biomolecules for biochemistry

7/30/2019 Biomolecules for Biochemistry

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UNIT 17 BIOMOLECULES

Syllabus

The Cell and Energy Cycle

Carbohydrates

Proteins

Nuclei acids

Lipids

Harmones

Vitamins

Biomolecules , common to living systems are carbohydrates, proteins , enzymes, lipids, vitamins,

hormones, nucleic acids and compounds for storage and exchange of energy such as adenosine

triphosphate (ATP) . Many of these biomolecules are polymers like the synthetic polymers. For example,

starch, proteins, nucleic acids are condensation polymers of simple sugars, aminoacids and nucleotidesrespectively. Most of the biochemical reactions take place in dilute solutions ( pH ~ 7) at body

temperatures (nearly 37C) and 1 atmospheric pressure. Biochemical reactions proceed with striking

selectivity and at incredible speed. Most of the biomolecules are very large and extremely complex.

Their reactions involve complex mechanisms. Biomolecules are related to the living organisms in the

following sequence :

Living organisms Organs Tissues Cells Organelles biomolecules (carbohydrates, proteins, lipids,

nucleic acids).

THE CELL

All the living creatures in the universe are made up of cells. The cells are the smallest units of life.

Their size is so small that they cannot be seen with a naked eye, but can be easily seen with a

microscope. The most remarkable characteristic of a cell is its ability to grow and reproduce daughter

cells which likewise produce new progeny cells.

The structure of the cell


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The important structural components of a cell are shown in Fig.

Structural components of a cell

1. Extra cellular matrix : This is the outermost wall of the cell. It is mainly made up of carbohydrates

such as cellulose, lignin etc. besides waxes and water.

2. Plasma membrane : It is a delicate elastic membrane present on the inner side of the extracellular

matrix. It is chiefly made up of phospholipids and proteins.

3. Cytosol : The cell is filled with a viscous translucent jelly like material called cytosol or the

cytoplasm. Within the cytoplasm are present a number of organelles as discussed below :

(i) Endoplasmic recticulum : It is either tubular or sac-like. Its outer surface is either smooth or

covered with ribosomes which make it rough. The ER provides a large surface area upon which

numerous biochemical reactions can occur. Ribosomes are made up of ribosomal RNA (60%) and

proteins (40%) . These assemble amino acids and synthesis proteins.

(ii) Golgi apparatus : It is packed with biomolecules such as polysaccharides, lipids etc. Since the golgi

apparatus secretes and delivers these macromolecules to other organelles , it is called export house of

the cell.

(iii) Mitochondria : It contains specific enzymes which are responsible for releasing storable and easilyusable energy in the form of ATP (adenosine triphosphate) through the oxidation of food materials

during respiration. It is called power house of the cell.

(iv) Lysosome : It contains several digestive enzymes. These are involved in a number of functions such

as digestion of food, defence against bacteria and viruses. They also destroy old and worn out organelles

of the cell. That is why lysosomes are called suicide bags of the cell.

(v) Nucleus : It is usually round in shape and contains a liquid substance called nucleoplasm in it. The

nucleoplasm contains DNA (deoxyribonucleic acid) and histone proteins. Since DNAs are units of genetic

information, nucleus is called control house of the cell.

Composition of the cell

A cell contains a number of organelles. Each organelle, in turn , contains a number of chemical

substances. The various substances present in the cell are mainly derived only from few elements, i.e.,

C, H, N, P and S. About 70% of the total mass of the cell is water; rest being mostly organic compounds.

These organic compounds are collectively referred to as biomolecules. Thus, biomolecules may be


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defined as complex lifeless chemical substances which form the basis of life, i.e., they not only build up

living creatures but are also responsible for their growth and maintenance.

Biomolecules are of two types :

(i) Micromolecules : These constitute about 3% of the total weight of the cell. Their molecular

masses lie in the range 100 to 1000 and contain upto 30 carbon atoms. Some important examples of

such biomolecules are lipids, vitamins, hormones etc.

(ii) Macromolecules : Some of the most important biomolecules present in the living cells are

carbohydrates, proteins and nucleic acids. All these are condensation polymers of simple monomer

molecules such as monosaccharides, a-aminoacids and nucleotides respectively. They are therefore

referred to macromolecules. These constitute about 26% of the total mass of the cell. The average

chemical composition of a cell is shown in Table.

Constituent

Percentage of total cell mass

Water

70

Proteins

15

Nucleic acids : DNA

RNA

1

6

Polysaccharides

2

Phospholipids

2

Miscellaneous small organic molecules

3

Inorganic ions


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(Na+, K+, Ca2+, Mg2+, Cl- etc.)

1

These macromolecules are essential for life.

