WS 2. Organic compounds of Living Things.pdf

Chemical Composition of Living Things ORGANIC COMPOUNDS This presentation designed for 1st year students of JFMED CU in Martin It is for internal use only and not to be distributed Copping is prohibited!!!!! ...

Chemical Composition of Living Things ORGANIC COMPOUNDS This presentation designed for 1st year students of JFMED CU in Martin It is for internal use only and not to be distributed Copping is prohibited!!!!!  Biopolymers ▪ Macromolecules are characterised by their large size (several thousands of atoms). By weight, they are the most abundant carbon-containing molecules in a living cell. ▪ The four major classes of biologically important macromolecules are: polysaccharides proteins lipids nucleic acids ▪ Macromolecules in the cells are polymers, formed by joining together the same small molecules, termed subunits or monomers. ▪ Each class of polymers is composed of subunits, which have a similar structure. ▪ Although each class of polymers consists of different type of monomers, their structure and synthesis have several features in common.  Biopolymers ▪ Biopolymer synthesis involves two steps: first the synthesis of subunits, and then the joining of them together, one by one. The overall process of joining two subunits involves a chemical reaction in which H2O is removed, termed a dehydration synthesis. http://oer2go.org/mods/en-boundless/www.boundless.com/biology/textbooks/boundless-biology-textbook/biological-macromolecules-3/synthesis-of-biological-macromolecules- 53/dehydration-synthesis-294-11427/images/fig-ch03_01_01/index.html / https://quizlet.com/154443575/21-molecule- to-metabolism-objectives-study-flash-cards  Biopolymers ▪ When the macromolecule is broken down into its subunits, the reverse reaction occurs, and the water molecule is added back, a reaction termed a hydrolytic reaction or hydrolysis. https://www.researchgate.net/publication/279810778_Kinetic_modeling_and_experimentation_of_ https://biologydictionary.net/hydrolyze/ anaerobic_digestion/figures?lo=1 CARBOHYDRATES  Carbohydrates ▪ Carbohydrates are the most abundant organic molecules in nature. More than half of all “organic” carbon is found in carbohydrates. ▪ The majority of these substances contain carbon, hydrogen, and oxygen in the ratio Cn(H2O)n, hence the name “hydrate of carbon”. ▪ They have been adapted for wide variety of biological functions, which include energy sources and structural elements (nucleic acids, membranes). ▪ Carbohydrates in the form of cereals, grains, fruits, and vegetables should make up the majority of our diet. ▪ On the basis of the number of simple sugar units they contain are classified as monosaccharides, oligosaccharides, and polysaccharides  Monosaccharides ▪ Monosaccharides, or simple sugars, are defined as polyhydroxy aldehydes and ketones. ▪ They are also classified according to the number of carbon atoms they contain. For example, the smallest sugars, called trioses, contain three carbon atoms. Four-, five-, and six-carbon sugars are called tetroses, pentoses, and hexoses, respectively. http://oregonstate.edu/instruct/bb450/450material/OutlineMaterials/16CarbohydrateStructure.html https://vivadifferences.com/difference-between-aldose-and-ketose-sugar-with-examples/  Monosaccharides ▪ The most abundant monosaccharides found in living cells are pentoses and hexoses. ▪ Five carbon sugars such as D-ribose and D-deoxyribose form the backbone of RNA (D-ribose) and DNA (D-deoxyribose) and have the greatest biological importance. https://www.assignmentpoint.com/science/chemistry/difference-between-deoxyribose-and-ribose.html  Important hexoses are glucose, fructose and galactose Glucose in animals, is the preferred energy source of brain cells and cells that have few or no mitochondria, such as erythrocytes. https://www.newworldencyclopedia.org/entry/Glucose Fructose is often referred to as fruit sugar because of its high content in fruit. This molecule is an important member of the ketose family of sugars. Fructose is utilized in large amounts in the male reproductive tract. The seminal vesicles produce a fluid characterized by a high https://fineartamerica.com/featured/2- content of fructose, which is used by sperm cells as an fructose-molecular-model-evan-oto.html energy source. Galactose is necessary for the synthesis of a variety of biomolecules. These include lactose, glycolipids, proteoglycans, and glycoproteins. This sugar is readily synthesised from glucose-1-phosphate. https://www.turbosquid.com/3d- models/galactose-molecule-structure-3d- model/466033  