CSIR NET Life Sciences System Physiology - Plant Syllabus

State the chemiosmotic basis of mitochondrial ATP synthesis.

Electron transport pumps protons across the inner membrane creating a proton-motive force (ΔpH + membrane potential); protons flow back through ATP synthase (F0F1), driving ATP synthesis (Mitchell's chemiosmotic theory).

What is the alternative oxidase (AOX) and where does it branch from the chain?

AOX is a cyanide-resistant terminal oxidase in plant mitochondria that accepts electrons directly from ubiquinol and reduces O2 to water, bypassing Complexes III and IV (no proton pumping, energy released as heat).

What is the physiological significance of the alternative oxidase pathway?

It allows continued carbon flux/respiration when the cytochrome path is restricted, prevents over-reduction of the ubiquinone pool and ROS formation, and generates heat (thermogenesis, e.g., in Arum spadix).

What triggers the oxygenase activity of Rubisco that initiates photorespiration?

When O2 competes with CO2 at Rubisco's active site (high O2/CO2 ratio, e.g., closed stomata, high temperature), Rubisco adds O2 to RuBP, producing one 3-PGA and one 2-phosphoglycolate (2C).

Name the three organelles involved in the photorespiratory (C2/glycolate) pathway.

Chloroplast, peroxisome, and mitochondrion cooperate in the photorespiratory cycle to metabolize 2-phosphoglycolate and recover carbon as 3-PGA.

What is released in the mitochondrial step of photorespiration, and the carbon cost?

In mitochondria, two glycine molecules are converted to one serine, releasing CO2 and NH3. Photorespiration thus loses fixed carbon (about 25% of fixed CO2) and nitrogen that must be reassimilated.

Write the reactions of nitrate assimilation including enzymes and their locations.

NO3- → NO2- by nitrate reductase (cytosol, uses NADH); NO2- → NH4+ by nitrite reductase (chloroplast/plastid, uses reduced ferredoxin).

Describe the GS-GOGAT pathway of ammonium assimilation.

Glutamine synthetase (GS) combines NH4+ with glutamate to form glutamine (uses ATP); glutamate synthase (GOGAT) transfers the amide to 2-oxoglutarate, forming two glutamate molecules (uses reduced ferredoxin or NADH).

What enzyme catalyzes biological nitrogen fixation and what is its overall reaction?

Nitrogenase: N2 + 8H+ + 8e- + 16 ATP → 2 NH3 + H2 + 16 ADP + 16 Pi. It is oxygen-sensitive and contains Fe and Mo-Fe cofactors.

How are amino acid families grouped by their carbon-skeleton precursors in plants?

Amino acids derive from key metabolic intermediates: e.g., glutamate family from 2-oxoglutarate; aspartate family from oxaloacetate; aromatic amino acids from the shikimate pathway (PEP + erythrose-4-P); serine family from 3-PGA.

What is the shikimate pathway and which amino acids does it produce?

The shikimate pathway (in plastids) converts phosphoenolpyruvate and erythrose-4-phosphate to chorismate, the precursor of the aromatic amino acids phenylalanine, tyrosine, and tryptophan (and many phenolics).

Name the five classical plant hormones and one key effect of each.

Auxin (cell elongation, apical dominance); Gibberellin (stem elongation, seed germination); Cytokinin (cell division, delays senescence); Abscisic acid (ABA; stomatal closure, dormancy); Ethylene (fruit ripening, senescence).

What is the principal naturally occurring auxin and its main biosynthetic precursor?

Indole-3-acetic acid (IAA) is the main natural auxin, synthesized primarily from the amino acid tryptophan.

Explain the chemiosmotic (acid-growth) hypothesis of auxin action.

Auxin activates plasma membrane H+-ATPases, acidifying the cell wall; low pH activates expansins that loosen the wall, allowing turgor-driven cell elongation.

What is polar auxin transport and which carriers mediate it?

Auxin moves unidirectionally (basipetally in shoots) cell-to-cell via influx carriers (AUX1/LAX) and asymmetrically localized efflux carriers (PIN proteins), whose polarity sets the direction of flow.

