addText("H⁺ pumped at: Complex I (4H⁺)  ·  Complex III (4H⁺)  ·  Complex IV (2H⁺)  →  Total: 10 H⁺ per NADH",
    { x:0.3, y:4.2, w:9.4, h:0.55,
      fontSize:12, bold:true, color:C.green, fontFace:"Calibri", align:"center", valign:"middle" });
}

// ══════════════════════════════════════════════════════════════
// SLIDE 8 – THE FOUR COMPLEXES
// ══════════════════════════════════════════════════════════════
{
  const sl = pres.addSlide();
  sl.addShape(pres.ShapeType.rect, { x:0, y:0, w:"100%", h:0.85,
    fill:{ type:"solid", color:C.navy } });
  sl.addShape(pres.ShapeType.rect, { x:0, y:0.85, w:"100%", h:0.06,
    fill:{ type:"solid", color:C.amber }, line:{ color:C.amber } });
  sl.addText("The Four ETC Complexes", { x:0.3, y:0.1, w:9.4, h:0.65,
    fontSize:22, bold:true, color:C.white, fontFace:"Calibri", valign:"middle" });
  sl.addShape(pres.ShapeType.rect, { x:0, y:0.91, w:"100%", h:4.72,
    fill:{ type:"solid", color:C.offWhite } });

  const complexes = [
    {
      num:"I", name:"NADH Dehydrogenase\n(NADH-CoQ Reductase)",
      sub:"Accepts 2e⁻ from NADH\nOxidizes NADH → NAD⁺\nTransfers to CoQ (ubiquinone)\nPumps 4H⁺ to IMS\nContains FMN + Fe-S centers\nInhibitor: Rotenone, Amytal",
      col:C.navy
    },
    {
      num:"II", name:"Succinate Dehydrogenase\n(Succinate-CoQ Reductase)",
      sub:"Accepts 2e⁻ from FADH₂\nOxidizes succinate → fumarate\n(TCA cycle enzyme!)\nTransfers to CoQ\nDoes NOT pump H⁺\nContains FAD + Fe-S centers",
      col:"3D5A80"
    },
    {
      num:"III", name:"Cytochrome bc₁ Complex\n(CoQ-Cyt c Reductase)",
      sub:"Accepts e⁻ from CoQ\nTransfers to cytochrome c\nPumps 4H⁺ to IMS\nContains cytochromes b, c₁\nand Fe-S (Rieske) protein\nInhibitor: Antimycin A",
      col:C.teal
    },
    {
      num:"IV", name:"Cytochrome c Oxidase\n(Complex IV)",
      sub:"Accepts e⁻ from Cyt c\nFinal electron acceptor: O₂\nReduces O₂ → H₂O\nPumps 2H⁺ to IMS\nContains Cu centers + heme a\nInhibitor: Cyanide, CO, Azide",
      col:C.green
    },
  ];

  complexes.forEach((c, i) => {
    const x = 0.15 + i * 2.45;
    // header
    sl.addShape(pres.ShapeType.roundRect, { x, y:1.0, w:2.3, h:0.55,
      rectRadius:0.07, fill:{ type:"solid", color:c.col }, line:{ color:c.col } });
    sl.addText(`Complex ${c.num}`, { x, y:1.0, w:2.3, h:0.55,
      fontSize:15, bold:true, color:C.white, fontFace:"Calibri", align:"center", valign:"middle" });
    // name
    sl.addShape(pres.ShapeType.rect, { x, y:1.55, w:2.3, h:0.7,
      fill:{ type:"solid", color:C.ltGray }, line:{ color:C.ltGray } });
    sl.addText(c.name, { x, y:1.55, w:2.3, h:0.7,
      fontSize:10, bold:true, color:C.navy, fontFace:"Calibri", align:"center", valign:"middle" });
    // body
    sl.addShape(pres.ShapeType.rect, { x, y:2.25, w:2.3, h:3.0,
      fill:{ type:"solid", color:"F0F4FA" }, line:{ color:C.ltGray, width:1 } });
    sl.addText(c.sub, { x:x+0.08, y:2.3, w:2.14, h:2.9,
      fontSize:10.5, color:C.darkTxt, fontFace:"Calibri", valign:"top",
      bullet:true });
  });
}

// ══════════════════════════════════════════════════════════════
// SLIDE 9 – MOBILE ELECTRON CARRIERS (CoQ & Cyt c)
// ══════════════════════════════════════════════════════════════
{
  const sl = contentSlide("Mobile Electron Carriers: CoQ & Cytochrome c", []);

