Plant biochemistry

                                                                                Biochemistry

             Biochemistry is the study of the chemical processes that occur within living organisms. It is a branch of science that combines biology and chemistry to understand the complex interactions between molecules that sustain life.

Branches of Biochemistry

1. Structural Biochemistry: Studies the 3D structure of biomolecules, such as proteins and nucleic acids.

2. Metabolic Biochemistry: Examines the chemical reactions that occur within cells, including energy production and nutrient metabolism.

3. Molecular Biochemistry: Focuses on the interactions between biomolecules, such as protein-protein interactions and gene expression.

4. Clinical Biochemistry: Applies biochemical principles to diagnose and treat diseases, including the analysis of bodily fluids and tissues.

5. Nutritional Biochemistry: Explores the biochemical processes involved in nutrition, including the metabolism of nutrients and the impact of diet on health.

6. Toxicological Biochemistry: Investigates the biochemical effects of toxins and pollutants on living organisms.

7. Pharmaceutical Biochemistry: Develops and tests new drugs, including the study of their biochemical mechanisms and interactions.

8. Environmental Biochemistry: Examines the biochemical processes that occur in the environment, including the impact of pollution on ecosystems.

9. Forensic Biochemistry: Applies biochemical techniques to analyze evidence and solve crimes.

10. Computational Biochemistry: Uses computational models and simulations to understand biochemical processes and predict the behavior of biomolecules.

These branches of biochemistry often overlap and intersect, providing a comprehensive understanding of the complex biochemical processes that underlie life.

Scope of Biochemistry in Agriculture

 Crop Improvement:

  Soil Science:

  Pest and Disease Management:

  Animal Nutrition:

  Food Science:

Applications of Biochemistry in Agriculture

 Genetic Engineering:

  Biotechnology:.

 Molecular Diagnostics:

 Nutrigenomics:

Climate-Smart Agriculture:

CARBOHYDRATES

Definition

         Carbohydrates are defined as polyhydroxy aldehydes or ketones, their derivatives and their polymers.)

Occurrence

           Carbohydrates occur in all animals, plants and microorganisms. In plants, 50-80% of dry matter is composed of carbohydrates.

         The structural material in plants is mainly cellulose, hemicelluloses and pectin.

Classification

   Carbohydrates are classified into three major groups as

             Monosaccharides

             Oligosaccharides

            Polysaccharides

Monosaccharides

        Monosaccharides are called simple sugars.

      They cannot be further hydrolyzed into simpler sugars.

        These are white, crystalline solids with sweet taste.

Based on functional group monosaccharides are classified into two groups

Aldoses: Sugars containing aldehyde group are called aldoses. E.g. glucose, mannose, galactose

Ketoses: Sugars that have ketone group are called ketoses. E.g. fructose

Based on number of carbon atoms monosaccharides are classified as Trioses (sugars having 3 carbon atoms), Tetroses (sugars having 4 carbon atoms), Pentoses (sugars having 5 carbon atoms), Hexoses (sugars having 6 carbon atoms), Heptoses (sugars having 7 carbon atoms)

Oligosaccharides

     Oligosaccharides are made up of two to ten monosaccharide units linked by glycosidic linkages.

Examples of oligosaccharides

Disaccharide: Sucrose is made up of glucose and fructose Maltose is made up of two units of glucose Lactose contains galactose and glucose

Trisaccharide: Raffinose contains glucose, fructose and galactose

Tetrasaccharide: Stachyose contains glucose, fructose and two galactose

Polysaccharides 

    Polysaccharides consist of many monosaccharides linked by glycosidic bond. Homopolysaccharides are composed of a single type of monosaccharide. E.g. starch, glycogen, cellulose, inulin.

Heteropolysaccharides are made up of repeating units of two or more different kinds of monosaccharides.

E.g. hemicelluloses, arabinogalactan, heparin

Polysaccharides may also be classified based on their function as structural and storage polysaccharides.

     Structural polysaccharides are usually present in the cell walls and give shape and rigidity to the cell

E.g. cellulose, hemicelluloses and pectin are components of plant cell wall. Chitin is a structural polysaccharide present in the exoskeletons of insects, crustaceans and certain fungi.

Disaccharides Maltose

  Maltose is a disaccharide made up of two a-D-glucose molecules joined by an alpha(1 -> 4) glycosidic linkage. Sucrose

    Sucrose is a disaccharide made up of an a-D-glucose and B-D-fructose linked by al→ ẞ 2 glycosidic bond.

Lactose

     Lactose is a reducing disaccharide made up of B-D-galactose linked to a-D-glucose by B-1,4 glycosidic linkage

    It is hydrolyzed by the enzyme lactase into galactose and glucose. It is also called milk sugar.

Sucrosyl oligosaccharides

             Sucrosyl oligosaccharides are formed by the transfer of galactopyranosyl, glucopyranosyl, or fructofuranosyl residue to either the glucosyl or fructosyl moiety of sucrose.

Starch

      It is a homopolymer of aD-glucose units. Starch has two main constituents, namely amylose and amylopectin. Most natural starches are a combination of these two.

     Starch is stored in the form of granules in the chloroplasts and amyloplasts.

 Amylopectin 

               Amylopectin is a branched polysaccharide. It contains 10 ^ 4 to 10 glucose units and is much larger than amylose and has a branch point at every 20 to 25 glucose residues.

     In amylopectin, glucose units are linked by alpha - 1, 4 and alpha - 1, 6 glycosidic linkages. alpha - 1, 6 glycosidic linkage occurs only at the branch points.

