CHEMISTRY OF CARBOHYDRATEI- DEFINITION :

Carbohydrate are aldehyde or ketone derivatives of polyhydric alcohols or any substances derived from them .

II- Importance of carbohydrates :carbohydrates are widely distributed both in plants and in animal

tissues . In plants , they are produced by photosynthesis . Carbohydrates constitute about 60% of our diet . They are important because :1- They serve as a source of energy e . g . glucose .2- They form structural elements in animal and plant cell .3- Carbohydrates may combine with lipids ( glycolipids ) or protein (glucoproteins) , Both enter in the structure of cell membrane and form the ground substances between tissues .

III- Classification of carbohydrates :A- Monosaccharides : contain one sugar unit .B- Disaccharides : contain two sugar units .C- Oligosaccarides : contain 3 – 10 sugar units .D- Polysaccarides : contain more than 10 sugar units .

IV- Monosaccarides: They are the simplest units of carbohydrate i . e . on hydrolysis , they can not give a simpler form . the general formula is Cn(H2O)n

A- Naming of monosaccarides : 1- According to the presence of aldehyde or ketone group :

a- Aldoses : monosaccarides containing aldehyde group ( -CHO ) , The suffix –ose means sugar .b- Ketoses : monosaccarides containing ketone group ( -C=O ) ,

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2- According to the number of carbon atoms :a- Trioses : monosaccharides containing 3 carbons .b- Tetroses : 4 carbons .c- Pentoses : 5 carbons .d- Hexoses : 6 carbons .e- Heptoses : 7 carbons . 3- According to both presence of aldehyde or ketone groups and number of carbon atoms :a- Aldotrioses and ketotrioses .b- Aldotetroses and ketotetroses .c- Aldopentoses and ketopentoses . d- Aldohexoses and ketohexoses .

4- System for numbering the carbons :The carbons are numbered starting from aldehyde group as carbon number 1. In case of ketoses the carbon of ketone group group is the carbon number 2.

B- Classification of monsaccharides :1- Trioses : monosaccharides containing 3 carbon atoms .

a- Aldotrioses : Glyceraldehyde “glycerose” . b- Ketotrioses : Dihydroxyacetone .

2- Tetroses : monosaccarides containing 4 carbon atoms : a- Aldotetroses : Erythrose and threose . b- Ketotetrose : Erythrulose .

Note : The suffix-ulose means Keto sugar . 3- Pentose : monosaccharides containing 5 carbon atoms . a- Types :

1) Aldopentoses : Ribose , arabinose , xylose and lyxose .2) Ketopentoses : Ribulose and xylulose .

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b- Importance ( function ) of pentoses : 1) Ribose and deoxyribose enter in the structure of nucleic acids RNA and DNA .2) Ribose enters in the structure of ATP , GTP and other high energy phosphate compounds .3) Ribose enters in the structure of coenzymes NAD , NADP and flavoproteins .4) Ribose phosphate and ribulose phosphate are intermediates in pentose phosphate shunt ( a minor pathway for glucose oxidation ).5) Arabinose and xylose are constituents of glycoprotein in plants and in animals .6) Lyxose is a constituent of lyxoflavin isolated from human heart muscle . 7) Xylulose is an intermediate in uronic acid pathway ( a minor pathway for glucose oxidation ) .

4- Hexoses :a- Types :

1) Aldohexoses : glucose , glactose and mannose . 2) Ketohexose : fructose .

b- Importance : 1) Glucose is the most importance sugar in carbohydrates :

a) Dietary carbohydrates are absorbed in the form of glucose . b) In the liver and other tissues , glucose is converted to all carbohydrates in the body e . g . glycogen , galactose , ribose and fructose . c) Glucose is the major source of energy in mammals .

2) Fructose “ Fruit sugar “ : a) It can be converted into glucose in liver . b) It is the main source of energy in mammals .

3) Galactose : a) It can be converted into glucose in liver .b) Synthesized in mammary gland to make the lactose of milk ( milk sugar ) .

4) Mannose : A constituent of many glucoproteins . 5- Heptoses :

As sedoheptulose : is formed in the oxidation of glucose through the pentose phosphate pathway .

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Ring ( cyclic ) Structure of sugars The simple open formula of sugars fails to explain some reactions e . g . glucose which has aldehyde group does not give all the reactions of aldehyde. This indicates that the –CHO group must be masked or combined in some way . In solution , the sugar which has an aldehyde group undergoes the following : 1- Hydration of aldehyde group to form group ( alcohol ) .2- Intermolecular reactions occur by subsequent condensation between one of the –OH of aldenol group and the –OH group of C4 or C5 to form ring structure ( hemiacetal structure ), here the carbonyl group becomes asymmetric carbon atoms . 3- If the remaining –OH is on the right side , so it is α - sugar . If the remaining –OH is on the left side , so it is β - sugar .

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4- Pyranose and furanose :A) The 1-5 ring form is called pyranose as it resembles the organic

compound pyran e . g . α and β glucopyranose .B) The 1-4 ring form is called furanose as it is resmbles the organic

compound furan e . g . α and β glucofuranose .

5- Haworth and chair forms : Cyclic structure of sugars may be present in the form of Haworth or Chair forms. In Haworth formula, the arrangement of H and –OH groups around carbon atoms is as follows :

1) All the –OH groups on the right side in old ring structure are written downwards in Haworth formula .

2) All the –OH groups on the left side in old ring structure are written upwards in Haworth formula .

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Glucose in solution is present mainly (99 %) as glucopyranose and (1% ) as glucofuranose, of 99 % of glucopyranose ( 36 % ) are present as α - D form and ( 63 % ) as β – D form .

V- ASYMMETRIC CARBON ATOM : is the carbon which attached to 4 different groups or atoms .

Any substances containing one or more asymmetric carbon atom shows 2 properties ; optical activity and optical isomerism . A- Optical activity :

is the ability of substance to rotate plane polarized light either to the right or to the left . 1- If the substance rorates plane polarized light to the right so it is

called : dextrorotatory or d or ( + ) . If it rotates it to the left so it is called : levorotatory or “l” or ( - ) .

2- Glucose contains 4 assymmetric carbon atoms . it is dextrorotatory , so it is sometimes named dextrose . Fructose contains 3 asymmetric carbon atoms . It is levorotatory so it is sometimes called : levulose .

3- Specific rotation : it is the angle of rotation specific for each optically active substance when the concentration of substance when the concentration of substance is 100 g / dl and the length of measuring tube is 10 cm . e.g specific rotation for glucose is ( +52.5º ) and for fructose is ( -91º )

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4- Racemic mixture : It is the mixture containing equal number of molecule of 2 optically active sugars ; one is dextrorotatory and the other is levorotatory . Thus , it shows no optical activity ( Provided that the angle of rotation is equal in both sides ) .

5- Resolution : It is the separation of optically inactive racemic mixture into its optically active substance .

B- Optical isomerism : It is the ability of substance to present in more than one form

(isomer) . A substance containing one asymmetric carbon atom can exist in a number of isomers = 2n where n is the number of asymmetric carbon atoms . e . g . glucose has 4 asymmetric carbon atoms so the number of its isomers equal 24 = 2 x 2 x 2 x 2 = 16 isomers . 1- Configuration ( Enantiomers )

A)The simplest carbohydrates are monosaccharides trioses ; for example glyceraldehyde which has one asymmetric carbon and thus 2 optically active forms : L and its mirror image D forms .

Reference sugar : It is glyceraldehyde which may be present in (D) form in which –OH group attached to asymmetric carbon atom is on the right side and ( L ) form in which the same –OH group is on the left side .

1) All other monosaccharides are considered to be derived from reference sugar glyceralddehyde . They are classified into D and L forms according to the position of –OH attached to the carbon atom adjacent to last -CH2OH e . g . carbon atom number 5 in glucose .

2) Most of the monosaccharides occuring in mammal are of D configuration ( form ) . However, a sugar may be dextrorotatory ( d ) or levorotatory ( l ) irrespective of its D or L forms .

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2- Anomeric carbon and anomers : A) Anomeric carbon : is the asymmetric carbon atom obtained from

active carbonyl sugar group : carbon number 1 in aldoses and carbon number 2 in ketoses .

B) Anomers : These are isomers obtained from the change of position of hydroxyl attached to the anomeric carbon e . g . α and β glucose are 2 anomers . Also α and β fructose are 2 anomers .

C) Mutarotation : It is a gradual change of specific rotation of any optically active substance having free aldehyde ( -CHO ) or ketone (C=O) group .

1) α -Glucose freshly dissolved in water has specific rotation of +112 . 2) β -Glucose when freshly dissolved in water , has specific ratation of

+19 . 3) when both anomers are left for some times , α and β sugars slowly

change into an equilibrium mixture which has specific rotation of +52.5

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3- Aldose – Ketose isomerism : Fructose has the same molecular formula as glucose but differs in structure formula . One contains keto group (C=O) and the other contains aldehyde group ( -CHO ) . Both are isomers. 4- Epimeric carbon and epimers :

A) Epimeric carbon is the asymmetric carbon atom other than carbon of aldehyde or Ketone gbroup e . g . carbons number 2 , 3 and 4 of glucose .