  // CoQ
  sl.addShape(pres.ShapeType.roundRect, { x:0.3, y:1.15, w:4.5, h:3.9,
    rectRadius:0.08, fill:{ type:"solid", color:"FFFDF0" }, line:{ color:C.amber, width:2 } });
  sl.addShape(pres.ShapeType.rect, { x:0.3, y:1.15, w:4.5, h:0.48,
    fill:{ type:"solid", color:C.amber }, line:{ color:C.amber } });
  sl.addText("CoQ (Ubiquinone / Q)", { x:0.3, y:1.15, w:4.5, h:0.48,
    fontSize:14, bold:true, color:C.white, fontFace:"Calibri", align:"center", valign:"middle" });
  sl.addText([
    { text:"• Small, hydrophobic, lipid-soluble molecule\n", options:{} },
    { text:"• Freely diffuses in inner mitochondrial membrane\n", options:{} },
    { text:"• Collects electrons from Complex I and II\n", options:{} },
    { text:"• Transfers to Complex III\n", options:{} },
    { text:"• Carries 2 electrons + 2 H⁺ (as ubiquinol, QH₂)\n\n", options:{} },
    { text:"Oxidized:  Q  (ubiquinone)\n", options:{ bold:true, color:C.amber } },
    { text:"Reduced:  QH₂  (ubiquinol)", options:{ bold:true, color:C.teal } },
  ], { x:0.4, y:1.73, w:4.3, h:3.2, fontSize:12.5, color:C.darkTxt, fontFace:"Calibri", valign:"top" });

  // Cyt c
  sl.addShape(pres.ShapeType.roundRect, { x:5.2, y:1.15, w:4.5, h:3.9,
    rectRadius:0.08, fill:{ type:"solid", color:"F0F6FF" }, line:{ color:C.teal, width:2 } });
  sl.addShape(pres.ShapeType.rect, { x:5.2, y:1.15, w:4.5, h:0.48,
    fill:{ type:"solid", color:C.teal }, line:{ color:C.teal } });
  sl.addText("Cytochrome c", { x:5.2, y:1.15, w:4.5, h:0.48,
    fontSize:14, bold:true, color:C.white, fontFace:"Calibri", align:"center", valign:"middle" });
  sl.addText([
    { text:"• Small, water-soluble heme protein\n", options:{} },
    { text:"• Located on outer face of inner membrane\n", options:{} },
    { text:"• Transfers electrons from Complex III → IV\n", options:{} },
    { text:"• Carries only ONE electron at a time\n", options:{} },
    { text:"• Contains iron (Fe²⁺/Fe³⁺) redox center\n\n", options:{} },
    { text:"Clinical Note:\n", options:{ bold:true, color:C.red } },
    { text:"Released from mitochondria in apoptosis\n→ activates caspase cascade", options:{ italic:true, color:C.red } },
  ], { x:5.3, y:1.73, w:4.3, h:3.2, fontSize:12.5, color:C.darkTxt, fontFace:"Calibri", valign:"top" });
}

// ══════════════════════════════════════════════════════════════
// SECTION 4 DIVIDER
// ══════════════════════════════════════════════════════════════
sectionDivider("Section 4: Oxidative Phosphorylation & ATP Synthesis",
               "Chemiosmotic theory and the F₀F₁-ATPase");

// ══════════════════════════════════════════════════════════════
// SLIDE 10 – CHEMIOSMOTIC THEORY
// ══════════════════════════════════════════════════════════════
{
  const sl = contentSlide("Chemiosmotic Theory (Mitchell, 1961)", []);

  sl.addText("Peter Mitchell proposed that ATP synthesis is driven by an electrochemical proton gradient (Δp) across the inner mitochondrial membrane — NOT by a direct chemical intermediate.",
    { x:0.4, y:1.1, w:9.2, h:0.65, fontSize:13, color:C.darkTxt, fontFace:"Calibri" });

  // 4 key steps numbered
  const steps = [
    { n:"1", title:"Electron Transport", body:"ETC complexes transfer electrons, releasing energy used to pump H⁺ from matrix → IMS" },
    { n:"2", title:"Proton Gradient (Δp)", body:"H⁺ accumulates in IMS → electrical potential (Δψ) + chemical gradient (ΔpH) = proton motive force" },
    { n:"3", title:"ATP Synthesis", body:"H⁺ flows back into matrix through F₀ channel of ATP synthase → drives rotation of F₁ subunit → ATP formed" },
    { n:"4", title:"Coupling", body:"Electron transport CANNOT proceed without ATP synthesis (coupled) — inhibit one, inhibit both" },
  ];

  steps.forEach((s, i) => {
    const x = i < 2 ? 0.3 : 5.1;
    const y = i % 2 === 0 ? 1.95 : 3.65;
    sl.addShape(pres.ShapeType.roundRect, { x, y, w:4.5, h:1.5,
      rectRadius:0.08, fill:{ type:"solid", color:"F5F8FF" }, line:{ color:C.teal, width:1.5 } });
    sl.addShape(pres.ShapeType.ellipse, { x:x+0.1, y:y+0.08, w:0.55, h:0.55,
      fill:{ type:"solid", color:C.teal }, line:{ color:C.teal } });
    sl.addText(s.n, { x:x+0.1, y:y+0.08, w:0.55, h:0.55,
      fontSize:16, bold:true, color:C.white, fontFace:"Calibri", align:"center", valign:"middle" });
    sl.addText(s.title, { x:x+0.75, y:y+0.1, w:3.6, h:0.4,
      fontSize:13, bold:true, color:C.navy, fontFace:"Calibri" });
    sl.addText(s.body, { x:x+0.75, y:y+0.55, w:3.6, h:0.85,
      fontSize:11.5, color:C.darkTxt, fontFace:"Calibri", valign:"top" });
  });

