Biochemistry PDF

1. Biochemistry Power to Understand What We Are!  What is Biochemistry? Generally biochemistry is the study of life at the molecular level. Uses basic laws of chemistry, biology and physics to explain processes of living cells.  Because life depends on biochemical reactions, biochemi...

1. Biochemistry Power to Understand What We Are!  What is Biochemistry? Generally biochemistry is the study of life at the molecular level. Uses basic laws of chemistry, biology and physics to explain processes of living cells.  Because life depends on biochemical reactions, biochemistry has become the basic language of all life sciences.  Why study biochemistry? ▪ Lead us to fundamental understanding of life. ▪ Understand important issues in medicine, health, and nutrition. Has led to greater molecular understanding of diseases such as diabetes, sickle cell anemia, and cystic fibrosis. Next frontier: AIDS, cancer, Alzheimer’s Disease. ▪ Advance biotechnology industries Biotechnology is the application of biological cells, cell components, and biological properties to technically and industrially useful operations. i. Major objective of biochemistry ▪ Complete understanding at the molecular level of all the chemical processes associated with living cells. Isolate-the numerous molecules found in cells, Determine-their structures, Analyze-how they function. ii. Further objective ▪ Attempt to understand how life began. ▪ An appreciation of the biochemistry of less complex form of life is often direct relevance to human biochemistry. 1.2 The major chemical constituents of cells Biochemistry = the chemistry of life Elements - These are single substances which cannot be broken down any more. there are 110 different elements that are known to man.  …cont’d  The living matter is composed of mainly six elements- Carbon, Hydrogen, Oxygen, Nitrogen, Phosphorus and Sulphur. (CHONPS)  These elements together constitute about 90% of the dry weight of the human body.  Several other functionally important elements are also found in the cells. These include Ca, K, Na, Cl, Mg, Fe, Cu, Co, Zn, F, Mo and Se.  Carbon-a unique element of life  Carbon is the most predominant and versatile element of life.  It possesses as unique property to form infinite number of compounds.  This is attributed to the ability of carbon to form: stable covalent bonds and C-C chains of unlimited length.  It is estimated that about 90% of compounds found in living system invariably contain carbon. Carbon can form immensely diverse compounds, from simple to complex. Compounds - These are two or more elements combined. These elements are bonded together. Complex Molecule Simple Molecule Methane with 1 Carbon atom DNA with tens of Billions of Carbon atoms  Organization of Life ▪ Life is composed of lifeless chemical molecules.  elements  simple organic compounds (monomers)  macromolecules (polymers)  supramolecular structures  organelles  cells  tissues  organisms  Complex Biomolecules ▪ As regards lipids, it may be noted that they are not biopolymers in a strict sense, but majority of them contain fatty acids.  Composition of the body and major classes of molecules  The human body is composed of a few elements that combine to form a great variety of biomolecules.  Biomolecules are compounds of carbon with a variety of functional groups Element  The simplest kind of matter which can not be split in to two or more simpler substances by chemical reactions. Chemical composition of a normal man (weight 65 kg) Constituent Percent (%) Weight (kg) Water 61.6 40 Protein 17.0 11 Lipid 13.8 9 Carbohydrate 1.5 1 Minerals 6.1 4 Fig. Some common functional groups of biomolecules. 1.3 Acid, Base and Buffer systems 14 5 coffee 15  The Body and pH  Homeostasis of pH is tightly controlled  Extracellular fluid = 7.4  Blood = 7.35 – 7.45 ✓ If pH is < 6.8 or > 8.0 death occurs  Acidosis (acidemia) below 7.35  Alkalosis (alkalemia) above 7.45 16  …cont’d  Acids are H+ donors.  Bases are H+ acceptors.  Acids and bases can be:  Strong – dissociate completely in solution  HCl, NaOH  Weak – dissociate only partially in solution  Lactic acid, carbonic acid  A weak acid has a characteristic dissociation constant, Ka.  The relationship between the pH of a solution, the Ka of an acid, and the extent of its dissociation are given by the Henderson-Hasselbalch 17 equation.  Acid/conjugate base pairs HA + H2O A - + H 3O + HA A- + H + HA = acid ( donates H+)(Bronstad Acid) A- = Conjugate base (accepts H+)(Bronstad Base) Ka = [H+][A-] Ka & pKa value describe tendency to loose H+ [HA] large Ka = stronger acid pKa = - log Ka small Ka = weaker acid  …cont’d  A buffer is a mixture of an undissociated acid and its conjugate base (the form of the acid having lost its proton).  It causes a solution to resist changes in pH when either H+ or OH- is added.  A buffer has its greatest buffering capacity in the pH range near its pKa (the negative log of its Ka).  Two factors determine the effectiveness of a buffer,: its pKa relative to the pH of the solution and its concentration.  Henderson-Hasselbalch Equation HA = weak acid 1) Ka = [H+][A-] [HA] A- = Conjugate base 2) [H+] = Ka [HA] [A-] 3) -log[H+] = -log Ka -log [HA] [A-] * H-H equation describes the relationship between pH, pKa and buffer 4) -log[H+] = -log Ka +log [A-] concentration [HA] 5) pH = pKa +log [A-] [HA]  …cont’d  If the pKa for a weak acid is known, this equation can be used  to calculate the ratio of the unprotonated to the protonated form at any pH.  From this equation, you can see that a weak acid is 50% dissociated at a pH equal to its pKa.  Most of the metabolic carboxylic acids have pKa ‘s between 2 and 5, depending on the other groups on the molecule. The pKa reflects the strength of an acid.  Acids with a pKa of 2 are stronger acids than those with a pKa of 5 because, at any pH, a greater proportion is dissociated.  The body produces more acids than bases Acids take in with foods. Cellular metabolism produces CO2. Acids produced by metabolism of lipids and proteins. CO2 Volatile acid H2CO3 CO2+ H2O CO2 CO2 H2SO4 H3PO4 Fixed acid Uric acid Lactic acid Ketone body 22  Maintenance of blood pH Three lines of defense to regulate the body’s acid-base balance – Blood buffers – Respiratory mechanism – Renal mechanism 23  Buffer systems Take up H+ or release H+ as conditions change Buffer pairs – weak acid and a base Exchange a strong acid or base for a weak one Results in a much smaller pH change 24  Principal buffers in blood in Plasma in RBC H2CO3 / HCO3- 35% 18% HHb / Hb- 35% HPro / Pro- 7% H2PO4- / HPO42- 5% Total 42% 58% 25  Bicarbonate buffer Predominant buffer system in ECF Sodium Bicarbonate (NaHCO3) and carbonic acid (H2CO3) HCO3- : H2CO3: Maintain a 20:1 ratio [HCO3－] pH=pKa+lg H2CO3 H+ + HCO3- [H2CO3] 24 = 6.1+ lg 1.2 20 = 6.1+ lg 1 26 = 6.1+1.3 = 7.4  Bicarbonate buffer HCl + NaHCO3 H2CO3 + NaCl NaOH + H2CO3 NaHCO3 + H2O 27  Phosphate buffer Major intracellular buffer NaH2PO4-Na2HPO4 H+ + HPO42- H2PO4- OH- + H2PO4- H2O + HPO42- 28  Protein Buffers Include plasma proteins and hemoglobin Carboxyl group gives up H+ Amino Group accepts H+ 29  2. Respiratory mechanisms CO2 CO2 Exhalation of CO2 Rapid, powerful, but only works with volatile acids H+ + HCO3- H2CO3 CO2 + H20 Doesn’t affect fixed acids like lactic acid Body pH can be adjusted by changing rate and depth of breathing 30  3. Kidney excretion Most effective regulator of pH The pH of urine is normally acidic (~6.0) – H+ ions generated in the body are eliminated by acidified urine. Can eliminate large amounts of acid (→H+) Reabsorption of bicarbonate (HCO3-) (←HCO3-) Excretion of ammonium ions(NH4+) (→NH4+) If kidneys fail, pH balance fails 31  Rates of correction Buffers function: almost instantaneously Respiratory mechanisms: take several minutes to hours Renal mechanisms: may take several hours to days 32 33  Acid-Base Imbalances pH< 7.35: acidosis pH > 7.45: alkalosis The body response to acid-base imbalance is called compensation – The body gears up its homeostatic mechanism and makes every attempt to restore the pH to normal level. – May be complete if brought back within normal limits – Partial compensation if range is still outside norms.34  Acid-Base Imbalances Acidosis- a decline in blood pH ↓ – Metabolic acidosis: due to a decrease in bicarbonate. ↓ – Respiratory acidosis: due to an increase in carbonic acid. ↑ Alkalosis- a rise in blood pH ↑ – Metabolic alkalosis: due to an increase in bicarbonate.↑ – Respiratory alkalosis : due to a decrease in carbonic acid. ↓ 35  Compensation If underlying problem is metabolic, hyperventilation or hypoventilation can help: respiratory compensation. If problem is respiratory, renal mechanisms can bring about metabolic compensation. 