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Chemistry of life (Biochemistry)
The study of chemical compounds that are vital for living organisms to sustain life is called biochemistry. The subject deals with the nature of these compounds and characteristic reactions they make inside the living organisms . We are not involved fundamentally with the study of biochemistry as a subject , but to give brief introduction to main classes of the organic compounds in this important field. It is beyond this discussion to present detailed explanation of these essential organic substances . We will give short introduction of the main classes and their active role in our body . Some of these groups are , carbohydrates , fats and proteins, etc..
· Carbohydrates.
Carbohydrates are classes of organic compounds that consist of carbon , hydrogen and oxygen with an empirical formula of Cm(H2O)n in most cases . The terms m and n can be the same as in the case of C6H12O6 (glucose) or different in the case of C12H22O11 (sucrose) . Another important feature of the carbohydrates is that oxygen and hydrogen are generally in ratio of 2:1 , so that it was historically called hydrates of carbon ; but not all compounds of carbohydrates necessarily maintain this hydrogen – oxygen ratio and not all compounds that fit this hydrogen-oxygen ratio are carbohydrates .
In biochemistry the term carbohydrate denotes different compounds called saccharides . These compounds include sugars , starch and cellulose . Saccharides (Greek word meaning sugars) are generally classified into monosaccharides , disaccharides and polysaccharides .
Monosaccharides are the simple sugars which are either aldoses (aldehydes) like glucose or ketoses ( ketones) like fructose . These simple sugars are further classified on the base of the number of carbon atoms they contain like pentose (containing five carbon atoms) , or hexose (containing six carbon atoms) .
Carbohydrates are naturally formed in a process called photosynthesis in which plants combine CO2 from the air and water from the soil in the presence of chlorophyll , sunlight and certain enzymes producing simple sugars .
6 CO2 + 6H2O (sun light) C6H12O6 + 6O2
sugar(glucose)
This above reaction is not simple process as it looks , but extremely complicated reaction with different intermediate steps before it gives the final product . since the final product is a monosaccharide , plants have the ability to synthesize disaccharides by combining two molecules of monosaccharides .
2 C6H12O6 C12H12O11 + H2O
monosaccharide disaccharide
This above natural chemical process is the reverse of hydrolysis . Both plants and animals have the ability to synthesize polysaccharides by combining large number of monosaccharide molecules .
n C6H12O6 (C6H10O5)n + n H2O
polysaccharide in plants are usually in the form of cellulose , stored in stalks and stems and in a form of starch in the roots and seeds .
Animals and plants depend on each other to sustain life ; plants can synthesize carbohydrates - as we mentioned before - from simple inorganic materials like CO2 and H2O while animals cannot. On the other hand , animals utilize these essential carbohydrates and metabolically oxidize to give CO2 , water and energy .
C6H12O6 + 6 O2 6 CO2 + 6H2O + energy
Note that this reaction is the reverse of that of the photosynthesis in plants ; we can combine both equations to establish the relationship .
The reaction to the right is endothermic and the energy is taken from the sunlight while the reaction to the left is exothermic in which the same energy is liberated and utilized by the body activity to sustain life .
It is clear from this cycle that the energy stored in the carbohydrates is originally from the sun .This energy is used by all living organisms in their metabolic process.
1- Monosaccharides
Monosaccharides are the basic units of the carbohydrates ; they are also called simple sugars . The term monosaccharide originally came from two Greek words mono- which means single and Sachar which means sugar . These simple sugars are usually colorless crystalline solid material . Almost all monosaccharides are soluble in water and have sweet taste .
Most monosaccharides have chemical formula of Cm(H2O)n where n < 2 . They are classified - as we already described - on the base of number of carbon atoms present in the molecule such as triose , pentose , and hexose representing glyceraldehyde , ribose and glucose respectively .
The carbon chain of the monosaccharides are numbered beginning from the carbon closest to the carbonyl group . We can also designate the structural nature of the monosaccharide by using the terms aldoses or ketoses so that if the carbonyl is at position 1 of the carbon chain , the sugar is an aldehyde and termed an aldose . On the other hand if the carbonyl group is in between two carbon atoms , then the sugar is ketone and termed ketose .
· Structures of monosaccharides – (optical isomers).
Monosaccharides exist in different stereo-isomeric forms . In section (10.3) of this chapter , we presented this property in detail and explained the two types of the stereoisomers ; the important one in our study of simple sugars is the optical isomerism .
Optical isomers are molecules that have the same molecular formula but differ in the arrangement of the atoms in space in such a way that they are mirror images to one another . Despite these isomers have the same physical and chemical properties , they differ in the direction of rotating planely polarized light (light waves vibrating in one plane ) . If polarized light is passed through these isomers, the plane of the vibrating light is rotated due to presence of chiral or asymmetric carbon in the molecule that is a carbon atom attached to four different groups . Suitable example is the glyceraldehyde molecule .
The central carbon atom is connected to aldehyde group , OH group , hydrogen and alcoholic group . Despite glyceraldehyde is the simplest carbohydrate , it is very important compound in the since that many complex sugars can be derived .