How does ABA cause stomatal closure at the guard-cell level?

ABA raises cytosolic Ca2+ and pH, activating anion channels (SLAC1) and K+ efflux channels while inhibiting inward K+ channels and the H+-ATPase; loss of solutes reduces guard-cell turgor, closing the stoma.

What is the gibberellin signaling mechanism involving DELLA proteins?

GA binds the GID1 receptor; the GA-GID1 complex promotes degradation of growth-repressing DELLA proteins via the SCF-ubiquitin/proteasome pathway, releasing growth and GA responses.

Describe the chromophore and two interconvertible forms of phytochrome.

Phytochrome carries a linear tetrapyrrole (phytochromobilin) chromophore. It exists as Pr (red-absorbing, ~660 nm, inactive) and Pfr (far-red-absorbing, ~730 nm, active); red light converts Pr→Pfr and far-red converts Pfr→Pr.

Where do active phytochromes act to control gene expression?

Light-activated Pfr translocates to the nucleus, where it interacts with and promotes degradation of PIF (Phytochrome-Interacting Factor) transcription factors, altering expression of light-responsive genes.

What light do cryptochromes and phototropins absorb, and what are their chromophores?

Both are blue-light/UV-A photoreceptors using flavin chromophores. Cryptochromes use FAD and pterin; phototropins use FMN bound in LOV domains.

What processes do phototropins (PHOT1/PHOT2) control?

Phototropins mediate blue-light responses: phototropism (bending toward light), chloroplast movement, stomatal opening, and leaf flattening/expansion.

Outline the ionic mechanism of light-induced stomatal opening.

Blue light activates the guard-cell H+-ATPase, hyperpolarizing the membrane; this drives K+ uptake through inward channels, accumulation of Cl- and malate, lowering water potential so water enters, increasing turgor and opening the pore.

Define short-day and long-day plants in terms of the critical night length.

Short-day (long-night) plants flower when the night exceeds a critical length; long-day (short-night) plants flower when the night is shorter than a critical length. The dark period length is the decisive factor.

What is florigen, and which gene encodes it?

Florigen is the mobile flowering signal produced in leaves and transported through the phloem to the shoot apex; it is the protein product of the FT (FLOWERING LOCUS T) gene.

What molecular components make up the plant circadian clock's core feedback loop?

A transcription-translation feedback loop: morning genes CCA1 and LHY repress the evening gene TOC1, while TOC1 (and the PRR proteins) feed back to regulate CCA1/LHY, producing ~24 h oscillations.

Distinguish apoplastic, symplastic, and transmembrane pathways of water/solute movement across roots.

Apoplastic: through cell walls and intercellular spaces (blocked at the Casparian strip). Symplastic: cell-to-cell through plasmodesmata. Transmembrane: repeatedly crossing plasma membranes. Water must enter symplast at the endodermis.

State the cohesion-tension theory of water transport (transpiration pull).

Transpiration from leaves lowers water potential, pulling water up the xylem; continuous water columns are held together by cohesion (H-bonding) and adhesion to xylem walls, creating tension that draws water from roots to leaves.

What is the proton-coupled mechanism of phloem loading (apoplastic loading)?

Companion cells use a plasma membrane H+-ATPase to pump protons out; sucrose is then co-transported into the sieve element–companion cell complex against its gradient via sucrose-H+ symporters (SUC/SUT), driving pressure-flow.

Explain Munch's pressure-flow hypothesis of phloem transport, including unloading.

At sources, sugar loading raises osmotic pressure drawing in water (high turgor); at sinks, unloading lowers turgor; the resulting pressure gradient drives bulk flow of phloem sap from source to sink, where assimilates are unloaded (symplastically or apoplastically).

From which precursor are all terpenes built, and what are the two biosynthetic routes in plants?

All terpenes derive from the C5 isoprene units IPP and DMAPP. Plants make these via the cytosolic mevalonate (MVA) pathway and the plastidic MEP (non-mevalonate/DOXP) pathway.

Classify terpenes by isoprene (C5) unit number with one example each.

