Carbohydrates Biochemistry PDF

BIOCHEMISTRY I Assistant Lecturer: MUKAYISENGA Josiane  Course overview Component 1 CHAP I : Carbohydrate Introduction Classification of carbohydrates Stereoisomerism monosaccharides Disaccharides Polysaccharides CHAP II : Amino acids and proteins Roles of pro...

BIOCHEMISTRY I Assistant Lecturer: MUKAYISENGA Josiane  Course overview Component 1 CHAP I : Carbohydrate Introduction Classification of carbohydrates Stereoisomerism monosaccharides Disaccharides Polysaccharides CHAP II : Amino acids and proteins Roles of proteins in living organisms Structure and properties of the 20 essential amino acids Formation and properties of the peptide bond  Protein folding; secondary, tertiary and quaternary protein structure  Protein denaturation CHAP II: Nucleic Acids Role of nucleic acids in living organisms  Nomenclature, chemical composition and structures of nucleosides and nucleotides  Structure of DNA double helix Packaging of DNA Replication  Mutations and repair mechanisms  Transcription  Genetic code Translation  DNA sequencing CHAP IV:Lipids Roles of lipids in living organisms  Classification of lipids  Fatty acids (saturated, unsaturated) Glycerides(neutral glycerides, phosphoglycerides)  Non-glycerol lipids (sphingolipids, steroids, waxes)  Biological membranes (structure, transport across membrane) Component II  Natural Product - General Definition - Classification - Semiochemicals and lipids - Alkaloids - Phenylpropanoids - Polyketides - Terpenoids - Saponines - Flavonoids  Biochemistry : General introduction Biochemistry is the study of the chemical substance and the chemical processes that occur in living organisms. The changes they undergo during development and life. This includes organic molecules and their chemical reactions. The principal biomolecules such as: Carbohydrates, Amino acids, Lipids, Proteins and Nucleic acids.  The importance of Biochemistry  Biochemistry is used in different domains :  In Food science: Determination of chemical composition of food, research, to invent ways to prolong the shelf life of food products.  In agriculture : To study the interaction of herbicides/insecticides with plants and pests, determine their ability to inhibit growth, and evaluate the toxicological effects on surrounding life.  In pharmacology, physiology, microbiology, toxicology, and clinical chemistry: -To investigate the mechanism of a drug action. -use chemical concepts, procedures, and techniques to study the diagnosis and therapy of disease and the assessment of  Biochemistry is important in industry: -Biotechnology industry: Produces seed that are resistant to diseases, plants that are drought resistant, Seed coatings with specific properties. -Pharmaceutical industry: Drugs production  Biochemistry is used to learn about the biological processes:-To study the properties of biological molecules (keratin in order to develop the shampoo). - To find uses for biomolecules (food additive), find a substitute for a usual biomolecule (artificial sweeteners).  Gene therapy is within the realm of biochemistry.(Biochemistry help to understand the chemical reaction involved).  I. Carbohydrates Introductory notes on carbohydrates  Carbohydrates are organic compound. They contain carbon, hydrogen and oxygen.  Carbohydrates are formed in the plants by photosynthesis from carbon dioxide and water in the presence of sunlight.  Among them we have the sugars ,starches and fibers found in fruits , grains, vegetables and milk products. Carbohydrates has general molecular formulas which makes them appear to be hydrates of carbon. The general formula is Cn (H2O) n. The simplest carbohydrates are called monosaccharides, Monosaccharide link together to form oligosaccharides and polysaccharides. All are aldehydes or ketones All contain several hydroxyl groups  Functions of carbohydrates Energy storage and production: Glycogen, starch in plant and animals are stored carbohydrate from which glucose can be mobilized for energy production.  It play a role in plant cell wall structure: cellulose (the most abundant polysaccharide in nature) and chitin the second next to cellulose, serve as structural elements in plant cell walls and exoskeletons of arthropods. It play a role in the immune response : cell–cell interactions, fertilization and viral infection. They exert a protein-saving action: whenever they are present in adequate amount in daily food , the body does not utilize proteins for energy purpose. it will need to eliminate nitrogen (ammonia) and sulfur present in some amino acids. Their presence is necessary for the normal lipids metabolism (Fats burn in the fire of carbohydrates): when carbohydrates are in excess may be converted in fatty acids and triglycerides (processes that occur mostly in the liver). Two sugars, ribose and deoxyribose, are