  // Nobel note
  sl.addShape(pres.ShapeType.roundRect, { x:0.3, y:5.05, w:9.4, h:0.45,
    rectRadius:0.06, fill:{ type:"solid", color:"FFF5D6" }, line:{ color:C.amber } });
  sl.addText("🏆  Peter Mitchell was awarded the Nobel Prize in Chemistry (1978) for the chemiosmotic theory",
    { x:0.3, y:5.05, w:9.4, h:0.45,
      fontSize:12, bold:true, color:C.navy, fontFace:"Calibri", align:"center", valign:"middle" });
}

// ══════════════════════════════════════════════════════════════
// SLIDE 11 – ATP SYNTHASE (F₀F₁-ATPase)
// ══════════════════════════════════════════════════════════════
{
  const sl = contentSlide("ATP Synthase (F₀F₁-ATPase)", []);

  // F0 box
  sl.addShape(pres.ShapeType.roundRect, { x:0.3, y:1.15, w:4.4, h:3.8,
    rectRadius:0.08, fill:{ type:"solid", color:"EAF2FB" }, line:{ color:C.navy, width:2 } });
  sl.addText("F₀ Subunit (Membrane sector)", { x:0.3, y:1.15, w:4.4, h:0.5,
    fontSize:13, bold:true, color:C.white, fontFace:"Calibri",
    fill:{ type:"solid", color:C.navy }, align:"center" });
  sl.addText([
    { text:"• Embedded in inner mitochondrial membrane\n", options:{} },
    { text:"• Forms the proton channel / pore\n", options:{} },
    { text:"• Consists of a, b, c subunits\n", options:{} },
    { text:"• c-ring rotation driven by H⁺ flow\n", options:{} },
    { text:"• Transmits rotation to F₁ via γ subunit\n\n", options:{} },
    { text:"Oligomycin blocks F₀ → inhibits ATP synthesis", options:{ bold:true, color:C.red, italic:true } },
  ], { x:0.4, y:1.75, w:4.2, h:3.1, fontSize:12.5, color:C.darkTxt, fontFace:"Calibri", valign:"top" });

  // F1 box
  sl.addShape(pres.ShapeType.roundRect, { x:5.3, y:1.15, w:4.4, h:3.8,
    rectRadius:0.08, fill:{ type:"solid", color:"FFF5EC" }, line:{ color:C.amber, width:2 } });
  sl.addText("F₁ Subunit (Matrix headpiece)", { x:5.3, y:1.15, w:4.4, h:0.5,
    fontSize:13, bold:true, color:C.white, fontFace:"Calibri",
    fill:{ type:"solid", color:C.amber }, align:"center" });
  sl.addText([
    { text:"• Projects into mitochondrial matrix\n", options:{} },
    { text:"• α₃β₃γδε subunit composition\n", options:{} },
    { text:"• β subunits contain catalytic sites\n", options:{} },
    { text:"• 3 catalytic sites cycle through states:\n", options:{} },
    { text:"   Open → Loose → Tight (binding change)\n", options:{ italic:true } },
    { text:"• Each 360° rotation produces 3 ATP\n\n", options:{} },
    { text:"3 H⁺ required per ATP synthesized", options:{ bold:true, color:C.amber, italic:true } },
  ], { x:5.4, y:1.75, w:4.2, h:3.1, fontSize:12.5, color:C.darkTxt, fontFace:"Calibri", valign:"top" });

  sl.addText("Stoichiometry: ~2.5 ATP per NADH  |  ~1.5 ATP per FADH₂", {
    x:0.3, y:5.05, w:9.4, h:0.42,
    fontSize:14, bold:true, color:C.white, fontFace:"Calibri",
    fill:{ type:"solid", color:C.teal }, align:"center", valign:"middle"
  });
}

// ══════════════════════════════════════════════════════════════
// SLIDE 12 – ATP YIELD
// ══════════════════════════════════════════════════════════════
{
  const sl = contentSlide("ATP Yield — Accounting Sheet", []);