37  Metabolic Acidosis Bicarbonate deficit (↓) - blood concentrations of bicarb drop below 22mEq/L (milliequivalents / liter) Causes: – Loss of bicarbonate through diarrhea or renal dysfunction – Accumulation of acids (lactic acid or ketones) – Failure of kidneys to excrete H+ Commonly seen in severe uncontrolled DM (ketoacidosis). 38  Respiratory Acidosis Carbonic acid excess caused by blood levels of CO2 above 45 mm Hg. Hypercapnia – high levels of CO2 in blood Causes: – Depression of respiratory center in brain that controls breathing rate – drugs or head trauma – Paralysis of respiratory or chest muscles – Emphysema 40  Metabolic Alkalosis Bicarbonate excess↑ - concentration in blood is greater than 26 mEq/L Causes: – Excess vomiting = loss of stomach acid – Excessive use of alkaline drugs – Certain diuretics – Endocrine disorders: aldosterone ↑ – Heavy ingestion of antacids 42  Respiratory Alkalosis Carbonic acid deficit↓ pCO2 less than 35 mm Hg (hypocapnea) Most common acid-base imbalance Primary cause is hyperventilation – Hysteria, hypoxia, raised intracranial pressure, excessive artificial ventilation and the action of certain drugs (salicylate) that stimulate respiratory centre. 44  Mixed acid-base disorders Sometimes, the patient may have two or more acid-base disturbances occurring simultaneously. In such instances, both HCO3- and H2CO3 are altered. 46 Reading Assignment 1. Biological importance of Water 2. Types of chemical bond 47 , , 2. Carbohydrates  Learning objectives At the end of this session the students will be able to:-  Explain what is meant by the terms monosaccharide, disaccharide, oligosaccharide, and polysaccharide.  Describe the formation of glycosides and the structures of the important disaccharides and polysaccharides.  Explain the roles of carbohydrates.  Definitions  Glycobiology is the study of the roles of sugars in health and disease.  The glycome is the entire complement of sugars of an organism, whether free or present in more complex molecules.  Glycomics, an analogous term to genomics and proteomics, is the comprehensive study of glycomes, including genetic, physiological, pathological, and other aspects.  Sources of Carbohydrates 4  Carbohydrates ▪ are the most abundant organic molecules in nature. Biomedical Importance(functions) 1.source and storage of energy, glucose and glycogen respectively. 2. Structural components. E.g. skin, bone, cell mm 3. Involved in cell-cell interaction 4. Their derivatives are drugs. E.g. erythromycin 5. Survival of Antarctic fish in icy environment is due to presence of anti-freeze glycoprotein's in their blood. 6. Ascorbic acid, a derivative of carbohydrate is a water-soluble vitamin.. Carbohydrates Metabolic/Nutritional  principal part of the energy  Carbohydrate intake can take place in different forms like sugar, starch, fibers etc.  Fiber does wonders in keeping your bowel function going smooth.  Carbohydrates add on to the taste and appearance of food item, thus making the dish tempting and mouth-watering  They are sometimes used as flavours and sweeteners.  Carbohydrates aid in regulating blood glucose and also do good to our body by breaking down fatty acids, thus preventing ketosis.  Chemical Nature of Carbohydrates ▪ They are polyhydroxy alcohols with a functional aldehyde or keto group. Most sugars have formula Cn(H2O)n, “hydrate of carbon.” Classification of Carbohydrates based on number of carbon chains present; they are: 1. Monosaccharides - simple sugars with multiple OH groups. Based on number of carbons (3, 4, 5, 6), a monosaccharide is a triose, tetrose, pentose or hexose. 2. Disaccharides - 2 monosaccharides covalently linked. 3. Oligosaccharides - a few monosaccharides covalently linked. (3-10 monomer) 4. Polysaccharides - polymers consisting of chains of monosaccharide or disaccharide units. (>10 monomer)  Types of Carbohydrates Simple Carbohydrates – monosaccharides – disaccharides Complex Carbohydrates – oligosaccharides – polysaccharides glycogen starches Fig. examples of an aldose (A) Fibers and a ketose(B) sugar.  1. Monosaccharides: Single Sugars Glucose – carbohydrate form used by the body, referred to as “blood sugar” – basic sub-unit of other larger carbohydrate molecules – found in fruits, vegetables, honey The oxidation of glucose by glucose oxidase (a highly specific test for glucose) is used by clinical and other laboratories to measure the amount of glucose in urine using a dipstick. 9  Monosaccharides: Single Sugars Fructose – sweetest of the sugars – occurs naturally in fruits & honey, “fruit sugar” – combines with glucose to form sucrose Galactose – combines with glucose to form lactose, “milk sugar” 10  , 1. Monosaccharides They can not be hydrolyzed to small compounds. Their general formula is Cn(H2O)n. They are also called as simple sugars. Nomenclature  have common (trivial) names and systematic names.  Systematic name indicates both the number of carbon atoms present and aldehyde or ketone group. ✓ E.g. glyceraldehyde is a simple sugars containing three carbon atoms and a aldehyde group. Simple sugars containing three carbon atoms are referred as trioses. In addition, sugars containing aldehyde group or keto group are called as aldoses or ketoses, respectively.  , Thus, the systematic name for glyceraldehyde is aldotriose.  Like wise a simple sugar with three carbon atoms and a keto group is called as ketotriose. Fig. examples of an aldose (A) and a ketose(B) sugar.  Properties of monosaccharides 1. Optical Isomerism All the monosaccharides except dihydroxyacetone contain at least one asymmetric carbon atom and hence they exhibit optical isomerism.  D and L-glyceraldehyde are used as parent compounds to designate all other sugars (compounds) as D or L forms. CHO CHO D & L designations are H C OH HO C H based on the configuration CH2OH CH2OH about the single D-glyceraldehyde L-glyceraldehyde asymmetric C in CHO CHO glyceraldehyde. H C OH HO C H CH2OH CH2OH The lower representations D-glyceraldehyde L-glyceraldehyde are Fischer Projections.  O H O H C C H – C – OH HO – C – H For sugars with more than one ‘ HO – C – H H – C – OH chiral center, D or L refers to H – C – OH HO – C – H the asymmetric C farthest H – C – OH HO – C – H from the aldehyde or keto CH2OH CH2OH group. D-glucose L-glucose If the hydroxyl group of the highest numbered chiral carbon is pointing to the right, the sugar is designated as D (Dextro: Latin for on the right side). If the hydroxyl group is pointing to the left, the sugar is designated as L (Levo: Latin for on the left side). Most naturally occurring carbohydrates are of the D-configuration  2.Optical Activity Monosaccharides except dihydroxy acetone exhibit optical activity because of the presence of at least 1 asymmetric carbon atom. If a sugar rotates plane polarized light to right then it is called as dextrorotatory and if a sugar rotates the plane polarized light to the left then it is called as levorotatory. Usually ‘+’ sign indicates dextrorotation and ‘–’ sign indicates levorotation of a sugar. CHO CHO H OH HO H CH2OH CH2OH D-glyceraldehyde L-glyceraldehyde R-(+)-glyceraldhyde S-(-)-glyceraldhyde (+)-rotation = dextrorotatory (-)-rotation = levorotatory  The Aldotetroses Glyceraldehyde is the simplest carbohydrate (C3, aldotriose, 2,3- dihydroxypropanal). The next carbohydrate are aldotetroses (C4, 2,3,4-trihydroxybutanal). aldotriose 2n H CHO OH CH2OH HO CHO H CH2OH D-glyceraldehyde L-glyceraldehyde aldotetroses 1 CHO 1 CHO H 2 OH HO 2 H highest numbered highest numbered "chiral" carbon H 3 OH HO 3 H "chiral" carbon 4 CH2OH 4 CH2OH D-erythrose L-erythrose CHO CHO HO H H OH highest numbered highest numbered H OH HO H "chiral" carbon "chiral" carbon CH2OH CH2OH D-threose L-threose 16  Aldopentoses and Aldohexoses Aldopentoses: C5, three chiral carbons, eight stereoisomers CHO CHO CHO CHO H OH HO H H OH HO H H OH H OH HO H HO H H OH H OH H OH H OH CH2OH CH2OH CH2OH CH2OH D-ribose D-arabinose D-xylose D-lyxose Aldohexoses: C6, four chiral carbons, sixteen stereoisomers CHO CHO CHO CHO CHO CHO CHO CHO H OH HO H H OH HO H H OH HO H H OH HO H H OH H OH HO H HO H H OH H OH HO H HO H H OH H OH H OH H OH HO H HO H HO H HO H H OH H OH H OH H OH H OH H OH H OH H OH CH2OH CH2OH CH2OH CH2OH CH2OH CH2OH CH2OH CH2OH D-allose D-altrose D- glucose D-mannose D-gulose D-idose D-galactose D-talose 17 3.Isomers and epimers ✓ Compounds that have the same chemical formula but have different structures are called isomers. ✓ E.g. fructose, glucose, mannose, and galactose are all isomers of each other, having the same chemical formula, C6H12O6. ✓ Carbohydrate isomers that differ in configuration around only one specific carbon atom (with the exception of the carbonyl carbon) are defined as epimers of each other. 