· Classification of monosaccharides
We have seen that simple sugars can be divided into different groups depending on the number of carbon atoms they contain designating them as trioses , tetroses, pentoses and hexoses.
A. Trioses: These are monosaccharides that consist of three carbon atoms . Glyceraldehyde is an example of this group . Trioses are the product of the metabolic breakdown of certain simple sugars .
B. Tetroses: Tetrodes are simple sugars with four-carbon structure . Erythrosine and throes are examples of these sugars .
C. Pentose: These are monosaccharides with five-carbon atoms . They are classified into two groups ; those with aldehyde functional groups called aldopentose and those with ketone functional groups called ketopentose .
The most significant of these sugars are the ribose and deoxyribose which are found in RNA (Ribonucleic acid) and in DNA (Deoxyribonucleic acid) . Both RNA and DNA are the main component of every living cell , especially in the nucleus of the cell .
D. Hexoses: They are monosaccharides with six carbon atoms . There are different kinds of hexoses but the most important ones in terms of human body are glucose , fructose and galactose . These sugars have the same chemical formula but differ in structure and can be called isomers of a given molecular formula .
We already explained that simple sugars are classified on the base of their functional groups . Hexose with aldehyde functional group are called aldohexose and those with ketone functional group are called ketohexose .
A. Glucose: glucose is an aldohexose with general formula C6H12O6 ; there are four asymmetric carbon atoms and 16 optical isomers . Glucose molecules can exist in solution in the form of open chain or in the form of ring structure . This ring structure is formed when the hydrogen of the carbon 5 -OH attaches with the oxygen atom of the aldehyde group on carbon 1 .
Open chain Ring structure
B. Galactose: galactose is an aldose sugar like glucose ; it can be considered as the isomer of glucose , they only differ in the configuration of a single carbon atom which is known as epimoric form of isomerism (differ in one stereoisomeric center) . Like any hexose , it can exist in solution as an open chain or ring form .
Open chain Ring structure
C. Fructose: fructose is ketohexose with a molecular formula of C6H12O6 , like glucose and galactose . Fructose or levulose is naturally occurring sugar found in fruits ; like any other hexoses , it is found in solution as a ring or as open chain structure . Fructose is the sweetest and most soluble of all sugars .
Reactions of the hexose monosaccharides
Aldoses and ketoses have reducing properties in common . These properties are the bases of the chemical tests undertaken to determine the sugar content in human blood and urine . The reactions involved in these chemical test are in the organic practical section . In these tests aldoses are oxidized into their corresponding acids .
RCHO + Cu2+ + 2 OH- RCOOH + Cu2O + H2O
Clinitest tablets are used to perform the above test to determine the sugar in the human urine . Note that these tablets contain copper ions in the form of Cu(II)sulfate.
Another test for reducing sugars is the Tollens test in a solution containing silver ions in basic solution .
Glucose + Ag+ + OH- gluconic acid + Ag + water
Another general qualitative test for carbohydrates is the Molisch test in which concentrated sulfuric acid is carefully added to the testing solution containing alpha-naphthol ; formation of purple ring at the interface of the acid and solution confirms the presence of carbohydrate substance .
Another important reduction reaction for some aldoses like glucose is the fermentation process in which an enzyme from the yeast catalyzes this reaction and without which this reaction cannot take place .
C6H12O6 enzyme CH3CH2OH + CO2
Aldoses can also undergo oxidation since they both contain aldehyde and hydroxyl group . We have seen that oxidation of the aldehyde group gives the corresponding acid , like gluconic acid in the case of glucose and glucuronic acid if the hydroxyl group oxidizes .
Aldohexoses can be converted to alcohols by reduction and in this case , glucose is reduced to sorbitol and fructose is reduced to mixture of mannitol and sorbitol.
Glucose Sorbitol
Since both sorbitol and mannitol are partially and slowly taken by the body , it is useful as sweetening agent for the diabetic people . When orally taken some of the sugar is excreted in the urine and other is taken by the body slowly .
1. Disaccharides
Disaccharides are the sugars formed when two monosaccharides are chemically joined together . The most common examples of the disaccharides are sucrose , lactose and maltose . They all have the general formula C12H22O11 , which means they are isomers .
Disaccharides formed as a result of condensation reaction of two monosaccharides which means elimination of water molecule . The reverse reaction is known as hydrolysis performed by certain enzyme .
These reactions are vital in the metabolism of living things . Different disaccharides hydrolyze to give two different or same simple sugars as shown above. Disaccharides are , like monosaccharides , white crystalline sweet solids . Their solubility varies from completely soluble to slightly soluble .
Disaccharide molecule from two simple sugars is formed by displacing hydroxyl group from one molecule and the hydrogen ion from the other producing water molecule a process known as condensation reaction .
