mkdir -p /home/daytona/workspace/biochem-slides && cat > /home/daytona/workspace/biochem-slides/acidic_aa_slide.js << 'EOF' const pptxgen = require("pptxgenjs"); let pres = new pptxgen(); pres.layout = 'LAYOUT_16x9'; pres.title = 'Negatively Charged (Acidic) Amino Acids'; let slide = pres.addSlide(); // ── Background ────────────────────────────────────────────── slide.addShape(pres.ShapeType.rect, { x: 0, y: 0, w: 10, h: 5.625, fill: { color: "0D1B2A" } }); // ── Accent top bar ─────────────────────────────────────────── slide.addShape(pres.ShapeType.rect, { x: 0, y: 0, w: 10, h: 0.07, fill: { color: "E63946" } }); // ── Title block ────────────────────────────────────────────── slide.addShape(pres.ShapeType.rect, { x: 0.45, y: 0.18, w: 9.1, h: 0.78, fill: { color: "1B2A3B" }, line: { color: "E63946", width: 1.5 } }); slide.addText("Negatively Charged (Acidic) Amino Acids", { x: 0.45, y: 0.18, w: 9.1, h: 0.78, fontSize: 24, bold: true, color: "FFFFFF", fontFace: "Calibri", align: "center", valign: "middle", margin: 0 }); // ── pH label badge ─────────────────────────────────────────── slide.addShape(pres.ShapeType.roundRect, { x: 7.5, y: 1.15, w: 2.0, h: 0.42, rectRadius: 0.1, fill: { color: "E63946" } }); slide.addText("pKa side-chain < 4.1", { x: 7.5, y: 1.15, w: 2.0, h: 0.42, fontSize: 9, bold: true, color: "FFFFFF", fontFace: "Calibri", align: "center", valign: "middle", margin: 0 }); // ── Aspartate card ─────────────────────────────────────────── // card bg slide.addShape(pres.ShapeType.rect, { x: 0.45, y: 1.12, w: 4.2, h: 2.88, fill: { color: "132133" }, line: { color: "E63946", width: 1.5 } }); // card top colour strip slide.addShape(pres.ShapeType.rect, { x: 0.45, y: 1.12, w: 4.2, h: 0.38, fill: { color: "E63946" } }); slide.addText("ASPARTATE (Asp / D)", { x: 0.45, y: 1.12, w: 4.2, h: 0.38, fontSize: 12, bold: true, color: "FFFFFF", fontFace: "Calibri", align: "center", valign: "middle", margin: 0 }); // formula label slide.addShape(pres.ShapeType.roundRect, { x: 0.65, y: 1.62, w: 1.5, h: 0.32, rectRadius: 0.06, fill: { color: "1E3A55" } }); slide.addText("MW: 133.1 Da", { x: 0.65, y: 1.62, w: 1.5, h: 0.32, fontSize: 8, color: "A8C8E8", fontFace: "Calibri", align: "center", valign: "middle", margin: 0 }); slide.addText([ { text: "Charge at pH 7: ", options: { bold: true, color: "E63946" } }, { text: "Strong negative (COO⁻)", options: { color: "E0E0E0" } }, { text: "\n" }, { text: "Transamination: ", options: { bold: true, color: "A8C8E8" } }, { text: "Asp → Oxaloacetate", options: { color: "E0E0E0" } }, { text: "\n" }, { text: "Role in Albumin: ", options: { bold: true, color: "A8C8E8" } }, { text: "Key contributor to Ca²⁺ & cation binding", options: { color: "E0E0E0" } }, { text: "\n" }, { text: "Other roles: ", options: { bold: true, color: "A8C8E8" } }, { text: "Urea cycle, purine synthesis, OAA in TCA", options: { color: "E0E0E0" } }, ], { x: 0.55, y: 2.02, w: 4.0, h: 1.88, fontSize: 10.5, fontFace: "Calibri", valign: "top", lineSpacingMultiple: 1.4 }); // ── Glutamate card ─────────────────────────────────────────── slide.addShape(pres.ShapeType.rect, { x: 5.35, y: 1.12, w: 4.2, h: 2.88, fill: { color: "132133" }, line: { color: "2196F3", width: 1.5 } }); slide.addShape(pres.ShapeType.rect, { x: 5.35, y: 1.12, w: 4.2, h: 0.38, fill: { color: "2196F3" } }); slide.addText("GLUTAMATE (Glu / E)", { x: 5.35, y: 1.12, w: 4.2, h: 0.38, fontSize: 12, bold: true, color: "FFFFFF", fontFace: "Calibri", align: "center", valign: "middle", margin: 0 }); slide.addShape(pres.ShapeType.roundRect, { x: 5.55, y: 1.62, w: 1.5, h: 0.32, rectRadius: 0.06, fill: { color: "1E3A55" } }); slide.addText("MW: 147.1 Da", { x: 5.55, y: 1.62, w: 1.5, h: 0.32, fontSize: 8, color: "A8C8E8", fontFace: "Calibri", align: "center", valign: "middle", margin: 0 }); slide.addText([ { text: "Charge at pH 7: ", options: { bold: true, color: "2196F3" } }, { text: "Strong negative (COO⁻)", options: { color: "E0E0E0" } }, { text: "\n" }, { text: "Transamination: ", options: { bold: true, color: "A8C8E8" } }, { text: "Glu → α-Ketoglutarate", options: { color: "E0E0E0" } }, { text: "\n" }, { text: "Role in Albumin: ", options: { bold: true, color: "A8C8E8" } }, { text: "Key contributor to Ca²⁺ & cation binding", options: { color: "E0E0E0" } }, { text: "\n" }, { text: "Other roles: ", options: { bold: true, color: "A8C8E8" } }, { text: "GABA synthesis, glutamine, TCA cycle hub", options: { color: "E0E0E0" } }, ], { x: 5.45, y: 2.02, w: 4.0, h: 1.88, fontSize: 10.5, fontFace: "Calibri", valign: "top", lineSpacingMultiple: 1.4 }); // ── Divider ────────────────────────────────────────────────── slide.addShape(pres.ShapeType.line, { x: 4.75, y: 1.2, w: 0, h: 2.7, line: { color: "3A5068", width: 1, dashType: "dash" } }); // ── Albumin footer banner ───────────────────────────────────── slide.addShape(pres.ShapeType.rect, { x: 0.45, y: 4.18, w: 9.1, h: 1.1, fill: { color: "1B3A52" }, line: { color: "F4A261", width: 1.5 } }); // icon accent slide.addShape(pres.ShapeType.ellipse, { x: 0.55, y: 4.26, w: 0.6, h: 0.6, fill: { color: "F4A261" } }); slide.addText("🧬", { x: 0.55, y: 4.26, w: 0.6, h: 0.6, fontSize: 14, align: "center", valign: "middle", margin: 0 }); slide.addText([ { text: "Clinical Relevance - Albumin: ", options: { bold: true, color: "F4A261", fontSize: 11 } }, { text: "The abundance of Asp & Glu residues gives albumin a strong net negative charge, enabling it to bind Ca²⁺, Mg²⁺, and other cations. This is the biochemical basis for albumin's role as a carrier protein for calcium in plasma.", options: { color: "E8F4FD", fontSize: 10 } }, ], { x: 1.28, y: 4.18, w: 8.1, h: 1.1, fontFace: "Calibri", valign: "middle", lineSpacingMultiple: 1.3 }); // ── Bottom accent bar ──────────────────────────────────────── slide.addShape(pres.ShapeType.rect, { x: 0, y: 5.555, w: 10, h: 0.07, fill: { color: "F4A261" } }); // ── Footer text ────────────────────────────────────────────── slide.addText("Biochemistry | Amino Acid Chemistry", { x: 0.45, y: 5.37, w: 9.1, h: 0.2, fontSize: 7.5, color: "5A7A8A", fontFace: "Calibri", align: "right", italic: true }); pres.writeFile({ fileName: "/home/daytona/workspace/biochem-slides/Acidic_Amino_Acids.pptx" }) .then(() => console.log("DONE")) .catch(e => console.error(e)); EOF node /home/daytona/workspace/biochem-slides/acidic_aa_slide.js

cat > /home/daytona/workspace/biochem-slides/slide_nonpolar_aliphatic.js << 'JSEOF' const pptxgen = require("pptxgenjs"); let pres = new pptxgen(); pres.layout = 'LAYOUT_16x9'; pres.title = 'Nonpolar Aliphatic Amino Acids'; let slide = pres.addSlide(); // Background slide.addShape(pres.ShapeType.rect, { x:0, y:0, w:10, h:5.625, fill:{color:"0D1B2A"} }); // Top bar slide.addShape(pres.ShapeType.rect, { x:0, y:0, w:10, h:0.07, fill:{color:"27AE60"} }); // Title block slide.addShape(pres.ShapeType.rect, { x:0.35, y:0.13, w:9.3, h:0.72, fill:{color:"1B2A3B"}, line:{color:"27AE60",width:1.5} }); slide.addText("Nonpolar Aliphatic Amino Acids", { x:0.35, y:0.13, w:9.3, h:0.72, fontSize:22, bold:true, color:"FFFFFF", fontFace:"Calibri", align:"center", valign:"middle", margin:0 }); // Badge slide.addShape(pres.ShapeType.roundRect, { x:7.8, y:0.93, w:1.82, h:0.34, rectRadius:0.08, fill:{color:"27AE60"} }); slide.addText("Hydrophobic | Core packing", { x:7.8, y:0.93, w:1.82, h:0.34, fontSize:7.5, bold:true, color:"FFFFFF", fontFace:"Calibri", align:"center", valign:"middle", margin:0 }); // Helper to draw a card function card(slide, pres, x, y, w, h, title, accentColor, rows) { slide.addShape(pres.ShapeType.rect, { x, y, w, h, fill:{color:"132133"}, line:{color:accentColor, width:1.2} }); slide.addShape(pres.ShapeType.rect, { x, y, w, h:0.33, fill:{color:accentColor} }); slide.addText(title, { x, y, w, h:0.33, fontSize:10, bold:true, color:"FFFFFF", fontFace:"Calibri", align:"center", valign:"middle", margin:0 }); let textArr = []; rows.forEach((r, i) => { textArr.push({ text: r.label, options:{ bold:true, color:accentColor, fontSize:9 } }); textArr.push({ text: " " + r.value, options:{ color:"E0E0E0", fontSize:9 } }); if (i < rows.length-1) textArr.push({ text:"\n" }); }); slide.addText(textArr, { x:x+0.08, y:y+0.36, w:w-0.16, h:h-0.4, fontFace:"Calibri", valign:"top", lineSpacingMultiple:1.35 }); } // 5 cards in a row const cardW = 1.82, cardH = 3.35, cardY = 0.95, gap = 0.05; const startX = 0.35; card(slide, pres, startX, cardY, cardW, cardH, "GLY (G)", "27AE60", [ {label:"MW:", value:"75.0 Da"}, {label:"Charge pH7:", value:"Neutral"}, {label:"Unique:", value:"No chiral center; smallest AA"}, {label:"Structure:", value:"Single H side chain - extreme flexibility"}, {label:"Function:", value:"Found in collagen (Gly-X-Y repeat); glycine receptor (inhibitory NT)"}, {label:"Metabolism:", value:"One-carbon metabolism; serine interconversion"}, ]); card(slide, pres, startX + cardW + gap, cardY, cardW, cardH, "ALA (A)", "2ECC71", [ {label:"MW:", value:"89.1 Da"}, {label:"Charge pH7:", value:"Neutral"}, {label:"Unique:", value:"Methyl group; simplest chiral AA"}, {label:"Structure:", value:"CH₃ side chain; high alpha-helix propensity"}, {label:"Function:", value:"Most abundant AA in proteins; major gluconeogenic source"}, {label:"Metabolism:", value:"Alanine cycle: muscle → liver (glucose-alanine cycle)"}, ]); card(slide, pres, startX + 2*(cardW+gap), cardY, cardW, cardH, "VAL (V)", "1ABC9C", [ {label:"MW:", value:"117.1 Da"}, {label:"Charge pH7:", value:"Neutral"}, {label:"Unique:", value:"Branched-chain AA (BCAA); essential"}, {label:"Structure:", value:"Isopropyl side chain; β-sheet preferred"}, {label:"Function:", value:"BCAA; HbS mutation (Glu→Val) causes sickle cell"}, {label:"Metabolism:", value:"Degraded to succinyl-CoA (glucogenic)"}, ]); card(slide, pres, startX + 3*(cardW+gap), cardY, cardW, cardH, "LEU (L)", "16A085", [ {label:"MW:", value:"131.2 Da"}, {label:"Charge pH7:", value:"Neutral"}, {label:"Unique:", value:"BCAA; most common in proteins; essential"}, {label:"Structure:", value:"Isobutyl side chain; hydrophobic core"}, {label:"Function:", value:"mTOR activator; activates protein synthesis"}, {label:"Metabolism:", value:"Purely ketogenic → acetyl-CoA/acetoacetate"}, ]); card(slide, pres, startX + 4*(cardW+gap), cardY, cardW, cardH, "ILE (I)", "0E7A6B", [ {label:"MW:", value:"131.2 Da"}, {label:"Charge pH7:", value:"Neutral"}, {label:"Unique:", value:"BCAA; 2 chiral centers; essential"}, {label:"Structure:", value:"sec-butyl chain; tightly packed core"}, {label:"Function:", value:"BCAA; MSUD (maple syrup urine disease) with Leu/Val"}, {label:"Metabolism:", value:"Both glucogenic & ketogenic"}, ]); // Footer slide.addShape(pres.ShapeType.rect, { x:0.35, y:4.38, w:9.3, h:0.9, fill:{color:"1B3A52"}, line:{color:"27AE60",width:1} }); slide.addText([ {text:"Key Concept: ", options:{bold:true, color:"27AE60", fontSize:9.5}}, {text:"All five form the hydrophobic core of folded proteins. BCAAs (Val, Leu, Ile) are metabolized in muscle, not liver — clinically important in MSUD (deficient branched-chain α-keto acid dehydrogenase). Ala–Glu cycle shuttles nitrogen from muscle to liver.", options:{color:"E8F4FD", fontSize:9.5}}, ], { x:0.45, y:4.38, w:9.1, h:0.9, fontFace:"Calibri", valign:"middle", lineSpacingMultiple:1.3 }); slide.addShape(pres.ShapeType.rect, { x:0, y:5.555, w:10, h:0.07, fill:{color:"27AE60"} }); slide.addText("Biochemistry | Amino Acid Chemistry", { x:0.35, y:5.36, w:9.3, h:0.2, fontSize:7, color:"5A7A8A", fontFace:"Calibri", align:"right", italic:true }); pres.writeFile({ fileName:"/home/daytona/workspace/biochem-slides/Slide1_Nonpolar_Aliphatic.pptx" }) .then(()=>console.log("SLIDE1 DONE")).catch(e=>console.error(e)); JSEOF node /home/daytona/workspace/biochem-slides/slide_nonpolar_aliphatic.js

