PLANT BIOCHEMISTRY/BIOCHEMISTRY (SYLLABUS FOR ICAR’S JRF/SRF(PGS) )

SYLLABUS FOR THE ALL INDIA COMPETITIVE EXAMINATION FOR ADMISSION TO DOCTORAL DEGREE PROGRAMMES AND THE AWARD OF

JRF/SRF (PGS)

08 PLANT BIOCHEMISTRY/BIOCHEMISTRY

Unit 1: Basic Biochemistry and Biomolecules 

Scope and importance of biochemistry and molecular biology in plants. Structural and functional organization of prokaryotic and eukaryotic cells, viruses and bacteriophages, cell organelles function and their fractionation. Chemical bonding in biological systems, pH and buffers. Thermodynamics and bioenergetics- concept of entropy, and free energy changes in biological reactions, Redox reactions, Role of high energy phosphates. Biomembranes. Classification structure, chemistry, properties and function of carbohydrates, proteins, lipids and nucleic acids. Components of immune system, Prostaglandins. 

Unit 2: Intermediary Metabolism 

Anabolism, catabolism and their regulation. Metabolism of carbohydrates – glycolytic pathway, HMP pathway, TCA cycle, glyoxylate pathway and gluconeogenesis. Biological oxidationelectron transfer and oxidative phosphorylation. Lipid metabolism, degradation and biosynthesis of fatty acids, ketogenesis and causes of ketosis. Biosynthesis of sterols and phospholipids.Protein degradation by proteases and ubiquitin-Proteasome System, Amino acid metabolism – catabolism of amino acids, transamination and deamination, urea cycle, biosynthesis of amino acids. Conversion of amino acids into bioactive compounds. Metabolism of nucleic acids-degradation and biosynthesis of purines, pyrimidines and nucleotides. Integration of carbohydrate, lipid and amino acid metabolism. Signal transduction mechanisms. Role of G-proteins, cyclic nucleotides and calcium in transduction. Disorders of lipid, carbohydrate, nucleic acid, amino acid metabolism. Inborn errors of metabolism. Secondary metabolites,Alkaloids, Phenolics and Isoprenoids, biotransformation and over expression. Role of oligosaccharides and polysaccharides in cellular metabolism. 

Unit 3: Enzymes, Vitamins and Hormones 

Major classes of enzymes, general properties, kinetics, active site and its mapping, activation energy and transition state. Mechanisms of enzyme action, inhibition and activation. Coenzymes and cofactors. Isoenzymes and immobilized enzymes. Abzymes, pseudoenzymes, bifunctional enzymes and enzyme promiscuity. Regulation of enzyme activity, allosteric regulation. Multi substrate reactions, kinetic experiments to determine the mechanism of multi substrate reactions. Isolation, purification and measurement of enzyme activity. Enzyme units. Enzyme engineering. Role of enzymes in agriculture, industry, and medicine. Structure, mode of action and metabolic functions of vitamins. Deficiency diseases associated with vitamins. General description of nature hormones and disorders associated with endocrine glands, viz. pituitary, thyroid, adrenal, pancreas and gonads. Peptide and steroid hormones. Phytohormones – auxins, gibberellins, cytokinins, ethylene, abscisic acid and new plant bio-regulators like SA, Brassinosteroids. Molecular mechanism of plant hormone action. 

Unit 4: Molecular Biology 

Structure of DNA and RNA Replication, transcription and translation. Post-transcriptional and translational modifications. Transcriptional and translation control of prokaryotes and eukaryotes. Features of genetic code in prokaryotes and eukaryotes. Gene expression - operon model, induction and repression, control of gene expression in prokaryotes and eukaryotes. Chloroplast and Mitochondrial genomes. Replication of viruses. Mutagens, oncogenes and carcinogenesis. General principles of recombinant DNA technology, restriction enzymes. Methods of gene transfer-plasmid and viruses as vectors, DNA and protein sequence analysis, oligonucleotide synthesis, genomic and cDNA library construction, site-directed mutagenesis, transposon tagging, chromosome walking. Basics of genome organization. Computer application in molecular biology, primer designing, sequence analysis and phylogenetic analysis. Benefits of gene manipulation in agriculture, nanobiotechnology, bio-chips. 