 Cellulose

Cellulose is the most abundant biomolecule found in nature. It is the leading constituent of cell walls in higher plants.

It occurs in almost pure form (98%) in cotton fibres and to lesser extent in flax (80%), jute (60-70%), wood (40-50%) and cereal straws (30-43%).

Cellulose is a linear polymer of ẞ-D-glucose units connected through B-1,4 glycosidic bonds.

 Chitin

   It is a structural polysaccharide found in the exoskeleton of insects and crustaceans and in the cell walls of fungi.

     It consists of N-acetylglucosamine units joined by ẞ-1,4 glycosidic linkages. Like cellulose it consists of parallel chains of molecules held together by hydrogen bonds.

Physical Properties of Carbohydrates

Monosaccharides and disaccharides are crystalline, sweet and water soluble compounds. Polysaccharides are amorphous or crystalline compounds.

They are water insoluble and are not sweet to tastwe

Mutarotation

     Mutarotation denotes to the change in optical rotation when an aqueous sugar solution is allowed to stand.

    Sugars having a potential free aldehyde or keto group (all reducing sugars) exhibit mutarotation. A freshly prepared solution of a-D-glucose has a specific rotation of +113° If the solution of a-D-glucose is allowed to stand, the specific rotation changes to +52.2.

Optical activity

   Optical activity is the ability of a chiral molecule to rotate the plane of plane-polarized light in either a clockwise or anti-clockwise direction.  Monosaccharides which causes rotation of plane polarized light to the right are called dextrorotatory and is designated (d) or (+).

    Those which rotate the plane polarized light towards left are said to be leavorotatory. (7) or (-).

 Isomerism in monosaccharides

       Isomerism is the existence of more than one compound with same molecular formula but different structural formula.

 Stereoisomerism

      Due to the presence of one or more asymmetric carbon atoms, sugars can exist in different stereoisomeric forms.

      When-OH group on this carbon atom is on the right, the sugar is the Disomer, if it is on the left, it is the L-isomer.

Epimers, diastereomers and enantiomers

  Monosaccharides differing in configuration around a single carbon atom other than carbonyl carbon are known as epimers.

 For example, D-mannose and D-galactose are epimers of D-glucose at carbon atom 2 and 4 respectively.

 Chemical Reactions of Carbohydrates Oxidation

Aldonic acids: Oxidation of an aldose with bromine water at neutral pH converts the aldehyde group to a carboxyl group. Ketoses are not readily axidized by bromine water.

Uronic acids: When aldoses are oxidized with hydrogen peroxide, uronic acids are formed. In this reaction only the primary alcohol group is oxidized to carboxyl group, whereas the aldehyde group remains unchanged.

Uronic acids are present in pectic polysaccharides.

Aldaric acid: When aldoses are oxidized with nitric acid, aldaric acids are formed. Both aldehyde and primary alcohol groups are oxidized to carboxyl groups. Glucose on oxidation with nitric acid produces glucaric acid or glucosaccharic acid. The aldaric acid of galactose is called mucic acid.

Reducing property

  Bb Sugars that have potentially free aldehyde or keto groups have the ability to reduce metal ions such as copper or silver under alkaline conditions.

  This reducing property is the basis of Fehling's and Benedict's tests. In these tests, cupric ion in copper sulphate is reduced to red cuprous oxide.

 Reaction with phenylhydrazine

    When reducing sugars are heated with phenylhydrazine at pH 4.7, a yellow precipitate is obtained.

   The precipitated compound is called as osazone.

     One molecule of reducing sugar reacts with three molecules of phenylhydrazine to form osazone.

With dilute alkali

      With dilute alkali and on standing, glucose undergoes transformation and is partly converted to fructose and mannose and hence, all the three sugars will exist at equilibrium.

Reaction with acids

      Monosaccharides are stable to hot dilute mineral acids. When heated with concentrated mineral acids, pentoses are dehydrated to furfural, while hexoses are dehydrated to hydroxymethylfurfural.

 Glycoproteins

    Glycoprotein is a type of protein molecule that contains a carbohydrate attached to it.

   The carbohydrate is an oligosaccharide chain (often branched) that is covalently bonded to the polypeptide side chains of the protein.

Functions of glycoproteins

           Glycoproteins act as structural components, involved in reproduction, immune system, hormones, and protection of cells and organisms.

          Glycoproteins allow for the binding of the sperm cell to the surface of the egg and thus essential for reproduction.

      The mucus secretions contain glycoproteins.

 Lectins

   Lectins are defined as specific carbohydrate binding proteins.

    They may bind to a soluble carbohydrate or to a carbohydrate moiety that is a part of a glycoprotein or glycolipid.

        Lectin usually contains two or more binding sites for carbohydrate units. They typically agglutinate red blood cells.

LIPIDS

Lipids are one of the four major classes of compounds found in living tissues, along with carbohydrates, proteins and nucleic acids.

      Lipids can be defined as “heterogeneous group of compounds that are not soluble in water, but soluble in non polar solvents

 Classification of Lipids

Lipids are classified into three major classes:

Simple lipids:

These are esters of fatty acid with alcoho Fats and oils Esters of fatty acid with glycerol 2. Waxes- Esters of fatty acid with long chain monohydric Alcohol

c.g. Insect wax: Bees wax, Plant wax: Carnauba wax,

Animal wax: Lanolin

B. Compound lipids: These are esters of fatty acid with alcohol and contain additional groups. Depending on the nature of these groups, it is further classified.