Cellular Reactions

A living system involves a number of complex reactions. The cell which is the smallest unit of life

synthesizes a number of macromolecules from simple molecules. Broadly speaking , there are three

categories of reactions which occur simultaneously in a cell. The set of chemical reactions by which

various molecules of the cell are synthesised is called anabolism. Another set of reactions which involve

the degradation of complex organic molecules into smaller ones and ultimately to carbon dioxide and

water with liberation of energy is called catabolism. The catabolic reactions serve dual purpose. They

not only provide energy for the various cellular functions but also provide starting materials for anabolic

reactions. It is interesting to note that these anabolic and catabolic reactions are not simple reverse of

each other but usually occur by different chemical pathways. Both anabolism and catabolism arecollectively referred to as metabolism.

Besides these two sets of reactions, there is yet another set of chemical reactions within the cells ,

which is neither anabolic or catabolic. These reactions carry out various functions such as cell movement

, conduction of nerve impulses, contraction of muscles etc. All these cellular reactions require a constant

source of energy and occur with a high efficiency.

ENERGY CYCLE

Free Energy changes in Biological Reactions

The principles of thermodynamics are usually applicable to living as well as non-living systems. A

reaction is said to be thermodynamically feasible (spontaneous) if it is accompanied by a decrease in

free energy, ie DG is negative. Several catabolic reactions in a cell (such as stepwise degradation of

sugars to CO2 and H2O) are accompanied by a negative DG and hence are spontaneous. In contrast ,

most of the anabolic reactions are not spontaneous, i.e., DG is positive and hence require energy to

occur.

A reaction with DG > 0 can still be made to occur provided it is coupled to another reaction in which

DG is large and negative so that the net DG of two reactions is negative. For example, consider the

following two reactions :

(i) A B ; DG1 > 0 (DG1 is positive)

(ii) S P ; DG2 < 0 (DG2 is negative)

In accordance with the principles of thermodynamics, reaction (i) is not energetically favourable but

reaction (ii) is enerergetically favourable.


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Now suppose that these two reactions are coupled , i.e.,

DG1 + DG2 = DG ( negative)

The energy evolved in reaction (ii) is transferred to reaction (i) provided the net DG is negative. The

coupled reaction then becomes energetically favourable. Coupled reactions are usually indicated by the

formalism as shown in Fig.

Coupled reaction, DG is negative, favoured

Thus, from the above discussion , it follows that energy requiring steps (DG positive) are made to occur

by coupling them with energy producing steps (DG negative) provided that the net free energy change

of the two steps is negative.

All energy-requiring cellular reactions occur by principle of coupling with energy-releasing reactions.

In most of the cellular reactions, the energy releasing step, i.e., equivalent reaction (ii) is the hydrolysis

of adenosine triphosphate (ATP).

Adonosine triphosphate (ATP) The Energy Currency of the cells

Adenosine triphosphate often acts as a link between energy-requiring and energy-releasing processes in

the cells. ATP functions as carrier of chemical energy from energy releasing to energy-requiring

processes in the cell.

Adenosine triphosphate is a nucleotide containing adenine as nitrogen base (purine) , ribose as the

sugar and three interlinked phosphate units.

Structure of adenosine triphosphate (ATP)

ATP is an energy rich compound. The bond between the ribose sugar and first phosphoric acid unit is

an ordinary low-energy phosphate bond (i.e., energy is consumed when the bond is broken), but the

oxygen-phosphorus bonds between the other two phosphoric acid residues (shown by wavy lines) are

high - energy phosphate bonds (i.e., energy is released when these bonds are broken).

In ATP, the four negatively charged oxygen atoms are very close and hence the repulsive forcesbetween them are quite high.

Within the cell, the enzyme catalysed hydrolysis of ATP to ADP (adenosine diphosphate) is

accompanied by release of energy.


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ATP ADP + Pi ( DG < 0 )

ATP AMP + 2 Pi ( DG < 0 )

(where Pi is the phosphoric acid unit)

This is due the reason that the hydrolysis of oxygen-phosphorus bond reduces the repulsive forces and

thus releases a large amount of free energy. The coupling of energy-releasing reactions to energy-

requiring reactions in a cell not only makes reactions feasible which are otherwise not favoured but also

provides energy to the cells for carrying out a number of functions such as :

(i) Movement of the cells.

(ii) To do mechanical work during muscle contraction.

(iii) Uptake of nutrients.

(iv) To transport substances across the cell membranes against the forces of osmotic pressure.

(v) To perform electrical work in the conductance of nerve impulses.

(vi) To carry out important processes such as cell division.

(vii) To produce bioluminscence as in fireflies ( glow-worms)

The energy needed to make ATP from ADP and AMP

ADP + Pi ATP ( DG > 0 )

AMP + 2 Pi ATP ( DG > 0 )

is obtained by :

(i) Photosynthesis and

(ii) Catabolism of nutrients such as carbohydrates and lipids.