  // Header note
  sl.addText("For complete oxidation of one glucose molecule (aerobic glycolysis + TCA + OXPHOS):",
    { x:0.4, y:1.05, w:9.2, h:0.4, fontSize:12.5, italic:true, color:C.midGray, fontFace:"Calibri" });

  const rows = [
    [{ text:"Pathway / Step", options:{ bold:true, color:C.white, fill:{type:"solid",color:C.navy} } },
     { text:"NADH", options:{ bold:true, color:C.white, fill:{type:"solid",color:C.navy} } },
     { text:"FADH₂", options:{ bold:true, color:C.white, fill:{type:"solid",color:C.navy} } },
     { text:"Direct ATP/GTP", options:{ bold:true, color:C.white, fill:{type:"solid",color:C.navy} } },
     { text:"ATP Equivalent", options:{ bold:true, color:C.white, fill:{type:"solid",color:C.navy} } }],
    ["Glycolysis (cytoplasm)", "2 NADH", "—", "2 ATP", "2 + 3–5"],
    ["Pyruvate Dehydrogenase (×2)", "2 NADH", "—", "—", "5"],
    ["TCA Cycle (×2)", "6 NADH", "2 FADH₂", "2 GTP", "6×2.5 + 2×1.5 + 2 = 20"],
    ["Subtotal", "10 NADH", "2 FADH₂", "4 ATP", "~30–32 ATP"],
    [{ text:"TOTAL (net)", options:{ bold:true, color:C.white, fill:{type:"solid",color:C.teal} } },
     { text:"10", options:{ bold:true, color:C.white, fill:{type:"solid",color:C.teal} } },
     { text:"2", options:{ bold:true, color:C.white, fill:{type:"solid",color:C.teal} } },
     { text:"4", options:{ bold:true, color:C.white, fill:{type:"solid",color:C.teal} } },
     { text:"~30–32 ATP", options:{ bold:true, color:C.white, fill:{type:"solid",color:C.teal} } }],
  ];
  sl.addTable(rows, {
    x:0.3, y:1.55, w:9.4, h:2.8,
    fontSize:12.5, fontFace:"Calibri",
    border:{ type:"solid", color:C.ltGray },
    colW:[3.4, 1.4, 1.4, 1.8, 2.4],
  });

  sl.addText("Note: Old textbooks stated ~36–38 ATP. Modern P/O ratio estimates give ~30–32 ATP (2.5 per NADH; 1.5 per FADH₂).",
    { x:0.3, y:4.55, w:9.4, h:0.5,
      fontSize:12, italic:true, color:C.midGray, fontFace:"Calibri" });

  // Energy efficiency box
  sl.addShape(pres.ShapeType.roundRect, { x:0.3, y:5.1, w:9.4, h:0.45,
    rectRadius:0.06, fill:{ type:"solid", color:"EAF7F0" }, line:{ color:C.green } });
  sl.addText("Energy efficiency: ~40% of energy from glucose → ATP  |  Remaining ~60% → HEAT (maintains body temperature)",
    { x:0.3, y:5.1, w:9.4, h:0.45,
      fontSize:11.5, bold:true, color:C.green, fontFace:"Calibri", align:"center", valign:"middle" });
}

// ══════════════════════════════════════════════════════════════
// SECTION 5 DIVIDER
// ══════════════════════════════════════════════════════════════
sectionDivider("Section 5: Inhibitors & Uncouplers",
               "Poisons of the electron transport chain");

// ══════════════════════════════════════════════════════════════
// SLIDE 13 – INHIBITORS
// ══════════════════════════════════════════════════════════════
{
  const sl = contentSlide("Inhibitors of the Electron Transport Chain", []);

  const rows = [
    [{ text:"Inhibitor", options:{ bold:true, color:C.white, fill:{type:"solid",color:C.navy} } },
     { text:"Site of Action", options:{ bold:true, color:C.white, fill:{type:"solid",color:C.navy} } },
     { text:"Mechanism", options:{ bold:true, color:C.white, fill:{type:"solid",color:C.navy} } },
     { text:"Clinical Relevance", options:{ bold:true, color:C.white, fill:{type:"solid",color:C.navy} } }],
    ["Rotenone / Amytal", "Complex I", "Block NADH → CoQ electron transfer", "Pesticide; experimental model of Parkinson's disease"],
    ["Antimycin A", "Complex III", "Block CoQ → Cyt c electron transfer", "Fish poison; experimental tool"],
    ["Cyanide (CN⁻)", "Complex IV", "Binds Fe³⁺ of Cyt c oxidase → blocks O₂ reduction", "Cyanide poisoning → cellular asphyxia; Rx: hydroxocobalamin"],
    ["Carbon Monoxide (CO)", "Complex IV", "Binds Fe²⁺ of Cyt c oxidase (like O₂)", "CO poisoning; cherry-red skin; Rx: 100% O₂"],
    ["Azide / H₂S", "Complex IV", "Inhibit Cyt c oxidase", "H₂S — 'rotten egg' poisoning"],
    ["Oligomycin", "F₀ subunit (ATP synthase)", "Block proton channel → no ATP synthesis", "Antibiotic; research tool"],
  ];
  sl.addTable(rows, {
    x:0.2, y:1.1, w:9.6, h:4.2,
    fontSize:11, fontFace:"Calibri",
    border:{ type:"solid", color:C.ltGray },
    fill:{ type:"solid", color:C.offWhite },
    colW:[2.0, 1.8, 2.8, 3.0],
  });

  sl.addText("Key concept: ETC inhibitors → ATP production stops → cell death (especially cardiac & neural tissue)",
    { x:0.3, y:5.38, w:9.4, h:0.38,
      fontSize:11.5, bold:true, italic:true, color:C.red, fontFace:"Calibri", align:"center" });
}

