from reportlab.lib.pagesizes import A4
from reportlab.lib import colors
from reportlab.lib.units import cm, mm
from reportlab.lib.styles import getSampleStyleSheet, ParagraphStyle
from reportlab.lib.enums import TA_CENTER, TA_LEFT, TA_JUSTIFY
from reportlab.platypus import (SimpleDocTemplate, Paragraph, Spacer, Image,
                                 Table, TableStyle, PageBreak, HRFlowable,
                                 KeepTogether)
from reportlab.platypus.flowables import BalancedColumns
from reportlab.pdfgen import canvas
from reportlab.lib.colors import HexColor
import os

IMG_DIR = "/home/daytona/workspace/vet-biochem-pdf/images"
OUT_PATH = "/home/daytona/workspace/vet-biochem-pdf/Vet_Biochemistry_Diagrams_Clinical.pdf"

W, H = A4

# ── Colour palette ────────────────────────────────────────────────
DARK_BLUE   = HexColor("#1a3a5c")
MED_BLUE    = HexColor("#2e6da4")
LIGHT_BLUE  = HexColor("#dce8f5")
ACCENT_GOLD = HexColor("#c8860a")
VET_GREEN   = HexColor("#2d6a2d")
LIGHT_GREEN = HexColor("#e6f4e6")
WARN_RED    = HexColor("#b22222")
LIGHT_RED   = HexColor("#fde8e8")
LIGHT_GRAY  = HexColor("#f5f5f5")
MID_GRAY    = HexColor("#888888")

styles = getSampleStyleSheet()

def S(name, **kw):
    """Create a ParagraphStyle inheriting from base."""
    base = styles.get(name, styles["Normal"])
    return ParagraphStyle(name + "_custom_" + str(id(kw)), parent=base, **kw)

# Custom styles
TITLE_STYLE = S("Title", fontSize=26, textColor=DARK_BLUE, spaceAfter=4,
                alignment=TA_CENTER, fontName="Helvetica-Bold")
SUBTITLE_STYLE = S("Normal", fontSize=13, textColor=MED_BLUE, spaceAfter=2,
                   alignment=TA_CENTER, fontName="Helvetica")
DATE_STYLE = S("Normal", fontSize=9, textColor=MID_GRAY, spaceAfter=0,
               alignment=TA_CENTER, fontName="Helvetica-Oblique")

SECTION_STYLE = S("Heading1", fontSize=14, textColor=colors.white,
                  spaceBefore=6, spaceAfter=4,
                  fontName="Helvetica-Bold", leading=18)
SUBSEC_STYLE = S("Heading2", fontSize=11, textColor=DARK_BLUE,
                 spaceBefore=4, spaceAfter=3,
                 fontName="Helvetica-Bold", leading=14)
BODY_STYLE = S("Normal", fontSize=9, textColor=colors.black,
               spaceBefore=2, spaceAfter=2, leading=13,
               fontName="Helvetica", alignment=TA_JUSTIFY)
BULLET_STYLE = S("Normal", fontSize=9, textColor=colors.black,
                 spaceBefore=1, spaceAfter=1, leading=12,
                 leftIndent=12, bulletIndent=0,
                 fontName="Helvetica")
CAPTION_STYLE = S("Normal", fontSize=8, textColor=MID_GRAY,
                  alignment=TA_CENTER, fontName="Helvetica-Oblique",
                  spaceBefore=2, spaceAfter=6)
VET_BOX_STYLE = S("Normal", fontSize=9, textColor=VET_GREEN,
                  leading=13, fontName="Helvetica", alignment=TA_JUSTIFY)
WARN_BOX_STYLE = S("Normal", fontSize=9, textColor=WARN_RED,
                   leading=13, fontName="Helvetica", alignment=TA_JUSTIFY)
TABLE_HEADER = S("Normal", fontSize=8, textColor=colors.white,
                 fontName="Helvetica-Bold", alignment=TA_CENTER)
TABLE_CELL = S("Normal", fontSize=8, textColor=colors.black,
               fontName="Helvetica", alignment=TA_LEFT, leading=11)

def img(filename, width_cm=14, height_cm=None):
    path = os.path.join(IMG_DIR, filename)
    if not os.path.exists(path):
        return Paragraph(f"[Image not found: {filename}]", BODY_STYLE)
    w = width_cm * cm
    from PIL import Image as PILImage
    pil = PILImage.open(path)
    iw, ih = pil.size
    ratio = ih / iw
    h = height_cm * cm if height_cm else w * ratio
    # clamp height
    max_h = 17 * cm
    if h > max_h:
        h = max_h
        w = h / ratio
    return Image(path, width=w, height=h, hAlign="CENTER")

def section_header(text, color=DARK_BLUE):
    """Returns a coloured banner paragraph."""
    tbl = Table([[Paragraph(text, SECTION_STYLE)]], colWidths=[W - 4*cm])
    tbl.setStyle(TableStyle([
        ("BACKGROUND", (0,0), (-1,-1), color),
        ("TOPPADDING",    (0,0), (-1,-1), 6),
        ("BOTTOMPADDING", (0,0), (-1,-1), 6),
        ("LEFTPADDING",   (0,0), (-1,-1), 10),
        ("ROUNDEDCORNERS", [4]),
    ]))
    return tbl

def vet_box(title, *lines, color=LIGHT_GREEN, border=VET_GREEN, title_color=VET_GREEN):
    content = [Paragraph(f"<b>{title}</b>", S("Normal", fontSize=9,
               textColor=title_color, fontName="Helvetica-Bold", leading=13))]
    for line in lines:
        content.append(Paragraph(f"• {line}", VET_BOX_STYLE))
    tbl = Table([[content]], colWidths=[W - 4*cm])
    tbl.setStyle(TableStyle([
        ("BACKGROUND",    (0,0), (-1,-1), color),
        ("BOX",           (0,0), (-1,-1), 1.5, border),
        ("TOPPADDING",    (0,0), (-1,-1), 6),
        ("BOTTOMPADDING", (0,0), (-1,-1), 6),
        ("LEFTPADDING",   (0,0), (-1,-1), 8),
        ("RIGHTPADDING",  (0,0), (-1,-1), 8),
    ]))
    return tbl

def warn_box(title, *lines):
    return vet_box(title, *lines, color=LIGHT_RED, border=WARN_RED, title_color=WARN_RED)

def key_table(headers, rows):
    data = [[Paragraph(h, TABLE_HEADER) for h in headers]]
    for row in rows:
        data.append([Paragraph(str(c), TABLE_CELL) for c in row])
    col_w = (W - 4*cm) / len(headers)
    tbl = Table(data, colWidths=[col_w]*len(headers), repeatRows=1)
    style = [
        ("BACKGROUND",    (0,0), (-1,0), MED_BLUE),
        ("ROWBACKGROUNDS",(0,1), (-1,-1), [colors.white, LIGHT_BLUE]),
        ("GRID",          (0,0), (-1,-1), 0.5, HexColor("#aaaaaa")),
        ("TOPPADDING",    (0,0), (-1,-1), 4),
        ("BOTTOMPADDING", (0,0), (-1,-1), 4),
        ("LEFTPADDING",   (0,0), (-1,-1), 5),
        ("VALIGN",        (0,0), (-1,-1), "TOP"),
    ]
    tbl.setStyle(TableStyle(style))
    return tbl

def divider():
    return HRFlowable(width="100%", thickness=0.5, color=LIGHT_BLUE, spaceAfter=4, spaceBefore=4)


# ── Page numbering canvas ─────────────────────────────────────────
class NumberedCanvas(canvas.Canvas):
    def __init__(self, *args, **kwargs):
        super().__init__(*args, **kwargs)
        self._saved_page_states = []

    def showPage(self):
        self._saved_page_states.append(dict(self.__dict__))
        self._startPage()

    def save(self):
        num_pages = len(self._saved_page_states)
        for state in self._saved_page_states:
            self.__dict__.update(state)
            self.draw_page_number(num_pages)
            canvas.Canvas.showPage(self)
        canvas.Canvas.save(self)

    def draw_page_number(self, page_count):
        page_num = self._saved_page_states.index(
            {k: v for k, v in self.__dict__.items()
             if k in self._saved_page_states[0]}) + 1
        self.setFont("Helvetica", 8)
        self.setFillColor(MID_GRAY)
        self.drawRightString(W - 2*cm, 1.2*cm,
                             f"Page {page_num} of {page_count}")
        self.drawString(2*cm, 1.2*cm, "Vet Biochemistry — Diagrams & Clinical Applications")
        self.setStrokeColor(LIGHT_BLUE)
        self.setLineWidth(0.5)
        self.line(2*cm, 1.5*cm, W - 2*cm, 1.5*cm)


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

# ── COVER PAGE ───────────────────────────────────────────────────
story.append(Spacer(1, 3*cm))
story.append(Paragraph("VET BIOCHEMISTRY", TITLE_STYLE))
story.append(Paragraph("Diagrams &amp; Clinical Applications", SUBTITLE_STYLE))
story.append(Spacer(1, 0.5*cm))
story.append(HRFlowable(width="60%", thickness=2, color=ACCENT_GOLD,
                         hAlign="CENTER", spaceBefore=4, spaceAfter=4))
story.append(Spacer(1, 0.3*cm))
story.append(Paragraph("Complete Illustrated Reference for Exam Preparation", SUBTITLE_STYLE))
story.append(Spacer(1, 0.5*cm))

# topic list on cover
topics = [
    ("Q.6", "Short Notes"),
    ("1.", "Cori Cycle"),
    ("2.", "Deamination Reactions of Amino Acids"),
    ("3.", "Effects of Temperature & pH on Enzyme Activity"),
    ("Q.7", "Brief Descriptions"),
    ("4.", "Beta-Oxidation of Fatty Acids"),
    ("5.", "TCA (Krebs) Cycle — Energy Production"),
    ("6.", "Glycogenolysis"),
    ("7.", "Enzyme-Substrate Complex Formation"),
    ("Bonus", "Oxidative Phosphorylation"),
]
cover_data = [[Paragraph(f"<b>{n}</b>", S("Normal", fontSize=10,
               textColor=MED_BLUE, fontName="Helvetica-Bold")),
               Paragraph(t, S("Normal", fontSize=10, fontName="Helvetica"))]
              for n, t in topics]
cover_tbl = Table(cover_data, colWidths=[2.5*cm, 12*cm])
cover_tbl.setStyle(TableStyle([
    ("ROWBACKGROUNDS", (0,0), (-1,-1), [colors.white, LIGHT_BLUE]),
    ("TOPPADDING",     (0,0), (-1,-1), 5),
    ("BOTTOMPADDING",  (0,0), (-1,-1), 5),
    ("LEFTPADDING",    (0,0), (-1,-1), 8),
    ("BOX",            (0,0), (-1,-1), 1, MED_BLUE),
    ("LINEBELOW",      (0,0), (-1,-2), 0.3, LIGHT_BLUE),
]))
story.append(cover_tbl)
story.append(Spacer(1, 1*cm))
story.append(Paragraph("Sources: Lippincott Illustrated Reviews Biochemistry 8e • Harper's Illustrated Biochemistry 32e •<br/>Basic Medical Biochemistry 6e • Guyton &amp; Hall Medical Physiology • Harper's 32e", DATE_STYLE))
story.append(PageBreak())


# ════════════════════════════════════════════════════════════════
#  SECTION 1 — CORI CYCLE
# ════════════════════════════════════════════════════════════════
story.append(section_header("Q.6 — SHORT NOTES", DARK_BLUE))
story.append(Spacer(1, 0.3*cm))
story.append(section_header("1.  Cori Cycle (Lactic Acid Cycle)", MED_BLUE))
story.append(Spacer(1, 0.2*cm))

story.append(Paragraph(
    "<b>Definition:</b> The Cori cycle is the metabolic pathway by which lactate "
    "produced by anaerobic glycolysis in peripheral tissues (muscle, RBCs) is "
    "transported to the liver, reconverted to glucose via gluconeogenesis, and "
    "returned to blood for re-use.", BODY_STYLE))
story.append(Spacer(1, 0.2*cm))
story.append(img("cori_cycle.png", width_cm=14))
story.append(Paragraph(
    "Fig 1. Cori Cycle — Basic Medical Biochemistry 6e, Fig. 22.12",
    CAPTION_STYLE))

story.append(key_table(
    ["Feature", "Detail"],
    [
        ["Tissues involved", "Muscle, RBCs (anaerobic) → Liver (aerobic)"],
        ["Key enzymes - Muscle", "LDH: Pyruvate → Lactate (uses NADH)"],
        ["Key enzymes - Liver", "LDH + Gluconeogenic enzymes (PCK, FBPase, G6Pase)"],
        ["ATP balance", "Muscle gains 2 ATP; Liver spends 6 ATP → Net loss of 4 ATP"],
        ["Function", "Recycles lactate carbon; prevents lactic acidosis; maintains blood glucose"],
    ]
))
story.append(Spacer(1, 0.3*cm))
story.append(vet_box(
    "Veterinary Clinical Applications",
    "Racing horses / greyhounds: Massive lactate production during sprint exercise; "
    "Cori cycle keeps blood glucose from crashing post-race",
    "Capture myopathy (wild deer, zebra, kangaroo): Extreme exertion → lactic acidosis when "
    "Cori cycle is overwhelmed → pH drops → muscle necrosis → death if untreated",
    "Cattle with dystocia (prolonged difficult birth): Calf undergoes anaerobic glycolysis "
    "→ elevated blood lactate at birth; correction with IV glucose + bicarbonate",
    "Exertional rhabdomyolysis ('tying-up') in horses: Pyruvate/lactate accumulation → "
    "muscle damage; serum CK and AST markedly elevated",
))
story.append(PageBreak())


