Introduction -PBB1 (4).pdf

Fundamentals of Plant Biochemistry and Biotechnology Introduction to Plant Biochemistry  Course Name: Fundamentals of Plant biochemistry and biotechnology Course Code : PBPT 111 Course Instructor : Dr. Santanu Mukherjee...

Fundamentals of Plant Biochemistry and Biotechnology Introduction to Plant Biochemistry  Course Name: Fundamentals of Plant biochemistry and biotechnology Course Code : PBPT 111 Course Instructor : Dr. Santanu Mukherjee Credit Hours: 3 (2+1) Course Objectives: This course is designed : Objectives  To cover the aspects of biochemistry unique and important to plants.  To see some of the many biochemical pathways critical to plants.  To learn about mode of regulation and metabolism of plant cellular constituents.  To impart understanding of the basic principles of the plant sciences and molecular biology, as well as the integration of these disciplines for food, non-food, feed and health applications.  Course Contents  Importance of Biochemistry. Properties of Water, pH and Buffer. Carbohydrate: Importance and classification. Structures of Monosaccharides, Reducing and oxidizing properties of Monosaccharides, Mutarotation; Structure of Disaccharides and Poly saccharides. Lipid: Importance and classification; Structures and properties of fatty acids; storage lipids and membrane lipids. Proteins: Importance of proteins and classification; Structures, titration and zwitterions nature of amino acids; Structural organization of proteins. Enzymes: General properties; Classification; Mechanism of action; Course Michaelis & Menten and Line Weaver Burk equation & plots; Introduction to allosteric enzymes. Nucleic acids: Importance and classification; Structure of Nucleotides, A, B & Z DNA; RNA: Types and Secondary & Tertiary Contents structure. Metabolism of carbohydrates: Glycolysis, TCA cycle, Glyoxylate cycle, Electron transport chain. Metabolism of lipids: Beta oxidation, Biosynthesis of fatty acids.  Concepts and applications of plant biotechnology: Scope, organ culture, embryo culture, cell suspension culture, callus culture, anther culture, pollen culture and ovule culture and their applications; Micro-propagation methods; organogenesis and embryogenesis, Synthetic seeds and their significance; Embryo rescue and its significance; somatic hybridization and cybrids; Somaclonal variation and its use in crop improvement; cryo-preservation; Introduction to recombinant DNA methods: physical (Gene gun method), chemical (PEG mediated) and Agrobacterium mediated gene transfer methods; Transgenics and its importance in crop improvement; PCR techniques and its applications; RFLP, RAPD, SSR; Marker Assisted Breeding in crop improvement; Biotechnology regulations.  Text Books 1. Stewart NC Jr. (2008). Plant Biotechnology and Genetics: Principles, Techniques and Applications. John Wiley & Sons Inc. 2. Voet D, Voet JG & Pratt CM. (2004). Fundamentals of Biochemistry. 2nd Ed. New York: Wiley. 3. Renneberg R. (2008). Biotechnology for Beginners. Academic Press Publishers. 4. William, H.E. and Daphne, C.E.(2005). Biochemistry and Molecular Biology, Oxford University Press. 5. Nelson, DL and Cox, MM. 2004. Lehninger Principles of Biochemistry. 4th Edn. MacMillan. 6. Wilson K & Walker J. (1994). Principles and Techniques of Biochemistry and Molecular Biology. 7th Ed. Cambridge University Press. 7. Kreuzer H & Massey A. (2008). Molecular Biology and Biotechnology: A Guide for Teachers. ASM Press. Lecture: 1 Pedagogy Power Point based lecture and interaction Topics to be Introduction to Plant Biochemistry covered Learning Students will acquire critical knowledge in Outcome problem solving within an interdisciplinary context of biotechnological production of secondary metabolites and recombinant proteins using plant cell technology. Readings  William, H.E. and Daphne, C.E.(2005). Biochemistry and Molecular Biology, Oxford University Press.  Conn, E.E. and Stumpf, P.K.(1989). Outlines of Biochemistry, Wiley Eastern Ltd., New Delhi.  Sadashiv, S and Manickam, A. (1996). Biochemical methods for Agricultural sciences. New age International publishers, New Delhi.  Lehninger, Nelson, D. L. and Michael, M. C. (2004). Principles of Biochemistry. Freeman Publishers.  Bio= life Chemistry = how things interact Biochemistry= the branch of science in which you study the chemical and physical processes that occur in an organism.  Biochemistry is the application of chemistry to the study of biological processes at the cellular and molecular level.  It emerged as a distinct discipline around the beginning of the 20th century when scientists combined chemistry, physiology and biology to investigate the chemistry of living systems by:  Contd………  Studying the structure and behavior of the complex molecules found in biological material and the ways these molecules interact to form cells, tissues and whole organism.  