CSIR-NET LIFE SCIENCES

Unit 6: System Physiology – Plant

Complete Topic-Wise Syllabus

Photosynthesis • Respiration • Nitrogen Metabolism • Plant Hormones • Photobiology • Transport • Secondary Metabolites • Stress Physiology

A. Photosynthesis

☀️ 1. Light Harvesting Complexes

• Concept of light harvesting
• Photosynthetic pigments
• Chlorophyll a
• Chlorophyll b
• Carotenoids
• Phycobilins
• Light-harvesting complexes
• Photosystems I and II
• Antenna pigments
• Energy transfer between pigments

🌿 2. Photosynthetic Apparatus

• Chloroplast structure
• Outer and inner chloroplast membranes
• Stroma
• Thylakoid membranes
• Grana
• Stroma lamellae
• Photosystem organization

⚡ 3. Photosynthetic Electron Transport

• Light absorption
• Excitation of chlorophyll
• Photosystem II
• Water splitting
• Oxygen evolution complex
• Plastoquinone
• Cytochrome b6f complex
• Plastocyanin
• Photosystem I
• Ferredoxin
• Ferredoxin-NADP⁺ reductase
• NADPH formation

🔋 4. Photophosphorylation

• Proton gradient
• Chemiosmotic mechanism
• ATP synthase
• Non-cyclic photophosphorylation
• Cyclic photophosphorylation
• ATP production
• NADPH production

☀️ Z-Scheme of Photosynthesis:

Water → PSII → Plastoquinone → Cytochrome b6f → Plastocyanin → PSI → Ferredoxin → NADP⁺ → NADPH

PSII: Water oxidation + O₂ evolution
PSI: NADPH production

🛡️ 5. Photoprotective Mechanisms

• Photoinhibition
• Non-photochemical quenching
• Thermal dissipation
• Carotenoid-mediated protection
• Xanthophyll cycle
• Reactive oxygen species management
• Antioxidant defense
• Superoxide dismutase
• Catalase
• Ascorbate peroxidase

🌱 6. CO₂ Fixation

• Calvin-Benson cycle
• Carbon fixation
• Rubisco
• Carboxylation
• Reduction
• Regeneration of RuBP
• Photorespiration
• ATP and NADPH utilization

🌿 7. C₃ Pathway

• Primary CO₂ acceptor: RuBP
• First stable product: 3-phosphoglycerate
• Role of Rubisco
• Reduction phase
• Regeneration phase
• Carbon balance

🌾 8. C₄ Pathway

• Kranz anatomy
• Mesophyll cells
• Bundle sheath cells
• PEP carboxylase
• Oxaloacetate
• Malate/aspartate
• CO₂ concentration mechanism
• Decarboxylation
• Calvin cycle in bundle sheath

🌵 9. CAM Pathway

• Crassulacean acid metabolism
• Night-time CO₂ fixation
• PEP carboxylase
• Malate storage
• Day-time decarboxylation
• Calvin cycle
• Water-use efficiency

🎯 C₃ vs C₄ vs CAM – Must Know:

C₃ → Spatially uncomplicated CO₂ fixation
C₄ → Spatial separation of initial fixation and Calvin cycle
CAM → Temporal separation of initial fixation and Calvin cycle

B. Respiration and Photorespiration

🔥 1. Citric Acid Cycle

• Location of TCA cycle
• Acetyl-CoA formation
• Citrate formation
• Isocitrate formation
• α-ketoglutarate
• Succinyl-CoA
• Succinate
• Fumarate
• Malate
• Oxaloacetate regeneration

⚡ 2. Plant Mitochondrial Electron Transport

• Mitochondrial electron transport chain
• Complex I
• Complex II
• Ubiquinone
• Complex III
• Cytochrome c
• Complex IV
• Oxygen reduction
• Proton gradient

🔋 3. ATP Synthesis

• Oxidative phosphorylation
• Proton motive force
• ATP synthase
• Chemiosmosis
• Electron transport and ATP coupling

🔀 4. Alternative Oxidase

• Alternative respiratory pathway
• Alternative oxidase
• Electron flow bypassing Complex III and IV
• Reduced ATP generation
• Heat production
• Role in plant stress responses
• Role in thermogenic plants

🌿 5. Photorespiration

• Rubisco oxygenase activity
• Formation of 2-phosphoglycolate
• Photorespiratory pathway
• Chloroplast
• Peroxisome
• Mitochondrion
• Glycolate
• Glycine
• Serine
• CO₂ release
• NH₃ release

🔬 Photorespiration:

Rubisco + O₂ → RuBP oxygenation → 2-phosphoglycolate → Glycolate → Glycine → Serine → Calvin cycle intermediates

The pathway involves chloroplast + peroxisome + mitochondrion.