4. Functional Isomers  same molecular formulae but different functional groups.  For example, glucose and fructose have same molecular formulae C6H12O6, but glucose contains aldehyde as functional group and fructose contains keto group.  H O C CH2OH H C OH C O HO C H HO C H H C OH H C OH H C OH H C OH CH2OH CH2OH D-glucose D-fructose Aldoses (e.g., Ketoses (e.g., glucose) have an fructose) have aldehyde group a keto group, at one end. usually at C2.  Cyclic Structure for Glucose Glucose cyclic hemiacetal formed by reaction of -CHO with - OH on C5. => 20 D-glucopyranose  Cyclic Structure for Fructose Cyclic hemiketal formed by reaction of C=O at C2 with -OH at C5. D-fructofuranose => 21  5. Anomers Cyclization of glucose produces a new asymmetric center at C1. The 2 stereoisomers are called anomers, α & β. Haworth projections represent the cyclic sugars as having essentially planar rings, with the OH at the anomeric C1:  α (OH below the ring)  β (OH above the ring). 6 CH2OH 6 CH2OH 5 O 5 O H H H OH H H 4 H 1 4 H 1 OH OH OH OH OH H 3 2 3 2 H OH H OH -D-glucose -D-glucose 6. Enantiomers  A special type of isomerism is found in the pairs of structures that are mirror images of each other.  These mirror images are called enantiomers. Enantiomers (mirror images) of glucose. Joining of monosaccharides  Monosaccharides can be joined to form disaccharides, oligosaccharides, and polysaccharides.  The bonds that link sugars are called glycosidic bonds. These are formed by enzymes known as glycosyltransferases. Joining and Cleaving Sugar Molecules 25  2. Disaccharides  They provide energy to human body.  They consist of two monosaccharide units held together by glycosidic bond. So, they are glycosides.  Most commons are maltose, lactose and sucrose a) Maltose (two glucose units )  The glycosidic linkage of maltose is symbolized as α (1→4). i.e. The anomeric carbon is bonded to oxygen on C4 of second sugar. And α-indicates the configuration of anomeric carbon atoms of both glucose units.  Systematic name for maltose is O-α-D glucopyranosyl-(1→4)- α-D glucopyranose.  Maltose is a reducing sugar because anomeric carbon of second glucose is free.  6 CH2OH 6 CH2OH Disaccharides: H 5 O H H 5 O H H H Maltose, a cleavage 4 OH H 1 4 OH H 1 product of starch (e.g., OH 3 2 O 3 2 OH amylose), is a H OH maltose H OH disaccharide with an α(1→ 4) glycosidic 6 CH2OH 6 CH 2OH 5 link between C1 - C4 H H O H 5 O OH H OH of 2 glucoses. 4 OH H 1 O 4 OH H 1 H H It is the α anomer (C1 OH 3 2 3 2 O points down). H OH cellobiose H OH Cellobiose, a product of cellulose breakdown, is the otherwise equivalent β anomer (O on C1 points up). The β(1 → 4) glycosidic linkage is represented as a zig-zag, but one glucose is actually flipped over relative to the other. Source for maltose  Maltose is present in germinating cereals and in barley.  Commercial malt sugar contains maltose  may be formed during the hydrolysis of starch.  b)Lactose Structure  It contains one glucose and one galactose.  It is symbolized as β (1→4).  O-β-D galactopyranosyl-(1→4)-β-D-glucopyranose.  It is a reducing sugar because anomeric carbon of glucose is free. Source for lactose  Lactose is synthesized in mammary gland and hence it occurs in milk.  Lactose  Galactose + glucose linked 1-4’.  “Milk sugar.” CH2OH CH2OH O O H OH..... H OH H 1 O 4 H H OH H OH H H..... OH H H OH H OH -Galactose Glucose − and −Lactose 30  c) Sucrose  It contains glucose and fructose.  common table sugar.  glucose is in α-form whereas fructose is in β-form in sucrose.  α, β(1→2).  O-α-D-glucopyranosyl-(1→2)-β-D-fructofuranose.  Nonreducing sugar b/c both the functional groups of glucose and fructose are involved in glycosidic linkage. Source of sucrose  Ripe fruit juices like pineapple, sugar cane, juice and honey are rich sources for sucrose.  It also occurs in juices of sugar beets, carrot roots and sorghum.  CH2OH O H H -Glucose H 1 OH H OH H OH CH2OH O O -Fructose OH 2 H H CH2OH OH H Sucrose  Oligosaccharides  Beans and peas contain some oligosaccharides.  These oligosaccharides contain 4 to 5 monosaccharide units.  Stachyose and verbascose are a few such oligosaccharides.  Usually these oligosaccharides are not utilized in human body.  Also found in glycoproteins where they have important functions. Oligosaccharides are also important constituents of glycolipids present in cell membrane  Complex Carbohydrates Oligosaccharides – short carbohydrate chains of 3 - 10 monosaccharides – found in legumes and human milk – Examples: cannot be broken down by human enzymes, though can be digested raffinose by colonic bacteria stachyose 34  Polysaccharides  They are polymers of monosaccharides.  They contain more than ten monosaccharide units.  The monosaccharides are joined together by glycosidic linkage. – alpha () bonds (starch) – beta () bonds (found in fiber)  Classification of Polysaccharides  Two types on the basis of the type of monosaccharide present. a) Homopolysaccharides  They are entirely made up of one type of monosaccharides.  On hydrolysis, they yield only one kind of monosaccharide. b) Heteropolysaccharides  They are made up of more than one type of monosaccharides.  On hydrolysis they yield more than one type of monosaccharides.  Homopolysaccharides  Important homopoly-saccharides are starch, glycogen, cellulose.  All these contain glucose as repeating unit.  Other name for homopolysaccharides are homoglycans. Starch Structure  It consist of two parts. A minor amylose component and a major amylopectin component.  CH2OH 6CH OH CH2OH CH2OH CH2OH 2 O 5 O H O H O H H O H H H H H H H H H H H OH H 1 4 OH H 1 OH H OH H OH H O O O O OH OH 2 3 H OH H OH H OH H OH H OH amylose Polysaccharides: Plants store glucose as amylose or amylopectin, glucose polymers collectively called starch. Glucose storage in polymeric form minimizes osmotic effects. Amylose is a glucose polymer with (1→4) linkages. The end of the polysaccharide with an anomeric C1 not involved in a glycosidic bond is called the reducing end.  CH2OH CH2OH H O H H O H amylopectin H H OH H OH H 1 O OH O H OH H OH CH2OH CH2OH 6 CH2 CH2OH CH2OH H O H H O H H 5 O H H O H H O H H H H H H OH H OH H OH H 1 4 OH H OH H 4 O O O O OH OH 2 3 H OH H OH H OH H OH H OH Amylopectin is a glucose polymer with mainly (1→4) linkages, but it also has branches formed by (1→6) linkages. Branches are generally longer than shown above. The branches produce a compact structure & provide multiple chain ends at which enzymatic cleavage can occur.  Function 1. It is the major polysaccharide present in our food. 2. It is also called as storage polysaccharide because it serve as reserve food material in plants. 3. It is present in food grains, tubers and roots like rice, wheat, potato and vegetables.  Complex Carbohydrates Glycogen – highly branched chains of glucose units – animal storage form of carbohydrate found in LIVER and MUSCLE Humans store ~ 100g in liver; ~ 400g in muscle – negligible source of carbohydrate in the diet (meat) 41  Glycogen  similar to that of amylopectin of starch. But the number of branches in glycogen molecule is much more than amylopectin.  There is one branch point for 6-7 glucose residues. Function 1. It is the major storage polysaccharide (carbohydrate) in human body. 2. It is mainly present in liver and muscle. 3. It is also called as animal starch.  CH2OH CH2OH H O O glycogen H H H H H OH H OH H 1 O OH O H OH H OH CH2OH CH2OH 6 CH2 CH2OH CH2OH H O H H O H H 5 O H H O H H O H H H H H H OH H OH H OH H 1 4 OH H OH H 4 O O O O OH OH 3 2 H OH H OH H OH H OH H OH Glycogen, the glucose storage polymer in animals, is similar in structure to amylopectin. But glycogen has more (1→6) branches. The highly branched structure permits rapid glucose release from glycogen stores, e.g., in muscle during exercise. The ability to rapidly mobilize glucose is more essential to animals than to plants.  Cellulose  It has linear chain of glucose residues, which are linked by β(1→4) glycosidic linkage.  It occurs as bundle of fibres in nature.  The linear chains are arranged side by side and hydrogen bonding between adjacent stands stabilizes the structure.  The role of cellulose is to impart strength and rigidity to plant cell walls, which can withstand high hydrostatic pressure gradients. Osmotic swelling is prevented. CH2OH 6CH OH CH2OH CH2OH CH2OH 2 O 5 O O H O H O OH H H H H H H H H OH H 1 O 4 OH H 1 O OH H O OH H O OH H OH H H H H 2 H 3 H OH H OH H OH H OH H OH cellulose  Starch Glycogen Cellulose 1.Nature: Stored form of Structural form of carbohydrate Stored form of carbohydrate in plants. carbohydrates in animals. in plant cells but prevents constipation in human. 