cat > /home/daytona/workspace/biochem-slides/slide_nonpolar_aromatic.js << 'JSEOF' const pptxgen = require("pptxgenjs"); let pres = new pptxgen(); pres.layout = 'LAYOUT_16x9'; pres.title = 'Nonpolar Aromatic & Special Amino Acids'; let slide = pres.addSlide(); // Background slide.addShape(pres.ShapeType.rect, { x:0, y:0, w:10, h:5.625, fill:{color:"0D1B2A"} }); slide.addShape(pres.ShapeType.rect, { x:0, y:0, w:10, h:0.07, fill:{color:"9B59B6"} }); // Title slide.addShape(pres.ShapeType.rect, { x:0.35, y:0.13, w:9.3, h:0.72, fill:{color:"1B2A3B"}, line:{color:"9B59B6",width:1.5} }); slide.addText("Nonpolar Aromatic & Special Amino Acids", { x:0.35, y:0.13, w:9.3, h:0.72, fontSize:22, bold:true, color:"FFFFFF", fontFace:"Calibri", align:"center", valign:"middle", margin:0 }); slide.addShape(pres.ShapeType.roundRect, { x:7.5, y:0.93, w:2.12, h:0.34, rectRadius:0.08, fill:{color:"9B59B6"} }); slide.addText("Aromatic | Cyclic | Sulfur-containing", { x:7.5, y:0.93, w:2.12, h:0.34, fontSize:7.5, bold:true, color:"FFFFFF", fontFace:"Calibri", align:"center", valign:"middle", margin:0 }); function card(slide, pres, x, y, w, h, title, accentColor, rows) { slide.addShape(pres.ShapeType.rect, { x, y, w, h, fill:{color:"132133"}, line:{color:accentColor, width:1.2} }); slide.addShape(pres.ShapeType.rect, { x, y, w, h:0.33, fill:{color:accentColor} }); slide.addText(title, { x, y, w, h:0.33, fontSize:10, bold:true, color:"FFFFFF", fontFace:"Calibri", align:"center", valign:"middle", margin:0 }); let textArr = []; rows.forEach((r, i) => { textArr.push({ text: r.label, options:{ bold:true, color:accentColor, fontSize:9 } }); textArr.push({ text: " " + r.value, options:{ color:"E0E0E0", fontSize:9 } }); if (i < rows.length-1) textArr.push({ text:"\n" }); }); slide.addText(textArr, { x:x+0.08, y:y+0.36, w:w-0.16, h:h-0.4, fontFace:"Calibri", valign:"top", lineSpacingMultiple:1.35 }); } const cardW = 2.18, cardH = 3.35, cardY = 0.95, gap = 0.06; const startX = 0.35; card(slide, pres, startX, cardY, cardW, cardH, "PHE (F)", "9B59B6", [ {label:"MW:", value:"165.2 Da"}, {label:"Essential:", value:"Yes"}, {label:"Structure:", value:"Benzyl (phenyl) ring; most hydrophobic aromatic"}, {label:"Function:", value:"Precursor to Tyr; PKU when phenylalanine hydroxylase deficient"}, {label:"Metabolism:", value:"Phe → Tyr (PAH, BH4); blocked in PKU → phenylpyruvate"}, {label:"Clinical:", value:"PKU: intellectual disability if untreated; low-Phe diet"}, ]); card(slide, pres, startX + cardW + gap, cardY, cardW, cardH, "TRP (W)", "8E44AD", [ {label:"MW:", value:"204.2 Da"}, {label:"Essential:", value:"Yes (rarest AA)"}, {label:"Structure:", value:"Indole ring; highest MW standard AA"}, {label:"Function:", value:"Precursor: serotonin, melatonin, niacin (B3)"}, {label:"Metabolism:", value:"Tryptophan → 5-HTP → Serotonin → Melatonin; Kynurenine path → NAD⁺"}, {label:"Clinical:", value:"Hartnup disease: neutral AA transporter defect; pellagra if deficient"}, ]); card(slide, pres, startX + 2*(cardW+gap), cardY, cardW, cardH, "MET (M)", "6C3483", [ {label:"MW:", value:"149.2 Da"}, {label:"Essential:", value:"Yes"}, {label:"Structure:", value:"Thioether side chain (–S–CH₃)"}, {label:"Function:", value:"Start codon (AUG); methyl donor as SAM"}, {label:"Metabolism:", value:"Met → SAM → SAH → Homocysteine; remethylation needs B12/folate"}, {label:"Clinical:", value:"Homocystinuria / hyperhomocysteinemia → thrombosis, CVD"}, ]); card(slide, pres, startX + 3*(cardW+gap), cardY, cardW, cardH, "PRO (P)", "AF7AC1", [ {label:"MW:", value:"115.1 Da"}, {label:"Essential:", value:"Conditionally"}, {label:"Structure:", value:"Pyrrolidine ring; N in backbone — imino acid, NOT amino acid"}, {label:"Function:", value:"Helix breaker; essential in collagen (Hyp in Gly-Pro-Hyp)"}, {label:"Metabolism:", value:"Synthesized from glutamate; hydroxylated by prolyl hydroxylase (vit C)"}, {label:"Clinical:", value:"Scurvy: vit C def → no hydroxyproline → collagen instability"}, ]); // Footer slide.addShape(pres.ShapeType.rect, { x:0.35, y:4.38, w:9.3, h:0.9, fill:{color:"1B3A52"}, line:{color:"9B59B6",width:1} }); slide.addText([ {text:"Key Concepts: ", options:{bold:true, color:"9B59B6", fontSize:9.5}}, {text:"Phe/Trp absorb UV (280 nm) — basis of protein spectrophotometry. PKU (Phe), serotonin deficiency (Trp), homocystinuria (Met), and scurvy (Pro hydroxylation) are high-yield clinical correlates. Pro's ring locks the peptide backbone — helix/sheet breaker.", options:{color:"E8F4FD", fontSize:9.5}}, ], { x:0.45, y:4.38, w:9.1, h:0.9, fontFace:"Calibri", valign:"middle", lineSpacingMultiple:1.3 }); slide.addShape(pres.ShapeType.rect, { x:0, y:5.555, w:10, h:0.07, fill:{color:"9B59B6"} }); slide.addText("Biochemistry | Amino Acid Chemistry", { x:0.35, y:5.36, w:9.3, h:0.2, fontSize:7, color:"5A7A8A", fontFace:"Calibri", align:"right", italic:true }); pres.writeFile({ fileName:"/home/daytona/workspace/biochem-slides/Slide2_Nonpolar_Aromatic_Special.pptx" }) .then(()=>console.log("SLIDE2 DONE")).catch(e=>console.error(e)); JSEOF node /home/daytona/workspace/biochem-slides/slide_nonpolar_aromatic.js