# ════════════════════════════════════════════════════════════════
#  SECTION 2 — DEAMINATION
# ════════════════════════════════════════════════════════════════
story.append(section_header("2.  Deamination Reactions of Amino Acids", MED_BLUE))
story.append(Spacer(1, 0.2*cm))
story.append(Paragraph(
    "<b>Definition:</b> Deamination is the removal of the amino (−NH₂) group from "
    "an amino acid, yielding an α-keto acid and releasing nitrogen. There are "
    "three main types: transamination, oxidative deamination, and non-oxidative "
    "deamination.", BODY_STYLE))
story.append(Spacer(1, 0.2*cm))

story.append(Paragraph("<b>Step 1 — Transamination (ALT &amp; AST):</b>", SUBSEC_STYLE))
story.append(img("transamination.png", width_cm=9))
story.append(Paragraph(
    "Fig 2a. Transamination reactions — ALT (top) and AST (bottom). "
    "Both require PLP (Vitamin B6). — Lippincott Biochemistry 8e, Fig. 19.8",
    CAPTION_STYLE))

story.append(Paragraph("<b>Step 2 — Oxidative Deamination (Glutamate Dehydrogenase):</b>", SUBSEC_STYLE))
story.append(img("oxidative_deamination.png", width_cm=9))
story.append(Paragraph(
    "Fig 2b. Panel A: Disposal of amino acids via transamination + oxidative "
    "deamination → free NH₃. Panel B: Reductive amination (synthesis). "
    "— Lippincott Biochemistry 8e, Fig. 19.12",
    CAPTION_STYLE))

story.append(key_table(
    ["Type", "Enzyme", "Coenzyme", "Product"],
    [
        ["Transamination", "ALT (GPT), AST (GOT)", "PLP (Vit B6)", "α-Keto acid + Glutamate"],
        ["Oxidative Deamination", "Glutamate Dehydrogenase (GDH)", "NAD⁺ (catabolism)", "α-KG + NH₃ + NADH"],
        ["Non-oxidative Deamination", "Serine dehydratase", "PLP", "Pyruvate + NH₃"],
        ["D-amino acid oxidase", "DAO (peroxisomal)", "FAD", "α-Keto acid + NH₃ + H₂O₂"],
    ]
))
story.append(Spacer(1, 0.2*cm))
story.append(vet_box(
    "Veterinary Clinical Applications",
    "ALT (SGPT): Liver-specific in dogs & cats. Elevated in hepatitis, hepatic lipidosis "
    "(fatty liver in obese cats), toxin ingestion (xylitol, aflatoxin). Normal dog ALT: 10-100 U/L",
    "AST (SGOT): Elevated in both liver AND muscle disease in horses and ruminants. "
    "Must interpret with CK to differentiate; if CK normal → liver origin",
    "GDH: Liver-specific in cattle and sheep. Best single enzyme marker of "
    "hepatocellular necrosis in ruminants (e.g., ragwort toxicity, aflatoxicosis)",
    "Ammonia toxicity: When GDH is impaired (liver failure) → NH₃ accumulates → "
    "hepatic encephalopathy in dogs, horses (head pressing, ataxia, seizures)",
    "Thiamin (B6) deficiency → PLP deficiency → transamination impaired → "
    "polioencephalomalacia in cattle/sheep (cerebrocortical necrosis)",
))
story.append(PageBreak())


# ════════════════════════════════════════════════════════════════
#  SECTION 3 — TEMP & pH
# ════════════════════════════════════════════════════════════════
story.append(section_header("3.  Effects of Temperature &amp; pH on Enzyme Activity", MED_BLUE))
story.append(Spacer(1, 0.2*cm))
story.append(img("temp_ph.png", width_cm=15))
story.append(Paragraph(
    "Fig 3. Left: Bell-curve effect of temperature (optimum 37-40°C for mammalian enzymes; "
    "denaturation above). Right: pH optima vary per enzyme — Pepsin (pH 2), "
    "Salivary amylase (pH 6.8), Trypsin (pH 7.5-8).",
    CAPTION_STYLE))

story.append(key_table(
    ["Enzyme", "Optimum pH", "Location / Species Relevance"],
    [
        ["Pepsin", "~2.0", "Stomach (monogastrics — dog, cat, pig, horse)"],
        ["Salivary amylase", "6.8–7.0", "Oral cavity (absent in cats; present in dogs, horses)"],
        ["Trypsin / Chymotrypsin", "7.5–8.0", "Pancreas → small intestine (all species)"],
        ["Alkaline Phosphatase (ALP)", "9–10", "Bone, liver, intestine — elevated in cholestasis"],
        ["Arginase", "~9.5", "Liver (urea cycle) — ruminants, dogs"],
        ["Acid Phosphatase", "~5.0", "Lysosomes, prostate"],
        ["Rumen microbial enzymes", "6.2–6.8", "Rumen — optimal for cellulolytic bacteria"],
    ]
))
story.append(Spacer(1, 0.2*cm))
story.append(vet_box(
    "Veterinary Clinical Applications — Temperature",
    "Fever (pyrexia) in animals: Moderate fever (39-40°C) initially enhances immune enzyme "
    "reactions. Hyperthermia >42°C (heat stroke in brachycephalic dogs, horses) denatures "
    "enzymes → multi-organ failure",
    "Hypothermia in neonates: Newborn lambs, piglets, foals in cold environments → "
    "metabolic enzyme rates halved per 10°C drop (Q10 effect) → hypoglycemia, bradycardia",
    "Thermostable enzymes: Rumen microbes have enzymes stable over wider temperature ranges; "
    "important in tropical veterinary nutrition",
    "Cold storage of blood/serum samples: Enzyme activity preserved at 4°C for clinical assays",
))
story.append(vet_box(
    "Veterinary Clinical Applications — pH",
    "Rumen acidosis (grain overload) in cattle/sheep: Rumen pH drops to 4.5-5.5 → "
    "inhibits cellulolytic bacteria enzymes → fermentation stops → D-lactic acidosis → "
    "ataxia ('drunken cow syndrome'), recumbency, death",
    "Abomasal displacement / volvulus in cows: Disrupts HCl production → enzyme pH disrupted",
    "Pancreatitis in dogs/cats: Trypsin activated prematurely within pancreas at wrong pH "
    "→ autodigestion of pancreatic tissue",
    "Alkalosis in milk fever (hypocalcaemia, parturient paresis): Systemic pH shift affects "
    "enzyme function; IV calcium gluconate treatment",
    "Clinical enzyme assays (ALT, ALP, CK): Must be run at controlled pH (phosphate "
    "buffer) and temperature (37°C) for accurate results",
))
story.append(PageBreak())


# ════════════════════════════════════════════════════════════════
#  SECTION 4 — BETA OXIDATION
# ════════════════════════════════════════════════════════════════
story.append(section_header("Q.7 — BRIEF DESCRIPTIONS", DARK_BLUE))
story.append(Spacer(1, 0.3*cm))
story.append(section_header("4.  β-Oxidation of Fatty Acids", MED_BLUE))
story.append(Spacer(1, 0.2*cm))
story.append(Paragraph(
    "<b>Definition:</b> β-Oxidation is the stepwise degradation of fatty acids in the "
    "<b>mitochondrial matrix</b> by sequential removal of 2-carbon (acetyl-CoA) units, "
    "producing NADH and FADH₂ per cycle.", BODY_STYLE))

story.append(Paragraph("<b>Full Pathway (activation + transport + 4 steps):</b>", SUBSEC_STYLE))
story.append(img("beta_oxidation_pathway.png", width_cm=9))
story.append(Paragraph(
    "Fig 4a. Complete β-oxidation pathway: activation → carnitine transport across "
    "inner mitochondrial membrane → 4-step repeating cycle → Acetyl-CoA → TCA cycle. "
    "— Harper's Illustrated Biochemistry 32e, Fig. 22-3",
    CAPTION_STYLE))

story.append(Paragraph("<b>Chemical equations for each step:</b>", SUBSEC_STYLE))
story.append(img("beta_oxidation_equations.png", width_cm=15))
story.append(Paragraph(
    "Fig 4b. β-oxidation reactions: (1) Activation by Thiokinase; (2) FAD-oxidation "
    "by Acyl dehydrogenase → FADH₂; (3) Hydration by Enoyl hydrase → β-OH-acyl-CoA; "
    "(4) NAD⁺-oxidation by β-Hydroxyacyl DH → NADH; (5) Thiolysis by Thiolase → "
    "Acetyl-CoA + shortened acyl-CoA. — Guyton & Hall Physiology",
    CAPTION_STYLE))

story.append(key_table(
    ["Step", "Enzyme", "Cofactor", "Product"],
    [
        ["0a. Activation", "Acyl-CoA synthetase (Thiokinase)", "ATP, CoA", "Fatty acyl-CoA + AMP + PPi (−2 ATP)"],
        ["0b. Transport", "CPT-I, CACT, CPT-II (Carnitine shuttle)", "Carnitine", "Acyl-CoA in mitochondrial matrix"],
        ["1. Oxidation", "Acyl-CoA dehydrogenase", "FAD", "trans-Δ²-Enoyl-CoA + FADH₂"],
        ["2. Hydration", "Enoyl-CoA hydratase", "H₂O", "L-3-Hydroxyacyl-CoA"],
        ["3. Oxidation", "L-3-Hydroxyacyl-CoA DH", "NAD⁺", "3-Ketoacyl-CoA + NADH"],
        ["4. Thiolysis", "β-Ketothiolase (Thiolase)", "CoA", "Acetyl-CoA + (n−2) Acyl-CoA"],
    ]
))
story.append(Spacer(1, 0.2*cm))
story.append(key_table(
    ["Palmitate (C16) Energy", "Cycles/Moles", "ATP/unit", "Total ATP"],
    [
        ["Activation cost", "—", "−2", "−2"],
        ["β-Oxidation FADH₂", "7", "×1.5", "+10.5"],
        ["β-Oxidation NADH", "7", "×2.5", "+17.5"],
        ["TCA (8 Acetyl-CoA)", "8", "×10", "+80"],
        ["NET TOTAL", "", "", "106 ATP"],
    ]
))
story.append(Spacer(1, 0.2*cm))
story.append(vet_box(
    "Veterinary Clinical Applications",
    "Ketosis / Acetonaemia in dairy cows (early lactation negative energy balance): "
    "Excess β-oxidation → Acetyl-CoA cannot enter TCA (OAA depleted) → ketone bodies "
    "(BOHB, acetoacetate, acetone). Blood BOHB >3 mmol/L = clinical ketosis. "
    "Treatment: IV glucose, propylene glycol, glucocorticoids",
    "Pregnancy toxaemia in ewes (twin-lamb disease): Same mechanism — twin fetuses "
    "consume glucose → ewe mobilises fat → ketosis. High mortality if untreated",
    "Feline hepatic lipidosis: Obese cats on starvation diet → massive fat mobilisation "
    "→ overwhelms hepatic β-oxidation → fat accumulates in liver → jaundice, liver failure",
    "CPT-I deficiency (dogs): Carnitine shuttle impaired → long-chain fatty acids cannot "
    "enter mitochondria → lipid myopathy, cardiomyopathy (seen in Boxers, Dobermans)",
    "L-carnitine supplementation: Used in dogs with dilated cardiomyopathy to improve "
    "fatty acid transport into cardiac mitochondria",
))
story.append(warn_box(
    "Exam Alert",
    "Remember: Activation uses 2 high-energy phosphates (ATP → AMP + PPi, equivalent to −2 ATP)",
    "FADH₂ from β-oxidation feeds directly into Complex II of ETC (bypasses Complex I) → 1.5 ATP each",
    "Odd-chain fatty acids (propionyl-CoA → succinyl-CoA via Vit B12) — glucogenic, "
    "important in ruminants (propionate from rumen)",
))
story.append(PageBreak())