// ══════════════════════════════════════════════════════════════
// SLIDE 14 – UNCOUPLERS
// ══════════════════════════════════════════════════════════════
{
  const sl = contentSlide("Uncouplers of Oxidative Phosphorylation", []);

  sl.addText("Uncouplers allow protons to re-enter the matrix WITHOUT going through ATP synthase → ETC continues but ATP synthesis stops → energy released as HEAT",
    { x:0.4, y:1.1, w:9.2, h:0.7, fontSize:13, color:C.darkTxt, fontFace:"Calibri" });

  const boxes = [
    {
      title:"2,4-Dinitrophenol (DNP)", col:C.red,
      body:"• Classic chemical uncoupler\n• Lipid-soluble weak acid\n• Carries H⁺ across membrane\n• Used as weight-loss drug (banned)\n• Hyperthermia, hyperpyrexia, death"
    },
    {
      title:"Thermogenin (UCP-1)", col:C.amber,
      body:"• Natural uncoupling protein\n• Found in brown adipose tissue\n• Creates a 'proton leak'\n• Generates heat (thermogenesis)\n• Critical for neonates & hibernating animals"
    },
    {
      title:"Thyroid Hormones", col:C.teal,
      body:"• Increase UCP expression\n• Increase basal metabolic rate\n• Hyperthyroidism → weight loss, heat\n• Hypothyroidism → cold intolerance\n• Regulate overall metabolic rate"
    },
  ];

  boxes.forEach((b, i) => {
    const x = 0.25 + i * 3.25;
    sl.addShape(pres.ShapeType.roundRect, { x, y:1.95, w:3.0, h:3.5,
      rectRadius:0.08, fill:{ type:"solid", color:"F5F8FF" }, line:{ color:b.col, width:2 } });
    sl.addShape(pres.ShapeType.rect, { x, y:1.95, w:3.0, h:0.52,
      fill:{ type:"solid", color:b.col }, line:{ color:b.col } });
    sl.addText(b.title, { x, y:1.95, w:3.0, h:0.52,
      fontSize:12, bold:true, color:C.white, fontFace:"Calibri", align:"center", valign:"middle" });
    sl.addText(b.body, { x:x+0.1, y:2.52, w:2.8, h:2.85,
      fontSize:11.5, color:C.darkTxt, fontFace:"Calibri", valign:"top" });
  });
}

// ══════════════════════════════════════════════════════════════
// SECTION 6 DIVIDER
// ══════════════════════════════════════════════════════════════
sectionDivider("Section 6: Regulation & Clinical Correlations",
               "Pathological conditions & clinical significance");

// ══════════════════════════════════════════════════════════════
// SLIDE 15 – REGULATION OF OXPHOS
// ══════════════════════════════════════════════════════════════
{
  const sl = contentSlide("Regulation of Oxidative Phosphorylation", []);

  sl.addText("The rate of ETC is tightly coupled to the ATP demand of the cell via the ADP/ATP ratio:",
    { x:0.4, y:1.1, w:9.2, h:0.5, fontSize:13, color:C.darkTxt, fontFace:"Calibri" });

  // Cycle diagram via boxes & arrows
  const cycle = [
    { txt:"ATP demand ↑\n(exercise, work)", col:C.navy, x:0.4, y:1.8 },
    { txt:"ADP + Pᵢ ↑\nin matrix", col:C.teal, x:3.3, y:1.8 },
    { txt:"H⁺ flux through\nATP synthase ↑", col:C.amber, x:6.2, y:1.8 },
    { txt:"ETC rate ↑\n(O₂ consumption ↑)", col:C.green, x:6.2, y:3.4 },
    { txt:"NADH/FADH₂\noxidized faster", col:C.teal, x:3.3, y:3.4 },
    { txt:"More ATP\nsynthesized", col:C.navy, x:0.4, y:3.4 },
  ];
  cycle.forEach((c, i) => {
    sl.addShape(pres.ShapeType.roundRect, { x:c.x, y:c.y, w:2.7, h:1.2,
      rectRadius:0.07, fill:{ type:"solid", color:c.col }, line:{ color:c.col } });
    sl.addText(c.txt, { x:c.x, y:c.y, w:2.7, h:1.2,
      fontSize:12, bold:true, color:C.white, fontFace:"Calibri", align:"center", valign:"middle" });
  });
  // Arrows
  [[3.1,2.4,0.2,0],[6.0,2.4,0.2,0],[8.9,2.4,0,0.5],[8.9,3.5,-0.2,0],[6.0,3.95,-0.3,0],[3.0,3.95,-0.3,0]].forEach(([x,y,w,h]) => {
    if (w !== 0) sl.addShape(pres.ShapeType.line, { x, y, w, h:0, line:{ color:C.amber, width:1.5 } });
    else sl.addShape(pres.ShapeType.line, { x, y, w:0, h, line:{ color:C.amber, width:1.5 } });
  });

  sl.addText("Respiratory Control Ratio (RCR): Rate of O₂ consumption (ADP present) ÷ Rate (no ADP)  — measures coupling efficiency",
    { x:0.3, y:4.8, w:9.4, h:0.6,
      fontSize:12, italic:true, color:C.midGray, fontFace:"Calibri",
      fill:{ type:"solid", color:C.ltGray }, margin:6 });
}

