BIO 221 — Plant Physiology | Interactive Lecture Notes

WEEK 01

Plants as Primary Food Producers

Autotrophy · Energy capture · Position in food chains · Scope of plant physiology

Learning Outcomes

Define plant physiology and its scope within biology
Explain why plants are called primary producers
Describe how solar energy is captured and stored as chemical energy
Outline the link between photosynthesis, food chains and human food security

1.1 What is Plant Physiology?

Plant physiology is the branch of botany that studies the functions and vital processes of plants — how they absorb water and minerals, manufacture food, breathe, grow, move and respond to their environment. It links plant structure (anatomy) and plant chemistry (biochemistry) to whole-plant performance in the field.

Term	Definition
Plant Physiology	Study of how plants live and function — nutrition, transport, respiration, growth, reproduction, response.
Autotroph	An organism that manufactures its own organic food from simple inorganic substances using an external energy source.
Photoautotroph	An autotroph that uses light energy (e.g., green plants, algae, cyanobacteria).
Primary Producer	The first trophic level in any food chain — the organism that introduces energy and fixed carbon into the ecosystem.

1.2 Plants as Primary Food Producers

Almost all life on Earth depends — directly or indirectly — on green plants. Through photosynthesis, plants capture solar energy and convert atmospheric CO₂ and soil water into carbohydrates, proteins, lipids and vitamins. These compounds become food for herbivores, which in turn become food for carnivores, so plants occupy the foundation of every terrestrial food web.

🌾 Why Plants Matter

Food: >80% of human calories come from cereals, legumes, tubers, fruits and vegetables.
Oxygen: Photosynthesis releases the O₂ we breathe.
Carbon sink: Forests and crops remove gigatons of CO₂ each year.
Medicines: ~25% of modern drugs are plant-derived (quinine, aspirin, vincristine).
Industrial raw materials: Timber, fibres, oils, dyes, biofuels.

1.3 The Energy Flow Diagram

Figure 1.1 — Energy flow through a simple food chain

About 90% of energy is lost as heat between trophic levels; only ~10% is passed on. This is why food chains rarely have more than 4–5 levels and why plant-based diets feed more people per hectare.

1.4 Scope of BIO 221

Theme	Topics covered
Water relations	Absorption, transpiration, water potential
Mineral nutrition	Macro- and micronutrients, deficiency diseases
Photosynthesis	Chloroplast, light reactions, Calvin cycle
Translocation & assimilation	Phloem transport, nitrate reduction, amino-acid synthesis
Respiration	Aerobic and anaerobic pathways
Growth & movement	Measurement, tropisms, nastic movements
Excretion	Removal of waste in plants

📝 Self-Check Quiz — Week 1

Plants are described as primary producers because they:

📝 Classwork & Assignment — Week 1

A. Classwork (in lecture, 15 min)

In one sentence, define plant physiology.
List four reasons why plants are essential to human life.
Sketch a food chain of four trophic levels found on your campus and label the producer.

B. Take-Home Assignment (due next class)

Write a short essay (300–400 words) titled "The Plant: Nature's First Factory" outlining how the seven physiological processes covered in BIO 221 each contribute to a plant's role as a primary producer.
Make a labelled poster of energy flow from sunlight to a top carnivore in a Nigerian savanna ecosystem.

Format: Hand-written or typed · Marks: 10 · Submit at start of Week 2 lecture

WEEK 02

Plant Water Absorption

Soil water · Osmosis · Water potential · Apoplast / Symplast / Transmembrane · Casparian strip

Learning Outcomes

Explain how plant roots absorb water from the soil
Define water potential (ψ) and its components
Describe the apoplast, symplast and transmembrane pathways
State the role of the Casparian strip in regulating uptake
Distinguish active from passive absorption of water

2.1 Why Plants Need Water

Water is the most abundant substance in plant tissues (often 80–95% by mass). It is the solvent for biochemical reactions, the raw material for photosynthesis, the medium of transport for minerals and sugars, and the source of turgor pressure that keeps cells rigid and leaves expanded.

2.2 Water Potential (ψ)

Water potential is the potential energy of water per unit volume relative to pure water at standard temperature and pressure. It is denoted by the Greek letter ψ (psi) and measured in megapascals (MPa). Water always moves from a region of higher ψ to a region of lower ψ.

🔬 Key Equation

ψ = ψs + ψp
ψs = solute (osmotic) potential — always negative; lower with more solutes.
ψp = pressure (turgor) potential — positive in turgid cells, negative under tension in xylem.
Pure water at atmospheric pressure: ψ = 0 MPa.

The water potential gradient that drives uptake into the plant is: Soil (−0.1 MPa) > Root (−0.3 MPa) > Stem > Leaf (−0.8 MPa) > Atmosphere (−50 to −100 MPa). [Georgia Tech]

2.3 Three Pathways Across the Root

Pathway	Route	Notes
Apoplast	Through cell walls and intercellular spaces only — never crosses a membrane.	Fastest; blocked at the endodermis by the Casparian strip.
Symplast	Through cytoplasm of cells, connected by plasmodesmata.	Selective; passes through living cytoplasm continuously.
Transmembrane	Crosses cell membranes via aquaporins; cell to cell.	Highly regulated; can be slowed in stress.

2.4 The Casparian Strip

⚠️

Definition. The Casparian strip is a band of suberin (a wax-like substance) deposited on the radial walls of endodermal cells. It is impermeable to water and solutes, so it forces all materials moving through the apoplast to cross the endodermal cell membrane before entering the xylem. This creates a checkpoint that excludes toxins and allows the plant to control mineral uptake.

Figure 2.1 — Root cross-section showing pathways

2.5 Active vs. Passive Absorption

Feature	Active Absorption	Passive Absorption
Energy	Requires ATP	None — driven by transpiration pull
When dominant	When transpiration is low (e.g., night)	During the day, when transpiration is high
Indicator	Root pressure / guttation	Wilting under heat stress
Site	Cortex & endodermis cells	Apoplast & xylem tension

📝 Self-Check Quiz — Week 2

A potato cell with ψs = −0.6 MPa and ψp = +0.2 MPa is placed in pure water (ψ = 0). Water will:

📝 Classwork & Assignment — Week 2

A. Classwork (in lecture, 20 min)

Calculate water potential for a cell with ψs = −1.2 MPa and ψp = +0.4 MPa.
Draw a labelled diagram of the three water uptake pathways across a root.
Predict the direction of water movement between two cells: Cell A (ψ = −0.5 MPa) and Cell B (ψ = −0.9 MPa).

B. Practical Assignment (lab, 1 week)

Osmosis experiment: Cut three potato cylinders of equal length. Place in (a) distilled water, (b) 0.5 M sucrose, (c) 1.0 M sucrose for 2 hours. Measure length and mass before and after, plot results, and explain in terms of water potential.
Submit a typed lab report: aim, materials, method, results table, graph, discussion, conclusion (max 1000 words).