             1.Phospholipids – Lipids containing, in addition to fatty acid and an alcohol, a phosphoric acid residue and a nitrogenous base.    2.Glycolipids- Lipids containing a fatty acid, sphingosine and carbohydrates like galactose (e.g. Cerebrosides).

            Sulpholipids Lipids containing sulphated hexoses, fatty acid and alcohol.

   Lipoproteins- Lipids containing protein subunits. Depending on the density of the protein and the lipid component, it is further classified as Very Low Density Lipoprotein (VLDL), Low Density Lipoprotein, (LDL) and High Density Lipoprotein (HDL).

C. Derived lipids: These are hydrolysis products of simple and compound lipids. In addition to fatty acids, glycerol, this also includes steroids, sterols, fatty aldehydes, ketones, alcohols, hydrocarbons, fat soluble vitamins and hormones.

Triacylglycerol, cholesterol and cholesteryl esters are uncharged and hence called neutral lipids.

Fatty Acids

Fatty acids are long aliphatic hydrocarbon chains with a carboxyl group at one end

For example, palmitic acid is a 16 carbon fatty acid with no double bonds and is indicated as 16:0, Oleic acid is a 18 carbon fatty acid with 1 double bond between 9th and 10th carbon and is indicated as 18:1 49, where A indicates the position of the double bond in the hydrocarbon chain.

Omega 3 and omega 6 fatty acids 

In the fatty acid structure, the carbon of the methyl group (on theMethyl end of the fatty acid) is referred as omega carbon and is given the number 1.

Simple Lipids

   Lipids containing only fatty acid and glycerol or long chain alcohol are termed simple lipids. This includes fats, oils and waxes.

Fats and Oils

Esters of fatty acid and glycerol are termed triacylglycerol or triglycerides.

A typical triacylglycerol has three molecules of fatty acid esterified to the three alcohol groups of one glycerol molecule.

Waxes

   Wax is an ester of long chain fatty acid with long chain monohydric alcohol

Compound Lipids

Lipids containing groups in addition to fatty acid and alcohol are termed compound lipids Phospholipids contain phosphate groups in addition to fatty acid andAlcohol. They are the major lipid components of biological membranes.

Physical and Chemical Properties

Triglycerides are solids or liquids at room temperature, and have a specific gravity of less than one and hence lighter than water.

   The melting point of fats is dependent on two factors: the chain length of the component fatty acids, and their degree of unsaturation.

Hydrolytic rancidity

  This type of rancidity is caused by lipase enzyme secreted by the microorganisms that grow in the fat.

Oxidative rancidity

  This type of rancidity occurs when atmospheric oxygen adds to the double bonds of the unsaturated fatty acids to produce either cleavage or polymerization.

Hydrogenation

Addition of hydrogen to the double bonds of unsaturated fatty acids in the presence of finely divided nickel catalyst at high temperature of 150°C and a pressure of 150psi is called hydrogenation..

Trans Fat

Fats containing double bonds in trans configuration are called trans fats. All naturally occurring fats contain cis double bonds.

Physical and chemical constants

        Saponification value is defined as the number of mg of alkali required to saponify the fatty acids present in 1 gram of oil. The saponification value of triacylglycerols gives comparative information about the chain length of the fatty acids it contains. High saponification values indicate the presence of significant amounts of short and medium chain length fatty acids.

 Iodine value is defined as the number of grams of iodine absorbed by 100 g of fat or oil. It is a measure of the reaction of iodine with the double bonds of unsaturated fatty acids. Iodine value indicates the degree of unsaturation. High iodine value indicates high degree of unsaturation.

Acid value is defined as the number of mg of alkali required to neutralize the free fatty acids present in 1 g of fat. It indicates the freshness of oil.When the acid value of a sample is high, it indicates that the oil has undergone rancidity.

Reichert Meisel number (RM number) is specific for volatile soluble fatty acids in butter and coconut oil. It is defined as the number of millilitres of 0.1N alkali required to neutralize the soluble volatile fatty acids distilled from 5 g of fat, RM number helps to detect adulteration in butter and ghee. When butter or ghee is adulterated with animal fat, the RM value is reduced

Polanski number is specific for insoluble non volatile fatty acids. Polanski number is defined as the number of millilitres of 0.1N alkali required to neutralize the insoluble non volatile fatty acids obtained from 5 g of fat. This helps in detection of animal fat in ghee.

      Amphipathic lipids

Generally lipids are insoluble in water due to the presence of non polar hydrocarbon groups. Phospholipids contain polar groups, making part of the molecule hydrophilic (water soluble) while part of the molecule is hydrophobic (water insoluble). Such molecules are said to be amphipathic

Proteins

Proteins are large biomolecules in comparison to carbohydrates and lipids

 A. Classification based on solubility and composition

Proteins are classified into three main groups based on solubility and composition as follows:

   Simple Proteins

  Conjugated proteins

  Derived proteins

  Simple proteins

Proteins that contain only a-amino acids are called simple proteins or in other words simple proteins on hydrolysis yield only amino acids.

iii). Derived proteins

   Derived proteins are formed when simple or conjugated proteins undergo complete or partial hydrolysis by the action of acid, alkali or enzymes. Two types of derived proteins are known.

1.   Primary derived proteins

2.   Secondary derived proteins

Primary derived proteins

     Primary derived proteins are formed during hydrolysis of simple or conjugated protein and there is only little modification in the structure of protein molecule and its properties.