Sucrose is formed by the reaction of the aldehyde group of glucose with the ketone group of fructose thus eliminating the reducing property of the carbonyl; and for this reason give negative test to reducing reagents. On the other hand , maltose and lactose have free aldehyde group and give positive test for both Fehling and Tollens reagents .
In the case of maltose formation , one aldehyde group of a glucose reacts with the hydroxyl group of another glucose leaving one aldehyde group free for reducing property . In the same way , lactose has one available aldehyde group ; for that reason maltose and lactose are reducing sugars while sucrose is not reducing sugar .
These sugars are differentiated analytically on the base of their fermentation and reducing properties . Both sucrose and maltose can be fermented by the addition of yeast which contains sucrase and maltase enzymes . Lactose does not ferment with the yeast since it does not contain lactase .
A. Sucrose:
This sugar is known as table sugar ; it is naturally occurring carbohydrate found in many fruits and vegetables like carrot roots and pineapples . Sucrose is extracted from cane and beet sugars and refined to be consumed by the people. Hydrolysis of sucrose gives a mixture of glucose and fructose .
This mixture of equal amounts of glucose and fructose is invert sugar . High concentration of this invert sugar is found in honey ; this kind of sugar is less prone to crystallization when cooled .
B. Maltose:
Maltose is a disaccharide formed from two units of glucose . It is commonly known as malt sugar . It is commercially prepared from hydrolysis of starch . It generally occurs in germinating seeds .
C. Lactose:
Lactose is also a disaccharide formed from joining of two units of glucose and galactose . It is found in milk and that is the reason why it is called milk sugar ; it differs from the above sugars in the sense that it comes from animals. We pointed out previously that lactose is fermented by the enzyme lactase forming lactic acid; this fermented milk is said to be sour milk. Lactose is also found in urine of pregnant woman and since it is reducing sugar , it gives positive test with Fehling or Benedict solution.
2. Polysaccharides:
Polysaccharides can be defined as the polymeric form of monosaccharides . These polymers hydrolyze to yield many monosaccharide molecules . These polysaccharides are generally formed from five-carbon or six-carbon sugars .
The most common polysaccharides are :
A. Starch
Starch is a polymer of glucose sugars which consist of around 20% amylose and 80% amylopectin . Amylose is linear chain of glucose molecules while amylopectin is branched form of the starch and contain much larger units of glucose in comparison to amylose . Starches are insoluble in water .
Starch (long chain of glucose units ) Amylopectin (branched form of starch)
Amylose (linear chain of glucose)
The presence of starch is tested with iodine which gives characteristic deep blue color . Hydrolysis of starch to simple sugars through several stages giving different dextrin’s on the process which can be followed by addition of iodine . Iodine gives no color with simple sugars and blue color with dextrin’s .
A. Cellulose
Cellulose is also polysaccharide consisting of linear chain of several hundred to thousands of linked glucose units . It is an important supporting and structural component of all plants . Unlike starch , cellulose is not affected by the digestive human enzymes and for that reason helps prevent constipation by making bulk feces of dietary fiber when taken by human .
Cellulose
Cellulose is digested and metabolized by certain animals like ruminants and termites with the help of micro-organisms which live in their abdomen . Cellulose is not soluble in water and in majority of solvents . Unlike starch , it does not give positive test to iodine or to Fehling reagent . Materials like cotton , wood and paper are mainly composed of cellulose . Cellulose is used to produce paper , cellophane and rayon.
B. Glycogen ,
Glycogen is multi-branched glucose polymer which is responsible for the storage of energy in animals . Glycogen is produced by the body and stored in the liver and the muscles ; it is originated from the animals while starch is basically from plant origin ; it acts as a reserve or long-term energy storage . Even though fats act as the primary energy stores , glycogen energy is necessary for immediate mobilization to cover a sudden need for glucose.
Glycogen is synthesized in the body cell from glucose through a process called glycogenesis and hydrolyzed to give glucose through a process known as glycogenolysis .
Glucose glycogenesis Glycogen glycogenolysis Glucose
C. Dextrin
Dextrin’s are lower molecular weight carbohydrates formed as a result of starch hydrolysis . Dextrin’s are considered as an intermediate between the starch and the disaccharides . It dissolves in water giving sticky colloidal suspension used in the preparation of adhesives like the glue on the back of the postage stamp .
1. Lipids (fats)
Lipids are naturally occurring organic compounds ; these include fats , waxes , fat soluble vitamins and sterols (steroid alcohols) . It is one of the main sources of food essential for animals and plants .
Lipids consist of carbon , hydrogen and oxygen and in certain cases nitrogen and phosphorus . They are insoluble in water but soluble in organic solvents like alcohol and acetone . Even though there are different categories of lipids , we will confine our discussion to simple lipids which are esters of fatty acids .
· Fatty acids:
There are two types of fatty acids ; saturated fatty acids which contain single bond between the carbon atoms and unsaturated fatty acids which contain double between the carbon atoms .