Marks: 15 · Submit before Week 4 lecture

WEEK 03

Plant Transpiration

Stomatal, cuticular, lenticular transpiration · Cohesion-tension theory · Regulation

Learning Outcomes

Define transpiration and list its three forms
Explain the mechanism of stomatal opening and closing
Describe the cohesion-tension theory of water ascent
State the benefits and costs of transpiration
Identify factors that affect the rate of transpiration

3.1 What is Transpiration?

Transpiration is the loss of water in the form of water vapour from the aerial parts of the plant, mainly the leaves. It is essentially the evaporation of water from the moist surfaces of mesophyll cells into the intercellular air spaces, followed by diffusion to the atmosphere through stomata. Although it is unavoidable, it is also the engine that pulls water up tall trees.

Type	Site	Share
Stomatal	Through stomatal pores in leaves	~80–90% of total
Cuticular	Through the leaf cuticle	~5–10%
Lenticular	Through lenticels in woody stems	~0.1–1%

3.2 Stomatal Mechanism

Each stoma is bordered by two guard cells. When guard cells take up K⁺ ions from neighbouring epidermal cells, their water potential drops, water enters by osmosis, they swell and bow apart — opening the pore. Loss of K⁺ (and accumulation of ABA in stress) reverses the process and closes it.

Figure 3.1 — Open vs. closed stoma

3.3 Cohesion-Tension Theory (Dixon & Joly, 1894)

STEP 1

Evaporation

Water vapour leaves stomata; mesophyll cells lose water to airspaces.

→

STEP 2

Tension

Negative pressure (suction) develops in the xylem column.

→

STEP 3

Cohesion

Hydrogen bonds keep water molecules attached to each other — the column does not break.

→

STEP 4

Adhesion + Pull

Adhesion to xylem walls + tension pulls water up from roots, hundreds of metres in tall trees.

3.4 Significance and Costs

Benefit	Cost
Pulls water and dissolved minerals up the xylem	~99% of water absorbed is lost — huge demand on uptake
Cools leaves through evaporative cooling	Excessive loss causes wilting and reduced photosynthesis
Maintains turgor for cell expansion and growth	Requires open stomata, which also lets CO₂ in but allows pathogen entry

3.5 Factors Affecting Transpiration

☀ Environmental & Plant Factors

Light: Stomata open in light → rate ↑
Temperature: Higher T → higher vapour pressure deficit → rate ↑
Humidity: Higher humidity → smaller gradient → rate ↓
Wind: Removes the boundary layer → rate ↑
Soil water availability: Drought → ABA closes stomata → rate ↓
Leaf surface area, thickness of cuticle, density of stomata.

📝 Self-Check Quiz — Week 3

In the cohesion-tension theory, the energy that ultimately pulls water up a 50 m tree is:

📝 Classwork & Assignment — Week 3

A. Classwork (in lecture)

List three reasons why an actively transpiring plant cools itself.
Draw a labelled diagram showing how guard cells open a stoma using K⁺ uptake.
Predict the effect on transpiration if a leaf's lower epidermis were sealed with petroleum jelly.

B. Practical Assignment (lab)

Bubble potometer: Set up a simple potometer using a leafy shoot. Record the rate of water uptake (cm/min) under (a) still air, (b) wind from a fan, (c) bright light, (d) shade. Tabulate, plot a bar chart, and explain results.
Cobalt chloride paper test: Compare colour change times on the upper vs. lower leaf surfaces of a Coleus or Hibiscus leaf. Explain the role of stomatal distribution.

Marks: 15 · Lab report due Week 5 · Group of 4

WEEK 04

Mineral Requirements

Sources · Macronutrients · Micronutrients (trace elements) · Roles in metabolism

Learning Outcomes

List the 17 essential mineral elements and their sources
Distinguish macronutrients from micronutrients (trace elements)
State the physiological role of each element
Explain mineral uptake mechanisms (active vs. passive)

4.1 Essential Elements — Arnon & Stout's Criteria (1939)

📦 An Element is "Essential" if:

The plant cannot complete its life cycle without it.
No other element can substitute for it.
It is directly involved in plant metabolism (component of an essential molecule, enzyme, or osmotic regulator).

Plants require 17 essential elements. Three (C, H, O) come from air and water. The remaining 14 are mineral nutrients absorbed from the soil as ions.

4.2 Macronutrients (required > 1000 mg/kg dry mass)

Element	Form Absorbed	Source	Main Role
Nitrogen (N)	NO₃⁻, NH₄⁺	Soil nitrate, fertiliser, fixation	Amino acids, proteins, chlorophyll, nucleic acids
Phosphorus (P)	H₂PO₄⁻, HPO₄²⁻	Phosphate rocks, organic matter	ATP, nucleic acids, phospholipids
Potassium (K)	K⁺	Soil minerals, fertiliser	Stomatal regulation, enzyme activator, osmotic balance
Calcium (Ca)	Ca²⁺	Limestone, gypsum	Cell wall (middle lamella), signalling
Magnesium (Mg)	Mg²⁺	Dolomite, soil minerals	Central atom of chlorophyll, enzyme activator
Sulphur (S)	SO₄²⁻	Soil organic matter, fertiliser	Cysteine, methionine, coenzyme A

4.3 Micronutrients / Trace Elements (required < 100 mg/kg)

Element	Form	Main Role
Iron (Fe)	Fe²⁺ / Fe³⁺	Cytochromes, electron carriers, chlorophyll synthesis
Manganese (Mn)	Mn²⁺	Photolysis of water at PS II; enzyme activator
Zinc (Zn)	Zn²⁺	Auxin synthesis; carbonic anhydrase
Copper (Cu)	Cu⁺ / Cu²⁺	Plastocyanin in light reactions; oxidases
Boron (B)	BO₃³⁻	Cell wall integrity, sugar transport, pollen tube growth
Molybdenum (Mo)	MoO₄²⁻	Cofactor of nitrate reductase and nitrogenase
Chlorine (Cl)	Cl⁻	Photolysis of water; osmotic balance
Nickel (Ni)	Ni²⁺	Cofactor of urease

💡

Mnemonic for the 8 micronutrients: "Mr B C MnCuZ FeNi" → Mo, B, Cl, Mn, Cu, Zn, Fe, Ni.

4.4 Mineral Uptake Mechanisms

Mode	Description	Energy?
Passive (diffusion)	Ions move down their electrochemical gradient through channels.	No
Active transport	Ions pumped against gradient by membrane proteins (e.g., proton pumps).	Yes (ATP)
Ion exchange	H⁺ from root displaces cations adsorbed on soil colloids.	Indirect
Mass flow	Ions carried passively by transpiration stream.	No

📝 Self-Check Quiz — Week 4

Which trace element is a cofactor for the enzyme nitrate reductase, the first step in nitrate assimilation?

📝 Classwork & Assignment — Week 4

A. Classwork

State Arnon & Stout's three criteria for an essential element.
Group the 14 mineral nutrients into macronutrients and micronutrients.
Write the chemical form in which N, P, K and Mg are absorbed by roots.