C. Nitrogen Metabolism

🌱 1. Nitrogen Uptake

• Importance of nitrogen
• Nitrate uptake
• Ammonium uptake
• Nitrate transporters
• Ammonium transporters
• Root nitrogen acquisition

🧪 2. Nitrate Assimilation

• Nitrate reduction
• Nitrate reductase
• Nitrite formation
• Nitrite reductase
• Ammonium formation

🔬 3. Ammonium Assimilation

• GS-GOGAT pathway
• Glutamine synthetase
• Glutamate synthase
• Glutamine formation
• Glutamate formation
• Integration with carbon metabolism

🎯 High-Yield:

NH₄⁺ → Glutamine synthetase → Glutamine → GOGAT → Glutamate

🧬 4. Amino Acid Biosynthesis

• Glutamate family
• Aspartate family
• Pyruvate family
• Serine family
• Aromatic amino acids
• Branched-chain amino acids

🦠 5. Biological Nitrogen Fixation

• Nitrogen fixation
• Nitrogenase complex
• Fe protein
• MoFe protein
• ATP requirement
• Oxygen sensitivity
• Rhizobium-legume symbiosis
• Root nodules
• Leghemoglobin

🧬 Nitrogenase Reaction:

N₂ + 8H⁺ + 8e⁻ + 16ATP → 2NH₃ + H₂ + 16ADP + 16Pi

D. Plant Hormones

🌱 1. Auxin

• Auxin biosynthesis
• IAA
• Polar auxin transport
• Cell elongation
• Apical dominance
• Root initiation
• Tropisms
• Fruit development

🌿 2. Cytokinins

• Cytokinin biosynthesis
• Cell division
• Meristem maintenance
• Delay of senescence
• Shoot formation
• Source-sink regulation

🌾 3. Gibberellins

• GA biosynthesis
• Seed germination
• Stem elongation
• Bolting
• Flowering
• Fruit growth
• α-amylase induction

🍂 4. Abscisic Acid

• ABA biosynthesis
• Seed dormancy
• Stomatal closure
• Drought response
• Stress signaling
• Seed maturation

🍌 5. Ethylene

• Ethylene biosynthesis
• Fruit ripening
• Abscission
• Senescence
• Triple response
• Stress responses

🌱 6. Other Plant Hormones

• Brassinosteroids
• Jasmonates
• Salicylic acid
• Strigolactones

🔄 7. Hormone Transport

• Local hormone transport
• Long-distance transport
• Polar transport
• Vascular transport
• Hormonal crosstalk

⚙️ 8. Hormonal Mechanisms of Action

• Hormone receptors
• Signal transduction
• Second messengers
• Protein phosphorylation
• Transcriptional regulation
• Hormone-responsive genes

🌿 Hormone Quick Association:

Auxin → Cell elongation & apical dominance
Cytokinin → Cell division & delayed senescence
GA → Growth & germination
ABA → Stress & dormancy
Ethylene → Ripening & senescence

E. Sensory Photobiology

💡 1. Light Perception

• Light as an environmental signal
• Photoreceptors
• Red and far-red light
• Blue light
• UV light
• Light-dependent signaling

🔴 2. Phytochromes

• Phytochrome structure
• Pr form
• Pfr form
• Red light
• Far-red light
• Photoconversion
• Phytochrome signaling
• Seed germination
• Shade avoidance
• De-etiolation

🔵 3. Cryptochromes

• Blue-light receptors
• Cryptochrome structure
• Photoreception
• Photomorphogenesis
• Circadian regulation
• Flowering responses

🔵 4. Phototropins

• Blue-light receptors
• Phototropism
• Chloroplast movement
• Stomatal opening
• Leaf positioning

🌿 5. Stomatal Movement

• Guard cells
• Stomatal opening
• Stomatal closure
• Potassium ion movement
• Anion transport
• Water movement
• ABA signaling
• Blue-light signaling