Disaccharides ▪ Disaccharides are glycosides that are composed of two monosaccharide units. ▪ Found in abundance in nature, disaccharides provide a significant source of energy in many human diets. ▪ Examples of important disaccharides include lactose, maltose, and sucrose. Sucrose (common table sugar: cane sugar or beet sugar) is produced in the leaves of plants. It serves as a transportable energy source throughout the entire plant. It consists of - glucose and -fructose. https://www.smartkitchen.com/resources/sucrose Maltose also known as malt sugar, is an intermediate product of starch hydrolysis and does not appear to exist free in nature. Maltose is a disaccharide with an (1,4) glycosidic linkage between two D- glucose molecules. https://www3.hhu.de/biodidaktik/zucker/bilder/maltose_gr.jpg Lactose (milk sugar) is a disaccharide found in milk. It is composed of one molecule of galactose linked through the hydroxyl group on carbon 1 in a -glycosidic linkage to the hydroxyl group of carbon 4 of a molecule of glucose. https://www.uoguelph.ca/foodscience/book-page/lactose  Disaccharides ▪ Digestion of disaccharides is mediated by enzymes synthesized by cells lining the small intestine. Deficiency of any of these enzymes results in unpleasant symptoms when the indigestible disaccharide sugar is ingested. ▪ Carbohydrate is absorbed principally into large intestine, where osmotic pressure draws water from the surrounding tissues (diarrhoea). Colonic bacteria digest disaccharides (fermentation), thus producing gas (bloating and cramps). ▪ The most commonly known deficiency is lactose intolerance, which occurs in human adults. Lactase deficiency appears to be inherited as an autosomal recessive trait. ▪ The prevalence of lactase deficiency in human populations varies greatly. For example 3% of Danes are deficient in lactase, compared with 97% of Thais. Lactose intolerance is treated by eliminating the sugar from the diet or by treating food with enzyme lactase.  Polysaccharides ▪ They are composed of large numbers of monosaccharide units connected by glycosidic linkages. ▪ Most commonly occurring polysaccharides are large molecules containing from hundreds to thousands of sugar units. ▪ Polysaccharide molecules are used as storage forms of energy or as structural materials. ▪ These molecules may have a linear structure like that of cellulose or amylose, or they may have branched shapes like those found in glycogen and amylopectin. ▪ Polysaccharides may be divided into two classes: homopolysaccharides, which are composed of one type of monosaccharide heteropolysaccharides, which contain two or more different types of monosaccharides  Homopolysaccharides ▪ The homopolysaccharides that are found in abundance in nature are starch, glycogen, and cellulose. In most plants, the major nutrient reserve is starch, which is a mixture of two polysaccharides, amylose and amylopectin. Amylose occurs as long, straight polymer chains composed of glucose units joined by glycosidic bonds. An amylose molecule is usually composed of at least 1,000 units of glucose, but this number can vary. Amylopectin is made up of glucose units bonded together, but the chains have many branches joined to the larger molecule via cross linkages. This results in separate chains of glucose units being bound together. An amylopectin polymer usually contains about 20,000 glucose monomers.  https://www.ernaeringslinjen.dk/tag/hvede/ https://kashimali44.files.wordpress.com/2013/02/polysaccharides-structure.jpeg ▪ Inside a seed, a supply of starch will often support the early growth of the tiny plantlet that germinates. ▪ Within the seed, there are enzymes, which hydrolyse the glycosidic bonds in starch, releasing the disaccharide maltose and, in turn, glucose, monomers to fuel the energy needs of the growing plant. ▪ Starch also makes grains (the seeds of wheat, corn, rice, etc.) a rich source of nutrition for humans and other animals. Glycogen is the carbohydrate storage molecule in vertebrates. It is found in greatest abundance in liver and muscle cells. Glycogen may make up as much as 8-10 % of the wet weight of liver cells and 2-3 % of that of muscle cells. Glycogen is similar in structure to amylopectin except for more frequent branch points, which may occur as often as every fourth glucose residue in the central core of the molecule. In the outer regions of glycogen molecules, branch points occur much less frequently. The resulting molecule is more compact than other polysaccharides. Therefore