 Secondary derived proteins

  Progressive hydrolytic cleavage of the peptide bonds of protein molecule results in formation of secondary derived proteins which are categorized into proteoses, peptones and peptides according to average molecular weight

 Classification of proteins based on functional aspects

  Proteins carry out all vital life processes. They perform various structural and dynamic functions in living organisms. Based on their functional aspects, proteins are classified as follows:

 Classification based on size and shape

Structure and shape of a protein depends on the axial ratio ie. length divided by width of the protein. In globular proteins, axial ratio is less than 10 and in fibrous proteins, axial ratio is greater than 10.

 Structure of proteins

Each protein in a biological system has a unique three-dimensional structure and biological activity. Conformation of a protein is the three-dimensional structure in its native state

 Four levels of structural organization are distinguished in the protein architecture. They are

1.   Primary

2.   Secondary

3.   Tertiary

4.   Quaternary

Primary structure of proteins

    Each protein has a unique, precisely defined amino acid sequence with one or more polypeptide chains

Secondary structure

  Secondary structure refers to folding of a linear polypeptide chain to form a specific coiled structure.

  Polypeptide chains can be folded

 Properties of protein

  Pure proteins are odourless and tasteless

   They are optically active.

  The magnitude of optical activity depends on temperature, wavelength of light and concentration of protein.

Denaturation of protein

Physical and chemical factors causing denaturation of protein are heat, UV radiation, organic solvents, acidic and basic reagents and heavy metal ions

   Exposure to heat and radiation causes excitation of protein molecules to higher energy levels and this disrupts the weak hydrogen bonds and salt linkages.

Renaturation

   Renaturation refers to the process of regaining the original regular three-Denaturation is found to be reversible at some instance

                                                                                         Enzymes

 Definition : enzymes are biological catalysts which bring about chemical reaction in the living cell and it is

 produced by the living organism in small amounts.

 Functions:

        Digestion

        breathing and

       synthesis

General properties of enzymes:

1. all enzymes are proteins.

2. enzymes accelerate the reaction but:   

     a. do not alter the reaction equilibrium       

     b. not consumed in overall  reaction             

     c. required in very small quantities.

3. enzymes are highly specific for their substrate.

4. enzymes possess active site, at which interaction with substrate take place.

Sources of enzymes:

  Endoenzymes: enzymes that function within the cells, most of enzymes are these types.

     Ex: metabolic oxidase.

  Exoenzymes: enzymes that are liberated by cells and catalyze reactions outside the cell.      Ex: digestive enzymes (amylase, lipase, protease).

Chemical composition of enzymes:

   Enzymes classified according to their chemical composition into.

1.  Enzyme consist of only protein.

            Ex:  pepsin, trypsin ( amino acids binding peptide bonds).   

2.  Enzyme consist of :   protein (enzyme)  +  Co - Enzyme  =  Holoenzyme

                                                   ( apoenzyme)

  3.  Enzyme consist of:

  Protein (enzyme)  +  prosthetic group (Co – factor)  =  Holoenzyme

 Classification of enzymes:

1.   Oxidoreductases: one compound oxidized, another reduced. Ex: lactate dehydrogenase, tyrosinase,

  2.   Transferase:

  Enzyme transfer group containing C, N or S, from one substrate to another substrate.

    Ex: Transaminase ( glutamate oxaloacetate transaminase(GOT)  or  Aspartate transaminase (AST).             and  glutamate pyruvate transaminase(GPT), alanine transaminase(ALT)         ( transfer of amine group(  

 Hydrolyase:

 Catalyse hydrolysis of ester, peptide or glycoside bound by addition of H2O across  the bond.

 2.   Lyasis: 

 Additional or removal of group without hydrolysis, oxidation, reduction producing double  Bond.

3.   Isomerase:

   Produce optical, geometric or position isomer of substrates by intermolecular rearrangement.

4.   Ligases or synthetase:

 link two substrate together usually by pyrophosphate bound.

  Three types of specificity:

 1. Steriospecificity: enzyme show specificities with only one specific group of substrate.    Ex: Urease      catalysis the hydrolysis of urea only     L- amino oxidase for L-alanine substrate.

 2. Substrate specificity: enzyme catalyze reaction with specific substrate, cannot acts on other   substrate. They are Like lock and key model. Ex: Trypsin, Chymotrypsin

        Trypsin: hydrolyze peptide bonds involving carboxyl group of basic amino acids (arginine and lysine).

    Chymotrypsin hydrolyze peptide bonds of aromatic amino acids (phenylalanine ,tyrosine).   

 3. Reaction specificity:  substrate can undergo many reactions,  but each reaction catalyzed by different  enzyme.   Ex: Oxalic acid undergo different reactions.

 Factors affecting enzyme activity: 

 1. Enzyme concentration.

   a. The rate of reaction depends directly on the amount of enzyme present.       

   b. At a specific time.

     c. Unlimited substrate concentration. 

   If the amount of enzyme is increased by two fold, the reaction rate is doubled.

  2. Substrate concentration.                           

a. The rate of reaction is directly proportional to the substrate avalible.

b. If the enzyme concentration is kept constant, and the amount of substrate is Increased.  

c.  Further increase in the substrate, does not increase the rate of the reaction any more.

  3. Temperature

a.  The rate of enzyme may increase with increase in temperature but up to a certain limit.

b.  All enzymes can work at their maximum rate at optimum temperature.

c.  For enzymes of human body 37°C is the optimum temperature.

d.  Enzymes denature at high temperatures.