B. Take-Home Assignment

Compile a one-page table titled "Essential Mineral Elements in Plants" with columns: element, ionic form, primary role, deficiency symptom (one line).
Visit a local farm or garden, photograph a maize/rice/cassava field, and identify any visible nutrient deficiency.

Marks: 10 · Submit at start of Week 5

WEEK 05

Nutrient Deficiency Diseases

Symptoms · Mobile vs. immobile elements · Diagnostic keys

Learning Outcomes

Recognise visual symptoms of common nutrient deficiencies
Distinguish symptoms of mobile vs. immobile element deficiencies
Use a simple diagnostic key for nutrient deficiencies
Suggest practical remedies for nutrient disorders

5.1 General Symptoms

Deficiencies reduce shoot growth and leaf size and cause foliage to discolour, fade, and distort, sometimes in a characteristic pattern. Severely deficient plants may exhibit dieback, remain undersized, and be predisposed to other maladies. Most symptoms result from chlorosis (loss of chlorophyll), necrosis (tissue death), stunting or distortion. [UC IPM]

5.2 Mobile vs. Immobile Elements — Where Symptoms Show

Mobility	Elements	Where symptoms first appear
Mobile in phloem	N, P, K, Mg	Older (lower) leaves first — plant relocates the element to growing tips
Immobile	Ca, S, Fe, Mn, B, Cu, Zn, Mo	Younger (upper) leaves first — cannot be re-translocated

5.3 Major Deficiency Diseases

Element	Classic Symptoms	Common Crop Example
Nitrogen (N)	General chlorosis of older leaves; pale, stunted plants; reduced tillering	Cereals, grasses
Phosphorus (P)	Dark green to purplish older leaves; delayed maturity; weak roots	Maize seedlings (purple stems)
Potassium (K)	Marginal scorch & necrosis of older leaves; weak stems	Cotton, banana
Calcium (Ca)	Distorted/dead growing points; blossom-end rot of fruit	Tomato, peanut
Magnesium (Mg)	Interveinal chlorosis on older leaves	Citrus, soybean
Sulphur (S)	Pale young leaves; yellowing similar to N but on new growth	Brassicas, legumes
Iron (Fe)	Severe interveinal chlorosis on young leaves; veins remain green	Citrus, soybean on alkaline soils
Manganese (Mn)	Interveinal chlorosis with grey speck (oats); reduced photolysis	Oats, sugarcane
Zinc (Zn)	Little leaf, rosetting, shortened internodes ("white bud" maize)	Maize, fruit trees
Copper (Cu)	Wilting of young shoots, dieback; reclamation disease in cereals	Wheat on peat soils
Boron (B)	Heart rot of beet; cracked stem of celery; failure of fruit set	Sugar beet, groundnut
Molybdenum (Mo)	Whiptail of cauliflower; reduced N fixation in legumes	Cauliflower, soybean

5.4 Simple Diagnostic Key

🔍 Where do symptoms appear first?

Older leaves: N, P, K or Mg — use leaf colour to differentiate (general yellowing = N; purple = P; marginal burn = K; interveinal yellow = Mg).
Younger leaves & growing tips: Ca, B (distortion); Fe, Mn (interveinal chlorosis); S (uniform pale).
Whole plant stunted with no clear chlorosis: consider P, K or root injury.

5.5 Remedies

Problem	Solution
Acid soil reducing Mo, Ca, Mg	Apply lime (CaCO₃) or dolomite
Alkaline soil locking up Fe, Mn, Zn	Acidify soil; foliar chelated micronutrient sprays
General N, P, K deficiency	Apply NPK fertiliser at recommended rate
Waterlogging-induced root damage	Improve drainage; avoid compaction

📝 Self-Check Quiz — Week 5

A maize plant shows interveinal chlorosis on its youngest leaves while older leaves remain green. The most likely deficiency is:

📝 Classwork & Assignment — Week 5

A. Classwork

State why N deficiency shows in older leaves but Fe deficiency shows in younger leaves.
Match each of the following symptoms to an element: heart rot of beet; whiptail of cauliflower; blossom-end rot of tomato; interveinal chlorosis of older leaves.

B. Take-Home Assignment / Field Exercise

Visit a campus farm or local garden. Photograph at least three plants showing suspected deficiency symptoms.
For each photo: describe symptom, propose deficient element, and suggest a corrective measure.
Write a short report (max 1500 words) titled "Diagnosing Plant Nutrient Disorders in My Locality".

Marks: 15 · Submit at end of Week 6

WEEK 06

Photosynthesis I — Chloroplast, Raw Materials & Products

Overall equation · Chloroplast structure · Pigments · Two stages

Learning Outcomes

Write and interpret the overall photosynthesis equation
Describe chloroplast structure and identify its compartments
Name the photosynthetic pigments and their absorption peaks
Distinguish the light reactions from the dark (Calvin) reactions

6.1 Definition and Significance

Photosynthesis is the anabolic process by which green plants, algae and some bacteria use light energy to synthesise organic compounds (mainly carbohydrates) from CO₂ and H₂O, releasing O₂ as a by-product. It is the principal route by which solar energy enters the biosphere.

📐 The Overall Equation

6 CO₂ + 12 H₂O —light, chlorophyll→ C₆H₁₂O₆ + 6 O₂ + 6 H₂O
Twelve waters are split (photolysis); only six waters appear as net product.
Glucose stores ~2870 kJ per mole, captured from sunlight.

6.2 Raw Materials and Products

Raw Material	Source	Product	Fate
Carbon dioxide (CO₂)	Atmosphere via stomata	Carbohydrate (glucose, sucrose, starch)	Food, growth, storage
Water (H₂O)	Soil via roots, xylem	Oxygen (O₂)	Released through stomata
Light energy	Sun (400–700 nm, PAR)	Chemical energy in C—H bonds	Drives all subsequent metabolism
Chlorophyll	Pigment in thylakoid	(Catalyst, not consumed)	—

6.3 The Chloroplast — Site of Photosynthesis

Chloroplasts are double-membrane plastids found mainly in mesophyll cells. A typical leaf cell contains 30–40 chloroplasts. Each chloroplast has the following compartments:

Structure	Description	Function
Outer membrane	Smooth, permeable to small molecules	Boundary; allows CO₂, O₂ exchange
Inner membrane	Selectively permeable	Controls flow of metabolites
Stroma	Fluid matrix containing DNA, ribosomes, enzymes	Site of Calvin cycle (dark reactions)
Thylakoid	Flattened sacs with embedded pigments	Site of light reactions
Granum (pl. grana)	Stack of thylakoids	Increases surface area for light capture
Stroma lamellae	Thylakoids connecting grana	Maintain proton gradient continuity

Figure 6.1 — Schematic chloroplast

6.4 Photosynthetic Pigments

Pigment	Colour Reflected	Absorption Peaks	Role
Chlorophyll a	Blue-green	430 nm, 662 nm	Primary pigment; reaction centre of PS I & II
Chlorophyll b	Yellow-green	453 nm, 642 nm	Accessory — broadens light capture
Carotenoids (carotene, xanthophyll)	Yellow / orange	~450 nm	Accessory; photoprotection from excess light

6.5 Two Stages of Photosynthesis — Overview

STAGE 1

Light Reactions

Thylakoid membrane. Light splits H₂O → O₂. Produces ATP & NADPH.