Monoterpenes (C10, e.g., menthol), sesquiterpenes (C15, e.g., farnesol), diterpenes (C20, e.g., gibberellins), triterpenes (C30, e.g., sterols), tetraterpenes (C40, e.g., carotenoids).

What is the general biosynthetic origin of plant phenolic compounds?

Most phenolics arise from the phenylpropanoid pathway, beginning with phenylalanine deaminated by phenylalanine ammonia-lyase (PAL) to cinnamic acid; this leads to flavonoids, lignin, tannins, and coumarins.

Give the major classes of nitrogen-containing secondary metabolites with examples.

Alkaloids (e.g., nicotine, morphine, caffeine), cyanogenic glycosides (release HCN), glucosinolates (mustard oils), and non-protein amino acids; many derive from amino acids and serve in defense.

List three ecological roles of plant secondary metabolites.

Defense against herbivores and pathogens (toxins, deterrents), protection from UV/abiotic stress (flavonoids), and attraction of pollinators/seed dispersers (pigments and scents); some are allelopathic.

What is systemic acquired resistance (SAR) and its key signaling molecule?

SAR is a broad, long-lasting whole-plant resistance induced after a local infection; salicylic acid is the key signal, leading to expression of PR (pathogenesis-related) proteins.

Differentiate PTI and ETI in plant immunity.

PTI (PAMP-triggered immunity) is the first layer, where surface receptors (PRRs) recognize conserved microbial patterns (PAMPs). ETI (effector-triggered immunity) is a stronger response where intracellular R proteins recognize pathogen effectors, often causing a hypersensitive response.

What is the hypersensitive response (HR) in plant defense?

HR is rapid, localized programmed cell death at the infection site that restricts pathogen spread (especially biotrophs), accompanied by ROS bursts and reinforcement of cell walls.

Which hormone signaling pathways defend against chewing insects versus biotrophic pathogens?

Jasmonic acid (JA) signaling defends mainly against chewing insects and necrotrophic pathogens; salicylic acid (SA) signaling defends against biotrophic pathogens. The two pathways are often mutually antagonistic.

What are compatible solutes (osmolytes) and give three examples used in osmotic/salt stress.

Compatible solutes are non-toxic organic molecules accumulated to lower osmotic potential and protect macromolecules without disrupting metabolism. Examples: proline, glycine betaine, and sugars/sugar alcohols (e.g., trehalose, mannitol).

What is the SOS pathway role in salt tolerance?

The Salt Overly Sensitive (SOS) pathway: salt raises cytosolic Ca2+; SOS3 senses Ca2+ and activates the SOS2 kinase, which activates the SOS1 plasma membrane Na+/H+ antiporter to extrude Na+, maintaining Na+/K+ homeostasis.

How do plants protect against high-temperature (heat) stress at the molecular level?

Heat stress triggers heat shock factors (HSFs) that induce heat shock proteins (HSPs/chaperones) which prevent protein aggregation and refold denatured proteins; plants also adjust membrane lipid saturation.

What are LEA proteins and when are they expressed?

Late Embryogenesis Abundant (LEA) proteins are hydrophilic protective proteins induced by ABA during seed desiccation and under water/cold/salt stress; they stabilize membranes and proteins during dehydration.

What protective mechanisms do plants use against cold/freezing stress?

Cold acclimation via the CBF/DREB transcription factors induces COR (cold-regulated) genes, accumulation of compatible solutes and antifreeze proteins, increased membrane lipid unsaturation, and dehydrins to limit ice damage.

Compare PEP carboxylase and Rubisco as CO2-fixing enzymes.

PEP carboxylase fixes HCO3- (no oxygenase activity, high affinity, no photorespiration) onto PEP. Rubisco fixes CO2 onto RuBP but also reacts with O2 (oxygenase activity causing photorespiration) and has lower CO2 affinity.

What are the three biochemical subtypes of C4 plants based on the decarboxylating enzyme?

NADP-malic enzyme (NADP-ME) type, NAD-malic enzyme (NAD-ME) type, and PEP carboxykinase (PEPCK) type, differing in the enzyme that releases CO2 in the bundle sheath.