Module I · Molecular Foundations
3 sections
14 units
1.1 Chemical Building Blocks
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Water properties: Cohesion, adhesion, high heat capacity, universal solvent, surface tension. All due to hydrogen bonding and polarity.
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pH and buffers: pH = -log[H⁺]; buffers resist pH change using weak acid/conjugate base pairs.
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Solutions: Molarity (M = mol/L), percent solutions (% w/v, % v/v), dilutions (C₁V₁ = C₂V₂).
1.2 Carbohydrates & Lipids
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Carbohydrates: Monosaccharides (glucose, fructose), disaccharides (sucrose), polysaccharides (starch, cellulose). Glycosidic bonds (α-1,4 in starch; β-1,4 in cellulose).
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Lipids: Triglycerides (energy storage), phospholipids (membranes), waxes (cuticle). Saturated (solid) vs unsaturated (liquid).
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Brix: Measures soluble solids (sugars). 1°Bx = 1g sucrose/100g. Export mangoes need ≥12°Bx.
1.3 Proteins & Enzymes
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Amino acids: General structure: amino group, carboxyl group, H, and variable R group. Peptide bonds form proteins.
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Protein structure: Primary (sequence), secondary (α-helix, β-sheet), tertiary (3D folding), quaternary (multiple subunits).
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Enzymes: Biological catalysts that lower activation energy. Active site binds substrate. Factors: temperature, pH, inhibitors.
1 U (enzyme unit) = 1 μmol product/min · Specific activity = U/mg protein
Cohesion
Adhesion
Molarity
Buffer
pH
Monosaccharide
Disaccharide
Polysaccharide
Starch
Cellulose
Lipid
Triglyceride
Phospholipid
Amino acid
Peptide bond
Enzyme
Active site
Module II · Metabolism & Energy Systems
4 sections
22 units
2.1 Photosynthesis
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Light reactions: In thylakoid membranes. PSII (P680) splits water → O₂, PSI (P700) reduces NADP⁺ to NADPH. ATP produced via photophosphorylation.
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Calvin cycle: In stroma. 3 phases: carbon fixation (RuBP + CO₂ → 3-PGA), reduction (3-PGA → G3P), regeneration (RuBP). Uses ATP and NADPH.
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C3 vs C4 vs CAM: C3 (rice, wheat), C4 (maize, sorghum) with Kranz anatomy, CAM (cactus, pineapple) fix CO₂ at night.
2.2 Respiration
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Glycolysis: Glucose → 2 pyruvate in cytoplasm. Net gain: 2 ATP + 2 NADH.
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Krebs cycle: In mitochondrial matrix. Per acetyl-CoA: 3 NADH + 1 FADH₂ + 1 ATP. Per glucose: 6 NADH + 2 FADH₂ + 2 ATP.
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ETC & oxidative phosphorylation: NADH/FADH₂ donate electrons to chain, proton gradient drives ATP synthase. ~32 ATP per glucose total.
C₆H₁₂O₆ + 6O₂ → 6CO₂ + 6H₂O + 36-38 ATP
2.3 Carbohydrate Transport
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Phloem structure: Sieve elements (conducting) + companion cells (support). Sieve plates allow flow.
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Source-sink: Sources (mature leaves) export sugars; sinks (fruits, roots) import. Sink strength = size × activity.
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Starch metabolism: Starch = amylose (linear) + amylopectin (branched). Cold-induced sweetening in potatoes: starch → sugars at low T.
2.4 Nitrogen & Lipid Metabolism
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Nitrogen assimilation: Nitrate reductase (NO₃⁻ → NO₂⁻), nitrite reductase (NO₂⁻ → NH₄⁺), GS-GOGAT pathway incorporates NH₄⁺ into amino acids.
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N₂ fixation: Rhizobia in legume nodules. Nitrogenase converts N₂ → NH₃ (requires 16 ATP). Leghemoglobin protects nitrogenase from O₂.
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Lipid synthesis: Fatty acids made in plastids via ACCase and FAS. Kennedy pathway assembles triglycerides (GPAT, LPAAT, DGAT).
Photosynthesis
Calvin cycle
Rubisco
C3
C4
CAM
Glycolysis
Krebs cycle
ETC
ATP synthase
Phloem
Source-sink
Starch
Nitrate reductase
GS-GOGAT
Nitrogenase
Module III · Productivity & Quality
5 sections
6 units
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Harvest index: HI = economic yield / total biomass. Modern wheat HI = 0.5 (vs 0.3 traditional). Green Revolution increased HI via dwarfing genes.
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Flavor biochemistry: Sweetness: fructose (1.7×) > sucrose (1.0) > glucose (0.7). Sugar/acid ratio key for fruit quality. Aroma compounds: esters (fruity), terpenes (citrus), aldehydes (green).
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Nutritional quality: Vitamin C (unstable, indicator of freshness), carotenoids (provitamin A), flavonoids (antioxidants). ORAC measures antioxidant capacity.