🌞 6. Photoperiodism

• Photoperiodic response
• Short-day plants
• Long-day plants
• Day-neutral plants
• Critical day length
• Phytochrome involvement
• Florigen

🕐 7. Biological Clock

• Circadian rhythm
• Oscillators
• Clock genes
• Light entrainment
• Free-running rhythm
• Period
• Phase
• Amplitude

💡 Photoreceptor Quick Revision:

Phytochrome → Red/Far-red light
Cryptochrome → Blue light
Phototropin → Blue light, phototropism & stomatal responses

F. Solute Transport and Photoassimilate Translocation

💧 1. Water Uptake

• Root water uptake
• Osmosis
• Water potential
• Solute potential
• Pressure potential
• Aquaporins
• Root pressure

🌊 2. Water Transport

• Apoplast pathway
• Symplast pathway
• Transmembrane pathway
• Casparian strip
• Xylem transport
• Cohesion-tension theory
• Transpiration pull

🧂 3. Ion Uptake and Transport

• Essential mineral nutrients
• Ion channels
• Transporters
• Primary active transport
• Secondary active transport
• Proton pumps
• H⁺-ATPase

🚰 4. Xylem Transport

• Water transport
• Mineral transport
• Xylem vessels
• Tracheids
• Cohesion
• Adhesion
• Transpiration-driven transport

🍃 5. Transpiration

• Stomatal transpiration
• Cuticular transpiration
• Lenticular transpiration
• Factors affecting transpiration
• Stomatal regulation

🍬 6. Photoassimilate Translocation

• Photosynthate production
• Sucrose transport
• Source tissues
• Sink tissues
• Phloem transport
• Pressure-flow hypothesis

⬆️⬇️ 7. Phloem Loading

• Apoplastic loading
• Symplastic loading
• Sucrose transporters
• Companion cells
• Sieve tube elements

📦 8. Phloem Unloading

• Symplastic unloading
• Apoplastic unloading
• Sink strength
• Source-sink relationship
• Storage tissues
• Growing tissues

🌿 Water vs Food Transport:

Xylem: Mainly water + minerals
Phloem: Mainly photoassimilates such as sucrose

G. Secondary Metabolites

🌿 1. Plant Secondary Metabolism

• Primary versus secondary metabolites
• Ecological functions
• Defense
• Signaling
• Plant-environment interactions

🌲 2. Terpenes and Terpenoids

• Isoprenoid biosynthesis
• IPP
• DMAPP
• MVA pathway
• MEP pathway
• Monoterpenes
• Sesquiterpenes
• Diterpenes
• Triterpenes
• Tetraterpenes

🍂 3. Phenolic Compounds

• Phenolic acids
• Flavonoids
• Tannins
• Lignin
• Anthocyanins
• Antioxidant activity
• UV protection

🌸 4. Phenylpropanoids

• Phenylalanine ammonia-lyase
• Phenylalanine-derived compounds
• Cinnamic acid
• Coumarins
• Flavonoids
• Lignin biosynthesis

☠️ 5. Alkaloids

• Nitrogen-containing secondary metabolites
• Alkaloid biosynthesis
• Nicotine
• Morphine
• Caffeine
• Defense mechanisms

🧪 6. Nitrogenous Compounds

• Alkaloids
• Glucosinolates
• Cyanogenic compounds
• Non-protein amino acids
• Plant defense

🛡️ 7. Roles of Secondary Metabolites

• Herbivore defense
• Pathogen defense
• Allelopathy
• Pollinator attraction
• UV protection
• Antioxidant defense
• Plant signaling

🧬 8. Metabolic Engineering

• Engineering metabolic pathways
• Overexpression of biosynthetic genes
• Gene silencing
• Pathway optimization
• Metabolic flux
• Production of high-value metabolites
• Plant biotechnology applications

🧬 Important Biosynthetic Routes:

Terpenes → MVA + MEP pathways
Phenylpropanoids → Shikimate → Phenylalanine → PAL pathway
Alkaloids → Amino-acid-derived pathways

H. Stress Physiology

🌡️ 1. Abiotic Stress

• Drought stress
• Salinity stress
• Heat stress
• Cold stress
• Oxidative stress
• Heavy metal stress
• Nutrient stress
• Flooding and hypoxia