it takes up a relatively small amount of space, an important http://bio1151.nicerweb.com/Locked/media/ch05/glycogen.html consideration in mobile animal bodies. Cellulose is the fibrous structural material that gives strength and rigidity to plant cells and wood. ▪ Like starch, cellulose is composed of long chains of glucose units connected by glycosidic bonds, yet the two polysaccharides have very different properties: We eat starch in potatoes and bread, but we build houses from cellulosic wood. ▪ These physical differences are entirely due to the orientation in space of a single bond. ▪ In starch and glycogen, the orientation of the bond allows the glucose chains to twist into compact spirals. ▪ In cellulose, the orientation of the bond prevents twisting, so that the chains are straight. This molecular rigidity explains the fibrous quality of cellulose and, in turn, the strength of leaves and stems and the hardness of wood. http://www.sliderbase.com/spitem-1467-4.html  Homopolysaccharides https://www.bankofbiology.com/2014/07/comparison-between-starch-glycogen-and.html  Homopolysaccharides ▪ Many organisms have the enzymes necessary to break the glycosidic bonds in starch and glycogen, but only some have those needed to break the bonds in cellulose. ▪ That is why sugar will break down in your mouth, but wood or cotton never will, no matter how long it remains there. ▪ A few organisms, such as termites and cows, have microorganisms in their guts that produce the necessary enzymes for hydrolysing cellulose, thus, these animals are able to feed on wood or on grass and leaves. ▪ Since the cellulose passes through the human gut without being degraded, it provides no calories but does serve as beneficial fibre, or roughage.  Heteropolysaccharides ▪ Heteropolysaccharides are high-molecular-weight carbohydrate polymers that contain more than one kind of monosaccharide. They can be also associated with other kinds of molecules. ▪ According to molecules they contain, they can be classified to: glycosaminoglycans (GAGs) glycoproteins glycolipids Glycosaminoglycans are linear polymers with repeating amino sugar units often with sulphate group. They have various function in organism. ▪ Classification of GAGs is made on the basis of: the identity of the sugar residues that they contain the type of linkages between these residues the presence and location of sulphate groups  Heteropolysaccharides https://onlinelibrary.wiley.com/doi/full/10.1111/j.1747-0285.2008.00741.x  Heteropolysaccharides Glycoproteins play different roles in the organisms: increasing the polarity of proteins influence on the solubility and electrical charge protection against proteolysis stabilisation of the structures receptors They are found in: cell membranes (antigens of red blood cells) mucosal fluid produced by epithelial cells (mucus) extracellular space (plasma proteins such as ceruloplasmin, plasminogen, prothrombin, immunoglobulins).  Heteropolysaccharides Glycolipids are compounds containing one or more monosaccharide residues bound by a glycosidic linkage to a hydrophobic moiety such as acylglycerol, sphingoid, ceramide (N-acylsphingoid), or prenyl phosphate. Their function is to: provide energy maintain the stability of the membranes help with attachment of cells to one another serve as markers for cellular recognition The most complex animal glycolipids are gangliosides. They contain glycosphingolipid with one or more sialic acid residues linked with the sugar chain. They are most abundant in nerve cells and as a part of cell membrane, play an important role in signal transduction. LIPIDS  Lipids ▪ Lipids are group of diverse molecules insoluble in water. ▪ Although lipids are not large macromolecular polymers like proteins, nucleic acids, and polysaccharides, many are formed by the chemical linking of several small constituent molecules. ▪ Functions: energy-storage molecules chemical messengers structural components of cells ▪ Examples of lipids include fats, oils, waxes, certain vitamins and hormones. ▪ Although the term lipid is sometimes used as a synonym for fat, fats are a subgroup of lipids called triglycerides. ▪ Lipids also encompass molecules such as fatty acids and their derivatives, phospholipids and sterol-containing metabolites such as cholesterol.  