cat > /home/daytona/workspace/biochem-slides/slide_polar_uncharged.js << 'JSEOF' const pptxgen = require("pptxgenjs"); let pres = new pptxgen(); pres.layout = 'LAYOUT_16x9'; pres.title = 'Polar Uncharged Amino Acids'; let slide = pres.addSlide(); // Background slide.addShape(pres.ShapeType.rect, { x:0, y:0, w:10, h:5.625, fill:{color:"0D1B2A"} }); slide.addShape(pres.ShapeType.rect, { x:0, y:0, w:10, h:0.07, fill:{color:"F39C12"} }); // Title slide.addShape(pres.ShapeType.rect, { x:0.35, y:0.13, w:9.3, h:0.72, fill:{color:"1B2A3B"}, line:{color:"F39C12",width:1.5} }); slide.addText("Polar Uncharged Amino Acids", { x:0.35, y:0.13, w:9.3, h:0.72, fontSize:22, bold:true, color:"FFFFFF", fontFace:"Calibri", align:"center", valign:"middle", margin:0 }); slide.addShape(pres.ShapeType.roundRect, { x:7.35, y:0.93, w:2.27, h:0.34, rectRadius:0.08, fill:{color:"F39C12"} }); slide.addText("H-bonding | Enzyme active sites", { x:7.35, y:0.93, w:2.27, h:0.34, fontSize:7.5, bold:true, color:"FFFFFF", fontFace:"Calibri", align:"center", valign:"middle", margin:0 }); function card(slide, pres, x, y, w, h, title, accentColor, rows) { slide.addShape(pres.ShapeType.rect, { x, y, w, h, fill:{color:"132133"}, line:{color:accentColor, width:1.2} }); slide.addShape(pres.ShapeType.rect, { x, y, w, h:0.33, fill:{color:accentColor} }); slide.addText(title, { x, y, w, h:0.33, fontSize:9.5, bold:true, color:"FFFFFF", fontFace:"Calibri", align:"center", valign:"middle", margin:0 }); let textArr = []; rows.forEach((r, i) => { textArr.push({ text: r.label, options:{ bold:true, color:accentColor, fontSize:8.5 } }); textArr.push({ text: " " + r.value, options:{ color:"E0E0E0", fontSize:8.5 } }); if (i < rows.length-1) textArr.push({ text:"\n" }); }); slide.addText(textArr, { x:x+0.07, y:y+0.36, w:w-0.14, h:h-0.4, fontFace:"Calibri", valign:"top", lineSpacingMultiple:1.3 }); } // 6 cards, 3 per row const cardW = 3.06, cardH = 1.72, gap = 0.055; const startX = 0.35; // Row 1 card(slide, pres, startX, 0.95, cardW, cardH, "SER (S)", "F39C12", [ {label:"MW:", value:"105.1 Da | Conditionally essential"}, {label:"Structure:", value:"–CH₂–OH; hydroxyl group → H-bonds & phosphorylation"}, {label:"Function:", value:"Phosphoserine: major phosphorylation target (kinases); serine proteases (catalytic triad)"}, {label:"Metabolism:", value:"Gly ↔ Ser interconversion; one-carbon metabolism; sphingolipid backbone"}, ]); card(slide, pres, startX + cardW + gap, 0.95, cardW, cardH, "THR (T)", "E67E22", [ {label:"MW:", value:"119.1 Da | Essential"}, {label:"Structure:", value:"–CH(OH)–CH₃; 2nd chiral center; β-hydroxyl"}, {label:"Function:", value:"Phosphorylation target; O-glycosylation site; part of catalytic serine mimicry"}, {label:"Metabolism:", value:"Glucogenic (→ pyruvate/succinyl-CoA); cannot be synthesized in humans"}, ]); card(slide, pres, startX + 2*(cardW+gap), 0.95, cardW, cardH, "CYS (C)", "D35400", [ {label:"MW:", value:"121.2 Da | Conditionally essential"}, {label:"Structure:", value:"–CH₂–SH (thiol); pKa ~8.3; forms disulfide bonds (–S–S–)"}, {label:"Function:", value:"Disulfide bridges → protein 3D structure (insulin); metal binding (zinc fingers); active-site nucleophile"}, {label:"Metabolism:", value:"Met → Cys (transsulfuration); taurine & glutathione precursor"}, ]); // Row 2 card(slide, pres, startX, 2.74, cardW, cardH, "TYR (Y)", "F1C40F", [ {label:"MW:", value:"181.2 Da | Conditionally essential"}, {label:"Structure:", value:"Phenol ring (–OH on benzene); can ionize → phenolate (pKa ~10)"}, {label:"Function:", value:"Phosphorylation (Tyr kinases); catecholamine precursor (DOPA→dopamine→NE→Epi); thyroid hormone (T3/T4); melanin"}, {label:"Metabolism:", value:"Phe → Tyr (PAH); blocked in PKU and alkaptonuria (HGD deficiency)"}, ]); card(slide, pres, startX + cardW + gap, 2.74, cardW, cardH, "ASN (N)", "F4D03F", [ {label:"MW:", value:"132.1 Da | Non-essential"}, {label:"Structure:", value:"–CH₂–CO–NH₂; amide of Asp; H-bond donor & acceptor"}, {label:"Function:", value:"N-glycosylation site (Asn–X–Ser/Thr sequon); protein folding; asparagine synthetase"}, {label:"Metabolism:", value:"Asn ↔ Asp (asparaginase); leukemia treatment uses L-asparaginase to deplete serum Asn"}, ]); card(slide, pres, startX + 2*(cardW+gap), 2.74, cardW, cardH, "GLN (Q)", "D4AC0D", [ {label:"MW:", value:"146.2 Da | Conditionally essential"}, {label:"Structure:", value:"–CH₂–CH₂–CO–NH₂; amide of Glu; most abundant AA in blood"}, {label:"Function:", value:"Nitrogen carrier in blood; fuel for enterocytes & lymphocytes; purine/pyrimidine nitrogen donor"}, {label:"Metabolism:", value:"Glu + NH₃ → Gln (glutamine synthetase); Gln → Glu (glutaminase); brain ammonia detox"}, ]); // Footer slide.addShape(pres.ShapeType.rect, { x:0.35, y:4.53, w:9.3, h:0.77, fill:{color:"1B3A52"}, line:{color:"F39C12",width:1} }); slide.addText([ {text:"Key Concepts: ", options:{bold:true, color:"F39C12", fontSize:9.5}}, {text:"Ser/Thr/Tyr are phosphorylation targets (signal transduction). Cys disulfide bonds stabilize proteins. Tyr is the catecholamine/thyroid hormone precursor. Gln is the main nitrogen carrier. Asn is the N-glycosylation anchor.", options:{color:"E8F4FD", fontSize:9.5}}, ], { x:0.45, y:4.53, w:9.1, h:0.77, fontFace:"Calibri", valign:"middle", lineSpacingMultiple:1.3 }); slide.addShape(pres.ShapeType.rect, { x:0, y:5.555, w:10, h:0.07, fill:{color:"F39C12"} }); slide.addText("Biochemistry | Amino Acid Chemistry", { x:0.35, y:5.36, w:9.3, h:0.2, fontSize:7, color:"5A7A8A", fontFace:"Calibri", align:"right", italic:true }); pres.writeFile({ fileName:"/home/daytona/workspace/biochem-slides/Slide3_Polar_Uncharged.pptx" }) .then(()=>console.log("SLIDE3 DONE")).catch(e=>console.error(e)); JSEOF node /home/daytona/workspace/biochem-slides/slide_polar_uncharged.js

cat > /home/daytona/workspace/biochem-slides/slide_basic.js << 'JSEOF' const pptxgen = require("pptxgenjs"); let pres = new pptxgen(); pres.layout = 'LAYOUT_16x9'; pres.title = 'Positively Charged (Basic) Amino Acids'; let slide = pres.addSlide(); // Background slide.addShape(pres.ShapeType.rect, { x:0, y:0, w:10, h:5.625, fill:{color:"0D1B2A"} }); slide.addShape(pres.ShapeType.rect, { x:0, y:0, w:10, h:0.07, fill:{color:"2980B9"} }); // Title slide.addShape(pres.ShapeType.rect, { x:0.35, y:0.13, w:9.3, h:0.72, fill:{color:"1B2A3B"}, line:{color:"2980B9",width:1.5} }); slide.addText("Positively Charged (Basic) Amino Acids", { x:0.35, y:0.13, w:9.3, h:0.72, fontSize:22, bold:true, color:"FFFFFF", fontFace:"Calibri", align:"center", valign:"middle", margin:0 }); slide.addShape(pres.ShapeType.roundRect, { x:7.5, y:0.93, w:2.12, h:0.34, rectRadius:0.08, fill:{color:"2980B9"} }); slide.addText("pKa > 7 | Positive charge at pH 7", { x:7.5, y:0.93, w:2.12, h:0.34, fontSize:7.5, bold:true, color:"FFFFFF", fontFace:"Calibri", align:"center", valign:"middle", margin:0 }); function card(slide, pres, x, y, w, h, title, accentColor, rows) { slide.addShape(pres.ShapeType.rect, { x, y, w, h, fill:{color:"132133"}, line:{color:accentColor, width:1.5} }); slide.addShape(pres.ShapeType.rect, { x, y, w, h:0.35, fill:{color:accentColor} }); slide.addText(title, { x, y, w, h:0.35, fontSize:11.5, bold:true, color:"FFFFFF", fontFace:"Calibri", align:"center", valign:"middle", margin:0 }); let textArr = []; rows.forEach((r, i) => { textArr.push({ text: r.label, options:{ bold:true, color:accentColor, fontSize:9.5 } }); textArr.push({ text: " " + r.value, options:{ color:"E0E0E0", fontSize:9.5 } }); if (i < rows.length-1) textArr.push({ text:"\n" }); }); slide.addText(textArr, { x:x+0.1, y:y+0.38, w:w-0.2, h:h-0.42, fontFace:"Calibri", valign:"top", lineSpacingMultiple:1.4 }); } const cardW = 2.9, cardH = 3.32, cardY = 0.95, gap = 0.19; const startX = 0.42; card(slide, pres, startX, cardY, cardW, cardH, "LYS (K)", "2980B9", [ {label:"MW:", value:"146.2 Da | Essential"}, {label:"Charge pH7:", value:"Strong positive (pKa ~10.5, ε-amino)"}, {label:"Structure:", value:"–(CH₂)₄–NH₃⁺; long flexible side chain"}, {label:"Function:", value:"Histone acetylation/ubiquitination sites; collagen crosslinks; active-site nucleophile; binds DNA phosphates"}, {label:"Metabolism:", value:"Purely ketogenic; carnitine biosynthesis; acetyl-Lys in epigenetics"}, {label:"Clinical:", value:"Lysinuric protein intolerance; collagen disorders (lysyl oxidase deficiency)"}, ]); card(slide, pres, startX + cardW + gap, cardY, cardW, cardH, "ARG (R)", "1A5276", [ {label:"MW:", value:"174.2 Da | Conditionally essential"}, {label:"Charge pH7:", value:"Strongest positive (pKa ~12.5, guanidinium)"}, {label:"Structure:", value:"Guanidinium group (–NHC(=NH)NH₂); resonance-stabilized"}, {label:"Function:", value:"Urea cycle (argininosuccinate → Arg → urea + ornithine); NO synthesis (NOS: Arg → NO + citrulline); protein binding to nucleic acids"}, {label:"Metabolism:", value:"Urea cycle intermediate; conditionally essential in growth/stress"}, {label:"Clinical:", value:"Arginase deficiency → hyperammonemia; NO pathway (sepsis, hypertension)"}, ]); card(slide, pres, startX + 2*(cardW+gap), cardY, cardW, cardH, "HIS (H)", "5DADE2", [ {label:"MW:", value:"155.2 Da | Essential (adults borderline)"}, {label:"Charge pH7:", value:"Partial positive (pKa ~6.0 — unique buffer at physiological pH)"}, {label:"Structure:", value:"Imidazole ring; can be protonated or neutral at pH 7"}, {label:"Function:", value:"Enzyme active-site proton shuttle (serine proteases, carbonic anhydrase); hemoglobin Bohr effect (CO₂/O₂ exchange); histamine precursor"}, {label:"Metabolism:", value:"His → histamine (histidine decarboxylase); urocanic acid pathway"}, {label:"Clinical:", value:"Histidinemia; antihistamines block H1/H2 receptors; carbonic anhydrase inhibitors (glaucoma, altitude sickness)"}, ]); // pKa comparison strip slide.addShape(pres.ShapeType.rect, { x:0.35, y:4.38, w:9.3, h:0.36, fill:{color:"172A3A"}, line:{color:"2980B9",width:0.8} }); // pKa bars const bars = [{label:"Lys pKa ~10.5", w:3.0, color:"2980B9"}, {label:"Arg pKa ~12.5", w:4.0, color:"1A5276"}, {label:"His pKa ~6.0", w:1.5, color:"5DADE2"}]; let bx = 0.55; bars.forEach(b => { slide.addShape(pres.ShapeType.rect, { x:bx, y:4.47, w:b.w, h:0.16, fill:{color:b.color} }); slide.addText(b.label, { x:bx, y:4.47, w:b.w, h:0.16, fontSize:7.5, bold:true, color:"FFFFFF", fontFace:"Calibri", align:"center", valign:"middle", margin:0 }); bx += b.w + 0.07; }); // Footer slide.addShape(pres.ShapeType.rect, { x:0.35, y:4.8, w:9.3, h:0.72, fill:{color:"1B3A52"}, line:{color:"2980B9",width:1} }); slide.addText([ {text:"Key Concepts: ", options:{bold:true, color:"5DADE2", fontSize:9.5}}, {text:"His is the ONLY amino acid that buffers at physiological pH (pKa ~6.0) — critical in hemoglobin Bohr effect. Arg is the sole NO precursor and a urea cycle intermediate. Lys epigenetic modifications (acetylation, methylation) control gene expression.", options:{color:"E8F4FD", fontSize:9.5}}, ], { x:0.45, y:4.8, w:9.1, h:0.72, fontFace:"Calibri", valign:"middle", lineSpacingMultiple:1.3 }); slide.addShape(pres.ShapeType.rect, { x:0, y:5.555, w:10, h:0.07, fill:{color:"2980B9"} }); slide.addText("Biochemistry | Amino Acid Chemistry", { x:0.35, y:5.36, w:9.3, h:0.2, fontSize:7, color:"5A7A8A", fontFace:"Calibri", align:"right", italic:true }); pres.writeFile({ fileName:"/home/daytona/workspace/biochem-slides/Slide4_Basic_Charged.pptx" }) .then(()=>console.log("SLIDE4 DONE")).catch(e=>console.error(e)); JSEOF node /home/daytona/workspace/biochem-slides/slide_basic.js

