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AGRICULTURAL PLANT BIOCHEMISTRY

Dr. G. Nagaraj
  • Country of Origin:

  • Imprint:

    NIPA

  • eISBN:

    9789389571387

  • Binding:

    EBook

  • Number Of Pages:

    266

  • Language:

    English

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Plant biochemistry is an important emerging field in the agricultural sciences. Basic knowledge of the chemistry and the biochemical mechanisms of the plant in synthesizing various components is essential for advancements needed in other areas of agriculture like plant breeding, plant protection, plant production, etc. In the recent past, biotechnology and biochemistry are moving hand in glove to solve many problems related to humans and other living beings. The book is aimed at providing good information to graduate and post-graduate students in agriculture and biology. It will also serve as a reference book to researchers in plant breeding, agronomy, plant physiology and plant protection and will come in handy to solve many global problems by the present and future generations.

0 Start Pages

Preface Plants have an important role on this globe. Being autotrophs they synthesize the most essential food components with the help of simple chemicals. They also have the ability to put together secondary nutrients, drugs and toxicants. Apart from sustaining their life, they help other forms of life including humans on this earth. They are also responsible for maintaining the climate and a congenial environment. Agriculture, which built up civilizations, has been the mainstay of human beings. Increasing population and changing needs of food with respect to quantity and quality has built up pressure to understand the biochemistry of plants and engineer them to suit to the requirements. This book is aimed at putting together the information on the various aspects of biochemistry of plants, their mechanism and utility. It has basic information and should be useful to beginners in agriculture, horticulture, biology and related disciplines. As a researcher for over forty years in agriculture, I have been collecting information on plant biochemistry. I also depended on some website and teaching material. I tried to put together most such information. I am sure the book will be useful not only to beginners, but also to some specific researchers. It should be my endevour to improve the content and quality based on expert advises. 

 
1 Introduction

All living organisms are basically made up of chemical components. The chemistry, composition and energy management of living organisms is what we call biochemistry. It tries to explain life processes at the molecular level. Although different organisms differ outwardly in their life processes, there are striking similarities in executing the different tasks. Genetic code, metabolic pathways, enzymes, coenzymes and even regulatory mechanisms are similar to a large extent in all the living organisms. Living organisms have certain extraordinary properties. They can grow, respond to stimuli and replicate themselves with high fidelity. All these activities are ultimately interpretable in chemical terms. The components that constitute organisms are all inanimate. The lifeless organic molecules with appropriate complexity and properties make a living being. Biochemistry helps us understand how the inanimate molecules that constitute living organisms interact with each other to maintain life. The basic life processes or the biochemistry remains broadly the same in either the unicellular microorganism or the higher organisms such as the plants or the human beings. Life is nothing but thousands of ordered chemical reactions. In other words, chemistry is the logic of all biological phenomena.

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2 Carbohydrates

Carbohydrates are the most abundant biomolecules on earth. They occur in nature as glucose, starch and cellulose etc. Each year, photosynthesis converts more than 100 billion metric tonnes of carbon dioxide and water into starch, cellulose and other plant products. Carbohydrates are polyhydroxy aldehydes or ketones and their derivatives. They provide 4k calories energy per gram. They promote utilization of lipids and reduce wastage of proteins. They are readily available in roots, tubers, cereal grains, sugarcane and sugar beet. Carbohydrates have the general formula Cn( H2O)n, indicting that they are the hydrates of carbon. Some carbohydrates also contain nitrogen, phosphorous or sulfur. They are characterized by the number of carbon atoms they contain. If n=3, they are trioses, n=4 tetroses, n=5 pentoses, n=6 hexoses and n=7 heptoses. The most common sugars in plants are the hexoses. Two or more simple carbohydrates condense together to form polymer sugars like sucrose, starch and cellulose etc. The basic condensing bond is glycosidic bond.