  4. Value of PH.

a.  Enzymes have specific range of PH at which will work.

b.  loose activity in low or high PH.

c.   Enzyme denature (change shape and become ineffective). (in temperature and PH).

  Enzyme inhibition:

Inhibitors :   a chemical substance, can react in place of substrate with the enzyme but is not transformed  into product(s). the process called enzyme inhibition.

    The Inhibitors : poisons, like cyanide, antibiotics, anti-metabolites and some drugs.

 Classification of inhibitors:

Inhibitors can be divided into two types:  

(i) Irreversible

           (ii) Reversible Irreversible inhibitors:

1.  The inhibitor occupying the active sites by forming covalent bonds or they may physically block  the active sites. 

2.  The inhibitor destroying the globular structure. 

     Reversible Inhibitors:

 Reversible inhibitors attach to enzymes with non-covalent interactions such as hydrogen bonds,  hydrophobic interactions and ionic bonds. Inhibitors form weak linkages with the enzyme.

        Elevated in serum in:   myocardial infarction,    acute liver cell damage,      viral hepatitis and      carbon tetrachloride poisoning.

      Moderate elevation: muscular dystrophy,     dermatomyositis,        acute pancreatitis and          crushed muscle injuries.

1.     Normal level of (GPT)  ( 7 to 56 units / liter )

Very high levels of ALT: (more than 10 times normal) are usually due to acute hepatitis, sometimes due  to a viral infection.

 moderate increases in ALT: include    obstruction of bile ducts,       cirrhosis,       chronic hepatitis,        heart damage, alcohol abuse,       tumors in the liver.

2.     Enzyme phosphatase: is agroup of enzyme , hydrolysis the monophosohate ester under acidic or  alkaline condition.

 Type of phosphatase are:   1. Acid phosphatase ACP 

                                             2. Alkaline phosphatase ALP

 Acid phosphatase(ACP). Normal level = 0.1 – 3.5 K. A.U /100ml

   Disease elevated in: 1. metastatic prostate carcinoma.

                                        2. carcinoma of blood.

 Alkaline phosphatase( ALP).   Normal level (3 – 13) K. U/ ml blood

 Disease elevated in:  1. Bon disease (paget disease)

                                          2. Rickets     

                                          3. Liver disease

3.     Enzyme amylase.             Normal value: 100 – 330 IU/L

  Disease elevated in:    1. Acute pancreatitis     2. Severe diabetic ( ketosis and acidosis).

 Lactate dehydrogenase LDH:  Normal level ( 70 – 240IU/L )

   Disease elevated in:   1.myocardial infarction (MI)

                                              2. pneumonia    

                                              3. Leukemia 

                                              4. Anemia

Nucleic acid

       Storage and transmission of biological information is fundamental for life and is carried out by nucleic acids.

      There are two types of nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).

     In 1869, Friedrich Miescher, a Swiss biochemist isolated a substance from the nucleic of pus cells and named it ‘nuclein’. Later it was realized that nuclein

 Composition of nucleic acid

        Nucleic acids are biopolymers made up of basic units called the nucleotides. Nucleotides have three characteristic components (1) nitrogenous bases (2) pentose sugar (3) phosphate. A unit made up of nitrogenous base and sugar is called as nucleoside.

   Nucleotides are nucleoside with phosphate group. Nitrogenous bases are formed from two parent compounds, pyrimidine and purine.

    The pentoses are ribose and deoxy ribose sugar moieties. The carbon and nitrogen atoms in the parent structures are conventionally numbered to facilitate the naming and identification of the derivative compounds.

 Structure of deoxyribonucleic acid (DNA) The structure of DNA was postulated by Watson and Crick in 1953,

   There are two helical DNA chains wound around the same axis to form a right handed double helix.

          The hydrophilic backbone of alternating deoxyribose and phosphate groups is on the outside of the double helix, facing the surrounding water.

           The purine and pyrimidine bases of both strands are stacked inside the double helix, with their hydrophobic and nearly planar ring structures very close together and perpendicular to the long axis.

 Forms and properties of DNA

Three forms of DNA are found to exist- A, B and Z- DNA of which B form is the predominant and most stable type.

B-DNA

      The Watson-Crick structure is also referred to as B form DNA or B-DNA.

        The B form is the most stable structure for a random-sequence DNA molecule under physiological conditions and is therefore the standard point of reference for studying the properties of DNA

A-DNA

A conformational change can be induced in DNA when the relative humidity of the sample is lowered below 75%. This double helix is formed under dehydrating conditions. Z-DNA

Renaturation

   DNA that has been denatured will often come back together when cooled below its Tm. This is referred to as Hybridization

Ribonucleic acid (RNA)

     Ribonucleic acid is present in the cytoplasm and it is single stranded. Several types of bacteriophages and many plant viruses contain RNA as genetic material and are devoid of DNA. RNA is very similar to DNA in that it is made up of 4 different building blocks of ribonucleotides.

Types of RNA

Messenger RNA (mRNA)

Transfer RNA (tRNA)

   Ribosomal RNA (rRNA)

   Messenger RNA

  mRNA is the most heterogenous in size and stability.

  They function as messengers conveying the information from a gene to the protein synthesizing machinery.

  mRNA molecules from prokaryotes are simple, whereas mRNAs from eukaryotes have some unique chemical characteristics.

