mkdir -p /home/daytona/workspace/biochem-notes && ls /home/daytona/workspace/bio…

~/biochem-notes/generate_notes.py

from reportlab.lib.pagesizes import A4
from reportlab.lib.styles import getSampleStyleSheet, ParagraphStyle
from reportlab.lib.units import cm
from reportlab.lib import colors
from reportlab.platypus import (
    SimpleDocTemplate, Paragraph, Spacer, Table, TableStyle,
    PageBreak, HRFlowable
)
from reportlab.lib.enums import TA_LEFT, TA_CENTER, TA_JUSTIFY
import datetime

OUTPUT = "/home/daytona/workspace/biochem-notes/Biochemistry_Exam_Notes.pdf"

doc = SimpleDocTemplate(
    OUTPUT,
    pagesize=A4,
    rightMargin=2*cm, leftMargin=2*cm,
    topMargin=2.5*cm, bottomMargin=2.5*cm,
    title="Biochemistry Exam Notes",
    author="Orris AI"
)

styles = getSampleStyleSheet()

# Custom styles
title_style = ParagraphStyle('MainTitle', parent=styles['Title'],
    fontSize=22, textColor=colors.HexColor('#1a237e'), spaceAfter=8,
    alignment=TA_CENTER, fontName='Helvetica-Bold')

subtitle_style = ParagraphStyle('Subtitle', parent=styles['Normal'],
    fontSize=11, textColor=colors.HexColor('#5c6bc0'), spaceAfter=20,
    alignment=TA_CENTER)

h1_style = ParagraphStyle('H1', parent=styles['Heading1'],
    fontSize=16, textColor=colors.white,
    backColor=colors.HexColor('#1a237e'),
    spaceAfter=8, spaceBefore=14,
    leftIndent=-0.5*cm, rightIndent=-0.5*cm,
    borderPad=6, fontName='Helvetica-Bold')

h2_style = ParagraphStyle('H2', parent=styles['Heading2'],
    fontSize=13, textColor=colors.HexColor('#1a237e'),
    spaceAfter=4, spaceBefore=10,
    borderPad=2, fontName='Helvetica-Bold',
    borderWidth=0, leftIndent=0)

h3_style = ParagraphStyle('H3', parent=styles['Heading3'],
    fontSize=11, textColor=colors.HexColor('#283593'),
    spaceAfter=3, spaceBefore=6,
    fontName='Helvetica-BoldOblique')

body_style = ParagraphStyle('Body', parent=styles['Normal'],
    fontSize=9.5, spaceAfter=4, leading=14,
    alignment=TA_JUSTIFY, fontName='Helvetica')

bullet_style = ParagraphStyle('Bullet', parent=styles['Normal'],
    fontSize=9.5, spaceAfter=3, leading=13,
    leftIndent=16, bulletIndent=4, fontName='Helvetica')

bold_style = ParagraphStyle('Bold', parent=styles['Normal'],
    fontSize=9.5, spaceAfter=3, fontName='Helvetica-Bold')

note_style = ParagraphStyle('Note', parent=styles['Normal'],
    fontSize=9, spaceAfter=4, leading=13,
    backColor=colors.HexColor('#e8eaf6'),
    borderPad=6, leftIndent=8, rightIndent=8,
    textColor=colors.HexColor('#1a237e'), fontName='Helvetica-Oblique')

warning_style = ParagraphStyle('Warning', parent=styles['Normal'],
    fontSize=9, spaceAfter=4, leading=13,
    backColor=colors.HexColor('#fff3e0'),
    borderPad=6, leftIndent=8, rightIndent=8,
    textColor=colors.HexColor('#e65100'), fontName='Helvetica-Bold')

def B(text): return f"<b>{text}</b>"
def I(text): return f"<i>{text}</i>"

def section_header(n, title, story):
    story.append(Spacer(1, 8))
    story.append(Paragraph(f"  TOPIC {n}: {title}", h1_style))
    story.append(Spacer(1, 4))

def h2(text, story):
    story.append(Paragraph(text, h2_style))

def h3(text, story):
    story.append(Paragraph(text, h3_style))

def p(text, story):
    story.append(Paragraph(text, body_style))

def bp(items, story):
    for item in items:
        story.append(Paragraph(f"• {item}", bullet_style))

def note(text, story):
    story.append(Paragraph(f"📌 {text}", note_style))
    story.append(Spacer(1, 3))

def warn(text, story):
    story.append(Paragraph(f"⚠ {text}", warning_style))
    story.append(Spacer(1, 3))

def table(data, story, col_widths=None):
    t = Table(data, colWidths=col_widths)
    t.setStyle(TableStyle([
        ('BACKGROUND', (0,0), (-1,0), colors.HexColor('#283593')),
        ('TEXTCOLOR', (0,0), (-1,0), colors.white),
        ('FONTNAME', (0,0), (-1,0), 'Helvetica-Bold'),
        ('FONTSIZE', (0,0), (-1,-1), 9),
        ('ROWBACKGROUNDS', (0,1), (-1,-1), [colors.white, colors.HexColor('#f5f5f5')]),
        ('GRID', (0,0), (-1,-1), 0.5, colors.HexColor('#bdbdbd')),
        ('VALIGN', (0,0), (-1,-1), 'TOP'),
        ('LEFTPADDING', (0,0), (-1,-1), 6),
        ('RIGHTPADDING', (0,0), (-1,-1), 6),
        ('TOPPADDING', (0,0), (-1,-1), 4),
        ('BOTTOMPADDING', (0,0), (-1,-1), 4),
    ]))
    story.append(t)
    story.append(Spacer(1, 6))

story = []

# ── COVER PAGE ──────────────────────────────────────────────────────────────
story.append(Spacer(1, 3*cm))
story.append(Paragraph("BIOCHEMISTRY", title_style))
story.append(Paragraph("RAPID EXAM NOTES", title_style))
story.append(Spacer(1, 0.5*cm))
story.append(HRFlowable(width="80%", thickness=2, color=colors.HexColor('#5c6bc0'), spaceAfter=10))
story.append(Paragraph("Complete Syllabus Coverage  •  Exam-Focused  •  High-Yield Points", subtitle_style))
story.append(Spacer(1, 1*cm))

cover_data = [
    ["Topics Covered", ""],
    ["1.", "Molecular Biology & Techniques"],
    ["2.", "Nucleic Acid Chemistry & Metabolism"],
    ["3.", "Enzyme & Enzyme Kinetics"],
    ["4.", "Immunology"],
    ["5.", "Organ Function Tests"],
    ["6.", "Cancer Biochemistry"],
    ["7.", "Recent Advances in Biochemistry"],
    ["8.", "Acid-Base Balance, Water & Electrolytes"],
    ["9.", "Digestion & Absorption"],
    ["10.", "Protein Chemistry, Haemoglobin, Myoglobin, Plasma Proteins"],
]
table(cover_data, story, col_widths=[1.5*cm, 13*cm])

story.append(Spacer(1, 1*cm))
story.append(Paragraph(f"Prepared: {datetime.datetime.now().strftime('%B %d, %Y')}  |  Target: 60%+ in 4 hours", subtitle_style))
story.append(PageBreak())

# ════════════════════════════════════════════════════════════════════════════
# TOPIC 1: MOLECULAR BIOLOGY & TECHNIQUES
# ════════════════════════════════════════════════════════════════════════════
section_header(1, "MOLECULAR BIOLOGY & TECHNIQUES", story)

h2("1.1 DNA Structure", story)
p("DNA is a double-stranded helix composed of nucleotides. Each nucleotide = phosphate + deoxyribose sugar + nitrogenous base. The two strands are antiparallel (one 5'→3', other 3'→5') and held together by hydrogen bonds between complementary base pairs.", story)
bp([
    f"{B('Purines:')} Adenine (A) pairs with Thymine (T) — 2 H-bonds; Guanine (G) pairs with Cytosine (C) — 3 H-bonds",
    f"{B('Chargaff Rule:')} A=T and G=C; (A+G) = (T+C) — purines equal pyrimidines",
    f"{B('Backbone:')} Sugar-phosphate backbone on outside; bases stacked inside",
    f"{B('Diameter:')} 2 nm; pitch of helix = 3.4 nm (10 bp per turn in B-DNA)",
    "B-DNA is the most common form under physiological conditions",
    "Z-DNA: left-handed helix; A-DNA: shorter, wider, right-handed",
], story)

h2("1.2 DNA Replication", story)
bp([
    f"{B('Semiconservative:')} Each daughter DNA has one old + one new strand (Meselson-Stahl experiment)",
    f"{B('Origin of replication:')} Begins at specific sequences (ori); bacteria have 1, eukaryotes have many",
    f"{B('Helicase:')} Unwinds double helix",
    f"{B('Primase:')} Synthesizes short RNA primer (needed to start synthesis)",
    f"{B('DNA Polymerase III (bacteria):')} Main polymerase; 5'→3' synthesis only; also has 3'→5' proofreading exonuclease",
    f"{B('Leading strand:')} Synthesized continuously in 5'→3' direction",
    f"{B('Lagging strand:')} Synthesized in short Okazaki fragments (5'→3'); fragments joined by DNA ligase",
    f"{B('DNA Pol I:')} Removes RNA primers, fills gaps",
    f"{B('Topoisomerase:')} Relieves supercoiling ahead of replication fork",
    f"{B('Telomerase:')} Extends chromosome ends in eukaryotes using RNA template",
], story)