Fats and Oils ▪ Fats and oils serve as long-term nutrient reserves in animals and plants (carbohydra- tes provide immediate fuels). They provide much more energy than sugars and proteins because of the huge number of C-H covalent bonds. ▪ Oils are lipids extracted from plant tissues and they are in liquid form at room temperature. Lard and butter are examples of animal fats, which are solids at room temperature. ▪ Fats and oils contain two basic units: glycerol and fatty acids – three fatty acids are usually joined to one glycerol molecule with ester bonds therefore, they are considered as triacylglycerols (triglycerides).  Fatty acids ▪ Fatty acids are long chain carboxylic acids (typically 16 or more carbon atoms) which may or may not contain carbon-carbon double bonds.  Fatty acids Saturated fatty acids ▪ The simplest fatty acids are unbranched, linear chains of -CH2 groups linked by carbon-carbon single bonds with one terminal carboxylic acid group, as shown in the diagram of stearic acid. ▪ The term saturated indicates that the maximum possible number of hydrogen atoms are bonded to each carbon in the molecule. ▪ Although the chains are usually between 16 and 24 carbons long, several shorter-chain fatty acids are biochemically important. For instance, butyric acid (C4) and caproic acid (C6) are found in milk.  Fatty acids Unsaturated fatty acids ▪ Unsaturated fatty acids have one or more carbon-carbon double bonds. ▪ The number of double bonds is indicated by the generic name – monounsaturated for molecules with one double bond or polyunsaturated for molecules with two or more double bonds. ▪ Oleic acid is an example of a monounsaturated fatty acid. It is the most abundant fatty acid in nature.  Fatty acids ▪ Two possible conformations, cis and trans, can be taken, according to spatial orientation of hydrogen atoms joined to the double-bonded carbons. ▪ In the cis configuration, the one occurring in all biological unsaturated fatty acids, the two hydrogen atoms adjacent to the double bond lie on the same side of the chain. ▪ In the trans configuration, the two hydrogen atoms adjacent to the double bond lie on opposite sides of the chain. ▪ Trans unsaturated fatty acids are produced by microorganisms in the gut of ruminant animals such as cows and goats, and they are also produced synthetically by partial hydrogenation of fats and oils in the manufacture of margarine. ▪ There is evidence that ingestion of these trans acids can have deleterious metabolic effects.  Fatty acids ▪ Fatty acids containing more than one carbon-carbon double bond – polyunsaturated fatty acids are found in relatively minor amounts. ▪ The multiple double bonds are almost always separated by a -CH2 groups (−CH2−CH=CH−CH2−CH=CH−CH2−), a regular spacing motif that is the result of the biosynthetic mechanism by which the double bonds are introduced into the hydrocarbon chain. ▪ Animals cannot synthesize two important fatty acids, linoleic (18:2) and alpha-linolenic (18:3) acids therefore, they must be obtained in the diet from plant sources. For this reason, these precursors are termed essential fatty acids. ▪ Arachidonic acid (20:4) is of particular interest as the precursor of a family of molecules, known as eicosanoids (from Greek eikosi, “twenty”), that include prostaglandins, thromboxanes, and leukotrienes. These compounds, produced by cells under certain conditions, have potent physiological properties.  Fatty acids Biological functions: ▪ Metabolic – they produce more than twice as much of energy as glucose. ▪ Structural – they are present in all biomembranes as a structural part of phospholipids and sphingolipids. ▪ Secretory – they make up serum lipoproteins and lung surfactant. ▪ Regulatory – they are important intracellular messengers (phosphatidyl- inositol, phosphatidylethanolamine, phosphatidylcholine, diacylglycerol, eicosanoids).  Phospholipids ▪ Phospholipids are a class of lipids that are a major component of all cell membranes as they can form lipid bilayers. ▪ Most phospholipids contain a diglyceride, a phosphate group, and a simple organic molecule such as choline. PROTEINS  Proteins ▪ The importance of proteins is implied by their name, which comes from the Greek word proteios, meaning “first place”. ▪ Proteins account for more than 50% of the dry weight of most cells. ▪ Proteins are a class of diverse macromolecules instrumental in almost everything organisms do and they determine many characteristics of cells and, in turn, of the whole organisms. ▪ Proteins are often classified according to their functions. Structural proteins, help to form bones, muscles, leaves, roots, and even the microscopic cell "skeleton" that provides shape and allows cell movement. Protein hormones serve as chemical messengers. Transport proteins act as carriers of other substances. Antibodies fight infections. Enzymes speed up, or catalyse, chemical reactions.  