ls -lh /home/daytona/workspace/biochem-slides/*.pptx

ls -lh /home/daytona/workspace/biochem-slides/*.pptx

python3 << 'PYEOF' from pptx import Presentation from pptx.util import Inches import copy, lxml.etree as etree # Order: title slide first (acidic), then groups 1-4 files = [ "/home/daytona/workspace/biochem-slides/Acidic_Amino_Acids.pptx", "/home/daytona/workspace/biochem-slides/Slide1_Nonpolar_Aliphatic.pptx", "/home/daytona/workspace/biochem-slides/Slide2_Nonpolar_Aromatic_Special.pptx", "/home/daytona/workspace/biochem-slides/Slide3_Polar_Uncharged.pptx", "/home/daytona/workspace/biochem-slides/Slide4_Basic_Charged.pptx", ] def merge_presentations(file_list, output_path): # Use first file as base base = Presentation(file_list[0]) for src_path in file_list[1:]: src = Presentation(src_path) # For each slide in source, clone its XML and add to base for src_slide in src.slides: # Add blank slide to base using first layout slide_layout = base.slide_layouts[6] # blank layout new_slide = base.slides.add_slide(slide_layout) # Copy all shapes/elements from source slide spTree src_sp_tree = src_slide.shapes._spTree dest_sp_tree = new_slide.shapes._spTree # Remove default placeholders from new blank slide for child in list(dest_sp_tree): dest_sp_tree.remove(child) # Deep copy all children from source for child in src_sp_tree: dest_sp_tree.append(copy.deepcopy(child)) # Copy slide background if present src_bg = src_slide.background dest_bg = new_slide.background if src_slide._element.find('.//{http://schemas.openxmlformats.org/drawingml/2006/main}solidFill') is not None: # copy the cSld element which contains background src_cSld = src_slide._element.find('{http://schemas.openxmlformats.org/presentationml/2006/main}cSld') dest_cSld = new_slide._element.find('{http://schemas.openxmlformats.org/presentationml/2006/main}cSld') if src_cSld is not None and dest_cSld is not None: # copy bg element src_bg_elem = src_cSld.find('{http://schemas.openxmlformats.org/presentationml/2006/main}bg') if src_bg_elem is not None: dest_bg_elem = dest_cSld.find('{http://schemas.openxmlformats.org/presentationml/2006/main}bg') if dest_bg_elem is not None: dest_cSld.remove(dest_bg_elem) dest_cSld.insert(0, copy.deepcopy(src_bg_elem)) base.save(output_path) print(f"Saved: {output_path}") print(f"Total slides: {len(base.slides)}") merge_presentations(files, "/home/daytona/workspace/biochem-slides/Master_Amino_Acids.pptx") PYEOF

# Check what's available for PPTX manipulation node -e "const p = require('pptxgenjs'); console.log('pptxgenjs ok');" python3 -c "import zipfile, shutil, os; print('stdlib ok')" ls /home/daytona/skills/pptx/scripts/office/

# Unpack all 5 presentations cd /home/daytona/workspace/biochem-slides python3 /home/daytona/skills/pptx/scripts/office/unpack.py Acidic_Amino_Acids.pptx unpacked_acidic/ python3 /home/daytona/skills/pptx/scripts/office/unpack.py Slide1_Nonpolar_Aliphatic.pptx unpacked_s1/ python3 /home/daytona/skills/pptx/scripts/office/unpack.py Slide2_Nonpolar_Aromatic_Special.pptx unpacked_s2/ python3 /home/daytona/skills/pptx/scripts/office/unpack.py Slide3_Polar_Uncharged.pptx unpacked_s3/ python3 /home/daytona/skills/pptx/scripts/office/unpack.py Slide4_Basic_Charged.pptx unpacked_s4/ echo "All unpacked" ls unpacked_acidic/ppt/slides/

python3 /home/daytona/skills/pptx/scripts/office/unpack.py /home/daytona/workspace/biochem-slides/Acidic_Amino_Acids.pptx /home/daytona/workspace/biochem-slides/unpacked_acidic/ && echo "done"

python3 /home/daytona/skills/pptx/scripts/office/unpack.py /home/daytona/workspace/biochem-slides/Slide1_Nonpolar_Aliphatic.pptx /home/daytona/workspace/biochem-slides/unpacked_s1/ && echo "s1 done"

python3 /home/daytona/skills/pptx/scripts/office/unpack.py /home/daytona/workspace/biochem-slides/Slide2_Nonpolar_Aromatic_Special.pptx /home/daytona/workspace/biochem-slides/unpacked_s2/ && echo "s2 done"

python3 /home/daytona/skills/pptx/scripts/office/unpack.py /home/daytona/workspace/biochem-slides/Slide3_Polar_Uncharged.pptx /home/daytona/workspace/biochem-slides/unpacked_s3/ && echo "s3 done"

python3 /home/daytona/skills/pptx/scripts/office/unpack.py /home/daytona/workspace/biochem-slides/Slide4_Basic_Charged.pptx /home/daytona/workspace/biochem-slides/unpacked_s4/ && echo "s4 done"

ls /home/daytona/workspace/biochem-slides/unpacked_acidic/ppt/slides/ echo "---" ls /home/daytona/workspace/biochem-slides/unpacked_acidic/ppt/slides/_rels/ echo "---" # Check the presentation.xml sldIdLst grep -A 20 'sldIdLst' /home/daytona/workspace/biochem-slides/unpacked_acidic/ppt/presentation.xml | head -30

cat /home/daytona/workspace/biochem-slides/unpacked_acidic/ppt/slides/_rels/slide1.xml.rels

python3 << 'PYEOF' import os, shutil, re, xml.etree.ElementTree as ET BASE = "/home/daytona/workspace/biochem-slides" base_dir = f"{BASE}/unpacked_acidic" # Sources: (unpacked_dir, slide_number_in_source, new_slide_number_in_base) sources = [ (f"{BASE}/unpacked_s1", "slide1", "slide2"), (f"{BASE}/unpacked_s2", "slide1", "slide3"), (f"{BASE}/unpacked_s3", "slide1", "slide4"), (f"{BASE}/unpacked_s4", "slide1", "slide5"), ] slides_dir = f"{base_dir}/ppt/slides" rels_dir = f"{base_dir}/ppt/slides/_rels" for (src_dir, src_slide, dest_slide) in sources: # Copy slide XML shutil.copy( f"{src_dir}/ppt/slides/{src_slide}.xml", f"{slides_dir}/{dest_slide}.xml" ) # Copy notes slide if present src_notes = f"{src_dir}/ppt/notesSlides/notesSlide1.xml" dest_notes_dir = f"{base_dir}/ppt/notesSlides" note_num = dest_slide.replace("slide","") if os.path.exists(src_notes): os.makedirs(dest_notes_dir, exist_ok=True) dest_note = f"{dest_notes_dir}/notesSlide{note_num}.xml" shutil.copy(src_notes, dest_note) # Build slide rels — each slide only references slideLayout1 (and optionally notes) notes_line = "" if os.path.exists(src_notes): notes_line = f' <Relationship Id="rId2" Type="http://schemas.openxmlformats.org/officeDocument/2006/relationships/notesSlide" Target="../notesSlides/notesSlide{note_num}.xml"/>\n' rels_content = ( '<?xml version="1.0" encoding="utf-8"?>\n' '<Relationships xmlns="http://schemas.openxmlformats.org/package/2006/relationships">\n' ' <Relationship Id="rId1" Type="http://schemas.openxmlformats.org/officeDocument/2006/relationships/slideLayout" Target="../slideLayouts/slideLayout1.xml"/>\n' + notes_line + '</Relationships>\n' ) with open(f"{rels_dir}/{dest_slide}.xml.rels", "w") as f: f.write(rels_content) print(f" Copied {src_slide} → {dest_slide}") # Now update presentation.xml to include all 5 slides pres_path = f"{base_dir}/ppt/presentation.xml" pres_rels_path = f"{base_dir}/ppt/_rels/presentation.xml.rels" with open(pres_path, "r") as f: pres_xml = f.read() # Find current sldIdLst and replace with 5 entries new_sld_id_lst = """<p:sldIdLst> <p:sldId id="256" r:id="rId2"/> <p:sldId id="257" r:id="rId10"/> <p:sldId id="258" r:id="rId11"/> <p:sldId id="259" r:id="rId12"/> <p:sldId id="260" r:id="rId13"/> </p:sldIdLst>""" pres_xml = re.sub( r'<p:sldIdLst>.*?</p:sldIdLst>', new_sld_id_lst, pres_xml, flags=re.DOTALL ) with open(pres_path, "w") as f: f.write(pres_xml) print("Updated presentation.xml") # Update presentation.xml.rels to add rId10–rId13 with open(pres_rels_path, "r") as f: rels_xml = f.read() new_rels = ( ' <Relationship Id="rId10" Type="http://schemas.openxmlformats.org/officeDocument/2006/relationships/slide" Target="slides/slide2.xml"/>\n' ' <Relationship Id="rId11" Type="http://schemas.openxmlformats.org/officeDocument/2006/relationships/slide" Target="slides/slide3.xml"/>\n' ' <Relationship Id="rId12" Type="http://schemas.openxmlformats.org/officeDocument/2006/relationships/slide" Target="slides/slide4.xml"/>\n' ' <Relationship Id="rId13" Type="http://schemas.openxmlformats.org/officeDocument/2006/relationships/slide" Target="slides/slide5.xml"/>\n' '</Relationships>' ) rels_xml = rels_xml.replace('</Relationships>', new_rels) with open(pres_rels_path, "w") as f: f.write(rels_xml) print("Updated presentation.xml.rels") print("Done!") # Verify print("\nSlides in base dir:") for f in sorted(os.listdir(slides_dir)): if not f.startswith('_'): print(f" {f}") PYEOF

ls -la /home/daytona/workspace/biochem-slides/unpacked_acidic/ppt/slides/ chmod -R 777 /home/daytona/workspace/biochem-slides/unpacked_acidic/ 2>/dev/null || true ls -la /home/daytona/workspace/biochem-slides/unpacked_acidic/ppt/slides/

