ORGANIC AND BIOLOGICAL CHEMISTRY SYSTEMATIC NOMENCLATURE Organic compounds are carbon containing compounds. Carbon has the following unique bonding properties: 1) it has a covalence of four 2) carbon atoms can bond to each other to form straight chains, branched chains and rings. 3) carbon atoms can form single, double and triple covalent bonds with other carbon atoms or non-metal elements. As a consequence of these bonding properties, there are thousands of different organic molecules. Since organic compounds with the same functional group behave in the same way chemically, the study of the chemistry of thousands of organic compounds can be simplified to a study of a small number of functional groups.
Table of Common Functional Groups Class of Functional Example Systematic Compound Group Name
SYSTEMATIC NAMING OF ORGANIC COMPOUNDS The systematic name of an organic compound is derived from a set of rules established by IUPAC (International Union of Pure and Applied Chemistry). They are named in such a way as to ensure easy identification Naming Alkanes 1. From the structural formula of the compound, find the longest continuous chain of carbon atoms and assign the parent name by combining the prefix from below with the suffix ane. Eg. CH 3 CH CH 2 CH 2 CH 2 CH 3 CH 3 Longest C chain is 6. 1 meth 2 eth 3 - prop 4 but 5 pent 6 hex 7 hept 8 oct 9 non 10 dec therefore the parent name is hexane 2. Locate the alkyl groups that are not part of the continuous chain and name them according to the number of carbon atoms present. Eg CH 3 methyl - CH 2 CH 3 ethyl therefore the above molecule is methyl hexane 3. the position of the branching alkyl group in the continuous chain is then indicated by a number, the numbering of the continuous chain starts at the end that gives the lower of the two possibilities 1 2 3 4 5 6 CH 3 CH - CH 2 - CH 2 CH 2 CH 3 CH 3 therefore 2 methyl hexane Note numbers are only required when other isomers are possible. - numbers in a name are separated from each by commas and from the words by hyphens.
4. If a compound contains two or more identical branches, the following prefixes are used: number of branches 2 3 4 prefix di - tri - tetra eg CH 3 CH CH CH 3 2,3 dimethyl butane CH 3 CH 3 5. If a molecule has two or more different branching alkyl groups, they are placed in alphabetical order in the name ie. ethyl before methyl. Eg Esters 3 ethyl 2 methylpeptane Esters are formed from reactions between alcohols and carboxylic acids. When writing the systematic of an ester, the organic acid suffix changes from oic acid to oate. The first part of the name is derived from the name of the alcohol eg Methanol form methyl esters, ethanol form ethyl esters Eg methyl ethanoate is shown in the diagram opposite. Amides Amides, like esters, have a more unique way of naming the compounds alkyl groups can be attached to the main carbon chain or to the nitrogen like in amines. Therefore those groups attached to the main chain are given a position identified by a number like we are used to. Those groups attached to the nitrogen are given a position N. 3,N-dimethyl-N-propyl-butanamide
PHYSICAL PROPERTIES The effect of length of carbon chain on melting and boiling points For compounds with identical functional groups, the boiling points increase as the length of the carbon chain increases. The secondary bonding forces operating between non-polar hydrocarbon chains are dispersion forces. The strength of dispersion forces increases with the length of the chain. For hydrocarbon chains, molar mass is proportional to the length of the chain. The pattern for melting points is not as clear as it is for boiling points, largely because melting does not involve complete separation of molecules. The Polarity of Functional Groups and boiling Points Alcohols, Aldehydes and Ketones In order to establish the effect of the polarity of functional groups on boiling points, it is necessary to compare compounds of similar molar mass. Looking at a data table, it can be seen that the alcohol has the highest boiling point, but there is little difference between aldehydes and ketones. This pattern can be explained in terms of the nature of the secondary bonds operating between them. In alcohols, the hydroxyl group forms strong hydrogen bonds with each other. Aldehyde and Ketone molecules both have carbonyl groups. This forms Dipole Dipole secondary bonds which hold the molecules together. The Dipole Dipole bonds are not as strong as hydrogen bonds, therefore lower boiling points.