   Transfer RNA (Smallest Soluble/SRNA)

1.         5’ terminus is always phosphorylated

i.              7 base pair stem acceptor or amino acid arm with CCA in 3’ terminus

ii.            3-4 bp stem and loop contains the base dihydrouridine (D-arm

iii.           5 bp stem and loop containing anti-codon triplet (anti-codon arm)

iv.           5 bp stem and loop contains sequence TC (y stands for pseudouridine

v.            Variable arm (between anti-codon and T arm) of length 3 -21 nucleotides

vi.           Ribosome assembly Teptidyl transferase activity

The predominant metabolic processes Involving carbohydrates are:

    Glycolysis: It is the pathway of reactions involving the conversion of glucose to pyruvate with the concomitant formation of the energy in the form of ATP.

   ii. Citric acid cycle/Tri Carboxylic Acid (TCA) cycle: This is the terminal common oxidative pathway for carbohydrates, fats and proteins. It is the continuous source of precursors for various biomolecule synthesis. The acetyl-CoA which enters this cycle is completely oxidized to carhon dioxide and water with the simultaneous production of reducing equivalents, NADH and FADH

  iii. Hexose Monophosphate Shunt / Pentose phosphate pathway: It is an alternative pathway to the glycolytic pathway and the citric acid cycle for the oxidation of glucose to carbon dioxide and water with the production of NADPH and ribose 5-phosphate. Not meant for Energy)

  iv. Gluconeogenesis / Neoglucogenesis: This biosynthetic pathway produces glucose from non-carbohydrate precursors.

  v. Glycogenesis: It is the major biosynthetic pathway for glycogen synthesis from glucose.

storway of glut

 vi. Glycogenolysis: It is the degradative pathway of glycogen to yield glucose. cytosol) Extrat mitochondrical)

  Glycolysis

The term "Glycolysis" is derived from the greek word 'Glykys meaning sweet and 'lysis' meaning splitting. It is also called as Embden-Meyerhof-Parnas pathway (EMP pathway) and involves a series of biological reactions through which glucose is converted to pyruvate with the production of adenosine triphosphate (ATP).

 Stage 1: Conversion of glucose to fructose 1, 6-bisphosphate

   Carbohydrates enter glycolysis in the form of Jucose. Monosaccharides in other forms are converted to glucose before entering this pathway.

   Glucose is phosphorylated to glucose 6-phosphate and the reaction is catalyzed by hexokinase, or specifically glucokinase.

 Stage 2: Conversion of fructose 1, 6-bisphosphate to 3-phosphoglycerate

Fructose 1, 6-bisphosphate from the first stage is acted upon by aldolase enzyme that splits the six carbon sugar to two triose sugars, viz., glyceraldehyde 3-phosphate and dihydroxy acetone phosphate.          The enzyme phosphotriose isomerase catalyzes the inter conversion of dihydroxyacetone phosphate to glyceraldehyde 3-phosphate in a rapid reversible reaction resulting in two molecules of glyceraldehyde 3-phosphate. Stage 3: Formation of pyruvate

Formation of 2-phosphoglycerate from 3-phosphoglycerate catalyzed by phosphoglycerate mutase involves an intramolecular rearrangement of the phosphoryl group from third carbon to second carbon. Dehydration of 2-phosphoglycerate results in the formation of phosphoenol pyruvate

Bioenergetics of glycolysis

Bioenergetics concerns with the energy flow in living system that leads to the production and utilization of energy.

  In glycolysis one molecule of glucose is converted to two molecules of pyruvate and seven molecules of ATP are generated.

TCA cycle (Aerobic)

Tricarboxylic acid cycle or TCA cycle was proposed by Sir Hans Krebs, an English biochemist in 1937. It consists of a cycle of reactions through which acetyl CoA is oxidized to carbon dioxide and water. This cycle is also called as Kreb’s cycle or citric acid cycle. The enzymes catalyzing the reactions of this cycle are found in the mitochondrial matrix.

CH3-CO-COOH + COASH+NAD+ Lipoate, Mg CH3-CO-S-CoA+NADH+H+CO,

TCA cycle has eight steps and they are described as follows:

i. Citrate formation

The initial step in TCA cycle is the condensation reaction between oxaloacetate and acetyl-CoA resulting in the formation of citrate and coenzyme A catalyzed by the enzyme citrate synthase.

ii. Isocitrate formation via cis-aconitate

Citrate is isomerized to isocitrate by the enzyme aconitase with the formation of cis-aconitate as an intermediate. The mechanism of this reaction involves both dehydration and hydration involving the interchange of hydrogen and a hydroxyl group. Fluoroacetate acts as an inhibitor

Oxidative decarboxylation of a-ketoglutarate to succinyl CoA

          Oxidative decarboxylation of a-ketoglutarate to succinyl-CoA and arbon dioxide takes place in the presence of a-ketoglutarate dehydrogenase complex utilizing NAD as coenzyme. Arsenite) is the inhibitor of a-ketoglutarate dehydrogenase complex.

Formation of succinate from succinyl CoA

Conversion of succinyl CoA to succinate involves a reversible reaction catalyzed by the enzyme, succinyl CoA synthetase or succinate thiokinase. This reaction also results in the formation of GTP and oenzyme A. in animal tissues succinate thiokinase utilizes GDP, whereas in plants and bacteria it uses ADP predominantly. GTP is produced in this reaction via substrate level phosphorylation.

Oxidation of succinate to fumarate

      Succinate is oxidized to fumarate by succinate dehydrogenase in the presence of FAD. Succinate dehydrogenase is the only enzyme in TCA which is membrane bound. Malonate is a strong competitive inhibitor of succinate dehydrogenase and blocks the citric acid cycle.