B) Epimers : are isomers resulting from the change of position of groups around the epimeric carbons . Glucose , glactose and mannose are epimers .

1) Glucose has 3 epimeric carbons , 2 , 3 and 4 . 2) Galactose : epimer of carbon 4 . 3) Mannose : epimer of carbon 2 .

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VI- PROPERTIES OF MONOSACCHARIDES :A- Physical properties :

1- All monosaccharides are soluble in water . 2- All monosaccharides show the property of optical activity . 3- All monosaccharides can exist in α and β forms . 4- All monosaccharides can undergo mutarotation .

B- Chemical Properties : 1- Oxidation : oxidation of sugars give acids 2- Reduction : Reduction of carbonyl group gives the corresponding

alcohol e . g . glucose gives sorbitol , ribose gives ribitol , galactose gives galacticol.

3- Reducing sugars : Sugars containing free aldehyde or ketone group can reduce other reagents e . g . they can reduce cupric ions of Fehling and Benedict’s reagents into cuprous ions :

Cupric ( blue ) + sugar Cuprous ( red ) + oxidized sugarA) These tests are one of the earlist tests for the presence of sugar in

urine of diabetics . B) These tests are nonspecific , because they can be reduced also by

other hexoses or other reducing compounds as vit . c . 4- Reactions with phosphoric and sulphuric acids : A) Reactions of phosphoric acid with monosaccharides gives

phosphate esters e . g . glucose gives glucose-6-phosphate and glucose-1-phosphate . Phsphorylated sugars are important intermediates in carbohydrate metabolism .

B) Reaction of sulphuric acids : This acid is a dehydrating agent ,

removing 3 molecules of H2O from the sugar giving a compound called furfural . This compound can condense with αβ -naphthol to give a violet ring . This is the idea of Molish’s test ; a general test for all carbohyrates .

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5- Fermentation : Fermentation is the action of bacterial or Yeast enzymes on carbohydrate .

A) Fermentation of sugas give ethyl alcohol and CO2 . B) All D-monosaccharides are fermentable .

C6H12O6 2 CH3-CH2-OH + 2 CO2

6- Osazone formation : Osazone are characteristic crystals resulting from the reaction of sugars with phenylhydrazine . All sugars having free carbonyl group can form osazone crystal .

SUGAR DERIVATIVES :A- Sugar acids : are produced by oxidation of carbonyl carbon , last hydroxyl carbon or both .

1- Aldonic acids : Oxidation of carbonyl carbon to carboxylic group gives aldonic acid e . g . glucose is oxidized to gluconic acid .

2- Uronic acid : Oxidation of last hydroxyl carbon gives uronic acid e. g . glucose is oxidized to glucuronic acid .

3- Aldaric acids : These are dicarboxylic acids produced by oxidation of both carbonyl carbon and last hydroxyl carbon e . g . glucose is oxidized to glucaric acid ( saccharic acid ) .

B- Sugar alcohols : Monosaccharides , both aldoses and ketoses may be reduced at carbonyl carbon to the corresponding alcohol ;

1- Glucose is reduced to sorbitol ( gulcitol ) .2- Galactose is reduced to galacticol ( dulcitol ) .3- Mannose is reduced to mannitol . 4- Fructose is reduced to mannitol and sorbitol . 5- Ribose is reduced to ribitol , a constituent of vitamin B2 ( riboflavin 6- Insitol = cyclitol

It is a sugar alcohol derived from glucose . It is a member of vitamin B complex .

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C- Deoxysugars : Are sugars in which one of the hydroxyl groups has been replaced by a hydrogen atom i.e one oxygen is missed .

1- Deoxyribose : occuring in nucleic acid DNA . 2- L-Fucose ( 6-deoxygalactose ) : occurring in glycoproteins .

D- Amino sugars : In these sugars , the hydroxyl group is replaced by an amino or an acetylamino group . 1- Amino sugars are constituents of glycoproteins , gangliosides and glucosaminoglycans . 2- Examples :

A) Glucosamine : occurring in heparin and hyaluronic acid . B) Galactosamine : occurring in chondroitin sulphate . C) Mannosamine : occurring in neuraminic and sialic acids .

E- Amino sugar acids : There are a condensation of amino sugars and some acids . They are occuring in glycoproteins . Examples include neuramnic acid ( NANA ) and sialic acid which is N-acetyl neuramininc acid .

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VIII- GLYCOSIDIC BOND AND GLYCOSIDES :Glycosidic bond : It is hhte bond between a carbohydrate and another compound to form a complex carbohydrate .

1- This bond is between the hydroxyl group of anomeric carbon of

monosaccharides ( carbon 1 in aldoses or carbon 2 in ketoses ) and another compound which may be : A) Another monosacccharides to form disaccharides glycosides as

maltose , lactose and sucrose .

B) Aglycone i.e . noncarbohydrate to form glycoside .

2- O and N-glycosides : A) If the monosaccharides is attached to –OH group of another sugar

glycogen , the resulting structure is an O-glycoside and the bond is called acetal link .

B) If the monosaccharides is attached to –NH2 of a glycone , the resulting structure is N-glycoside .

C) All sugar-sugar glycosidic bonds are O type linkage . If the fitst sugar is glucose , the resulting compound is glucoside . if galactose , a galactoside and so on .

B- Examples of glycosides : 1- Disaccharides 2- Sugar nucleotide as ATP , GTP and other nucleotides : a

glycone here is purines and pyrimidines . 3- Glycolipids : as cerebrosides . 4- Glycoproteins . 5- Cardiac glycosides : Aglycone here is steroid

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II- DISACCHARIDES :These are formed by condensation of 2 molecules of

monosaccharides bond together by glycosidic bond . Its general formula is Cn(H2O)n-1 A- The most important disaccharides are :

1- Maltose = α- glucose + α-glucose (α 1-4 glucosidic bond ) .2- Isomaltose = α-glucose + α-glucose (α 1-6 glucosidic bond ) .3- Lactose = β-glucose + β -galactose (β 1-4 glucosidic bond ) . 4- Sucrose = α-glucose + β -fructose (α 1-B2 glucosidic bond ) . 5- Cellobinose = β-glucose + β -glucose (β 1-4 glucosidic bond ) . 6- Trehalose = α-glucose + α-glucose (α 1-1 glucosidic bond ) .

B- Naming of glycosidic bonds : glycosidic bonds sugars are named according to :

1- The numbers of the connected carbons . 2- The position of the anomeric carbon of the sugar , If it is in α

position , the linkage is an α-bond . If it is in the β position . the linkage is a β -bond .

3- Example : lactose consists of β -glucopyranose and β -galactopyranose . The bond is between carbon 1 of β -galactopyranose and carbon 4 of glucopyranose . The bond is therefore β 1-4 galactosidic linkage .

C- Maltose : Also called malt sugar : 1- Structure : It is formed of 2 molecules of α-D glucopyranose

linked together by α 1-4 glucosidic bond . 2- Sources :

Malt . Maltose is produced during digestion of starch by amylase enzyme

3- Properties : Maltose contains free carbonyl ( aldehyde ) group so having the following properties :

A) It is a reducing agent ( can reduce Benedict’s reagent) . B) It can be present in α and β forms . C) It can show mutarotation . D) It can form characterstic osazone crystals .

D- Isomaltose : 1- Structure : It is similar to maltose , being formed of 2 molecules

of α-D glucopyranose , but linked together by α 1-6 glucosidic bond .

2- Sources : Isomaltose is produced during digestion of starch and glycogen by amylase enzyme .

3- Properties : The same as maltose .

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E- Lactose : 1- Structure : It is formed of 2 molecules of β -D-galactopyranose

and β -D-glucopyranose linked together by β 1-4 glucosidic ( galactosidic ) bond.

2- Sources : it is the sugar present in milk . In human milk , its concentration is 7.4 g/dl . It may appear in urine in late pregnancy and during lactation .

3- Properties : Lactose contains free carbonyl group , so having the following properties :

A) It is reducing sugar ( can reduce Benedict’s reagent ) . B) It can present in α and β forms . C) It can be show mutarotation .D) It can form characteristic osazone crystals . E) Lactose is digested by intestinal enzyme called : Lactase into

galactose and glucose. Deficiency of this enzyme stops the digestion of lactose. this leads to its fermentation by intestinal bacteria , diarrhea and abdominal distension .

F- Sucrose : 1- Structure : it is formd of 2 molecules of α-D-glucopyranose and β -D-fructofuranose linked by α1 B 2 glycosidic bond . 2- Sources : cane and beet sugar . It is also present in pine apple and carrot . 3- Properties : sucrose contains no free carbonyl group ( because both the anomeric carbons ; carbon 1 of α-glucose and carbon 2 of β -fructose are involved in glycosidic bond ) so fructose has the following properties :

A) It is not a reducing sugar ( can not reduce Benedict’s reagent ) . B) It can not be present in α and β forms . C) It can not show mutarotation . D) It can not form osazone crystals . E) Sucrose is dextrorotatory . On hydrolysis by inverase ( sucrase )

enzyme , it gives a mixture of equal number of glucose and fructose molecules . This mixture is called invert sugar and it is levorotatory .