# ════════════════════════════════════════════════════════════════
#  SECTION 5 — TCA CYCLE
# ════════════════════════════════════════════════════════════════
story.append(section_header("5.  TCA (Krebs / Citric Acid) Cycle", MED_BLUE))
story.append(Spacer(1, 0.2*cm))
story.append(Paragraph(
    "<b>Definition:</b> The TCA cycle is a series of 8 enzyme-catalysed reactions in "
    "the <b>mitochondrial matrix</b> that completely oxidise <b>Acetyl-CoA</b> to CO₂, "
    "capturing energy as NADH, FADH₂, and GTP.", BODY_STYLE))
story.append(Spacer(1, 0.2*cm))
story.append(img("tca_cycle.png", width_cm=13))
story.append(Paragraph(
    "Fig 5. Complete TCA (Krebs) Cycle showing all 8 steps, enzymes, cofactors, and "
    "inhibitors (red lines: Fluoroacetate blocks Aconitase; Arsenite blocks α-KG DH; "
    "Malonate blocks Succinate DH). — Harper's Illustrated Biochemistry 32e, Fig. 16-3",
    CAPTION_STYLE))

story.append(key_table(
    ["Step", "Reaction", "Enzyme", "Energy"],
    [
        ["1", "OAA (4C) + Acetyl-CoA (2C) → Citrate (6C)", "Citrate synthase", "—"],
        ["2", "Citrate → cis-Aconitate → Isocitrate", "Aconitase (Fe²⁺)", "—"],
        ["3", "Isocitrate → Oxalosuccinate → α-KG + CO₂", "Isocitrate DH (Mn²⁺)", "1 NADH"],
        ["4", "α-KG (5C) → Succinyl-CoA (4C) + CO₂", "α-KG DH complex (TPP, Lipoate, FAD)", "1 NADH"],
        ["5", "Succinyl-CoA → Succinate", "Succinyl-CoA synthetase (Mg²⁺)", "1 GTP"],
        ["6", "Succinate → Fumarate", "Succinate DH (Complex II of ETC)", "1 FADH₂"],
        ["7", "Fumarate + H₂O → L-Malate", "Fumarase", "—"],
        ["8", "L-Malate → OAA", "Malate dehydrogenase", "1 NADH"],
    ]
))
story.append(Spacer(1, 0.2*cm))
story.append(key_table(
    ["Product per turn", "Number", "ATP equivalent", "Cumulative"],
    [
        ["NADH (Steps 3,4,8)", "3", "× 2.5 = 7.5 ATP", "7.5"],
        ["FADH₂ (Step 6)", "1", "× 1.5 = 1.5 ATP", "9.0"],
        ["GTP (Step 5)", "1", "= 1 ATP", "10.0"],
        ["TOTAL per turn", "", "", "~10 ATP"],
        ["CO₂ released", "2", "—", "Metabolic waste"],
    ]
))
story.append(Spacer(1, 0.2*cm))
story.append(vet_box(
    "Veterinary Clinical Applications",
    "Acetonaemia/ketosis in dairy cattle: Negative energy balance → OAA diverted to "
    "gluconeogenesis → TCA cycle slows → Acetyl-CoA accumulates → ketogenesis. "
    "Blood glucose <2.2 mmol/L + BOHB >3 mmol/L = diagnosis",
    "Fluoroacetate (compound 1080) poisoning: Used as rodenticide; highly toxic to dogs, "
    "cats, foxes, livestock. Fluoroacetate → fluorocitrate → irreversibly blocks Aconitase "
    "→ citrate accumulates → TCA stops → cardiac arrest. No antidote; supportive care only",
    "Arsenite toxicity (arsenic poisoning in livestock from dipping vats, pasture): "
    "Inhibits α-KG dehydrogenase → TCA blocked → energy failure in heart and nervous system",
    "Thiamin (Vit B1) deficiency: α-KG DH complex requires TPP (thiamin pyrophosphate). "
    "Deficiency in ruminants (polioencephalomalacia) and horses (bracken fern toxicity) "
    "→ TCA impaired → brain energy failure. Treatment: IV thiamin",
    "Succinate dehydrogenase is Complex II of ETC — important junction between TCA and OXPHOS",
))
story.append(PageBreak())


# ════════════════════════════════════════════════════════════════
#  SECTION 6 — GLYCOGENOLYSIS
# ════════════════════════════════════════════════════════════════
story.append(section_header("6.  Glycogenolysis", MED_BLUE))
story.append(Spacer(1, 0.2*cm))
story.append(Paragraph(
    "<b>Definition:</b> Glycogenolysis is the enzymatic <b>degradation of stored glycogen</b> "
    "to yield glucose (liver) or glucose-6-phosphate (muscle). It is NOT the reverse of "
    "glycogen synthesis — it uses entirely different enzymes.", BODY_STYLE))
story.append(Spacer(1, 0.2*cm))
story.append(img("glycogenolysis.png", width_cm=13))
story.append(Paragraph(
    "Fig 6. Steps in Glycogenolysis: Phosphorylase cleaves α-1,4 bonds → Glucan transferase "
    "moves trisaccharide to expose branch → Debranching enzyme cleaves α-1,6 bond releasing "
    "free glucose. Blue = α-1,4 linked glucose; Orange = branch glucose; "
    "Branch point = α-1,6 bond. — Harper's Illustrated Biochemistry 32e, Fig. 18-4",
    CAPTION_STYLE))

story.append(key_table(
    ["Step", "Enzyme", "Bond cleaved", "Product"],
    [
        ["1. Chain shortening", "Glycogen phosphorylase (needs PLP)", "α-1,4 (phosphorolysis)", "Glucose-1-phosphate"],
        ["2. Branch transfer", "Glucan transferase (part of debranching enzyme)", "Transfers 3 units", "Exposed α-1,6 branch"],
        ["3. Branch removal", "α-1,6-Glucosidase (debranching enzyme)", "α-1,6 (hydrolysis)", "Free glucose (unphosphorylated!)"],
        ["4. Isomerisation", "Phosphoglucomutase", "—", "Glucose-6-phosphate"],
        ["5. Liver only", "Glucose-6-phosphatase (ER membrane)", "—", "Free glucose → blood"],
    ]
))
story.append(Spacer(1, 0.2*cm))
story.append(key_table(
    ["Hormone/Signal", "Mechanism", "Tissue", "Effect"],
    [
        ["Glucagon (low blood glucose)", "↑cAMP → PKA → Phosphorylase kinase → Phosphorylase b→a", "Liver", "↑ Glycogenolysis; glucose released to blood"],
        ["Epinephrine (stress/exercise)", "Same cAMP cascade + Ca²⁺", "Liver + Muscle", "↑ Glycogenolysis for fight-or-flight"],
        ["Ca²⁺ (muscle contraction)", "Directly activates phosphorylase kinase", "Muscle", "↑ Glycogenolysis during exercise"],
        ["AMP (low ATP)", "Allosteric activation of phosphorylase b", "Muscle", "↑ Glycogenolysis when energy low"],
        ["Insulin (fed state)", "Activates phosphatase → dephosphorylates phosphorylase", "Both", "↓ Glycogenolysis; ↑ Glycogen synthesis"],
    ]
))
story.append(Spacer(1, 0.2*cm))
story.append(vet_box(
    "Veterinary Clinical Applications",
    "Neonatal hypoglycaemia (piglets, lambs, foals): At birth, umbilical cord clamped → "
    "maternal glucose supply cut → epinephrine + glucagon activate glycogenolysis to restore "
    "blood glucose. Neonates with limited glycogen stores → fatal hypoglycaemia within hours. "
    "Rx: Oral or IV glucose",
    "Glycogen Storage Diseases (GSD) — Pompe disease (GSD Type II) in Brahman cattle: "
    "Acid maltase (lysosomal α-glucosidase) deficiency → glycogen accumulates in muscle "
    "and heart → cardiomyopathy, muscle weakness, respiratory failure",
    "GSD Type III (Debranching enzyme deficiency): Reported in German Shepherds → "
    "cannot debranch → glycogen accumulates → hypoglycaemia + hepatomegaly",
    "Capture myopathy in wild animals: Epinephrine surge → rapid glycogenolysis → "
    "glucose used for intense muscle work → lactate + glycogen depletion → muscle necrosis",
    "Hypoglycaemia in toy breed dogs (Chihuahuas, Yorkshire Terriers): "
    "Limited hepatic glycogen stores; stress → rapid glycogen depletion → seizures",
    "Diabetes mellitus in dogs/cats: Glucagon dominance → unregulated glycogenolysis "
    "→ persistent hyperglycaemia despite glucose excess",
))
story.append(PageBreak())


# ════════════════════════════════════════════════════════════════
#  SECTION 7 — ENZYME-SUBSTRATE COMPLEX
# ════════════════════════════════════════════════════════════════
story.append(section_header("7.  Enzyme-Substrate Complex Formation", MED_BLUE))
story.append(Spacer(1, 0.2*cm))
story.append(Paragraph(
    "<b>Definition:</b> The enzyme-substrate (ES) complex is the transient molecular "
    "association formed when a substrate binds to the <b>active site</b> of an enzyme, "
    "preceding catalysis: <b>E + S ⇌ ES → E + P</b>", BODY_STYLE))
story.append(Spacer(1, 0.2*cm))

story.append(Paragraph("<b>Active site hydrogen bonding (basis of specificity):</b>", SUBSEC_STYLE))
story.append(img("es_hbonds.png", width_cm=11))
story.append(Paragraph(
    "Fig 7a. Glucose binding site in glucokinase — each -OH of glucose (red) is held by "
    "specific H-bonds (dashed) to Asp-205, Asn-204, Asn-231, Glu-256, Glu-290, Gly-229. "
    "Panel B: Galactose (differs by one -OH) is NOT phosphorylated → explains enzyme "
    "specificity. — Basic Medical Biochemistry 6e, Fig. 8.5",
    CAPTION_STYLE))

story.append(Paragraph("<b>Induced Fit Model — Before and After substrate binding:</b>", SUBSEC_STYLE))

# side by side images
before_img = img("es_before.png", width_cm=7)
after_img  = img("es_after.png",  width_cm=7)
side_tbl = Table([[before_img, after_img]], colWidths=[8*cm, 8*cm])
side_tbl.setStyle(TableStyle([
    ("ALIGN",         (0,0), (-1,-1), "CENTER"),
    ("VALIGN",        (0,0), (-1,-1), "MIDDLE"),
    ("LEFTPADDING",   (0,0), (-1,-1), 4),
    ("RIGHTPADDING",  (0,0), (-1,-1), 4),
]))
story.append(side_tbl)
story.append(Paragraph(
    "Fig 7b (left): Glucokinase BEFORE binding — open cleft, substrate approaching. "
    "Fig 7c (right): AFTER binding — cleft closes around glucose (red sphere) "
    "= Induced Fit. — Basic Medical Biochemistry 6e, Fig. 8.6",
    CAPTION_STYLE))

story.append(key_table(
    ["Model", "Proposed by", "Concept", "Status"],
    [
        ["Lock and Key", "Emil Fischer, 1894",
         "Enzyme has rigid pre-formed active site; substrate fits exactly like key in lock",
         "Outdated — does not explain enzyme flexibility"],
        ["Induced Fit", "Daniel Koshland, 1958",
         "Substrate binding induces conformational change in enzyme; cleft closes, "
         "improving catalysis, improving co-substrate binding, excluding water",
         "Currently accepted model"],
    ]
))
story.append(Spacer(1, 0.2*cm))
story.append(key_table(
    ["Stabilising Force", "Example in Glucokinase ES complex"],
    [
        ["Hydrogen bonds", "Each -OH of glucose H-bonds to Asp, Asn, Glu, Gly residues"],
        ["Electrostatic interactions", "Charged Asp/Glu attract polar glucose -OH groups"],
        ["Hydrophobic interactions", "Non-polar regions of substrate near hydrophobic pockets"],
        ["Van der Waals forces", "Short-range attractive forces at close contact"],
        ["Transient covalent bonds", "Serine proteases (trypsin) — acyl-enzyme intermediate"],
    ]
))
story.append(Spacer(1, 0.2*cm))
story.append(vet_box(
    "Veterinary Clinical Applications",
    "Organophosphate (OP) poisoning (cattle, dogs, sheep from pesticide/dip tank exposure): "
    "OP covalently binds Serine in active site of acetylcholinesterase (AChE) → ES complex "
    "permanently blocked → ACh accumulates at synapses → SLUD signs "
    "(Salivation, Lacrimation, Urination, Defaecation) + bradycardia, miosis, seizures. "
    "Treatment: Atropine (competitive blocker) + Pralidoxime/2-PAM (reactivates AChE if given early)",
    "Competitive enzyme inhibitors: Many drugs work by mimicking substrate to occupy active "
    "site — e.g., allopurinol (xanthine oxidase inhibitor) used in Dalmatians for urate urolithiasis",
    "Substrate specificity explained by ES complex: Glucokinase phosphorylates glucose but "
    "NOT galactose (differs by one -OH) → explains galactosaemia pathology in calves",
    "Km and Vmax: Derived from ES complex kinetics. High Km = weak substrate binding. "
    "Low Km = tight binding = high affinity. Clinically, enzyme Km determines drug dosing "
    "interactions in liver metabolism",
))
story.append(PageBreak())


# ════════════════════════════════════════════════════════════════
#  BONUS — OXIDATIVE PHOSPHORYLATION
# ════════════════════════════════════════════════════════════════
story.append(section_header("BONUS: Oxidative Phosphorylation (OXPHOS)", HexColor("#5a1e82")))
story.append(Spacer(1, 0.2*cm))
story.append(Paragraph(
    "<b>Definition:</b> Oxidative phosphorylation is the process by which ATP is synthesised "
    "from ADP + Pi, driven by the energy of electron flow through the mitochondrial electron "
    "transport chain (ETC) coupled to the proton-motive force (Mitchell's chemiosmotic theory).",
    BODY_STYLE))
story.append(Spacer(1, 0.2*cm))
story.append(img("oxphos.png", width_cm=15))
story.append(Paragraph(
    "Fig 8. Complete Oxidative Phosphorylation concept map and ETC diagram. "
    "TCA + β-oxidation → NADH/FADH₂ → ETC (Complexes I-IV) → H⁺ pumped out → "
    "gradient drives ATP synthase (Complex V). — Lippincott Biochemistry 8e, Fig. 6.18",
    CAPTION_STYLE))

story.append(key_table(
    ["Complex", "Name", "Electron carrier", "H⁺ pumped", "Inhibitor"],
    [
        ["I", "NADH-CoQ reductase", "NADH → FMN → Fe-S → CoQ", "4 H⁺", "Rotenone (insecticide); Amytal"],
        ["II", "Succinate-CoQ reductase", "FADH₂ → Fe-S → CoQ", "0 H⁺", "Malonate (competitive)"],
        ["III", "CoQ-Cyt c reductase", "CoQ → Cyt b → Fe-S → Cyt c₁ → Cyt c", "4 H⁺", "Antimycin A"],
        ["IV", "Cytochrome c oxidase", "Cyt c → CuA → Haem a → CuB/Haem a3 → O₂", "2 H⁺", "Cyanide, CO, Azide"],
        ["V", "ATP synthase (F₀F₁)", "H⁺ flows back in", "—", "Oligomycin (blocks F₀)"],
        ["Uncouplers", "Dissipate gradient without ATP", "DNP, Thermogenin (UCP1)", "—", "Heat produced instead of ATP"],
    ]
))
story.append(Spacer(1, 0.2*cm))
story.append(vet_box(
    "Veterinary Clinical Applications — Oxidative Phosphorylation",
    "Cyanide toxicity (cattle from sorghum/sudangrass/wild cherry leaves; dogs from "
    "smoke inhalation): CN⁻ binds Complex IV (cytochrome oxidase) → blocks O₂ reduction "
    "→ OXPHOS stops → histotoxic hypoxia → bright red venous blood (oxyHb not used). "
    "Treatment: Sodium nitrite + sodium thiosulphate (cattle); hydroxocobalamin (dogs)",
    "Carbon monoxide (CO) poisoning (animals in barn fires, faulty heaters): CO blocks "
    "Complex IV + binds Hb → double impairment of O₂ delivery and utilisation",
    "Rotenone: Natural insecticide/piscicide, inhibits Complex I. Toxic to fish and "
    "insects; used in aquaculture. Toxic to dogs and cats if ingested",
    "Thermogenin (UCP1) in brown adipose tissue: Present in neonatal lambs, piglets, "
    "foals, calves — uncouples OXPHOS to generate heat instead of ATP. "
    "Critical for thermoregulation at birth in cold environments",
    "Mitochondrial myopathies in horses and dogs: Defects in ETC complexes → exercise "
    "intolerance, lactic acidosis, muscle weakness",
    "ATP yield summary: NADH=2.5 ATP, FADH₂=1.5 ATP; 1 glucose → ~30-32 ATP total",
))
story.append(PageBreak())