Hydration of fumarate to malate

Fumarase is the enzyme catalyzing the reversible hydration of fumarate to L-malate.

Conversion of malate to oxaloacetate

    The last reaction of the citric acid cycle involves the enzyme NAD-linked malate dehydrogenase catalyzing the oxidation of L-malate to oxaloacetate. Thus oxaloacetate is regenerated and ready to fuse the second acetyl-CoA molecule in TCA cycle.

Glyoxylate cycle

    Glyoxylate cycle is a modified TCA cycle which occurs in plants, fungi and bacteria, in which four carbon dicarboxylic acids are obtained from acetyl-CoA.

   In plants, the glyoxylate cycle takes place in glyoxysomes. Glyoxylate cycle allows microbial cells to use the two carbon compound acetate as the carbon source in the absence of glucose or fructose

Stage I: Formation of NADPH and ribulose 5-phosphate

The enzymes involved in the first three reactions of the pathway are glucose-6-phosphate dehydrogenase, phosphogluconolactonase and phosphogluconate dehydrogenase respectively. Ultimately, Ribulose 5-phosphate and NADPH are formed.

Hexose monophosphate shunt

       Hexose Mono Phosphate shunt (HMP shunt) is an alternate pathway for the oxidation of glucose. Otto Warburg found the first evidence for the existence of this pathway in 1930 and later it was elucidated by Frank Dickens group in the year 1950

MADPH + Pentose FA bio Sugar & Erythocer 3 NA Phosphd 1

      In non-photosynthetic tissues such as germinating seeds, differentiating tissues and during the hours of darkness, HMP shunt plays an important role.

      In animals, along with the Embden - Meyerhof pathway, HMP shunt occurs in certain tissues, notably liver, adipose tissue and lactating mammary gland. HMP shunt is a multistep process in which the three molecules of CO2 and three 5-carbon residues are obtained from three molecules of glucose 6-phosphate. The important products of HMP shunt is to generate NADPH and ribose 5-phosphate.

Stage II

      Conversion of the ribulose 5-phosphate to ribose 5-phosphate and subsequently to xylulose-5 phosphate takes place catalyzed by the enzymes nbulose 5-phosphate isomerase and ribulose 5-phosphate epimerase respectively. Ribose 5-phosphate serves as a precursor for the biosynthesis of nucleic acids. Stages I and II comprise the oxidative phase of HMP shunt.

Stage III

   In the final stage, two molecules of 6- carbon sugars and one molecule of 3-carbon sugar, glyceraldehyde 3- phosphate are obtained from three molecules of the 5-carbon sugars.

  This phase of HMP is the non-oxidative phase and involves two enzymes, transaldolase and transketolase, A C₂ is transferred from xylulose 5-phosphate to ribose 5-phosphate resulting in sedoheptulose 7-phosphate and glyceraldehyde 3-phosphate catalyzed by the enzyme transketolase.

i. Production of NADPH for the biosynthesis of fatty acids.

ii. Production of ribose for the synthesis of nucleotide and nucleic acids.

iii. Production of erythrose 4-phosphate which serves as a precursor for the biosynthesis of phenolics and aromatic amino acids through shikimate pathway.

iv. Interconversion of 3, 4, 5, 6 and 7 carbon sugars

Comparison between HMP shunt and glycolysis pathway

Catabolism of glucose involves these two major pathways i.c., glycolysis and HMP shunt. These two pathways have minute similarities, for example, the presence of metabolites like glucose 6-phosphate. Major differences found in both pathways are

(1) HMP pathway does not involve ATP generation, whereas in glycolysis, ATP molecules are generated.

(ii) Pentose phosphates are formed in the HMP shunt but not in glycolysis.

(iii) NADH is produced in glycolysis whereas NADPH is produced in HMP pathway.

Secondary metabolits

 Introduction

       Secondary metabolites are organic compounds produced by plants which have no direct function in growth and development. They are generally produced by plants to protect themselves from various predators.

       Secondary metabolites have a restricted distribution in the plant kingdom. They are often found in only one plant species or related group of species

Phenolic Compounds

  Plants produce wide variety of compounds that contain a phenol group.

   Secondary metabolites having at least one aromatic ring to which one or more hydroxyl groups are attached are regarded as phenolic compounds

Classification of phenolic compounds

Phenolics are classified according to their carbon skeleton

Simple phenols

These are compounds having at least one hydroxyl group attached to an aromatic ring as a basic skeleton. Catechol is the simplest phenolic compound occurring in plants.

Hydroxybenzoates

      Phenolic compounds with one carboxylic acid group directly attached to the aromatic ring are classified as hydroxybenzoates. Coumarins

     Coumarins are derived from cinnamic acid by cyclization of the side chain of the coumaric acid. The coumarins, such as umbelliferone, esculetin and scopoletin, are mainly found in olive oil, oats and spices.

Stilbenes

     Stilbenes have the C6-C2-Co structure. They act as phytoalexins, and are produced by plants in response to attack by fungal, bacterial and viral pathogens

Flavonoids

       Flavonoids are the major group of naturally occurring phenolics. These are compounds with two aromatic rings connected by a three-carbon bridge. They occur in the epidermis of leaves and the skin of fruits and have different roles as secondary metabolites

Tannins

   Tannins are polyphenols which have astringent taste and are capable of precipitating proteins. These compounds are used for tanning leuther.