💧 2. Drought Stress

• Water deficit
• Stomatal closure
• ABA accumulation
• Osmotic adjustment
• Proline accumulation
• Reactive oxygen species
• Antioxidant defense

🧂 3. Salinity Stress

• Osmotic stress
• Ion toxicity
• Na⁺ accumulation
• K⁺/Na⁺ balance
• Ion transport
• Osmoprotectants
• Antioxidant mechanisms

🔥 4. Heat Stress

• Protein denaturation
• Membrane damage
• Heat shock proteins
• Heat shock factors
• Antioxidant response
• Acclimation

❄️ 5. Cold Stress

• Membrane rigidification
• Cold-responsive genes
• CBF/DREB pathway
• Osmoprotectants
• Antioxidant defense

⚡ 6. Oxidative Stress

• Reactive oxygen species
• Superoxide
• Hydrogen peroxide
• Hydroxyl radical
• Singlet oxygen
• ROS signaling

🛡️ 7. Antioxidant Defense

• Superoxide dismutase
• Catalase
• Ascorbate peroxidase
• Glutathione peroxidase
• Ascorbate
• Glutathione
• Non-enzymatic antioxidants

🦠 8. Biotic Stress

• Pathogenic bacteria
• Pathogenic fungi
• Viruses
• Insects
• Nematodes
• Herbivores

🌿 9. Plant Innate Immunity

• Pattern recognition receptors
• PAMP recognition
• PTI – Pattern-triggered immunity
• Effector-triggered immunity
• Effector recognition
• Hypersensitive response
• Systemic acquired resistance

🧬 10. Molecular Stress Responses

• Stress-responsive transcription factors
• DREB
• WRKY
• NAC
• MYB
• Heat shock factors
• Stress-responsive genes

🔬 11. Plant Defense Signaling

• Salicylic acid signaling
• Jasmonic acid signaling
• Ethylene signaling
• Calcium signaling
• ROS signaling
• MAP kinase cascades
• Defense gene activation

🛡️ Plant Immunity Sequence:

Pathogen-associated signal → Pattern recognition receptor → PAMP recognition → PTI → Pathogen effector → Effector recognition → ETI → Defense responses

🎯 Major Stress-Response Components:

Stress perception → Signal transduction → Ca²⁺ signaling → ROS/ROS signaling → Hormonal signaling → Transcription factors → Stress-responsive genes → Physiological adaptation

📚 Unit 6 – Plant Physiology Quick Revision Map

A → Photosynthesis

B → Respiration & Photorespiration

C → Nitrogen Metabolism

D → Plant Hormones

E → Sensory Photobiology

F → Solute Transport

G → Secondary Metabolites

H → Stress Physiology

🎯 Most Important CSIR-NET Topics

• Light-harvesting complexes
• Photosystem I and Photosystem II
• Z-scheme of electron transport
• Photophosphorylation
• Photoprotection and non-photochemical quenching
• Calvin cycle
• C₃, C₄ and CAM pathways
• Photorespiration
• TCA cycle
• Plant mitochondrial electron transport chain
• Alternative oxidase pathway
• Nitrate assimilation
• GS-GOGAT pathway
• Biological nitrogen fixation
• Nitrogenase complex
• Auxin transport and signaling
• Cytokinin signaling
• Gibberellin and seed germination
• ABA and drought response
• Ethylene and fruit ripening
• Phytochrome photoconversion
• Cryptochromes and phototropins
• Stomatal movement
• Photoperiodism
• Circadian clock
• Water potential
• Cohesion-tension theory
• Xylem transport
• Phloem loading and unloading
• Pressure-flow hypothesis
• Terpenoid biosynthesis
• Phenylpropanoid pathway
• Alkaloid biosynthesis
• Plant metabolic engineering
• Drought and salinity stress
• Heat and cold stress
• ROS and antioxidant defense
• PTI and ETI
• Systemic acquired resistance
• Plant innate immunity

📖 Recommended Study Sequence:

☀️ Photosynthesis → 🔥 Respiration → 🧪 Nitrogen Metabolism → 🌱 Plant Hormones → 💡 Photobiology → 💧 Transport → 🧬 Secondary Metabolism → 🛡️ Stress Physiology