CH3-CH2-CH2-CH2-COOH CH3-(CH2)7-CH=CH-(CH2)7-COOH
Saturated fatty acid unsaturated fatty acids
Table.10.6 Common saturated fatty acids.
|
Name |
Formula |
Source |
|
Butyric acid |
C3H7COOH |
Butter fat |
|
Caproic acid |
C5H11COOH |
Goat fat |
|
Caprylic acid |
C7H15COOH |
Coconut oil |
|
Capric acid |
C9H19COOH |
Palm oil |
|
Lauric acid |
C11H23COOH |
Laurel (plant) |
Table.10.7 Common unsaturated fatty acids .
|
Name |
Formula |
Source |
|
Oleic acid |
C17H33COOH (1 double bond) |
Olive oil |
|
Linoleic oil |
C17H31COOH (2 double bond) |
Linseed oil |
|
Linolenic acid |
C17H29COOH (3 double bond) |
Linseed oil |
Unsaturated fatty acids can exist in two structural forms , cis in which the two hydrogen atoms adjacent to the double bond are on the same side of the carbon chain and trans in which the adjacent two hydrogen atoms are on the opposite sides of the carbon atom (discussed in section 10.3) .
Iodine number
Human body cannot sufficiently synthesize some of the fatty acids they need and must be obtained from the food they take . These fatty acids are known as essential fatty acids . linoleic and linolenic acids are among the essential acids ; they are found in certain plant oils like peanut , soybeans and corn but not in olive oil or cocoanut.
Essential fatty acids have important function in the body such as the synthesis of prostaglandins (hormone-like substance with wide physiological activities) .
Iodine number:
The degree or the amount of unsaturation in a given fatty acid is determined by its iodine number , which is the amount of iodine consumed by 100 g of the acid. Iodine reacts with the double bond of the unsaturated fatty acid , so the higher the iodine consumed the more double bonds present in that fatty acid .
Despite there are different methods for determining iodine value , they all fall under the iodiometry procedures . We indicated that the higher the unsaturation for a fatty acid the higher the iodine value . Linseed oil has much more iodine value than coconut oil which means the linseed oil is highly unsaturated oil with respect to coconut oil . In general , vegetables oils have higher iodine number than animal fats .
Fats and oils
We defined the fats as esters of fatty acids (already discussed in carboxylic acids unit) which are formed from the reactions between a fatty acid and specific alcohol called glycerol .
There are three OH groups available in glycerol and each one can react with a fatty acid molecule forming a fat molecule . These fatty acids can be of same fatty acids or different fatty acid molecules .
The esters formed when the alcohol is glycerol is called glyceride . It can be monoglyceride , diglyceride or triglyceride depending on the number of fatty acids reacted with the glycerol .
In general if the reacting fatty acid is saturated , the ester formed is called fat and if it is unsaturated the resulting ester will be an oil . Most fats have iodine value less than 70 while most oils have iodine value more than 70 . Keep in mind that mineral oil is a saturated hydrocarbon different than fats and oils which are either from animal , vegetable origin and petroleum distillate .
Those oils are different from essential oils which are volatile liquids used as flavors and perfumes , while mineral oils are mixtures of higher alkanes . The name may be inappropriate and sometimes other names are applied such as liquid paraffin , paraffin oil etc. .
· Properties and uses of fats
Fats can be considered as body fuel , they produce more energy for the body than any other nutrient such as carbohydrates or proteins . Another important function of the fats is their essential role in reserving food supply for the body . They protect the vital organs by keeping them rigid in their place and helping to absorb shocks .
In terms of physical properties , fats and oils are either in liquid or solid state with white or yellow color in most cases . They are colorless and tasteless in their pure state but get rancid as the time goes on creating unpleasant odor and taste. Since both fats and oils are insoluble in water ; they form transient emulsions which can be stabilized by adding emulsifiers from the bile to make them digestible .
In terms of chemical properties , fats hydrolyze in the presence of certain enzymes to form fatty acids and glycerol . We have seen that when a fat is formed water is the product (see the preceded equation) ; the reverse process is called hydrolysis.
After the hydrolysis of the fat , the glycerol is separated and purified for medical and industrial purposes . It is used as humectant (against loss of moisture) for skin and hair care products . It is also used in the preparation of medical and pharmaceutical products . Glycerol has also an important industrial applications ; it is found in food , beverages and sweetener as sugar substitute besides many other uses .
We briefly explained in this chapter , that basic hydrolysis of fats yield glycerol and salt of the fatty acid ; this process is called saponification and the sodium or potassium salt formed is called soap .
Sodium soaps are solid bars and potassium soaps are liquid . In preparing soaps, various materials are added to give pleasant odor and color ; in certain soaps , germicidal substances are added to protect the skin from the germs as in the case scouring soap .
In hard water , calcium and magnesium ion react with the soap rendering it insoluble and inactive to give more lather and more cleansing result . This problem is overcome by using detergents . Detergents are synthetic cleaning substances consisting of mixtures of surfactants (lower the surface tension) used as a soap . They can be used both in soft and hard water ; which means calcium and magnesium salts of detergents are soluble in water thus overcoming the disadvantage of soap .