part of the bearing structure, respectively of the RNA and DNA and obviously find themselves in the nucleotide structure. Flavor and Sweeteners A less important function of carbohydrates is to provide sweetness to foods. Receptors located at the tip of the tongue bind to tiny bits of carbohydrates and send what humans perceive as a "sweet" signal to the brain. However, different sugars vary in sweetness. For example, fructose is almost twice as sweet as sucrose and sucrose is approximately 30% sweeter than glucose. Biological Recognition Processes Carbohydrates not only serve nutritional functions, but are also thought to play important roles in cellular recognition processes. For example, many immunoglobulin's(antibodies) and peptide hormones contain glycoprotein sequences. These sequences are composed of amino acids linked to carbohydrates.  Classes of carbohydrates a) on the basic of the major forming units there are three classes: Monosaccharide: Carbohydrates that cannot be hydrolyzed to simpler carbohydrates(Simple sugars like Glucose, fructose and galactose). Oligosaccharides: are formed by short chains of monosaccharidic units (from 2 to 20) linked one to the next by chemical bounds, called glycosidic bounds The most abundant oligosaccharides are disaccharides, formed by two monosaccharides, and especially in the human diet the most important are sucrose (common table sugar), lactose and maltose. Polysaccharides: are polymers consisting of 20 to thousands of monosaccharide. In the plant kingdom several types of polysaccharides are present, in vertebrates there are only a small number. The polysaccharides cannot be directly utilized by the body They must first be broken down into monosaccharides, the only sugar form the body can use. There are types of polysaccharides that are important in the study of nutritional science: starch, dextrin, glycogen and cellulose, Chitin. 1. Starch :-Is abundant in the plant world and is found in granular form in the cells of plants. -They provide a reserve food supply for the plant, sustain the root or tuber and nourish the growing embryo during germination. - Most starches are a mix of two different molecular structures, amylose and amylopectin. 2. Dextrin: Are intermediary products of starch digestion. - Are formed by the action of amylases on starches. - Most commonly consumed in cooked starch foods.  3)Glycogen: Is the reserve carbohydrate in humans, animals ,fungi and bacteria 4)Cellulose: is composed of thousands of glucose molecules. Is the structural constituent of the cell walls of plants. -Is the most abundant naturally occurring organic substance. -It can be digested only by herbivores such as cows, sheep, horses, etc., -These animals have bacteria in their rumens (stomachs) whose enzyme systems break down cellulose molecules. -Humans do not have the enzyme needed to digest cellulose, so it is passed through the digestive tract unchanged. 5) Chitin: Chitin makes up the hard exoskeleton of crustaceans and insects -Fungal cell walls are made of chitin a polymer of N- acetyl glucosamine. -The fact that true fungi have chitin cell walls makes them more like animals than plants. Based on their composition Polysaccharide can be: omopolysaccharides:They contain one type of monosaccharide (EX: starch,glycogen and chitin). Eteropolysaccharides: : They contain two or more different kinds (e.g. hyaluronic acid). b)On the basis of their degree of polymerization, they can be classified as: simple: mono and disaccharides(also known as “sugars”) and tri- and tetra saccharides. (oligosaccharides).  complex: Those are polysaccharides. Classification of carbohydrate  Nomenclature Functional group Ketone Aldehyde 4 Tetrose Tetrulose Number of carbons 5 Pentose Pentulose 6 Hexose Hexulose 7 Heptose Heptulose 8 Octose Octulose  Monosaccharides  Are simple sugar , are the basic units of carbohydrates.  They are fundamental units of carbohydrates and cannot be further hydrolyzed to simple compounds.  Common monosaccharides contain from 3 to 6 carbon atoms.  They are classified based on number of carbon atoms as trioses, tetroses,pentoses,hexoses and heptoses  From all of these structures, pentoses and hexoses are the most common  They have to be obtained by chemical reactions  Only few are free in plant  They provide energy- readily broken down to release energy(metabolism).Therefore Primary fuel for the body. They serve as building blocks of other carbohydrates (Disaccharides, Polysaccharides) Ex: Glucose (C6H12O6), fructose, galactose (with 6 C) Food sources for simple sugars are: Fruits ,honey, syrup, Candy. Converts to glucose in the body.  