# ════════════════════════════════════════════════════════════════
#  QUICK REVISION TABLE (last page)
# ════════════════════════════════════════════════════════════════
story.append(section_header("QUICK REVISION — Complete Summary Table", DARK_BLUE))
story.append(Spacer(1, 0.3*cm))
story.append(key_table(
    ["Topic", "Key Enzyme(s)", "Key Product(s)", "ATP Yield", "Vet Relevance"],
    [
        ["Cori Cycle",
         "LDH, Glucokinase, G6Pase",
         "Glucose ↔ Lactate",
         "Net −4 ATP",
         "Exercise lactate; capture myopathy; neonatal asphyxia"],
        ["Transamination",
         "ALT (GPT), AST (GOT)",
         "Glutamate + α-keto acid",
         "—",
         "ALT elevated in dog/cat liver disease; AST in horse muscle/liver"],
        ["Oxidative Deamination",
         "GDH (mitochondrial)",
         "α-KG + NH₃ + NADH",
         "+1 NADH",
         "GDH elevated in ruminant hepatocellular necrosis; hepatic encephalopathy"],
        ["Temp/pH effects",
         "All enzymes",
         "Optimum bell curve",
         "—",
         "Rumen acidosis; heat stroke; pancreatitis in dogs"],
        ["β-Oxidation",
         "Acyl-CoA DH, Enoyl hydratase, HADH, Thiolase",
         "Acetyl-CoA + NADH + FADH₂",
         "106 ATP (palmitate)",
         "Ketosis (cows/ewes); feline hepatic lipidosis; carnitine deficiency"],
        ["TCA Cycle",
         "Citrate synthase, Isocitrate DH, α-KG DH, Succinate DH, Malate DH",
         "3NADH + 1FADH₂ + 1GTP + 2CO₂",
         "~10 ATP/turn",
         "Ketosis; fluoroacetate poisoning; thiamin deficiency; arsenic toxicity"],
        ["Glycogenolysis",
         "Glycogen phosphorylase, Debranching enzyme, G6Pase",
         "Glucose (liver) / G-6-P (muscle)",
         "No ATP cost",
         "Neonatal hypoglycaemia; GSD in Brahman cattle; diabetes mellitus"],
        ["ES Complex",
         "Enzyme-specific",
         "Transition state complex",
         "—",
         "OP poisoning (AChE inhibition); allopurinol in Dalmatians; drug interactions"],
        ["Oxidative Phosphorylation",
         "Complexes I-IV + ATP Synthase (V)",
         "ATP + H₂O",
         "~30-32 ATP/glucose",
         "Cyanide poisoning; CO toxicity; thermogenin in neonates; mitochondrial myopathy"],
    ]
))
story.append(Spacer(1, 0.5*cm))
story.append(Paragraph(
    "<b>Sources:</b> Lippincott Illustrated Reviews Biochemistry 8e • "
    "Harper's Illustrated Biochemistry 32e • Basic Medical Biochemistry 6e • "
    "Guyton &amp; Hall Textbook of Medical Physiology • Goldman-Cecil Medicine",
    DATE_STYLE))


# ── BUILD ─────────────────────────────────────────────────────────
doc = SimpleDocTemplate(
    OUT_PATH,
    pagesize=A4,
    leftMargin=2*cm, rightMargin=2*cm,
    topMargin=2*cm,  bottomMargin=2.5*cm,
    title="Vet Biochemistry — Diagrams & Clinical Applications",
    author="Orris AI",
    subject="Veterinary Biochemistry Exam Reference",
)
doc.build(story, canvasmaker=NumberedCanvas)
print(f"PDF created: {OUT_PATH}")

Successfully replaced 1 instance(s) of the string in '/home/daytona/workspace/vet-biochem-pdf/build_pdf.py'

from reportlab.lib.pagesizes import A4
from reportlab.lib import colors
from reportlab.lib.units import cm
from reportlab.lib.styles import getSampleStyleSheet, ParagraphStyle
from reportlab.lib.enums import TA_CENTER, TA_LEFT, TA_JUSTIFY
from reportlab.platypus import (SimpleDocTemplate, Paragraph, Spacer, Image,
                                 Table, TableStyle, PageBreak, HRFlowable)
from reportlab.pdfgen import canvas
from reportlab.lib.colors import HexColor
from PIL import Image as PILImage
import os

IMG_DIR  = "/home/daytona/workspace/vet-biochem-pdf/images"
OUT_PATH = "/home/daytona/workspace/vet-biochem-pdf/Vet_Biochem_Complete_Answers.pdf"
W, H = A4

# ── Palette ──────────────────────────────────────────────────────
DARK_BLUE   = HexColor("#1a3a5c")
MED_BLUE    = HexColor("#2e6da4")
LIGHT_BLUE  = HexColor("#dce8f5")
DARK_GREEN  = HexColor("#1a5c2a")
MED_GREEN   = HexColor("#2e8a42")
LIGHT_GREEN = HexColor("#e0f4e4")
GOLD        = HexColor("#b8860b")
LIGHT_GOLD  = HexColor("#fdf6dc")
PURPLE      = HexColor("#5a1e82")
LIGHT_PURP  = HexColor("#f0e6fa")
WARN_RED    = HexColor("#b22222")
LIGHT_RED   = HexColor("#fde8e8")
MID_GRAY    = HexColor("#777777")
LIGHT_GRAY  = HexColor("#f8f8f8")

styles = getSampleStyleSheet()

def PS(base="Normal", **kw):
    return ParagraphStyle("x"+str(hash(str(kw))), parent=styles.get(base, styles["Normal"]), **kw)

# ── Styles ───────────────────────────────────────────────────────
TITLE_S   = PS("Title",   fontSize=28, textColor=DARK_BLUE, alignment=TA_CENTER,
                fontName="Helvetica-Bold", spaceAfter=6)
SUB_S     = PS("Normal",  fontSize=12, textColor=MED_BLUE,  alignment=TA_CENTER,
                fontName="Helvetica", spaceAfter=4)
DATE_S    = PS("Normal",  fontSize=8,  textColor=MID_GRAY,  alignment=TA_CENTER,
                fontName="Helvetica-Oblique")
Q_HEAD_S  = PS("Normal",  fontSize=13, textColor=colors.white, fontName="Helvetica-Bold",
                leading=18, spaceAfter=0)
ANS_HEAD_S= PS("Normal",  fontSize=11, textColor=DARK_BLUE, fontName="Helvetica-Bold",
                spaceBefore=6, spaceAfter=3, leading=15)
SUBHEAD_S = PS("Normal",  fontSize=10, textColor=MED_BLUE,  fontName="Helvetica-Bold",
                spaceBefore=4, spaceAfter=2, leading=13)
BODY_S    = PS("Normal",  fontSize=9,  textColor=colors.black, fontName="Helvetica",
                leading=13, spaceBefore=2, spaceAfter=2, alignment=TA_JUSTIFY)
BULLET_S  = PS("Normal",  fontSize=9,  textColor=colors.black, fontName="Helvetica",
                leading=12, spaceBefore=1, spaceAfter=1, leftIndent=14)
FORMULA_S = PS("Normal",  fontSize=9,  textColor=DARK_GREEN, fontName="Helvetica-Bold",
                leading=13, spaceBefore=2, spaceAfter=2, leftIndent=10)
CAPTION_S = PS("Normal",  fontSize=7.5,textColor=MID_GRAY,  fontName="Helvetica-Oblique",
                alignment=TA_CENTER, spaceBefore=1, spaceAfter=5)
TH_S      = PS("Normal",  fontSize=8,  textColor=colors.white, fontName="Helvetica-Bold",
                alignment=TA_CENTER)
TD_S      = PS("Normal",  fontSize=8,  textColor=colors.black, fontName="Helvetica",
                alignment=TA_LEFT, leading=11)
TD_C_S    = PS("Normal",  fontSize=8,  textColor=colors.black, fontName="Helvetica",
                alignment=TA_CENTER, leading=11)
MARK_S    = PS("Normal",  fontSize=9,  textColor=GOLD, fontName="Helvetica-Bold",
                alignment=TA_CENTER)

# ── Helpers ──────────────────────────────────────────────────────
def get_img(fname, max_w_cm=14, max_h_cm=16):
    path = os.path.join(IMG_DIR, fname)
    if not os.path.exists(path):
        return Paragraph(f"[Image missing: {fname}]", BODY_S)
    pil = PILImage.open(path)
    iw, ih = pil.size
    ratio = ih / iw
    w = max_w_cm * cm
    h = w * ratio
    if h > max_h_cm * cm:
        h = max_h_cm * cm
        w = h / ratio
    return Image(path, width=w, height=h, hAlign="CENTER")

def q_banner(text, bg=DARK_BLUE):
    row = [Paragraph(text, Q_HEAD_S)]
    t = Table([row], colWidths=[W - 4*cm])
    t.setStyle(TableStyle([
        ("BACKGROUND",    (0,0),(-1,-1), bg),
        ("TOPPADDING",    (0,0),(-1,-1), 7),
        ("BOTTOMPADDING", (0,0),(-1,-1), 7),
        ("LEFTPADDING",   (0,0),(-1,-1), 12),
    ]))
    return t

def marks_tag(marks):
    return Paragraph(f"[{marks}]", MARK_S)

def info_box(title, lines, bg=LIGHT_BLUE, border=MED_BLUE, tc=DARK_BLUE):
    content = [Paragraph(f"<b>{title}</b>",
                PS("Normal", fontSize=9, textColor=tc, fontName="Helvetica-Bold", leading=13))]
    for l in lines:
        content.append(Paragraph(f"• {l}", PS("Normal", fontSize=8.5, textColor=colors.black,
                                               fontName="Helvetica", leading=12)))
    t = Table([[content]], colWidths=[W - 4*cm])
    t.setStyle(TableStyle([
        ("BACKGROUND",    (0,0),(-1,-1), bg),
        ("BOX",           (0,0),(-1,-1), 1.5, border),
        ("TOPPADDING",    (0,0),(-1,-1), 6),
        ("BOTTOMPADDING", (0,0),(-1,-1), 6),
        ("LEFTPADDING",   (0,0),(-1,-1), 8),
        ("RIGHTPADDING",  (0,0),(-1,-1), 8),
    ]))
    return t

def vet_box(title, *lines):
    return info_box(f"🐾 Vet Relevance — {title}", list(lines),
                    bg=LIGHT_GREEN, border=MED_GREEN, tc=DARK_GREEN)

def warn_box(title, *lines):
    return info_box(f"⚠ Exam Tip — {title}", list(lines),
                    bg=LIGHT_RED, border=WARN_RED, tc=WARN_RED)

def def_box(title, defn):
    return info_box(f"Definition: {title}", [defn],
                    bg=LIGHT_GOLD, border=GOLD, tc=GOLD)

def make_table(headers, rows, col_widths=None):
    data = [[Paragraph(h, TH_S) for h in headers]]
    for row in rows:
        data.append([Paragraph(str(c), TD_S) for c in row])
    cw = col_widths if col_widths else [(W - 4*cm)/len(headers)]*len(headers)
    t = Table(data, colWidths=cw, repeatRows=1)
    t.setStyle(TableStyle([
        ("BACKGROUND",    (0,0),(-1,0), MED_BLUE),
        ("ROWBACKGROUNDS",(0,1),(-1,-1), [colors.white, LIGHT_BLUE]),
        ("GRID",          (0,0),(-1,-1), 0.4, HexColor("#bbbbbb")),
        ("TOPPADDING",    (0,0),(-1,-1), 4),
        ("BOTTOMPADDING", (0,0),(-1,-1), 4),
        ("LEFTPADDING",   (0,0),(-1,-1), 5),
        ("VALIGN",        (0,0),(-1,-1), "TOP"),
    ]))
    return t

def sp(h=0.25): return Spacer(1, h*cm)
def hr(): return HRFlowable(width="100%", thickness=0.5, color=LIGHT_BLUE,
                             spaceBefore=4, spaceAfter=4)
def pb(): return PageBreak()