Thus , it is clear from the above discussions that ATP acts as an intermediate compound capable of

receiving energy from one reaction and transferring this energy to carry out another reaction. In

otherwords, ATP is the most important biomolecule in which the energy is easily transferred,

transformed and stored. That is why, ATP is usually referred to as the energy currency of the cells.

Photosynthesis and Energy

Energy for life processes basically comes from sun. During photosynthesis, green plants absorb

energy from the sun to make glucose and oxygen from carbon dioxide and water. Photosynthesis is a

complex process which occurs in a sequence of steps leading to the net reaction.


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The oxygen produced in the photosynthesis is the source of all the oxygen in the atmosphere.

Photosynthesis takes place generally in a series of light reactions which occur only in presence of light

energy and a series of dark reactions which can occur in dark because they do not depend on light

energy. The dark reactions proceed on high energy produced by the hydrolysis of ATP. Chloroplasts

present in the plant cell absorb the released energy. Here, through a series of reactions, water is

oxidised to oxygen and energy released is stored in bonds of energy storage compounds such as ATP. In

fact, ATP drives the dark reactions which convert CO2 and hydrogen (from water) into glucose and

other carbohydrates.

In presence of a suitable catalyst, ATP releases energy by undergoing a three step hydrolysis of

the P-O bond of its triphosphate groups (P-O bond). In the first step, ATP is hydrolysed to ADP and

releases 31 kJ mol-1 Gibbs energy. In the second step , ADP is converted into AMP (adenosine

monophosphate) and produces approximately the same amount of energy. In the last step of hydrolysis

of AMP to adenosine, only 14 kJ mol-1 Gibbs energy is released.

The living plants may convert the glucose produced during photosynthesis into disaccharides

polysaccharides , starches, cellulose, proteins or oils. The end product depends upon the type of plants

involved and complexity of its biochemistry. Plants thus, are primary source of energy for animals and

humans. This can be represented by oxidation of glucose which is reverse of photosynthesis.

C6H12O6 + 6 O2 6 CO2 + 6 H2O : DG = - 2880 kJ mol-1

Part of the energy is utilized while part of it is stored leading to the next reaction :

C6H12O6 + 36 ADP + 36 H3PO4 + 6 O2

6 CO2 + 36 ATP + 42 H2O

CARBOHYDRATES

Carbohydrates have the general formula Cx(H2O)y . These can be described as optically active

polyhydroxy aldehydes or ketones. Carbohydrates are also known as saccharides. They are the ultimate

source of most of our food . We clothe ourselves with cellulose in the form of cotton, linen and rayon.

We build furniture and houses from cellulose in the form of wood. Thus carbohydrates provide us with

basic necessities of life, food, clothing and shelter.

Classification

The carbohydrates can be divided into three major classes, depending upon whether theseundergo hydrolysis and if so, on the number of products formed.

(i) Monosaccharides : These cannot be hydrolysed to simpler compounds. Depending upon the total

number of carbon atoms in monosaccharides and aldehyde or ketone functional groups present, the

terms used for their classification are given in the Table.

Carbon atoms


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General terms

Aldehydes

Ketones

3

Triose

Aldotriose

Ketotriose

4

Tetrose

Aldotetrose

Ketotetrose

5

Pentose

Aldopentose

Ketopentose

6

Hexose

Aldohexose

Ketohexose

7

Heptose

Aldoheptose

Ketoheptose

(ii) Oligosaccharides : The oligosaccharides ( oligo , few) are carbohydrates which yield a few but

definite number ( 2 10) of monosaccharide molecule on hydrolysis.

For example, a disaccharide on hydrolysis yields two monosaccharide molecules.


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A trisaccharide like raffinose on hydrolysis gives glucose, fructose and galactose.

(iii) Polysaccharides : These are high molecular mass carbohydrates which yield many molecules of

monosaccharides on hydrolysis. Examples are starch and cellulose, both having general formula

(C6H10O5)n

In general monosaccharides and oligosaccharides are crystalline solids, soluble in water and sweet in

taste. These are collectively known as sugars. The polysaccharides , on the other hand are amorphous ,

insoluble in water and tasteless and are known as non-sugars.

The carbohydrates may also be classified as either reducing or non-reducing sugars. All those

carbohydrates which contain free aldehyde or ketonic group and reduce Fehlings solution and Tollens

reagent are referred to as reducing sugars. All monosaccharides whether aldose or ketose are reducing

sugars. In disacchaides if reducing group of the monosaccharides i.e., aldehydic or ketonic groups are

bonded , these are non-reducing sugars e.g sucrose, while others in which these functions are free are

reducing sugars e.g. maltose and lactose.

Monosaccharides

All carbohydrates are either mono-saccharides or get converted to monosaccharides on

hydrolysis. The most well known monosaccharides are ribose C5H10O5, glucose C6H12O6 and fructose

C6H12O6. Ribose is aldopentose, glucose is aldohexose while fructose is ketohexose as shown below :

D and L Designations

The sugars are divided into two families ; the D-family and L-family which have definite

configurations. These configurations are represented with respect to glyceraldehyde as the standard.