MONOSACCHARIDES No of C-atoms Potentially active carbonyl group Trioses Tetroses Pentoses Aldoses Ketoses Hexoses Heptoses “These carbohydrates cannot Octoses be hydrolyzed into simpler compounds” Physical properties of monosaccharides Sugars(simple sugars) Small molecules Sweet Readily soluble in water Crystalline Name always ends in-ose eg. Glucose Chemical properties All reducing sugars; They reduce mild oxidizing agents such as Tollens or Benedict’s reagents. The structure of some monosaccharides  Based on number of carbons Trioses C3H6O3 eg. Glyceraldehyde (glycerose), dihydroxyacetone. Intermediates in cellular respiration (see glycolysis),photosynthesis(dark r(x)) and other branches of carbohydrate metabolism. PENTOSES Ribose Found in nucleic acids Forms structural elements of nucleic acid and coenzymes Intermediates of pentose phosphate pathway Also involves in synthesis of ATP, NAD, NADP, flavoproteins.  HEXOSES Glucose  Found in fruits , fruit juices, hydrolysis of starch, maltose and lactose.  Body sugar and the principal one used by the tissues.  Excess in the blood is called hyperglycemia and presence in urine (glucosuria) indicates diabetes mellitus.  Fructose Latin word for fruit — "fructus" Found in fruit juices, honey  Main nutritional source of energy for the spermatozoa and is found in the seminal fluid Can be converted to glucose in the liver It is the sweetest sugar Lack of enzymes of metabolism( Hepatic Fructokinase) can lead to essential fructosuria.  Galactose Greek word for milk-"galact", found as a component of lactose in milk Formed by the hydrolysis of lactose It can be converted to glucose in the liver Accumulation of galactose in blood can lead Lactose intolerance : – missing digestive enzyme needed to split into two monosaccharide parts to absorb it.  Glycosidic bond Glycosidic bond or glycosidic linkage is a type of covalent bond that joins a carbohydrate (sugar) molecule to another group, which may or may not be another carbohydrate. Formation of ethyl glucoside :  Glucose and ethanol combine to form ethyl glucoside and water.  The reaction often favors formation of the glycosidic bond as shown due to the anomeric effect A glycosidic bond is formed between the hemiacetal or hemiketal group of a saccharide (or a molecule derived from a saccharide) and the hydroxyl group of some compound such as an alcohol. A substance containing a glycosidic bond is a glycoside. Hemiacetals and hemiketals are compounds that are derived from aldehydes and ketones respectively. The Greek word hèmi means half. A glycoside is a molecule present in many plants and some animal , these compound upon hydrolysis gives one or more sugar( Glycone) moities and non sugar moiety ( Aglycone ). Glycoside =sugar molecule (Glycone)+ non sugar molecule( Aglycone)  Glycone and an Aglycone are linked by a glycosidic bond Example of Glycosidic bonds formed between disaccharides Maltose= D-glucose + D-glucose (Alpha –(1,4) glycosidic bond) Lactose= D-galactose + D-glucose (Beta –(1,4) glycosidic bond) Sucrose=D-glucose + D-fructose (Alpha –(1,2) Beta glycosidic bond) Cellobiose =D-glucose + D-glucose (Beta –(1,4) glycosidic bond)  Based on functional group Monosaccharides are either aldehydes or ketones Aldoses or ketoses Combining these terms describes the essential structure of sugars - Glyceraldehyde is an aldotriose - Glucose is an aldohexose Fructose is a ketohexose The simplest aldose is Glyceraldehyde Contains an aldehyde Contains a chiral center (Means carbon with 4 different groups bonded to it) Because of chiral center, it has two Enantiomers (non superimporsable mirror images) Called D and L forms Almost all sugars are D Stereoisomerism in carbohydrates Some definitions Stereoisomerism: is the study of chemical molecules which have the same chemical formula, same structure but different arrangement in space. Structural isomerism : is defined as isomers having identical molecular formulas but differing in the order in which the individual atoms are connected. Isomers = Those are molecule with the same chemical formula, but different in structure Example: C2H60, ethanol ,dimethyl ether. Epimers = isomers that differ at only one carbon. For example : D-glucose and D-galactose are epimers because their structure differ only in the configuration of the OH group at carbon 4 Enantiomers = isomers that are mirror images (D and L) Dextrorotatory compound :are compounds which rotate the plane of polarized light to the right (positive +) Levorotatory compound: are compounds which rotate the plane of polarized light to the left (negative sign). Anomers = isomers that differ only at keto/ aldo carbon. Chirality: is a geometric property of some molecules and ions. When a molecules is chiral, it means it is optically active and has a chiral carbon also known as one which has four different groups attached to it.  