# ── Numbered canvas ───────────────────────────────────────────────
class NC(canvas.Canvas):
    def __init__(self, *a, **kw):
        super().__init__(*a, **kw)
        self._pages = []
        self._pn = 0

    def showPage(self):
        self._pn += 1
        self._pages.append(dict(self.__dict__))
        self._startPage()

    def save(self):
        n = len(self._pages)
        for i, st in enumerate(self._pages):
            self.__dict__.update(st)
            self._draw_footer(i+1, n)
            canvas.Canvas.showPage(self)
        canvas.Canvas.save(self)

    def _draw_footer(self, pn, total):
        self.setFont("Helvetica", 7.5)
        self.setFillColor(MID_GRAY)
        self.drawString(2*cm, 1.1*cm, "Vet Biochemistry — Complete Answers | Q.5, Q.6, Q.7")
        self.drawRightString(W-2*cm, 1.1*cm, f"Page {pn} of {total}")
        self.setStrokeColor(LIGHT_BLUE)
        self.setLineWidth(0.5)
        self.line(2*cm, 1.4*cm, W-2*cm, 1.4*cm)

# ═════════════════════════════════════════════════════════════════
#  BUILD STORY
# ═════════════════════════════════════════════════════════════════
story = []

# ── COVER ────────────────────────────────────────────────────────
story += [sp(3)]
story.append(Paragraph("VET BIOCHEMISTRY", TITLE_S))
story.append(Paragraph("Complete Exam Answers with Diagrams", SUB_S))
story += [sp(0.3)]
story.append(HRFlowable(width="55%", thickness=2.5, color=GOLD, hAlign="CENTER",
                         spaceBefore=4, spaceAfter=4))
story += [sp(0.3)]
story.append(Paragraph("Q.No.5 &nbsp;|&nbsp; Q.No.6 &nbsp;|&nbsp; Q.No.7", SUB_S))
story += [sp(0.5)]

cover_rows = [
    ("Q.5", "Definitions (2 × 5 = 10 marks)",
     "Intermediary Metabolism • Turnover Number • Specific Activity • Coenzymes • Oxidative Phosphorylation"),
    ("Q.6", "Short Notes — Any Two (2.5 × 2 = 5 marks)",
     "Cori Cycle • Deamination of Amino Acids • Effects of Temperature & pH on Enzyme Activity"),
    ("Q.7", "Brief Descriptions — Any Three (5 × 3 = 15 marks)",
     "β-Oxidation • TCA Cycle • Glycogenolysis • Enzyme-Substrate Complex Formation"),
]
for qn, title, topics in cover_rows:
    story.append(Table([[
        Paragraph(f"<b>{qn}</b>", PS("Normal", fontSize=11, textColor=colors.white,
                                      fontName="Helvetica-Bold", alignment=TA_CENTER)),
        [Paragraph(f"<b>{title}</b>", PS("Normal", fontSize=10, textColor=DARK_BLUE,
                                          fontName="Helvetica-Bold")),
         Paragraph(topics, PS("Normal", fontSize=8.5, textColor=MID_GRAY,
                               fontName="Helvetica-Oblique"))]
    ]], colWidths=[1.8*cm, W-5.8*cm],
        style=TableStyle([
            ("BACKGROUND",    (0,0),(0,-1), MED_BLUE),
            ("BACKGROUND",    (1,0),(1,-1), LIGHT_GRAY),
            ("BOX",           (0,0),(-1,-1), 1, MED_BLUE),
            ("TOPPADDING",    (0,0),(-1,-1), 8),
            ("BOTTOMPADDING", (0,0),(-1,-1), 8),
            ("LEFTPADDING",   (0,0),(-1,-1), 8),
            ("VALIGN",        (0,0),(-1,-1), "MIDDLE"),
        ])))
    story.append(sp(0.15))

story += [sp(1)]
story.append(Paragraph("Sources: Lippincott Illustrated Reviews Biochemistry 8e • Harper's Illustrated "
                        "Biochemistry 32e • Basic Medical Biochemistry 6e • Guyton &amp; Hall Physiology",
                        DATE_S))
story.append(pb())

# ═════════════════════════════════════════════════════════════════
#  Q.No.5  —  DEFINITIONS
# ═════════════════════════════════════════════════════════════════
story.append(q_banner("Q.No.5   Define the following                          (2 × 5 = 10 marks)", DARK_BLUE))
story += [sp(0.3)]

# ── i. Intermediary Metabolism ────────────────────────────────────
story.append(ANS_HEAD_S and Paragraph("<b>i. &nbsp; Intermediary Metabolism</b>", ANS_HEAD_S))
story.append(def_box("Intermediary Metabolism",
    "The totality of chemical reactions occurring in living cells that involve the "
    "breakdown (catabolism) and synthesis (anabolism) of molecules, and the "
    "interconversion of metabolic intermediates linking carbohydrate, lipid, and "
    "amino acid metabolism."))
story += [sp(0.15)]
story.append(Paragraph(
    "Intermediary metabolism refers to the reactions that connect the major metabolic pathways. "
    "It is the 'metabolic crossroads' of the cell.", BODY_S))
story.append(Paragraph("<b>Key features:</b>", SUBHEAD_S))
for pt in [
    "Occurs in all living cells; regulated by enzyme phosphorylation, allosteric control, and hormones",
    "Central hub = <b>Acetyl-CoA</b>, which links glycolysis, fatty acid oxidation, and amino acid catabolism",
    "Key intermediates: Pyruvate, Acetyl-CoA, Oxaloacetate, Glucose-6-phosphate, α-Ketoglutarate",
    "Pathways are interconvertible: Glucose → Fatty acids; Amino acid carbons → TCA cycle intermediates",
    "<b>Vet note:</b> In ruminants, intermediary metabolism revolves around propionate (from rumen fermentation) → gluconeogenesis, rather than dietary glucose as in monogastrics",
]:
    story.append(Paragraph(f"• {pt}", BULLET_S))
story += [sp(0.3)]
story.append(hr())

# ── ii. Turnover Number ───────────────────────────────────────────
story.append(Paragraph("<b>ii. &nbsp; Turnover Number (k<sub>cat</sub>)</b>", ANS_HEAD_S))
story.append(def_box("Turnover Number (kcat)",
    "The number of substrate molecules converted to product per enzyme molecule "
    "(or per active site) per unit time (per second), when the enzyme is fully "
    "saturated with substrate at Vmax."))
story += [sp(0.15)]
story.append(Paragraph("<b>Formula:</b>", SUBHEAD_S))
story.append(Paragraph("k<sub>cat</sub> = V<sub>max</sub> / [E<sub>t</sub>]     "
                        "(where E<sub>t</sub> = total enzyme concentration)", FORMULA_S))
story.append(Paragraph("k<sub>cat</sub> = V<sub>max</sub> / S<sub>t</sub>     "
                        "(where S<sub>t</sub> = total active sites)", FORMULA_S))
story += [sp(0.1)]
story.append(make_table(
    ["Parameter", "Value / Detail"],
    [
        ["Units", "reactions per second (s⁻¹) or per minute (min⁻¹)"],
        ["Typical range (mammalian enzymes)", "10² to 10⁴ s⁻¹"],
        ["Carbonic anhydrase (fastest)", "~4 × 10⁵ s⁻¹ — one of the fastest known enzymes"],
        ["Lysozyme (slowest common)", "~0.5 s⁻¹ (2 seconds per reaction)"],
        ["Acetylcholinesterase", "~14,000 s⁻¹"],
        ["Catalytic efficiency", "kcat / Km — best measure of enzyme performance"],
        ["Diffusion-limited enzymes", "kcat/Km approaches 10⁸–10¹⁰ M⁻¹s⁻¹ (catalytically perfect)"],
    ],
    col_widths=[7*cm, 9*cm]
))
story += [sp(0.15)]
story.append(vet_box("Turnover Number",
    "Organophosphate poisoning in cattle, dogs, sheep: OP compounds covalently inhibit "
    "acetylcholinesterase (AChE), reducing its effective kcat to near zero → ACh accumulates "
    "→ SLUD syndrome. Treatment: Pralidoxime (2-PAM) reactivates AChE if given early",
    "Measuring kcat helps evaluate enzyme deficiencies in Glycogen Storage Diseases "
    "(e.g., low phosphorylase kcat in GSD Type V — McArdle disease in horses/dogs)",
))
story += [sp(0.3)]
story.append(hr())

# ── iii. Specific Activity ────────────────────────────────────────
story.append(Paragraph("<b>iii. &nbsp; Specific Activity</b>", ANS_HEAD_S))
story.append(def_box("Specific Activity",
    "The enzyme activity (units of catalytic activity) per milligram of total protein "
    "in a preparation. It is a measure of enzyme purity — the higher the specific "
    "activity, the purer the enzyme."))
story += [sp(0.15)]
story.append(Paragraph("<b>Formula:</b>", SUBHEAD_S))
story.append(Paragraph("Specific Activity = V<sub>max</sub> (or enzyme units) / mg total protein",
                        FORMULA_S))
story.append(Paragraph("<b>Units:</b> μmol substrate/min/mg protein &nbsp; OR &nbsp; U/mg &nbsp; OR &nbsp; nmol/min/mg",
                        FORMULA_S))
story += [sp(0.1)]
story.append(make_table(
    ["Term", "Formula", "Meaning"],
    [
        ["Total Activity", "Units × total volume (mL)", "Total enzyme present in whole preparation"],
        ["Specific Activity", "Units / mg total protein", "Purity indicator — rises as enzyme is purified"],
        ["Turnover Number", "Vmax / [Et]", "Speed of catalysis by pure enzyme"],
        ["Pure enzyme", "Highest possible specific activity", "All protein present is the enzyme of interest"],
    ],
    col_widths=[4.5*cm, 5.5*cm, 6*cm]
))
story += [sp(0.15)]
story.append(Paragraph("<b>Purification steps and specific activity:</b>", SUBHEAD_S))
story.append(Paragraph(
    "As enzyme is purified (e.g., ammonium sulfate precipitation → dialysis → "
    "ion-exchange chromatography → affinity chromatography), total protein decreases "
    "while enzyme activity is preserved → specific activity increases progressively.",
    BODY_S))
story.append(vet_box("Specific Activity",
    "Clinical enzyme assays in vet diagnostics (ALT, AST, ALP, CK, LDH, GGT, GDH) are "
    "reported in U/L (units per litre of serum) — analogous to specific activity",
    "Elevated ALT specific activity in dogs/cats → hepatocyte damage (hepatitis, lipidosis, toxins)",
    "Elevated CK (creatine kinase) → muscle damage in horses (tying-up), cattle, dogs",
    "GDH most specific for hepatocellular necrosis in ruminants (cattle, sheep)",
))
story += [sp(0.3)]
story.append(hr())

# ── iv. Coenzymes ─────────────────────────────────────────────────
story.append(Paragraph("<b>iv. &nbsp; Coenzymes</b>", ANS_HEAD_S))
story.append(def_box("Coenzymes",
    "Small, nonprotein organic molecules that associate with certain enzymes and are "
    "essential for their catalytic activity. They act as carriers of specific chemical "
    "groups, electrons, hydrogen atoms, or atoms from one reaction to another."))
story += [sp(0.15)]
story.append(Paragraph("<b>Key terminology:</b>", SUBHEAD_S))
story.append(make_table(
    ["Term", "Definition"],
    [
        ["Apoenzyme", "Inactive protein portion of an enzyme alone (without cofactor)"],
        ["Cofactor", "Nonprotein component required for activity (metal ion OR organic molecule)"],
        ["Holoenzyme", "Apoenzyme + Cofactor = ACTIVE, functional enzyme"],
        ["Coenzyme", "Small organic cofactor; transiently associated; dissociates after reaction (e.g., NAD⁺)"],
        ["Prosthetic group", "Coenzyme permanently/covalently bound to enzyme (e.g., FAD, biotin)"],
    ],
    col_widths=[4.5*cm, 11.5*cm]
))
story += [sp(0.2)]
story.append(Paragraph("<b>Classification of coenzymes:</b>", SUBHEAD_S))
story.append(make_table(
    ["Coenzyme", "Derived from", "Function", "Example enzyme"],
    [
        ["NAD⁺/NADH", "Niacin (Vit B3)", "Oxidation-reduction (electron carrier)", "LDH, GDH, Malate DH"],
        ["FAD/FADH₂", "Riboflavin (Vit B2)", "Oxidation-reduction (electron carrier)", "Succinate DH, Acyl-CoA DH"],
        ["NADP⁺/NADPH", "Niacin (Vit B3)", "Anabolic redox reactions", "G6P-DH, Fatty acid synthase"],
        ["Coenzyme A (CoA)", "Pantothenic acid (Vit B5)", "Acyl group transfer", "Citrate synthase, Thiolase"],
        ["Thiamin PPi (TPP)", "Thiamin (Vit B1)", "Aldehyde/ketone transfer; decarboxylation", "Pyruvate DH, α-KG DH"],
        ["Pyridoxal phosphate (PLP)", "Pyridoxine (Vit B6)", "Amino group transfer (transamination)", "ALT, AST"],
        ["Biotin", "Biotin (Vit B7)", "CO₂ transfer (carboxylation)", "Pyruvate carboxylase"],
        ["Tetrahydrofolate (THF)", "Folic acid (Vit B9)", "One-carbon group transfer", "Thymidylate synthase"],
        ["Cobalamin (Vit B12)", "Cobalamin", "Methyl group transfer; rearrangements", "Methylmalonyl-CoA mutase"],
    ],
    col_widths=[3.8*cm, 3.2*cm, 4.5*cm, 4.5*cm]
))
story += [sp(0.15)]
story.append(vet_box("Coenzymes",
    "Thiamin (Vit B1 / TPP) deficiency in ruminants → Polioencephalomalacia (PEM / "
    "cerebrocortical necrosis): Pyruvate DH and α-KG DH require TPP → blocked → "
    "brain energy failure → blindness, opisthotonus, seizures. Treat: IV thiamin",
    "Riboflavin (Vit B2 / FAD) deficiency: Rare but causes dermatitis, peripheral "
    "neuropathy in poultry; reduced β-oxidation and TCA cycle activity",
    "Niacin (Vit B3 / NAD⁺) deficiency: 'Black tongue' in dogs (= pellagra equivalent); "
    "Tryptophan can be converted to niacin in liver (cats cannot do this efficiently)",
    "Vit B12 (cobalamin) deficiency in cobalt-deficient pastures: Methylmalonyl-CoA "
    "mutase impaired → propionate metabolism blocked in ruminants → 'pine' disease in sheep",
))
story += [sp(0.3)]
story.append(hr())