Detergents are made from different petrochemicals besides fat and oils . They are generally neutral unlike the soaps which are alkaline . The sodium salt of the detergents is prepared by the reaction of long chain alcohols with concentrated sulfuric acid and the product is neutralized by sodium hydroxide .
R-OH + H2SO4 R- OSO3H + H2O
long chain alcohol
R- OSO3H + NaOH R-OSO3Na + H2O
Detergent
The unbranched straight chain detergents are less harmful in terms of environmental pollution .
2. Proteins
Another essential nutrient for living organisms is the protein . Proteins are complex organic substance which consist of carbon , hydrogen , oxygen and nitrogen besides some other elements like sulfur and phosphorus . Proteins consist of long chain of simple molecules called amino acids arranged in a specific order. There are 20 known amino acids .
All of these amino acids cannot be synthesized by the human body and must be externally supplied . The first three amino acids are shown below with their symbol and names
Amino acid molecule contains amino group and carboxylic group .
Despite the amino group can be structurally anywhere in the molecule , the amino group of the naturally occurring amino acids are bonded with the alpha – carbon (the one next to acid group ). Almost all amino acids have alpha chiral carbon (except glycine) and show L-configuration .
Amphoteric nature of the amino acids
Amphoteric substance is one that shows both acidic and basic character ; which means it behaves as an acid and base. As the name denotes , amino acids contain carboxylic group which is an acid since it furnishes proton in solution and also contain amino group which accepts the proton and on the base of Brnsted – Lowry acid-base definition , amino acids act as an acid and as a base at the same time; therefore amino acids react with both acidic and basic substances ; consequently amino acids can be called amphoteric substance as long as they donate and accept protons .
Amino acid molecules react together in which the amino group of one amino acid reacts with the carboxylic group of another forming a long chain of amino acid molecules connected through a bond known as peptide bond . This bond is formed as a result of condensation reaction in which one molecule of water is produced for every two reacting amino acids .
A combination between two amino acids form a product called dipeptide , and that of three amino acids form tripeptide and more than three amino acids form polypeptide. There are two different ways for two amino acids to combine .
It is very important to know that for combined amino acids , their name is abbreviated by taking the first three letters of the amino acid and in the order of their combination in the peptide ; the first amino acid is the one that furnishes the OH from the acid group .
· Isoelectric point
We have seen that amino acids contain both basic and acidic functional groups. In the crystalline forms , amino acids exist as zwitterions , which is a neutral molecule having both positive and negative electrical charges resulting no net electric charge. These solid forms usually have high melting point and less solubility in organic solvents but soluble in water . In aqueous solution , these amino acids establish an equilibrium dependent on the pH of the solution .
isoelectric point
In basic solution , the equilibrium is shifted towards the right and in acidic solution the equilibrium is shifted towards the left . If two electrodes are placed in this amino acid solution , there will be net migration of the solute molecules towards either the positive electrode (cathode) or the negative electrode (anode) depending on the alkalinity or acidity of the solution .
In basic solution a negatively charged carboxylic group is formed and the migration takes place towards the positively charged electrode and in acidic solution , a positively charged amino group will be formed and the migration takes place towards the negatively charged electrode .
At certain pH , characteristic of each amino acid , the positive and the negative ions will be equal and there will be no net migration of the amino acid molecules towards the electrodes . This specific pH value is called isoelectric point .
Proteins like amino acids have an isoelectric point which is characteristic property for each protein . Proteins have the minimum solubility in their isoelectric point .
For the pH of the amino acid above the isoelectric point , the basicity dominates , that is there will be more basic sites and the pH below the isoelectric point , the acidity will dominate and there will be more acidic sites .
· Structure and the properties
Proteins hydrolyze in acidic or basic media , or by the action of certain enzymes . This hydrolysis breaks the protein molecule into the constituent amino acids . In the reverse process , amino acids combine together with the help of specific enzymes to form polypeptides which are the basic molecular structures of the proteins ; the more units of amino acids combined the bigger the molecular weight of the protein .
As a result of the large molecular sizes of the proteins , different structural forms are created which are referred to as primary , secondary and tertiary structures based on the shape and spatial orientation of the protein molecule .
The bases of these shapes and their biological significances is beyond our discussion. The main properties of the proteins can be summarized as follows :
A. Colloidal
The aqueous solution of protein form colloidal dispersion of the protein molecules in water . These colloidal particles have the ability to pass through the filter paper but inable to pass thhrough the cellular membranes ; this phenomenon is physiologically important since it keeps the protein in the bloodstream and impedes the diffusion of protein molecules into the urine indicating the damage of kidney membranes .
B. Denaturation
Denaturation refers to change of protein structure loosing its biological function . When proteins become denaturated , they coagulate or precipitate . This effect takes place under the influence of several reasons :
1. Effect of alcohol: 70% aqueous solution of alcohol (ethanol) precipitates almost all proteins and for this reason we use this alcohol concentration as a disinfectant because it coagulates the protein of the bacteria rendering it inactive .