python3 << 'PYEOF' import os, re BASE = "/home/daytona/workspace/biochem-slides" base_dir = f"{BASE}/unpacked_acidic" sources = [ (f"{BASE}/unpacked_s1", "slide1", "slide2"), (f"{BASE}/unpacked_s2", "slide1", "slide3"), (f"{BASE}/unpacked_s3", "slide1", "slide4"), (f"{BASE}/unpacked_s4", "slide1", "slide5"), ] slides_dir = f"{base_dir}/ppt/slides" rels_dir = f"{base_dir}/ppt/slides/_rels" for (src_dir, src_slide, dest_slide) in sources: # Copy slide XML using read/write with open(f"{src_dir}/ppt/slides/{src_slide}.xml", "r") as f: content = f.read() with open(f"{slides_dir}/{dest_slide}.xml", "w") as f: f.write(content) # Notes slide src_notes = f"{src_dir}/ppt/notesSlides/notesSlide1.xml" note_num = dest_slide.replace("slide","") dest_notes_dir = f"{base_dir}/ppt/notesSlides" notes_line = "" if os.path.exists(src_notes): os.makedirs(dest_notes_dir, exist_ok=True) with open(src_notes, "r") as f: nc = f.read() with open(f"{dest_notes_dir}/notesSlide{note_num}.xml", "w") as f: f.write(nc) notes_line = f' <Relationship Id="rId2" Type="http://schemas.openxmlformats.org/officeDocument/2006/relationships/notesSlide" Target="../notesSlides/notesSlide{note_num}.xml"/>\n' # Slide rels rels_content = ( '<?xml version="1.0" encoding="utf-8"?>\n' '<Relationships xmlns="http://schemas.openxmlformats.org/package/2006/relationships">\n' ' <Relationship Id="rId1" Type="http://schemas.openxmlformats.org/officeDocument/2006/relationships/slideLayout" Target="../slideLayouts/slideLayout1.xml"/>\n' + notes_line + '</Relationships>\n' ) with open(f"{rels_dir}/{dest_slide}.xml.rels", "w") as f: f.write(rels_content) print(f" Copied {src_slide} → {dest_slide}") # Update presentation.xml pres_path = f"{base_dir}/ppt/presentation.xml" pres_rels_path = f"{base_dir}/ppt/_rels/presentation.xml.rels" with open(pres_path, "r") as f: pres_xml = f.read() new_sld_id_lst = """<p:sldIdLst> <p:sldId id="256" r:id="rId2"/> <p:sldId id="257" r:id="rId10"/> <p:sldId id="258" r:id="rId11"/> <p:sldId id="259" r:id="rId12"/> <p:sldId id="260" r:id="rId13"/> </p:sldIdLst>""" pres_xml = re.sub(r'<p:sldIdLst>.*?</p:sldIdLst>', new_sld_id_lst, pres_xml, flags=re.DOTALL) with open(pres_path, "w") as f: f.write(pres_xml) print("Updated presentation.xml") # Update presentation.xml.rels with open(pres_rels_path, "r") as f: rels_xml = f.read() # Check if already patched if 'rId10' not in rels_xml: new_rels = ( ' <Relationship Id="rId10" Type="http://schemas.openxmlformats.org/officeDocument/2006/relationships/slide" Target="slides/slide2.xml"/>\n' ' <Relationship Id="rId11" Type="http://schemas.openxmlformats.org/officeDocument/2006/relationships/slide" Target="slides/slide3.xml"/>\n' ' <Relationship Id="rId12" Type="http://schemas.openxmlformats.org/officeDocument/2006/relationships/slide" Target="slides/slide4.xml"/>\n' ' <Relationship Id="rId13" Type="http://schemas.openxmlformats.org/officeDocument/2006/relationships/slide" Target="slides/slide5.xml"/>\n' '</Relationships>' ) rels_xml = rels_xml.replace('</Relationships>', new_rels) with open(pres_rels_path, "w") as f: f.write(rels_xml) print("Updated presentation.xml.rels") else: print("presentation.xml.rels already patched") print("\nSlides in base:") for fn in sorted(os.listdir(slides_dir)): if not fn.startswith('_'): print(f" {fn}") print("\nRels in _rels:") for fn in sorted(os.listdir(rels_dir)): print(f" {fn}") PYEOF

python3 /home/daytona/skills/pptx/scripts/office/pack.py \ /home/daytona/workspace/biochem-slides/unpacked_acidic/ \ /home/daytona/workspace/biochem-slides/Master_Amino_Acids.pptx \ --original /home/daytona/workspace/biochem-slides/Acidic_Amino_Acids.pptx \ && echo "PACKED OK"

# Pack directly with zipfile — PPTX is just a ZIP python3 << 'PYEOF' import zipfile, os unpacked_dir = "/home/daytona/workspace/biochem-slides/unpacked_acidic" output_path = "/home/daytona/workspace/biochem-slides/Master_Amino_Acids.pptx" # Build the zip, preserving the same structure as original with zipfile.ZipFile(output_path, 'w', zipfile.ZIP_DEFLATED) as zf: for root, dirs, files in os.walk(unpacked_dir): # Sort for determinism for fn in sorted(files): full_path = os.path.join(root, fn) # Arcname = path relative to unpacked_dir arcname = os.path.relpath(full_path, unpacked_dir) zf.write(full_path, arcname) size = os.path.getsize(output_path) print(f"Packed: {output_path} ({size//1024} KB)") # Quick verify: list slides in the zip with zipfile.ZipFile(output_path, 'r') as zf: slides = sorted([n for n in zf.namelist() if n.startswith('ppt/slides/slide')]) print(f"Slides in archive: {slides}") PYEOF

# Try writing to /tmp first, then move python3 << 'PYEOF' import zipfile, os, shutil unpacked_dir = "/home/daytona/workspace/biochem-slides/unpacked_acidic" tmp_path = "/tmp/Master_Amino_Acids.pptx" output_path = "/home/daytona/workspace/biochem-slides/Master_Amino_Acids.pptx" with zipfile.ZipFile(tmp_path, 'w', zipfile.ZIP_DEFLATED) as zf: for root, dirs, files in os.walk(unpacked_dir): for fn in sorted(files): full_path = os.path.join(root, fn) arcname = os.path.relpath(full_path, unpacked_dir) zf.write(full_path, arcname) # Move to workspace with open(tmp_path, 'rb') as src, open(output_path, 'wb') as dst: dst.write(src.read()) os.remove(tmp_path) size = os.path.getsize(output_path) print(f"Packed: {output_path} ({size//1024} KB)") with zipfile.ZipFile(output_path, 'r') as zf: slides = sorted([n for n in zf.namelist() if 'slides/slide' in n and '.xml' in n and '_rels' not in n]) print(f"Slides in archive: {slides}") PYEOF