→

STAGE 2

Calvin Cycle (Dark)

Stroma. Uses ATP & NADPH to fix CO₂ → sugars. Does not need light directly.

Both stages run together in daylight; the dark reaction is "dark" only in the sense that it does not directly need photons. [NCBI]

📝 Self-Check Quiz — Week 6

In a chloroplast, the Calvin cycle takes place in the:

📝 Classwork & Assignment — Week 6

A. Classwork

Write the overall balanced equation for photosynthesis using 12 H₂O.
Label a diagram of a chloroplast (outer membrane, inner membrane, stroma, granum, thylakoid, lumen).
State why chlorophyll a appears green although it absorbs at 430 nm and 662 nm.

B. Practical / Take-Home

Pigment separation: Extract pigments from a fresh leaf using ethanol; perform paper chromatography. Identify chlorophyll a, b, and carotenoids by their Rf values.
Essay (300–500 words): "Why life on Earth depends on a 0.04% gas (CO₂) and a green pigment."

Marks: 15 · Lab + essay due Week 8

WEEK 07

Light Reactions & Photolysis of Water

Photosystems I & II · Z-scheme · Photophosphorylation · Water splitting

Learning Outcomes

Describe the structure and role of photosystems I and II
Explain non-cyclic and cyclic photophosphorylation (Z-scheme)
State the equation and significance of photolysis of water (Hill reaction)
Identify the products of the light reactions

7.1 Two Photosystems

Feature	Photosystem II (PS II)	Photosystem I (PS I)
Reaction-centre chlorophyll	P680 (absorbs at 680 nm)	P700 (absorbs at 700 nm)
Discovered first?	Numbered 2 but discovered second	Numbered 1; discovered first
Electron source	H₂O (via photolysis)	PS II via electron transport chain
Final electron acceptor	Plastoquinone (PQ)	NADP⁺ → NADPH
Released gas	O₂	None

7.2 Photolysis of Water (Hill Reaction)

At PS II, light energy drives the splitting of water molecules — a process called photolysis or the Hill reaction. It supplies the electrons used to reduce P680⁺, releases molecular oxygen, and contributes protons (H⁺) to the thylakoid lumen.

💧 Photolysis Equation

2 H₂O —light, Mn cluster→ 4 H⁺ + 4 e⁻ + O₂
Catalysed by the oxygen-evolving complex (OEC) containing four manganese (Mn) atoms.
Provides the only source of atmospheric O₂ of biological origin.

7.3 The Z-Scheme — Non-Cyclic Photophosphorylation

Figure 7.1 — Z-scheme of electron flow

1

PS II excited

Photon raises P680 electrons to a high-energy level.

→

2

Photolysis

H₂O split; electrons replace those lost by P680; O₂ released.

→

3

ETC

Electrons flow PQ → cyt b₆f → PC; H⁺ pumped to lumen → ATP via ATP synthase.

→

4

PS I excited

Second photon re-energises electrons to ferredoxin.

→

5

NADP⁺ reduction

Ferredoxin-NADP⁺ reductase makes NADPH.

7.4 Cyclic vs. Non-Cyclic Photophosphorylation

Feature	Non-cyclic	Cyclic
Photosystems	Both PS I and PS II	Only PS I
Electron path	H₂O → PS II → PS I → NADPH	Loops back to PS I
Products	ATP, NADPH, O₂	ATP only
Function	Main energy and reductant supply	Extra ATP when NADPH is in surplus

7.5 Summary of Light-Reaction Products

✨ Outputs to the Calvin Cycle

ATP — chemical energy currency.
NADPH — reducing power.
O₂ — by-product, released to atmosphere.

📝 Self-Check Quiz — Week 7

The oxygen released during photosynthesis comes from:

📝 Classwork & Assignment — Week 7

A. Classwork

Draw and label the Z-scheme; mark where ATP and NADPH are formed.
Write the equation for photolysis of water and identify the metal cluster involved.
State two differences between cyclic and non-cyclic photophosphorylation.

B. Take-Home

Carry out the Hill reaction demonstration: dichlorophenol-indophenol (DCPIP) decolourised by isolated chloroplasts in light. Record colour change times in light vs. dark and explain.
Write a structured 1-page report.

Marks: 15 · Submit Week 9

WEEK 08

Calvin Cycle (Dark Reactions)

Carboxylation · Reduction · Regeneration of RuBP · C3, C4, CAM

Learning Outcomes

Describe the three phases of the Calvin cycle
Identify RuBisCO, RuBP, 3-PGA, G3P and their roles
Explain how ATP and NADPH from light reactions are used
Compare C3, C4 and CAM pathways

8.1 Overview

The Calvin cycle (also called the C3 pathway, dark reaction, or Calvin–Benson cycle) takes place in the chloroplast stroma. It uses the ATP and NADPH made in the light reactions to fix atmospheric CO₂ into a stable carbohydrate, glyceraldehyde-3-phosphate (G3P), from which glucose, sucrose and starch are synthesised.

8.2 Three Phases of the Calvin Cycle

PHASE 1

Carboxylation

3 CO₂ + 3 RuBP (5C) → 6 × 3-PGA (3C). Enzyme: RuBisCO.

→

PHASE 2

Reduction

6 × 3-PGA + 6 ATP + 6 NADPH → 6 × G3P. Net 1 G3P leaves cycle.

→

PHASE 3

Regeneration

5 × G3P + 3 ATP → 3 × RuBP. Cycle restarts.

🧮 Net Stoichiometry

Per 1 glucose (2 × G3P): 6 CO₂ + 18 ATP + 12 NADPH consumed.
RuBisCO is the most abundant enzyme on Earth.

8.3 Diagram of the Calvin Cycle

Figure 8.1 — Calvin cycle

8.4 C3, C4 and CAM Pathways

Feature	C3	C4	CAM
First fixed product	3-PGA (3 C)	OAA (4 C)	OAA at night
Initial enzyme	RuBisCO	PEP carboxylase	PEP carboxylase
Anatomy	Mesophyll only	Kranz: mesophyll + bundle sheath	Single cell, time-separated
Climate	Cool, moist	Hot, sunny	Arid (succulents)
Examples	Wheat, rice, soybean	Maize, sugarcane, sorghum	Cactus, pineapple, agave
Photorespiration	High	Suppressed	Suppressed

📝 Self-Check Quiz — Week 8

During the Calvin cycle, the carboxylation step is catalysed by:

📝 Classwork & Assignment — Week 8

A. Classwork

List the three phases of the Calvin cycle in order with the key enzyme of phase 1.
Calculate the number of ATP and NADPH needed to synthesise one molecule of glucose.
Explain why RuBisCO is described as the most abundant protein on Earth.