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3 Lipids

Lipids are non polar substances of biological origin that are sparingly soluble in water, but soluble in organic solvents like chloroform, hexane, benzene etc. The word lipid comes from the Greek word lipos meaning lard or fat. The lipids present in biological systems are either hydrophobic (non polar) or amphipathic (both polar and non polar). Lipids like fats, oils or glycerophospholipids can be hydrolyzed to get fatty acids and other products. Hydrophobic nature is useful in making lipids as membranes which act as effective barriers to more polar molecules. Steroids are also considered lipids, but cannot be hydrolysed and are components of non-saponifiables in fats. Waxes, which are esters of fatty acids with long chain alcohols are also considered as lipids.

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4 Amino Acids

Amino acids are the building blocks of proteins. They occur in all living plant cells as constituents of proteins and as free acids or amides. More than 200 naturally occurring amino acids have been identified in higher plants. Around 20 different amino acids have been observed to be incorporated into proteins. They have two functional groups, an amino group (-NH2) and a carboxylic group(-COOH). Both these groups are attached to the a carbon atom only. Amino acids with this structure are called a amino acids or 2-aminoacids. The unique characteristics of the 20 amino acids are due to the side chain (R), which can be an alkyl, hydroxyl, thiol, amino, sulphide, aromatic, or heterocyclic group. Amino acids have the general formula, R-CH(NH2)-COOH. The R represents a side chain. If R=H, the simplest amino acid glycine (NH2 -CH2 –COOH) results. Amino acids are alpha (a ) amino carboxylic acids. The carbon atom is tetrahedral in shape. The various groups attached to it are placed in different positions. Since the valence of the carbon atom is four, four groups can be attached to the carbon atom. Based on the groups attached to the carbon atom it may be of two types.

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5 Peptides

An amine reacts with a carboxylic acid to form an amide. Similarly, the amino group  on one amino acid molecule reacts with the carboxyl group of another amino acid  to form a compound called peptide. A peptide bond is an amide bond that forms when the –COO- group of one amino acid reacts with the -NH3+ group of another amino acid. The resulting compounds are called peptides. Even after this there is a reactive amino group and a carboxyl group in the peptide. If these groups react further a poly peptide can form and later a polymer called protein can form.

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6 Proteins

The word protein was first coined in 1838 to emphasize the importance of this class of molecules. The word is derived from the Greek word proteios which means “of the first- rank”. Proteins are polymers/macro molecules made up of several amino acids. When there are more than 50 amino acids in a chain, the polypeptide is normally called a protein. Each protein in the cells of living beings has a unique sequence of amino acids that determines its biological function. The proteins are folded into specific defined structures, which are maintained by a large number of relatively weak bonds. The  three  dimensional structure is well defined and suited to it’s specific function. Very small changes in the structure can modify the function. Hence, it is important to know the structure of proteins to understand their behavior and function. The biological activity of proteins depends on maintenance of folded conformation. Proteins fold into well defined three dimensional shapes and they are able to recognize their corresponding substrates or antigen molecules and bind them tightly. The protein structure has been classified into four different levels based on the folded conformation of the protein.

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7 Enzymes

Enzymes are organic catalysts produced by living organisms. They make possible biochemical reactions. Hence they are called biocatalysts. They are mostly a specialized class of proteins. However, there are some non-protein enzymes like ribozymes, which are RNAses. Enzymes speed up reactions at ambient temperatures. This is in contrast to chemical reactions like saponification of lipids which take place when lipids are boiled for a few hours with concentrated alkali.  Enzymes, namely, lipases, hydrolyze lipids at body temperatures in minutes. They are superior to chemical catalysts by a factor of 107 to 1014 .  An enzyme may be a simple protein or a complex protein. They are produced by cells and are mostly globular proteins. Each cell contains an estimated 3000 different enzymes.