h2("1.3 Transcription (RNA Synthesis)", story)
p("DNA → RNA; occurs in nucleus (eukaryotes). RNA Polymerase II transcribes mRNA.", story)
bp([
    f"{B('Template strand:')} Read 3'→5'; mRNA synthesized 5'→3'",
    f"{B('Promoter:')} TATA box (~-25), CAAT box (~-75), GC box",
    f"{B('Steps:')} Initiation → Elongation → Termination",
    f"{B('mRNA processing (eukaryotes):')} 5' 7-methylguanosine cap (export/translation initiation), 3' poly-A tail (stability), splicing of introns by spliceosomes",
    f"{B('Types of RNA:')} mRNA (carries code), tRNA (adaptor, anticodon), rRNA (ribosome structure), snRNA (splicing), miRNA (gene regulation)",
], story)

h2("1.4 Translation (Protein Synthesis)", story)
bp([
    f"{B('Genetic code:')} Triplet codons; 64 codons, 61 encode amino acids + 3 stop codons (UAA, UAG, UGA)",
    f"{B('Start codon:')} AUG (codes Met/fMet); Wobble hypothesis: flexibility at 3rd codon position",
    f"{B('Ribosomes:')} 70S in prokaryotes (50S+30S); 80S in eukaryotes (60S+40S)",
    f"{B('Steps:')} Aminoacyl-tRNA synthetase charges tRNA + AA (uses ATP) → Initiation (small subunit binds mRNA) → Elongation (A site: aminoacyl-tRNA; P site: peptidyl-tRNA; E site: exit) → Translocation by EF-G (GTP) → Termination at stop codon (release factors)",
    f"{B('Post-translational modification:')} Glycosylation, phosphorylation, hydroxylation, acetylation",
], story)
note("Key exam point: AUG = start; UAA/UAG/UGA = stop; ribosome subunits add up (30+50=70S, 40+60=80S)", story)

h2("1.5 Molecular Biology Techniques", story)
tbl_data = [
    ["Technique", "Principle", "Application"],
    ["PCR", "Thermocyclic amplification of DNA using Taq polymerase", "DNA diagnosis, forensics, cloning"],
    ["Southern Blot", "DNA separated by gel → transferred → probed with labeled DNA", "Detect specific DNA sequences"],
    ["Northern Blot", "RNA detection using labeled DNA probe", "Gene expression analysis"],
    ["Western Blot", "Protein separated by SDS-PAGE → antibody probe", "Protein identification (e.g., HIV confirmation)"],
    ["ELISA", "Antigen-antibody reaction with enzyme-linked reporter", "HIV, hepatitis, hormone detection"],
    ["DNA Sequencing (Sanger)", "Chain termination with ddNTPs", "Determine nucleotide sequence"],
    ["RFLP", "Restriction enzymes cut DNA at specific sites → size differences", "Genetic fingerprinting"],
    ["Gel Electrophoresis", "Molecules separated by size in electric field", "DNA/protein sizing"],
    ["Flow Cytometry", "Laser-based cell counting/sorting by surface markers", "CD4 count in HIV"],
    ["FISH", "Fluorescent probes hybridize to chromosomes", "Chromosomal abnormalities"],
    ["RT-PCR", "RNA → cDNA (reverse transcriptase) → PCR", "Viral RNA detection (COVID-19)"],
    ["Recombinant DNA", "Foreign DNA inserted into vector → host cell expression", "Insulin production, vaccines"],
]
table(tbl_data, story, col_widths=[4*cm, 7*cm, 5*cm])

story.append(PageBreak())

# ════════════════════════════════════════════════════════════════════════════
# TOPIC 2: NUCLEIC ACID CHEMISTRY & METABOLISM
# ════════════════════════════════════════════════════════════════════════════
section_header(2, "NUCLEIC ACID CHEMISTRY & METABOLISM", story)

h2("2.1 Nucleotide Structure", story)
bp([
    f"{B('Nucleoside:')} Base + sugar (no phosphate)",
    f"{B('Nucleotide:')} Base + sugar + phosphate (mono/di/triphosphate)",
    f"{B('Purines:')} Adenine, Guanine (double ring)",
    f"{B('Pyrimidines:')} Cytosine, Thymine (DNA), Uracil (RNA) (single ring)",
    f"{B('Sugars:')} Deoxyribose in DNA; Ribose in RNA (has 2'-OH group)",
    "Bond: N-glycosidic bond links base to sugar (N9 for purines, N1 for pyrimidines)",
], story)

h2("2.2 Purine Synthesis (De Novo)", story)
p("Synthesized as IMP (inosine monophosphate) first, then converted to AMP or GMP.", story)
bp([
    f"Starting material: Ribose-5-phosphate → PRPP (by PRPP synthetase, using ATP)",
    f"Ring built on PRPP using: glutamine, glycine, formyl-THF, aspartate, CO2 (10 steps)",
    f"IMP → AMP (needs GTP) or IMP → GMP (needs ATP) — cross-regulation",
    f"{B('Rate-limiting step:')} PRPP amidotransferase (inhibited by AMP, GMP — feedback inhibition)",
    f"Purine bases are {B('recycled')} efficiently by salvage pathway (HGPRT, adenine phosphoribosyltransferase)",
    f"{B('Lesch-Nyhan syndrome:')} HGPRT deficiency → cannot salvage purines → gout, self-mutilation, neurological problems",
], story)

h2("2.3 Pyrimidine Synthesis (De Novo)", story)
bp([
    "Ring formed first (outside ribose), then attached to PRPP",
    f"Steps: Carbamoyl phosphate (CPS II, cytosol) + Aspartate → Orotic acid → OMP → UMP",
    f"{B('CPS II:')} Rate-limiting, inhibited by UMP (feedback), activated by PRPP",
    f"UMP → UDP → UTP; UTP → CTP (by CTP synthetase)",
    f"Thymidylate: dUMP → dTMP by thymidylate synthase (needs 5,10-methylene-THF); regenerated by dihydrofolate reductase (DHFR)",
    f"{B('5-Fluorouracil (5-FU):')} Inhibits thymidylate synthase — anti-cancer drug",
    f"{B('Methotrexate:')} Inhibits DHFR — anti-cancer/anti-folate",
    f"{B('Orotic aciduria:')} UMP synthase deficiency → megaloblastic anemia, orotic acid in urine; Rx: uridine",
], story)

h2("2.4 Purine Catabolism & Gout", story)
bp([
    f"AMP → IMP → Hypoxanthine → Xanthine → Uric acid (by xanthine oxidase)",
    f"GMP → Guanosine → Guanine → Xanthine → Uric acid",
    f"{B('Uric acid:')} Final product in humans (other mammals have uricase → allantoin)",
    f"{B('Gout:')} Hyperuricemia → monosodium urate crystals in joints (big toe, tophi)",
    f"{B('Allopurinol:')} Inhibits xanthine oxidase → reduces uric acid; also converted to alloxanthine (suicide inhibitor)",
    f"{B('Rasburicase (uricase):')} Used in tumor lysis syndrome",
    f"{B('Colchicine:')} Inhibits neutrophil migration; used in acute gout",
    f"{B('Secondary hyperuricemia:')} High cell turnover (leukemia, psoriasis), renal disease, drugs (thiazides)",
], story)

note("Mnemonic: Purines = Pure As Gold (Adenine, Guanine). Pyrimidines = CUT (Cytosine, Uracil, Thymine)", story)

story.append(PageBreak())

# ════════════════════════════════════════════════════════════════════════════
# TOPIC 3: ENZYME & ENZYME KINETICS
# ════════════════════════════════════════════════════════════════════════════
section_header(3, "ENZYME & ENZYME KINETICS", story)

h2("3.1 Enzyme Basics", story)
bp([
    f"Enzymes are {B('biological catalysts')} — lower activation energy, not consumed in reaction",
    f"{B('Apoenzyme:')} Protein part alone (inactive)",
    f"{B('Cofactor:')} Non-protein component (metal ions: Mg, Zn, Fe, Cu; or coenzymes: NAD, FAD, CoA)",
    f"{B('Holoenzyme:')} Apoenzyme + cofactor (active)",
    f"{B('Coenzyme:')} Organic cofactor (often derived from vitamins — e.g., NAD+ from niacin, FAD from riboflavin, CoA from pantothenate)",
    f"{B('Active site:')} Specific 3D region that binds substrate; made of catalytic and binding residues",
    f"{B('Lock and key model:')} Rigid fit (Fischer); {B('Induced fit model:')} Enzyme changes shape on binding (Koshland) — more accepted",
], story)

h2("3.2 Michaelis-Menten Kinetics", story)
p("E + S ⇌ ES → E + P", story)
bp([
    f"{B('Km (Michaelis constant):')} [S] at which reaction rate = Vmax/2; low Km = high affinity for substrate",
    f"{B('Vmax:')} Maximum velocity; proportional to total enzyme concentration",
    f"{B('kcat (turnover number):')} Number of substrate molecules converted per enzyme per second",
    f"{B('Lineweaver-Burk plot (double reciprocal):')} 1/V vs 1/[S]; y-intercept = 1/Vmax; x-intercept = -1/Km; slope = Km/Vmax",
], story)