2. Salting out process: at high concentration of salt solution , proteins become almost insoluble and precipitate . This is one of the techniques used to separate proteins from solutions . Salts like Na2SO4 , NaCl are used for this purpose . The separation from the solution is achieved through filteration and the traces of the remaining salt is eliminated by a process known as dialysis .
3. Heavy metal salt : Saturated salt solutions of certain heavy metals such as silver and mercury(II) precipitate the protein . These heavy metal salts coagulate the protein making it biologically inactive . This is the reason why these metals are poisonous if taken internally .
4. Heating :
Almost all protein coagulate on heating . Heating is common method to sterilize materials because the protein of the bacteria is destroyed by coagulating it . Presence of protein in urine (which is kidney malfunction) can be determined by heating given sample of urine to precipitate the protein .
5. Concentrated inorganic acids:
Concentrated strong mineral acids can be used to precipitate the protein. HCl , H2SO4 , and nitric acid are among the mineral acids that can be employed to precipitate proteins . Concentrated HCl from the gastric glands precipitate the milk protein , casein , in the form of curds .
C. Qualitative tests for proteins
Most qualitative tests for proteins depend on specific color formation . These tests are not always decisive since it depends on the presence of certain amino acids . Some of these tests are :
Xanthoprotic : Which is the formation of yellow precpitate due to action of nitric acid on proteins . Contact of nitric acid on your finger usually produces yellow color on the skin of the finger . This test is only positive for the amino acids that contain benzene ring .
There are other well known tests like , Biuret , Millon’s , Hopkin-Cole and ninhydrin tests in which their procedures are explained in the organic practical section. Different chromatographic methods are used to separate and identify different mixture of proteins or amino acids .
Quantatively the amount of protein in a sample is estimated by determining the nitrogen content and multiplying the result by factor 6. This factor came from the fact that the average percent of nitrogen in protein is 16% by weight ; that is approximately 1/6 of the total weight of the protein . If for example the total nitrogen of a sample is 2.5 g , the amount of protein present in the sample = . The result is always expressed in percent .
Nucleoproteins can be defined as conjugated propteins that consist of acidic part which is nonprptein section called nucleic acid and a protein part . Nucleoproteins hydrolyze during the digestion process into nucleic acids and proteins . Proteins further hydrolyze into amino acids while nucleic acids hydrolyze into nucleotides .
Nucleic acids are biological polymers that consist of repeating units of nucleotides so that nucleic acids can be called polynucleotides . Each nucleotide consist of heterocyclic nitrogen base , pentose sugar and phosphoric acid . The number of nucleotide units in a nucleolic acid depends on the nature of the nucleic acid and may range from approximately one hundred units to several million units .
Nucleotide
There are mainly two branches of nucleic acids :
a) Deoxyribonucleic acid (DNA) which is found in the nucleus of the cell and contains pentose sugar , deoxyribose , which is the only sugar on hydrolysis.
b) Ribonucleic acid (RNA) which is mainly found in cytoplasm and contain ribose as the only sugar on hydrlysis .
Parts of nucleotides
We have showed that a nucleotide consist of nitrogen base , pentose sugar (ribose or deoxyribose ) and phosphoric acid . Let us investigate them one by one .
A. Nitrogen bases:
The two groups of heterocyclic nitrogen – containing bases in the nucleic acids are derivatives of purine or pyrimidine with following structures .
The most common purine bases in nucleic acids are adenine and quinine . They are present in both DNA and RNA .
The pyrimidines that are most common in both DNA and RNA are cytosine , uracil and thymine .
(2-oxy-6-aminopyrimidine) (2,4-dioxy-5-methylpyrimdine) (2,dioxypyrimidine)
Nucleosides ,
Nucleosides are units formed by combination of nitrogenous base and one of the two pentose sugars (ribose or deoxyribose) in the structure of nucleic acids . In this combination the glycosidic bond between the sugar and the nitrogenous base is formed at C – 1 of the sugar and the position 9 of the purine base or position 1 of the pyrimidine base .
Glyosidic between C1 of ribose Glyosidic between C1 of deoxyribose and
and positon-9 of purine postion-1 of pyrimidine
Nomenclature
Nucleosides from the pyrimidines have names ending in -idine and those from the purines have names ending in -osine Purines with ribose sugars are named as follows :
Adenine + ribose Adenosine
Guanine + ribose Guanosine
Purines with deoxyribose sugars are named as follows :
Adenine + deoxyribose Deoxyadenosine
Guanine + deoxyribose Deoxy guanosine
Pyrimidines containing ribose sugars are named as follows :
Uracil + ribose Uridine
Cytosine + ribose Cytidine
Thymine + ribose Thymidine
Pyrimidines containing deoxyribose sugars are named as :
Uracil + deoxyribose Deoxy uridine
Cytosine + deoxyribose Deoxycytidine
Thymine + deoxyribose Deoxythymidine
It is known that glycosides are quite stable in alkaline medium and the situation is the same in the nucleosides but hydrolyze in aqueous acid solution to produce base and pentose sugar .