1.Source: Muscles and liver Linen and cotton are nearly pure Cereals, e.g., wheat, rice, and tubers, e.g., cellulose. potatoes. 1.Solubility: Water soluble forming Water insoluble. Amylose is water soluble and amylopectin is colloidal solution. insoluble. 1.Nature of the chains: Branched chain similar to Straight chain (large number of Amylose is helical straight chain (-glucose amylopectin but its -glucose units linked by - units linked by -1,4-glucosidic bonds). trees are shorter and 1,4- glucosidic bonds). Amylopectin is branched chain (-glucose have more branches units linked by -1,4- and -1,6-glucosidic than amylopectin tree. bonds). 1.Reaction with iodine: Gives red color. No color. Amylose gives blue color and amylopectin gives red color. 1.Digestibility: Digestible by amylase into Non-digestiblebut HCl hydrolysis Is hydrolyzed by HCl or amylase into dextrins dextrins and maltose. gives cellobiose. and maltose. HETEROPOLYSACCHARIDES  also called mucopolysaccharides & glycosaminoglycans.  Mucopolysaccharides consist of repeating disaccharide units(of two types monosaccharides.)  mucopolysaccharides are component of connective tissue, hence often called structural polysaccharides.  Mucopolysaccharides are also components of extracellular matrix of bone, cartilage and tendons.  The complex of mucopolysaccharide and protein is called as proteoglycan.  Mucopolysaccharides also function as lubricants and shock absorbers Heparin  The repeating disaccharide unit of heparin consist of glucosamine and either iduronic acid or glucuronic acid.  Majority of uronic acids are iduronic acids. Further amino groups of glucosamine is sulfated. iduronate-2-sulfate N-sulfo-glucosamine-6-sulfate H CH2OSO3− H O H O H COO− H OH H O OH H H O H OSO3− H NHSO3− heparin or heparan sulfate - examples of residues  Functions 1. Heparin is a normal anti-coagulant present blood. 2. It is produced by mast cells present in the arteries, liver, lung and skin. 3. Unlike other glycosaminoglycans, heparin is an intracellular component. 4. It can be used during the treatment of myocardial infarction as well as for the prevention of deep venous thrombosis during hospitalizations.  Complex Carbohydrates Fiber Dietary Fiber – non-digestible carbohydrates (chains of monosaccharides) and lignin that are intact and intrinsic in plants (includes oligosaccharides) Functional Fiber – isolated, non-digestible carbohydrates that have beneficial physiological effects in humans 49  Complex Carbohydrates Fiber cont. dietary fiber found in all types of plant foods refining removes fiber from whole grains and other foods 50  Complex Carbohydrates Fiber cont. types of non-starch polysaccharides include: cellulose hemicelluloses pectins gums & mucilages -glucans chitin & chitosan lignans 51  Summery Functions of Carbohydrates 1) Energy glucose fuels the work of most of the body’s cells – preferred fuel of NERVOUS TISSUE (the brain, nerves) and RED BLOOD CELLS (RBC) excess glucose is stored as GLYCOGEN in liver and muscle tissue 52  Functions of Carbohydrates 2) Sparing Body Protein if diet does not provide enough glucose, then other sources of glucose must be found if carbohydrate intake < 50 - 100 g, body protein will be used to make glucose an adequate supply of carbohydrate spares body proteins from being broken down to synthesize glucose 53  Functions of Carbohydrates 3) Preventing Ketosis (Anti-ketogenic) carbohydrates required for the complete metabolism of fat incomplete fat metabolism produces KETONES an adequate supply of carbohydrate (> 50 – 100 g per day) prevents KETOSIS 54  Fiber beneficial for weight control by contributing to satiety & delay gastric emptying soluble fibers lower blood cholesterol to help reduce risk of cardiovascular disease minimizes risk of and helps control Type II Diabetes insoluble fibers help promote intestinal health by enlarging stool size and easing passage of stool 55  Soluble Fiber examples include gums, pectins, mucilages, some hemicelluloses functions: – delay gastric emptying – slow transit through the digestive system – delay glucose absorption – bind to bile, help decrease cholesterol food sources: fruits 56  Insoluble Fiber examples include cellulose, hemicellulose functions: – speed transit through the digestive tract – delay glucose absorption – increase fecal weight and soften stool to ease passage – reduces risk of hemorrhoids, diverticulitis and appendicitis food sources: cereal grains, legumes, vegetables, nuts 57  Fiber: Too much of a good thing? Excessive amounts of fiber may lead to: – displacement of other foods in the diet – intestinal discomfort – interference with the absorption of other nutrients 58  Summary Carbohydrates are major constituents of human food and human tissues. They are characterized by the type and number of monosaccharide residues in their molecules. Glucose is the major metabolic fuel of humans and a universal fuel of the fetus. The physiologically important monosaccharides include glucose, the "blood sugar," and ribose, an important constituent of nucleotides and nucleic acids. The important disaccharides include maltose (glucosyl-glucose), sucrose(glucosyl-fructose), and lactose (galactosyl-glucose),. Starch and glycogen are storage polymers of glucose in plants and animals, respectively. Starch is the major metabolic fuel in the diet. 59  References  DM Vasudevan, Sreekumari S. Text Book of Biochemistry for Medical Students, 5th Edition. 2007.  Murray R.K et al. Harper's illustrated Biochemistry 30th edition.  Pamela C.C, and Richard A.H., Lippincott's Illustrated Reviews: Biochemistry 5th edition, J.B.  Thomas M. Devlin. Text Book of Biochemistry with Clinical Correlations. 6th Edition, 2006, Wiley-Liss Publication, USA  Marks' Essential Medical Biochemistry, 2nd Edition Copyright 2007 Lippincott Williams & Wilkins. , Lipids  Introduction ▪ Lipids are a heterogeneous group of organic compounds defined by their solubility in nonpolar solvents such as chloroform, ether, and benzene and by their poor solubility in water.  Unlike the polysaccharides ,proteins and nucleic acids, lipids are not polymers. Further, lipids are mostly small molecules. ▪ Lipids may be polar or nonpolar (amphipathic). Major polar lipids include fatty acids, cholesterol, glycerophosphatides, and glycosphingolipids. ✓ Very short chain fatty acids and ketone bodies are readily soluble in water. Nonpolar lipids serve principally as storage and transport forms of lipid. E.g triacylglycerols (also called triglycerides) and cholesteryl esters. Occurrence Lipids present in humans, animals, plants and micro- organisms to some extent. ✓ Animal fat, egg yolk, butter and cheese are lipids of animal origin. ✓ vegetable or cooking oils are lipids are plant origin. Functions of lipids 1. Under skin it serve as thermal insulator against cold. 2. Fat around kidney serve as padding against injury. 3. Serve as a source of energy for cell like carbohydrates. 4. It is an ideal form of storing energy in the human body compared to carbohydrates and proteins because: (a) Energy content of fat is higher. (b) Only fat can be stored in a water free form which is not possible with carbohydrates and proteins  , 5. Lipids are structural components of cell membrane and nervous tissue. 6. Some lipids serve as precursors for the synthesis of complex molecules. For example, acetyl-CoA is used for the synthesis of cholesterol. 7. Lipoproteins, which are complexes of lipids and proteins are involved in the transport of lipids in the blood and components of cell membrane. 8. Some lipids serve as hormones and fat soluble vitamins are lipids. 9. Fats are essential for the absorption of fat soluble vitamins. 10. Fats serve as surfactants by reducing surface tension.  , 11. Eicosanoids which have profound biological actions are derived from the essential fatty acids. 12. Lipids present in myelinated nerves act as insulators for propagation of depolarization wave. 13. Some saturated fatty acids are anti-microbial and anti-fungal agents. 14.Lipids are an important group of antigens of parasites that cause filariasis, cysticercosis, leishmaniasis and schistosomiasis in third world countries. Anti-lipid antibodies are found in the blood of individuals affected with these diseases. 15. Saturated free fatty acids (SFFAs) are pheromones of animals like tiger etc... Classification of Lipids  Lipids Simple Complex /Compou Derived nd Fat or oil Waxes Fatty Fat Sol Carotenoid Acids/Ster Vitamin s oids s Glycolipid s Phospholipids Lipoproteins Sulfolipids  Classification of Lipids  Lipids are broadly classified into simple, complex, derived and miscellaneous lipids, which are further subdivided into different groups. 