tbl_data = [
    ["Inhibition Type", "Effect on Vmax", "Effect on Km", "Lineweaver-Burk", "Example"],
    ["Competitive", "Unchanged", "Increased", "Same y-int, different slope", "Statins (HMG-CoA reductase), Allopurinol"],
    ["Noncompetitive", "Decreased", "Unchanged", "Different y-int, same x-int", "Cyanide, Heavy metals"],
    ["Uncompetitive", "Decreased", "Decreased", "Parallel lines (same slope)", "Lithium"],
    ["Mixed", "Decreased", "Variable", "Lines intersect above x-axis", "Various"],
    ["Suicide/Irreversible", "Decreased", "Unchanged initially", "Enzyme destroyed", "Aspirin (COX), Penicillin (transpeptidase)"],
]
table(tbl_data, story, col_widths=[3.5*cm, 2.5*cm, 2.5*cm, 3.5*cm, 4*cm])

h2("3.3 Allosteric Enzymes", story)
bp([
    f"Show {B('sigmoidal')} kinetics (not Michaelis-Menten hyperbola)",
    f"{B('Allosteric activators:')} Increase activity; T-state (tense/inactive) → R-state (relaxed/active)",
    f"{B('Allosteric inhibitors:')} Stabilize T-state, decrease activity",
    f"Examples: ATCase (pyrimidine synthesis), Phosphofructokinase-1 (AMP activates, ATP/citrate inhibit), Hemoglobin (O2 binding cooperative)",
    f"{B('Cooperativity:')} Binding of one substrate facilitates subsequent binding (positive cooperativity)",
], story)

h2("3.4 Enzyme Regulation", story)
bp([
    f"{B('Covalent modification:')} Phosphorylation (kinases activate; phosphatases deactivate) — e.g., glycogen phosphorylase",
    f"{B('Proteolytic cleavage:')} Zymogens activated by cleavage — e.g., trypsinogen → trypsin; pepsinogen → pepsin; prothrombin → thrombin",
    f"{B('Feedback inhibition:')} End product inhibits early enzyme — most common regulation in biosynthesis",
    f"{B('Gene expression regulation:')} Induction or repression at transcriptional level",
    f"{B('Isoenzymes (isozymes):')} Catalyze same reaction, differ in properties; e.g., LDH (5 isoforms), CK (MM, MB, BB)",
], story)

h2("3.5 Clinically Important Enzymes (Serum Markers)", story)
tbl_data = [
    ["Enzyme", "Source/Isoform", "Clinical Significance"],
    ["AST (SGOT)", "Liver, heart, muscle, RBC", "Elevated in hepatitis, MI, muscle disease"],
    ["ALT (SGPT)", "Liver (specific)", "Most specific for hepatocellular damage"],
    ["ALP", "Liver, bone, intestine, placenta", "Elevated in cholestasis, bone disease, pregnancy"],
    ["GGT", "Liver, kidney", "Sensitive for alcohol abuse, cholestasis"],
    ["LDH", "All tissues; LDH1 (heart), LDH5 (liver)", "MI (LDH1>LDH2 = 'flip'), hemolysis"],
    ["CK", "CK-MB (heart), CK-MM (muscle), CK-BB (brain)", "MI: CK-MB rises 4-6h, peaks 24h"],
    ["Troponin I & T", "Cardiac-specific", "Most sensitive/specific for MI; rises 3-6h, lasts 7-14 days"],
    ["Amylase", "Pancreas, salivary glands", "Elevated in pancreatitis (rises early, lasts 3-5 days)"],
    ["Lipase", "Pancreas (specific)", "More specific than amylase for pancreatitis (lasts longer)"],
    ["Acid phosphatase", "Prostate, RBC, bone", "Prostate cancer (replaced by PSA)"],
    ["Cholinesterase", "Liver", "Decreased in liver disease, organophosphate poisoning"],
]
table(tbl_data, story, col_widths=[4*cm, 5*cm, 7*cm])

story.append(PageBreak())

# ════════════════════════════════════════════════════════════════════════════
# TOPIC 4: IMMUNOLOGY
# ════════════════════════════════════════════════════════════════════════════
section_header(4, "IMMUNOLOGY", story)

h2("4.1 Overview of Immunity", story)
tbl_data = [
    ["Feature", "Innate Immunity", "Adaptive Immunity"],
    ["Specificity", "Non-specific", "Highly specific (clonal)"],
    ["Speed", "Immediate (minutes-hours)", "Slow (days-weeks)"],
    ["Memory", "No memory", "Immunological memory"],
    ["Components", "Skin, mucosa, NK cells, complement, phagocytes, cytokines", "T cells, B cells, antibodies"],
    ["Recognition", "Pattern recognition receptors (PRRs), TLRs", "Antigen-specific receptors (TCR, BCR)"],
]
table(tbl_data, story, col_widths=[4*cm, 6*cm, 6*cm])

h2("4.2 Cells of the Immune System", story)
bp([
    f"{B('T lymphocytes (T cells):')} Mature in thymus; cell-mediated immunity",
    f"  - CD4+ Helper T cells: Th1 (activate macrophages/cytotoxic T cells), Th2 (help B cells, antibody production)",
    f"  - CD8+ Cytotoxic T cells (CTL): Kill virus-infected/tumor cells via perforin/granzyme",
    f"  - Regulatory T cells (Treg): Suppress immune response, prevent autoimmunity",
    f"{B('B lymphocytes:')} Mature in bone marrow; humoral immunity; differentiate into plasma cells (antibody factories) and memory B cells",
    f"{B('NK cells:')} Kill without prior sensitization; no CD3; recognize 'missing self' (no MHC class I)",
    f"{B('Macrophages:')} Phagocytosis, antigen presentation (MHC II), cytokine secretion (IL-1, TNF, IL-6, IL-12)",
    f"{B('Dendritic cells:')} Best APCs; process antigens and present to naive T cells",
    f"{B('Neutrophils:')} First responders; phagocytosis; respiratory burst (MPO, NADPH oxidase)",
    f"{B('Mast cells/Basophils:')} IgE receptor; degranulate histamine in allergic reactions",
    f"{B('Eosinophils:')} Anti-parasitic; involved in allergic diseases",
], story)

h2("4.3 Antibody (Immunoglobulin) Structure", story)
bp([
    f"Y-shaped glycoprotein; 2 heavy chains + 2 light chains linked by disulfide bonds",
    f"Variable region (Fab): antigen-binding; hypervariable loops = CDRs (complementarity-determining regions)",
    f"Constant region (Fc): effector functions (complement activation, receptor binding)",
    f"Light chains: kappa (κ) or lambda (λ)",
    f"Heavy chains determine class (isotype): μ(IgM), γ(IgG), α(IgA), ε(IgE), δ(IgD)",
    f"Fab fragment (papain cleavage): antigen-binding; F(ab')2 (pepsin cleavage): bivalent",
], story)

tbl_data = [
    ["Isotype", "Structure", "Key Functions", "Key Feature"],
    ["IgG", "Monomer (4 subclasses)", "Main serum Ab; opsonization; complement; crosses placenta (maternal immunity)", "Most abundant; secondary response"],
    ["IgM", "Pentamer (J chain)", "First Ab in infection; best complement activator; ABO blood group Ab", "First responder; largest Ig"],
    ["IgA", "Dimer (secretory IgA in mucosa)", "Mucosal immunity: saliva, tears, breast milk, GI/respiratory secretions", "Secretory component (SIgA) protects against proteases"],
    ["IgE", "Monomer", "Allergy (type I hypersensitivity); anti-parasite; binds mast cells/basophils", "Lowest serum concentration"],
    ["IgD", "Monomer", "B cell surface receptor; signals naive B cell activation", "Function not fully clear"],
]
table(tbl_data, story, col_widths=[2.5*cm, 3.5*cm, 6*cm, 4*cm])

h2("4.4 Complement System", story)
bp([
    f"{B('Classical pathway:')} Activated by Ag-Ab (IgG/IgM) complexes; C1 → C4 → C2 → C3",
    f"{B('Lectin pathway:')} MBL binds carbohydrates on pathogens → MASP1/2 → C4 → C2 → C3",
    f"{B('Alternative pathway:')} Spontaneous C3 hydrolysis; amplification; Factor B, D, Properdin",
    f"{B('C3b:')} Opsonization (marks for phagocytosis)",
    f"{B('C3a, C5a (anaphylatoxins):')} Chemotaxis, mast cell degranulation, vasodilation",
    f"{B('MAC (C5b-C9):')} Membrane attack complex; lyses gram-negative bacteria",
    f"{B('C1-INH deficiency:')} Hereditary angioedema",
    f"{B('CD55/CD59 deficiency (PNH):')} Paroxysmal nocturnal hemoglobinuria",
], story)