Esters and Carboxylic Acids The boiling points of esters are much lower than those of their isomeric acids. eg methyl methanoate 31.5 OC ethanoic acid 117.9 OC (C 2 H 4 O 2 ) (C 2 H 4 O 2 ) This pattern is explained in terms of the greater strength of the secondary bonds between carboxyl groups relative to the secondary bonds between ester groups. Ester groups only have polar This is not as strong as hydrogen bonds.
The Solubility of Organic Compounds in Water Non polar organic compounds, such as the hydrocarbons, are not soluble in water because they cannot form hydrogen bonds with the polar water molecules. Molecules with polar functional groups but long carbon chains ( 6 carbon atoms or more ) Are also classified as non polar because the non polar carbon chain is the dominant structural feature of these molecules Polar groups with the capacity to form hydrogen bonds with water can render an organic compound soluble in water, so long as the carbon chain is small enough not to be the dominant structure The influence of functional groups is increased when more than one functional group is present, eg. diols, dicarboxylic acids and diamines This pattern of solubility is also evident with amino acids Eg.
ALCOHOL Ethanol Production On an industrial scale ethanol is produced in 2 ways. Approximately 20% is produced from ethene, which is from crude oil or natural gas. Ethanol produced in this way is called synthetic ethanol. 80% is produced by fermentation of glucose, a monosaccharide, which is either obtained from fruits, (eg grapes), or from the hydrolysis of disaccharides or polysaccharides (starches in vegetables or grains) When using grains like wheat or barley, eg for beer or whisky making, the grains are first soaked in water. As the seeds germinate, enzymes are produced that catalyse the hydrolysis of the starch molecules into glucose. Yeast is then added to the mixture. The glucose passes through the cell walls into yeast cells where enzymes catalyse the fermentation of the glucose into ethanol and carbon dioxide. The products pass out through the cell walls. The hydrolysis and fermentation reactions are as follows: (All equations are important) There are special conditions for ethanol production by fermentation optimum temperature are between 20 0 C - 30 0 C. At temperatures outside this range, the enzymes are rendered either totally or partly ineffective. Since fermentation is exothermic, it is necessary to cool the fermentation vessel to avoid excessively high temperatures fermentation is an anaerobic process and oxygen must be almost totally excluded from the fermentation vessel. A small amount is needed for the growth of yeast cells. If oxygen does enter the vessel, ethanol turns to ethanoic acid. In wine making, the CO 2 produced by fermentation provides a protective blanket against oxygen.
PRIMARY, SECONDARY AND TERTIARY ALCOHOLS Alcohols are classified as primary, secondary or tertiary depending on the position of the hydroxyl group in the molecular structure. Primary Secondary alcohols -OH group bonded to a carbon atom that is in turn bonded to two alkyl groups Tertiary alcohols -OH group bonded to a carbon atom that is in turn bonded to three alkyl groups
OXIDATION OF ALCOHOLS The type of product, if any, formed by the reaction of an alcohol with an oxidising agent such as acidified potassium dichromate solution depends on whether the alcohol is primary, secondary or tertiary. A primary alcohol is oxidised first to a corresponding aldehyde. Further contact with the oxidising agent, the aldehyde is further oxidised to a carbolic acid. A secondary alcohol is oxidised to the corresponding ketone. The ketone does not undergo further oxidisation. A tertiary alcohol is not oxidised by acidified dichromate solution Primary and Secondary alcohols reduce orange dichromate ions to green chromium ions. Tertiary alcohols do not make a colour change. Cr 2 O -2 7 + 14H + + 6e orange 2Cr +3 + 7H 2 O green The oxidation of primary and secondary alcohols by acidified dichromate is slow at room temperature. Heat must be used to show a colour change within a reasonable time.
Aldehydes and Ketones Aldehyde and Ketone molecules contain the carbonyl group c = o Aldehydes and Ketones are widely used as solvents, flavourings and fragrances Preparation of aldehydes and Ketones Aldehydes are prepared by the controlled oxidation of primary alcohols. A solution of the oxidising agent is dropped into the alcohol acid mixture as it is heated. The aldehyde boils off immediately it forms, preventing it s further oxidation to the carboxylic acid. The aldehyde is the lowest boiling point substance in the mixture no hydrogen bonding and consequently distils off at the lowest temperature. Ketones are prepared by the oxidation of secondary alcohols. Thus the ketone product does not have to be distilled off as it is formed. Heating is required to increase the rate of reaction.