1. Simple lipids:- esters of fatty acids with different alcohols. a. Fats and oils ( TAGs) :- These are esters of fatty acids with glycerol. The difference between fat and oil is only physical. Thus, oil is a liquid while fat is a solid at room temperature. b. Waxes:- Esters of fatty acids(usually long chain) with alcohols other than glycerol like mericyle and cetyle.  2. Complex (Compound) lipids  These are esters of fatty acids with alcohols containing additional groups such as phosphate, nitrogenous base, carbohydrate, protein …etc. A. Phospholipids:- Esters of the above type containing phosphoric acid and frequently a nitrogenous base. i) Glycerophospholipids These phospholipids contain glycerol as the alcohol E.g. lecithin, cephalin. ii) Sphingophospholipids The alcohol is sphingosine. E.g. sphingomyelin B. Glycolipids  These lipids contain a fatty acid, carbohydrate and nitrogenous base. The alcohol is sphingosine, hence they are also called as glycosphingolipids. Glycerol and phosphate are absent. E.g. Cerebrosides, gangliosides. C. Lipoproteins: Macromolecular complexes of lipids with proteins. D. Other complex lipids: Sulfolipids, amino lipids and lipopolysaccharides are among the other complex lipids. 3. Derived lipids  These are the derivatives obtained on the hydrolysis of simple and complex lipids which possess the characteristics of lipids. These include fatty acids, mono- and diacylglycerols, lipid(fat) soluble vitamins, steroid hormones, cholesterol and ketone bodies. 4. Miscellaneous lipids: These include a large number of compounds possessing the characteristics of lipids. E.g., carotenoids, squalene,hydrocarbons such as pentacosane(in bees wax), terpenes etc. Neutral Lipids: These are lipids which are uncharged. These are mono-, di-, and triacylglycerols, cholesterol and cholesteryl esters.  Fatty acids ▪ Are carboxylic acids with hydrocarbon side chain. ▪ They are the simplest form of lipids. The anionic group has an affinity for water, giving the fatty acid its amphipathic nature (having both a hydrophilic and a hydrophobic region).  …cont’d ▪ Fatty acids with less than 12 and more than 24 carbon atoms are uncommon in biological systems.  Palmitic acid (l6C) and stearic acid(18) are the most common.  Most of the fatty acids have even number of carbon atoms. This is due to biosynthesis of fatty acids mainly occurs with the sequential addition of 2 carbon units. ▪ They rarely occur in free form and are usually found in esterified form as the major components of various lipids.  ,,  Long-chain fatty acids (LCFAs), the hydrophobic portion is predominant.  highly water-insoluble, and must be transported in the circulation in association with protein.  More than 90% of the fatty acids found in plasma are in the form of fatty acid esters (primarily triacylglycerol, cholesteryl esters, and phospholipids) contained in circulating lipoprotein particles.. ▪ Unesterified (free) fatty acids are transported in the circulation in association with albumin. ▪ Based on the nature of …cont’d hydrocarbon side chain, they are divided into: A. Saturated fatty acids: ✓ contain no double bonds—that is, be saturated ✓ they can not undergo further hydrogenation. B. Unsaturated fatty acids: contain one or more double Fig. A saturated (A) and bonds—that is, be mono- or polyunsaturated fatty acids. an unsaturated (B) fatty acid. which may further be NB: Cis double bonds cause a fatty hydrogenated. acid to “kink.”. A. Saturated fatty acids All C bonded to H  No double bonds  long, straight chain  most animal fats  solid at room temp. contributes to cardiovascular disease (atherosclerosis) = plaque deposits  B. Unsaturated fatty acids  Have a double bonds in the fatty acids  plant & fish fats  vegetable oils  liquid at room temperature  the kinks made by double bonded C prevent the molecules from packing tightly together  In which hydrocarbon side chain is unsaturated (one or more , double bonds are present).  All the naturally occurring unsaturated fatty acids are cis- isomers.  Cis and trans isomers are not interchangeable in cells.  Only cis isomers can fit into cell membrane because of bend at double bond.  Trans Fats – The Double Whammy  Trans fats come from adding hydrogen to vegetable oil (unsaturated fats) through a process called hydrogenation.  “Partially hydrogenated” oils may contain higher levels of trans fats.  Trans fats are more solid than oils.  Trans fats increase the shelf life of foods.  Unlike other fats, trans fats both raise your "bad" (LDL) cholesterol and lower your 20 "good" (HDL) cholesterol.  Fatty Acid Structure  Why would the type of fatty acid determine its state at room temperature?  Double bonds create the kinks in the structure→ can’t be packed as closely together → lessVan der waals forces intraction.  This makes them more fluid at room temperature → lower melting temperature The peanut butter puzzle…  Fats are usually found in animals  Oils are usually found in plants  So why is peanut butter solid?  hydrogenation Saturated vs. unsaturated saturated unsaturated  Nomenclature of fatty acids  The naming of a fatty acid (systematic name) is based on the hydrocarbon from which it is derived.  The saturated fatty acids end with a suffix -anoic (e.g. octadecanoic acid) while the unsaturated fatty acids end with a suffix –enoic (e.g. octadecenoic acid).  In addition to systematic names/ fatty acids have common names which are more widely used.  Numbering of carbon atoms  It starts from the carboxyl carbon which is taken as number 1.  The carbons adjacent to this (carboxyl C) are 2, 3, 4 and so on or alternately α , β, γ and so on.  The terminal carbon containing methyl group is known omega (ω) carbon. Starting from the methyl end, the carbon atoms in a fatty acid are numbered as omega 1, 2, 3 etc.  Shorthand representation of fatty acids  The total number of carbon atoms are written first,  followed by the number of double bonds and  finally the (first carbon) position of double bonds, starting from the carboxyl end.  Thus, saturated fatty acid, palmitic acid is written as l6:0  oleic acid as 18:1;9,  Arachidonic acid as 20 : 4; 5, 8, 11, 14.  Δ9 indicates that the double bond is between 9 and 10 of the fatty acid.  ω9 represents the double bond position (9 and 10) from the ω end.  Essential fatty acids  They are not synthesized in the body.  Two fatty acids are dietary essentials in humans : ▪ linoleic acid- which is the precursor of arachidonic acid, the substrate for prostaglandin synthesis. ▪ α-linolenic acid- important for growth and development. ▪ Arachidonic acid becomes essential if linoleic acid is deficient in the diet. ❖ Essential fatty acid deficiency can result in a scaly dermatitis, as well as visual and neurologic abnormalities. Essential fatty acid deficiency, however, is rare.  Alpha-linolenic acid – omega-3 fatty acid Linoleic acid - omega-6 fatty acid Table. Common names and structures of some fatty acids of physiologic importance. 28  Shorthand representation of fatty acids Linoleic acid CH3(CH2)4CH=CHCH2CH=CH(CH2)7COOH 18:2 n-6 Alpha-linolenic acid CH3CH2CH=CHCH2CH=CHCH2CH=CH(CH2)7COOH 18:3 n-3 Eicosapentaenoic acid(EPA, fish oil) CH3CH2CH=CHCH2CH=CHCH2CH=CHCH2CH=CHCH2CH=CH(CH2)3COOH 20:5 n-3   NB: Humans have carbon 9, 6, 5 and 4 desaturases, but lack the enzymes to insert double bonds at carbon atoms beyond C-9 in , the fatty acid chain.  This is the basis for the nutritional essentiality of the polyunsaturated linoleic (cis double bonds) ,and α-linolenic acids(has all cis double bonds).  Essential fatty acids are required for:  membrane structure and function,  transport of cholesterol,  formation of lipoproteins, prevention of fatty liver etc.  also needed for the synthesis of another important group of compounds, namely eicosanoid. Good sources of ‘omega-3 fatty acids’ Oily fish (salmon, mackerel, sardines, tuna) Pumpkin seeds, sesame seeds soybean oil  Good sources of ‘omega-6 fatty acids’ Most vegetable oil, Sunflower oil, Corn oil, Soybean oil Cotton seeds oil Pumpkin seeds Nuts and cereals Poultry, eggs Avocado 1. Storage lipids ▪ The fats and oils used almost universally as stored forms of energy in living organisms are derivatives of fatty acids. ▪ Two types of fatty acid–containing compounds, triacylglycerols and waxes. ▪ They are esters of fatty acids with alcohols. ▪ An ester is formed when acid reacts with alcohol. Eg. Fats and waxes Formation of an ester: O O R'OH + HO-C-R" R'-O-C-R'' + H2O Fats , ▪ Esters of fatty acids with glycerol. ▪ Also called as triglycerides or triacylglycerols. because all the three hydroxyl groups of glycerol are esterified.  