B. Take-Home Assignment

Compare C3, C4 and CAM plants in a table; give two crop examples of each adapted to West Africa.
Short essay (400 words): "Why C4 plants outperform C3 plants under high light and high temperature."

Marks: 15 · Submit Week 10

WEEK 09

Translocation of Manufactured Food

Phloem structure · Pressure-flow hypothesis · Source–sink · Loading & unloading

Learning Outcomes

Define translocation and identify the tissue involved
Describe phloem composition: sieve elements and companion cells
Explain the pressure-flow (Münch) hypothesis of phloem transport
Distinguish source from sink and outline loading and unloading
Compare xylem and phloem transport

9.1 What is Translocation?

Translocation is the long-distance transport of manufactured food (mainly sucrose, but also amino acids and hormones) from a source (where it is made or stored) to a sink (where it is used or stored). It occurs in the phloem.

9.2 Phloem Anatomy

Cell	Living?	Role
Sieve-tube element	Yes (no nucleus)	Conducts sap; sieve plates between cells
Companion cell	Yes (full organelles)	Provides ATP and proteins; loads sucrose
Phloem fibre	No (sclerenchyma)	Mechanical support
Phloem parenchyma	Yes	Storage

9.3 Source and Sink

Source	Sink
Mature photosynthetic leaves	Growing roots, fruits, seeds, tubers
Storage organs in spring (when mobilising starch)	Same organs in summer (when storing)

The same organ can switch between source and sink during the season. Example: a potato tuber is a sink in summer (storing starch) but a source in spring (when sprouting and supplying sugars to new shoots).

9.4 Pressure-Flow Hypothesis (Ernst Münch, 1930)

1

Loading

Sucrose actively pumped into sieve element at source → lowers ψs.

→

2

Water in

Water enters from xylem by osmosis → turgor (ψp) rises.

→

3

Bulk flow

High turgor pushes phloem sap toward sink (positive pressure).

→

4

Unloading

Sucrose removed at sink → ψs rises → water leaves → ψp drops.

The continuous gradient in pressure between source and sink keeps the phloem sap flowing. [Georgia Tech]

9.5 Xylem vs. Phloem

Feature	Xylem	Phloem
Cells	Dead vessels & tracheids	Living sieve-tube + companion cells
Substance moved	Water + minerals	Sucrose, amino acids, hormones
Direction	Upward (one way)	Source → sink (any direction)
Driving force	Transpiration pull (negative pressure)	Pressure-flow (positive pressure)
Energy	Passive	Active loading at source (ATP)

📝 Self-Check Quiz — Week 9

According to the pressure-flow hypothesis, the immediate cause of bulk flow in the phloem is:

📝 Classwork & Assignment — Week 9

A. Classwork

Define translocation, source and sink in your own words.
List four differences between xylem and phloem transport.
Identify the source and sink of: a sprouting potato; a ripening mango; a flowering cassava.

B. Take-Home Assignment

Ringing experiment essay: Describe Malpighi's classic ringing experiment on a tree trunk. Explain the observation in light of phloem function.
Diagram and annotate the four steps of the pressure-flow mechanism.

Marks: 10 · Submit Week 11

WEEK 10

Nitrate Reduction & Amino-Acid Synthesis

Nitrate reductase · Nitrite reductase · GS–GOGAT · Transamination

Learning Outcomes

Outline how plants assimilate nitrate from the soil
Describe the steps of nitrate → nitrite → ammonium reduction
Explain the GS–GOGAT cycle for ammonium assimilation
Describe transamination as a route to other amino acids

10.1 Why Nitrogen Matters

Nitrogen is required for amino acids, proteins, nucleic acids, chlorophyll and many cofactors. Although ~78% of the atmosphere is N₂, plants cannot use the gas directly. They take up nitrate (NO₃⁻) or ammonium (NH₄⁺) from the soil and reduce nitrate to ammonium before incorporating it into organic molecules. [MicrobeNotes]

10.2 Nitrate Reduction — Two Enzymatic Steps

STEP 1

Nitrate → Nitrite

NO₃⁻ + NADH → NO₂⁻ + NAD⁺ + H₂O. Enzyme: Nitrate reductase (NR); cytosolic; cofactors FAD, haem-Fe, Mo. Rate-limiting step.

→

STEP 2

Nitrite → Ammonium

NO₂⁻ + 6 Fd_red + 8 H⁺ → NH₄⁺ + 6 Fd_ox + 2 H₂O. Enzyme: Nitrite reductase (NiR); chloroplast/plastid; uses ferredoxin.

💡

Why two compartments? Nitrite is toxic, so it is rapidly transported to the chloroplast where ferredoxin (from PS I) provides the reducing power to make harmless NH₄⁺.

10.3 Ammonium Assimilation — The GS–GOGAT Cycle

GS

Glutamine Synthetase

Glutamate + NH₄⁺ + ATP → Glutamine + ADP + Pᵢ

→

GOGAT

Glutamate Synthase

Glutamine + 2-oxoglutarate + NADPH → 2 Glutamate (one returns to GS, one exits to biosynthesis)

The cycle continually rebuilds glutamate while channelling fixed nitrogen into glutamine — the gateway amino acid for all other amino acids and nucleotides.

10.4 Transamination — From Glutamate to Other Amino Acids

Other amino acids are made by transamination: the –NH₂ group of glutamate is transferred to a keto-acid acceptor by aminotransferases (transaminases), generating a new amino acid and α-ketoglutarate.

Keto-acid acceptor	Amino acid produced
Pyruvate	Alanine
Oxaloacetate	Aspartate
3-Phosphoglycerate	Serine
2-Oxoglutarate	Glutamate (cycle)

10.5 Why Mo and Fe Matter Here

🧭 Trace Elements in Action

Molybdenum (Mo) — cofactor of nitrate reductase. Mo deficiency → nitrate accumulates, plant becomes effectively N-deficient even when nitrate is plentiful.
Iron (Fe) — component of haem in NR and Fe–S clusters in NiR.
Manganese (Mn) and ferredoxin pool — link photosynthesis to nitrogen assimilation.

📝 Self-Check Quiz — Week 10

In the GS–GOGAT cycle, the reaction catalysed by GS uses which energy source?

📝 Classwork & Assignment — Week 10

A. Classwork

Write the two reduction reactions catalysed by NR and NiR with their cofactors.
Draw a flow chart from soil NO₃⁻ to glutamate via GS–GOGAT.
Define transamination and give one example.

B. Take-Home

Mini-research (1–1.5 pages): "Why molybdenum deficiency mimics nitrogen deficiency."
Construct a concept map linking N source → NR → NiR → GS → GOGAT → transamination → protein.