The glyceraldehyde may be presented by two forms as :

The D-configuration hasOH attached to the carbon adjacent to CH2OH on right while L-configurationhasOH attached to the carbon adjacent toCH2OH on left. The sugars are called D- or L

configuration depending upon whether the configuration of the molecule is related to D-glyceraldehyde

or L-Glyceraldehyde . By convention, a molecule is assigned D-configuration if theOH group attached

to the carbon adjacent to theCH2OH group (last chiral carbon) is on the right hand side irrespective of

the position of other groups. On the other hand, the molecule is assigned L-configuration if theOH

group attached to the carbon adjacent to theCH2OH group is on the left.


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It has been found that all naturally occurring sugars belong to D-series e.g. D-glucose, D-ribose

and D-fructose .

Presence of Asymmetric Carbon Atoms

On carefully examining the monosaccharide molecules, we observe that they contain one or

more chiral carbon atoms. For example, glucose has four chiral carbon atoms (carbons 2, 3, 4 and 5). We

know that if there are n chiral carbon atoms in a molecule, it will have 2n optical isomers. Therefore ,

glucose has 24 or 16 optical isomers. Three of these sixteen aldohexoses which occur as D-Glucose , D-

Galactose and D-mannose.

It is noted in all these three molecules , the configuration at C-5 is same (-OH on the right ) and

therefore , they belong to D-family.

Cyclic Structure of Monosaccharides

The monosaccharides give the characteristic reactions of alcohols and carbonyl group (aldehyde

or ketones). It has been found that these monosaccharides exist in the form of cyclic structures. We

know that aldehydes and ketones react with the hydroxyl group to form hemiacetals and acetals as,

Monosaccharides contain a number ofOH groups and an aldehyde or keto group. Therefore these canundergo intramolecular reaction (within the molecule) to form hemiacetals which result in cyclic

structures. In cyclization, theOH groups (generally of C5 or C4 in aldoses and C5 or C6 in ketoses)

combine with the aldehyde or keto groups. As a result , cyclic structures of five or six membered rings

containing one oxygen atom are formed. For example, glucose forms a ring structure. It forms six

membered ring of five carbon atoms and one oxygen atom.

Cyclic Structure of Glucose

Glucose forms a hemiacetal between theCHO group andOH group on the C5 atom. As aresult, C1 becomes asymmetric (chiral ) and forms two isomers (I) and (II) . These two isomers differ in

the orientation of H and -OH groups around C1 atom. These isomers are known as a-D-Glucose and b-D-

Glucose. Such pairs of optical isomers which differ in the configuration only around C1 is atom are called

anomers. The C1 atom is known as anomeric carbon atom.


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The above representations are called Fischer projection formulae.

Mutarotation

The two forms of a- and b-glucose exist in separate crystalline forms and have different melting

points and optical rotations. When either of these two forms are dissolved in water and allowed to

stand , these get converted into other form and the equilibrium mixture is formed with small amount of

the open chain form :

The formation of equilibrium mixture can be explained as :

The a- D glucose has specific rotation of +112 while b-D-glucose has a specific rotation of + 19.

When a-form is dissolved in water its specific rotation falls until a constant value of + 52.7 is reached.

On the other hand, when b-form is dissolved in water , its specific rotation increases and becomes

constant at + 52.7. This change in optical rotation of a solution with time to an equilibrium value is

called mutarotation (muto means to change). During mutarotation the ring opens and then again closes

either in the inverted position or in the original position giving a mixture of a- and b- forms. Thus, there

is an equilibrium mixture of a- and b-forms in the solution.

Pentose Structures

The structures of a-D-Glucose and b-D-glucose may be drawn in simple six membered ring called

pyranose structures. These resemble pyran which has a a six membered heterocyclic ring containing five

carbon atoms and one oxygen atom.

These structures were suggested by Haworth and are known as Haworth projection formulae or

pyranose structures.


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Note: To write pyranose structures for any monosaccharide (a- and b-D-glucose), draw a hexagon

with its oxygen atom at the upper right hand corner. The terminalCH2OH group is always placed above

the plane of the hexagon ring (in D-series) . Place all the groups ( on C1, C2, C3 and C4) which are

present on the left hand side in Fischer projection above the plane of the ring and all those groups onthe right hand side below the plane of the ring.