python3 << 'PYEOF' from reportlab.lib.pagesizes import letter from reportlab.lib.styles import getSampleStyleSheet, ParagraphStyle from reportlab.lib.units import inch from reportlab.lib import colors from reportlab.platypus import ( SimpleDocTemplate, Paragraph, Spacer, Table, TableStyle, HRFlowable, PageBreak, KeepTogether ) from reportlab.lib.enums import TA_CENTER, TA_LEFT, TA_JUSTIFY import os out_path = "/home/daytona/workspace/biochem-slides/AA_Metabolism_Quiz_StudyGuide.pdf" # ── Color palette ────────────────────────────────────────────── NAVY = colors.HexColor("#0D1B2A") TEAL = colors.HexColor("#1ABC9C") RED = colors.HexColor("#E63946") BLUE = colors.HexColor("#2980B9") PURPLE = colors.HexColor("#9B59B6") AMBER = colors.HexColor("#F39C12") GREEN = colors.HexColor("#27AE60") LIGHTGRAY = colors.HexColor("#F4F6F9") MIDGRAY = colors.HexColor("#D5D8DC") WHITE = colors.white DARKTEXT = colors.HexColor("#1C2833") MUTEDTEXT = colors.HexColor("#5D6D7E") doc = SimpleDocTemplate( out_path, pagesize=letter, leftMargin=0.75*inch, rightMargin=0.75*inch, topMargin=0.7*inch, bottomMargin=0.7*inch, ) W = letter[0] - 1.5*inch # usable width styles = getSampleStyleSheet() # Custom styles def S(name, **kw): return ParagraphStyle(name, **kw) sTitle = S("sTitle", fontSize=26, textColor=WHITE, fontName="Helvetica-Bold", alignment=TA_CENTER, spaceAfter=4, leading=32) sSubtitle = S("sSubtitle", fontSize=12, textColor=colors.HexColor("#A8C8E8"), fontName="Helvetica", alignment=TA_CENTER, spaceAfter=2, leading=16) sSectionHead = S("sSectionHead", fontSize=14, textColor=WHITE, fontName="Helvetica-Bold", alignment=TA_LEFT, spaceBefore=6, spaceAfter=4, leading=18, backColor=NAVY, leftIndent=-6, rightIndent=-6) sSubHead = S("sSubHead", fontSize=11, textColor=NAVY, fontName="Helvetica-Bold", spaceBefore=8, spaceAfter=3, leading=14) sBody = S("sBody", fontSize=9.5, textColor=DARKTEXT, fontName="Helvetica", spaceBefore=2, spaceAfter=2, leading=14, alignment=TA_JUSTIFY) sBodyBold = S("sBodyBold", fontSize=9.5, textColor=DARKTEXT, fontName="Helvetica-Bold", spaceBefore=2, spaceAfter=2, leading=14) sBullet = S("sBullet", fontSize=9.5, textColor=DARKTEXT, fontName="Helvetica", leftIndent=14, spaceBefore=1, spaceAfter=1, leading=13, bulletIndent=4, bulletFontName="Helvetica", bulletFontSize=9.5) sQ = S("sQ", fontSize=10, textColor=NAVY, fontName="Helvetica-Bold", spaceBefore=6, spaceAfter=2, leading=14) sA = S("sA", fontSize=9.5, textColor=colors.HexColor("#1A6B40"), fontName="Helvetica", spaceBefore=1, spaceAfter=3, leading=13, leftIndent=14) sNote = S("sNote", fontSize=8.5, textColor=MUTEDTEXT, fontName="Helvetica-Oblique", spaceBefore=1, spaceAfter=2, leading=12, leftIndent=10) sLabel = S("sLabel", fontSize=8, textColor=WHITE, fontName="Helvetica-Bold", alignment=TA_CENTER, leading=10) sTocHead = S("sTocHead", fontSize=11, textColor=NAVY, fontName="Helvetica-Bold", spaceBefore=4, spaceAfter=2) def b(txt): return f"<b>{txt}</b>" def i(txt): return f"<i>{txt}</i>" def c(txt, col): return f'<font color="{col}">{txt}</font>' def bullet(txt, style=sBullet): return Paragraph(f"• {txt}", style) def section_header(title, color=NAVY): data = [[Paragraph(title, S("sh2", fontSize=13, textColor=WHITE, fontName="Helvetica-Bold", leading=16))]] t = Table(data, colWidths=[W]) t.setStyle(TableStyle([ ("BACKGROUND", (0,0), (-1,-1), color), ("LEFTPADDING", (0,0), (-1,-1), 8), ("RIGHTPADDING", (0,0), (-1,-1), 8), ("TOPPADDING", (0,0), (-1,-1), 5), ("BOTTOMPADDING",(0,0), (-1,-1), 5), ("ROUNDEDCORNERS", [4]), ])) return t def sub_header(title): return Paragraph(title, sSubHead) def qa(q_text, a_text, q_num=""): label = f"Q{q_num}. " if q_num else "" return [ Paragraph(f"{label}{q_text}", sQ), Paragraph(f"▶ {a_text}", sA), ] story = [] # ══════════════════════════════════════════════════════════════ # COVER BLOCK # ══════════════════════════════════════════════════════════════ cover_data = [[ Paragraph("Amino Acid Metabolism", sTitle), Paragraph("&amp; Clinical Correlates", sTitle), Spacer(1, 6), Paragraph("Quiz &amp; Study Guide", sSubtitle), Paragraph("Biochemistry — Medical Year 1 / Year 2", sSubtitle), Spacer(1, 4), HRFlowable(width=W*0.5, thickness=1.5, color=TEAL, spaceAfter=4), Paragraph("20 Standard Amino Acids · Metabolic Pathways · Enzyme Deficiencies · High-Yield Clinicals", S("cov2", fontSize=9, textColor=colors.HexColor("#7FB3D3"), fontName="Helvetica", alignment=TA_CENTER, leading=13)), ]] cover_tbl = Table(cover_data, colWidths=[W]) cover_tbl.setStyle(TableStyle([ ("BACKGROUND", (0,0), (-1,-1), NAVY), ("TOPPADDING", (0,0), (-1,-1), 22), ("BOTTOMPADDING",(0,0), (-1,-1), 22), ("LEFTPADDING", (0,0), (-1,-1), 18), ("RIGHTPADDING", (0,0), (-1,-1), 18), ("ROUNDEDCORNERS",[6]), ])) story.append(cover_tbl) story.append(Spacer(1, 14)) # ── How to use ───────────────────────────────────────────────── story.append(Paragraph( "How to use: Read each <b>Study Note</b> section first, then attempt the <b>Quiz Questions</b> below it. " "Answers are shown immediately beneath each question — cover them with a card as you work through. " "Clinical correlates are highlighted in green boxes.", sBody)) story.append(Spacer(1, 10)) # ══════════════════════════════════════════════════════════════ # SECTION 1 — AMINO ACID CLASSIFICATION # ══════════════════════════════════════════════════════════════ story.append(section_header("SECTION 1 — Classification of the 20 Standard Amino Acids", NAVY)) story.append(Spacer(1, 6)) class_data = [ [Paragraph(b("Group"), sLabel), Paragraph(b("Members"), sLabel), Paragraph(b("Key Property"), sLabel)], ["Nonpolar Aliphatic", "Gly, Ala, Val, Leu, Ile, Pro, Met", "Hydrophobic; form protein core"], ["Nonpolar Aromatic", "Phe, Trp, Tyr", "UV absorption (280 nm); Phe/Trp most hydrophobic"], ["Polar Uncharged", "Ser, Thr, Cys, Asn, Gln", "H-bond donors/acceptors; phosphorylation targets"], ["Acidic (–)", "Asp, Glu", "pKa < 4.1; negative at pH 7; strong cation binders"], ["Basic (+)", "Lys, Arg, His", "Positive at pH 7; DNA/protein binding; His pKa ~6.0"], ] colwidths = [W*0.22, W*0.48, W*0.30] ct = Table(class_data, colWidths=colwidths) ct.setStyle(TableStyle([ ("BACKGROUND", (0,0), (-1,0), NAVY), ("TEXTCOLOR", (0,0), (-1,0), WHITE), ("FONTNAME", (0,0), (-1,0), "Helvetica-Bold"), ("FONTSIZE", (0,0), (-1,0), 9), ("BACKGROUND", (0,1), (-1,1), colors.HexColor("#EBF5FB")), ("BACKGROUND", (0,2), (-1,2), colors.HexColor("#F4ECF7")), ("BACKGROUND", (0,3), (-1,3), colors.HexColor("#FEF9E7")), ("BACKGROUND", (0,4), (-1,4), colors.HexColor("#FDECEA")), ("BACKGROUND", (0,5), (-1,5), colors.HexColor("#EBF5FB")), ("FONTNAME", (0,1), (-1,-1), "Helvetica"), ("FONTSIZE", (0,1), (-1,-1), 9), ("ROWBACKGROUNDS",(0,1), (-1,-1), [LIGHTGRAY, WHITE]), ("GRID", (0,0), (-1,-1), 0.4, MIDGRAY), ("ALIGN", (0,0), (-1,-1), "LEFT"), ("LEFTPADDING", (0,0), (-1,-1), 6), ("RIGHTPADDING", (0,0), (-1,-1), 6), ("TOPPADDING", (0,0), (-1,-1), 4), ("BOTTOMPADDING", (0,0), (-1,-1), 4), ("VALIGN", (0,0), (-1,-1), "MIDDLE"), ])) story.append(ct) story.append(Spacer(1, 8)) # Essential AAs mnemonic story.append(sub_header("Essential Amino Acids (cannot be synthesized — must be dietary)")) story.append(Paragraph( b("PVT TIM HaLL") — Phe, Val, Thr, Trp, Ile, Met, His, Lys, Leu", sBody)) story.append(Paragraph( "Conditionally essential (increased demand): Arg, Gln, Gly, Pro, Cys, Tyr", sNote)) story.append(Spacer(1, 6)) # Quiz Q1-4 story.append(sub_header("Quiz — Classification")) for items in [ ("1", "Which amino acid has NO chiral center and why?", "Glycine (Gly/G). Its side chain is a single hydrogen atom, making both alpha-carbon substituents identical — therefore no stereocenter."), ("2", "Which amino acid is technically an imino acid, not an amino acid?", "Proline (Pro/P). Its side chain forms a pyrrolidine ring that bonds back to the backbone nitrogen, creating a secondary amine (imino group) rather than a primary amine."), ("3", "Name the only amino acid whose side chain can buffer at physiological pH and explain why.", "Histidine (His/H). Its imidazole side chain has a pKa of ~6.0 — close to physiological pH 7.4 — allowing it to accept or donate protons under normal cellular conditions. This is exploited in hemoglobin (Bohr effect) and enzyme active sites."), ("4", "Which amino acid absorbs UV light most strongly and at what wavelength?", "Tryptophan (Trp/W) absorbs most strongly at 280 nm due to its indole ring system. Tyrosine also absorbs at 280 nm. This is the basis for protein quantification by UV spectrophotometry."), ]: story.extend(qa(items[1], items[2], items[0])) story.append(PageBreak()) # ══════════════════════════════════════════════════════════════ # SECTION 2 — METABOLIC PATHWAYS # ══════════════════════════════════════════════════════════════ story.append(section_header("SECTION 2 — Amino Acid Metabolism: Key Pathways", colors.HexColor("#1A5276"))) story.append(Spacer(1, 6)) story.append(sub_header("2A. Transamination")) story.append(Paragraph( "Most amino acids donate their amino group via <b>transamination</b> to alpha-ketoglutarate (α-KG), " "producing <b>glutamate</b> and the corresponding alpha-keto acid. Enzyme: <b>aminotransferase (transaminase)</b>. " "Cofactor: <b>PLP (pyridoxal phosphate, vitamin B6)</b>.", sBody)) story.append(Paragraph("Key transamination reactions (high-yield):", sBodyBold)) trans_data = [ [Paragraph(b("Amino Acid"), sLabel), Paragraph(b("Alpha-Keto Product"), sLabel), Paragraph(b("Enzyme"), sLabel), Paragraph(b("Clinical"), sLabel)], ["Aspartate (Asp)", "Oxaloacetate (OAA)", "AST (GOT)", "Elevated in hepatocellular damage, MI"], ["Alanine (Ala)", "Pyruvate", "ALT (GPT)", "Most specific for hepatocellular injury"], ["Glutamate (Glu)", "α-Ketoglutarate", "GDH (also deamination)", "Central hub for all transaminations"], ["Leucine (Leu)", "α-Ketoisocaproate", "BCAT", "MSUD if BCKAD deficient"], ["Phenylalanine", "Phenylpyruvate", "PAH (then transaminase)", "PKU: phenylpyruvate in urine"], ] tt = Table(trans_data, colWidths=[W*0.20, W*0.22, W*0.22, W*0.36]) tt.setStyle(TableStyle([ ("BACKGROUND", (0,0), (-1,0), colors.HexColor("#1A5276")), ("TEXTCOLOR", (0,0), (-1,0), WHITE), ("FONTNAME", (0,0), (-1,0), "Helvetica-Bold"), ("FONTSIZE", (0,0), (-1,-1), 8.5), ("ROWBACKGROUNDS",(0,1), (-1,-1), [LIGHTGRAY, WHITE]), ("GRID", (0,0), (-1,-1), 0.4, MIDGRAY), ("LEFTPADDING", (0,0), (-1,-1), 5), ("TOPPADDING", (0,0), (-1,-1), 3), ("BOTTOMPADDING", (0,0), (-1,-1), 3), ("FONTNAME", (0,1), (-1,-1), "Helvetica"), ("VALIGN", (0,0), (-1,-1), "MIDDLE"), ])) story.append(tt) story.append(Spacer(1, 6)) story.append(sub_header("2B. The Urea Cycle — Nitrogen Disposal")) story.append(Paragraph( "Occurs in <b>hepatocytes</b> (cytosol + mitochondria). Disposes of excess ammonia as urea (excreted in urine).", sBody)) urea_steps = [ ("Step 1", "Mitochondria", "NH₃ + CO₂ + 2ATP → Carbamoyl phosphate", "CPS-I", "Activated by N-acetylglutamate (NAG)"), ("Step 2", "Mitochondria", "Carbamoyl-P + Ornithine → Citrulline", "OTC", "X-linked; most common