# ── v. Oxidative Phosphorylation ──────────────────────────────────
story.append(Paragraph("<b>v. &nbsp; Oxidative Phosphorylation</b>", ANS_HEAD_S))
story.append(def_box("Oxidative Phosphorylation (OXPHOS)",
    "The metabolic process by which ATP is synthesised from ADP and inorganic phosphate (Pi), "
    "driven by the energy released during the transfer of electrons along the mitochondrial "
    "electron transport chain (ETC) to molecular oxygen, coupled to the pumping of protons "
    "across the inner mitochondrial membrane (Mitchell's Chemiosmotic Theory)."))
story += [sp(0.2)]
story.append(Paragraph("<b>Diagram — Oxidative Phosphorylation:</b>", SUBHEAD_S))
story.append(get_img("oxphos.png", max_w_cm=15, max_h_cm=13))
story.append(Paragraph(
    "Fig. Oxidative Phosphorylation — ETC Complexes I–IV pump H⁺ from matrix to "
    "intermembrane space; H⁺ re-enters via ATP synthase (Complex V) → ATP synthesis. "
    "Source: Lippincott Illustrated Reviews Biochemistry 8e", CAPTION_S))
story += [sp(0.1)]
story.append(make_table(
    ["ETC Complex", "Name", "Inhibitor (Vet toxicology)"],
    [
        ["Complex I",  "NADH-CoQ reductase",      "Rotenone (insecticide; toxic to fish, cats)"],
        ["Complex II", "Succinate-CoQ reductase",  "Malonate (competitive inhibitor)"],
        ["Complex III","CoQ-Cyt c reductase",      "Antimycin A"],
        ["Complex IV", "Cytochrome c oxidase",     "Cyanide (CN⁻), Carbon monoxide (CO), Azide"],
        ["Complex V",  "ATP synthase (F₀F₁)",      "Oligomycin (blocks F₀ proton channel)"],
        ["Uncouplers", "Dissipate H⁺ gradient → heat instead of ATP",
         "DNP (2,4-dinitrophenol); Thermogenin/UCP1 in neonatal brown fat"],
    ],
    col_widths=[2.5*cm, 5.5*cm, 8*cm]
))
story += [sp(0.15)]
story.append(vet_box("Oxidative Phosphorylation",
    "Cyanide toxicity (cattle/horses from sorghum, sudangrass, wild cherry): CN⁻ blocks "
    "Complex IV → OXPHOS stops → bright red venous blood (oxyHb cannot unload O₂ as cells "
    "cannot use it). Rx: Sodium nitrite + sodium thiosulphate",
    "CO poisoning (barn fires, faulty heaters): Blocks Complex IV AND binds haemoglobin "
    "→ dual impairment. Animals found dead or unconscious",
    "Thermogenin (UCP1) in neonatal lambs, piglets, foals, calves: Uncouples OXPHOS "
    "→ heat generation for thermoregulation at birth. Hypothermic neonates lack this reserve",
    "ATP yield: NADH → 2.5 ATP; FADH₂ → 1.5 ATP; 1 glucose → ~30–32 ATP total",
))
story.append(pb())

# ═════════════════════════════════════════════════════════════════
#  Q.No.6  —  SHORT NOTES
# ═════════════════════════════════════════════════════════════════
story.append(q_banner("Q.No.6   Write short notes on Any TWO               (2.5 × 2 = 5 marks)", MED_BLUE))
story += [sp(0.3)]

# ── 1. Cori Cycle ─────────────────────────────────────────────────
story.append(Paragraph("<b>1. &nbsp; Cori Cycle — Diagrammatic Representation</b>", ANS_HEAD_S))
story.append(def_box("Cori Cycle (Lactic Acid Cycle)",
    "The metabolic cycle in which lactate produced by anaerobic glycolysis in peripheral "
    "tissues (muscle, RBCs) is transported to the liver, reconverted to glucose by "
    "gluconeogenesis, and returned to the blood — completing the cycle."))
story += [sp(0.2)]
story.append(get_img("cori_cycle.png", max_w_cm=14, max_h_cm=10))
story.append(Paragraph(
    "Fig. Cori Cycle — RBCs/Muscle: Glucose → Glycolysis → 2 Lactate (+ 2 ATP); "
    "Blood carries lactate to Liver: Lactate → Gluconeogenesis → Glucose (uses 6 ATP). "
    "Source: Basic Medical Biochemistry 6e, Fig. 22.12", CAPTION_S))
story += [sp(0.1)]
story.append(Paragraph("<b>Steps:</b>", SUBHEAD_S))
for step in [
    "<b>1.</b> Glucose delivered from liver via blood to muscle/RBC",
    "<b>2.</b> Anaerobic glycolysis in muscle/RBC: Glucose → Pyruvate → Lactate (LDH, uses NADH)",
    "<b>3.</b> Lactate transported via blood to <b>liver</b>",
    "<b>4.</b> In liver: Lactate → Pyruvate (LDH, NAD⁺ used) → Glucose (gluconeogenesis — needs 6 ATP)",
    "<b>5.</b> New glucose released back into blood → cycle repeats",
]:
    story.append(Paragraph(step, BULLET_S))
story += [sp(0.1)]
story.append(make_table(
    ["Feature", "Muscle/RBC", "Liver"],
    [
        ["Process", "Anaerobic glycolysis", "Gluconeogenesis"],
        ["ATP", "+2 ATP produced", "−6 ATP consumed"],
        ["Key enzyme", "LDH (Lactate DH)", "LDH + PEPCK, FBPase, G6Pase"],
        ["Net for cycle", "—", "Net energy cost = 4 ATP"],
    ],
    col_widths=[5*cm, 5.5*cm, 5.5*cm]
))
story.append(vet_box("Cori Cycle",
    "Exercising horses/greyhounds: Massive lactate production → Cori cycle recycles it",
    "Capture myopathy: Overwhelmed Cori cycle → fatal lactic acidosis in wild animals",
    "Neonatal asphyxia in calves (dystocia): Anaerobic metabolism → elevated blood lactate; Rx: IV glucose + NaHCO₃",
))
story += [sp(0.3)]
story.append(hr())

# ── 2. Deamination Reactions ──────────────────────────────────────
story.append(Paragraph("<b>2. &nbsp; Deamination Reactions of Amino Acids</b>", ANS_HEAD_S))
story.append(def_box("Deamination",
    "The removal of the amino (−NH₂) group from an amino acid, resulting in production "
    "of an α-keto acid and release of nitrogen, chiefly as ammonia (NH₃)."))
story += [sp(0.2)]
story.append(Paragraph("<b>Step 1 — Transamination (ALT &amp; AST reactions):</b>", SUBHEAD_S))
story.append(get_img("transamination.png", max_w_cm=9, max_h_cm=8))
story.append(Paragraph(
    "Fig. A: ALT — Alanine + α-KG → Pyruvate + Glutamate (coenzyme: PLP/Vit B6). "
    "B: AST — Aspartate + α-KG ↔ OAA + Glutamate (coenzyme: PLP). "
    "Source: Lippincott Biochemistry 8e, Fig. 19.8", CAPTION_S))
story += [sp(0.15)]
story.append(Paragraph("<b>Step 2 — Oxidative Deamination (Glutamate Dehydrogenase):</b>", SUBHEAD_S))
story.append(get_img("oxidative_deamination.png", max_w_cm=10, max_h_cm=9))
story.append(Paragraph(
    "Fig. Panel A: Disposal — NH₂ groups → Transamination → Glutamate → Oxidative "
    "Deamination (GDH + NAD⁺) → free NH₃ + NADH + α-KG. "
    "Panel B: Synthesis — Reverse via Reductive Amination (GDH + NADPH). "
    "Source: Lippincott Biochemistry 8e, Fig. 19.12", CAPTION_S))
story += [sp(0.1)]
story.append(make_table(
    ["Type", "Enzyme", "Coenzyme", "Products"],
    [
        ["Transamination", "ALT (SGPT), AST (SGOT)", "PLP (Vit B6)", "α-Keto acid + Glutamate"],
        ["Oxidative deamination", "Glutamate DH (GDH)", "NAD⁺ (catabolism)", "α-KG + NH₃ + NADH"],
        ["Non-oxidative deamination", "Serine dehydratase", "PLP", "Pyruvate + NH₃ (Serine)"],
        ["D-amino acid oxidase (DAO)", "DAO (peroxisomal, FAD-dep.)", "FAD", "α-Keto acid + NH₃ + H₂O₂"],
    ],
    col_widths=[4*cm, 4.5*cm, 3.5*cm, 4*cm]
))
story += [sp(0.1)]
story.append(Paragraph(
    "<b>Fate of NH₃:</b> Toxic → rapidly converted to <b>Urea</b> (liver urea cycle) "
    "for safe excretion. In birds/reptiles → uric acid.", BODY_S))
story.append(vet_box("Deamination",
    "ALT (SGPT): Liver-specific in dogs & cats. Reference range dog: 10–100 U/L. "
    "Elevated in hepatitis, hepatic lipidosis, aflatoxin/xylitol toxicity",
    "AST (SGOT): Elevated in both liver AND muscle disease in horses & ruminants. "
    "Always interpret alongside CK to differentiate source",
    "GDH: Best hepatocellular marker in cattle/sheep — elevated in ragwort toxicity, "
    "aflatoxicosis; hepatic encephalopathy when NH₃ accumulates",
))
story.append(pb())

# ── 3. Temperature and pH effects ────────────────────────────────
story.append(q_banner("Q.No.6 continued", MED_BLUE))
story += [sp(0.3)]
story.append(Paragraph("<b>3. &nbsp; Effects of Temperature and pH on Enzyme Activity</b>", ANS_HEAD_S))
story += [sp(0.2)]
story.append(get_img("temp_ph.png", max_w_cm=15, max_h_cm=9))
story.append(Paragraph(
    "Fig. Left: Effect of temperature — bell-shaped curve; optimum 37–40°C for mammalian enzymes; "
    "above optimum → denaturation. Right: Effect of pH — different enzymes have different "
    "optima (Pepsin pH 2; Salivary amylase pH 6.8; Trypsin pH 7.5–8).", CAPTION_S))
story += [sp(0.2)]
story.append(Paragraph("<b>A. Effect of Temperature:</b>", SUBHEAD_S))
story.append(make_table(
    ["Phase", "Mechanism", "Effect on Activity"],
    [
        ["Rising (below optimum)", "↑ kinetic energy → more frequent enzyme-substrate collisions; Q₁₀ = 2 (rate doubles per 10°C rise)",
         "Activity increases"],
        ["Optimum (~37–40°C)", "Maximum collision frequency + enzyme still properly folded",
         "Maximum activity"],
        ["Above optimum (>40–42°C)", "Heat breaks H-bonds, disrupts hydrophobic interactions → protein denaturation → active site lost",
         "Rapid, often irreversible decrease"],
    ],
    col_widths=[3.5*cm, 8.5*cm, 4*cm]
))
story += [sp(0.2)]
story.append(Paragraph("<b>B. Effect of pH:</b>", SUBHEAD_S))
story.append(make_table(
    ["Enzyme", "Optimum pH", "Location"],
    [
        ["Pepsin",                  "~2.0",    "Stomach (monogastrics — dog, cat, pig, horse)"],
        ["Salivary amylase",        "6.8–7.0", "Oral cavity (absent in cats; present in dogs, horses)"],
        ["Trypsin / Chymotrypsin",  "7.5–8.0", "Pancreas → small intestine (all species)"],
        ["Alkaline Phosphatase (ALP)", "9–10", "Bone, liver, intestinal mucosa"],
        ["Arginase",                "~9.5",    "Liver (urea cycle)"],
        ["Acid Phosphatase",        "~5.0",    "Lysosomes, prostate"],
        ["Rumen cellulases",        "6.2–6.8", "Rumen microbiota — cellulose digestion in cattle/sheep"],
    ],
    col_widths=[5*cm, 2.5*cm, 8.5*cm]
))
story += [sp(0.1)]
story.append(Paragraph(
    "<b>Why pH affects activity:</b> Changes ionisation state of active site amino acids "
    "(His, Asp, Glu, Lys, Cys) → alters substrate binding and catalytic mechanism. "
    "Extreme pH denatures the enzyme by breaking ionic bonds and H-bonds.", BODY_S))
story.append(vet_box("Temperature & pH Effects",
    "Rumen acidosis (grain overload) in cattle/sheep: pH 4.5–5.5 → inactivates cellulolytic "
    "enzymes → bloat, ataxia, death. Rx: NaHCO₃ + rumen transfaunation",
    "Heat stroke in brachycephalic dogs (Bulldogs, Pugs) and horses: Core temp >42°C → "
    "enzyme denaturation → multi-organ failure. Immediate cooling is life-saving",
    "Pancreatitis in dogs/cats: Premature trypsinogen activation at wrong pH within "
    "pancreas → autodigestion → acute abdomen, peritonitis",
    "Hypothermia in neonatal piglets/lambs in cold: Metabolic enzyme activity halved → "
    "hypoglycaemia, failure to thrive. Provide supplemental heat and colostrum",
    "Clinical assay quality control: ALT, ALP, CK assays run at 37°C in phosphate buffer "
    "(pH 7.4) for accurate results",
))
story.append(pb())