Unit 5: Techniques in Biochemistry

 Principles of optical, phase contrast, fluorescence and electron microscopy, spectrophotometry, UV and VIS, fluorimetry, turbidometry and atomic absorption spectrophotometry. Radioisotopic techniques – scintillation counters and autoradiography and their application in biological sciences. Electrophoresis - general principles and application, gel electrophoresis, isoelectric focusing, pulsed field gel electrophoresis, immunoelectrophoresis. Chromatographic techniques - paper, thin layer, column chromatography, GC and HPLC. Centrifugation - principles of sedimentation in various rotors, differential centrifugation, density gradient centrifugation and ultracentrifugation. PCR, Quantitative PCR and application of RFLP, RAPD, AFLP, microsatellite and mitochondrial and ribotyping techniques.. Southern, Northern and Western blotting, ELISA. Microarray and DNA chips. MALDI-TOF and metabolite profiling techniques such as ICP-MS. X-ray diffraction, IR, NMR, FTIR, GC-MS, LC-MS. Preliminary methods of statistical analysis as applied to agricultural data – standard deviation, standard error, ANOVA, correlation and regression., 

Unit 6: Biochemistry of Food-grains, Fruits and Vegetables 

Fundamentals of nutrition, concept of balanced diet. Nutritional quality of protein and its evaluation. Dietary fibre. Vitamins- biochemical functions and deficiency diseases. Fats and lipids-types of fatty acids and their significance in health. Biochemical composition and food value of various food grains (including cereals, pulses, oil seeds), fruits and vegetables. Biochemistry of fruit ripening, Biochemical aspects of post-harvest technology, storage and preservation of cereals, pulses, oilseeds, fruits and vegetables. Food enzymes. Biochemical basis of quality improvement of food grains, vegetables and fruits. Antioxidants, nutraceuticals. Food toxins and anti-metabolites, food additives, storage proteins. Processability of food grains. Bioavailability of nutrients and effect of food matrices, storage and processing on the functionality and bioavailability of nutrients. 

Unit 7: Photosynthesis

 Photosynthesis – photosynthetic pigments, light reactions, photosystems. Photophosphorylation, dark reactions: C3, C4 and CAM pathways. Conversion of C3 to C4 plants. Regulation of Rubisco. Chemisomotic coupling. Carbon cycle and its regulation, Ion fluxes and conformational changes during photosynthesis. Photorespiration. Relationship between photosynthesis, photorespiration and crop productivity. Chloroplasm morphology, structure and biochemical anatomy. Cytosolic and organelle interactions. Nature and exchange of metabolites through translocators. Seed reserve biosynthesis.

 Unit 8: Plant Metabolic Processes

 Uptake and metabolism of mineral nutrients in plants. Sulphur metabolism. Nitrogen cycle, nitrate and nitrite reduction, denitrification, symbiotic and non-symbiotic nitrogen fixation. Biochemical and physiological role of hydrogenase. Chemoautrotrophy in rhizobia and nitrifying bacteria. Cell cycle. Growth regulation in plants. Role of oligosaccharides and polysaccharides in cellular metabolism. Metabolism of cyanogenic glycosides and glucosinolates. 

Unit 9: Plant Molecular Biology

 General organization of nuclear, mitochondrial and chloroplast genomes. Genomics and functional genomics. Transcriptomics and Proteomics. Tissue specific expression of genes. Molecular biology of various stresses – drought, salinity and temperature. Signal transduction and its molecular basis: Structure, organization and regulation of nuclear genes. Genes involved in photosynthesis and nitrogen fixation. Regulation of chloroplast gene expression. Mitochondrial control of fertility. Molecular markers in plants and their uses. 

Unit 10: Plant Biotechnology/Genetic Engineering 

Totipotency, application of tissue culture for plant improvement, cryopreservation. Protoplasm fusion. General principles of gene cloning. Isolation and characterization of plant genes and promoters. Different methods of gene transfer –direct and vector mediated. Gene silencing. Site directed mutagenesis. Molecular analysis of transformants. Potential applications of plant genetic engineering for crop improvement – nutritional and processing quality improvement, shelf life enhancement, insect-pest resistance (insect, viral, fungal and bacterial diseases), abiotic stress tolerance and herbicide resistance, Biosafety and IPR issues. Genome editing techniques and tools.