All carbohydrates contain at least one asymmetrical (chiral) carbon and are, therefore, optically active carbohydrates can exist in either of two conformations, as determined by The orientation of the hydroxyl group about the asymmetric carbon furthest from the carbonyl: D-conformation and L- conformation. The chiral carbon furthest from the carbonyl group determines the absolute configuration L or D of the sugar. If in the fischer projection, the OH group on the chiral carbon furthest from the carbonyl is pointing left, then it's L.If it's pointing right, then it's D. Determination of chiral carbon Compounds can have more than one chiral carbon: The maximum number of stereoisomers is 2n where n= number of chiral carbon atoms. Therefore, this compound with two chiral carbon atoms has 22 or 4stereoisomers.  Fischer and Haworth projection Fischer and Haworth projections are two standard ways of illustrating the stereochemistry of a carbohydrate. They are two types of illustration which are used to represent the 3D arrangement of atoms in carbohydrates. They are also used to compare different carbohydrates. The Fischer projection was studied by German chemist Emil Fischer in 1891. A Haworth projection was studied by the English chemist Sir Norman Haworth who expanded on the work of Fischer In the representation, the numbering of the carbons in carbohydrates proceeds from the furthest carbonyl carbon, for aldoses, or the carbon nearest the carbonyl, for ketoses.  Fischer projections:is a two-dimensional representation of a three-dimensional organic molecule by projection In a Fischer projection, the carbon atoms of a sugar molecule are connected vertically by solid lines, while carbon-oxygen and carbon-hydrogen bonds are shown horizontally. Stereochemical information is conveyed by a simple rule: vertical bonds point into the plane of the page, while horizontal bonds point out of the page Carbon atoms may or may not be shown in a Fischer projection.  The advantage of Fischer projections, it is easy to visually identify the stereochemical properties of a carbohydrate and compare the difference between two carbohydrates quickly and easily. Example, it is easy to tell the difference between two enantiomers (molecules that are a mirror image of each other.) The above is Fischer projection of D-glucose and D- fructose in its open chain form  CHO CHO CHO CHO CHO CHO H OH HO H HO H H OH H OH HO H H OH HO H H OH HO H HO H H OH H OH HO H H OH HO H H OH HO H H OH HO H H OH HO H H OH HO H CH2OH CH2OH CH2OH CH2OH CH2OH CH2OH CHO CHO CHO CHO CHO CHO HO H H OH H OH HO H HO H H OH HO H H OH H OH HO H H OH HO H H OH HO H HO H H OH HO H H OH H OH HO H H OH HO H H OH HO H CH2OH CH2OH CH2OH CH2OH CH2OH CH2OH CHO CHO CHO CHO H OH HO H HO H H OH HO H H OH HO H H OH HO H H OH HO H H OH H OH HO H H OH HO H CH2OH CH2OH CH2OH CH2OH  Haworth projection A Haworth projection differs from a Fischer projection in that it is used to represent the carbohydrate in its cyclical form. It is useful for sugars which have a ring structure. The above structure is the representation of the Haworth projection for the cyclic form of D-glucose. How to convert A Fischer to a Haworth projection  Some tips are used to convert Fischer to a Haworth projection.  Starting from Fischer projection of the above molecule. C-2, C-3, and C-4, if the OH is on the right hand side of the Fischer, it will be down in the Haworth. When it is on the left hand side of the Fischer, it will be up in the Haworth. If the sugar is D, draw the C-5 CH2OH pointing up. For D-sugars, draw the C-1 OH pointing down for the alpha (and up for the beta). Converting Fischer to Haworth Projection  Reactions of monosaccharides The monosaccharide contains carbonyl group which can be reduced or oxidized by the reducing agents.  Biologically relevant reactions used to identify carbohydrates.  Carbohydrate may be classified as reducing or non- reducing based on their reactivity with Tollens', Benedict's ,fehling’s solution. If a carbohydrate is oxidized by these reagents it is called reducing sugar. All monosaccharides are reducing sugars Oxidation-Reduction Complete oxidation of sugars supplies energy Sugars that can be oxidized are called reducing sugars Contain a free aldehyde group (found in open chain form) Aldehyde in aldose readily get oxidized Ketose isomerizes and get oxidized  Aldehyde get oxidized to carboxylic acid Differentiating aldehyde from ketone a tollen test is used.  