h2("4.5 Hypersensitivity Reactions (Gell & Coombs)", story)
tbl_data = [
    ["Type", "Mechanism", "Mediator", "Examples"],
    ["I - Immediate", "IgE on mast cells/basophils; cross-linking by antigen", "Histamine, leukotrienes, prostaglandins", "Anaphylaxis, asthma, hay fever, urticaria"],
    ["II - Cytotoxic", "IgG/IgM bind cell-surface antigens; complement + phagocytosis", "Complement, ADCC", "Hemolytic anemia, ABO incompatibility, myasthenia gravis, Graves' disease"],
    ["III - Immune Complex", "Ag-Ab complexes deposited in tissues; complement activation", "Neutrophils, complement", "SLE, post-strep GN, serum sickness, Arthus reaction"],
    ["IV - Delayed (Cell-mediated)", "Sensitized T cells (CD4+/CD8+) activated by antigen", "Lymphokines, cytotoxic T cells", "TB (Mantoux test), contact dermatitis, graft rejection, type 1 DM"],
]
table(tbl_data, story, col_widths=[3*cm, 4*cm, 3*cm, 6*cm])

h2("4.6 Major Histocompatibility Complex (MHC)", story)
bp([
    f"{B('MHC class I (HLA-A, B, C):')} On all nucleated cells; present endogenous (intracellular) antigens to CD8+ T cells",
    f"{B('MHC class II (HLA-DR, DP, DQ):')} On APCs (dendritic cells, macrophages, B cells); present exogenous antigens to CD4+ T cells",
    f"Remember: {B('CD8 × 1 = 8')} (class I); {B('CD4 × 2 = 8... no:')} Class II + CD4 (both have even numbers: II, 4)",
    f"{B('HLA associations:')} HLA-B27: ankylosing spondylitis; HLA-DR3/DR4: type 1 DM; HLA-DR2: multiple sclerosis, narcolepsy; HLA-DR5: Hashimoto's; HLA-A3: hemochromatosis",
], story)

story.append(PageBreak())

# ════════════════════════════════════════════════════════════════════════════
# TOPIC 5: ORGAN FUNCTION TESTS
# ════════════════════════════════════════════════════════════════════════════
section_header(5, "ORGAN FUNCTION TESTS", story)

h2("5.1 Liver Function Tests (LFTs)", story)
tbl_data = [
    ["Test", "Normal Range", "Clinical Significance"],
    ["Total Bilirubin", "0.3-1.2 mg/dL", "Elevated in jaundice (pre-hepatic, hepatic, post-hepatic)"],
    ["Direct (conjugated) Bilirubin", "<0.3 mg/dL", "Elevated in obstructive/hepatic jaundice"],
    ["Indirect (unconjugated) Bilirubin", "0.2-0.9 mg/dL", "Elevated in hemolysis, Gilbert's, Crigler-Najjar"],
    ["ALT (SGPT)", "7-40 U/L", "Most specific for hepatocellular damage"],
    ["AST (SGOT)", "10-40 U/L", "Elevated in hepatitis, MI; AST:ALT > 2:1 in alcoholic hepatitis"],
    ["ALP", "40-120 U/L", "Elevated in cholestasis, bone disease, pregnancy"],
    ["GGT", "5-50 U/L", "Sensitive for alcohol use; elevated in cholestasis"],
    ["Albumin", "3.5-5 g/dL", "Decreased in chronic liver disease (marker of synthetic function)"],
    ["PT/INR", "11-13 sec / 0.8-1.2", "Prolonged in liver disease (factor synthesis impaired)"],
    ["Total Protein", "6-8 g/dL", "Decreased in liver/nutritional disease"],
]
table(tbl_data, story, col_widths=[4.5*cm, 3.5*cm, 8*cm])

h2("5.2 Bilirubin Metabolism (Key for Exam)", story)
bp([
    f"RBCs destroyed (80%) → Heme → Biliverdin (biliverdin reductase) → {B('Indirect/Unconjugated bilirubin')} (fat-soluble, bound to albumin)",
    f"Liver: Unconjugated + glucuronide (by UDP-glucuronosyltransferase) → {B('Direct/Conjugated bilirubin')} (water-soluble)",
    f"Excreted in bile → Gut bacteria convert to urobilinogen → Urobilin (stool - brown colour) / Urobilinogen reabsorbed → kidneys → excreted in urine",
    f"{B('Van den Bergh reaction:')} Direct bilirubin: immediate reaction; Indirect: requires methanol (indirect reaction)",
], story)

tbl_data = [
    ["Type of Jaundice", "Indirect Bili", "Direct Bili", "Urine Bili", "Urine Urobilinogen", "Stool colour", "Cause"],
    ["Pre-hepatic (Hemolytic)", "↑↑", "Normal", "Absent", "↑", "Normal/dark", "Hemolysis, G6PD, sickle cell"],
    ["Hepatic (Hepatocellular)", "↑", "↑", "Present", "↑ or ↓", "Pale/normal", "Hepatitis, cirrhosis"],
    ["Post-hepatic (Obstructive)", "Normal/↑", "↑↑", "Present", "Absent", "Clay/pale", "Gallstones, pancreatic cancer"],
]
table(tbl_data, story, col_widths=[3.5*cm, 2*cm, 2*cm, 2*cm, 2.5*cm, 2.5*cm, 5.5*cm])

h2("5.3 Kidney Function Tests (RFTs)", story)
tbl_data = [
    ["Test", "Normal", "Significance"],
    ["Serum Creatinine", "0.6-1.2 mg/dL", "Best endogenous marker of GFR; derived from creatine in muscle"],
    ["Blood Urea Nitrogen (BUN)", "8-20 mg/dL", "Raised in pre-renal, renal failure; BUN:Cr ratio >20 → pre-renal"],
    ["GFR", ">90 mL/min/1.73m²", "Best overall marker of kidney function"],
    ["Creatinine Clearance", "90-130 mL/min", "Estimates GFR; 24-hour urine collection"],
    ["Uric Acid", "3.5-7.0 mg/dL (M), 2.5-6.0 (F)", "Raised in gout, renal failure, tumor lysis"],
    ["Serum Cystatin C", "0.5-1.0 mg/L", "More sensitive marker of early GFR decline than creatinine"],
    ["Urinalysis", "—", "Proteinuria (nephrotic), hematuria (nephritic), casts (ATN: granular casts)"],
    ["Microalbuminuria", "30-300 mg/day", "Early diabetic nephropathy marker"],
]
table(tbl_data, story, col_widths=[4.5*cm, 3.5*cm, 8*cm])

h2("5.4 Cardiac Function Tests", story)
bp([
    f"{B('Troponin I & T:')} Rise 3-6h, peak 12-24h, persist 7-14 days; most sensitive/specific for MI",
    f"{B('CK-MB:')} Rise 4-6h, peak 24h, normal by 48-72h; used for re-infarction",
    f"{B('Myoglobin:')} Earliest marker (1-3h), not cardiac-specific; useful to rule out MI",
    f"{B('LDH1 > LDH2 (flip):')} Seen in MI (after 12-24h, persists longest)",
    f"{B('BNP/NT-proBNP:')} B-type natriuretic peptide; elevated in heart failure; BNP < 100 pg/mL rules out HF",
    f"{B('hs-CRP:')} High-sensitivity CRP; cardiovascular risk marker",
], story)

h2("5.5 Pancreatic Function Tests", story)
bp([
    f"{B('Serum Amylase:')} Rises within 6h, normalizes by 3-5 days in pancreatitis",
    f"{B('Serum Lipase:')} More specific; rises 4-8h, peaks 24h, lasts 8-14 days; preferred test",
    f"{B('Fecal elastase-1:')} < 200 μg/g stool → exocrine pancreatic insufficiency",
    f"{B('Secretin stimulation test:')} Gold standard for exocrine function",
    f"{B('Glucose & HbA1c:')} Endocrine function (beta cells)",
], story)

h2("5.6 Thyroid Function Tests (TFTs)", story)
tbl_data = [
    ["Test", "Hypothyroidism", "Hyperthyroidism", "Note"],
    ["TSH", "↑ (primary)", "↓", "Most sensitive screening test"],
    ["Free T4 (FT4)", "↓", "↑", "Active hormone"],
    ["Free T3 (FT3)", "↓", "↑↑", "Most potent"],
    ["T3 resin uptake", "↓", "↑", "Indirect measure of TBG"],
    ["TBG", "↑ (pregnancy, OCP)", "—", "Affects total but not free hormones"],
    ["Anti-TPO Ab", "+", "+(Hashimoto's)", "Hashimoto's thyroiditis"],
    ["TSI (TSHR-Ab)", "—", "+(Graves')", "Stimulating Ab → Graves'"],
]
table(tbl_data, story, col_widths=[3.5*cm, 3.5*cm, 3.5*cm, 5.5*cm])

story.append(PageBreak())