Glucose-Fructose Glucose + Fructose Sucrose dextrorotatory levorotatory Dextrorotatory +52.5 -91

Invert sugarLevorotatory

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G- Cellobiose : 1- Structure : It is formed of 2 units of β -D- glucopyranose linked by β 1----------4 glucosidic bond . 2- Sources : It is obtained by partial hydrolysis of cellulose .

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POLYSACCARIDES :These are carbohydrates , formed of more than 10 sugar units .

They are classified into : A- Homopolysaccharides which contain repeated same sugar units . B- Heteropolysaccharides which contain repeated different sugar units .

A- Homopolysaccharides : They include : 1- Starch ( also called glucoson or glucan ) . Structure : Starch granule is formed of inner (a) and outer (b) layers :

1) Inner layer : called amylose . It constitutes 15-20 % of the granule and formed of non branching helical structure of glucose units linked together by α 1 – 4 glucosidic bonds . 2) Outer layer : called amylopectin . It constitutes 80-85 % of the granule and formed of branched chain . Each chain is composed of 24-30 glucose units linked together by α 1-6 glycosidic bonds at the branch points .

Sources : It is the most important food source of carbohydrate , it is found in cereals , potatoes , legumes and other vegetables .

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Properties : 1- Starch gives blue colour with iodine . Amylopectin gives red

colour with iodine . 2- Partial hydrolysis ( digestion ) by amylase enzyme gives various

forms of dextrins . 2- Dextrins : These are hydrolytic products of starch . They are formed of α-glucose units but simpler than starch . They include amylodextrin , erythrodextrin and achrodextrin . 3- Glycogen : ( also called animal starch ) : Structure : It is highly branched chain homopolysaccharide . Each branch is composed of 12-14 glucose units , linked together by 1-4 glycosidic bonds and by 1-6 glycosidic bond at branch point (like amylopectin) .Sources : Glycogen is the storage form of carbohydrates in human and animals . It is synthesized and stored in liver , muscles and tissues . Properties : It gives red colour with iodine . 4- Cellulose : a- Structure : It is long straight non branching chains of glucose units (β -D-glucopyranose ) linked together by β 1---4 glycosidic bond . The chains are strenthened by cross linked hydrogen bonds . b- Sources : Cellulose is the chief constituent of the framework of plant ; leaved vegetables , fruits , wood , cotton , …etc . c- Properties :

1- Cellulose gives no colour with iodine . 2- Cellulose is insoluble in water . 3- Cellulose in diet cannot be digested by many mammals including

humans because of the absence of hydrolase enzyme that attachs β -linkage .

4- Its presence in diet is important because it cannot be digested , so it will increase the bulk of stool . This stimulates the intestinal movement and prevents constipation .

5- Cellulose can be utilized and serve as a source of energy in herbivores because their gut contain bacterial enzymes that can attach β -Linkage .

5- Inulin a- Structure : it is frutosan i.e . formed of repeated units of fructose linked together by β 1-2 bonds . A) Sources : Root of artichokes and other plants . B) Properties : soluble in warm water . C) Medical importance : Inulin clearance is one of a diagnostic tests

for investigation of glomerular filtration rate .

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6- Chitin : A) Structure : It is a polymer of N-acetylglucosamine linked together

by glycosidic bonds . B) Sources : It is important polysaccharides invertebrates .

B- Heteropolysaccharides : They include glucosaminoglycans , proteoglycans and glycoproteins . GLYCOSAMINOGLYCANS, (MUCOPOLYSACCHARIDES) : A – Introduction : 1- They are formed of repeating disaccharides units [ acidic sugar amino sugar ]n .

The acidic sugar is either D-glucuronic acid or its carbon 5 epimer L-induronic acid . The amino sugar is either D-glucoamine or D=galactosamine in which the amino group is usually acetylated . The amino sugar may also be sulphated at carbon 4 or 6 .

2- Most of GAGs are present extracellulary except heparine . 3- Most of them form the structural components of connective tissue such as bone , elastin and collagen . 4- They act as lubricants and cushion for other tissues because they have the property of holding large quantities of water . 5- When a solution of glycosaminoglycans is compressed , the water is “squeezed out” and the glycosaminoglycans are forced to occupy a smaller volume , when the compression is released , the glycosaminoglycans return back to their original , hydrated volume because of the repulsion of their nagative charges . This property is the cause of resilence of synovial fluid and the vitreous humor of the eye . B- Glycosaminoglycans include : 1- Hyaluronic acid : Structure : Repeated disaccharides unit consists of

1) glucuronic acid . 2) N-acetylglucosamine .

N . B . It is the only GAGs which contains no sulfate group .Site :

1) Synovial fluid . 2) Vitrous body of the eye . 3) Embryonic tissue .4) Cartilage .5) Loose connective tissue .

C- Function : 1) It permits cell migration during wound repair and morphogenesis ,

i . e . differentiation of cells in the form of organs and tissues in the early embryo .

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2) It makes extracellular matrix loose because of its ability to attract water .

3) It makes cartilage compressible because of its high concentration in this tissue .

4) It acts as a lubricant in joints . d- Role in disease :

Hyaluronic acid facilitates cell migration .It is produced in increased amounts by tumor cells . This facilitates migration of these cells through the extracellular matrix and spread of the tumor . 2- Chondritin 4 – and 6 – sulfate : Structure : It is usually present in association with protein to form proteoglycan aggregates . The repeated disaccharides unit consists of :

1) Glucouronic acid .2) N-acetylgalactosamine with sulfate on either C-4 or C-6 .

Site : It is the most abundant GAGs in the body . It is found in : 1) Cartilage , tendons , ligements and bones .2) Aorta , skin , cornes , umbilical cord and in certain neurons .

c- Functions : 1) In cartilage : it binds collagen and hold fibers in strong network .2) Help to maintain the shape of skeletal system . 3) Have role in compressibility of cartilage in weight bearing .

3- Keratan sulfate : Structure : The repeated disaccharides unit consists of :

1) Galactose ( no uronic acid ) , with sulfate on C-6 . 2) N-Acetylglucosamine with sulfate on C-6 .

Site : 1) Cornea . 2) It is found as proteoglycan in cartilage .

C- Functions : 1) It plays an important role in corneal transparency .4- Dermatan sulfate : One- Structure : The repeated disaccharide unit consists of :

1) L-Induroic acid . 2) N-Acetylgalactosamine with sulfate on C-6 .

Sits : 1) Cornea .2) Selera .3) Skin , blood vessels and heart valves .

Functions : 1) In cornea , it plays together with keratan sulfate an important role

in corneal transparency . 2) Its presence in sclera may play a role in maintaining the overall

shape of the eye .

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5- Heparine : Structure : The repeated disaccharides unit consists of :

1) Induronic acid with sulfate on C-2 . 2) Glucosamine with sulfate on C-3 and C-6 .

Site : Heparine present in mast cells ( intracellular compound ) Mast cells are located along the wall of blood vessels of liver , lungs , skin , heart , kidney and spleen . Functions :

1) It act as anticoagulant . 2) Heparine sulfate ( which is the same as heparine in structure except

some glucosamines are acetylated and there are fewer sulfate groups ) ; has the following functions :

1) It is a component of cell membrane and act as receptors . 2) It participates in cell adhesion and cell-cell interaction .3) It is present in basement membrane of the kidney and plays

an important role determining the charge selectiveness of golmerular filtration .

- PROTOGLYCANS AND GLUCOPROTEINS :Both are proteins containing carbohydrates , They differ from each

other in that they present in different sites , contain different sugars and have different shape and size . Proteoglycans : These are chains of glycosaminoglycans attached to protein molecule e . g . hyaluronic acid , chondroitin sulfate , keratan sulfate , dermatan sulfate , heparine and heparan sulfate . They serve as a ground substance and associated with structure elements of tissues as bone elastin and cartilage. The carbohydrate part is present in very long unbranched chains ( more than 50 monosaccharides molecules ) attached to protein core .Glycoproteins ( mucoproteins ) : 1- Structure : They consist of : Protein core : Carbohydrate chains which are branched short chain ( from 2-15 monosaccharides units ) such usually called oligosaccharides chain . They include :

1) Hexoses : Galactose and mannose .2) Acetylhexosamines : N-acetyl glucosamine and N-acetyl-

galactosamine .3) Pentoses : Arabinose and xylose . 4) Methylpentose 5) Sialic acid .6) They contain no uronic acids or sulfate groups .

2- Functions :Glycoproteins are components of extracellular matrix .

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They are components of mucins of gastrointestinal and urogental tracts , where they act as protective biologic lubricants .Glycoproteins are components of cell membrane as :

1) Blood group antigens ( A , B , AB ) .2) Cell surface recognition receptors : for hormones , other cells and

viruses .3) Glycophorin : Which is glycoprotein present in human red cell

membrane . It spans the lipid membrane . It has free polypeptide portions outside both the external and internal ( cytoplasmic ) surfaces.

4) Plasma proteins : globular proteins – except albumin – present in plasma are glycoproteins .

5) Most secreted enzymes and proteins ( as hormones ) are glycoproteins.

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¬

ENZYMEDefinitions A- Catalysts: These are organic or inorganic substances that acce¬lerate the rate of chemical reactions.

1- The organic catalysts are enzymes: They are:a- Highly specific i.e. catalyze one or two reactions only.b- Protein in nature, so they are denaturated by heat.