Marks: 10 · Submit Week 12

WEEK 11

Aerobic Respiration

Glycolysis · Krebs cycle · Electron transport chain · ATP yield

Learning Outcomes

Define respiration and contrast it with photosynthesis
Describe the four stages of aerobic respiration and their locations
State the ATP and NADH yields per stage
Explain the importance of respiration for plant growth

11.1 What is Respiration?

Respiration is the controlled oxidation of food (mainly glucose) to release energy stored as ATP. Aerobic respiration uses oxygen as the final electron acceptor. The overall equation:

⚡ Overall Equation

C₆H₁₂O₆ + 6 O₂ → 6 CO₂ + 6 H₂O + ~32 ATP
ΔG° ≈ −2870 kJ/mol — most lost as heat, ~40% captured in ATP.

11.2 Photosynthesis vs. Respiration

Feature	Photosynthesis	Respiration
Reactants	CO₂ + H₂O + light	Glucose + O₂
Products	Glucose + O₂	CO₂ + H₂O + ATP
Energy	Stored	Released
Site	Chloroplast	Cytoplasm + mitochondrion
When	Daylight	Day & night

11.3 Four Stages of Aerobic Respiration

Stage	Location	Inputs	Outputs (per glucose)
1. Glycolysis	Cytoplasm	Glucose, 2 ATP, 2 NAD⁺	2 Pyruvate, 4 ATP (net 2), 2 NADH
2. Pyruvate oxidation (link reaction)	Mitochondrial matrix	2 Pyruvate, 2 NAD⁺, 2 CoA	2 Acetyl-CoA, 2 CO₂, 2 NADH
3. Krebs (citric acid) cycle	Mitochondrial matrix	2 Acetyl-CoA	4 CO₂, 6 NADH, 2 FADH₂, 2 ATP
4. Electron transport & oxidative phosphorylation	Inner mitochondrial membrane	10 NADH, 2 FADH₂, 6 O₂	6 H₂O, ~26 ATP

Total per glucose: ~32 ATP, 6 CO₂, 6 H₂O. [NCBI]

11.4 Diagram — Respiration Overview

Figure 11.1 — Stages of aerobic respiration

11.5 Significance for Plants

Respiration provides ATP for active uptake of minerals, protein synthesis, growth and movement.
It supplies carbon skeletons (e.g., α-ketoglutarate, oxaloacetate) for amino-acid synthesis (link with Week 10).
It releases heat that contributes to flower thermogenesis (e.g., Arum, Symplocarpus) to volatilise scents.

📝 Self-Check Quiz — Week 11

During aerobic respiration, the bulk of ATP is produced at:

📝 Classwork & Assignment — Week 11

A. Classwork

Write the overall equation for aerobic respiration.
State the location, net ATP, and net NADH for each of the four stages.
Explain why O₂ is essential despite not appearing until the last step.

B. Practical / Take-Home

Germinating seed respiration: Use a thermos flask with germinating bean seeds + thermometer; record temperature rise over 24 h. Compare with boiled (dead) seeds. Explain.
Short essay: "Plants respire all day and all night; why does this not exhaust their food?"

Marks: 15 · Submit Week 13

WEEK 12

Anaerobic Respiration in Plants

Fermentation · Ethanol & lactate · Flooded soils · Comparison with aerobic

Learning Outcomes

Define anaerobic respiration and fermentation in plants
Write the equations for ethanol and lactate fermentation
Compare aerobic and anaerobic respiration in ATP yield
Explain anaerobic adaptations (e.g., rice, flood-tolerant crops)

12.1 When Plants Respire Without Oxygen

When O₂ is limited — in flooded soils, deep within bulky tissues, or in submerged seeds — plants switch to anaerobic respiration (fermentation). Glycolysis still occurs, but pyruvate is no longer fed into the Krebs cycle; instead it is reduced to ethanol or lactate to regenerate NAD⁺ so glycolysis can continue.

12.2 Two Routes

Pathway	Equation	Where
Ethanol fermentation	Pyruvate → acetaldehyde + CO₂; acetaldehyde + NADH → ethanol + NAD⁺	Most plants under hypoxia; yeast
Lactate fermentation	Pyruvate + NADH → lactate + NAD⁺	Brief or partial hypoxia; some root tips; animal muscle

⚡ Overall Equation

C₆H₁₂O₆ → 2 C₂H₅OH + 2 CO₂ + 2 ATP (ethanol fermentation)

12.3 Aerobic vs. Anaerobic Respiration

Feature	Aerobic	Anaerobic
O₂ required?	Yes	No
Final product of glucose	CO₂ + H₂O	Ethanol + CO₂ (or lactate)
ATP yield	~32 per glucose	2 per glucose
Site	Cytoplasm + mitochondrion	Cytoplasm only
Heat	Moderate	Low

12.4 Adaptations to Anaerobic Conditions

Rice (Oryza sativa): aerenchyma tissue carries O₂ from leaves to submerged roots.
Mangrove pneumatophores: aerial breathing roots above tidal mud.
Cypress knees in swamp species.
Tolerant species accumulate alanine rather than ethanol to avoid self-poisoning.

12.5 Practical Significance

Application	Use
Bread & alcohol industry	Yeast (and plant-cell ethanol fermentation) produce CO₂ and ethanol.
Silage making	Lactic-acid fermentation preserves animal feed.
Storage of grains/tubers	Reducing O₂ in airtight silos slows respiration; but excess hypoxia ruins quality.

📝 Self-Check Quiz — Week 12

A plant root in a flooded field switches to ethanol fermentation. The cell's main energetic disadvantage is:

📝 Classwork & Assignment — Week 12

A. Classwork

Write the overall equation for ethanol fermentation in plants.
State four differences between aerobic and anaerobic respiration.
Explain how rice survives in waterlogged paddy fields.

B. Take-Home Practical

Place yeast in a glucose solution inside a sealed flask connected to limewater. Record the time taken for limewater to turn milky and explain.
Optional: repeat with germinating pea seeds kept in nitrogen gas to simulate hypoxia.

Marks: 10 · Submit Week 14

WEEK 13

Plant Growth & Its Measurement

Meristems · Growth zones · Auxometer/arc indicator · Sigmoid curve · Growth analysis

Learning Outcomes

Define plant growth and identify the meristems involved
Describe zones of cell division, elongation and maturation
Use simple instruments (auxometer, horizontal microscope) to measure growth
Interpret a sigmoid growth curve and growth indices (RGR, NAR)

13.1 What is Plant Growth?

Growth is the irreversible increase in size, mass or number of cells in a plant, driven by cell division and cell expansion. Unlike animals, plants grow throughout their life through specialised tissues called meristems. [NCBI]

13.2 Types of Meristems

Meristem	Location	Result
Apical	Tips of shoots and roots	Primary growth (length)
Lateral (cambium)	Cylindrical layers in stems and roots of dicots	Secondary growth (girth) — absent in most monocots
Intercalary	Bases of internodes (e.g., grasses)	Rapid stem elongation; allows regrowth after grazing

13.3 Three Growth Zones at a Root or Shoot Tip

ZONE 1

Cell Division

Apical meristem cells divide actively. Small, square, dense cytoplasm.

→

ZONE 2

Cell Elongation

Cells take up water into vacuoles and stretch lengthwise; auxin loosens walls.