# ════════════════════════════════════════════════════════════════════════════
# TOPIC 6: CANCER BIOCHEMISTRY
# ════════════════════════════════════════════════════════════════════════════
section_header(6, "CANCER BIOCHEMISTRY", story)

h2("6.1 Molecular Basis of Cancer", story)
bp([
    f"{B('Cancer:')} Uncontrolled cell proliferation due to accumulation of mutations in genes regulating cell growth/death",
    f"{B('Proto-oncogenes:')} Normal genes promoting growth; when mutated → oncogenes (gain of function); act as dominant",
    f"{B('Oncogenes:')} RAS (G-protein, point mutation in 30% cancers), MYC (transcription factor), HER2/ERBB2, BCL2 (anti-apoptosis), SRC (kinase)",
    f"{B('Tumor suppressor genes:')} Inhibit growth; loss of function (recessive — both alleles lost); Knudson's 'two-hit hypothesis'",
    f"{B('Key TSGs:')} TP53 (most commonly mutated gene in cancer — guardian of genome), RB1 (retinoblastoma), BRCA1/2 (breast/ovarian), APC (colon), VHL (renal cell), PTEN, p16/CDKN2A",
    f"{B('Apoptosis:')} p53 triggers apoptosis via BAX; BCL2 is anti-apoptotic; cytochrome c release → apoptosome → caspases",
    f"{B('Hallmarks of cancer (Hanahan & Weinberg):')} Self-sufficiency in growth signals, insensitivity to anti-growth signals, evasion of apoptosis, limitless replication, angiogenesis, invasion/metastasis, metabolic reprogramming, immune evasion",
], story)

h2("6.2 Cell Cycle & Cancer", story)
bp([
    f"Cell cycle: G1 → S (DNA synthesis) → G2 → M (mitosis) → G0 (quiescent)",
    f"{B('Cyclins + CDKs:')} Drive cell cycle forward; CDK inhibitors (p21, p27, p16) act as brakes",
    f"{B('Rb protein:')} In hypophosphorylated state → binds E2F → blocks S-phase entry; CDK4/6-cyclin D phosphorylates Rb → releases E2F",
    f"{B('p53:')} Responds to DNA damage → arrests cell in G1 (via p21) → allows repair or triggers apoptosis",
    f"{B('Telomeres:')} Shorten with each division; cancer cells upregulate telomerase → immortality",
], story)

h2("6.3 Tumor Markers (High Yield!)", story)
tbl_data = [
    ["Tumor Marker", "Cancer", "Notes"],
    ["PSA (Prostate-Specific Antigen)", "Prostate", "Screening; also elevated in BPH, prostatitis"],
    ["AFP (Alpha-fetoprotein)", "Hepatocellular carcinoma, Yolk sac tumor", "Also elevated in liver regeneration, pregnancy; neural tube defect screening"],
    ["CEA (Carcinoembryonic Antigen)", "Colorectal, gastric, pancreatic, lung", "Not specific; used for monitoring recurrence"],
    ["CA 125", "Ovarian cancer (serous)", "Also elevated in endometriosis, PID"],
    ["CA 19-9", "Pancreatic, cholangiocarcinoma", "Not specific; monitoring"],
    ["CA 15-3", "Breast cancer", "Monitoring; not for diagnosis"],
    ["hCG (beta-hCG)", "Choriocarcinoma, testicular (non-seminoma)", "Also pregnancy; gestational trophoblastic disease"],
    ["LDH", "Lymphoma, testicular seminoma, all cancers", "Non-specific; marker of tumor burden"],
    ["Calcitonin", "Medullary thyroid carcinoma", "C cells; MEN 2A/2B"],
    ["Thyroglobulin", "Differentiated thyroid cancer (after thyroidectomy)", "Monitoring recurrence"],
    ["Chromogranin A", "Neuroendocrine tumors (carcinoid)", "Most sensitive for carcinoid"],
    ["5-HIAA (urine)", "Carcinoid syndrome", "Serotonin metabolite; flushing, diarrhea"],
    ["Bence-Jones protein", "Multiple myeloma", "Free light chains in urine (kappa/lambda)"],
    ["M-protein (serum)", "Multiple myeloma, MGUS", "Monoclonal immunoglobulin peak (M-spike) on SPEP"],
    ["BRCA1/2", "Breast, ovarian cancer risk", "Genetic marker; counseling/prophylaxis"],
]
table(tbl_data, story, col_widths=[5*cm, 4.5*cm, 6.5*cm])

h2("6.4 Warburg Effect", story)
p(f"Cancer cells preferentially use {B('aerobic glycolysis')} (glucose → lactate even in presence of O2) rather than oxidative phosphorylation. This provides rapid ATP generation and biosynthetic intermediates (pentose phosphate pathway, lipid synthesis). PET scan exploits this: FDG (18F-labeled glucose) accumulates in metabolically active cancer cells.", story)

h2("6.5 Carcinogens & Cancer Types", story)
tbl_data = [
    ["Carcinogen", "Cancer"],
    ["Aflatoxin B1 (Aspergillus)", "Hepatocellular carcinoma (TP53 R249S mutation)"],
    ["Vinyl chloride", "Angiosarcoma of liver"],
    ["Nitrosamines, H. pylori", "Gastric cancer"],
    ["Benzene", "AML, aplastic anemia"],
    ["Aromatic amines (β-naphthylamine)", "Bladder cancer"],
    ["Asbestos", "Mesothelioma, lung cancer"],
    ["UV light", "Melanoma, basal cell carcinoma (C→T mutations in TP53)"],
    ["HPV 16/18", "Cervical, oropharyngeal cancer (E6 inactivates p53, E7 inactivates Rb)"],
    ["EBV", "Burkitt lymphoma (c-MYC translocation t(8;14)), Hodgkin lymphoma"],
    ["HBV/HCV", "Hepatocellular carcinoma"],
    ["HTLV-1", "Adult T-cell leukemia/lymphoma"],
    ["Ionizing radiation", "Thyroid cancer, leukemia, bone sarcomas"],
]
table(tbl_data, story, col_widths=[7*cm, 9*cm])

story.append(PageBreak())

# ════════════════════════════════════════════════════════════════════════════
# TOPIC 7: RECENT ADVANCES IN BIOCHEMISTRY
# ════════════════════════════════════════════════════════════════════════════
section_header(7, "RECENT ADVANCES IN BIOCHEMISTRY", story)

h2("7.1 CRISPR-Cas9 Gene Editing", story)
bp([
    f"{B('Principle:')} Guide RNA (gRNA) directs Cas9 endonuclease to specific DNA sequence → double-strand break → repair by NHEJ (error-prone, gene knockout) or HDR (precise editing with template)",
    f"{B('Origin:')} Bacterial adaptive immune system against phages",
    f"{B('Applications:')} Sickle cell disease (CTX001/Casgevy approved 2023 — first CRISPR therapy), beta-thalassemia, cancer immunotherapy (CAR-T), hereditary transthyretin amyloidosis",
    f"{B('Base editing:')} Point mutations without DSB (Adenine/Cytosine base editors)",
    f"{B('Prime editing:')} 'Search and replace' genome editing — greater precision",
], story)

h2("7.2 RNA Therapeutics", story)
bp([
    f"{B('mRNA vaccines:')} COVID-19 vaccines (Pfizer-BioNTech, Moderna); mRNA encodes antigen → immune response; no integration into genome; can be rapidly designed",
    f"{B('siRNA/RNAi:')} Small interfering RNA; degrades target mRNA → silences gene; inclisiran (siRNA targeting PCSK9 for LDL reduction, approved 2020)",
    f"{B('Antisense oligonucleotides (ASO):')} Complementary to mRNA → block translation or trigger degradation; e.g., nusinersen (SMA), eteplirsen (Duchenne MD)",
    f"{B('miRNA:')} Endogenous ~22 nt RNAs; post-transcriptional gene regulation; dysregulated in cancer (oncomiRs)",
    f"{B('Aptamers:')} Short ssDNA/RNA oligonucleotides that bind proteins; pegaptanib (anti-VEGF aptamer, AMD)",
], story)

h2("7.3 Proteomics & Genomics", story)
bp([
    f"{B('Human Genome Project (HGP):')} Completed 2003; ~3 billion bp; ~20,000-25,000 protein-coding genes; only ~2% of genome codes proteins",
    f"{B('Next-generation sequencing (NGS):')} Massively parallel sequencing; whole genome (WGS), whole exome (WES), targeted panels; used in cancer genomics, NIPT, rare disease diagnosis",
    f"{B('Proteomics:')} Large-scale study of proteins; mass spectrometry (LC-MS/MS) is primary tool; identifies disease biomarkers",
    f"{B('Metabolomics:')} Comprehensive analysis of metabolites; NMR spectroscopy and mass spectrometry",
    f"{B('Pharmacogenomics:')} Genetic variants affect drug metabolism; CYP2D6 (codeine metabolism), CYP2C19 (clopidogrel activation), TPMT (6-MP toxicity), HLA-B*5701 (abacavir hypersensitivity)",
    f"{B('Liquid biopsy:')} Circulating tumor DNA (ctDNA) in plasma; minimal residual disease monitoring; early cancer detection",
], story)

h2("7.4 Stem Cells & Regenerative Medicine", story)
bp([
    f"{B('iPSCs (induced pluripotent stem cells):')} Adult cells reprogrammed by 4 Yamanaka factors (Oct4, Sox2, Klf4, c-Myc) to pluripotent state",
    f"{B('Gene therapy:')} AAV vectors most common; approved: Luxturna (RPE65 mutation, blindness), Zolgensma (SMA, most expensive drug)",
    f"{B('CAR-T cell therapy:')} T cells engineered with chimeric antigen receptor; e.g., axicabtagene ciloleucel (diffuse large B cell lymphoma, CD19 target)",
    f"{B('Organoids:')} 3D mini-organs from stem cells; drug testing, disease modeling",
], story)

h2("7.5 Epigenetics", story)
bp([
    f"{B('Definition:')} Heritable changes in gene expression without changes in DNA sequence",
    f"{B('DNA methylation:')} CpG island methylation → gene silencing; methylated in most cancer TSGs",
    f"{B('Histone modification:')} Acetylation (HATs → open chromatin, activate genes); Deacetylation (HDACs → closed chromatin); Methylation (complex effects)",
    f"{B('Chromatin remodeling:')} SWI/SNF complex repositions nucleosomes",
    f"{B('X-inactivation:')} One X chromosome inactivated → Barr body; by XIST RNA; epigenetic mechanism",
    f"{B('Imprinting:')} Only one parental allele expressed; Prader-Willi (paternal 15q deletion) and Angelman syndrome (maternal 15q deletion/imprinting)",
], story)

story.append(PageBreak())