2- The inorganic catalysts are metals as zinc, magnesium chloride ions. They are:a- Non specific i.e. catalyze many reactions.b- Not affected by heat.B- Enzymes: These are specific protein catalysts, that accelerate the rate of chemical reactions. Enzyme structure is not changed by entering the reactions, and it does not affect the equilib¬rium constant (i.e. end products) of the reactions.C- Rate of chemical reaction: It is the change in the amount (moles, grams) of starting materials (substrates) or products per unit time.D- Substrate: Is the substance upon which the enzyme acts.

cell. They accelerate all the biochemical reaction that occur in biologically systemwhich aim to :A- Prevent uncontrolled and spontaneous reactions .B- Allow reactions to occur at a rate appropriate to the needs of the cells Substrates -------------------------------- Products ENZYMES:

(en = in , zyme = yeast).Enzymes are biologically active proteins that are synthesized within the

General Characteristic of enzymes

A- Properties of enzymes:1. They are invariably protein2. They act within a moderate PH and temperature range3. They are highly specific, catalyzing only one type of chemical reaction.

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B. Enzyme specificity: The specificity of the enzyme is determined by1. The functional group of the enzyme and its co-factor2. .The functional group of the substrate3. The physical proximity of these various functional groups There are 4 types of specificitya- Optical specificity: Enzymes act on one of 2 isomers. The glycolytic enzymes act on D- not L- sugar. maltase acts on α-glycosides and not β-glycosides.b- Group specificity: Enzymes need the presence of certain group to act e.g. pepsin acts on peptide bonds.c- Absolute specificity: one enzyme acts only on one subst¬rate e.g. urease enzyme acts only on urea.d- Relative specificity: These are the lowest grade of the specificity in which the enzyme acts on a group of comp¬ounds having the same type of bonds e.g. lipase enzymes act on different triacylglycerols.

C- Genetic expression of enzymes:Enzymes are the major means for the genetic expression 1- Living cells contain a unique set of enzymes

2- The set of enzymes in each cell is genetically determined.3- Genetic disorders may lead to various diseases.

D- Enzyme activity: 1- Requirements for enzyme activity:

*- Enzymes are either simple or conjugated proteins.*- If the enzyme is a simple protein, only the native conformation of the protein is required for activity.*- If the enzyme is a conjugated protein, it is called: holo¬enzyme and its activiy will depend upon: 1) Conformation of the protein which is called a apoenzyme2) The availability of a non-protein part, which is called cofactor.. Some enzymes require metals as Mg2+ and Cu2+as co-factors.Some enzymes require coenzymes as NAD+ and FAD.

In some enzyme systems, the cofactor is tightly bound to the enzyme protein as in case of flavin adenine dinucleotide (FAD). In such cases, the cofactor is called a prosthetic group.

Differences between apoenzyme and cofactor:

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Apoenzyme Cofactor

Protein in nature. Non protein. Big molecular weight. Small molecular weight.Non dialyzable.¬ Dialyzable.Heat liable. Stable

E- Coenzymes The co-enzymes are heat stable organic compound responsible for the catalytic action of the enzymes. Co-enzymes are frequently containing Vit B complex. They are classified according to their function into1) Hydrogen carriers: NAD and NADP . FAD and FMN . Lipoic acid. Coenzyme Q.

2) Carriers of groups other than hydrogen: Coenzyme A = acid carrier.

Thiamine diphosphate (TPP) = Acetal group

Biotin = CO2 carrier Pyridoxal phosphate = amino group carrier. Tetrahydrofolate = one carbon group carrier. Cobalamine = methyl group carrier.

Co-enzymes for transfer of 2 hydrogen

A. Nicotinamide Adenine Dinucleotide (NAD)Nicotiamide Adenine Dinucleotide Phosphate (NADP)The vitamin niacin (Nicotinic acid) is involved in the formation of NAD which acts as electron carrier in oxidation reduction reaction

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B. Co-enzyme Q or UbiquinoneIt is a component of the respiratory chain in the mitochondria and acts as electron carrier

C. Flavin nucleotide co-enzymeRiboflavin (vitamin B2) is the constituent of several enzymes which are involved in intermediary metabolism1. Riboflavin monophosphate also knowen as flavin mono-nucleotide (FMN): It is the constituent of cytochrome C reductase and the amino acid dehydrogenase

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2. Flavin adenine dinucleotide (FAD) It is the prosthetic group of acyl-CoA dehydrogenase

D. Lipoic acidIt is involved in the complete system of oxidative decarboxylation of pyruvate or ketoglutarate

Co-enzymes for transfer of groups other than hydrogen

A. Thiamine pyrophosphate (TPP)Thiamine (Vit B1) is a component of the co-enzyme TPP that acts as decarboxylase in the oxidative decarboxylation of α-keto acids. It is component of the enzyme pyruvate dehydrogenase

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B. Co-enzyme APantothenic acid is a component of Co-enzyme A. It acts as Co-acylase in the acyl transfer reaction.

C-Pyridoxal PhosphatePyridoxine (vit B6) is involved in the enzyme system of transaminases, cystathionine synthetase and heme biosynthesis

D. Biotin or Vitamin H

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It acts as co-carboxylase in the transfer of pyruvate to oxalacetate and acetyl CoA into malonyl CoA

F- Measures of enzyme activity:a- The unit of enzyme activity: is the amount of enzyme cau¬sing transformation of one micromole (1 µmol) of a subs¬trate per minute at 25 ºC under optimal conditions of measurement.b- The specific activity is the number of units of enzyme activity per milligram of enzyme protein.c- The katal (Kat) is the amount of enzyme activity that transforms 1 mol of substrate per second.

ENZYMES NOMENCLATURE (NAMING):Enzyme nomenclature has histori¬cally been a source of confusion. There are several ways of naming enzymes:A- Trivial names e.g. trypsin, pepsin.B- Some enzymes were named by attaching the suffix -ase to the name of the substrates e.g. maltose & maltase.C- Some enzymes were named according to the type of the reaction

e.g. aminotransferase. D- To standardize enzyme nomenclature, the International Union of Biochemistry (lUB) made a systemic name to each enzyme. This name can indicates:1- The substrate acted upon.2- The coenzyme involved in the reaction. 3- The type of reaction catalyzed.e.g. Lactate - NAD+ - oxidoreductase enzyme. (Its old name was lactate dehydrogenase)

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It catalyze the following reactionLactate + NAD ----------------------------- Pyruvate + NADH+HE- In addition to naming enzymes, the IUB classifies the enzymes by giving each enzyme a number. This number called: Enzyme commi¬ssion numerical code (EC) and it contains 4 digits: 1- First digit: indicates the class of the enzyme. There are 6 classes of enzymes. 2- Second digit: indicates the functional group upon which the enzyme acts e.g. -OH , -CHO 3- Third digit: indicates the coenzyme e.g. NAD, FAD. 4- Fourth digit: indicates the substrate

Alcohol DehydrogenaseE.C (1) : Class of enzyme: oxidoreductase.E.C. 1.1) : Group upon which the enzyme acts is : CH-OH E.C. 1.1.(1) : The coenzyme is NAD+.E.C. 1.1.1.(1) : Alcohol e.g. ethanol is the substrate.

CLASSIFICATION OF ENZYMES:- There are 6 classes of enzymes which are:A- Oxidoreductases : This group of enzymes catalyzes an oxidation¬ reduction reaction between two substrates: S (oxidized) + Y (reduced) --------------- S (reduced) + Y (oxidized).1- Oxidoreductases are further classified according to the sub¬strate oxidized and to the mechanism of oxidation. The mechanism of oxidation is either by addition of oxygen (oxidases) or by removal of hydrogen (dehydrogenases).* Dehydrogenase are group of the enzymes catalyzes the removal of 2 H or electron from the substrate to the coenzymes e.g Lactate dehydrogenase* Oxidase: they are group of the enzyme catalyze transfer of hydrogen or electron to oxygen with the formation of hydrogen peroxide e.g Glucose oxidase* Oxygenase: enzymes catalyzes the incorporation of either molecular oxygen into the substrate e.g lipoxygenase or one oxygen e.g monoxygenase

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2- Transferases : This group of enzyme catalyzes transfer of group other than hydrogen

SX + Y-----------------------------S + YX .* They are further classified according to the group transfe¬rred: phosphotransferases, transaminases, transketolases, transacylases, transformylases and transmethylases.Example: Phosphotransferases : Kinases :Glucose + ATP Glucokinase Glucose-6-phosphate + ADP3. Hydrolases : This group catalyzes hydrolysis i.e. breakdown of a chemical bond by addition of water: A-B HOH AH + BOH

Example: peptidase:

4. Lyases : This group of enzymes catalyzes removal of groups from substrates by mechanism other than hydrolysis. Pyruvate Decarboxylase CH3 COCOOH ---------------------------- CH3CHOFructose 1,6 Bisphosphate------------- Dihydroxyacetone Phosphate

5- Isomerases: This group of enzymes catalyzes the inter conversion of one isomer into the other. *- This group includes: isomerases, mutases and epimerases. Example: phosphohexose isomerase:

Phosphohexose isomerase_Glucose-6-phosphate Fructose-6-phosphate

6- Ligases (or synthetases): This group of enzymes catalyzes join¬ing of two substrates using the energy released in the hydroly¬sis of a high energy phosphate compound as ATP or GTP.. Example: Glutamine synthetase.Glutamate + NH3---------------------------- Glutamine + H2O MECHANISM OF ENZYME ACTION:A- Energy of activation:1- All the reactions that proceed from initial substrates (ini¬tial state) to products (final state) consume energy. This is called free energy of the reaction.2- However the substrates do not become products directly, but must be energized (absorb energy) to reach an activated or transition state. This energy is called activation energy.3- At transition state, there is a high probability that a che¬mical bond will be made or broken to form the product.