Fats are also called as neutral fats. , Triacylglycerol Formation of an ester: O O R'OH + HO-C-R" R'-O-C-R'' + H2O  Structure of Triacylglycerol/ fats ✓ 3 fatty acids linked to glycerol. i.e. three molecules of fatty acids esterified with one molecule of glycerol. All the three fatty acids can be same or different. Functions of Triglycerides 1.They function as storage lipids in animals and in plants. 2. In man adipose tissue or fat tissue found under the skin, in the abdominal cavity and in the mammary gland contain triacylglycerols.  …Cont’d. 3. In other animals and plant cells also triacylglycerols are found as tiny droplets in cytosol. 4. The fat stored under the skin serve as energy store and as insulator against cold. 5. Women have more fat than men. 6. In obese (fat) people, many kilograms of triacylglycerol is stored under the skin. 7. The antarctic and arctic animals like seals and penguins appear bloated because of high concentration of triglycerides in their bodies. Physical Properties of TAGs 1. Pure fats have no colour, taste and odour. 2. At room temperature, ✓ fat of plant origin remains oil because it contains more unsaturated fatty acids where as ✓animal fat remain as solid, because it contains mostly saturated fatty acids. 3. Triglycerides containing asymmetric carbon atom are optically active.  Steroids ▪ Steroids are complex molecules containing four fused rings.  The four fused rings makeup ‘cyclopentanoperhydrophenanthrene’(CPPP) or ‘sterane’ ring.  Sterane ring is also called as steroid nucleus. The most abundant steroids are sterols which are steroid alcohols. Fig. structure of steroid nucleus Fig. structure of steroid Cholesterol.  COMPOUND LIPIDS When a lipid contains an element or moiety in addition to fatty acids and alcohol present in simple fats, it is known as a compound or conjugated lipid.  Saturated C16 or C18 FA Phosphodiester Unsaturated C16 – C20 FA linkage Derived from polar alcohol smallest = H (from H-OH) least common in membranes phosphatidic acid  Cardiolipin ▪Cardiolipin is an important component of the inner mitochondrial membrane ▪ This the only human glycerophospholipid that is antigenic. ▪ For example,cardiolipin is recognized by antibodies raised against Treponema pallidum, the bacterium that causes syphylis. ▪ Cardiolipins are used in serological diagnosis of syphilis and autoimmune diseases. Plasmalogens Platelet-activating factor (PAF) PAF is synthesized /released by a variety of cell types. binds to surface receptors, triggering potent thrombotic and acute inflammatory events. PAF activates inflammatory cells and mediates hypersensitivity, acute inflammatory, and anaphylactic reactions. neutrophils causes platelets to aggregate and degranulate, and alveolar macrophages to generate superoxide radicals  Sphingophospholipids S Sphingomyelin is an important constituent of the myelin of nerve fibers. T T The myelin sheath is a layered, membranous structure that insulates and protects neuronal fibers of the central nervous system. Sphingophospholipids  Ceramide OH O CH3 (H2C)12 CH CH CH CH NH C R1 Sphingosine Fatty acid CH2 O CH3 Phosphate O P O CH2 CH2 N+ CH3 Choline OH CH3 Sphingomyelin Sphingomyelins are found in large amounts in brain and nerves and in smaller amounts in lung, spleen, kidney, liver and blood. Sphingomyelins differ from lecithins and cephalins in that they contain sphingosine as the alcohol instead of glycerol, they contain two nitrogenous bases: sphingosine itself and choline.  Glycolipids Glycolipids are lipids that contain carbohydrate residues in addition to the alcohol (sphingosine) and a very long-chain fatty acid (24-carbon series). They are present in cerebral tissues and, therefore, are called cerebrosides. They are also referred to as sphingogalactolipids or galactosides as galactose is an important constituent of their structure. Classification of glycolipids: According to the number and nature of the carbohydrate residue(s) present in the glycolipids the following types exist: Cerebrosides: They have one galactose molecule (galactosides). Sulfatides: They are cerebrosides with sulfate substitution on the sugar (sulfated cerebrosides). Gangliosides: They have several sugar and sugaramine residues and at least one residue of N-acetyl neuraminic acid (NANA). Glycolipids help form insulation for nervous system electrical activity Negatively charged gangliosides in glia membrane Repel negative ions & attract positive ions Myelin insulation greatly increases the speed of action potentials  Glycolipids Pattern of sugar residues is variable Always in outer leaflet of cell membrane, & inner leaflet of organelles Hydrophilic (soluble) Hydrophobic (not soluble = lipophilic)  Cerebrosides ▪ The cerebrosides, as the name suggest (cerebral = related to brain), occur in myelin sheath of nerves and white matter of the brain tissues and cellular membranes. ▪ They are important for nerve conductance. They contain sugar, usually -galactose (sometimes glucose or lactose), sphingosine and fatty acid, but no phosphoric acid. Cerebron (Phrenosin) contains Ceramide cerebronic acid (2- hydroxylignoceric acid) and OH O galactose. CH3 (H2C)12 CH CH CH CH NH C R1 Nervon contains nervonic acid Sphingosine Fatty acid (lignoceric acid unsaturated at CH2 C15) and galactose. CH2OH Oxynervon contains oxynervonic O OH H O acid (2-hydroxynervonic acid) and Galactose galactose. OH H H H Other Cerebrosides: Some H OH cerebrosides contain carbohydrates other than Psychosin galactose Cerebroside  Gangliosides They are compound lipids present in gray matter of the brain, ganglionic cells, and RBCs. They are composed of a glycosphingolipid (ceramide and oligosaccharide) with one or more sialic acids (i.e., N- acetylneuraminic acid; NANA) linked as a branch to the sugar chain. Gangliosides are classified according to the oligosaccharide attached to ceramide. The basic oligosaccharide unit attached to ganglioside GM1 consists of five monosaccharides, i.e., Ceramide-Glucose  Galactose (NANA)  N-Acetylgalactosamine  Galactose (with NANA attached to the first galactose). GM1ganglioside is the site of attachment of the Vibrio cholerae exotoxin that causes the acute diarrhea of cholera. GM2 and GM3 gangliosides are derived from GM1 by removal of terminal galactose and N-acetylgalactosamine, respectively.  Although a minor membrane component (~2%), glycolipids have some special functions ▪ Gangliosides in neurons Oligosaccharides with negatively charged sialic acid residues Attract positive ions, e.g. Ca++ Affects electrical properties & signaling  Gangliosides act as Receptors Gangliosidoses As components of the cell plasma membrane, gangliosides modulate cell signal transduction events. They have recently been found to be highly important in immunology. They transfer biogenic amines across the cell membrane and act as cell membrane receptors. They work as the receptors for cholera toxin on the human intestine mucosal cells and as receptors for certain viruses. Natural and semi-synthetic gangliosides are considered the potential therapeutic agents for neurodegenerative disorders.  Sphingolipids at Cell Surfaces are Sites of Biological Recognition ▪ In humans, at least 60 different sphingolipids have been identified in cellular membranes  Many of these are prominent in the plasma membranes of neurons Glycosphingolipids as determinants of blood groups:   The carbohydrate moieties of certain sphingolipids;  define the human blood groups  therefore determine the type of blood  that individuals can safely receive in blood transfusions Fuc sugar fucose 58 Lipid rafts have higher concentrations of - Sphingolipid Cholesterol Glycolipids Lipoproteins ▪ Lipoproteins are lipids combined with proteins in the tissues. The lipid component could be a phospholipids, cholesterol or triglycerides. The lipoproteins could be described as of two types. ▪ Structural lipoproteins: These are widely distributed in tissues, being present in cellular and subcellular membranes. In lung tissues, they act as surfactants in a complex of a protein and lecithin. In the eye, rhodopsin of rods is a lipoprotein complex. ▪ Transport lipoproteins: These are the forms present in blood plasma. They are composed of a protein called apolipoprotein and different types of lipids. (Cholesterol, cholesterol esters, phospholipids and triglycerides). As the lipid content increases, the density of plasma lipoproteins decreases and the diameter increases and vice versa.  