# ════════════════════════════════════════════════════════════════════════════
# TOPIC 8: ACID-BASE BALANCE, WATER & ELECTROLYTES
# ════════════════════════════════════════════════════════════════════════════
section_header(8, "ACID-BASE BALANCE, WATER & ELECTROLYTES", story)

h2("8.1 pH and Buffers", story)
bp([
    f"Normal blood pH: {B('7.35-7.45')} (acidosis < 7.35; alkalosis > 7.45); death outside 6.8-7.8",
    f"{B('Henderson-Hasselbalch:')} pH = pKa + log([A⁻]/[HA]) = 6.1 + log([HCO3⁻]/[CO2 × 0.03])",
    f"{B('Normal values:')} HCO3⁻ = 22-26 mEq/L; pCO2 = 35-45 mmHg",
    f"{B('Buffers:')} Bicarbonate (blood, extracellular main); Phosphate (intracellular, urine); Protein/hemoglobin (intracellular, blood)",
    f"{B('Compensation:')} Respiratory: immediate (minutes-hours, changes pCO2); Renal: slow (days, changes HCO3⁻)",
], story)

h2("8.2 Acid-Base Disorders", story)
tbl_data = [
    ["Disorder", "pH", "Primary Change", "Compensation", "Common Causes"],
    ["Metabolic Acidosis", "↓ (<7.35)", "↓ HCO3⁻", "↓ pCO2 (hyperventilation, Kussmaul)", "DKA, lactic acidosis, renal failure, diarrhea (high AG vs normal AG)"],
    ["Metabolic Alkalosis", "↑ (>7.45)", "↑ HCO3⁻", "↑ pCO2 (hypoventilation)", "Vomiting, NG suction, diuretics, hyperaldosteronism"],
    ["Respiratory Acidosis", "↓", "↑ pCO2", "↑ HCO3⁻ (renal retention)", "COPD, respiratory failure, sedatives, pneumonia"],
    ["Respiratory Alkalosis", "↑", "↓ pCO2", "↓ HCO3⁻ (renal excretion)", "Hyperventilation (anxiety, PE, early salicylate, pregnancy, altitude)"],
]
table(tbl_data, story, col_widths=[3.5*cm, 1.5*cm, 3*cm, 3.5*cm, 5.5*cm])

h2("8.3 Anion Gap", story)
bp([
    f"{B('Anion Gap (AG):')} Na⁺ - (Cl⁻ + HCO3⁻); Normal = 8-12 mEq/L (unmeasured anions: albumin, phosphate, sulfate)",
    f"{B('High AG Metabolic Acidosis (MUDPILES):')} Methanol, Uremia, DKA, Propylene glycol, Isoniazid/Infection (lactic), Lactic acidosis, Ethylene glycol, Salicylates",
    f"{B('Normal AG Metabolic Acidosis (HARDUPS):')} Hyperalimentation, Addison's disease, Renal tubular acidosis, Diarrhea, Ureteroenterostomy, Pancreatic fistula, Saline infusion",
    f"{B('Delta-delta ratio:')} (AG-12)/(24-HCO3⁻); < 1 → non-AG component; 1-2 → pure AG; > 2 → concurrent metabolic alkalosis",
], story)

h2("8.4 Water Balance & Body Fluid Compartments", story)
bp([
    f"{B('Total Body Water (TBW):')} 60% of body weight in males (50% in females, 75% in infants)",
    f"{B('ICF:')} 2/3 of TBW (~40% body weight); K⁺, Mg²⁺, phosphate are dominant ions",
    f"{B('ECF:')} 1/3 of TBW (~20% body weight); subdivided: Plasma (25% ECF) + Interstitial fluid (75% ECF)",
    f"{B('Plasma volume:')} ~3.5 L; dominant cation Na⁺, dominant anion Cl⁻",
    f"{B('Osmolality:')} 280-295 mOsm/kg; mainly from Na⁺; Calculated: 2×Na⁺ + Glucose/18 + BUN/2.8",
    f"{B('Osmolal gap:')} Measured - Calculated > 10 → exogenous osmoles (methanol, ethanol, ethylene glycol)",
    f"{B('ADH (Vasopressin):')} Released from posterior pituitary in response to increased osmolality or decreased blood volume; acts on V2 receptors in collecting duct → inserts AQP2 → water reabsorption",
    f"{B('Aldosterone:')} Released by zona glomerulosa (adrenal cortex) in response to angiotensin II/high K⁺; Na⁺ reabsorption + K⁺ & H⁺ secretion in distal nephron",
], story)

h2("8.5 Sodium Disorders", story)
tbl_data = [
    ["Disorder", "Serum Na⁺", "Cause", "Features", "Treatment"],
    ["Hyponatremia", "<135 mEq/L", "SIADH (↑ADH), heart failure, cirrhosis, hypothyroidism, psychogenic polydipsia", "Nausea, confusion, seizures (if severe)", "Fluid restriction (SIADH); hypertonic saline if severe; tolvaptan (V2 receptor antagonist) in SIADH"],
    ["Hypernatremia", ">145 mEq/L", "Diabetes insipidus (central or nephrogenic), inadequate water intake, insensible losses", "Thirst, confusion, lethargy, brain shrinkage", "Free water replacement; DDAVP for central DI"],
    ["SIADH", "Low Na⁺", "Lung cancer (small cell), CNS disease, drugs (carbamazepine, SSRIs), pain", "Euvolemic hyponatremia; urine osmolality > serum osmolality; urine Na > 40", "Fluid restriction; demeclocycline; tolvaptan"],
]
table(tbl_data, story, col_widths=[3*cm, 2.5*cm, 4*cm, 4*cm, 2.5*cm])

h2("8.6 Potassium & Other Electrolytes", story)
bp([
    f"{B('Hypokalemia (<3.5 mEq/L):')} Causes: vomiting, diarrhea, diuretics, hyperaldosteronism, insulin, alkalosis; Features: muscle weakness, arrhythmias (U wave on ECG, prolonged QT); Rx: KCl supplementation",
    f"{B('Hyperkalemia (>5.5 mEq/L):')} Causes: renal failure, ACEi, K+-sparing diuretics, acidosis, cell lysis, Addison's; Features: peaked T waves, wide QRS, VF; Rx: calcium gluconate (stabilize membrane), insulin+glucose, sodium bicarbonate, kayexalate, dialysis",
    f"{B('Hypocalcemia (<8.5 mg/dL):')} Hypoparathyroidism, vit D deficiency, CKD, hypomagnesemia; Chvostek sign (tap facial nerve → facial twitch), Trousseau sign (inflate BP cuff → carpal spasm), tetany, prolonged QT",
    f"{B('Hypercalcemia (>10.5 mg/dL):')} 'Bones, Stones, Groans, Psychic Moans' — Primary hyperparathyroidism (outpatient), malignancy (inpatient) most common; Rx: IV saline + furosemide, bisphosphonates, calcitonin",
    f"{B('Hypomagnesemia:')} Causes: alcoholism, diuretics, malabsorption; causes refractory hypokalemia and hypocalcemia",
    f"{B('Phosphate:')} Hypophosphatemia → hemolytic anemia, muscle weakness, rhabdomyolysis (seen in refeeding syndrome)",
], story)

story.append(PageBreak())