Biochemistry has become the foundation for understanding all biological processes. It has provided explanations for the causes of many diseases in humans, animals and plants.“  Fundamentals of Biochemistry  Cells (basic structural units of living organisms) are highly organized and constant source of energy is required to maintain the ordered state.  Living processes contains thousands of chemical reactns. Precise regulation and integration of these reactns. are required to maintain life  Certain important reactions E.g. Glycolysis is found in almost all organisms.  All organisms use the same type of molecules: CHO, proteins, lipids & nucleic acids.  Instructions for growth, reproduction and developments for each organism is encoded in their DNA.  Evolution of Biochemistry Early 19th Century World made of either "living matter" (organic) or "non-living matter" (inorganic).(Vitalism) 1828 Friedrich Wohler accomplished the synthesis of Urea from inorganic matter. 1897 Edvard and Hans Buchner showed dead cell extracts can perform reactions of living cells. The molecules responsible for performing these reactions are called enzymes Late 1800's Emil Fischer suggested key/lock picture. Substrate = Key, Enzyme = Lock Early 1900's Field of biochemistry emerges Structure and function of enzymes Elucidating enzymatic pathways 1944 Genes composed of DNA 1953 Watson and Crick determine the structure of DNA Biological function linked to the information in genes  Foundations of Biochemistry Universe is 15-20 billion years old –BIG BANG Initially H2 was made then condensed to He Stars formed-Stars died, Super novas exploded creating higher atomic number elements. Over the billions of years under the right conditions complex molecules formed. Complicated chemical reactions started occurring - intermolecular interactions and carbon based chemistry developed. From this milieu sprang the property of LIFE Biochemistry is the study of this process on a chemical level  What is a cell?  The word cell comes from the Latin word "cella", meaning "small room", and it was first coined by a microscopist observing the structure of cork.  The cell is the basic unit of all living things, and all organisms are composed of one or more cells.  Cells are so basic and critical to the study of life, in fact, that they are often referred to as "the building blocks of life".  Organisms - bacteria, amoebae and yeasts, for example - may consist of as few as one cell, while a typical human body contains about a trillion cells. Three domains of Organisms Prokaryotic Cell  The organisms made of prokaryotic cells are called prokaryotes e.g. bacteria and cyanobacteria.  These cells lack a membrane bound nucleus.  The hereditary material (DNA) is found in cytoplasm.  These cells lack membrane bound organelles.  Ribosome’s are of small size in and freely scattered cytoplasm.  Cellulose is absent in cell wall, rather it is made up of peptido-glycan or murrain.  These cells are simple and of smaller size (average diameter 0.5 – 10 nm) Eukaryotic Cell  The organisms made of Eukaryotic cells are called Eukaryotes, e.g. animals, plants fungi and protista.  These cells have a membrane bound nucleus; and hereditary material is found inside the nucleus.  These cells have membrane bound organelles.  Ribosome’s are of large size and are present in endoplasmic reticulum free in cytoplasm.  Cellulose is present in cell wall of plant cells. The cell wall of most of fungi is composed of chitin.  These cells are complex and of larger size (Average diameter 10-100nm).  Biochemical Reactions  Metabolism: total sum of the chemical reaction happening in a living organism (highly coordinated and purposeful activity)  Anabolism- energy requiring biosynthetic pathways  Catabolism- degradation of fuel molecules and the production of energy for cellular function  All reactions are catalyzed by enzymes  The primary functions of metabolism are:  acquisition & utilization of energy  Synthesis of molecules needed for cell structure and functioning (i.e. proteins, nucleic acids, lipids, & CHO  Removal of waste products Even though thousands of reactn. sound very large and complex in a tiny cell:  The types of reactn. are small  Mechanisms of biochemical reactn. are simple  Reactions of central importance (for energy production & synthesis and degradation of major cell components) are relatively few in number Frequent reaction encountered in biochemical processes 1. Nucleophilic Substitution  One atom of group substituted for another 2. Elimination Reactions  Double bond is formed when atoms in a molecule is removed 3. Addition Reactions:  Two molecules combine to form a single product.  A. Hydration Reactions  Water added to alkene > alcohol (common addition reactn.) 4. Isomerization Reactions.  Involve intramolecular shift of atoms or groups 5. Oxidation-Reduction (redox) Reactions  Occur when there is a transfer of e- from a donor to an electron acceptor 6. Hydrolysis reactions  Cleavage of double bond by water.  