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8 Nucleic Acids

Nucleic acids were first discovered in 1868 by Friedrich Meischer. Nucleic acids are high molecular weight polymers that are present in our cells. They  store and transfer genetic material from generation to generation. Knowledge of how genes are expressed and how they can be manipulated is becoming increasingly important for understanding   of nearly every aspect of biochemistry. These macromolecules pass on information for cellular growth and reproduction.  All the genetic information in the cells is called the genome. Every time a cell divides, the information is copied and passed on to the new cells.   Nucleic acids fall into two main classes according to the type of sugar they contain: the Deoxyribonucleic acids (DNA) and Ribonucleic acids (RNA). Some sections  of  the  DNA  called  genes contain the information to make a protein. RNA translates the genetic information in the DNA to the ribosomes, where the synthesis of proteins takes place.

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9 Plant Metabolism

Plants are responsible for highly useful molecular reactions. All the enzymatic  reactions  that  occur in the cell are  termed  as metabolic reactions.  They  take place within organisms in an orderly and regulated way.  They  are  the  metabolic pathways and the compounds  resulting from the process, namely,  metabolism are called  the metabolites. Metabolism in Greek means change. It is the set of life sustaining chemical transformations within the cells of living organisms. These enzyme-catalyzed reactions allow organisms to grow and reproduce, maintain their structures, and respond to the environments around them.   Metabolism is a highly organized,   coordinated and purposeful enzymatic activity inside a cell. Metabolism has four functions: 1. To obtain energy from the environment, 2. To convert molecules into building blocks, 3. To convert the building blocks into proteins, lipids, sugars, nucleic acids and other cell components and 4. To synthesize and degrade organic molecules for specific needs of the cell.

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10 Carbohydrate Metabolism

Carbohydrate metabolism in the cell is essentially the metabolism of glucose and other substances related to glucose in their metabolic processes. The chemical reactions involved in carbohydrate metabolism represents complex groups, sequences, and cycles of reactions which integrate at various points with the reactions concerned in the metabolism of lipids and proteins. The major types of chemical processes involved in carbohydrate metabolism may be grouped as follows: a) Anabolism of starch – Photosynthesis, b) Catabolism of starch, c) Catabolism of glucose – 1. Glycolysis and TCA cycle and 2. Oxidative pentose   phosphate pathway.   Plant cells “burn “ glucose for energy. Plants also produce sugars through photosynthesis. This is roughly the reverse of the burning process.

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11 Lipid Metabolism

The importance of lipids have already been elaborated. They play a major role as source of energy and as components of membranes which have implications in plant growth regulation. The complete metabolism of fat leads to oxidation, the final products being CO2 and water. The burning of one mole of palmitic acid gives 2340 kcal.  The molecular weight of palmitic acid is 256. This works out to approximately 9 kcal/g of palmitic acid. This energy is twice that derived from either sugars or proteins. Fats and oils are thus better and more efficient forms of storage of energy in living beings.

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12 Amino Acid Metabolism

Plants can synthesize all the 20 amino acids, which include essential and non-essential amino acids. They can be degraded by removal of the amino group and conversion of the remaining skeleton to useful metabolic intermediates which participate in the synthesis of glucose and other ketone bodies.   Biosynthesis of amino acids   The biosyntheses of amino acids have an important feature. Their carbon skeletons come from intermediates from glycolysis, pentose phosphate pathway and citric acid cycle etc. The biosynthetic pathways depend on the intermediates from which they are derived. The primary amino group normally comes from the transamination of glutamate. Glutamine synthetase is a central control point in nitrogen metabolism, since glutamine is the amino group donor in the formation of many biosynthetic products as well as being a storage form of ammonia. Glutamate is the precursor of proline, ornithine, and arginine. Serine, cysteine, and glycine are derived from 3-phosphoglycerate. Glycine is synthesized from serine by removing CH2OH group. Tyrosine is synthesized from phenylalanine. Asparagine and glutamine are amides that are synthesized from aspartate and glutamate.