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4- The definition of activation energy: is the amount of energy required to raise all the molecules in one mole of a substa¬nce to the transition state.5- The effect of enzymes is to decrease the energy of activation of substrates

Active site:The substrate is bounded to a specific region on the enzyme called active site which is characterized bySmal portion of the total volume of the enzymeIt is composed of R group comes from side chain of the amino acids and the specificity depends on arrangement of these groups1) During enzyme action, there is a temporary combination between the enzyme and its substrate forming enzyme¬ substrate complex. This occurs at active site of enzyme. 2)This is followed by dissociation of this complex into enzyme again and products. E + S------- ES ------- E + P

Two theories have been proposed to explain the specificity of enzyme actiona. The lock and key theory Model of Fischer or template model :The active site of the enzyme is complementary in conformation to the substrate, so that enzyme and substrate recognize one another. This theory postulate that active site of the enzyme has fixed shape.

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B. The induced fit theory Model of Koschland: An essential feature of this model is the flexibility of the catalytic site. The enzyme changes shape upon binding the substrate, so that the conformation of subst¬rate and enzyme protein are only complementary after the binding reaction. Catalytic site is presumed to be preshaped to fit with the substrate. Fig 3

ENZYME KINETICS:It is the study of the rate or velocity of reac¬tions catalyzed by enzymes.A- Initial velocity: the rate (velocity) at which a reaction pro¬ceeds is measured as the decrease in the concentration of reac¬tants (substrate) or the increase in concentration of the products with time.1- If an enzyme is incubated with its substrate and the appea¬rance of the product with time is recorded on a graph, the resulting line will have the hyperbolic shape as in the fo¬llowing figure 4

2- The rate (velocity) of the reaction, which corresponds to the slope of this curve, is initially constant but gradually decreases.3- The decline in the rate of the reaction may be due to deple¬tion of the substrate, inhibition of the enzyme by its pro¬duct, or denaturation of the enzyme. Each of these events affects the conditions of the reaction, and in turn affects the velocity of the reaction.4- Thus only in the initial portion of the reaction are the con¬ditions accurately known. For this reason, only the initial velocity (Vi) is used in

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calculating the kinetic parameters of the reaction. The units of velocity are concentration per unit time, e.g. micromoles per minute.

Factors affecting enzyme activity:1- Concentration of enzyme: The initial velocity of a reaction is directly proportion to the amount of the enzyme present, provided that all other conditions remain constant i.e. when the amount of enzyme in a reaction is doubled, the amount of substrate converted to product is doubled. Also when the amount of enzyme is trippled, the amount of substrate conve¬rted to product is trippled and so on. Fig 5

2- Concentration of substrate: The initial velocity of a reac¬tion is directly proportional to the amount of substrate present till it reaches a maximum point known as maximum velocity (Vmax), where any further increase in the amount of substrate causes no increase in the velocity of the reaction. This is true if all other conditions especially enzyme concentration remain constant. At low substrate concentration, not all enzymes are saturated. So the rate of reaction will increase. At higher substrate concentration, all enzymes get satura¬ted with substrates and any more increase of substrate concentration will result in no increase in the rate of the reaction (plateau curve). The following diagram can explain:

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A- Michaelis-Menten Equation:1) This equation describes the dependence of reaction ve¬locity on substrate concentration.2) Michaelis and Menten proposed that in any enzymatic reaction, the enzyme (E) combines with substrate (S) to form an enzyme-substrate (ES) complex.

K1 E + S -------------------- ESES then breaks down either to enzyme and substrate again or to enzyme and product (P)

K2ES-------------------- E + P K-1 ES------------------------ E + S 4) The rates(velocities) at which the partial reactions of this model occur are described by the rate constants K1 , K-1 and K2.5) According to this model, the increase in the initial velocity (Vo) observed with an increase in (S) is due to an increase in the amount of ES formed. At Vmax , all of the enzyme is involved in an ES complex.

6) Using the previous model, Michaelis and Menten develop¬ed an equation that expresses the initial velocity (Vi) of a reaction in terms of the Vmax , [S] and the rate constants K1, K-1and K2.

Vmax [S] Vi = ------------------------------- [S] + Km

K1 + K2

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Km = -------------------------- K-1 If Km = [S] then

Vmax Vi = --------------------- 2

Thus Km can be defined as substrate concentration that produces half maximum concentration

Important conclusions about Michaelis-Menten equationKm is a constant, characteristic for every enzyme and paticular substrate. Km reflect the affinity of the enzyme for the substrateThe smaller Km value, more active enzyme ( high affinity of the enzyme toward the substrate)Large or high Km value reflect the low affinity of the enzyme toward the substrate

Hexokinase is more active than glucokinase because the amount of glucose (substrate) needed to produce ½ Vmax in case of hexokinase is less than in case of glucokinase i.e. Km of hexokinase is less than glu¬cokinase

Lineweaver-Burk plot:-Here the reciprocal of V i.e 1/V is plotted versus the reciprocal of [S] 1/S. The curve is straight line and it becomes more practical to estimate Km because a few give saturation curve.

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3- Effect of temperature:a- The optimal temperature for enzymatic activity in human body is that temperature similar of that of the cells 37 ºCb- At zero temperature, the enzyme is inactive. The re¬action velocity increases with increase of temperature until a maximum velocity is reached. This increase in reaction velocity is due to the increase in the number of molecules having sufficient energy to pass over the energy barrier and form the products of the reaction. Further elevation in temperature resulted in decrease in reaction velocity.

4. Effect of pH The optimal pH for an enzyme activity is that pH at which the enzymes acts maximally. Increase or decrease in pH, the ionic state of both enzyme and substrate will be changed and the rate of the reaction decline Each enzyme has its own optimal pH , pancreatic lipase 7.5 while pepsin 2

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Enzyme-inhibitorAny substance that can diminish the velocity of an enzymatic reaction is called inhibitor. The inhibition of the enzymes can be classified either reversible or irreversible1.Reversible inhibitors:- these inhibitors bind to the enzyme through non- covalent bond*- Dilution of the enzyme-inhibitor complex results in diss¬ociation of the reversibly bound inhibitor and recovery of enzyme activity.

*- Reversible inhibition may be competitive or non competitive2- Irreversible inhibitors: This type of inhibition occurs when an inhibited enzyme does not regain activity upon dilution of the enzyme inhibitor complex

Competitive and noncompetitive inhibitors:1- Competitive inhibitors: This type of inhibition occurs when the inhibitor binds reversibly to the active site where the substrate normally would occupy. Therefore, both inhibitor and substrate compete for active site.*- Here is structural similarity between substrate and inhibitore.g. malonic and succinic acids on succinate dehydrogenase

*- Effect of competitive inhibitor on Vmax The effect of a competitive inhibitor is reversed by increa¬sing substrate concentration. Therefore, at a sufficiently high substrate concentration, the reaction velocity reaches Vmax observed in absence of the inhibitorEffect on Km: A competitive inhibitor increase Km of the substrate i.e more substrate is neededEffect on Line-weaver-Burk plot: Inhibited and uninhibited reactions show different X axis intercepts indicate increase in Km

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2.Non competitive inhibitors: This type of inhibition occurs when the inhibitor and substrate can bind at different site of the enzyme. There is no structural similarities between substrate and inhibitor e.g heavy metals or oxidizing agentEffect of noncompetitive inhibitors on Vmax : Non competi¬tive inhibition cannot be overcome by increasing the concentration of substrate. Thus, noncompetitive inhibitors decrease the Vmax.Effect on Km: Non competitive inhibitor do not interfere with the binding of the substrate with enzymes. Thus the enzyme show the same Km Effect on Lineweaver-Burke plot: Noncompetitive inhibition is readily differentiated from competitive inhibition by plotting l/V versus l/S and noting that Vmax decreases in of noncompetitive inhibitor, wherease Km is unchanged.

Uncompetitive inhibitorThis inhibitors binds only on [ES] complex. This results in apparent changes in both Vmax and Km which is reflected in double reciprocal plot

Allosteric ( Regulatory) Enzymes

1.Allosteric enzymes generally catalyze irreversible reaction in metabolic pathways.

2.The term allosteric means "other site". It indicates that a molecules called effectors (also called modifiers or modu¬lators) can bind non-covalently at a site other than active site.

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Effectors are positive if they enhance the catalytic reaction and negative if they attenuate the reaction rate.*- Effectors may be the end product of a metabolic pathway.