OXIDATION OF ALDEHYDES When aldehydes are heated with an acidified solution of dichromate, they undergo oxidation to carboxylic acids. Aldehydes also undergo oxidation to carboxylate ions when they are heated with ammoniacal silver nitrate solution (Tollen s reagent). The oxidising agent is the silver diamine ion, which is reduced to metallic silver. Under certain conditions, the silver can be made to deposit on the inside walls of the reaction vessel as a silver mirror. The formation of a silver mirror is a positive test for the presence of an aldehyde functional group. The oxidation product is a carboxylate ion, not a carboxylic acid, because the reaction is carried out under alkaline conditions due to the ionisation of ammonia. Distinguishing between an aldehyde and a Ketone A Ketone will not be oxidised by orange acidified dichromate, aldehydes will react with the silver mirror. Ketones will not. The monosaccharide glucose exists in two structural forms, straight chain and ring. In the chain form, there is an aldehyde group present, glucose is an example of a polyhydroxl aldehyde. Thus glucose is able to reduce Tollen s reagent to produce a silver mirror, therefore it is called a reducing sugar.
CARBOXYLIC ACIDS Carboxylic acid molecules contain the carboxylic group -COOH Carboxylic acids can be prepared by heating primary alcohols or aldehydes with excess acidified dichromate solution. Ionisation of Carboxylic acids in water Ionisation is the term for a reaction in which molecular substances react to form ionic products. They are weak acids, if soluble in water they partially ionise in water to form hydronium and carboxylate ions. The ionisation is an equilibrium process with the position to the left. Neutralisation of Carboxylic acids Carboxylic acids are neutralised by hydroxide ions, carbonate ions and hydrogencarbonate ions. These reactions occur at a fast rate at room temperature and are exothermic Water soluble carboxylic salts are formed if sodium or potassium hydroxide, carbonate or hydrogencarbonate are used. If the carboxylic acid is insoluble in water it will appear to dissolve as the water soluble carboxylate salt forms. CO 2 gas can also be produced.
The Solubility of Carboxylate salts Potassium and sodium carboxylates are soluble in water. This is because of the strong ion dipole bond between the negative carboxylate ions and polar water molecules. The full negative charge on a carboxylate ion forms stronger bonds with water molecules than do the partial charges on the polar OH groups found in carboxylic acids. Drugs with Carboxyl groups as part of their Molecular Structure Two of the most common pain relief drugs are aspirin and ibuprofen. A carboxyl group forms part of the structure of both of the components. Both structures have large non polar parts, therefore not soluble in water. They are both solids at room temperature. In tablet form these drugs are mixed with solid sodium hydrogencarbonate. When mixed with water, the carboxylic acid is converted to water soluble carboxylate form. In this form the drug is easier to administer and is faster acting. Once the carboxylate form is in the stomach, it reacts with hydrochloric acid and is converted back to the molecular form.
AMINES Amines may be regarded as derivatives of ammonia in which one or more of the hydrogen atoms of the ammonia molecule have been replaced by one or more alkyl groups They are classified as primary, secondary or tertiary depending on the number of hydrogen atoms replaced. Due to the presence of an unbonded pair of electrons on the nitrogen atom, the molecules can accept one proton each from an acid. This makes the amines, like ammonia, act as bases Solubility of Protonated Amines Protonated amines are soluble in water. This is because of the strong ion dipole bond, which forms between the positively charged Protonated amine ions and polar water molecules. The full positive charge on a Protonated amine ion forms stronger bonds with water molecules than do the partial charges on the polar N H groups found in amines. When amines that are insoluble in water are reacted with an acid, they appear to dissolve because of the formation of the water soluble Protonated form of the amine.