Cyclic structures for Fructose

Like glucose, fructose has also six membered hemiacetal ring structure. The hemiacetal is formed

by the intramolecular combination of keto group andOH group of C6 atom. As a result, C2 atom

becomes asymmetric and therefore , D-fructose has two possible isomers as a-D-frucose and b-D-

fructose which differ in the arrangement of CH2OH and OH groups around C2. These are shown below :

The above structures may be written in the Haworth forms as pyranose ring structures as :

In the free state D-fructose exists as a six membered ring or as a pyranose ring. However, in the

combined state as a component of disaccharides, it exists in the furanose form (5-membered

hemiketal). This structure is similar to furan ring which is five membered heterocyclic ring with one

oxygen atom.

The furanose structure can be obtained by internal ketal formation by combining keto group ( of C2) and

OH group of C5 as shown below.

These cyclic structures can also be written in the same way as for glucose.

Glucose (Dextrose ; Grape sugar) C6H12O6

Glucose occurs in nature in free as well as in combined form. It is present in sweet fruits and

honey. Ripe grapes contain 20% of glucose.

Preparation of Glucose


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1. From Sucrose (cane sugar) : If sucrose is boiled with dil HCl or H2SO4 in alcoholic solution, glucose

and fructose are obtained in equal amounts.

2. From starch : Commercially glucose is obtained by hydrolysis of starch by boiling it with dilute

H2SO4 at 393 K under pressure.

Properties of Glucose

Glucose has alcoholic and aldehydic groups and therefore , gives characteristic reactions of these

groups. However, the presence of the two functional groups influences their individual characteristics to

some extent.

Glucose undergoes the following chemical reactions.

1. Acetylation : Glucose reacts with acetic anhydride in presence of anhydrous zinc chloride to form

penta-acetyl glucose ( or gluose penta-acetate).

The formation of pentaacetyl derivaive shows the presence of five OH groups in glucose molecule.

2. Formation of glycosides : Glucose reacts with methyl alcohol in the presence of dry HCl gas

forming five isomeric ( a and b-) glycosides. The reaction indicates the presence of ring structures in

glucose in which freeCHO group is not present but is converted to -CHOH group.

The isolation of a-D-glucoside and b-D-glucoside indicates the existence of a-D-glucose and b-D-glucose

(cyclic hemiacetal ) structures for glucose.

3. Reduction : When an aqueous solution of glucose is treated with sodium amalgam or sodium

borohydride, it is reduced to sorbitol ( or glucitol ) a hexahydric alcohol.

4. Prelonged heating with HI acid and red phosphorus at 373 K gives n-hexane.


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The formation of n-hexane proves the straight chain open structure of glucose.

5. Oxidation : The oxidation of glucose occurs as :

(i) Mild oxidising agent such as bromine water, silver oxide , sodium hypobromite etc. oxidise

glucose to gluconic acid convertingCHO group toCOOH group.

Since glucose is readily oxidised , it acts as a strong reducing agent and reduces Tollens reagent

(ammoniacal silver nitrate) and Fehling solution.

(ii) Strong oxidising agents like nitric acid oxidise both the terminal groups ( -CHO andCH2OH ) of

glucose to give the dibasic acid, glucaric acid (also known as saccharic acid).

6. Reaction with hydrogen cyanide: Like aldehydes, glucose reacts with hydrogen cyanide forming

cyanohydrin.

It may be noted that this reaction creates a new asymmetric carbon atom and therefore, two

cyanohydrins differing only in the configuration at the aldehydic carbon are obtained. These are known

as D-Gluconitrile and D-mannonitrile.

Hydrolysius of cyanohydrin and reduction of the corresponding acid formed gives a clue regarding

the nature of the monosaccharide carbon chain.

6. Action with hydroxyl amine : Glucose condenses with hydroxylamine , NH2OH to form glucose

oxime.

7. Action with phenyl hydrazine : Glucose reacts with phenyl hydrazine like normal aldehydes

to form phenyl hydrazone. However, unlike normal aldehydes, glucose on warming with excess of the

reagent gives diphenyl hydrazones called osazones. It has been observed that during the reaction, three

equivalents of the reagent are consumed but the product contained only two phenyl hydrazine residues.

It has been found that after formation of phenyl hydrazone (II) the adjacentCHOH group is oxidised by


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a second phenyl hydrazene molecule to carbonyl group (III) and itself is reduced to aniline and ammonia.

Phenyl hydrazone of glucose (III) thus produced reacts with phenyl hydrazine to form glucosazone.

Glucosazone is a yellow crystalline compound, sparingly soluble in water and has a sharp melting point.

It is used in the identification of glucose.

It is very important to note that glucose, fructose and mannose form the same glucosazone. This

shows that they differ only in the configuration at C1 and C2.

8. Action with alkalies : When warmed with dilute alkalies, glucose is converted into a mixture of

glucose, fructose and mannose.

Same results are obtained when mannose or fructose are treated with alkali. The reaction is called Lobry

de Bruyn Van Ekenstein rearrangement.

10. Fermentation : A solution of D-glucose is readily fermented by the enzyme zymase present in yeast,

in the absence of air to form ethanol and carbondioxide.