Lignins

    Lignin is the second abundant natural compound present on earth next to cellulose

     It is a polymer of the three phenylpropanoid alcohols, coniferyl alcohol, sinapyl alcohol and p-courmaryl alcohol.

Shikimic acid pathway

         Shikimic acid pathway is an important pathway through which plants synthesize phenolics. The precursors of shikimate pathway are erythrose 4-phosphate and phosphoenolpyruvate derived from pentose phosphate pathway and glycolysis respectively.

 Functions of phenolics

      Phenolic compounds provide mechanical support and defense to plants.

     Lignins present in cell wall provide mechanical strength to plant parts such as cell wall, stems and twigs and provide stability for the vascular tissues of the xylem

      The mechanical strength and chemical composition of cell wall make plant tissues difficult for herbivores to digest and also inhibits the growth of pathogenic microorganisms

      Lignin is synthesized in response to wounding

       Viniferin, a constituent of grape vine is a fungicide. Rotenoids (isoflavonoids) found in legumes have strong insecticidal actions.

    Flavonoids secreted into the soil by legume roots mediate the interaction of legumes and nitrogen-fixing bacteria, thereby help in symbiotic nitrogen fixation. Flavonoids also protect plant cells from UV irradiation

 Terpenes

      The terpenes or terpenoids constitute a diverse class of secondary metabolites that are generally insoluble in water.

       The basic structural element of terpenes is the branched 5-carbon unit called isoprene. Terpenes can decompose at high temperatures to give isoprene.

      Hence all terpenes are also called as isoprenoids.

Structure of isoprene

    Isoprenoids are dimers, trimers, tetramers or polymers of isoprene units that are generally linked together in head to tail manner

   The structures of terpenes may be cyclic or non-cyclic with simple and complex polymeric structures.

Classification

Hemiterpenes

        Hemiterpenes are the simplest among the terpenes containing 5 carbon atoms.

       The most prominent hemiterpene, isoprene is emitted from the leaves of many trees such as conifers, poplars, oaks and willows.

Monoterpenes

Monoterpenes consist of ten carbon atoms with 2 isoprene units.

Sesquiterpenes

   Sesquiterpenes consist of three isoprene units and exist in linear, cyclic, bicyclic, and tricyclic forms. They also exist with cyclic lactone ring structure

Diterpenes

      Diterpenes contain four isoprene units and are derived from geranylgeranyl pyrophosphate. Phytol, the side chain present in chlorophyll> molecule and gibberellic acid, the phytohormone are diterpenes. Diterpenes exhibited inhibitory effects against pathogenic microbes, herbivores, and weeds.

Sesterterpenes

    Sesterterpenes consist of 25 carbon atoms with five isoprene units which are rare among terpene compounds.

Triterpenes

       Triterpenes consists of thirty carbon atoms with 6 isoprene units They are derived from the precursor squalene which is a C30 compound.

     They are mostly cyclic compounds. A group of triterpenes called as saponins, protect plants against pathogenic microbes and insect pests.

    Cholesterol and other phytosterols are triterpenes.

Tetraterpenes

     Tetraterpenes are terpenes consisting of eight isoprene units with 40 carbon atoms. Carotenoids are tetraterpenes

Polyterpenes

          Polyterpenes are polymeric terpenes formed from many isoprene units. Rubber, which occurs in the latex of the rubber tree (Hevea braziliensis), is a polyterpene (cis-1,4-polyisoprene). Gutta-percha latex

 Functions of terpenes

  Terpenes have important defence function in plants.

    They are toxins and feeding deterrents to many insects and mammals that feed on plants.

.   Certain monoterpenes and sesquiterpenes are synthesized and emitted only after the insect begin feeding.

    These substances repel egg laying pests and attract natural enemies, including predatory and parasitic insects, which kill the plant-feeding insects.

Alkaloids

      The alkaloids are a large family of organic nitrogen containing secondary metabolites with therapeutic significance.

     Alkaloids can be defined as naturally occurring organic nitrogen containing heterocyclic basic compounds.

 Classification of alkaloids

Alkaloids are broadly classified into three types based on the biosynthetic origin and nature of cyclic ring.

1. True alkaloids contain nitrogen in the heterocycle and originate from amino acids.

o.g. Atropine, nicotine, morphine

2. Protoalkaloids contain nitrogen but not in the heterocycle and originate from amino acids. e.g. Hordenine, mescaline, ephedrine

3. Pseudoalkaloids contain heteroéyclic ring with nitrogen, but does not originate from amino acids. This group includes purine type of alkaloids. e.g. Caffeine

Waxes

         The aerial surfaces of plants are covered with a layer of chloroform soluble non-volatile lipids, collectively called wax.

     The wax layer reduces water loss, thereby making terrestrial plant life possible.

      The amount and composition of wax deposited are controlled by the plant in response to environmental factors such as relative humidity, soil moisture and light.

Cutin

    A major component of the cuticle is cutin, which in turn is covered by surface waxes.

     Cutin is lipid polyester with polymeric network of oxygenated C1s and Cis fatty acids cross-linked by ester bonds, such that the carboxyl group of one fatty acid is linked to a primary or secondary hydroxyl group of another.

Suberin

      The major aliphatic components of suberin (20-50%) are -hydroxy acids, the corresponding dicarboxylic acids, very long (C20) acids, and similarly long alcohols

     Among the w-hydroxy and dicarboxylic acids, monounsaturated Cis and saturated C16 acids are often the dominant components.