# ════════════════════════════════════════════════════════════════════════════
# TOPIC 9: DIGESTION & ABSORPTION
# ════════════════════════════════════════════════════════════════════════════
section_header(9, "DIGESTION & ABSORPTION", story)

h2("9.1 Carbohydrate Digestion & Absorption", story)
bp([
    f"{B('Salivary amylase:')} Begins in mouth; cleaves α-1,4 bonds of starch → dextrins (inactivated by stomach acid)",
    f"{B('Pancreatic amylase:')} Major digestive enzyme; cleaves starch → maltose, maltotriose, α-limit dextrins",
    f"{B('Brush border enzymes:')} Maltase, sucrase, lactase, isomaltase; convert disaccharides → monosaccharides at intestinal epithelium",
    f"{B('Absorption:')} Glucose + Galactose: SGLT1 (Na⁺-dependent, secondary active transport); Fructose: GLUT5 (facilitated diffusion); All exit via GLUT2 into portal blood",
    f"{B('Lactase deficiency:')} Most common in non-Europeans; osmotic diarrhea, bloating, flatulence after dairy",
    f"{B('Sucrase-isomaltase deficiency:')} Diarrhea with sucrose/starch ingestion",
], story)

h2("9.2 Protein Digestion & Absorption", story)
bp([
    f"{B('Stomach:')} Pepsinogen → pepsin (by HCl + autocatalysis); pepsin cleaves peptide bonds at Phe, Tyr, Trp",
    f"{B('Pancreatic proteases (as zymogens):')} Trypsinogen → trypsin (by enteropeptidase/enterokinase from brush border); Trypsin then activates chymotrypsinogen, proelastase, procarboxypeptidase, prolipase",
    f"{B('Brush border peptidases:')} Aminopeptidases, dipeptidases cleave to amino acids",
    f"{B('Absorption:')} Free AAs, di/tripeptides absorbed via PepT1 (H+-dependent); several carrier systems for different AA groups",
    f"{B('Hartnup disease:')} Neutral AA transporter defect (tryptophan malabsorption) → pellagra-like symptoms (niacin deficiency); blue diaper syndrome",
    f"{B('Cystinuria:')} Defective renal/intestinal transport of COLA (Cystine, Ornithine, Lysine, Arginine) → cystine kidney stones",
], story)

h2("9.3 Fat (Lipid) Digestion & Absorption", story)
bp([
    f"{B('Emulsification:')} Bile salts from liver emulsify fat → small droplets (increase surface area)",
    f"{B('Lingual & gastric lipases:')} Minor role; cleave short/medium chain TGs",
    f"{B('Pancreatic lipase + colipase:')} Main enzyme; hydrolyzes TG → 2-monoglyceride + 2 FFA",
    f"{B('Bile salts form micelles:')} Solubilize products of digestion; deliver to enterocyte brush border",
    f"{B('Absorption into enterocytes:')} 2-monoglyceride + FFA passively diffuse into cells",
    f"{B('Re-esterification:')} In smooth ER → TG re-formed; packaged into chylomicrons (apolipoprotein B-48) in Golgi",
    f"{B('Chylomicrons:')} Released into lymphatics (lacteals) → thoracic duct → systemic circulation",
    f"{B('Short/medium chain FAs:')} Don't need micelles; directly enter portal blood (not lymphatics)",
    f"{B('Fat-soluble vitamins (A, D, E, K):')} Absorbed with fats; deficiency in malabsorption, cholestatic liver disease",
    f"{B('Steatorrhea:')} Fatty stools; >7g fat/day; seen in pancreatic insufficiency, celiac disease, Crohn's, bile salt deficiency",
], story)

h2("9.4 Gastrointestinal Hormones", story)
tbl_data = [
    ["Hormone", "Source", "Stimulus", "Actions"],
    ["Gastrin", "G cells (antrum)", "Protein, distension, vagus (ACh)", "↑ Gastric acid (HCl), ↑ pepsinogen, ↑ gastric motility; trophic to gastric mucosa"],
    ["Secretin", "S cells (duodenum)", "Acid (low pH) in duodenum", "↑ HCO3⁻ from pancreas; ↓ gastric acid; ↑ bile secretion"],
    ["CCK (Cholecystokinin)", "I cells (duodenum)", "Fat and protein in duodenum", "↑ Pancreatic enzymes; ↑ bile release (gallbladder contraction); ↓ gastric emptying; satiety"],
    ["GIP (Gastric Inhibitory Peptide)", "K cells (duodenum)", "Fat, protein, carbohydrate", "↓ Gastric acid; ↑ insulin release (incretin effect)"],
    ["GLP-1 (Glucagon-like peptide-1)", "L cells (ileum/colon)", "Nutrients in gut", "↑ Insulin; ↓ glucagon; ↓ gastric emptying; satiety; target of GLP-1 agonists (liraglutide, semaglutide)"],
    ["Motilin", "M cells (duodenum/jejunum)", "Fasting (interdigestive)", "Initiates migrating motor complex (MMC); erythromycin is motilin agonist"],
    ["VIP", "Neurons throughout GI", "—", "Relax smooth muscle; ↑ water/electrolyte secretion; ↓ gastric acid"],
    ["Somatostatin", "D cells (pancreas, stomach)", "Acid, fat, protein", "Inhibits gastrin, secretin, CCK, GIP, glucagon, insulin; ↓ gastric acid; octreotide is analog"],
]
table(tbl_data, story, col_widths=[3*cm, 3*cm, 3.5*cm, 6.5*cm])

h2("9.5 Vitamins & Cofactors (Absorption Summary)", story)
tbl_data = [
    ["Vitamin", "Absorbed In", "Deficiency"],
    ["B12 (Cobalamin)", "Terminal ileum (requires intrinsic factor from gastric parietal cells)", "Megaloblastic anemia, subacute combined degeneration of spinal cord"],
    ["B9 (Folate)", "Duodenum/Jejunum (proximal small intestine)", "Megaloblastic anemia, neural tube defects (no neurological disease)"],
    ["Iron", "Duodenum; Fe2+ (ferrous) absorbed better than Fe3+ (ferric); vitamin C helps", "Iron deficiency anemia (microcytic, hypochromic)"],
    ["Calcium", "Duodenum (active, vitamin D-dependent) and jejunum (passive)", "Osteoporosis, tetany"],
    ["Fat-soluble (ADEK)", "Small intestine with fat + bile", "A: night blindness; D: rickets/osteomalacia; E: hemolytic anemia; K: bleeding"],
    ["B1 (Thiamine)", "Small intestine", "Beriberi, Wernicke-Korsakoff"],
    ["B3 (Niacin)", "Small intestine (some from tryptophan)", "Pellagra (4Ds: Dementia, Dermatitis, Diarrhea, Death)"],
]
table(tbl_data, story, col_widths=[4*cm, 5*cm, 7*cm])

story.append(PageBreak())

# ════════════════════════════════════════════════════════════════════════════
# TOPIC 10: PROTEIN CHEMISTRY, HAEMOGLOBIN, MYOGLOBIN, PLASMA PROTEINS
# ════════════════════════════════════════════════════════════════════════════
section_header(10, "PROTEIN CHEMISTRY, HAEMOGLOBIN, MYOGLOBIN & PLASMA PROTEINS", story)

h2("10.1 Protein Structure", story)
bp([
    f"{B('Primary structure:')} Sequence of amino acids linked by peptide bonds (N–C bond); determined by DNA sequence",
    f"{B('Secondary structure:')} Local folding patterns stabilized by H-bonds: α-helix (3.6 aa/turn, H-bonds between N-H and C=O 4 residues apart); β-pleated sheet (parallel or antiparallel, H-bonds between strands)",
    f"{B('Tertiary structure:')} 3D folding of single polypeptide; stabilized by: disulfide bonds (Cys–Cys), H-bonds, ionic bonds, hydrophobic interactions, van der Waals forces",
    f"{B('Quaternary structure:')} Multiple polypeptide subunits; e.g., hemoglobin (2α + 2β subunits); stabilized by same forces as tertiary",
    f"{B('Denaturation:')} Loss of 2°/3°/4° structure (heat, pH, detergents, urea); primary structure maintained; may be reversible",
    f"{B('Chaperones (HSP70, HSP90):')} Help proteins fold correctly; prevent aggregation; upregulated by heat stress",
], story)

h2("10.2 Amino Acids", story)
bp([
    f"{B('Essential AAs (must be obtained from diet):')} PVT TIM HaLL = Phenylalanine, Valine, Threonine, Tryptophan, Isoleucine, Methionine, Histidine (semi), Leucine, Lysine",
    f"{B('Acidic AAs:')} Aspartate (Asp, D), Glutamate (Glu, E) — negative charge at physiological pH",
    f"{B('Basic AAs:')} Lysine (Lys, K), Arginine (Arg, R) — positive charge; Histidine (His, H) — positive at slightly acidic pH",
    f"{B('Sulfur-containing AAs:')} Cysteine (disulfide bonds), Methionine (start AA, methylation reactions via SAM)",
    f"{B('Aromatic AAs:')} Phe, Tyr, Trp (absorb UV at 280 nm → used to measure protein concentration)",
    f"{B('Imino acid:')} Proline (rigid, breaks α-helix; abundant in collagen → converted to hydroxyproline by Vit C)",
    f"{B('Glucogenic AAs:')} Can be converted to glucose (enter TCA as OAA, α-KG, fumarate, succinyl-CoA, pyruvate)",
    f"{B('Ketogenic AAs:')} Leucine, Lysine (purely ketogenic); Ile, Phe, Thr, Trp, Tyr (both glucogenic + ketogenic)",
], story)