Polynucleotides Hydrolyze Nucleotides Hydrolyze Nucleosides Hydrolyze Base + sugar
Nucleotides are the phosphate esters of the nucleosides . The phosphoric acid reacts with one of the hydroxyl groups in the sugar forming phosphate ester bond.
Condensation reaction
In the case of ribonucleoside , the phosphate ester bond can be formed at three possible -OH groups at C1 , C3 and C5 and for that reason we have to specify the point of the attachment in naming the nucleotide .
We already pointed out that nucleotides are phosphate esters of nucleosides ; and because the compound contains phosphoric acid , acidic name is given according to the following table.
|
Nucleoside + H3PO4 |
Acidic name of the nucleotide |
|
Adenosine |
Adeynilic acid |
|
Guanosine |
Guanilic acid |
|
Cytidine |
Cytidilic acid |
|
Uridine |
Uridylic acid |
|
Thymidine |
Thymidilic acidic |
The nucleoside formed from the reaction of one molecule of a nucleoside with one molecule of a phosphoric acid is called monophosphate of that nucleoside . In the case of adenosine , it is called adenosine monophosphate (AMP) or Adeynilic acid . If it reacts with one more phosphoric acid molecule , it is called adenosine diphosphate (ADP) ; and if three groups are involved it is called adenosine triphosphate (ATP) .
) AMP) (ADP) (ATP)
These phosphate esters , AMP , ADP and ATP perform vital role in cellular metabolism as high storage of energy and release that energy from the hydrolysis of phosphate bonds and pass to the specific reactions that require this energy to take place . ATP contains the highest amount of energy in comparison to ADP and AMP. Besides being body building blocks , certain nucleotides perform biological activities of their own . Appropriate example can be taken in the case of cyclic adenosine monophosphate (cyclic – AMP) which is formed as a result of phosphate group attached to carbon-3 and carbon-5 of the ribose sugar . It (cyclic-AMP) acts as messenger in regulating enzymatic activities in cells that store fats and carbohydrates.
Cyclic adenosine monophosphate (camp)
Certain nucleotides act as Coenzyme . Nicotinamide adenine dinucleotide (NAD+) is essential for many biological oxidation-reductions reactions to take place . It exists in oxidized form (NAD+) and reduced form transferring electrons from reaction to another .
Exercises:
1. What is the modern definition of organic chemistry ? Briefly explain the role of organic chemistry in our daily life.
2. What was the vital force theory and how was it disproved ?
3. Account for the fact that element carbon has the unique property of forming so many millions of chemical compounds .
4. Briefly compare , in general , the physical and chemical properties of organic and inorganic compounds .
5. Explain the role of carbon dioxide in the natural formation of certain organic substances like coal , petroleum , and natural gas .
6. What are the hydrocarbons ? mention the different classes of the hydrocarbons on the base of their general structure . Give an example of each class .
7. Name the following hydrocarbon compounds .
8. Write the structural formula for each of the following compounds .
B. 2,3-Dimethylpentane
C. 2-Chloro-3-ethylpentane
D. 1,1,2,2-Tetrabromobutane
E. e) 2-Butyne
F. 3,4-Diethyl-1-hexyne
G. 3-Ethyl-2-heptene
9. Write the possible isomers for the following hydrocarbons .
A. C7H16
B. C6H12
C. C5H10
D. C4H8
E. C6H10
10. How can you determine the nature of the following hydrocarbons as alkanes, alkenes, alkynes and cycloalkanes .
A. C7H14
B. C6H12
C. C5H12
D. C4H6
E. C3H4
11. How can you distinguish by simple qualitative test between the following pairs of compounds ?
A. Ethanol and pentane .
B. Acetaldehyde and acetone .
C. Acetic acid and ethylamine .
D. Phenol and benzene .
E. Pentane and pentene .
12. Account for the extra stability of benzene in comparison to ethene (ethylene).
13. Explain what we mean by a functional group . Why it is important to classify organic compounds on the base of their functional group ?
14. Distinguish the following compounds as alcohol , aldehyde , ketone , carboxylic acid and amine .
A. CH3-COCH3
B. CH3CH(OH)CH3
C. HCHO
D. CH3CH2CO2H
E. CH3CH(NH2)CH3 .
15. Draw the possible structural formula of the following compounds .
A. C2H6O
B. CH4O
C. C3H6O2
D. C3H8O
E. C2H7N.
16. Complete and balance the following equations .
17. Define the following terms .
A. Fatty acids
B. Esters
C. Oils
D. Acid chlorides
18. Give an example of each of the following reactions .
A. Addition reaction
B. Substitution reaction
C. Elimination reaction
19. What are nucleoproteins ?
20. Explain briefly the hydrolysis product of nucleic acid .
21. What is the basic difference between the RNA and DNA in terms of structure ?
22. Write T at the end of the true statement and F at the end of the false one.
A. Adenosine consist of ribose sugar and pyrimidine base .
B. Hydrolysis of nucleotide gives phosphoric acid and nucleoside .
C. The nucleoside urosine is made up of uracil and ribose .
D. The nitrogen containing bases in the nucleic acids are either derivatives of pyrimidine or pyridine .
E. Uracil is found in both RNA and DNA .
23. Explain the relationship between the plants and animals in terms of synthesis and utilization of carbohydrates .
24. Despite that lactose and sucrose have the same formula (C12H22O11), they give different results to reducing agents . Explain why ?