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Pigments: Chlorophylls (green), carotenoids (yellow/orange), anthocyanins (red/purple, pH-dependent), betalains (red/yellow). Color indicates ripeness.
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Post-harvest quality: Q₁₀ (respiration rate doubles/10°C). Ethylene triggers climacteric ripening. 1-MCP blocks ethylene receptors. Chilling injury in tropical fruits <12°C.
Harvest Index = Economic Yield / Total Biomass · Q₁₀ = R₂/R₁ for 10°C increase
Harvest index
Brix
Sugar/acid ratio
Esters
Terpenes
ORAC
Anthocyanins
Carotenoids
Chlorophyll
Ethylene
1-MCP
Chilling injury
Climacteric
Module IV · Stress & Environmental Biochemistry
5 sections
6 units
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Drought stress: ABA triggers stomatal closure. Compatible solutes: proline, glycine betaine maintain turgor. LEA proteins protect cellular structures.
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Salinity stress: SOS pathway: SOS3 senses Ca²⁺, activates SOS2 kinase, which activates SOS1 Na⁺/H⁺ antiporter for ion exclusion.
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Temperature stress: Heat shock proteins (HSPs) refold denatured proteins. Cold acclimation via CBF pathway increases membrane unsaturation.
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Secondary metabolites: Terpenes (isoprene units), phenolics (phenylpropanoid pathway, PAL key enzyme), alkaloids (nitrogen-containing, from amino acids).
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ROS and antioxidants: ROS: O₂⁻, H₂O₂, OH•, ¹O₂. Enzymatic antioxidants: SOD, CAT, APX. Non-enzymatic: ascorbate, glutathione, vitamin E.
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Tolerance strategies: Escape (early maturity), avoidance (deep roots, stomatal closure), tolerance (osmotic adjustment, HSPs). Sub1A rice survives flooding.
ABA
Proline
Glycine betaine
SOS pathway
HSP
CBF
Terpenes
Phenolics
Alkaloids
ROS
SOD
CAT
APX
Ascorbate
Glutathione
Sub1A
Module V · Analytical & Biochemical Techniques
7 sections
8 units
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Lab fundamentals: Safety (PPE: lab coat, goggles, gloves). Molarity (M = n/V), percent solutions, dilutions (C₁V₁ = C₂V₂). Buffers resist pH change.
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Spectrophotometry: Beer-Lambert law: A = εcl. Standard curves determine unknown concentrations. Bradford assay (595 nm) for proteins.
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Chromatography: Paper/TLC: stationary phase (paper/silica), mobile phase (solvent). Rf = distance compound / distance solvent front. HPLC, GC-MS for advanced analysis.
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Enzyme assays: 1 U = 1 μmol product/min. Specific activity = U/mg protein. Michaelis-Menten: Vmax, Km. Lineweaver-Burk plot for kinetic analysis.
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Data analysis: Mean, SD (data spread), SEM (precision). t-test (2 groups), ANOVA (>2 groups). p < 0.05 significant. R² > 0.98 for good standard curve.
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Field methods: Liquid nitrogen (-196°C) for enzymes/RNA, dry ice (-78°C), ice packs (0-4°C), silica gel for DNA. GPS coordinates, sample documentation essential.
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Applied techniques: Brix (refractometer), titratable acidity (titration), oil content (Soxhlet). Export standards: mango 12°Brix, avocado 21% dry matter.
A = εcl · C₁V₁ = C₂V₂ · 1 U = 1 μmol/min · Specific Activity = U/mg protein
Molarity
Buffer
Beer-Lambert
Standard curve
Rf
HPLC
GC-MS
Enzyme unit
Km
Vmax
SD
SEM
t-test
ANOVA
Brix
Titration
Module VI · Ethiopian Case Studies
5 sections
6 units
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Coffee biochemistry: Caffeine biosynthesis: xanthosine → theobromine → caffeine. Chlorogenic acids (5-10% in green beans) degrade 50-80% during roasting. Regional variation: Yirgacheffe (high caffeine), Hararge (high lipids).
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Enset fermentation: Kocho (pseudostem + corm, 1-6 months), bulla (fine flour, 5 days), amicho (boiled corm). pH 5.7 → 3.8. LAB dominate; phytate reduction increases mineral bioavailability.
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Mango export chain: Harvest at mature green (9-11°Brix), export at ≥12°Brix. Floatation test (1% salt) for maturity. Evaporative cooling extends shelf life 3→28 days.
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Teff & injera: Teff: smallest grain, gluten-free, high iron (5-15 mg/100g). Injera fermentation: ersho starter, two-stage (LAB then yeasts), pH 6.0→3.8, CO₂ creates eyes.
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Flower export: Roses harvested at tight bud stage. Ethylene management: STS (silver thiosulfate) or 1-MCP. Grading by stem length: premium (70-100cm), Grade 1 (50-70cm), Grade 2 (30-50cm).
Caffeine
Chlorogenic acid
Yirgacheffe
Enset
Kocho
Bulla
LAB
Brix
Evaporative cooling
Teff
Injera
Ersho
STS
1-MCP
Vase life