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13 Protein Metabolism

Amino acids serve as the building blocks of proteins and as precursors of many other important biomolecules such as hormones, purines, pyrimidines, porphyrins and some vitamins. They also serve as sources of energy when present in excess amounts and when they are used as fuel, amino acids undergo deamination reactions. The remaining carbon skeleton will either convert itself into glucose or undergoes oxidation to CO2 via TCA cycle. Central dogma: The Central dogma of molecular biology, which has been formulated as a simple linear progression of information from DNA to RNA to Protein, is summarized in the illustration. The replication process on the left consists of   passing  information from a parent DNA molecule to daughter molecules. The middle  transcription process copies this information to a mRNA molecule.  Finally, this information is used by the chemical machinery of the ribosome to make polypeptides.

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14 Terpenes

Primary metabolism in a plant comprises all metabolic pathways that are essential to the plant’s survival. Primary metabolites, namely, carbohydrates, lipids and proteins are compounds that are directly involved in the growth and development of a plant whereas the secondary metabolites are compounds produced in other metabolic pathways that, although important, are not essential to the functioning of the plant. However, secondary plant metabolites are useful in the long term, often for defense purposes, and give plants characteristics such as color.   Secondary plant metabolites are used in signalling and regulation of primary metabolic pathways. Plant hormones, which are secondary metabolites, are often used to regulate the metabolic activity within cells. Secondary plant metabolites help the plant maintain an intricate balance with the environment, often adapting to match the environmental needs. Plant metabolites that color the plant are a good example of this, as the coloring of a plant can attract pollinators and also defend against attack by animals. Terpenes, alkaloids, sterols, pigments, growth regulators, and phenolics are the important secondary plant metabolites.

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15 Phenolics

Phenol is normally a benzene ring containing an –OH group, and hence an aromatic alcohol. The term phenolic refers to similar aromatic compounds with one or more -OH groups. Phenolics constitute one of the most widespread classes of secondary metabolites. Commonly talked about class of compounds like anthocyanins, flavonoids, lignins, tannins, coumarins and chalcones are all phenolic substances. Phenolics are water insoluble substances. However, the water solubility increases with the increase in the number of -OH groups. Phenolics absorb electromagnetic radiation strongly. Many of the phenolics absorb in the visible part of the spectrum (Ex. anthocyanins) and are coloured. Phenolics are produced in plants by 1. Shikimate pathway through phenylalanine (C6.C3)  and 2. Acetate/ malonate pathway.

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16 Plant Pigments

Plant pigments impart colour to the different components like leaves, flowers, fruits etc. They in turn are responsible for the colour of raw food, we eat. Pigments like chlorophyll, anthocyanins, flavonoids, tannins, xanthones etc. are the different pigments that are present in plants. The primary function of pigments in plants is photosynthesis, which uses the green pigment chlorophyll along with several red and yellow pigments that help to capture as much light energy as possible. Other functions of pigments in plants include attracting insects to flowers to encourage pollination.

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17 Sterols

Sterols are derivatives of a complex ring system called cyclopentano perhydro phenanthrene. The term sterol means solid alcohol. Sterols, though alcohols, are solids with a M.P. of 100-120ºC. The 27 carbon atoms impart hydrocarbon character, namely, solubility in non-polar solvents. Free sterols in plants are mono hydroxy  secondary alcohols varying in the constitution of methyl or ethyl group and in double bonds. Cholesterol, ergosterol, bile acids, sex harmones, cortical harmones and D-vitamins are some of the sterol derivatives.     The most widely distributed sterols in higher plants are the C29 sterols, stigmasterol, β sitosterol and g sitosterol. Together, they are called steroids. In plants, steroids are present as glycosides. Cholesterol was first isolated from gall stones. The word cholesterol means “solid alcohol from bile”. Bile is a fluid which is formed and stored in the gall bladder. It aids in the digestion of fats in the digestive tract. Sterols form an important group among the steroids. Unsaturated steroids with most of the skeleton of cholestane containing a 3β-hydroxyl group and an aliphatic side chain of 8 or more carbon atoms attached to position 17 form the group of sterols.