DISACCHARIDES

The disaccharides are composed of two molecules of monosaccharides. On hydrolysis with dilute

acids or enzymes they yield two molecules of either same or different monosaccharides, e.g.

The disaccharides may be reducing or non-reducing depending upon the position of linkages between

the two monosaccharide units. If this glycoside linkage involves the carbonyl functions of both the

monosaccharide units, the resulting disaccharide would be non-reducing e.g. sucrose. If one of the

carbonyl functions in anyone of the monosaccharide units is free, the resulting disaccharide would be

reducing sugar, e.g. maltose and lactose.

SUCROSE , CANE SUGAR, C12H22O11

It is the most common disaccharide widely distributed in plants. It is manufactured either from

cane sugar or beet root. It is a colourless , crystalline and sweet substance soluble in water. Its aqueous

solution is dextrorotatory, [a]D = + 66.5. On hydrolysis with dilute acids or enzyme invertase, cane sugar

gives equimolar mixture of D-(+)-glucose and D-(-)-fructose.


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Sucrose is dextrorotatory but after hydrolysis gives dextrorotatory glucose and laevorotatory fructose.

Since the laevorotation of fructose (-92.4) is more than dextrorotation of glucose (+52.5) , the mixture

is laevorotatory. Thus, hydrolysis of sucrose brings about a change in the sign of rotation, from dextro

(+) to laevo(-) and such a change is known as inversion and the mixture is known as invert sugar.

Sucrose solution is fermented by yeast when the enzyme invertase hydrolyses sucrose to glucoseand fructose, enzyme zymase converts these monosaccharides to ethyl alcohol.

Haworth (1927) suggested the following structure for sucrose. It is a non-reducing sugar.

Haworths representation of sucrose

Maltose (Malt sugar ) C12H22O11

It is obtained by partial hydrolysis of starch by diastase , an enzyme present in malt (sprouted barley

seed).

On hydrolysis one mole of maltose yields two moles of D-glucose. It is a reducing sugar. The two glucose

units are linked through a-glycosidic linkage between C-1 of one unit and the C-4 of other unit.

Lactose (C12H22O11)

Lactose occurs in milk and is also called milk sugar. Hydrolysis of lactose with dilute acid yields equimolar

mixture of D-glucose and D-galctose. It is a reducing sugar. It gets hydrolysed by emulsin, an enzyme

which specifically hydrolyses b-glycosidic linkages.


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PLOYSACCHARIDES

These carbohydrates in which hundreds or even thousands of monosaccharide units are joined

together by glycosidic linkages. Some examples of polysaccharides are starch, cellulose and dextrins.

However, starch and cellulose are most important of polysaccharides.

STARCH , AMYLUM (C6H10O5)n

Starch occurs in all plants, particularly in their seeds. The main sources are wheat, maize, rice,

potatoes, barley and sorghum. Starch occurs in the form of granules, which vary in size and shape

depending on their plant source. Starch is a white amorphous powder , insoluble in cold water. Its

solution in water gives a blue colour with iodine solution. The blue colour disappears on heating and

reappears on cooling. On hydrolysis with dilute acids or enzyme, starch breaks down to molecules of

variable complexity ( n > n) , maltose and finally D-glucose.

Starch does not reduce Fehlings solution or Tollens reagent and does not form an osazone, indicating

that all hemiacetal hydoxyl group of glucose (C -1) are linked with glycosidic linkages. Starch is a mixture

of two polysaccharides, amylose and amylopectin. Natural starch has approximately 10 20 % of

amylose and 80 90 % of amylopectin.

Amylose is water soluble and gives a blue colour with iodine. It is a straight chain polysaccharide

having only D-glucose units joined together by a-glycosidic linkages involving C-1 of one glucose and C-4

of the next. It can have 100 3000 D-glucose units i.e., its molecular mass range from 10,000 to

500,000.

Amylopectin is a branched chain polysaccharide insoluble in water which does not give blue

colour with iodine. It is composed of chains of 25 30 D-glucose units joined by a-D glycosidic linkages

between C-1 of one glucose unit and C-4 of the next glucose unit (similar to amylose). However, these

chains are connected with each other by 1,6-linkages. Starch is a major food material for us. It is

hydrolysed by enzyme amylase present in saliva. The end product is glucose which is an essential

nutrient.


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CELLULOSE, (C6H10O5)n

It is the chief constituent of the cell walls of plants. Wood contains 45 50 % while cotton contains 90

95 % cellulose. It is a colourless amorphous solid which decomposes on heating. It is largely linear and its

individual strands align with each other through multiple hydrogen bonding. This lends rigidity to its

structure. It is thus used effectively as a cell wall material.

Cellulose does not reduce Tollens reagent or Fehlings solution. It does not form osazone and is not

fermented by yeast. It is not hydrolysed so easily as starch, but on heating with dilute sulphuric acid

under pressure yields only glucose.