Reducing sugars test When a reducing sugar is heated with Benedict’s solution (alkaline copper sulfate),the solution changes color from blue to orange - red. The orange- red is a precipitate This is Benedict’s test or Fehling test  Mixing fructose and Fehling solution( oxidizing agent),then heat the blue color of oxidizing agent change to red The same result will be found for lactose and maltose All carbohydrate that react with Fehling solution and change their bleu color from bleu to red are reducing sugars The compound that bear a free aldehyde group can be readily oxidized by Fehling solution  Non reducing sugar test Sucrose is a non reducing sugar so, it can not react with Benedict’s solution(no color change) If your sample does not react with Benedict’s solution, is non reducing sugar. Sucrose is composed of glucose and fructose joined by a glyosidic bond. The glycosidic bond in sucrose is slightly different from that in maltose. Glucose unit has hemiacetal group whereas fructose unit has one hemiketal group  Both group take part in glycosidic bond of fructose. No free hemiketal or hemiacetal group in the cyclic structure. Thus in the solution phase the cyclic structure of glucose does not open therefore no free aldehyde Therefore it can’t react with Fehling solution  Disaccharides Maltose : Malt sugar 1. Glucose + Glucose 2. Found in germinating seeds & used in fermentation to produce malted beverages (beer, whiskey). Condensation Hydrolysis  Alpha and Beta The alpha and beta glucose differ on the position of one of the four -OH groups. The carbon to the right of the oxygen atom in the hexagonal ring is called the anomeric carbon. When the -OH group attached to it is below the ring, the molecule is alpha glucose. when the -OH group is above the ring, the molecule is beta glucose. Since the linear and cyclic forms of glucose inter- convert with each other, alpha glucose can turn into beta glucose and vice versa. Cellobiose Is a disaccharide which has a role of support, protective in cell wall of plants. It is composed by two glucose monomers through beta-(1,4) linkage. Structure of cellobiose  POLYSACCHARIDES Like disaccharides, polysaccharides cannot be directly utilized by the body. They must first be broken into monosaccharide, the only sugar form the body can use. They can be:-Homopolysaccharides: Are polymers of a single monosaccharide. -Heteropolysaccharides: They made by more than one type of monosaccharide. FUNCTIONS POLYSACCHARIDES: Energy storage  Structure Storage Polysaccharides:  Starch : Found in chloroplast of the plants cell , especially abundant in potatoes, corn and wheat.  Starch : Is made up of amylose and amylopectin. Amylose : Consists of a linear chain of several hundred glucose molecules. Amylopectin : Is a branched molecule made of several thousand glucose units The formation of starches are the ways that plants store glucose. Starch test To show the presence of starch, you can add a solution of iodine(in potassium iodide) to the sample. If the starch is present, the iodine solution changes color from yellow to blue – black  Glycogen: Glycogen serves as the secondary long-term energy storage in animal and fungal cells. Glycogen: is made primarily by the liver and the muscles, but can also be made by glycogenesis within the brain and stomach Glycogen is analogous to starch, and is sometimes referred to as animal starch Glycogen have a similar structure to amylopectin but more extensively branched and compact than starch.  Cellulose Cellulose is a structural polysaccharide made up of thousands of glucose units (10000-15000 glucose molecules) In this case, beta glucose units are held together by 1,4 glycosidic bonds (1st glucose is beta –linked to the 4th carbon of another glucose) Beta points up,so draw the bond as curved or wavy line (Up from C1 and down from C4) Cellulose formation  These chains are linked together to form long microfibrils The microfibrils are held together by hydrogen bonds to form strong cellulose fibres It is these that give plant cell walls their strength and rigidity Human do not have the capacity to digest cellulose We don’t have cellulase that breaks linkage between glucose monomers Ruminant animals (cattles,giraffes) can digest cellulose  Bacteria live in the digestive track of rumen that degrade cellulose Termites also have bacteria in digestive tract that secrete cellulase to digest wood fibers The cellulase breakdown the bonds between the cellulose molecule to release units of glucose. Three bacterial species—Fibrobacter succinogenes, Ruminococcus albus and Ruminococcus flavefaciens—have long been considered to be the predominant agents of cellulolysis in the rumen This is an example of mutualism: both herbivore and bacterium benefit The bacterium gets a food source and a sheltered environment and the herbivore get energy (glucose) Roles of cellulose It is used in manufacturing of paper Cellulose is used in manufacturing of cellophane (a clear film used in food packaging ) Celluloid is used in the manufacturing of photographic film. Celluloid is created from nitrocellulose (cellulose nitrate). Cellulose films are used in the production of dialysis membranes, sellotape and sweet wrappers  Even cotton clothers and toilet towels are made from cellulose Viscose is a synthetic fibers delivered from cellulose and used in a range of textiles