Proteins ▪ All proteins are polymers constructed of subunits called amino acids. There are 20 types of amino acids in proteins. ▪ In each amino acid there is one central carbon atom, called the alpha () carbon bound to a hydrogen atom, an amino group (-NH2), a carboxyl group (- COOH), and a side chain, represented by radical (R). ▪ In water, the carboxyl group may dissociate, giving up a hydrogen ion. Meanwhile, the amino group can accept a hydrogen ion. Thus, a molecule contains one positive group and one negative group, and those charges help to determine protein behaviour. ▪ Some amino acid side chains are hydrophobic, some are hydrophilic, and the others are ambivalent, or partially soluble in water. The properties of a protein are determined in good measure by the R group of its constituent amino acids. https://www.researchgate.net/publication/332440930_PROTEIN_ACIDIC_HYDROLYSIS_FOR_AMINO _ACIDS_ANALYSIS_IN_FOOD_-PROGRESS_OVER_TIME_A_SHORT_REVIEW/figures?lo=1 https://www.philpoteducation.com/mod/book/tool/print/index.php?id=782&chapterid=1126  Proteins ▪ Proteins are polymers, where the amino acid subunits are linked covalently by peptide bonds. These bonds are the result of a condensation reaction between the carboxyl group of one amino acid and the amino group of another one. ▪ Two joined amino acid units, or residues, are called a dipeptide. A carboxyl group protrudes from one end of a dipeptide and an amino group protrudes from the other end. https://www.philpoteducation.co m/mod/book/tool/print/index.ph p?id=782&chapterid=1126  Proteins ▪ Condensation reactions can occur again and again, forming longer chains. ▪ Regardless of length, each chain will have an amino terminus and a carboxyl terminus. A protein molecule can consist of one, two, or several polypeptide chains bound to one another in various ways. http://what-when-how.com/wp-content/uploads/2011/05/tmp10104_thumb.jpg  Proteins ▪ There are no chemical restrictions on the number of times an amino acid can appear in a protein or on where it can be located along a chain, and there is nothing in the chemistry of the amino acids themselves that restricts the length of chains. ▪ Thus, the different numbers and the different orders of 20 amino acids result in seemingly endless variety of proteins. ▪ Short peptide chains formed by 2-10 of amino acids are referred to as oligopeptides, the chains longer than 10 are referred to as polypeptides. The peptides have important biological functions, especially regulatory functions (hormones, neurotransmitters) or are a part of more complex macromolecules. ▪ Proteins are molecules whose polypeptide chain comprises of many amino acids (typically several hundreds). The molecular weight of the protein most often ranges from 10,000 to 50,000 Daltons.  Protein structure ▪ In 1950, Frederik Sanger of Cambridge University made the great discovery by explaining the precise amino acid sequence of the protein hormone called insulin. The innovative work of Sanger and his colleagues revealed that the order of amino acids is the key to the structure and function of proteins and that a specific sequence characterises each type of protein. ▪ The sequence of amino acids, called primary structure, determines not just the structure and the function of the protein but the way the chain twists, bends, and folds into a characteristic complex shape as well. ▪ This shape consists of a series of higher order configurations called secondary, tertiary, and quaternary structure, which ultimately determine a protein´s activity in a living thing. https://ib.bioninja.com.au/higher-level/topic-7-nucleic-acids/73-translation/protein- structure.html  Protein structure Secondary Structure ▪ The work of chemists Linus Pauling and Robert Corey helped to reveal the hierarchy of protein structure and function by focusing on the spatial relationships of amino acids in polypeptide chains. They knew that the subunits of some proteins tend to occur in regularly repeating patterns. These patterns form the secondary structure of the protein. ▪ Formation of the secondary protein structure is realised by formation of hydrogen bonds between N-H and C=0 groups along the protein chain. The polypeptide chain assumes a regular conformation that allows the maximum number of hydrogen bonds to form. ▪ The most common secondary structures are -helix and -pleated sheet.  