// ══════════════════════════════════════════════════════════════
// SLIDE 16 – CLINICAL CORRELATIONS
// ══════════════════════════════════════════════════════════════
{
  const sl = contentSlide("Clinical Correlations", []);

  const cards = [
    {
      title:"Mitochondrial Myopathies\n(OXPHOS Diseases)",
      col:C.navy,
      body:"• Mutations in mtDNA (maternal inheritance)\n• Affects tissues with high energy demand\n• Features: myopathy, encephalopathy, lactic acidosis\n• Examples: MELAS, MERRF, Leigh syndrome\n• Diagnosis: ragged red fibres on Gomori stain"
    },
    {
      title:"Cyanide Poisoning",
      col:C.red,
      body:"• Inhibits Complex IV (Cyt c oxidase)\n• Venous blood bright red (O₂ not consumed)\n• Bitter almond smell\n• Lactic acidosis (anaerobic glycolysis)\n• Treatment: hydroxocobalamin (binds CN⁻)"
    },
    {
      title:"Carbon Monoxide Poisoning",
      col:C.amber,
      body:"• Inhibits Complex IV AND haemoglobin\n• Cherry-red skin\n• Cannot use O₂ for electron transport\n• Headache, confusion, coma, death\n• Treatment: 100% O₂ / hyperbaric O₂"
    },
    {
      title:"Ischemia-Reperfusion Injury",
      col:C.teal,
      body:"• Ischaemia → ETC stops → ATP depletion\n• Reperfusion → burst of O₂ → reactive O₂ species (ROS)\n• ROS damage mitochondria & cells\n• Seen in: MI, stroke, organ transplant\n• Antioxidants (Vit E, C) may limit damage"
    },
  ];

  cards.forEach((c, i) => {
    const x = i < 2 ? 0.25 + i * 4.85 : 0.25 + (i-2) * 4.85;
    const y = i < 2 ? 1.1 : 3.2;
    sl.addShape(pres.ShapeType.roundRect, { x, y, w:4.5, h:1.9,
      rectRadius:0.07, fill:{ type:"solid", color:"F5F8FF" }, line:{ color:c.col, width:2 } });
    sl.addShape(pres.ShapeType.rect, { x, y, w:4.5, h:0.48,
      fill:{ type:"solid", color:c.col }, line:{ color:c.col } });
    sl.addText(c.title, { x, y, w:4.5, h:0.48,
      fontSize:12, bold:true, color:C.white, fontFace:"Calibri", align:"center", valign:"middle" });
    sl.addText(c.body, { x:x+0.1, y:y+0.52, w:4.3, h:1.3,
      fontSize:10.5, color:C.darkTxt, fontFace:"Calibri", valign:"top" });
  });
}

// ══════════════════════════════════════════════════════════════
// SLIDE 17 – SHUTTLE SYSTEMS
// ══════════════════════════════════════════════════════════════
{
  const sl = contentSlide("Cytoplasmic NADH — Shuttle Systems", []);

  sl.addText("Cytoplasmic NADH cannot cross the inner mitochondrial membrane directly. Two shuttle systems transfer electrons from cytoplasmic NADH into the mitochondria:",
    { x:0.4, y:1.1, w:9.2, h:0.6, fontSize:13, color:C.darkTxt, fontFace:"Calibri" });

  // Malate-Aspartate shuttle
  sl.addShape(pres.ShapeType.roundRect, { x:0.3, y:1.85, w:4.4, h:3.5,
    rectRadius:0.08, fill:{ type:"solid", color:"EAF7F0" }, line:{ color:C.green, width:2 } });
  sl.addText("Malate-Aspartate Shuttle", { x:0.3, y:1.85, w:4.4, h:0.5,
    fontSize:13, bold:true, color:C.white, fontFace:"Calibri",
    fill:{ type:"solid", color:C.green }, align:"center" });
  sl.addText([
    { text:"Tissues: heart, liver, kidney\n\n", options:{ bold:true } },
    { text:"Cytoplasmic NADH → mitochondrial NADH\n", options:{} },
    { text:"Yield: 2.5 ATP per cytoplasmic NADH\n\n", options:{} },
    { text:"Steps:\n", options:{ bold:true } },
    { text:"OAA reduced to malate (cytoplasm)\n→ Malate enters mitochondria\n→ Malate reoxidized to OAA\n→ Generates mitochondrial NADH", options:{} },
  ], { x:0.4, y:2.42, w:4.2, h:2.8, fontSize:12, color:C.darkTxt, fontFace:"Calibri", valign:"top" });