If it inhibits the reaction (negative regulation), it is called feed back inhibition. *-Positive effector : It gives the enzyme a configuration which binds the substrate.Classes of allosteric enzymes: there are two major classesa- Homotropic enzymes in which the substrate is also the effectorb- Heterotropic enzymes : in which the effector is other substance than the substrateExamples of allosteric enzymesPhosphofructokinase is an allosteric enzyme in the glycolytic oxidation of glucose. It is allosterically inhibited by high level of ATP and stimulated by ADPAcetyl CoA carboxylase is the allosteric enzyme stimulated by citrate and inhibited by fatty acid

Effect of allosteric regulation on Km and Vmax :Allosteric regulation of enzymes causes conformational chan¬ges at the catalytic site. This leads to :a- Altering Km for a substrate and Vmax . Therefore Michael-Menten does not applyb- They have characteristi sigmoid shape or S-shape curve

IsoenzymesIsozymes are physically distinct forms of the enzyme with the same catalytic activity: they catalyze the same reaction but at different rates( have different Km value). They migrate differently in an electric field. - The best known example is:

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. Lactate dehydrogenase enzyme (LD) which is a tetrameric i.e. contains 4 polype¬ptide chains. These 4 chains are a mixture of different proportions of 2 chains H and M. chains Hand M (H from heart & M from muscle).These two subunit combined in 5 different ways so that there are 5 isoenzymes of LDH

Type Composition LocationLDH1 H4 HeartLDH2 H3M HeartLDH3 H2M2 BrainLDH4 HM2 ---LDH5 M4 Muscles

Isoenzymes differ significantly in their Km and Vmax. For example isoenzyme in heart (H4) and skeletal muscles (M4) have distinctly different kinetics properties which are related to their physiological role in the tissuesLDH5 (M4) have low Km i.e high affinity for pyruvate so will rapidly oxidize glucose to lactate instead of pyruvate, which is really fit with physiological state of skeletal muscle which mainly function under anaerobic condition. On the other hand LDH1 (H4) have high Km value low affinity to pyruvate so will prevent accumulation of lactate in heart tissues which function under aerobic conditionSerum isoenzymes are valiable in the diagnosis of certain disease serum LDH5 increases in certain liver diseases while LDH1 in heart disease

Regulation of the enzyme activityControl of metabolic regulation of a pathway occurs through modi- fication of the enzymatic activity of the key enzyme in the pathway( rate limiting enzyme). The activity of rate limiting enzyme can be regulated in a number of ways

1. Control of enzyme levelThis is determined by rate of enzyme synthesis, which is stimulated by substance called inducers, and the process is called induction. Also the enzyme synthesis is inhibited by other substance is called repressor and the process is called repression.

Induction

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It is the increase in enzyme production through hormonal activation of the mechanism controlling their gene expressionExample: Insulin hormone is hypoglycemic hormone induced the synthesis of group of the enzyme responsible for glucose oxidation ( glucokinase or phosphofructokinase) or glycogen synthesis (glycogen synthetase)

Repression and DerepressionInsulin hormone is hypoglycemic hormone that represses the bio -synthesis of gluconeogenic enzymes responsible for synthesis of glucose from non carbohydrate sources. While in case of fasting gluconeogenic enzyme are derepressed by glucocorticoid hormoneProenzymes Zymogens : Some enzymes are synthesized as inactive forms called zymogens or proenzymes e. g. trypsinogen and pepsinogen. Zymogens are inactive because a polypeptide chain masks their catalytic sites. To activate zymogens, cleavage of the polypeptide chain should occur to open the catalytic site for its substrate.

2. Modulation of catalytic efficiency of the enzyme A-Covalent modification: The activity of some enzyme may be regulated by reversible modification. This can be done by covalent attachment of phosphate group to seryl residue of the enzyme. Phosphrylation/dephosphorylation :1- Some enzymes may be regulated by co¬valent modification, most frequently by the addition or removal of phosph¬ate groups from the enzymes (through -OH group of serine, threonine or tyrosine residues of the enzyme).2- Phosphorylation reactions are catalyzed by a family of enzymes, called protein kinase. It utilizes ATP as a phosphate donor. Phosphate groups are cleaved from phosphorylated en¬zymes by the action of phosphoprotein¬ phosphatase.3- Depending on the specific enzyme, the phosphorylated form may be more or less active than the unphosphorylated enzyme. For example, phosphorylation of glycogen phosphorylase increases activity, whereas the addition of phosphate to glycogen syn¬thase results in a less active enzyme.B. Non covalent modification This is done by non-covalent binding of certain metabolities to allosteric site. De novo synthesis of fatty acids acetyl CoA carboxylase is regulated by feed back nhibition by non-covalent binding of fatty acids It means that the end product of a series of reactions directly inhibits the first enzyme of that series.

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Enzyme CompartmentationCompartmentalization of the metabolic pathway allows the separation of the process that proceeds in opposite direction and may otherwise interfere with one another e.g the anabolic process involved in the biosynthesis of fatty acids from acetyl CoA are located in cytosol while catabolic process concerned with the oxidation of fatty acids are located with the mitochondria.

Clinical EnzymologyEnzyme level determination in plasma can be used ax an index or diagnostic agent in the diagnosis of certain diseases. There are two types of plasma enzymeFunctional EnzymesThey are the enzymes that are normally present in plasma in higher concentration as they perform certain physiological function. E.g Blood clotting factors and lipoprotein lipase

Non-Functional enzymesThey perform no known physiological function in plasma as their names implies. Their presence in plasma at levels higher than normal level reflect tissues destructione.g ALT and AST in liver diseaseCPK in heart diseaseLDH in heart disease

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NUCLEOTIDESThe nucleotides are important intracellular molecules having the following functions1- They enter in the structure of the nucleic acids RNA and DNA.2- Purines enter in the structure of a- ATP (a source of energy) is the main form chemical energy available. b- The physiological mediators Cyclic AMP: the second messenger involves in the action of many hormones c- Component of some coenzymes ; FAD , NAD and NADP. d-S~adenosylmethionine (methyl donner).3- Pyrimidines enter in the structure of a- UDP-glucose (glycogen and glucouronic acid synthesis).

b- UDP-galactose (lactose synthesis).c- CDP - acylglycerol (phospholipid synthesis).

Polynucleotides----------Nucleotides--------- Nucleosides+ PO4The nucleosides are ---------- nitrogen bases, sugar and phosphate. The nitrogen bases are Purine and Pyrimidine

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Purine bases are Adenine , guanine , hypoxanthine and xanthine.

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SOURCES OF DIFFERENT ATOMS OF PURINEAND PYRIMIDINE BASESAlthough human ingest dietary nucleic acids and nucleotides, survival does not requir their absorption and utilization. Human can synthesize ample amounts of purine and pyrimidine nucleotides de novo ( from intermediates).

Biosynthesis of PurineDe- novo synthesis pathway

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Inhibitors of purine biosynthesis1- AzaserineIt is a glutamine antagonist , stop purine synthesis at the reaction 5.2- DiazonorleucineBlocks reaction 23- 6- MercaptopurineBlocks the formation of AMP and GMP

IMP--------/----------- AMP--------/--------GMPSite of purine biosynthesis:Liver is the major site for purine biosynthesis.

*Other tissues are less capable of de novo synthesis of purines.*RBCs leukocytes and the brain are incapable of de novo synthesis ofpurine. They depend on exogenous purines (adenine and guanine) for the formation of purine nucleotides (AMP and GMP). The conversion of adenine and guanine to AMP and GMP is called PURINE SALVAGE PATHWAY.

Regulation of purine biosynthesisPurine biosynthesis utilizes 6 ATP molecules and requires glycine glutamine aspartate and methenyltetrahydrofolate. To avoid the loss of unnecessary energy and nutrients. this pathway should be regulated to provide, the exact needs of purines. The regulation depends upon the activity of PP-ribose-P synthetase enzyme. It is allosterically inhibited by GMP, GDP, AMP and ADP i.e. excess purines-inhibit more formation and vice versa.

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Catabolism of purinesIn humans , the end products of purine catabolism is uric acid.Site Mainly liver.Mechanism

Sources of uric acid1- Catabolism of purines in the liver (99%).2-Uric acid produced in the intestine by the action of bacteria on puri¬nes present in diet (1%).Regulation of uric acid formation*This depends on the activity of xanthine oxidase enzyme , which is present in the liver kidney and intestine.*Absence of this enzyme led to decrease uric acid formation.

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Plasma level of uric acid2.5- 7 mg/l00 mlThe form of uric acid in the plasma and other body fluids depends upon the pH of that fluidAt the pH around 7. The uric acid is present in the form of a salt sodium urate. e.g. Blood , CSF.At the pH below 5.75: The predominant form is uric acid e.g. urine.

CLINICAL DISORDERS OF PURINE KETABOLISM HYPERURICEMIA (GOUT)

Hyperuricemia is the increased in blood uric acid level above 7 mg/100 ml.CausesHyperuricemia may result either from1-Increase the activity of PP-ribose-P synthetase------ Purine over¬production and excretion.2-Increase the rate of cell division as in leuckemia ------Purine overproduction and excretion.3-Decrease the rate of uric acid excretion as in nephritis and lead poisoning this leads to renal damage.