h2("10.3 Haemoglobin Structure & Function", story)
bp([
    f"{B('Structure:')} Tetramer — Adult HbA: α2β2; HbA2: α2δ2; Fetal HbF: α2γ2",
    f"{B('Heme group:')} Porphyrin ring + Fe²⁺ (ferrous); Fe³⁺ (ferric/methemoglobin) cannot carry O2",
    f"{B('O2 binding:')} Cooperative (allosteric); sigmoidal O2-dissociation curve (not hyperbola like myoglobin)",
    f"{B('Hill coefficient:')} n = 2.8 for hemoglobin (positive cooperativity); n = 1 for myoglobin (no cooperativity)",
    f"{B('Tense (T) state:')} Low O2 affinity; stabilized by 2,3-BPG, H⁺, CO2 (Bohr effect), Cl⁻",
    f"{B('Relaxed (R) state:')} High O2 affinity",
    f"{B('Bohr effect:')} ↑ pCO2 / ↓ pH → ↑ H⁺ → stabilizes T state → right shift of O2 curve → O2 released to tissues",
    f"{B('2,3-BPG:')} Binds β chains, stabilizes T state → right shift; increased in anemia, altitude, chronic hypoxia",
    f"Right shift: ↑ T, ↑ pCO2, ↓ pH, ↑ 2,3-BPG → {B('decreased O2 affinity')} (releases O2 to tissues)",
    f"Left shift: ↓ T, ↓ pCO2, ↑ pH, ↓ 2,3-BPG, CO binding, HbF → {B('increased O2 affinity')} (binds O2 tightly)",
    f"{B('CO poisoning:')} CO binds Hb with 200x affinity vs O2; left shift; cherry-red color; Rx: 100% O2",
    f"{B('Carbamate:')} CO2 binds amino groups of Hb to form carbamates (Haldane effect)",
], story)

h2("10.4 Haemoglobin Disorders", story)
tbl_data = [
    ["Disorder", "Mutation/Defect", "Features"],
    ["Sickle Cell Anemia (HbS)", "β-globin Glu→Val (point mutation, GAG→GTG)", "Polymerize when deoxygenated → sickling; hemolytic anemia, vaso-occlusive crises, splenomegaly then auto-splenectomy; malaria protection in trait"],
    ["HbC Disease", "β-globin Glu→Lys", "Mild hemolytic anemia; target cells; splenomegaly"],
    ["β-Thalassemia Major", "β-chain synthesis absent/reduced (mutations)", "Severe hemolytic anemia, hepatosplenomegaly, iron overload, bone deformities (crew-cut skull X-ray), chipmunk facies; needs transfusions"],
    ["α-Thalassemia", "Deletion of α-globin genes (4 genes total)", "1 gene: silent; 2 genes: α-thal trait; 3 genes: HbH disease (β4); 4 genes: hydrops fetalis (Hb Barts γ4 — fatal)"],
    ["Methemoglobinemia", "Fe²⁺ → Fe³⁺ (nitrites, dapsone, lidocaine)", "Cyanosis; blood is chocolate brown; O2 saturation falsely normal by pulse ox; Rx: methylene blue → reduces Fe³⁺ back to Fe²⁺ (via NADPH by G6PD)"],
    ["G6PD Deficiency", "X-linked; cannot regenerate NADPH (needed to reduce glutathione)", "Episodic hemolytic anemia triggered by oxidant stress (primaquine, dapsone, fava beans, infections); Heinz bodies; bite cells"],
    ["Pyruvate Kinase Deficiency", "Autosomal recessive; glycolysis defect", "Hemolytic anemia; ↑ 2,3-BPG (actually protective somewhat); RBC cannot generate ATP"],
]
table(tbl_data, story, col_widths=[3.5*cm, 4.5*cm, 8*cm])

h2("10.5 Myoglobin", story)
bp([
    f"{B('Structure:')} Single polypeptide chain (153 aa); one heme group; α-helical (8 helices labeled A-H)",
    f"Mb stores O2 in muscle; {B('hyperbolic O2 dissociation curve')} (no cooperativity, no Bohr effect, no 2,3-BPG effect)",
    f"Mb has {B('higher O2 affinity than Hb')} → picks up O2 from Hb in muscle; releases only when pO2 is very low",
    f"{B('Myoglobinuria:')} Rhabdomyolysis → myoglobin in urine → tea-colored urine; nephrotoxic; causes acute renal failure",
    f"{B('Myoglobin as cardiac marker:')} Earliest to rise (1-3h) after MI; not cardiac-specific",
    f"Mb vs Hb key difference: Mb is monomer (no cooperativity, hyperbolic) vs Hb tetramer (cooperative, sigmoidal)",
], story)
note("Exam trick: Mb = Hyperbolic (one subunit). Hb = Sigmoidal (four subunits, cooperative). HbF has higher O2 affinity than HbA (less 2,3-BPG binding because γ-chain doesn't bind 2,3-BPG well)", story)

h2("10.6 Plasma Proteins", story)
tbl_data = [
    ["Protein", "Produced By", "Normal Level", "Function & Clinical Significance"],
    ["Albumin", "Liver", "3.5-5 g/dL", "Main plasma protein; osmotic pressure; transport (fatty acids, bilirubin, drugs, Ca²⁺, hormones); negative acute phase reactant; decreased in liver disease, nephrotic syndrome, malnutrition"],
    ["Globulins (α, β, γ)", "Liver, plasma cells", "2-3.5 g/dL", "Multiple functions; γ-globulins = immunoglobulins (antibodies); M-spike in myeloma"],
    ["Fibrinogen", "Liver", "200-400 mg/dL", "Clotting factor I; converted to fibrin by thrombin; positive acute phase reactant"],
    ["Haptoglobin", "Liver", "30-200 mg/dL", "Binds free Hb after hemolysis → prevents renal loss; decreased in hemolysis; positive acute phase reactant"],
    ["Transferrin", "Liver", "200-360 mg/dL", "Iron transport protein; TIBC inversely related to iron stores; ↑ in iron deficiency, ↓ in iron overload"],
    ["Ceruloplasmin", "Liver", "20-60 mg/dL", "Copper transport (90% of plasma copper); decreased in Wilson's disease; ferroxidase activity"],
    ["α1-antitrypsin (AAT)", "Liver", "100-200 mg/dL", "Inhibits neutrophil elastase; AAT deficiency → emphysema (lower lobes), neonatal cholestasis/liver cirrhosis"],
    ["C-reactive protein (CRP)", "Liver", "<1 mg/L", "Binds phosphocholine; activates complement; major acute phase reactant; marker of inflammation/infection"],
    ["Prealbumin (Transthyretin)", "Liver", "10-40 mg/dL", "Transport of T4 and retinol (with RBP); short half-life (2 days) → best indicator of nutritional status & acute liver synthetic function"],
    ["Retinol-binding protein (RBP)", "Liver", "3-6 mg/dL", "Transports vitamin A; complex with prealbumin; decreased in protein malnutrition"],
    ["α2-Macroglobulin", "Liver", "100-300 mg/dL", "Protease inhibitor; increased in nephrotic syndrome; too large to be lost in urine"],
    ["β2-Microglobulin", "All nucleated cells", "<2 mg/L", "Part of MHC class I; increased in multiple myeloma, renal failure; renal function marker"],
    ["Ferritin", "All cells", "12-300 ng/mL", "Iron storage; ↑ in iron overload, anemia of chronic disease, acute phase reaction; ↓ in iron deficiency (first marker to drop)"],
]
table(tbl_data, story, col_widths=[4*cm, 3*cm, 2.5*cm, 6.5*cm])

h2("10.7 Acute Phase Reactants", story)
bp([
    f"{B('Positive APRs (increase in inflammation):')} CRP, Fibrinogen, Ferritin, Haptoglobin, Ceruloplasmin, Complement (C3,C4), α1-antitrypsin, Serum Amyloid A (SAA), α1-acid glycoprotein",
    f"{B('Negative APRs (decrease in inflammation):')} Albumin, Prealbumin (Transthyretin), Transferrin, Retinol-binding protein",
    f"{B('ESR:')} Erythrocyte sedimentation rate; fibrinogen/globulins coat RBCs → rouleaux → faster settling; non-specific inflammation marker; elevated in infection, autoimmune, cancer",
    f"{B('CRP vs ESR:')} CRP rises faster (within hours) and falls faster; ESR more delayed but useful in monitoring chronic inflammation (e.g., RA, temporal arteritis)",
], story)

warn("High-yield: In nephrotic syndrome: Albumin ↓, total protein ↓, α2-Macroglobulin ↑ (large, not lost), Fibrinogen ↑, LDL ↑ (liver compensates by making more lipoproteins)", story)

story.append(Spacer(1, 1*cm))
story.append(HRFlowable(width="100%", thickness=1.5, color=colors.HexColor('#1a237e'), spaceAfter=6))
story.append(Paragraph("END OF NOTES — Good luck on your exam! You've got this.", ParagraphStyle('Footer',
    parent=styles['Normal'], fontSize=11, textColor=colors.HexColor('#1a237e'),
    alignment=TA_CENTER, fontName='Helvetica-Bold')))

doc.build(story)
print(f"PDF successfully created: {OUTPUT}")

cd /home/daytona/workspace/biochem-notes && python generate_notes.py 2>&1

ls -lh /home/daytona/workspace/biochem-notes/Biochemistry_Exam_Notes.pdf