  // Glycerol-3-phosphate shuttle
  sl.addShape(pres.ShapeType.roundRect, { x:5.3, y:1.85, w:4.4, h:3.5,
    rectRadius:0.08, fill:{ type:"solid", color:"FFF8EC" }, line:{ color:C.amber, width:2 } });
  sl.addText("Glycerol-3-Phosphate Shuttle", { x:5.3, y:1.85, w:4.4, h:0.5,
    fontSize:13, bold:true, color:C.white, fontFace:"Calibri",
    fill:{ type:"solid", color:C.amber }, align:"center" });
  sl.addText([
    { text:"Tissues: brain, skeletal muscle\n\n", options:{ bold:true } },
    { text:"Cytoplasmic NADH → mitochondrial FADH₂\n", options:{} },
    { text:"Yield: 1.5 ATP per cytoplasmic NADH\n\n", options:{} },
    { text:"Steps:\n", options:{ bold:true } },
    { text:"DHAP reduced to G3P (cytoplasm)\n→ G3P oxidized by mitochondrial G3PDH\n→ Generates FADH₂\n→ Enters ETC at CoQ", options:{} },
  ], { x:5.4, y:2.42, w:4.2, h:2.8, fontSize:12, color:C.darkTxt, fontFace:"Calibri", valign:"top" });
}

// ══════════════════════════════════════════════════════════════
// SLIDE 18 – REACTIVE OXYGEN SPECIES
// ══════════════════════════════════════════════════════════════
{
  const sl = contentSlide("Reactive Oxygen Species (ROS) from ETC", []);

  sl.addText("~1–3% of electrons 'leak' from the ETC (mainly at Complex I and III) and react with O₂ to form reactive oxygen species:",
    { x:0.4, y:1.1, w:9.2, h:0.55, fontSize:13, color:C.darkTxt, fontFace:"Calibri" });

  const ros = [
    { f:"O₂ + e⁻ →", n:"Superoxide (O₂•⁻)", col:C.red },
    { f:"O₂•⁻ + e⁻ + 2H⁺ →", n:"Hydrogen Peroxide (H₂O₂)", col:C.amber },
    { f:"H₂O₂ + Fe²⁺ →", n:"Hydroxyl Radical (OH•)", col:C.red },
  ];
  ros.forEach((r, i) => {
    const y = 1.85 + i * 0.6;
    sl.addText(r.f, { x:0.4, y, w:3.2, h:0.5, fontSize:13, color:C.midGray, fontFace:"Calibri", align:"right" });
    sl.addShape(pres.ShapeType.roundRect, { x:3.7, y:y+0.02, w:3.6, h:0.45,
      rectRadius:0.06, fill:{ type:"solid", color:r.col }, line:{ color:r.col } });
    sl.addText(r.n, { x:3.7, y:y+0.02, w:3.6, h:0.45,
      fontSize:13, bold:true, color:C.white, fontFace:"Calibri", align:"center", valign:"middle" });
  });

  // Defenses
  sl.addShape(pres.ShapeType.rect, { x:0.3, y:3.8, w:9.4, h:0.4,
    fill:{ type:"solid", color:C.navy }, line:{ color:C.navy } });
  sl.addText("Antioxidant Defenses", { x:0.3, y:3.8, w:9.4, h:0.4,
    fontSize:13, bold:true, color:C.white, fontFace:"Calibri", align:"center" });

  const def = [
    { e:"Superoxide Dismutase (SOD)", r:"O₂•⁻ → H₂O₂ + O₂", col:C.teal },
    { e:"Catalase", r:"H₂O₂ → H₂O + O₂", col:C.green },
    { e:"Glutathione Peroxidase", r:"H₂O₂ + 2GSH → GSSG + 2H₂O", col:C.amber },
    { e:"Vitamin E & C, β-carotene", r:"Non-enzymatic scavengers", col:C.midGray },
  ];
  def.forEach((d, i) => {
    const x = 0.3 + (i % 2) * 4.85;
    const y = 4.3 + Math.floor(i / 2) * 0.55;
    sl.addText(`${d.e}:  `, { x, y, w:2.8, h:0.48, fontSize:11.5, bold:true, color:d.col, fontFace:"Calibri", align:"right" });
    sl.addText(d.r, { x:x+2.8, y, w:2.0, h:0.48, fontSize:11.5, color:C.darkTxt, fontFace:"Calibri" });
  });
}