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Cellulose is straight chain polysaccharide composed of only D-glucose units , which are joined by b-

glycoside linkages between C-1 of one glucose unit and C-4 of the next glucose unit. The molecular mass

of cellulose is in the range of

50,000 500,000 ( 300 2500 D-glucose units). It is used in the manufacture of rayon and gun cotton.

Large population of cellulolytic bacteria present in the stomach (rumen) of ruminant mammals

(cattle, sheep etc.) breaks down cellulose with the help of enzyme cellulase. It is then digested and

converted into glucose. Human stomach is different and does not have enzyme capable of breaking

cellulose molecules.

PROTEINS

Proteins are high molecular mass complex biopolymers of amino acids present in all living cells.

The protoplasm of plant and animal cell contains 10 20% proteins. The name protein is derived from

Greek word proteios meaning of prime importance. As enzymes these catalyze biochemical reactions, as

hormones they regulate metabolic processes and as antibodies they protect the body against toxic

substances. All proteins contain the elements carbon, hydrogen, oxygen , nitrogen and sulphur. Some of

these may also contain phosphorus, iodine and traces of metals like iron, copper , zinc and manganese.

All proteins on partial hydrolysis gives peptides of varying molecular masses which on complete

hydrolysis give amino acids.

AMINO ACIDS

Amino acids contain amino (-NH2) and carboxyl (-COOH) functional groups. Depending upon the

relative position of two functional groups in the alkyl chain the amino acids can be classified as a,b,g ,d

and so on. Only a-amino acids are obtained on hydrolysis of proteins. These may contain other

functional groups also.

Nomenclature of Amino acids

All amino acids have trivial names, even those for which IUPAC names are not cumbersome e.g.

H2NCH2COOH is better known as glycine rather than -amino acetic acid or 2-aminoethanoic acid.

These trivial names usually reflect the property of the compound or its source e.g glycine is so named

since it has sweet taste ( glykos means sweet) and tyrosine was first obtained from cheese ( tyros


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means cheese). Amino acids are generally represented by a three letter symbol, sometimes one letter

symbol is also used. The structures of some commonly occurring amino acids along their 3-letter and

1-letter symbols are given in the TABLE.

Name of the amino acid

Characteristic feature of side chain, R

Three letter Symbol

One letter code

1. Glycine

H

Gly

G

2. Alanine

-CH3

Ala

A

3. Valine*

(CH3)2CH-

Val

V

4. Leucine*

(CH3)2CH-CH2-

Leu

L

5. Isoleucine*


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Ile

I

6. Arginine*

Arg

R

7. Lysine*

H2N-(CH2)4-

Lys

K

8. Glutamic acid

HOOCCH2CH2-

Glu

E

9. Aspartic acid

HOOCCH2-

Asp

D

10. Glutamine

H2NCOCH2CH2-

Gln

Q

11. Asparagine

H2NCOCH2-

Asn


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N

12. Threonine*

CH3CHOH-

Thr

T

13. Serine

HOCH2-

Ser

S

14. Cysteine

HS-CH2-

Cys

C

15. Methionine*

CH3-S-CH2CH2-

Met

M

16. Phenylalanine*

C6H5CH2-

Phe

F

17. Tyrosine

(p)HO-C6H4-CH2-

Tyr

Y


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18. Tryptophan*

Trp

W

19. Histidine

His

H

20. Proline

Pro

P

*Essential amino acid

Classification of Amino Acids

Amino acids are classified as acidic, basic or neutral depending upon the relative number of

amino and carboxyl groups in their molecule. Equal number of amino and carboxyl groups make it

neutral, more number of amino than carboxyl groups make it basic and more carboxyl as compared to

amino make it acidic. The amino acids, which can be synthesized in the body , are known as non-

essential amino acids and those which cannot be synthesized in the body must be obtained through

diet, are known as essential amino acids.

Physical properties of a-amino acids

Amino acids are usually colourless, crystalline solids. These are water soluble high melting solids

and behave like salts rather than simple amines or carboxylic acids. This behaviour is due to the

presence of both an acidic(carboxyl group) and a basic amino group in the same molecule. In aqueous

solution the carboxyl group can lose a proton and amino acid can accept a proton, giving rise to a dipolarion known as zwitter ion. This is neutral but contains both positive and negative charges.

In zwitter ionic form, amino acids show amphoteric behaviour as they react both with acids and

bases.


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In acidic solution, the carboxylate function (-COO-) accepts a proton and gets converted to carboxyl

substituent (-COOH) , while in basic solution the ammonium substituent (+NH3) changes to amino group

(-NH2) by loosing a proton.