Protein structure ▪ In the -helix, the long chain of amino acids residues is wrapped. The chain is held in position by hydrogen bonds joining the N-H group of one peptide bond with the C=0 group of a peptide bond four subunits up the chain. ▪ The spiral -helix is a more stable configuration than other conformations that do not allow such hydrogen bonding and it forms spontaneously in regions wherever the amino acid sequence (primary structure) allows a bond to form. https://masteringcollegebiochemistry.wordpress.com/category/proteins/secondary-structure/  Protein structure ▪ In the configuration called the -pleated sheet, two or more polypeptide chains, or two regions of one polypeptide chain, lying side by side become cross-linked by hydrogen bonds and form an accordion-like sheet of connected molecules. ▪ The protein keratin, found in mammalian hair and fingernails is composed mainly of -helix regions, while in fibroin, a protein in the silk strands, - sheets are the common secondary structure. https://www.quia.com/jg/1165527list.html Prions ▪ A prion (PrP) is an infectious agent composed of protein in a misfolded form. ▪ Prions are responsible for the transmissible spongiform encephalopathies in a variety of mammals, including bovine spongiform encephalopathy (BSE, also known as "mad cow disease") in cattle. ▪ In humans, prions cause Creutzfeldt-Jakob disease (CJD), Gerstmann–Sträussler–Scheinker http://drugster.info/medic/term/subacute-spongiform- syndrome, fatal familial insomnia and kuru. encephalopathy/ ▪ All known prion diseases affect the structure of the brain or other neural tissues and all are currently untreatable and universally fatal. ▪ All known prions induce the formation of an amyloid fold, in which the protein polymerises into an aggregate consisting of tightly packed https://www.researchgate.net/publication/326330981_FHSU_Scho lars_Repository_Polymorphism_In_The_PrPC_Prion_Protein_Ge beta sheets except of the alpha helices present ne_In_Pigs more frequently in original protein.  Protein structure Tertiary Structure Superimposed on the patterns of secondary structure is a protein's tertiary structure, which is stabilised by different types of bonds between side chains of protein. ▪ A type of covalent bond, called a disulfide bond or bridge (-S-S-), results from the linking of two sulfhydryl (-SH) groups in cysteine residues. Disulfide bonds can cause a kink or loop in a chain or join two polypeptide chains into one molecule. ▪ Other type of bonding that contributes to tertiary structure is called a hydrophobic interaction. As a polypeptide folds into its functional conformation, amino acids with hydrophobic (non-polar) side chains usually congregate in clusters at the core of the protein out of contact with water. Once the non-polar amino acid chains are close together, van der Waals interactions reinforce the hydrophobic interactions. ▪ Hydrogen bonds between polar side chains and ionic bonds between positively and negatively charged chains also help stabilise tertiary structure.  Protein structure Quaternary Structure Some proteins consist of two or more polypeptide chains aggregated into one functional macromolecule. Quaternary structure is the overall protein structure that results from the aggregation of these polypeptide subunits. ▪ For example, collagen is a fibrous protein that has helical subunits supercoiled into a larger triple helix. This supercoiled organization of collagen, which is similar to the construction of a rope, gives the long fibres great strength. This suits collagen fibres to their function as the girders of connective tissue such as tendons and ligaments. ▪ Haemoglobin, the oxygen- binding protein of red blood cells, is an example of a globular protein with quaternary structure. It consists of two kinds of polypeptide chains with two of each kind per haemoglobin molecule. https://www.researchgate.net/publication/221925240_The_Use_of_Blood_and_Derived_Products_as_Food_Ad ditives/figures?lo=1  Protein structure According to realisation of the bonds within one protein chain or between different chains, proteins are divided to two groups: 1. Fibrous proteins are wire- or rod-like shaped, e.g. keratins, collagens, elastins. They are usually important structural proteins involved in construction of connective tissues, tendons, bones or muscles. 2. Globular proteins have spherical shape. They are usually involved in metabolic reactions, e.g. enzymes, or haemoglobin. https://ib.bioninja.com.au/standard-level/topic-2-molecular- biology/24-proteins/fibrous-vs-globular-protein.html https://animalphys4e.sinauer.com/boxex0201.html