// ══════════════════════════════════════════════════════════════
// SLIDE 19 – SUMMARY / TAKE-HOME MESSAGES
// ══════════════════════════════════════════════════════════════
{
  const sl = pres.addSlide();
  sl.addShape(pres.ShapeType.rect, { x:0, y:0, w:"100%", h:"100%",
    fill:{ type:"solid", color:C.navy } });
  sl.addShape(pres.ShapeType.rect, { x:0, y:0, w:"100%", h:0.12,
    fill:{ type:"solid", color:C.amber }, line:{ color:C.amber } });
  sl.addShape(pres.ShapeType.rect, { x:0, y:5.5, w:"100%", h:0.12,
    fill:{ type:"solid", color:C.amber }, line:{ color:C.amber } });

  sl.addText("KEY TAKE-HOME MESSAGES", {
    x:0.5, y:0.2, w:9.0, h:0.7,
    fontSize:26, bold:true, color:C.white, fontFace:"Calibri", charSpacing:2
  });
  sl.addShape(pres.ShapeType.line, { x:0.5, y:0.95, w:9.0, h:0,
    line:{ color:C.amber, width:2 } });

  const msgs = [
    ["ΔG < 0", "Reaction proceeds spontaneously (exergonic)"],
    ["ETC has 4 complexes", "I → CoQ → III → Cyt c → IV → O₂ (Complex II bypasses CoQ pathway)"],
    ["Proton gradient", "Established by Complexes I, III, IV; drives ATP synthase (chemiosmosis)"],
    ["ATP yield", "~2.5 ATP/NADH; ~1.5 ATP/FADH₂; ~30-32 ATP per glucose"],
    ["Inhibitors", "Rotenone (I), Antimycin A (III), Cyanide/CO (IV), Oligomycin (synthase)"],
    ["Uncouplers", "Allow H⁺ re-entry bypassing ATPase → heat not ATP (DNP, UCP-1)"],
    ["Clinical link", "OXPHOS diseases, cyanide poisoning, ischaemia-reperfusion injury"],
  ];

  msgs.forEach(([key, val], i) => {
    const y = 1.1 + i * 0.59;
    sl.addShape(pres.ShapeType.roundRect, { x:0.4, y, w:2.1, h:0.48,
      rectRadius:0.06, fill:{ type:"solid", color:C.teal }, line:{ color:C.teal } });
    sl.addText(key, { x:0.4, y, w:2.1, h:0.48,
      fontSize:12, bold:true, color:C.white, fontFace:"Calibri", align:"center", valign:"middle" });
    sl.addText(val, { x:2.65, y:y+0.03, w:7.1, h:0.44,
      fontSize:12, color:C.ltGray, fontFace:"Calibri", valign:"middle" });
  });
}

// ══════════════════════════════════════════════════════════════
// SLIDE 20 – QUESTIONS / REFERENCES
// ══════════════════════════════════════════════════════════════
{
  const sl = pres.addSlide();
  sl.addShape(pres.ShapeType.rect, { x:0, y:0, w:"100%", h:"100%",
    fill:{ type:"solid", color:C.offWhite } });
  sl.addShape(pres.ShapeType.rect, { x:0, y:0, w:0.18, h:"100%",
    fill:{ type:"solid", color:C.teal } });

  sl.addText("?", { x:0.3, y:0.3, w:9.4, h:2.5,
    fontSize:120, bold:true, color:C.ltGray, fontFace:"Calibri", align:"center" });

  sl.addText("QUESTIONS & DISCUSSION", { x:0.3, y:2.8, w:9.4, h:0.7,
    fontSize:28, bold:true, color:C.navy, fontFace:"Calibri", align:"center" });

  sl.addShape(pres.ShapeType.line, { x:1.0, y:3.55, w:8.0, h:0,
    line:{ color:C.amber, width:2 } });

  sl.addText("References:", { x:0.4, y:3.7, w:9.2, h:0.35,
    fontSize:14, bold:true, color:C.navy, fontFace:"Calibri" });

  const refs = [
    "1. Harvey RA, Ferrier DR. Lippincott Illustrated Reviews: Biochemistry, 8th ed. Wolters Kluwer; 2023.",
    "2. Lieberman MA, Marks AD. Basic Medical Biochemistry: A Clinical Approach, 6th ed. Wolters Kluwer; 2022.",
    "3. Harper's Illustrated Biochemistry, 32nd ed. McGraw-Hill; 2023.",
  ];
  sl.addText(refs.join("\n"), { x:0.4, y:4.1, w:9.2, h:1.2,
    fontSize:11.5, color:C.midGray, fontFace:"Calibri", valign:"top" });
}

// ══════════════════════════════════════════════════════════════
// WRITE FILE
// ══════════════════════════════════════════════════════════════
const outPath = "/home/daytona/workspace/biological-oxidation-ppt/Biological_Oxidation_MBBS.pptx";
pres.writeFile({ fileName: outPath })
  .then(() => console.log("SUCCESS: " + outPath))
  .catch(e => { console.error("ERROR:", e); process.exit(1); });

cd /home/daytona/workspace/biological-oxidation-ppt && node create_ppt.js

ls -lh /home/daytona/workspace/biological-oxidation-ppt/