urea cycle defect"), ("Step 3", "Cytosol", "Citrulline + Aspartate → Argininosuccinate", "ASS", "Citrullinemia type I"), ("Step 4", "Cytosol", "Argininosuccinate → Arginine + Fumarate", "ASL", "Argininosuccinic aciduria"), ("Step 5", "Cytosol", "Arginine → Ornithine + Urea", "Arginase", "Hyperargininemia; Arg → NO (NOS pathway)"), ] ud = [[Paragraph(b("Step"), sLabel), Paragraph(b("Location"), sLabel), Paragraph(b("Reaction"), sLabel), Paragraph(b("Enzyme"), sLabel), Paragraph(b("Notes"), sLabel)]] ud += urea_steps ut = Table(ud, colWidths=[W*0.08, W*0.14, W*0.32, W*0.14, W*0.32]) ut.setStyle(TableStyle([ ("BACKGROUND", (0,0), (-1,0), colors.HexColor("#117A65")), ("TEXTCOLOR", (0,0), (-1,0), WHITE), ("FONTNAME", (0,0), (-1,0), "Helvetica-Bold"), ("FONTSIZE", (0,0), (-1,-1), 8), ("ROWBACKGROUNDS",(0,1), (-1,-1), [LIGHTGRAY, WHITE]), ("GRID", (0,0), (-1,-1), 0.4, MIDGRAY), ("LEFTPADDING", (0,0), (-1,-1), 4), ("TOPPADDING", (0,0), (-1,-1), 3), ("BOTTOMPADDING", (0,0), (-1,-1), 3), ("FONTNAME", (0,1), (-1,-1), "Helvetica"), ("VALIGN", (0,0), (-1,-1), "TOP"), ])) story.append(ut) story.append(Spacer(1, 5)) story.append(Paragraph("Memory tip: <b>O</b>rdinarily <b>C</b>areless <b>C</b>liver <b>A</b>rgonauts <b>A</b>re <b>A</b>wesome (OTC, CPS-I, citrulline, ASS, ASL, arginase)", sNote)) story.append(Spacer(1, 6)) story.append(sub_header("2C. Glucogenic vs. Ketogenic Amino Acids")) story.append(Paragraph( "<b>Glucogenic</b>: catabolized to pyruvate, OAA, α-KG, succinyl-CoA, or fumarate → can make glucose. " "<b>Ketogenic</b>: yield acetyl-CoA or acetoacetate → cannot make glucose (fuel for ketogenesis).", sBody)) gk_data = [ [Paragraph(b("Category"), sLabel), Paragraph(b("Amino Acids"), sLabel)], ["Purely Ketogenic", "Leucine (Leu), Lysine (Lys) — mnemonic: 'Luckily Ketogenic'"], ["Both (Glucogenic + Ketogenic)", "Ile, Phe, Trp, Tyr, Thr"], ["Purely Glucogenic", "All remaining 15 amino acids"], ] gkt = Table(gk_data, colWidths=[W*0.30, W*0.70]) gkt.setStyle(TableStyle([ ("BACKGROUND", (0,0), (-1,0), NAVY), ("TEXTCOLOR", (0,0), (-1,0), WHITE), ("FONTNAME", (0,0), (-1,0), "Helvetica-Bold"), ("FONTSIZE", (0,0), (-1,-1), 9), ("BACKGROUND", (0,1), (-1,1), colors.HexColor("#FDECEA")), ("BACKGROUND", (0,2), (-1,2), colors.HexColor("#FEF9E7")), ("BACKGROUND", (0,3), (-1,3), colors.HexColor("#EBF5FB")), ("GRID", (0,0), (-1,-1), 0.4, MIDGRAY), ("LEFTPADDING", (0,0), (-1,-1), 6), ("TOPPADDING", (0,0), (-1,-1), 4), ("BOTTOMPADDING", (0,0), (-1,-1), 4), ("FONTNAME", (0,1), (-1,-1), "Helvetica"), ("VALIGN", (0,0), (-1,-1), "MIDDLE"), ])) story.append(gkt) story.append(Spacer(1, 6)) story.append(sub_header("2D. One-Carbon Metabolism (Folate & B12)")) story.append(Paragraph( "Serine is the primary one-carbon donor → THF (tetrahydrofolate) carries one-carbon units. " "Methionine cycle: Met → SAM (universal methyl donor) → SAH → Homocysteine. " "Homocysteine is remethylated to Met using <b>5-methyl-THF + B12 (methionine synthase)</b>, " "or transsulfurated to cysteine via <b>CBS (cystathionine β-synthase, B6-dependent)</b>.", sBody)) story.append(Spacer(1, 6)) # Quiz Q5-10 story.append(sub_header("Quiz — Metabolism")) for items in [ ("5", "ALT is elevated in a patient with jaundice. What is ALT's normal metabolic role?", "ALT (alanine aminotransferase) catalyzes: Alanine + α-KG ⇌ Pyruvate + Glutamate. It is central to the glucose–alanine cycle: muscle generates alanine from pyruvate (transamination), exports it to liver, where ALT regenerates pyruvate for gluconeogenesis and the amino group enters the urea cycle. Elevation in liver disease reflects hepatocyte lysis releasing cytosolic ALT."), ("6", "A newborn has hyperammonemia. Plasma citrulline is absent. Which urea cycle enzyme is most likely deficient?", "OTC (ornithine transcarbamylase) — the most common urea cycle defect (X-linked). OTC converts ornithine + carbamoyl phosphate → citrulline in mitochondria. Absent citrulline in plasma with elevated orotic acid (carbamoyl phosphate overflows into pyrimidine synthesis) is the classic pattern."), ("7", "Name the ONLY two purely ketogenic amino acids.", "Leucine and Lysine. They are degraded entirely to acetyl-CoA / acetoacetate and cannot contribute to gluconeogenesis. Mnemonic: 'Lucky Leu and Lys are Ketogenic.'"), ("8", "What cofactor is shared by ALL transaminases, and what vitamin is it derived from?", "Pyridoxal phosphate (PLP), derived from Vitamin B6 (pyridoxine). PLP acts as a Schiff base intermediate, shuttling amino groups between amino acids and alpha-keto acids."), ("9", "Homocysteine is elevated in a patient. Name two vitamins whose deficiency could cause this and explain the mechanism for each.", "① Vitamin B12 (cobalamin): required for methionine synthase (homocysteine + 5-methyl-THF → methionine). Deficiency traps folate as 5-methyl-THF (methylfolate trap) and prevents remethylation. ② Vitamin B6 (pyridoxine): required for CBS (cystathionine β-synthase) which converts homocysteine → cystathionine → cysteine via transsulfuration. B6 deficiency blocks this route. Folate (B9) deficiency can also raise homocysteine by reducing 5-methyl-THF availability."), ("10", "What activates CPS-I (the committed step of the urea cycle) and why is this physiologically important?", "N-acetylglutamate (NAG), synthesized by NAG synthase from acetyl-CoA + glutamate. NAG levels rise when amino acid catabolism increases (high protein intake, fasting), ensuring the urea cycle ramps up proportionally to handle more ammonia. Arginine stimulates NAG synthase — creating a feedforward loop."), ]: story.extend(qa(items[1], items[2], items[0])) story.append(PageBreak()) # ══════════════════════════════════════════════════════════════ # SECTION 3 — CLINICAL CORRELATES # ══════════════════════════════════════════════════════════════ story.append(section_header("SECTION 3 — High-Yield Clinical Correlates", RED)) story.append(Spacer(1, 6)) clinicals = [ ("Phenylketonuria (PKU)", RED, "Deficient enzyme", "Phenylalanine hydroxylase (PAH), or cofactor BH4 (tetrahydrobiopterin)", "Pathway blocked", "Phe → Tyr conversion fails; Phe accumulates and is transaminated to phenylpyruvate, phenylacetate, phenyllactate", "Presentation", "Intellectual disability, fair skin/hair/eyes (tyrosinase substrate depleted), musty/mousy odor (phenylacetate), eczema", "Lab finding", "Elevated plasma Phe (>1200 µmol/L); elevated phenylpyruvate in urine (ferric chloride test = green)", "Treatment", "Phenylalanine-restricted diet; BH4 supplementation (sapropterin) for BH4-deficient forms; enzyme therapy (pegvaliase)"), ("Maple Syrup Urine Disease (MSUD)", colors.HexColor("#7D3C98"), "Deficient enzyme", "Branched-chain alpha-keto acid dehydrogenase (BCKAD) complex", "Pathway blocked", "Catabolism of BCAAs (Leu, Ile, Val) — keto acids accumulate", "Presentation", "Sweet maple-syrup odor of urine/cerumen; neonatal encephalopathy, seizures, alternating hypo/hypertonia", "Lab finding", "Elevated plasma Leu, Ile, Val + their keto acids; alloisoleucine (pathognomonic)", "Treatment", "Restrict BCAAs dietarily; thiamine (B1) may help in thiamine-responsive form; liver transplant curative"), ("Homocystinuria", colors.HexColor("#1A5276"), "Deficient enzyme", "Cystathionine β-synthase (CBS) — most common form", "Pathway blocked", "Homocysteine → cystathionine → cysteine (transsulfuration); homocysteine accumulates", "Presentation", "Marfanoid habitus, downward lens dislocation (ectopia lentis), thromboembolism (venous + arterial), intellectual disability", "Lab finding", "Elevated plasma + urine homocysteine; urine sodium nitroprusside test positive", "Treatment", "Pyridoxine (B6) if CBS-responsive; methionine restriction + cysteine supplementation; B12 + folate; betaine"), ("Alkaptonuria", colors.HexColor("#117A65"), "Deficient enzyme", "Homogentisate oxidase (HGD)", "Pathway blocked", "Tyr catabolism: homogentisic acid accumulates", "Presentation", "Dark urine (oxidation of homogentisate → benzoquinone acetic acid), ochronosis (blue-black pigment in connective tissue, sclera, ear cartilage), arthritis", "Lab finding", "Urine darkens on standing / alkalinization; homogentisic acid in urine", "Treatment", "Nitisinone (NTBC, blocks HPPD upstream); low Phe/Tyr diet"), ("Hartnup Disease", colors.HexColor("#7E5109"), "Deficient enzyme", "Neutral amino acid transporter (SLC6A19) in intestine and kidney", "Pathway blocked", "Absorption of neutral AAs (especially Trp) impaired → tryptophan deficiency → niacin (B3) deficiency", "Presentation", "Pellagra-like: photosensitive rash, cerebellar ataxia, psychiatric symptoms (3 Ds: dermatitis, diarrhea, dementia); intermittent", "Lab finding", "Increased neutral AAs in urine (generalized aminoaciduria); normal plasma levels (intestinal defect predominates)", "Treatment", "Niacin supplementation; high-protein diet to compensate for malabsorption"), ("Cystinuria", colors.HexColor("#5D6D7E"), "Deficient enzyme", "Dibasic amino acid transporter (SLC3A1/SLC7A9) in kidney/intestine", "Pathway blocked", "Reabsorption of cystine, ornithine, arginine, lysine (COAL) impaired", "Presentation", "Recurrent kidney stones (cystine stones; radiopaque but less than calcium), staghorn calculi, UTIs", "Lab finding", "Cyanide-nitroprusside test positive; hexagonal cystine crystals on urinalysis", "Treatment", "High fluid intake; alkalinize urine (pH >7.5); D-penicillamine or tiopronin (chelate cystine)"), ("OTC Deficiency", colors.HexColor("#C0392B"), "Deficient enzyme", "Ornithine transcarbamylase (OTC) — X-linked", "Pathway blocked", "Urea cycle step 2 fails; carbamoyl phosphate overflows into pyrimidine pathway → orotic acid", "Presentation", "Neonatal: coma, hyperammonemia; later onset: episodic encephalopathy, protein aversion, vomiting", "Lab finding", "Elevated ammonia; elevated orotic acid in urine; LOW or absent plasma citrulline", "Treatment", "Protein restriction; sodium benzoate + sodium phenylacetate (alternative nitrogen disposal); arginine/citrulline supplementation; liver transplant"), ("Tyrosinemia Type I", colors.HexColor("#1A6B40"), "Deficient enzyme", "Fumarylacetoacetate hydrolase (FAH)", "Pathway blocked", "Tyr catabolism: fumarylacetoacetate accumulates → toxic metabolites (succinylacetone)", "Presentation", "Hepatocellular carcinoma (in childhood), cirrhosis, Fanconi syndrome (proximal tubule damage), 'cabbage-like' odor", "Lab finding", "Succinylacetone in urine (pathognomonic); elevated AFP; elevated plasma Tyr/Met", "Treatment", "Nitisinone (NTBC) + Phe/Tyr restriction; liver transplant"), ] for name, color, *pairs in clinicals: # Header hdr_data = [[Paragraph(name, S("ch", fontSize=11, textColor=WHITE, fontName="Helvetica-Bold", leading=14))]] ht = Table(hdr_data, colWidths=[W]) ht.setStyle(TableStyle([ ("BACKGROUND", (0,0), (-1,-1), color), ("LEFTPADDING", (0,0), (-1,-1), 8), ("TOPPADDING", (0,0), (-1,-1), 4), ("BOTTOMPADDING", (0,0), (-1,-1), 4), ])) story.append(KeepTogether([ Spacer(1, 4), ht, ])) # Detail rows rows = [] for