Drugs with amine groups as part of their molecular structure A large number of drugs are high molar mass amines that are insoluble in water. Taken this way they are ineffective. They are commonly administered in the Protonated water soluble form. Procaine and Lidocaine are anaesthetics with tertiary amine groups as part of their molecular structure. They are usually administered as water soluble chloride salts in which amine is in the Protonated form. Only the tertiary amine group is protonated. The primary amine group attached to the benzene ring is difficult to protonate.
ESTERS Esters contain the ester functional group COO- Esters can be regarded as two alkyl groups linked by an ester functional group. Common naturally occurring esters include fragrances of flowers and fruits and animal fats and vegetable oils, as long chain triesters. eg Preparation of Esters An ester is prepared by reacting, under reflux, an alcohol with a carboxylic acid in the presence of concentrated sulphuric acid as a catalyst. This is called esterification. Water is also produced, hence this is called a condensation reaction. These reactions are slow and an extended period of heating is required to achieve a satisfactory yield of ester in a reasonable time. Reflux is a process by which a mixture of the reactants and products are boiled for a prescribed period of time. The reflux process allows extended heating of the reaction mixture without loss of reactants and products by evaporation. These acid catalysed esterification reactions are reversible and equilibrium is established in the reaction vessel during reflux. The equilibrium mixture contains appreciable quantities of both reactants and products.
Hydrolysis of Esters Esters undergo hydrolysis when refluxed with aqueous acid or base. Hydrolysis can be regarded as the reverse of esterification water is consumed as a reactant in a hydrolysis reaction. In acidic conditions, the products of hydrolysis are a carboxylic acid and an alcohol. The reaction is catalysed by the acid. If there is a large excess of water, the position of the equilibrium favours the formation of the carboxylic acid and alcohol. The reaction is slow at room temperature, therefore do it under reflux. In basic conditions, such as with sodium hydroxide solution, the products of hydrolysis are a carboxylate salt and an alcohol. Refluxing is necessary to bring about a reaction at a reasonable rate Under these alkaline conditions, carboxylate ions, not carboxylic acid molecules are formed. To form the carboxylic acid following alkaline hydrolysis of an ester, a solution of a strong acid such as hydrochloric acid must be added after the refluxing is completed.
AMIDES Amides have the following functional group as part of their molecular structure: While small molar mass amides are not very common in nature, polymeric proteins with amide groups as linkages are very common. Eg propenamide (monomer used for polymer production) Preparation of Amides Theoretically, an amide could be prepared from a condensation reaction between ammonia or an amine with a carboxylic acid In practice, when a carboxylic acid is reacted with ammonia or an amine, a proton is transferred from the acid to the basic ammonia or amine, forming an ammonium or substituted ammonium salt. Usual production methods are heating an ammonium carboxylate above it s melting point refluxing an ester with ammonia or an amine
Hydrolysis of Amides Amides are more difficult to hydrolise than esters, they require extended refluxing under strongly acidic or alkaline conditions. Hydrolysis of the amine linkages in proteins occurs more readily when catalysed by specific enzymes. Without the assistance of enzymes, the hydrolysis of proteins requires reflux under acid conditions for several hours. Alkaline hydrolysis of amides using concentrated sodium hydroxide solution produces ammonia or an amine and a carboxylate salt. Acid hydrolysis of amides with concentrated hydrochloric acid produces ammonium or substituted ammonium salt and a carboxylic acid.
PROTEINS Amino Acids Amino acids are the building blocks of proteins. They consist of small molecules with at least one amine group and one carboxyl functional group and one of twenty different R groups as part of the molecular structure. All amino acids have a structure in which there is a central carbon atom (the "alpha carbon) that is covalently bonded to one hydrogen atom one amine functional group (usually primary amine) one carboxyl functional group one other atom or group of atoms represented as R in the structural formula. This R group can contain additional functional groups. Zwitterion In a ph neutral environment, amino acids undergo self ionisation whereby a proton is transferred from the carboxyl group to the amine group in the same molecule. The self - ionisation is a dipolar ion, called a Zwitterion. eg The Zwitterion does not carry an overall charge. It can be regarded as a molecule with unit positive and negative charge separation.