25. Write (√ ) at the end of the correct statement and (X) at the of the incorrect one .
A. Carbohydrates were historically known as hydrates of carbon . ( )
B. Carbohydrates are synthesized by plants and animals from inorganic materials . ( )
C. Proteins are essential for living organisms as source of energy only .
D. Alkaline hydrolysis of fats gives fatty acids .
E. Proteins are polymeric units of amino acids .
F. Large value of iodine number for fats shows more unsaturated sites of that fat .
G. All the compounds in which the ratio of C to H is 2:1 are necessarily carbohydrates .
H. Nucleosides do not contain phosphate units.
26. Explain the following terms :
a) Fatty acids
b) Isoelectric point
c) Saturated fatty acids
d) Detergents
e) peptide bond.
27. Give reasons for the following statements.
A. All the naturally occurring amino acids are optically active except glycine .
B. 70% aqueous ethanol is better disinfectant than 100% ethanol (absolute) .
C. Chiral compounds are optically classified as D and L forms in their aqueous solutions .
D. Pentose and hexose sugar molecules can exist as ring form structure .
E. Enantiomers are different than epimers .
C
C
CH
2
OH
OH
OHH
C
C
CH
2
OH
OH
HOH
D -glyceraldehydeL-glyceraldehyde
CHO
C
C
CH
2
OH
OHH
OHH
CH
2
OH
C
C
CH
2
OH
O
OHH
ErythroseErythrulose
CHO
C
C
C
CH
2
OH
OH
OH
H
H
H
H
RiboseDeoxyribose
CHO
C
C
C
CH
2
OH
OH
OH
OH
H
H
H
C
C
C
C
C
CH
2
OH
OH
OHH
HOH
OH
OHH
H
CHO
C
C
C
C
CH
2
OH
HOH
OH
OHH
H
C
C
C
C
C
CH
2
OH
OH
OHH
HOH
H
OHH
OH
O
D-(+)-Glucose
D-(-)-Fructose
D-(+)-Galactose
C
C
C
C
C
CH
2
OH
OH
OHH
HOH
OH
OHH
H
D-(+)-Glucose
CHO
C
C
C
C
CH
2
OH
HOH
OH
OHH
H
O
D-(-)-Fructose
H
2
C
CH
H
2
C
OH
OH
OH
+
RCOOH
RCOOH
RCOOH
H
2
C
HC
H
2
C
O
CH
R
O
OC
R
O
OCR
O
+
3H
2
O
glycerol
fatty acids
triglyceride
Fatty acid+alcohol
Fat+H
2
O
esterification
Hydrolysis
H
2
N - C - H
COOH
H
H
2
N - C - H
CH
3
COOH
H
2
N - C - H
CH
2
OH
COOH
Glycine
Alanine
Serine
H
2
N - C - COOH
R
H
Amino group
Carboxylic group
HOOC - C - NH
2
H
H
+HCl
HOOC - C - NH
3
+
+Cl
-
H
H
NH
2
- C- COOH + NaOH
NH
2
- C- COO- + Na
+
+ H
2
O
H
H
H
H
reactas base
reactas an acid
H
2
N - CH - C
R
1
O
NH - CH - COOH
R
2
Peptide bond
H
2
N - CH
2
- C
O
OH
+ H
2
N - CH - C
O
OH
NH
2
- CH
2
- C -NH - CH - COOH
O
CH
3
Glycine
Gly-ala
+ H
2
O
CH
3
Alanine
O
OH
H
2
N - CH
2
- C
O
OH
Glycine
NH
2
- CH - C - NH - CH
2
- COOH
CH
3
O
H
2
N - CH - CH3
+
Alanine
Ala-gly
H
2
O
+
CH
3
6 CO
2
+ 6H
2
O + ENERGY
plant photosynthesis.
animal metabolism
C
6
H
12
O
6
+6O
2
CH
3
CH
3
Br
CH
3
- CH
2
- CH - CH - CH
3
A-
B-
C-
CH
3
COOH + CH
3
CH
2
OH
C
3
H
8
+ O
2
CH
3
CH
2
OH
[O]
[O]
C
6
H
5
OH + NaOH
C
C
C
C
C
CH
2
OH
OH
OHH
HOH
OH
OHH
H
CH
2
O
C
C
C
C
CH
2
OH
HOH
OH
OHH
H
C
C
C
C
C
CH
2
OH
OH
OHH
HOH
H
OHH
OH
O
D-(+)-Glucose
D-(-)-Fructose
D-(+)-Galactose