→

ZONE 3

Cell Maturation

Cells differentiate into tissues (xylem, phloem, parenchyma). Growth complete.

13.4 Methods of Measuring Growth

Method	Principle	What it measures
Direct measurement (ruler/calipers)	Increase in length, diameter	Stem height, leaf length, root length
Auxometer / Arc indicator	Pivoting pointer amplifies tip growth	Rapid (minutes–hours) shoot elongation
Horizontal microscope	Cross-hairs track tip movement against scale	Very small or slow growth
Crescograph (Bose)	Magnifies movement up to 10⁶×	Minute changes in length
Fresh / dry mass	Weighing	Total biomass over time
Leaf area (graphical or planimeter)	Area calculation	Total photosynthetic surface

Figure 13.1 — Sigmoid (S-shaped) growth curve

The classic plant growth curve is sigmoid: a slow lag phase, an exponential log phase (most rapid increase), and a stationary phase (growth tapers as resources or developmental signals limit it).

13.5 Quantitative Growth Analysis

📊 Growth Indices

Relative Growth Rate (RGR) = (ln W₂ − ln W₁) / (t₂ − t₁) — mass added per unit existing mass per unit time.
Net Assimilation Rate (NAR) = increase in mass per unit leaf area per unit time — photosynthetic efficiency.
Leaf Area Ratio (LAR) = leaf area / total dry mass.
RGR = NAR × LAR.

📝 Self-Check Quiz — Week 13

Most rapid stem elongation in grasses (e.g., maize, sugarcane) is driven by:

📝 Classwork & Assignment — Week 13

A. Classwork

Distinguish apical, lateral and intercalary meristems with one example each.
Sketch the sigmoid growth curve and label the lag, log and stationary phases.
Calculate the RGR of a plant whose dry mass rose from 5 g to 20 g in 30 days.

B. Practical Assignment (lab + field)

Grow 10 maize seedlings; measure shoot height and leaf number every 2 days for 3 weeks. Tabulate, plot a growth curve, identify the phases, and calculate RGR.
Construct a simple auxometer using a pin, lever, and pulley; demonstrate growth of a Coleus shoot over 24 h.

Marks: 20 · Lab report due Week 15

WEEK 14

Plant Movements

Tropisms · Thigmotropism · Nastic movements · Hormonal control

Learning Outcomes

Define tropism and nastic movement and distinguish them
List the major tropisms with examples
Explain thigmotropism and tendril coiling
Describe nastic movements and the role of the pulvinus
Outline hormonal control of movement (auxin, ABA)

14.1 Two Big Classes of Plant Movement

Feature	Tropism	Nastic
Direction	Determined by stimulus direction	Independent of stimulus direction
Mechanism	Differential growth	Reversible turgor changes (osmotic)
Reversible?	No (growth is permanent)	Yes
Example	Shoot bending toward light	Mimosa leaf folding on touch

14.2 Tropisms — Directional Growth Responses

Tropism	Stimulus	Example
Phototropism	Light	Shoot bends toward light (positive); roots away (negative)
Geotropism (Gravitropism)	Gravity	Roots grow downward (positive); shoots upward (negative)
Hydrotropism	Water	Roots grow toward moisture
Chemotropism	Chemicals	Pollen tube grows toward ovule
Thigmotropism	Touch / mechanical contact	Tendrils of cucumber, passion fruit, grapevine coil around supports
Thermotropism	Temperature	Some flowers track warmth
Traumatotropism	Wounding	Roots grow away from injured side

Most tropic responses are mediated by auxin (IAA) migrating to the shaded or lower side of an organ, where it promotes elongation, causing the curvature. [Britannica]

14.3 Thigmotropism — The Touch Response

🌿

When a tendril contacts a support, contact-side cells shorten while the opposite side elongates, producing a tight coil within minutes to hours. The response is potentiated by auxin and ethylene and shows thigmomorphogenesis — long-term changes in plant form due to repeated mechanical stimulation (wind-pruned trees stay shorter).

14.4 Nastic Movements

Type	Stimulus	Example
Thigmonasty	Touch	Mimosa pudica leaf folding; Venus fly-trap closure
Photonasty	Light intensity	Dandelion / morning glory opening at dawn
Nyctinasty	Day/night cycle	Prayer plant (Maranta) leaves fold up at night
Thermonasty	Temperature	Tulip / crocus flower opens with warmth
Chemonasty	Chemicals	Sundew tentacles bend on contact with prey
Seismonasty	Vibration / shock	Mimosa leaf collapse on touch

💧

The pulvinus. Many leaf nastic movements depend on a swollen pulvinus (cushion) at the leaflet base. Sudden K⁺ movement causes water to rush out of parenchyma cells on one side, collapsing turgor; the leaf folds. Recovery within minutes restores turgor. [CK-12]

14.5 Plant Hormones in Movement & Growth (Quick Reference)

Hormone	Main role(s)
Auxin (IAA)	Phototropism, gravitropism, apical dominance, root initiation
Gibberellins (GA)	Cell elongation, stem growth, breaking seed dormancy
Cytokinins	Cell division, delay of senescence
Ethylene	Fruit ripening, leaf abscission
Abscisic acid (ABA)	Stomatal closure, dormancy, stress response

[Oregon State Extension]

📝 Self-Check Quiz — Week 14

When a Mimosa leaf collapses upon touch, the underlying mechanism is:

📝 Classwork & Assignment — Week 14

A. Classwork

State two clear differences between tropic and nastic movements.
List five tropisms with their stimuli and one example each.
Explain the role of auxin in shoot phototropism.

B. Practical / Take-Home

Phototropism demo: Place a bean seedling on a windowsill with light only from one direction; record the angle of curvature daily for a week and explain.
Mimosa investigation: Time the leaf-folding response of Mimosa pudica after a single touch and after repeated touches. Discuss any habituation observed.
Essay (300–500 words): "How plants 'see', 'feel' and 'choose' — the physiology of plant movement."

Marks: 15 · Submit Week 16

WEEK 15

Excretion in Plants & Course Synthesis

Removal of waste · Secondary metabolites · Integration of all topics · Exam prep

Final Learning Outcomes

Describe how plants excrete gases, water and solid waste
Identify common secondary metabolites that act as excretory products
Integrate all course themes — absorption, photosynthesis, translocation, respiration, growth, movement, excretion
Prepare effectively for the BIO 221 examination

15.1 Excretion in Plants — Why So Quiet?

Plants do not have specialised excretory organs comparable to animal kidneys. Their metabolism produces less nitrogenous waste because nitrogen is recycled into amino acids. Most of what would be "waste" is either re-used, deposited as inert deposits, or released through diffusion. [Britannica]

15.2 Routes of Excretion

Substance	Route of removal
O₂ (from photosynthesis)	Diffuses out through stomata, lenticels, root cell walls
CO₂ (from respiration)	Diffuses out through stomata and lenticels
Excess water	Transpiration (evaporation) and guttation (liquid drops via hydathodes)
Mineral salts	Crystallised as raphides or cystoliths inside vacuoles, or stored in older leaves shed at leaf-fall
Organic acids, tannins, alkaloids	Stored in vacuoles, bark, heart-wood; also leached by rain
Resins, latex, gums, mucilage	Exuded passively via specialised ducts after wounding (e.g., rubber tree, pine, papaya)

Many excretory products serve secondary roles — alkaloids deter herbivores, resins seal wounds, latex traps insects, tannins resist decay.