# ═════════════════════════════════════════════════════════════════
#  Q.No.7  —  BRIEF DESCRIPTIONS
# ═════════════════════════════════════════════════════════════════
story.append(q_banner("Q.No.7   Describe briefly Any THREE                (5 × 3 = 15 marks)", DARK_GREEN))
story += [sp(0.3)]

# ── 1. Beta Oxidation ─────────────────────────────────────────────
story.append(Paragraph("<b>1. &nbsp; Steps of β-Oxidation of Fatty Acids</b>", ANS_HEAD_S))
story.append(def_box("β-Oxidation",
    "The stepwise degradation of fatty acids in the mitochondrial matrix by sequential "
    "removal of 2-carbon acetyl-CoA units, producing NADH and FADH₂ per cycle, "
    "with the acetyl-CoA entering the TCA cycle for complete oxidation."))
story += [sp(0.15)]
story.append(Paragraph("<b>Pre-steps: Activation and Transport</b>", SUBHEAD_S))
story.append(Paragraph(
    "<b>Step 0a — Activation (cytoplasm / outer mitochondrial membrane):</b>", BODY_S))
story.append(Paragraph(
    "Fatty acid + CoA + ATP  ──[Acyl-CoA synthetase/Thiokinase]──▶  "
    "Fatty acyl-CoA + AMP + PPi  (costs 2 ATP equivalents)", FORMULA_S))
story.append(Paragraph(
    "<b>Step 0b — Carnitine shuttle (transport across inner mitochondrial membrane):</b>", BODY_S))
for pt in [
    "Long-chain acyl-CoA cannot cross inner mitochondrial membrane alone",
    "Transferred to <b>carnitine</b> by CPT-I (carnitine palmitoyltransferase-I) on outer membrane → acylcarnitine",
    "Acylcarnitine crosses via <b>CACT</b> (carnitine-acylcarnitine translocase)",
    "Reconverted to acyl-CoA inside by CPT-II; free carnitine returns",
]:
    story.append(Paragraph(f"• {pt}", BULLET_S))
story += [sp(0.2)]
story.append(Paragraph("<b>The 4 Repeating Steps of β-Oxidation:</b>", SUBHEAD_S))
story.append(get_img("beta_oxidation_pathway.png", max_w_cm=9, max_h_cm=13))
story.append(Paragraph(
    "Fig. β-Oxidation pathway: activation → carnitine transport → 4-step repeating cycle "
    "→ Acetyl-CoA → TCA cycle → 2CO₂. Each cycle shortens fatty acid chain by 2C. "
    "Source: Harper's Illustrated Biochemistry 32e, Fig. 22-3", CAPTION_S))
story += [sp(0.15)]
story.append(get_img("beta_oxidation_equations.png", max_w_cm=15, max_h_cm=5))
story.append(Paragraph(
    "Fig. Chemical equations for each step: (1) Activation; (2) FAD-oxidation → FADH₂; "
    "(3) Hydration → β-hydroxy intermediate; (4) NAD⁺-oxidation → NADH; "
    "(5) Thiolysis → Acetyl-CoA. Source: Guyton & Hall Medical Physiology, Fig. 69.3",
    CAPTION_S))
story += [sp(0.1)]
story.append(make_table(
    ["Step", "Enzyme", "Cofactor", "Product"],
    [
        ["1. FAD-dependent oxidation", "Acyl-CoA dehydrogenase",     "FAD",  "trans-Δ²-Enoyl-CoA + FADH₂"],
        ["2. Hydration",               "Enoyl-CoA hydratase",         "H₂O",  "L-3-Hydroxyacyl-CoA"],
        ["3. NAD⁺-dependent oxidation","L-3-Hydroxyacyl-CoA DH",     "NAD⁺", "3-Ketoacyl-CoA + NADH"],
        ["4. Thiolysis",               "β-Ketothiolase (Thiolase)",   "CoA",  "Acetyl-CoA + (n−2) Acyl-CoA"],
    ],
    col_widths=[4.5*cm, 5*cm, 2*cm, 4.5*cm]
))
story += [sp(0.15)]
story.append(Paragraph("<b>Energy yield for Palmitate (C16):</b>", SUBHEAD_S))
story.append(make_table(
    ["Stage", "Moles formed", "ATP per mole", "Total ATP"],
    [
        ["Activation (cost)", "—", "−2", "−2"],
        ["β-Oxidation: FADH₂ (7 cycles)", "7", "× 1.5", "+10.5"],
        ["β-Oxidation: NADH (7 cycles)",  "7", "× 2.5", "+17.5"],
        ["TCA cycle: 8 Acetyl-CoA",       "8", "× 10",  "+80"],
        ["NET TOTAL", "", "", "106 ATP"],
    ],
    col_widths=[7*cm, 3*cm, 3*cm, 3*cm]
))
story.append(vet_box("β-Oxidation",
    "Ketosis/Acetonaemia in dairy cows (periparturient): Negative energy balance → "
    "excess β-oxidation → acetyl-CoA cannot enter TCA (OAA depleted) → ketone bodies "
    "(BOHB, acetoacetate, acetone). Blood BOHB >3 mmol/L = clinical ketosis. "
    "Rx: IV 50% glucose, propylene glycol, dexamethasone",
    "Pregnancy toxaemia in ewes (twin-lamb disease): Same mechanism; high twin fetal "
    "demand depletes ewe's glucose → ketosis → CNS signs, recumbency, death",
    "Feline hepatic lipidosis: Obese cat anorexia → fat mobilisation overwhelms "
    "hepatic β-oxidation → fat accumulation → jaundice, liver failure",
    "CPT-I deficiency: Carnitine shuttle impaired → long-chain FA cannot enter "
    "mitochondria → lipid myopathy + dilated cardiomyopathy (Boxers, Dobermans)",
))
story.append(warn_box("β-Oxidation Exam Points",
    "Activation COSTS 2 high-energy phosphates (ATP → AMP + PPi); NOT just 1 ATP",
    "Odd-chain FA → propionyl-CoA → succinyl-CoA (requires Vit B12) → TCA; glucogenic; "
    "important in ruminants (propionate from rumen fermentation)",
    "Unsaturated FA: Require additional enzymes (isomerase / reductase); yield slightly less ATP",
))
story.append(pb())

# ── 2. TCA Cycle ──────────────────────────────────────────────────
story.append(Paragraph("<b>2. &nbsp; Steps of TCA Cycle including Energy Production</b>", ANS_HEAD_S))
story.append(def_box("TCA Cycle (Krebs / Citric Acid Cycle)",
    "A cyclic series of 8 enzyme-catalysed reactions in the mitochondrial matrix that "
    "completely oxidise acetyl-CoA (2C) to CO₂, capturing energy as NADH (3), "
    "FADH₂ (1), and GTP (1) per turn, yielding ~10 ATP per acetyl-CoA."))
story += [sp(0.2)]
story.append(get_img("tca_cycle.png", max_w_cm=13, max_h_cm=14))
story.append(Paragraph(
    "Fig. Complete TCA (Krebs) Cycle — all 8 steps with enzymes, cofactors, and inhibitor "
    "sites (red lines): Fluoroacetate → blocks Aconitase; Arsenite → blocks α-KG DH complex; "
    "Malonate → competitively inhibits Succinate DH. "
    "Source: Harper's Illustrated Biochemistry 32e, Fig. 16-3", CAPTION_S))
story += [sp(0.15)]
story.append(make_table(
    ["#", "Reaction", "Enzyme", "Cofactors", "Energy"],
    [
        ["1", "OAA (4C) + Acetyl-CoA (2C) → Citrate (6C)", "Citrate synthase", "CoA-SH, H₂O", "—"],
        ["2", "Citrate → cis-Aconitate → Isocitrate (6C)", "Aconitase", "Fe²⁺, H₂O", "—"],
        ["3", "Isocitrate → Oxalosuccinate → α-KG (5C) + CO₂", "Isocitrate dehydrogenase", "NAD⁺, Mn²⁺", "1 NADH"],
        ["4", "α-KG (5C) → Succinyl-CoA (4C) + CO₂", "α-KG dehydrogenase complex", "TPP, Lipoate, FAD, NAD⁺, CoA", "1 NADH"],
        ["5", "Succinyl-CoA → Succinate", "Succinyl-CoA synthetase", "Mg²⁺, GDP/ADP", "1 GTP"],
        ["6", "Succinate → Fumarate", "Succinate dehydrogenase (Complex II)", "FAD", "1 FADH₂"],
        ["7", "Fumarate + H₂O → L-Malate", "Fumarase", "H₂O", "—"],
        ["8", "L-Malate → Oxaloacetate", "Malate dehydrogenase", "NAD⁺", "1 NADH"],
    ],
    col_widths=[0.5*cm, 5.2*cm, 4*cm, 3.3*cm, 1.8*cm]
))
story += [sp(0.15)]
story.append(Paragraph("<b>Energy production per turn of TCA cycle:</b>", SUBHEAD_S))
story.append(make_table(
    ["Product", "Number per turn", "ATP equivalent", "Total ATP"],
    [
        ["NADH (steps 3, 4, 8)", "3", "× 2.5 ATP each", "7.5 ATP"],
        ["FADH₂ (step 6)",       "1", "× 1.5 ATP each", "1.5 ATP"],
        ["GTP (step 5)",         "1", "= 1 ATP",         "1.0 ATP"],
        ["CO₂ released",         "2", "—",               "Metabolic waste"],
        ["TOTAL per turn",       "",  "",                 "~10 ATP"],
    ],
    col_widths=[5.5*cm, 3.5*cm, 3.5*cm, 3.5*cm]
))
story += [sp(0.1)]
story.append(Paragraph("<b>Regulation — Key allosteric enzymes:</b>", SUBHEAD_S))
story.append(make_table(
    ["Enzyme", "Activated by", "Inhibited by"],
    [
        ["Citrate synthase", "ADP, low [NADH], low [Acetyl-CoA]", "ATP, NADH, Succinyl-CoA, Citrate"],
        ["Isocitrate DH",    "ADP, Ca²⁺ (muscle/heart)",          "ATP, NADH"],
        ["α-KG DH complex",  "Ca²⁺, ADP",                         "ATP, NADH, Succinyl-CoA"],
    ],
    col_widths=[5*cm, 5.5*cm, 5.5*cm]
))
story.append(vet_box("TCA Cycle",
    "Ketosis in dairy cows: Negative energy balance → OAA diverted to gluconeogenesis "
    "→ TCA cycle slows → acetyl-CoA excess → ketogenesis. BOHB, acetoacetate, acetone "
    "elevated. 'Sweet/acetone breath' in affected cows",
    "Fluoroacetate (compound 1080) poisoning: Dogs, foxes, native wildlife especially "
    "vulnerable. Fluoroacetate → fluorocitrate → blocks Aconitase (Step 2) → citrate "
    "accumulates → TCA stops → cardiac arrhythmia, seizures, death. No antidote",
    "Thiamin (Vit B1) deficiency: α-KG DH complex requires TPP. Polioencephalomalacia "
    "in cattle/sheep (bracken fern in horses) → brain energy failure → seizures, "
    "blindness. IV thiamin 10–20 mg/kg is curative if given early",
    "Arsenite/arsenic poisoning (old sheep dip vats): Binds lipoate in α-KG DH → TCA "
    "block → energy failure. Chelation with DMSA or BAL",
))
story.append(pb())