Effect of hyperuricemiaWhen the plasma level of sodium urate exceeds certain level (above 7 mg/100 ml)-------- formation of crystals of sodium urates--------depositionof these crystals in soft tissues (these urate deposits are called : tophi);1- In JointsUrate crystals will be phagocytosed by leukocytes---------- Acute inflammatory reaction called acute gouty arthritis. The joints that firstly affected are the small joints especially those of big toes.

2 In kidneysDeposition of uric acid tophi may lead to uric acid stone.3-In the cartilageAs that of the ear----------- distruction of cartilage.

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HYPOURICEMIAIt is the decrease of blood uric acid level below 2 mg/l00 ml.Causes1-Deficiency of activity of xanthine oxidase enzyme. Here xanthine and hypoxanthine can not be converted to uric acid. This leads toa-Hypouricemia.b-Excess xanthine and hypoxanthine excretion (xanthinurea).2-Drugse.g.acetylsalicylic acid (aspirine) inhibits urate excretion.

PYRIMIDINE BIOSYNTHESIS

Regulation of pyrimidine biosynthesis Carbamoyl phosphate synthetase II isa- Stimutated by PP-ribose-phosphate. b- Inhibited by UTP and other purines.

NUCLEIC ACIDNucleic acid are polymers of nucleotides. The nucleotides are linked together by phosphodiester bonds between 3' –hydroxyl on the sugar of

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one nucleotides and the 5'-phosphate on the sugar of the another nucleotides. In long chains formed. One end contains the phosphate group (5' end) and the other contains the free hydroxyl at 3' end.

DNA :. Deoxyribonucleic acidSite : Nucleus.Structure*DNA is formed of many nucleotides (it may reach millions of nucleotide.units). Each nucleotide is formed of base , sugar and phosphoric acid.The bases are : Adenine , guanine . cytosine and thymine. The sugar is deoxy-ribose.*The nucleotides are arranged in chains linked together by a phosphodi¬ester bonds between 5' carbon atom of a deoxyribose of one nucleotide and 3' carbon atom of the next. Phosphodiester bond = one phosphate is linked to 2 sugars----2 ester bonds.The chain begins with 5' and ends with 3'

*DNA is formed of two antiparallel double chains (strands) of nucleotides in the form of double helix. The sugar and phosphate molecules form the backbone outside while the bases are arranged inside. So the bases are not part of the backbone but lie between the 2 strands.

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The helix is 20µ in diameter. In crystalline DNA, the bases are separated by 3.4 A and there is a complete turn of the helix every 10 base pair.

The genetic information of DNA is stored as a sequence of purine and pyrimidine nucleotides in the DNA molecule.Pairing ruleIt was found that in DNA molecules the concentration of deoxy-adenosinenucleotides (adenine-ribose~P) = Deoxy-Thymidine nucleotides (thymine-ribose-P) , and the concentration of deoxy-guanosine nucleotides (guanine-rihose-p)=Deoxy-cytidine nucleotides (cytosine-ribose-P).The pairing of bases of both strands of DNA are complementary and not identicalalways adenine is paired only with thymine and Guanine is paired only with cytosine A------- T G------CShape of DNA:Chromosomal DNA may be linear or circular DNA is complexed with histones in eukaryotic chromosome which profoundly influence the structure of the chromosome. Histones are small proteins rich in positive

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charge amino acids (Basic amino acids as arginine and lysine). Histone are divided into five classes H1 H2A H2B H3 and H4. Also non histone proteins and possibly RNA affect the packing of DNA. When single DNA is complexed with histones it forms chromatin threat.Sense and anti-sense strandsThe 2 strands of DNA molecules are anti-parallel. i.e. one strand runs in the 5' to 3' direction and the other strand runs in the 3' to 5' direc¬tion. This resembles 2 parallel streets each going one way but in opposite directions. Accordingly , one strand is considered as the sense strand , the opposite strand might be considered comple -mentary or anti-sense strand.

Bonds between the basesIn double stranded DNA1 adenine is paired with thymine by 2 hydrogen bonds and guanine is paired with cytosine by 3 hydrogen bonds. Thus G-C bond is stronger than A -T bond. The higher the G-C content of a DNA molecule , the more difficult is to separate the 2 strands Functions of DNA1) Replication of DNA (=Reproduction)The genetic information are stored in the nucleotide sequence of DNA of parent cell passes to daughter cell. So the new DNA is typically identical to that of parent cell. 2) Transcription :

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DNA is the source of information for the synthesis of all protein molecules formed in the same cell. This can be done by a process called transcription.

REPLICATION OF DNAIt is the process for transferring genetic information on DNA from generation to generation. When a cell divides to give 2 daughter cells, replication of DNA allows the daughter cells to have the same DNA formation of the mother cells. Replication is semiconservative process i.e on the two strands of DNA molecules, there is always one strand of old DNA and the other is newly synthesized.The 2 strands of parent DNA are separated from each other. Then each one acts as a template upon which a new strand is formed.Semiconservative replicationDuring cell division the double strands of DNA molecule are separated. By using free nucleotides which are present in the nucleus (ATP GTP ,TTP and CTP), each strand of DNA induces the formation of a complementary stra¬nd which is identical in structure to the one which has separatedThis reactions need a large amount of energy i.e. each nucleotide that incorporated in the DNA molecule utilize 2 high energy phosphate.Steps of replication1. The parent strands unwind at a unique site (called oriC site) with the help of an unwinding helicase enzyme, using ATP hydrolysis as a source of energy2. Another protein, a single strand binding protein binds to the unwind DNA to prevent reannealing3.The exosed bases on the separated strands serve as a templete for the new strand4. The replication is continous in one strand “leading strand” and discontinous for the other “ lagging stand”5.The leading strand is synthesized continously by DNA polymerase III that can bind nucleotide only from 5' ---3' direction. 6. Because there is no DNA polymerase III that can bind nucleotide from 3' ---5' direction, The enzyme replicate the other strand by turning it on its back (3' to 5' direction Turned on 5' to 3' direction). It is called Okasaki fragments7.DNA polymerase I fills the gap between the fragments by nucleotides then DNA ligase cause ligation of the fragments to form continous strand

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Ribonucleic acid = RNAThere are 3 types of RNA- Messenger RNA mRNA- Transfer RNA tRNA -Ribosomal RNA rRNA

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All are formed in the nucleus under the control of DNA and the enzymeRNA polymerase.RNA is differ from DNA in the following features RNA DNASugar Ribose DeoxyriboseBase Uracil ThymineStrands Single DoubleStability Breaks down at high pH Resistant Due to presence of 2 OH

Messanger RNA

mRNA is a one stranded nucleic acid. It is formed under the control of DNA in the nucleus ( transcription ). It encodes the information directing protein synthesis and make up about 21% of RNA in the cell. Formation of mRNA from coding (sense) strand of the DNA is the first step in the transcriptionIt is composed of 400 - 4000 nucleotides.Structure- Bases Adenine , guanine , cytosine and uracil- Sugar Ribose.- PhosphateFunctionmRNA is a nucleic acid which carries the genetic information from DNA of the nucleus to the ribosomes where the proteins are synthesized.

Transfer RNA = tRNA:* It is a single strand of nucleotides formed of Bases Adenine guanine cytosine and uracil.- Sugar : Ribose.- Phosphate* This single strand is arranged to form 3 loops and 2 free ends as shown

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* It is the amino acids carrying RNA. It has the shape of clove leaf

Transfer RNA (tRNA) serves: as adapter molecule for translation of mRNA into amino acid sequence in protein synthesis. The tRNA is formed as large precursors which are acted upon by ribonuclease P to reduce its size. The ribonuclease P removes 18 ribonucleotides from tRNA precursor close to the anticodon region. tRNA is formed in the nucleus and pass to the cyto¬plasm. There are at least 20 species of tRNA in every cells at lease one to each of the 20 amino acids- So tRNA are the carriers of amino acid. tRNA has 2 different regions the anti¬codon region and the terminal region for amino acid which has three nucleotides at 3 terminus CCA. Amino acids attaches to 3-OH of the terminal adenine-The middle arm contain the anticodon region which is formed of 3 bases complementary to a cer¬tain codon on mRNA.

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So for each codon in mRNA specific tRNA will be attached which means a specific amino acids.RIBOSOMAL RNA = (rRNA )

*The cytoplasmic ribosomes are the site of protein synthesis i.e. They contain enzymes needed for this process.*Ribosomes contain only proteins and RNA (rRNA).*rRNA are formed in the nucleus as a large precursor molecule. In the nucleolus , this precursor will undergo alteration to be converted to ribosome subunits.*Each ribosome consists of 2 subunits : one about twice the size of the other.*The whole ribosome and each subunit have its own sedimentation rate. This rate is measured by what is called Svedberg units

Whole ribosome Large subunit Small subunit

Eukaryotes 80 S 60 S 40 S

Prokaryota 70 S 50 S 30 S

The large subunit (60 S) is the binding site for t RNA , while the small subunit (40 S) is the binding site for mRNA.

PROTEIN BIOSYNTHESISPrinciple of protein biosynthesis* Body proteins are of various types plasma proteins contractile proteins of muscle all enzymes , some hormones * Protein biosynthesis is subdivided among the various tissues.