15.3 Important Plant Secondary Products

Class	Examples	Significance
Alkaloids	Caffeine, nicotine, quinine, morphine	Defence; major medicinal value
Tannins	Found in oak, mangrove bark	Antimicrobial; leather industry
Resins	From pine, frankincense	Wound sealing; varnish
Latex	Hevea (rubber), Carica (papaya)	Defence; commercial rubber
Essential oils	Citrus, mint, eucalyptus	Pollinator attraction; aroma industry
Crystals (Ca-oxalate)	Raphides in cocoyam, dieffenbachia	Sequester calcium; deter herbivores

15.4 Course Integration — The Big Picture

Topic	Connects to	Why it matters
Water absorption	Transpiration, mineral uptake	Without uptake there is no transport stream
Photosynthesis	Translocation, respiration	Source of organic carbon for the entire plant and ecosystem
Mineral nutrition	Photosynthesis (Mg, Fe), N assimilation (Mo)	Limits productivity
Translocation	Photosynthesis, growth, storage	Distributes assimilates to non-photosynthetic tissues
Respiration	All energy-requiring processes	Uses sugars; provides ATP & carbon skeletons
Growth & movement	Hormonal regulation	Outcome of internal physiology + environmental cues
Excretion	Photosynthesis, respiration, defence	Removes by-products and produces useful secondary metabolites

15.5 Examination Preparation

📚 Revision Checklist by Week

Wk 1: Define plant physiology; explain plants as primary producers.
Wk 2–3: Water potential equation; pathways of uptake; cohesion-tension; factors affecting transpiration.
Wk 4–5: 14 mineral elements; symptoms of deficiency in N, P, K, Ca, Mg, Fe, Zn.
Wk 6–8: Equation of photosynthesis; chloroplast structure; Z-scheme; photolysis; Calvin cycle phases; C3/C4/CAM.
Wk 9: Pressure-flow hypothesis; xylem vs. phloem.
Wk 10: NR, NiR, GS-GOGAT; transamination.
Wk 11–12: Stages of aerobic respiration; ATP yields; ethanol fermentation; aerobic vs. anaerobic.
Wk 13: Meristems; growth zones; sigmoid curve; RGR.
Wk 14: Tropism vs. nastic; auxin in phototropism; pulvinus mechanism.
Wk 15: Routes of plant excretion; major secondary metabolites.

📝 Final Review Quiz — Week 15

A maize plant in a flooded field shows yellowing of older leaves and weak roots. Drawing on the whole course, the most likely combined explanation is:

📝 Classwork & Final Assignment — Week 15

A. Classwork

List four routes by which plants excrete waste.
Identify three commercially important plant secondary metabolites.
Draw a single integrated diagram showing water uptake → transpiration → photosynthesis → translocation → respiration in the same plant.

B. Final Course Project

Choose one local crop (e.g., cassava, maize, rice, tomato, cocoa, oil palm).
Write a 1500-word case study covering: water relations, mineral needs, photosynthetic pathway (C3/C4/CAM), translocation, key respiration considerations, growth pattern, hormonal/movement response, and notable excretory products.
Include at least two diagrams and three primary references.

Marks: 30 (counts toward CA) · Submit by examination week

COURSE COMPLETE

Congratulations!

You have completed BIO 221 Plant Physiology — from soil water and stomata to chloroplasts, sugars, sap streams, growth and movement. Plants quietly do most of the work that keeps our planet alive. Carry that perspective into your next course.

BIO 221 — PlantPhysiology

Welcome to Plant Physiology

Plants as Primary Food Producers

Learning Outcomes

1.1 What is Plant Physiology?

1.2 Plants as Primary Food Producers

1.3 The Energy Flow Diagram

1.4 Scope of BIO 221

A. Classwork (in lecture, 15 min)

B. Take-Home Assignment (due next class)

Plant Water Absorption

Learning Outcomes

2.1 Why Plants Need Water

2.2 Water Potential (ψ)

2.3 Three Pathways Across the Root

2.4 The Casparian Strip

2.5 Active vs. Passive Absorption

A. Classwork (in lecture, 20 min)

B. Practical Assignment (lab, 1 week)

Plant Transpiration

Learning Outcomes

3.1 What is Transpiration?

3.2 Stomatal Mechanism

3.3 Cohesion-Tension Theory (Dixon & Joly, 1894)

3.4 Significance and Costs

3.5 Factors Affecting Transpiration

A. Classwork (in lecture)

B. Practical Assignment (lab)

Mineral Requirements

Learning Outcomes

4.1 Essential Elements — Arnon & Stout's Criteria (1939)

4.2 Macronutrients (required > 1000 mg/kg dry mass)

4.3 Micronutrients / Trace Elements (required < 100 mg/kg)

4.4 Mineral Uptake Mechanisms

A. Classwork

B. Take-Home Assignment

Nutrient Deficiency Diseases

Learning Outcomes

5.1 General Symptoms

5.2 Mobile vs. Immobile Elements — Where Symptoms Show

5.3 Major Deficiency Diseases

5.4 Simple Diagnostic Key

5.5 Remedies

A. Classwork

B. Take-Home Assignment / Field Exercise

Photosynthesis I — Chloroplast, Raw Materials & Products

Learning Outcomes

6.1 Definition and Significance

6.2 Raw Materials and Products

6.3 The Chloroplast — Site of Photosynthesis

6.4 Photosynthetic Pigments

6.5 Two Stages of Photosynthesis — Overview

A. Classwork

B. Practical / Take-Home

Light Reactions & Photolysis of Water

Learning Outcomes

7.1 Two Photosystems

7.2 Photolysis of Water (Hill Reaction)

7.3 The Z-Scheme — Non-Cyclic Photophosphorylation

7.4 Cyclic vs. Non-Cyclic Photophosphorylation

7.5 Summary of Light-Reaction Products

A. Classwork

B. Take-Home

Calvin Cycle (Dark Reactions)

Learning Outcomes

8.1 Overview

8.2 Three Phases of the Calvin Cycle

8.3 Diagram of the Calvin Cycle

8.4 C3, C4 and CAM Pathways

A. Classwork

B. Take-Home Assignment

Translocation of Manufactured Food

Learning Outcomes

9.1 What is Translocation?

9.2 Phloem Anatomy

9.3 Source and Sink

9.4 Pressure-Flow Hypothesis (Ernst Münch, 1930)

9.5 Xylem vs. Phloem

A. Classwork

B. Take-Home Assignment

BIO 221 — Plant
Physiology