Classification of Lipoproteins Lipoproteins are classified by their density which, in turn, reflects size. The greater the lipid/protein ratio in the complex, the larger it is and the lower its density. There are five main classes of lipoproteins. Triglyceride-rich particles include : Chylomicrons, which transport exogenous lipid from the intestine to all the cells. VLDL (very low density lipoproteins), which transport endogenous lipid from the liver to cells;. IDL (intermediate density lipoproteins), which are usually undetectable in normal plasma. It is normally a transient intermediate lipoprotein formed during the conversion of VLDL to LDL. It contains both cholesterol and endogenous triglycerides. Classification of Lipoproteins LDL (low density lipoproteins): formed from VLDL, transport cholesterol to cells. HDL (high density lipoproteins): These are involved in the transport of cholesterol from the cells to the liver. LDL and HDL are two smaller lipoproteins contain mostly cholesterol. The classes of lipoproteins are chylomicrons, VLDLs, IDLs, LDLs, and HDLs. Classification of Lipoproteins Chylomicrons: synthesized in small intestine and secreted into the lymph. Apolipoprotein present:- Apo-B, Apo AI, ApoAII, ApoAIV, ApoCII, ApoCIII, ApoE. composition: 1 % protein. 87 % triglyceride. 8 % phospholipid. 3 % cholesteryl ester. 1 % free cholesterol.  Lipoprotein Classification Very low density lipoproteins (VLDL) synthesized in the liver, rich in triglyceride apo-lipoproteins: Apo-B100, ApoC-III, Apo-E, ApoA-I, ApoA-II composition: 7 - 10 % protein. 50 - 55 % triglyceride. 18 - 20 % phospholipid. 12 - 15 % cholesteryl ester. 8 - 10 % free cholesterol.  Low density lipoproteins (LDL) LDL and IDL, are the catabolic products of VLDL apo-lipoproteins present: Apo-B Composition: 20 - 22 % protein 12 - 15 % triglyceride 20 - 28 % phospholipid 37 - 48 % cholesteryl ester 8 - 10 % free cholesterol  High density lipoproteins (HDL) formed around ApoAI secreted from liver and intestine. apo –lipoproteins present: Apo A-I, Apo A-II, ApoAIV, ApoCIII, ApoE Composition: 33 - 57 % protein 3 - 15 % triglyceride 26 - 43 % phospholipid 15 - 30 % cholesteryl ester 2 - 10 % free cholesterol HDLs are used for the transport of lipid through the circulatory system to the liver, and high levels of HDLs forecast a low risk of heart attack. In contrast, high levels of LDLs (which transport cholesterol to the non-hepatic tissues) are considered cautionary. D stands for “density” in these acronyms because fat has a density of about 0.88 g/ml, whereas protein has a density of about 1.0 g/ml. In consequence, the higher the fat content, the lower the density of the particle.   Since cholesterol is hydrophobic (water fearing) and blood is hydrophilic (water loving), the two do not mix.  Cholesterol is carried through the bloodstream in protein packages called lipoproteins, made up of lipid on the inside and protein on the outside.  Two kinds of lipoproteins carry cholesterol throughout your body. - High density lipoproteins (HDL) - Low density lipoproteins (LDL) 70  LDL and HDL …cont’d  LDL cholesterol is sometimes called bad cholesterol.  High LDL cholesterol leads to a buildup of cholesterol in arteries.  The higher the LDL level in your blood, the greater chance you have of getting heart disease.  HDL cholesterol is sometimes called good cholesterol.  HDL carries cholesterol from other parts of your body back to your liver. The liver removes the cholesterol from your body.  The higher your HDL cholesterol level, the lower your chance of getting heart disease. 71 Chemistry of Amino Acids and Proteins - I 1  Outline of the topic  General structure of Amino Acids  Classification of Amino acids  Function of Amino Acids  Acid-Base property of amino acids  Peptide bond structure and functional peptides  Protein structure  Biological functions of proteins  Protein classification 2  Objectives of the topic At the end of this session, you will be able to Describe general structure of amino acids List the biochemical functions of amino acids Categorize amino acids by different basis of classification Explain acid-base property of amino acids Explain peptide bond and its character Mention functional peptides Give details of protein structure Elucidate biological functions of proteins Classify proteins 3 What are Proteins? Unbranched Polymers of amino acids linked head to tail Major constituent of most cells Usually form multi-molecular complexes They are folded into specific conformations Their conformation and functional-group chemistry controls function Responsible for most of our phenotype (define what an organism is, what it looks like, how it behaves, etc.) Made from almost 20 different types of standard amino- acids Special condition: Selenocysteine incorporated during co- translation in human 4  Amino acids  Structure:  central carbon H O  amino group H | ||  Carboxyl group —N— —C— C—OH H | Side chain (R group)  variable group R  confers unique chemical functionality  Chiral/ Optically active  Acid–base properties  Capacity to polymerize 5  Classification of Amino Acids Amino acids can be classified based on  Side chain character  Nutritional value  Metabolic fate  Presence/ absence in proteins 6 Amino Acid Classification by Side Chain Character  Hydrophobic side chain: stabilize protein structure by hydrophobic interactions.  Tyrosine can form hydrogen bonding. 7 Classification...  Reversible formation of a disulfide bond by the oxidation of two molecules of cysteine 8  Classification… Acidic side chain: H+ (proton) donor 9  Classification … Basic side chains: H+ acceptors  Histidine side chain pKa= 6.0  10% protonated at pH= 7  Serving as a proton donor/ acceptor in many enzymatic reactions  Identification of carbon atoms in amino acids 10  Names and Codes of Amino Acids Name One Three R-Group Properties letter Letter Glycine G Gly Hydrophobic Alanine A Ala Hydrophobic Valine V Val Hydrophobic Leucine L Leu Hydrophobic Isoleucine I Ile Hydrophobic, two chiral carbons Proline P Pro Cyclic, not terribly hydrophobic Phenylalanine F Phe Hydrophobic, bulky Tyrosine Y Tyr Less hydrophobic (than Phe), bulky Tryptophan W Trp Hydrophobic, bulky (indole ring) Cysteine C Cys Hydrophobic, highly reactive (S-S link) Methionine M Met Hydrophobic (start a.a.) Serine S Ser Hydrophilic, reactive Threonine T Thr Hydrophilic, reactive, two chiral carbons Lysine K Lys Highly hydrophilic, positively charged Arginine R Arg Highly hydrophilic, positively charged Histidine H His Highly hydrophilic, positive or neutral Aspartate D Asp Highly hydrophilic, negatively charged Glutamate E Glu Highly hydrophilic, negatively charged Asparagine N Asn Polar, Uncharged Glutamine Q Gln Polar, Uncharged 11 Amino Acid Classification Based on Nutritional Value  Basedupon whether the AAs can be synthesized in human body or not  Indispensable or essential amino acids: 9 amino acids  Not synthesizable in the body in adequate amounts  Val, Ile, Thr, Trp, Leu, Lys, Met, Phe and His.  Dispensable or non-essential AAs o Can be synthesizable in the body from the essential ones  Conditionally essential amino acids: During illness or stress  Tyrosine, cysteine, arginine, glutamine, glycine, proline, and serine. 12  CLASSIFICATION BASED ON METABOLIC FATE  Based upon the catabolic fate of Carbon skeleton of amino acids Ketogenic Mixed Glucogenic Type  Ketogenic Catabolically give intermediates Leu IIe convertible into Acetyl-CoA or Acetoacetyl-CoA Lys Tyr Ala, Arg Asp,  Glucogenic Asn Glu, Gln 14 of them give rise to intermediates of Ser, Met Pro, Trp glycolysis or Kreb’s cycle Gly His, Thr Val, Cys  Mixed type Carbon-skeleton of which is catabolized to Phe produce glycolytic intermediates or acetyl CoA derivatives 13 Some Common Biological Functions of Amino Acids  Formation of peptides and proteins  Stabilize 3D structure of proteins by forming multiple bonds  Specific AAs at the active site are vital for enzyme catalysis  Some AAs as source of glucose  Cys and Met are sources of S in the body (e.g. for Fe-S center formation)  Carbon skeleton and Nitrogen of AAs used for nucleic acid synthesis  Gly and Met help in the detoxification mechanisms  Met can act as a methyl group donor in methylation reactions 14 Amino Acids as Precursors of Biologically Important Derivatives  Gycine is a precursor for  Heme  Creatine  Tyrosine is the precursor for number of hormones:  Thyroxine & Triiodothyronine  Epinephrine & nor-epinephrine  Skin pigment melanin  Tryptophan can give rise to Niacin Serotonin  Histidine can be converted to Histamine 15 Uncommon Amino Acids – Found in proteins Hydroxylysine and hydroxyproline - Mainly in collagen - Found in connective tissues Tyroxine and Triiodotyronine - Produced from degradation of thyroglobulin - Act as hormones for growth & development N-methylarginine and N-acetyllysine - found in histone proteins 16 Uncommon Amino Acids – Found in proteins Methylhistidine, -N-methyllysine, & N,N, N-trimethyllysine - Methylated amino acids in myosin -Carboxyglutamic acid - In blood clotting proteins & Ca2+ containing proteins