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Mamary gland makes milk proteins Muscle makes contractile proteinsLiver makes plasma proteins Lymphocytes make gamma globulin

* Nucleic acids (DNA andRNA) are molecules concerned with protein biosyn thesis.* DNA are present in chromosomes , while RNA is formed under the control ofDNA.Proteins are composed of amino acids arranged in certain sequence. The function of this protein depends on the sequence of these amino acids. Genetic informations about protein biosynthesis are present in the genes of DNA molecule in the nucleus. These information are represented by the sequence of bases in DNA and translated to sequence of amino acids in the cytoplasm.

Codons and Genetic CodeCodon is the sequence of 3 nucleotides (bases) in DNA molecules which determines the type and position of the amino acid that enter in the structure of protein molecules Twenty different amino acids are required for protein synthesis. So there must be at least 20 different genetic codes for the amino acids. DNA or mRNA contains only 4 different nucleotides. If the genetic code is represented by two nucleotides only, we can have4x4 =16 code wordsbut the genetic code is represented by 3 nucleotides and can provide x34x4x4 = 643 codons which are called non-sense codons, do not code for any amino acids. This leaves 61 codons for 20 amino acids i.e the number of codons is about three times the number of amino acids. This exess in the genetic code is explained by the fact that many amino acids are represented by more than one genetic code.

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Three codons (term*) indicate the termination of polypeptide chain. Two codons ( Met+ Init) and (Valine + Int) are used for initiation as well as for methionine and valineIn this way the genetic information are sent from the nucleus to cyto¬plasm where the process of protein biosynthesis occurs.STEPS OF PROTEIN BIOSYNTHESISThis occurs in 3 steps1- Activation of amino acids and their carriage by tRNA.2- Transcription of mRNA.3- Translation.ACTIVATION OF AMINO ACIDSThis process occurs in cytosol. For each amino acid there is specific activating enzyme called : the aminoacyl-tRNA synthetase e.g. alanine acyl-¬tRNA synthetase, glycine acyl-tRNA synthetase. They help the trans¬fer of different amino acids to tRNA as follows

-The amino acid becomes attached to the terminal nucleotide of the tRNA (the base of which is adenine). The aminoacyl-tRNA is travelled to the ribosomes where protein biosyn¬thesis occurs.

TranscriptionTranscription is the synthesis of mRNA of a certain protein under the control of RNA polymerase

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Transcription is local. It means that it occurs in a certain area of DNA that carries the genetic infor¬mation (=codons) about this protein(s). This area of DNA is a genome or structural gene.Transcription is conservative, DNA is used only as a templet and unchanged after transcription

Transcription begins by recognition of the RNA polymerase -enzyme to the initiation point of the genome. This initiation point is called promoter.

This is the signal after which the 2 strands of DNA molecule in the genome are separated from each other.

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Then under the control of RNA polymerase enzyme ,one strand acts as a tempelate upon which mRNA is formed. This strand is termed: sense strand. The other DNA strand is termed : antisense strand. Moreover , one strand of DNA molecule will act as a sense strand for one gene and antisense for another gene.

The formation and elongation of RNA molecules begins by its 5' end and elongates towards its 3' end. This occurs anti-parrallel to the sense strand that acts as a tempelate for it.

The high energy phosphate compound, ATP, GTP, CTP and UTP act as a donner for different nucleotides needed for the formation and elongation of RNA. This consumes a large amounts of energy.

e.g. ATP--------------------------------AMP

RNA molecule ends at a certain site in the sense strand. This site is termed : stop site. The newly formed RNA leaves the nucleus to the cytoplasm (ribosomes) where protein synthesis occurs.

Summary of transcription

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1. RNA polymerase holoenzyme is formed of 5 subunits 2α, 2β and 2σ. 2σ is responsible for recognition and binding of RNA polymerase to the initiation site while the core 2α and 2β that are very rich in GC nucleotides are responsible for elongation of RNA. 1- Binding of RNA polymerase enzyme to the promoter sequence site.2- The 2 strands of genome in the DNA are separated into sense and anti-sense strands (enzyme unwinds a short stretch of DNA).3- At the sense strand of the genome , the enzyme select the correct ribonucleotides and catalyze the formation of RNA molecule which begins at its 5' end.4- Then elongation of the RNA molecule from the 5' to the 3' end continuous antiparrallel to its tempelate.5- The high energy phosphate compounds ATP , GTP , CTP and U'TP act as a donners for different nucleotides needed for the formation and elongation of RNA. This consumes a large amounts of energy.

e.g. ATP---------------- AMP6- RNA molecule ends at a certain site in the sense strand. This site is termed stop site.7- The newly formed RNA leaves the nucleus to the cytoplasm (ribosomes) where protein synthesis occurs.

Posttranscriptional changes of RNA moleculesi.e. changes of RNA after their synthesismRNA together with tRNA and rRNA undergo some modification after their transcription and before they are released from the nucleus to the cyto¬plasm. These changes may be1- Addition of some new nucleotides (AMP) to the 3' end of the transcripted mRNA. This addition helps the transfer of mRNA from the nucleus to the cytoplasm.2- Cleavage of the transcripted RNAe.g. r RNA is synthesized as one simple long strand , which is cleaved to give 2 fragments (40S) and (60S) so, the rRNA molecules are ready to be incorporated into the ribosome.

TRANSLATION (Protein synthesis)The mRNA migrates from the nucleus to the cytoplasm (ribosomes) where protein biosynthesis occurs.* The ribosome is the cellular structure on which various mechanisms occur to assemble the protein molecule. Many of these ribosomes can aggregate to translate a single mRNA , and is called polyribosomes.

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* Translation of genetic code that are carried by mRNA to the ribosome can be divided into 3 stages

a- Initiation b-Elongation c-Termination

a- INITIATION* mRNA binds to 40S ribosomal subunit. This binding needs a protein fac¬tor which is termed : initiation factor 3 (IF-3)..

*The aminoacyl-tRNA interacts with GTP and another protein factor that is termed : Initiation factor 2. (IF-2) ----- complex

This complex together with a third protein factor which is termed initia¬tion factor 3 (IF-l) will attach the anticodon of t-RNA to the first codon (on mRNA) to form an initiation complex with 40 S ribosomal subunit.

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The initiation complex attaches with 60 S ribosomal~subunit with releaseof initiation factors 1 , 2 , 3 and hydrolysis of GTP into GDP +Pi. The formation of 80S ribosome is thus complete.

*The complete ribosome contains 2 sites for tRNA molecules. These areP site (Peptidyl site) and A site (aminoacyl site).*The first amino acid in the polypeptide chain (first aminoacyl tRNA)gets attached to the P site. The subsequent aminoacyl tRNA are attached to A site.

b- ELONGATIONThe binding of the proper aminoacyl tRNA in A site depends on proper codon recognition. Aminoacyl tRNA enters A site as follows Aminoacyl tRNA + Elongation factor 1 (EF-1) + GTP--------- Complex

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Aminoacyl tRNA site A

The free NH2 group of amino acid 2 (aa2) attracts the COOH group of the amino acid 1 (aa1). This leads to the transfer of peptide chain to site A under the influence of peptidyl transferase enzyme with release of the peptidyl tRNA.Site P is now free. In the presence of the translocase enzyme , GTP and elongation factor 2 , the ribosome moves in the direction of a 5'------3' direction on mRNA to translocate the newly formed peptidyl tRNA in site P,

* Site A is now free. It occupies by a third aminoacyl~tRNA according to codon-anticodon and the process is repeated. The polypeptide chain is thus increased each time by one amino acid.

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C- TERMINATIONAfter many cycles of elongation , the terminating codon of mRNA is reached at site A. There is no tRNA with anticodon to recognize the terminating codon of mRNA. Releasing factor hydrolyzes the bond between the peptide and tRNA at site P , and release the protein molecule.

POST-TRANSLATIONAL REGULATIONSome proteins after being translated undergo additional changes to be active. These changes may be1- Addition of carbohydrateTo form glycoprotein e.g. Immunoglobulin.

2- Conversion of inactive to active forme.g. proinsulin is converted to active insulin by removal of C chain.

3- Conversion of proline to hydroxyproline.

REGULATION OF PROTEIN SYNTHESIS : OPERON MODELOperon can regulate protein biosynthesis . Operon is a group of compo¬nents in DNA that are essential for the transcription of structural gene(s) of certain protein(s). Each component is formed of a number of nucleotidein DNA molecule. These components are1- Promoter.2- Operator.3- Structural gene(s).4- Regulator gene.

Structural genes

Regulator gene Promotor Operator

Transcription of regulator gene leads to the formation of a protein termed : repressor. This repressor has a high affinity for the operator.The operator is between the promoter site (at which the RNA polymerase is attached) and the structural genes (G1 , G2 G3). When repressor is atta¬ched to the operator , this prevents the transcription of the structural genes.

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Inducer is a substance that can bind with the repressor -------- Opera¬tor is free ------------- Promotor together with RNA-polymerase enzyme will initiate transcription of structural genes to synthesize proteins. Examples of inducers and repressors1- Clucocorticoids act as inducers for the synthesis of gluconeogenic enzv¬mes.2- Insulin acts as an inducer for glycolytic enzymes and as repressor for gluconeogenic enzymes.

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