In acidic solution, an amino acid exists as a positive ion and migrates towards the cathode in an electric

field, while in alkaline solution it exists as a negative ion and migrates towards anode. At certain

hydrogen ion concentration (pH) , the dipolar ion exists as a neutral ion and does not migrate to either

electrode. This pH is known as isoelectric point of amino acid. The isoelectric point depends on other

functional groups in the amino acid, and neutral amino acids have isoelectric points in the range of pH

5.5 to 6.3. At the isoelectric point the amino acids have least solubility in water and this property is

exploited in the separation of different amino acids obtained from the hydrolysis of proteins.

Except glycine, all other naturally occuring a-amino acids are optically active, since the a-carbon

atom is asymmetric. These exist both in D and L forms. Their Fischer projection formulae are written

with carboxyl group (-COOH) at the top. In the D form amino group (-NH2) is written on the right side

and L-form on the left hand side. This is similar to the placement of hydroxyl group (-OH) in

glyceraldehydes, the reference compound for carbohydrates.

D and L refer to the configuration of the amino acid molecule about the asymmetric carbon

atom. Most naturally occurring amino acids have L-configuration.

Chemical properties of a-amioacids

Amino acids form salts with acids as well with bases. Their chemical reactions are similar to primary

amines and carboxylic acids.

PEPTIDES

Proteins on hydrolysis breaks down into smaller fragments called peptides which finally give a-

amino acids.

The peptide bond : The reaction between two molecules of the same or different amino acids, proceed

through the combination of the amino acid group of one molecule with carboxyl group of the other. This

results in the elimination of a water molecule and the formation of a peptide bondCO-NH. For

example, when carboxyl group of glycine combines with the amino group of the alanine, we get,

glycylalanine.


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Glycylalanine ( Gly Ala)

Alternatively, the amino group of glycine may react with carboxyl group of alanine , resulting in the

formation of a different dipeptide, alanylglycine ( Ala- Gly ).

In both the dipeptides i.e., glycylalanine or alanylglycine, there are free functional groups at both

ends. These groups can further react with relevant groups of the other amino acids forming tri, tetra,

penta peptides and so on.

PLYPEPTIDES

As a convention the structure of polypeptides is written in a way that the amino acid with free

amino(-NH2) group is known as N-terminal residue is written on the left hand side of the polypeptide

chain and the amino acid with free carboxyl group ( C- terminal residue) is written on the right hand

side of the chain. Thus, a tripeptide , alanylglycylphenylalanine is represented as follows :

Ala Gly - Phe

The name of any polypeptide is written starting from the N-terminal residue. The suffix ine in the

name of the amino acid is replaced by -yl (as glycine to glycyl, alanine to alanyl etc.) for all amino acids

except the C-terminal acid. This nomenclature is not used frequently. Instead , the three letter or one

letter abbreviation for the amino acid is used., e.g. the above tripeptide is named as Ala Gly Phe or

A G F.

Relatively shorter peptides are known as oligopeptides whereas longer polymers are called

polypeptides. A polypeptide with more than hundred or so amino acid residues , having molecular mass

higher than 10,000 is called protein. However, the distinction between a polypeptide and a protein is

not sharp. Polypeptides with fewer amino acids are likely to be called proteins if they ordinarily have a

well-defined conformation of a protein.

Polypeptides are amphoteric because of the presence of terminal ammonium and carboxylate

ions as well as the ionised side chains of amino acid residues. Therefore, they titrate as acids or bases

and have an isoelectric point at which they are frequently least soluble and have the greatest tendency

to aggregate.

The functions of proteins are important and varied in bio-systems, however, the smaller peptides

have important functions though their total content in tissues is small compared to proteins. Some of

these are very potent. Most of the toxins (poisonous substances) in animal venoms and in plant sources

are polypeptides. Minute amount of some oligopeptides with as few as three modified amino acid

residues are effective as hormones. A derivative of the dipeptide, aspartylphenylalanine methyl ester

(aspartame ) is 160 times as sweet as sucrose and is used as a sugar substitute.


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Problem

01. What is the name of the polypeptide whose structure is shown ?

02. A tripeptide on complete hydrolysis gives glycine, alanine and phenylalanine. Using three letter

symbols write down the possible sequences of the tripeptide.

Labels: UNIT 17 BIOMOLECULES

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PLUS TWO

Atomic Structure and Chemical Bonding

Solid State

Chemical Equilibrium -II ( Ionic Bonding)

Thermodynamics

Electrochemistry

Chemical Kinetics

Surface Chemistry

The P-block elements

d & f Block Elements

Metallurgy

Co-Ordination Compounds and Organometallics

Stereochemistry

Organic Compounds with Functional Groups Containing Oxygen-I

Organic Compounds with Functional Graoups Containing Oxygen-II

Organic compounds with Functional Groups Containing Nitrogen

Polymers


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Bio Molecules

Chemistry in Everyday Life

QUESTIONS

Atoms and Molecules

1.

biomolecules for biochemistry

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