Proteins In nature, the carboxylic group from one amino acid can undergo a condensation reaction with an amine group from another amino acid, with the aid of specific enzymes. The product is a dipeptide. The formed amide group is called a peptide link. Eg glycine alanine The other product is water from this condensation reaction. The continuation of this type of condensation process involving more amino acids lead to the formations of a long chain molecule called a polypeptide. The polypeptides are proteins that have the following general structure The R groups are different, therefore this is not a repeating unit. Hydrogen Bonding within and between protein chains The peptide links within protein chains are polar. Hydrogen bonding between these links can occur both within a protein chain and between protein chains. The polar peptide links in protein chains also forms hydrogen bonds with water molecules. Muscle tissue contains between 50% and 80% water, some of which is directly bonded to proteins that make up muscle. This water is responsible for the moistness of fresh meat. Natural protein fibres such as wool and silk absorb water readily because peptide links form hydrogen bonds with water.
The Structure and Function of Proteins The structure of a protein molecule and it s biological function are inextricably linked. A protein molecule that transports molecules in living organisms such as myoglobin or haemoglobin that transport oxygen, must have sites within it s structure that can precisely accommodate the molecule being transported. The structure of proteins is usually described at four levels primary, secondary, tertiary and quaternary structure. Primary Structure is the sequence in which the amino acids are linked together by peptide bonds to form the polypeptide chain. In living cells, the sequencing of amino acids in the synthesis of a particular protein is coded in the DNA and is carried out by the RNA molecules in the cell nucleus. Each particular protein has its own unique sequence of amino acids that can be determined in some cases through modern analytical techniques. Secondary Structures have shapes where the polypeptide chain folds or twists into. There are two fundamental folding patterns for a polypeptide chain, - the α helix and the β pleated sheet. The α helix has a spiral or coiled spring shape that is held in place by numerous intramolecular hydrogen bonds. β pleated sheets consist of extended polypeptide chain with neighbouring chains running in antiparallel directions. The C=O and the H N - groups lie in the plane of the sheet and are approximately perpendicular to the long axis of the sheet. Tertiary Structure Refers to the folding that the α helix and β pleated sheets exhibit. Many proteins consist of more than one polypeptide chain. Haemoglobin consists of four polypeptide chains. The Quaternary Structure of a multi chain protein refers to the 3-D arrangement in which these chains pack together. Dispersion forces between non-polar R groups are mainly responsible for the stabilisation of the quaternary structure.
Denaturation of Proteins The spatial arrangement of a protein is what creates its biological function. If the normal secondary, tertiary or quaternary structure of a protein is altered, it loses its capacity to perform biological functions. The protein is said to be denatured. Structural alterations are commonly caused by changes in the temperature or ph of the environment of the protein Eg. Congealing of albumin in egg white by heating and the curdling of milk by adding acid. Effect of ph change Changes in ph have their greatest effect on ionic bonding between NH + 2 and COO - side groups. Adding concentrated acid converts COO - -COOH. Adding Alkali converts -NH 3 + to non ionic NH 2 groups. In both cases ionic bonds can no longer form between the side groups and the structure is destabilised. Effect of Heat Raising the temperature above 50 0 C to 60 0 C is sufficient to break secondary bonds. dispersion forces and hydrogen bonds that stabilise the secondary tertiary or quaternary structures. The protein structure consequently unravels.
TRIGLYCERIDES Triglycerides are fats and oils derived from plants and animals. They are triesters of the 1,2,3 propantriol (commonly called glycerol) and long straight chain carboxylic acids. The carboxylic acids are often referred to as fatty acids. Almost without exception they contain an even number of carbon atoms (usually 12 to 22) in the chain. The chains are both saturated and unsaturated. If there is more than one C=C bond is present, it is called polyunsaturated. Fatty acids are commonly written as number indicates the length of chain naturally occurring triesters of propane,1,2,3 triol nearly always have three different fatty acids forming ester linkages. HYDROLYSIS OF TRIGLYCERIDES Fats and oils are highly concentrated stores of energy. The first stage in the use of fats as an energy source is the hydrolysis of the triglyceride molecules catalysed by enzymes called lipases. The products of the hydrolysis of each fat molecule are one molecule of glycerol and three fatty acid molecules. Without the aid of lipases, this hydrolysis of triglycerides requires severe reaction conditions.