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18 Alkaloids

Alkaloids are naturally occurring substances of plant origin that are alkaline in reaction. They are optically active, contain nitrogen as part of a heterocyclic ring and have varying degrees of psychological responses in man and animals. They exhibit significant pharmacological activity. Alkaloids are mostly basic in character but also includes some related compounds with neutral and even weakly acidic properties. Presently more than 2000 alkaloids are known. Nomenclature of alkaloids Alkaloids are named by adding the suffix ‘ine’ to various distinguishable features such as sources, physiological action in animals, their properties etc. Thus, 1. The name of the genera of the plants containing them Ex. Atropine (Atropa), nicotine (Nicotiana) etc. 2. The names of the species of the plants producing them Ex. Cocaine (Erythroxolon coca). 3. The common name of the organism producing them Ex. Ergotamine (ergot fungus). 4. The specific physiological activity observed in animals Ex. Emetine (emetic – causing vomiting), narcotine (narcotic-alters mind).

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19 Vitamins

Vitamins are essential organic nutrients required by an organism in small quantities. They are essential since they cannot be synthesized in sufficient quantities by an organism, and must be obtained from the diet. The term vitamin does not include other essential nutrients like dietary minerals, essential fatty acids, or essential amino acids which are needed in larger quantities than vitamins. The term vitamin is derived from “vitamine,” coined in 1912 by the Polish biochemist Funk. The name is from vital and amine, meaning amine of life. Thirteen vitamins are generally recognized presently. Vitamins are used in small quantities by an organism to keep it in a healthy condition. Vitamins are given letters of alphabet (A,B, C, D, etc.) in the order in which they have been discovered. The letters do not bear any relation to their structures or their importance. Vitamins are classified by their biological and chemical activity and not by their structure. Thus, each “vitamin” refers to a number of vitamer compounds that all show the biological activity associated with a particular vitamin. Vitamin A includes the compounds retinal, retinol, and four known carotenoids. Vitamers by definition are convertible to the active form of the vitamin in the body, and are sometimes inter-convertible to one another, as well.

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20 Plant Growth Regulators

Plant hormones (phytohormones) are chemicals that regulate plant growth and are termed as ‘plant growth substances’. Plant hormones are signal molecules produced within the plant, and are present in extremely low concentrations. Hormones regulate cellular processes in targeted cells. Hormones also determine the formation of flowers, stems, leaves, the shedding of leaves, and the development and ripening of fruit. Every cell is capable of producing hormones in plants. They shape the plant, affecting seed growth, time of flowering, the sex of flowers, senescence of leaves, and fruits. Plant hormones affect gene expression and transcription levels, cellular division, and growth.They direct which tissues grow upward and which grow downwards. Hormones are vital to plant growth. Hence, they are also known as growth factors or growth regulators.

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21 Nitrogen Metabolism

Before the invention of N fertilizer, mineralization of organic N ( present in dead plants and animals or manure) was the main method used to obtain ammonium and nitrate nitrogen. Mineralization is conducted by soil microbes resulting in ammonium ion. Most Nitrogen is absorbed by plants in the form of Nitrate (NO-3). Ammonium is converted to Nitrate with the help of  soil bacteria. Nitrogen is a very mobile element and is easily lost from the soil. Ammonium (NH4+) can be converted to Ammonia (NH3). The gaseous ammonia can be lost to the atmosphere.  Nitrate can be lost through denitrification. Nitrate nitrogen is reduced to nitrous oxide (N2O), elemental nitrogen (N2) and nitric oxide (NO). All are volatile. Denitrification occurs under conditions of high water availability and temperatures higher than 10ºC.

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22 Plant Cell

The word cell was coined by Robert Hooke with the help of compound microscope. Cell is the basic unit of life. A plant cell has three distinct components a). Cell wall b). Protoplasm and c). Vacuole. Cell wall  and  vacuole are considered as non-living substances. The protoplasm which is living is  composed of 1. Cytoplasm and 2. Nucleus. The cytoplasm contains several organelles such as mitochondria, chloroplast, ribosomes, endoplasmic reticulum, golgi complex, lysosomes, plastids etc.

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23 End Pages

Appendix Conversion factors

 
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