# ── 3. Glycogenolysis ─────────────────────────────────────────────
story.append(Paragraph("<b>3. &nbsp; Glycogenolysis</b>", ANS_HEAD_S))
story.append(def_box("Glycogenolysis",
    "The enzymatic degradation of stored glycogen to yield glucose (in liver, for blood "
    "glucose maintenance) or glucose-6-phosphate (in muscle, for ATP synthesis via "
    "glycolysis). It is NOT the reverse of glycogen synthesis."))
story += [sp(0.2)]
story.append(get_img("glycogenolysis.png", max_w_cm=13, max_h_cm=10))
story.append(Paragraph(
    "Fig. Steps in Glycogenolysis: Phosphorylase cleaves α-1,4 bonds → Glucan transferase "
    "moves 3 glucose units to expose branch → Debranching enzyme (α-1,6-glucosidase) "
    "releases free glucose at branch point. Blue circles = α-1,4 linked glucose; "
    "Orange = branch chain glucose; branch point = α-1,6 bond. "
    "Source: Harper's Illustrated Biochemistry 32e, Fig. 18-4", CAPTION_S))
story += [sp(0.15)]
story.append(Paragraph("<b>Steps of Glycogenolysis:</b>", SUBHEAD_S))
story.append(make_table(
    ["Step", "Enzyme", "Bond", "Product"],
    [
        ["1. Chain removal", "Glycogen phosphorylase (PLP cofactor, Vit B6)",
         "Cleaves α-1,4 (phosphorolysis)", "Glucose-1-phosphate"],
        ["2. Branch transfer (debranching)", "Glucan transferase (part of debranching enzyme)",
         "Transfers 3 glucose units to main chain", "Exposed α-1,6 branch"],
        ["3. Branch cleavage", "α-1,6-Glucosidase (debranching enzyme)",
         "Cleaves α-1,6 (hydrolysis)", "Free glucose (only unphosphorylated product!)"],
        ["4. Isomerisation", "Phosphoglucomutase",
         "Isomerisation", "Glucose-6-phosphate"],
        ["5. Liver only", "Glucose-6-phosphatase (ER lumen)",
         "Hydrolysis", "Free glucose → released to blood"],
    ],
    col_widths=[3*cm, 5*cm, 4*cm, 4*cm]
))
story += [sp(0.15)]
story.append(Paragraph("<b>Hormonal Regulation:</b>", SUBHEAD_S))
story.append(Paragraph(
    "Glucagon/Epinephrine → adenylate cyclase → ↑ cAMP → "
    "Protein Kinase A (PKA) → phosphorylates Phosphorylase kinase (active) → "
    "phosphorylates Glycogen phosphorylase b → <b>Phosphorylase a (ACTIVE)</b> → "
    "Glycogenolysis ↑", FORMULA_S))
story += [sp(0.1)]
story.append(make_table(
    ["Signal", "Tissue", "Mechanism", "Result"],
    [
        ["Glucagon (low blood glucose)", "Liver",         "↑cAMP → PKA cascade",        "Glycogenolysis ↑; glucose → blood"],
        ["Epinephrine (stress/exercise)","Liver + Muscle","↑cAMP + Ca²⁺ cascade",        "Glycogenolysis ↑ (fight-or-flight)"],
        ["Ca²⁺ (muscle contraction)",   "Muscle",        "Direct activation of Phos. kinase","Glycogenolysis ↑ during exercise"],
        ["AMP (energy depletion)",       "Muscle",        "Allosteric activation of Phos. b","Glycogenolysis ↑ when ATP low"],
        ["Insulin (fed state)",          "Both",          "Activates phosphatase",        "Glycogenolysis ↓; glycogen synthesis ↑"],
    ],
    col_widths=[4*cm, 2.5*cm, 4*cm, 5.5*cm]
))
story += [sp(0.1)]
story.append(make_table(
    ["Tissue", "Final product", "Fate"],
    [
        ["Liver",  "Free glucose (via Glucose-6-phosphatase)", "Released to blood → maintains blood glucose ~80 mg/dL"],
        ["Muscle", "Glucose-6-phosphate (NO G-6-Pase)", "Enters glycolysis → ATP for muscle contraction"],
    ],
    col_widths=[2.5*cm, 6*cm, 7.5*cm]
))
story.append(vet_box("Glycogenolysis",
    "Neonatal hypoglycaemia (piglets, lambs, foals): After birth cord is clamped → "
    "epinephrine + glucagon activate hepatic glycogenolysis to restore blood glucose. "
    "Neonates with limited stores → fatal hypoglycaemia within hours. Rx: Oral/IV glucose",
    "GSD Type II (Pompe disease) in Brahman cattle: Acid maltase deficiency → glycogen "
    "accumulates in muscle/heart → cardiomyopathy, progressive muscle weakness",
    "GSD Type III (Debranching enzyme deficiency) in German Shepherds: Cannot debranch "
    "→ glycogen accumulates → hypoglycaemia + hepatomegaly",
    "Capture myopathy in deer, zebra, kangaroo: Epinephrine surge → rapid glycogenolysis "
    "+ lactate accumulation → muscle necrosis → fatal rhabdomyolysis",
    "Diabetes mellitus in dogs/cats: Glucagon dominance → uncontrolled glycogenolysis "
    "→ hyperglycaemia despite adequate glucose. Insulin therapy required",
))
story.append(pb())

# ── 4. Enzyme-Substrate Complex Formation ────────────────────────
story.append(Paragraph("<b>4. &nbsp; Enzyme-Substrate Complex Formation</b>", ANS_HEAD_S))
story.append(def_box("Enzyme-Substrate (ES) Complex",
    "The transient non-covalent molecular complex formed when a substrate molecule "
    "binds to the specific active site of an enzyme, preceding catalytic conversion "
    "to product. General equation: E + S ⇌ ES → E + P"))
story += [sp(0.2)]
story.append(Paragraph("<b>Nature of the Active Site:</b>", SUBHEAD_S))
for pt in [
    "A 3-dimensional cleft or pocket formed by a small number of specific amino acid residues",
    "Contains a <b>binding site</b> (holds substrate in correct orientation) and a <b>catalytic site</b> (performs chemical transformation)",
    "Key residues: Ser, His, Asp, Cys, Lys, Glu — vary by enzyme type",
    "Represents only ~10–15% of total enzyme surface area",
]:
    story.append(Paragraph(f"• {pt}", BULLET_S))
story += [sp(0.15)]
story.append(Paragraph("<b>Active site H-bond interactions (basis of substrate specificity):</b>",
                        SUBHEAD_S))
story.append(get_img("es_hbonds.png", max_w_cm=11, max_h_cm=8))
story.append(Paragraph(
    "Fig. Glucose binding site in glucokinase — each -OH of glucose (red) is held by "
    "multiple H-bonds (dashed lines) to specific amino acid residues: Asp-205, Asn-204, "
    "Asn-231, Glu-256, Glu-290, Gly-229. Panel B: Galactose (one -OH differs) is NOT "
    "phosphorylated — demonstrates exquisite enzyme specificity. "
    "Source: Basic Medical Biochemistry 6e, Fig. 8.5", CAPTION_S))
story += [sp(0.15)]
story.append(Paragraph("<b>Two Models of ES Complex Formation:</b>", SUBHEAD_S))
story.append(make_table(
    ["Model", "Proposed", "Key Concept", "Status"],
    [
        ["Lock and Key", "Emil Fischer, 1894",
         "Enzyme has rigid, pre-formed active site; substrate fits exactly like key in lock; "
         "no conformational change occurs",
         "Outdated — cannot explain enzyme flexibility or allosteric effects"],
        ["Induced Fit", "Daniel Koshland, 1958",
         "Substrate binding induces conformational change in enzyme; active site cleft "
         "closes around substrate; improves co-substrate binding; excludes water from active site",
         "Currently accepted model"],
    ],
    col_widths=[2.5*cm, 2.5*cm, 7*cm, 4*cm]
))
story += [sp(0.15)]
story.append(Paragraph("<b>Induced Fit — Before and After substrate binding:</b>", SUBHEAD_S))
before = get_img("es_before.png", max_w_cm=7.2, max_h_cm=7)
after  = get_img("es_after.png",  max_w_cm=7.2, max_h_cm=7)
side = Table([[before, after]], colWidths=[8.2*cm, 8.2*cm])
side.setStyle(TableStyle([
    ("ALIGN",         (0,0),(-1,-1), "CENTER"),
    ("VALIGN",        (0,0),(-1,-1), "MIDDLE"),
    ("LEFTPADDING",   (0,0),(-1,-1), 3),
    ("RIGHTPADDING",  (0,0),(-1,-1), 3),
]))
story.append(side)
story.append(Paragraph(
    "Fig. Left (Before): Glucokinase in open conformation; D-glucose (red) approaching. "
    "Right (After): Cleft closes completely around glucose = Induced Fit. Conformational "
    "change improves ATP binding site and excludes water. "
    "Source: Basic Medical Biochemistry 6e, Fig. 8.6", CAPTION_S))
story += [sp(0.1)]
story.append(Paragraph("<b>Forces stabilising the ES complex:</b>", SUBHEAD_S))
story.append(make_table(
    ["Force", "Description"],
    [
        ["Hydrogen bonds",          "Between -OH, -NH₂ of substrate and enzyme Asp, Asn, Glu, Gly residues"],
        ["Electrostatic/ionic",     "Charged groups on substrate ↔ oppositely charged enzyme residues"],
        ["Hydrophobic interactions","Nonpolar substrate regions fit into hydrophobic pockets in active site"],
        ["Van der Waals forces",    "Short-range attractive forces at very close contact distances"],
        ["Transient covalent bonds","E.g., acyl-enzyme intermediate in serine proteases (trypsin, chymotrypsin)"],
    ],
    col_widths=[4*cm, 12*cm]
))
story += [sp(0.1)]
story.append(Paragraph(
    "<b>Significance of ES complex:</b> Lowers activation energy (Ea) by correctly "
    "orienting substrate and stressing key bonds; explains substrate specificity and "
    "competitive inhibition (inhibitor occupies active site).", BODY_S))
story.append(vet_box("ES Complex",
    "Organophosphate (OP) poisoning (cattle from dips, dogs/cats from sprays): OP forms "
    "covalent bond with Ser in AChE active site → ES complex permanently blocked → "
    "ACh accumulates → SLUD syndrome (salivation, lacrimation, urination, defaecation) + "
    "bradycardia, miosis, seizures, bronchospasm. "
    "Rx: Atropine (competitive ACh blocker) + Pralidoxime/2-PAM (reactivates AChE if early)",
    "Competitive inhibition in vet pharmacy: Allopurinol blocks xanthine oxidase active "
    "site (competitive) → used in Dalmatians for urate urolithiasis",
    "Substrate specificity explained: Glucokinase phosphorylates only glucose (not galactose) "
    "→ basis of galactosaemia in calves (congenital galactose-1-phosphate uridyltransferase deficiency)",
    "Drug-enzyme Km: High Km = weak binding = lower drug efficacy at physiological "
    "substrate concentrations; important for antimicrobial target selection",
))
story.append(pb())

# ── MASTER REVISION TABLE ─────────────────────────────────────────
story.append(q_banner("COMPLETE QUICK REVISION — All Questions Summary", PURPLE))
story += [sp(0.3)]
story.append(make_table(
    ["Question", "Topic", "Key Enzyme(s)", "Key Product(s)", "ATP", "Vet Relevance"],
    [
        ["Q5-i",  "Intermediary metabolism", "All metabolic enzymes",
         "Acetyl-CoA, OAA, α-KG", "—",
         "Ruminant propionate metabolism; ketosis"],
        ["Q5-ii", "Turnover number (kcat)", "Any enzyme",
         "Reactions/sec at Vmax", "—",
         "OP poisoning reduces AChE kcat to zero"],
        ["Q5-iii","Specific activity", "Any enzyme",
         "Units/mg protein", "—",
         "ALT, AST, ALP, CK in serum biochemistry"],
        ["Q5-iv", "Coenzymes", "ALT (PLP), LDH (NAD⁺), Succinate DH (FAD)",
         "Varied (NADH, FADH₂, etc.)", "—",
         "B-vitamin deficiencies; PEM, black tongue, B12 deficiency"],
        ["Q5-v",  "Oxidative phosphorylation", "Complex I–IV + ATP synthase",
         "ATP + H₂O", "30–32 ATP/glucose",
         "Cyanide poisoning; CO toxicity; thermogenin in neonates"],
        ["Q6-1",  "Cori cycle", "LDH, G6Pase", "Glucose ↔ Lactate", "Net −4 ATP",
         "Capture myopathy; exercising horses; neonatal asphyxia"],
        ["Q6-2",  "Deamination", "ALT, AST, GDH, DAO",
         "α-Keto acids + NH₃ → Urea", "+1 NADH (GDH)",
         "Liver enzyme panels in dogs/cats; hepatic encephalopathy"],
        ["Q6-3",  "Temp & pH on enzymes", "All enzymes",
         "Bell-shaped activity curve", "—",
         "Rumen acidosis; heat stroke; pancreatitis; hypothermic neonates"],
        ["Q7-1",  "β-Oxidation", "Acyl-CoA DH, Enoyl hydratase, HADH, Thiolase",
         "Acetyl-CoA + NADH + FADH₂", "106 ATP (C16)",
         "Ketosis in cows/ewes; hepatic lipidosis in cats; CPT deficiency"],
        ["Q7-2",  "TCA cycle", "Citrate synthase, Isocitrate DH, α-KG DH, Succinate DH, Malate DH",
         "3NADH + 1FADH₂ + 1GTP + 2CO₂", "~10 ATP/turn",
         "Acetonaemia; fluoroacetate poisoning; thiamin deficiency"],
        ["Q7-3",  "Glycogenolysis", "Glycogen phosphorylase, Debranching enzyme, G6Pase",
         "Glucose (liver) / G-6-P (muscle)", "None",
         "Neonatal hypoglycaemia; GSD in Brahman cattle; DM in dogs"],
        ["Q7-4",  "ES Complex", "Glucokinase (example)",
         "Transition state complex → Product", "—",
         "OP poisoning; allopurinol in Dalmatians; substrate specificity"],
    ],
    col_widths=[1.2*cm, 3*cm, 4*cm, 3.2*cm, 1.8*cm, 3*cm]
))
story += [sp(0.5)]
story.append(Paragraph(
    "<b>Sources:</b> Lippincott Illustrated Reviews Biochemistry 8e • "
    "Harper's Illustrated Biochemistry 32e • Basic Medical Biochemistry 6e • "
    "Guyton &amp; Hall Textbook of Medical Physiology • Goldman-Cecil Medicine",
    DATE_S))

# ── BUILD ─────────────────────────────────────────────────────────
doc = SimpleDocTemplate(
    OUT_PATH,
    pagesize=A4,
    leftMargin=2*cm, rightMargin=2*cm,
    topMargin=2*cm,  bottomMargin=2.5*cm,
    title="Vet Biochemistry — Complete Exam Answers with Diagrams",
    author="Orris AI",
    subject="Veterinary Biochemistry Q5 Q6 Q7 Complete Answers",
)
doc.build(story, canvasmaker=NC)
print(f"PDF created: {OUT_PATH}")
import os
size = os.path.getsize(OUT_PATH)
print(f"File size: {size/1024/1024:.1f} MB")