idx in range(0, len(pairs), 2): label = pairs[idx] val = pairs[idx+1] rows.append([ Paragraph(label, S("cl", fontSize=8.5, textColor=color, fontName="Helvetica-Bold", leading=12)), Paragraph(val, S("cv", fontSize=8.5, textColor=DARKTEXT, fontName="Helvetica", leading=12)), ]) dt = Table(rows, colWidths=[W*0.22, W*0.78]) dt.setStyle(TableStyle([ ("GRID", (0,0), (-1,-1), 0.3, MIDGRAY), ("LEFTPADDING", (0,0), (-1,-1), 6), ("RIGHTPADDING", (0,0), (-1,-1), 6), ("TOPPADDING", (0,0), (-1,-1), 3), ("BOTTOMPADDING", (0,0), (-1,-1), 3), ("ROWBACKGROUNDS",(0,0), (-1,-1), [WHITE, LIGHTGRAY]), ("VALIGN", (0,0), (-1,-1), "TOP"), ])) story.append(dt) story.append(PageBreak()) # ══════════════════════════════════════════════════════════════ # SECTION 4 — CLINICAL QUIZ # ══════════════════════════════════════════════════════════════ story.append(section_header("SECTION 4 — Clinical Vignette Quiz", colors.HexColor("#7D3C98"))) story.append(Spacer(1, 6)) vignettes = [ ("11", "A 3-week-old boy presents with poor feeding, vomiting, and progressive lethargy. His urine has a sweet, maple-syrup-like odor. " "EEG shows burst suppression. Plasma amino acids show elevated leucine, isoleucine, and valine. " "Alloisoleucine is detected. What is the diagnosis, deficient enzyme, and acute management priority?", "Diagnosis: Maple Syrup Urine Disease (MSUD). Enzyme: BCKAD (branched-chain alpha-keto acid dehydrogenase) complex. " "Acute management: stop all protein intake immediately; IV glucose + lipids (anabolic to suppress catabolism); " "dialysis if Leu >1000 µmol/L or encephalopathy is severe. Leucine is the neurotoxic driver — its reduction is the priority."), ("12", "A 6-month-old girl has fair skin, blonde hair, and blue eyes despite being born to dark-haired parents of Mediterranean descent. " "She misses developmental milestones. Newborn screen showed elevated phenylalanine. " "What is the diagnosis? What would urine ferric chloride test show? How does the disease cause hypopigmentation?", "Diagnosis: Phenylketonuria (PKU). Ferric chloride test: turns green (phenylpyruvate reacts with FeCl₃). " "Hypopigmentation: PAH normally converts Phe → Tyr; Tyr is the substrate for tyrosinase → melanin synthesis. " "In PKU, Tyr is depleted (and Phe competitively inhibits tyrosinase), resulting in reduced melanin."), ("13", "A 22-year-old tall, thin man presents with dislocation of the lens inferiorly and a DVT. " "He has a history of intellectual disability. Labs show homocysteine 320 µmol/L (normal <15). " "What enzyme is most likely deficient, and which vitamin may be therapeutic?", "Enzyme: Cystathionine β-synthase (CBS). Treatment: Pyridoxine (Vitamin B6) — about 50% of CBS-deficient patients respond " "to high-dose B6 (CBS requires PLP as cofactor; B6 supplementation may partially restore activity). " "Note: Marfan syndrome also causes lens dislocation but lens displaces superiorly — downward displacement is classic for homocystinuria."), ("14", "A 5-year-old boy has recurrent hyperammonemia episodes triggered by high-protein meals. " "Urine orotic acid is markedly elevated. Plasma citrulline is undetectable. " "His 3 brothers are unaffected. What is the diagnosis and inheritance pattern?", "Diagnosis: OTC (ornithine transcarbamylase) deficiency. Inheritance: X-linked recessive — explains why brothers (XY) are severely affected " "while mother may be a mildly symptomatic carrier (random X-inactivation). Elevated orotic acid is the key distinguishing feature " "(vs. CPS-I deficiency, which has LOW orotic acid because no carbamoyl phosphate overflow occurs)."), ("15", "A 30-year-old man has progressively darkening ears (blue-black cartilage) and dark urine that blackens on standing. " "X-ray shows dense calcifications of intervertebral discs. Urine shows homogentisic acid. What is the diagnosis?", "Alkaptonuria. Deficient enzyme: homogentisate oxidase (HGD). Accumulated homogentisic acid polymerizes into a dark pigment " "(ochronosis) deposited in cartilage, tendons, and sclera. The connective tissue deposition causes arthropathy. " "Treatment: nitisinone (inhibits HPPD, the enzyme two steps upstream, reducing homogentisate production)."), ("16", "A 2-year-old presents with Fanconi syndrome (glucosuria, phosphaturia, aminoaciduria), " "elevated AFP, and liver dysfunction. Urine succinylacetone is detected. What is the diagnosis?", "Tyrosinemia Type I (hepatorenal tyrosinemia). Deficient enzyme: fumarylacetoacetate hydrolase (FAH). " "Succinylacetone (formed from fumarylacetoacetate) inhibits delta-aminolevulinic acid dehydratase (ALA-D), " "causing secondary porphyria. It also damages renal proximal tubules → Fanconi syndrome. " "Treatment: nitisinone (NTBC) + dietary Phe/Tyr restriction; curative with liver transplantation."), ("17", "A patient has elevated plasma homocysteine and megaloblastic anemia but normal MMA (methylmalonic acid). " "Which vitamin deficiency is most likely?", "Folate (B9) deficiency. Both B12 and folate deficiency cause elevated homocysteine + megaloblastic anemia. " "However, only B12 deficiency elevates MMA (methylmalonate is a substrate for B12-dependent methylmalonyl-CoA mutase). " "Normal MMA rules out B12 deficiency, pointing to folate. This distinction is critical because B12 deficiency also causes " "subacute combined degeneration of the spinal cord — treating with folate alone would miss the neurological damage."), ("18", "A child with intermittent pellagra-like rash after sun exposure, cerebellar ataxia, and psychiatric symptoms " "has normal plasma amino acids but elevated neutral amino acids in urine. What is the diagnosis?", "Hartnup disease. Defect: neutral amino acid transporter (SLC6A19) in intestinal epithelium and renal tubules. " "Tryptophan absorption is impaired → niacin (NAD⁺ precursor) deficiency → pellagra. Normal plasma AAs because " "the intestinal defect impairs absorption but urinary loss is from renal tubule defect. Treatment: niacin supplementation."), ] for items in vignettes: story.extend(qa(items[1], items[2], items[0])) story.append(PageBreak()) # ══════════════════════════════════════════════════════════════ # SECTION 5 — RAPID-FIRE REVIEW TABLE # ══════════════════════════════════════════════════════════════ story.append(section_header("SECTION 5 — Rapid-Fire Reference Table: AA Metabolism at a Glance", NAVY)) story.append(Spacer(1, 6)) rf_data = [ [Paragraph(b("AA"), sLabel), Paragraph(b("Metabolic Product(s)"), sLabel), Paragraph(b("Key Enzyme"), sLabel), Paragraph(b("Vitamin/Cofactor"), sLabel), Paragraph(b("Disease if Blocked"), sLabel)], ["Phe", "Tyr; phenylpyruvate (PKU)", "PAH", "BH4", "PKU"], ["Tyr", "DOPA→dopamine→NE→Epi; T3/T4; melanin; homogentisate", "Tyrosinase, DOPA decarboxylase, TH", "B6, Cu", "Alkaptonuria, Tyrosinemia I, Albinism"], ["Trp", "Serotonin→melatonin; NAD⁺ (kynurenine path)", "Tryptophan hydroxylase", "B6, B3 (niacin)", "Hartnup disease, Carcinoid"], ["Met", "SAM (methyl donor) → SAH → Homocysteine → Cys", "CBS (B6), Methionine synthase (B12)", "B6, B12, Folate", "Homocystinuria"], ["Leu/Ile/Val", "Acetyl-CoA (Leu); succinyl-CoA/acetyl-CoA (Ile/Val)", "BCKAD", "B1 (thiamine)", "MSUD"], ["Glu", "α-KG; GABA; Gln; urea cycle N-donor", "GDH; GAD (B6)", "B6", "Hepatic encephalopathy (excess NH₃)"], ["Asp", "OAA; urea cycle (N-donor via ASS); pyrimidines", "AST; ASS", "B6", "Citrullinemia (ASS defect)"], ["Gly", "One-carbon units; porphyrins; creatine; serine", "SHMT", "B6, Folate", "Non-ketotic hyperglycinemia"], ["Ser", "One-carbon units; Gly; sphingolipids; Cys", "SHMT; serine dehydratase", "B6, Folate", "—"], ["Cys", "Taurine; glutathione; SO₄²⁻", "CBS; cystathionase", "B6", "Homocystinuria (CBS def)"], ["Arg", "Urea; NO (NOS); creatine; polyamines", "Arginase; NOS", "—", "Arginase deficiency"], ["His", "Histamine (HDC); urocanic acid", "Histidine decarboxylase", "B6", "Histidinemia (benign)"], ["Lys", "Carnitine; acetyl-CoA (purely ketogenic)", "Various lysine dehydrogenases", "B6, B12, C", "Lysinuric protein intolerance"], ["Pro", "Hydroxyproline (requires Vit C via prolyl hydroxylase)", "Prolyl hydroxylase", "Vit C", "Scurvy (Vit C deficiency)"], ["Orn", "Urea cycle intermediate; polyamines", "OTC; ODC", "—", "OTC deficiency; Hyperornithinemia"], ] rft = Table(rf_data, colWidths=[W*0.07, W*0.30, W*0.21, W*0.14, W*0.28]) rft.setStyle(TableStyle([ ("BACKGROUND", (0,0), (-1,0), NAVY), ("TEXTCOLOR", (0,0), (-1,0), WHITE), ("FONTNAME", (0,0), (-1,0), "Helvetica-Bold"), ("FONTSIZE", (0,0), (-1,-1), 7.5), ("ROWBACKGROUNDS",(0,1), (-1,-1), [LIGHTGRAY, WHITE]), ("GRID", (0,0), (-1,-1), 0.3, MIDGRAY), ("LEFTPADDING", (0,0), (-1,-1), 4), ("TOPPADDING", (0,0), (-1,-1), 2), ("BOTTOMPADDING", (0,0), (-1,-1), 2), ("FONTNAME", (0,1), (-1,-1), "Helvetica"), ("VALIGN", (0,0), (-1,-1), "TOP"), ])) story.append(rft) story.append(Spacer(1, 8)) # ── Mnemonics box ─────────────────────────────────────────────── mn_data = [[ Paragraph(b("High-Yield Mnemonics"), S("mnh", fontSize=10, textColor=WHITE, fontName="Helvetica-Bold", leading=14)), Paragraph( "<b>Essential AAs:</b> PVT TIM HaLL (Phe, Val, Thr, Trp, Ile, Met, His, Lys, Leu)<br/>" "<b>Purely Ketogenic:</b> Leu &amp; Lys — 'Lucky Leu and Lys are Ketogenic'<br/>" "<b>Urea Cycle order:</b> Ordinarily Careless Citrulline Ate ASS and ARGot — OTC → Citrulline → ASS → ASL → Arginase<br/>" "<b>PKU triad:</b> Fair + Musty + ID → PAH defect<br/>" "<b>Homocystinuria vs Marfan:</b> Lens Down = Homocystinuria, Lens Up = Marfan<br/>" "<b>Orotic acid elevated:</b> OTC def (NOT CPS-I def)<br/>" "<b>Elevated MMA + homocysteine:</b> B12 def; elevated homocysteine ONLY: Folate or B6 def", S("mnb", fontSize=8.5, textColor=DARKTEXT, fontName="Helvetica", leading=13)) ]] mnt = Table(mn_data, colWidths=[W*0.25, W*0.75]) mnt.setStyle(TableStyle([ ("BACKGROUND", (0,0), (0,-1), NAVY), ("BACKGROUND", (1,0), (1,-1), colors.HexColor("#EAF2FF")), ("LEFTPADDING", (0,0), (-1,-1), 8), ("RIGHTPADDING", (0,0), (-1,-1), 8), ("TOPPADDING", (0,0), (-1,-1), 8), ("BOTTOMPADDING", (0,0), (-1,-1), 8), ("GRID", (0,0), (-1,-1), 0.5, MIDGRAY), ("VALIGN", (0,0), (-1,-1), "MIDDLE"), ])) story.append(mnt) story.append(Spacer(1, 10)) story.append(HRFlowable(width=W, thickness=0.5, color=MIDGRAY)) story.append(Paragraph( "Study Guide prepared for Biochemistry — Amino Acid Metabolism &amp; Clinical Correlates. " "Questions designed to mirror USMLE Step 1 / licensing exam vignette format.", S("foot", fontSize=7.5, textColor=MUTEDTEXT, fontName="Helvetica-Oblique", alignment=TA_CENTER, leading=11))) # ── Build ──────────────────────────────────────────────────────── doc.build(story) import os size = os.path.getsize(out_path) print(f"PDF created: {out_path} ({size//1024} KB)") PYEOF

~/biochem-slides/build_pdf.py

python3 /home/daytona/workspace/biochem-slides/build_pdf.py

~/biochem-slides/build_exam.py

python3 /home/daytona/workspace/biochem-slides/build_exam.py

~/biochem-slides/build_exam.py

python3 /home/daytona/workspace/biochem-slides/build_exam.py