WATER  Life is inconceivable without water.  Water constitutes 45%-75% of total human body weight.  It is distributed in intracellular and extracellular compartments and provides a continuous solvent phase between body compartments.  As the biological solvent, water plays a major role in all aspects of metabolism:  Absorption, transport, digestion, excretion as well as maintenance of body temperature.  Water is not just the solvent in biological reactions.  Water is a good nucleofile and it is very often a direct participant in reactions such as hydrolysis and condensation  The unique properties of water are derived from its structure.  Structure of water  H2O  Water is a hydride of oxygen in which the highly electronegative oxygen atom attracts the bonding electrons from two hydrogen atoms.  This leads to polar H-O bonds in which the hydrogen atoms have a slight positive charge and the oxygen atom has a slight negative charge.  Therefore a water molecule has a dipole structure  Neighboring liquid water molecules interact with one another.  The intermolecular bonding between water molecules arises from the attraction between the partial negative charge on the oxygen atom and the partial positive charge on the hydrogen atom of adjacent water molecules.  This type of attraction involving a hydrogen atom is known as hydrogen bond.  Hydrogen bonds contain a hydrogen atom between two electronegative atoms (e.g., O and N).  Hydrogen bonds are weaker than covalent bonds.  However the cumulative effect of many hydrogen bonds is equivalent to the stabilizing effect of covalent bonds.  In proteins, nucleic acids and water, hydrogen bonds are essential to stabilize overall structure.  Water is an excellent solvent for both ionic compounds and low-molecular weight nonionic polar compounds such as sugars, urea and alcohols.  Ionic compounds are soluble because water can overcome the electrostatic attraction between ions through solvation of the ions.  Non-ionic polar compounds are soluble because water molecules can form hydrogen bonds to polar groups.  Amphipathic compounds  Amphipathic compounds are the molecules which contain both hydrophobic groups (large nonpolar hydrocarbon chains) and polar or ionic groups (hydrophilic groups).  They don’t dissolve in water as individual molecules.  When they reach at a definite concentration (critic micelle concentration) in water, they associate with each other in submicroscopic aggregations of molecules called micelles.  Micelles have hydrophilic groups on their exterior (bonding with solvent water), and hydrophobic groups clustered in their interior.  They occur in spherical shapes.  Micelle structures are stabilized by hydrogen bonding with water, by van der Waals attractive forces between hydrocarbon groups in the interior, and by energy of hydrophobic interactions. Examples : Soap, Detergents, Phospholipids, Cholesterol, Glycolipids, and fatty acids  Hydrophobic interactions are also weaker than covalent bonds. However, many such interactions result in large, stable structures.  When amphipathic compounds are available at a considerably higher concentration than critic micelle concentration, they form liposome vesicles after the sonication.  Liposome vesicles are two-bilayer lipid spheres.  Liposomes have potential applications in medicine.  Drugs and some macromolecules encapsulated in liposome systems can be targeted to a particular cell population or organ.  Water’s Unique Properties…  The STRUCUTRE of the water molecule gives water its unique properties  Water is a polar molecule, which means that it has a region with a slight negative charge (the oxygen atom) and a region with a slight positive charge (the hydrogen atoms)  The oppositely charged regions of water molecules interact to form hydrogen bonds  Hydrogen bond is an attraction between a hydrogen atom and a negative atom  Water has many characteristics that make it vital to our bodies  Water is a very small molecule, so it moves fast and can squeeze into tiny crevasses between other molecules  Hydrogen has a slightly positive charge while oxygen has a slightly negative charge. This makes it easy for water to pry apart other charged molecules, dissolving them (Polarity).  Due to polarity, water forms a crystal structure that is less dense than liquid water (structure).  Water absorbs and releases heat energy slowly, and can hold a great deal of heat energy. This helps organisms maintain their body temperature in the safe range (heat capacity).  Polarity allows water to stick to itself (cohesion) and to any charged material (adhesion). Water can glue materials together (Cohesion and adhesion).  Water can act as either an acid or a base, maintaining a stable pH in our bodies (buffer). ACID-BASE BALANCE AND BUFFERING SYSTEMS……………………… Thank you Dr Santanu Mukherjee School of Agriculture Shoolini University Village Bajhol, Solan (H.P) [email protected] +91 8697601370