e.g. Prothrombin 17 Uncommon Amino Acids – Found in proteins Desmosine - Derivative of four Lys residues - Found in fibrous protein elastin Selenocysteine - Derived from serine - Introduced during protein synthesis - Role in antioxidant activity e.g. Gluthione peroxidase active site 18  Amino Acids not found in proteins GABA (decarboxylation of glutamic acid) - a potent neurotransmitter. Histamine (decarboxylation of histidine) & Serotonin (from tryptophan) - function in smooth muscle contraction, as nurotransmitter, vascular permeability, etc -Alanine - for synthesis of carnosine (for muscle endurance) 19  Amino Acids not found in proteins Epinephrine Ornithine & Citrulline - in urea cycle, Arg synthesis. Dopa (3,4-dihydroxyphenylalanine): Precursor of melanin S-adenosyl methionine (SAM): a methyl donor in transmethylation rxn 20 Acid-Base Properties of Amino Acids  Ammonium form acts as an acid, the carboxylate as a base. 21  pI of Neutral Amino Acids  The PI can be calculated as the average of pKa1 and pKa2 22 pI of Amino Acids - Alanine 23 Amino Acids with Ionizable Side Chains Lysine 24 pI of Amino Acids – With Acidic, Neutral and Basic Side Chains 25 pKa and PI Values of Common Amino Acids 26  Peptide Bond & Functional Peptides 27  Peptide Bonds (Amide bond) Condensation rxn Formation of dipeptide, tripeptides, etc....  Forms N-terminal and C-terminal Acid-base behavior of a peptide can be predicted from its free -amino and -carboxyl groups as well as the nature and number R groups.  Have characteristic characteristic pI  pKa value for an ionizable R group can Serylglycyltyrosylalanylleucine change somewhat when an amino acid or becomes a residue in a peptide. Ser–Gly–Tyr–Ala–Leu 28  Planar peptide groups in a polypeptide chain Amide nitrogen are non-basic because their unshared electron pair is delocalized by interaction with the carbonyl group. Rotation around C-N bond is restricted due to the double bond nature Peptide groups are therefore planar Planar Structure of peptide 29  Biologically Active Peptides  Glutathione – Formed from -glutamic acid, Cysteine & Glycine – It protects the cell membrane from damage,  e.g., prevents hemolysis of erythrocytes Slightly larger peptides/ Oligopeptides  Insulin – contains two polypeptide chains one having 30 and the other has 21amino acid residues  Corticotropin – is a 39-residue hormone of the anterior pituitary gland – stimulates the adrenal cortex 30  Commercial peptide: Example O O O H2N CH C NH C CH C OCH3  Aspartame/ L-Aspartyl- CH2 CH2 L-phenylalanine methyl Methyl ester ester/ Neurasweet C OH  Artificial sweetener O Aspartic Acid Phenylalanine 31  Structure and Classification of Proteins 32  Protein structure  The 3-D structure mainly depends on types, number and sequence of amino acids  twisted, folded, coiled into unique shape Pepsin  Structure determines the function of a protein  Native, folded structure of the protein depends on several factors Collagen (1) interactions with solvent molecules (2) the pH and ionic composition of the solvent (3) the sequence of amino acid in a protein. Hemoglobin 33 Primary structure of proteins  Describes sequence and number of amino acids in chain ◦ Determined by gene (DNA sequence) ◦ Contain all information necessary for folding into its “native” structure  Amino acid sequence of Lysozyme 34  Primary structure... Does Amino Acid Sequence determine protein function? Oxytocin Ile Gln Tyr Asn - Initiates contractions of the uterus during childbirth Cys Cys Pro-Leu-GlyNH 2 - Plays a role in the release of milk during lactation S S Vasopressin (ADH) Phe Gln Tyr Asn - Regulate the amount of water Cys Cys present in the body Pro-Arg-GlyNH2 S S 35  Primary structure... Change in amino acid sequence may cause problem! Hemoglobin – 574 amino acids 36 Secondary structure of proteins: Local folding  Formed by H-bonding  Describes about folding pattern along short sections of polypeptide  The Development of regular patterns of hydrogen bonding result in distinct folding patterns 37 Secondary structure: Examples  -helix  Peptide carbonyl H-bonded to peptide N- H group four residues farther  One turn of the helix represents 3.6 amino acid residues (13 atoms from the O to the H of the H-bond - 3.613 helix)  All of the H-bonds lie parallel to the helix axis  All of the carbonyl groups are pointing in one direction along the helix axis 38 Secondary (2°) structure: Examples e.g. Myoglobin – 153 AAs - Eight stretches of  -helix forming a box to contain the heme prosthetic grp. Other forms of Helix 310 helix - 3.0 residues per turn (with 10 atoms in the ring formed by making the hydrogen bond three residues up the chain) 27 ribbon 39 Secondary (2°) structure: Examples  -Pleated Sheet  Each strip of paper as a single peptide strand  Peptide backbone makes a zigzag pattern along the strip  –carbons lying at the folds of the pleats.  Formation of interstrand H- bonds  Side chains oriented perpendicular to the plane of the sheet,  Side chains extending out from the plane on alternating sides 40  Secondary (2°) structure: Examples Two types Parallel pleated sheet - Typically large structures Usually > five strands Antiparallel pleated sheet - Usually having hydrophobic side chain on one side, so it requires alternating hydrophobic & hydrophilic residues arrangement in primary structure 41  Secondary (2°) structure: Examples -Turn/ tight turn/ -bend - A tight loop formed by the carbonyl O of the 1st is H-bonded with amide N of the 4th residue down the chain - Proline & glycine, occur frequently in -turn sequences - Abundant in globular structures 42  Secondary (2°) structure: Examples -Bulge  A small piece of non-repetitive structure that can occur by itself  Most often occurs as an irregularity in antiparallel -structures  Occurs between two normal – structure H-bonds and comprises 2 residues on one strand and one residue on the opposite strand  Bulges thus cause changes in the direction of the polypeptide chain, but to a lesser degree than -turns. 43 Super Secondary Common motifs: Examples 44 Super-secondary structures commonly found in some DNA- binding proteins 45 Tertiary (3°) structure: All things hold together  Shows the whole molecule folding pattern ◦ Describes about overall 3-D structure of a polypeptide ◦ Determined by interactions between R groups ◦ Bonds that determine 3D-structure are:  Hydrogen bond  Hydrophobic interactions  Disulfide bridges  Ionic bonds  Van der Waals Force 46 Bonds determining 3° structure of proteins 47 Examples of some domains -Barrel Bundle Saddle 48  Quaternary (4°) structure  Formed from more than one polypeptide chain  Organized by the same types of bonds as tertiary structure  Most intracellular enzymes are oligomers C) Immunoglobulin49  Advantages of Quaternary Association Stability - Favorable reduction of the protein’s surface-to-volume ratio - Interactions stabilizes the protein energetically - Shield hydrophobic residues from solvent water Genetic Economy and Efficiency - Less DNA is required to code for a monomer 50  Advantages of … Bringing Catalytic Sites Together  Monomer may not constitute a complete enzyme active site  May also carry out different but related reactions on different subunits e.g. Tryptophan synthase (22) -subunit: - subunit : Cooperativity - Regulate catalytic activity by subunit interactions - Some proteins are inactive when oligomers e.g. Insulin hexamer formation in solution - Ligand binding at one site changes affinity of Hb the other site for O2 51 Examples of Proteins with Quaternary Structure 52  Summary of Levels of Protein Structure aa sequence peptide bonds determined by DNA H bonds of carbonyl O and Amide H of peptide R groups Hydrophobic, Ionic, Disulfide bridges, H-bond Multiple polypeptides All bond types like tertiary53 Classification of Proteins – Based on Function  a. Enzymes:  e.g. Glucokinase  b. Regulatory Proteins  Regulating other proteins  Eg. Insulin  Regulation of gene expression e.g. Transcription activators c. Transport Proteins e.g. Hb: Serum albumin: Fatty acid transport Membrane transporters (channels): e.g. AA & Glucose transporters 54  Functional classes … d. Storage Proteins: e.g. Casein: Major source of Calcium phosphate in mammalian infants E.g. Ferritin: for Hb synthesis e. Contractile and Motile Proteins፡ For cell motility, muscle contraction , cell division e.g. Actin & Myosin: muscle contraction Dynein and Kinesin (Motor proteins): drive the movement of vesicles, granules, and organelles along microtubules 55  Functional classes … f. Structural Proteins - Provide strength & protection to cells & tissues e.g. -keratin: hair, horns, and fingernails Collagen: bone, connective tissue, tendons, cartilage, Elastin: an impor