Source of edible fats and oils Edible fats are solid at room temperature and are generally derived from animals. Edible oils are liquids at room temperature and are usually derived from plants and fish. Animal fats contain a greater percentage of saturated fatty acids than vegetable oils. Generalisation about melting points of fats and oils. melting points increase as the length of the hydrocarbon chains increase (dispersion forces are the reason) melting points decrease as the degree of unsaturation increases. Unsaturated chains are much less ordered, therefore chains can t pack together, therefore lower melting points. Determining the degree of Unsaturation of a Triglyceride Alkenes, which contain C=C groups, undergo additional reactions with diatomic molecules, eg Br 2, I 2, and H 2. fats and oils with unsaturated groups will undergo the same type of addition reactions when mixed with a solution of bromine (orange) in saturated hydrocarbon solvent (cyclohexane) the orange colour of the Br 2 disappears as the products of the addition reaction are colourless. The amount of unsaturation can be determined by a titration of the unknown against a standard solution of Bromine. The higher the amount of Bromine used, the greater the unsaturation. The addition of Iodine, I 2, across the C=C double bonds in a fat or oil molecule does not occur as readily as the addition of Bromine. The reaction is slow and incomplete, equilibrium reaction lies to the left. Despite Iodine s lack of reactivity, the degree of unsaturation is usually quoted as an Iodine number. The Iodine number of a fat or oil is the mass of I 2 that reacts exactly with 100 grams of the fat or oil. The greater the value, the greater the degree of unsaturation. Hydrogenation of Oils Liquid oils can be converted to solid fats by a process called hydrogenation. Margarine and Peanut Butters are prepared in this way. A vegetable oil is heated in the presence of hydrogen gas under pressure with a nickel catalyst. Sufficient hydrogen is added to the oil to make it solid at room temperature
CARBOHYDRATES Carbohydrates are naturally occurring substances with a general formula C x (H 2 O) y often x = y. from this formula it can be seen that they can be regarded as hydrates of carbon. In structural terms, they are polyhydroxyaldehydes or polyhydroxyketones. They are also classified as monosaccharides, disaccharides and polysaccharides depending on the number of simple sugar units that comprise the molecular structure. Monosaccharides These are the monomers from which all disaccharides and polysaccharide molecules are constructed. The following generalisations can be applied to monosaccharides their general formula is C x H 2x O x with x of values 3 to 8 they are water-soluble compounds they have the name ending..ose eg glucose they are sweet to taste and are often called simple sugars structurally the molecules of six carbon polyhydroxyketones and five and six carbon polyhydroxyaldehydes can exist in chain or cyclic form the two forms exist in equilibrium with each other, equilibrium lies with the cyclic form they are solids at room temperature (extensive hydrogen bonding) Polysaccharides These are insoluble in water (because of the large molecular size) but do absorb water and are virtually tasteless. They are formed by successive condensation reactions of monosaccharides. Complete hydrolysis of a polysaccharide produces monosaccharides such as glucose. The four most common and biologically important polysaccharides are all composed of glucose units. They are: Cellulose main structural material of plants Glycogen main storage of polysaccharides in animals Amylox amylopectin make up starch Cellulose and amylose are straight chain polysaccharides whereas glycogen and amylopectin are branched chain polymers
Glucose as a Reducing Agent Glucose exists in both chain and cyclic forms, which in aqueous solution are in equilibrium. The aldehyde functional group in the chain can be oxidised by Tollen s Reagent. (Silver mirror test). The aldehyde group is oxidised to a carboxylate group. There is no aldehyde group present in the cyclic form and therefore does not react with Tollen s reagent. However consumption of the chain form by the Tollen s reagent mean more chain form will be produced (Le Chatelier s) Carbohydrate molecules can undergo extensive hydrogen bonding with polar water molecules because of the presence of hydroxyl groups as part of their molecular structure. However only the mono and disaccharides have molecules small enough in size to actually mix with the water molecules to form aqueous solutions