Biochemistry - Unit 3 Sugars and Lipids PDF

# Unit-3: Sugars and Lipids ## Dr. Mukul Godbole Assistant Professor Department of Biosciences and Technology, MIT WPU This presentation is for educational purposes only. # Unit III. Sugars and Lipids - Classification of sugars. - Glycoconjugates: proteoglycans, glycoproteins, and glycolipids....

# Unit-3: Sugars and Lipids ## Dr. Mukul Godbole Assistant Professor Department of Biosciences and Technology, MIT WPU This presentation is for educational purposes only. # Unit III. Sugars and Lipids - Classification of sugars. - Glycoconjugates: proteoglycans, glycoproteins, and glycolipids. - Glycolysis - TCA cycle - Gluconeogenesis - Carbohydrate metabolism and disorders. - Classification of Fatty acids and lipids. - Lipids as signals, cofactors, and pigments. - Metabolism of fatty acids and triacylglycerols. - Lipid metabolism disorders. ## Carbohydrates - Carbohydrates are polyhydroxy aldehydes or ketones, or substances that yield such compounds on hydrolysis. - Many, but not all, carbohydrates have the empirical formula (CH₂O)n. Some also contain nitrogen, phosphorus, or sulfur. - Mono-, oligo-, and poly-saccharides. - Oligosaccharides consist of short chains of monosaccharide units, or residues, joined by characteristic linkages called glycosidic bonds. ### Monosaccharides - Aldehydes or ketones with two or more hydroxyl groups - Many carbon atoms are chiral centers - Colorless, crystalline solids that are freely soluble in water but insoluble in nonpolar solvents. Most have a sweet taste. - Backbone: unbranched carbon chains in which all the carbon atoms are linked by single bonds. In the open-chain form, one of the carbon atoms is double-bonded to an oxygen atom to form a carbonyl group. Each of the other carbon atoms has a hydroxyl group. - If the carbonyl group is at an end of the carbon chain the monosaccharide is an aldose; if the carbonyl group is at any other position the monosaccharide is a ketose. ## Carbohydrates - Most monosaccharides are enantiomers - chiral carbon atoms forming optically active isomeric forms. - A molecule with n chiral centers can have 2n stereoisomers. - Glyceraldehyde is a reference molecule for deciding L or D isomers. - D-ribulose is the ketopentose corresponding to the aldopentose D-ribose. - D-glucose and D-mannose (which differ in the stereochemistry at C-2) or D-glucose and D-galactose (which differ at C-4) are epimers. - In aqueous solutions, monosaccharides exist as cyclic (ring) structures, wherein the carbonyl group has formed a covalent bond with the oxygen of a hydroxyl group along the chain. - These are outcomes of a general reaction between alcohols and aldehydes or ketones to form derivatives called hemiacetals or hemiketals, which contain an additional asymmetric carbon atom, and thus, can exist in two stereoisomeric forms. - Isomeric forms of monosaccharides that differ only in their configuration about the hemiacetal or hemiketal carbon atom are called anomers. The hemiacetal (or carbonyl) carbon atom is called anomeric carbon. ## Carbohydrates - In the synthesis and metabolism of carbohydrates, the intermediate forms are phosphorylated derivatives and not the actual sugars. - Condensation of phosphoric acid with one of the hydroxyl groups of a sugar forms a phosphate ester, as in glucose-6-phosphate. Sugar phosphates are relatively stable at neutral pH and bear a negative charge. - One effect of sugar phosphorylation within cells is to trap the sugar inside the cell; most cells do not have plasma membrane transporters for phosphorylated sugars. - Phosphorylation also activates sugars for subsequent chemical transformation. - Monosaccharides are reducing sugars. Their carbonyl carbon is oxidized to carboxyl group. ### Disaccharides - Two monosaccharides joined covalently by an O-glycosidic bond formed when a hydroxyl group of one sugar reacts with the anomeric carbon of the other. The product is also called 'glycoside'. - N-glycosyl bonds join the anomeric carbon of a sugar to a nitrogen atom in glycoproteins and nucleotides. ## Carbohydrates ### Polysaccharides - Also called glycans. They differ from each other in the identity of their recurring monosaccharide units, in the length of their chains, in the types of bonds linking the units, and in the degree of branching. - Homopolysaccharides contain only a single monomeric species (e.g., starch, glycogen, cellulose); heteropolysaccharides contain two or more different kinds (peptidoglycan). - The process of formation of polysaccharides has no definite limits; thus, the size and molecular weight of polysaccharides and the number of monosaccharide repeating units depends on the synthesizing enzyme. ## Carbohydrates - Starch and glycogen molecules occur intracellularly, and are heavily hydrated because they have many exposed hydroxyl groups available to hydrogen-bond with water. ### Starch - Starch is a polymer of amylose and amylopectin. ## Carbohydrates - Dextrans are bacterial and yeast polysaccharides made up of (a1->6)-linked poly-D-glucose; all have (a1->3) branches, and some also have (a1->2) or (a1->4) branches. - Dental plaque, formed by bacteria growing on the surface of teeth, is rich in dextrans. Synthetic dextrans are used in several commercial products (for example, Sephadex) that serve in the fractionation of proteins by size-exclusion chromatography. ### Cellulose - Cellulose is also a straight polymer of glucose repeating units, like amylose. But, they both have different structures and properties. Cellulose has ẞ(1->4) linkages. - Glycogen and starch ingested in the diet are hydrolyzed by a-amylases and glycosidases, enzymes in the saliva and intestine that break (a1->4) glycosidic bonds between glucose units. Most animals cannot use cellulose as a fuel source because they lack an enzyme to hydrolyze the (ẞ1->4) linkages. - The intestinal tract of termites harbors a symbiotic microbe, Trichonympha, which secretes cellulase and hydrolyzes the (ẞ1->4) linkages. ### Chitin - Chitin, present in the exoskeleton of arthropods - insects, lobsters, crabs – is the second most abundant polysaccharide after cellulose. It is a linear homopolysaccharide composed of N- acetylglucosamine residues in (ẞ1->4) linkage, with an acetyl group instead of a hydroxyl group on the C-2. ## Carbohydrates ### Peptidoglycan - Peptidoglycan is a heteropolymer of alternate (ẞ1->4)-linked N-acetylglucosamine (NAG) and N- acetylmuramic acid (NAM) residues. The linear polymers lie side by side in the cell wall, cross-linked by short peptides, and the exact structure depends on the bacterial species. - The enzyme lysozyme lyses bacterial cell wall by hydrolyzing the (ẞ1->4) glycosidic bond between NAG and NAM. Lysozyme is present in tears as a defense mechanism against bacterial infections. ### Hyaluronan - Hyaluronan (hyaluronic acid), present in the synovial fluid of joints, contains alternating residues of D-glucuronic acid and N-acetylglucosamine. Hyaluronidase, secreted by some pathogenic bacteria, can hydrolyze the glycosidic linkages of hyaluronan, rendering tissues more susceptible to bacterial invasion. - In many species, a similar enzyme in sperm hydrolyzes an outer glycosaminoglycan coat around the ovum, allowing sperm penetration. - Heparin - Chondroitin-4-sulfate ## Carbohydrates - Spaces outside animal cells comprises extracellular matrix (ECM) that holds cells together, and provides a porous pathway for the diffusion of nutrients and oxygen to individual cells. - These are heteropolysaccharides and fibrous proteins such as fibrillar collagens, elastin, and fibronectin. - Basement membrane is a specialized ECM that underlies epithelial cells; it comprises specialized collagens, laminin, and heteropolysaccharides. These heteropolysaccharides, the glycosaminoglycans, are a family of linear polymers composed of repeating disaccharide units. Repeating units of N-acetylglucosamine or N-acetylgalactosamine and D-glucuronic acid or L-iduronic acid. - Glycosaminoglycans form rodlike-helical structures to avoid repulsion between carboxyl and sulfate groups. These carboxyl and sulfate groups can then interact with proteins, forming proteoglycans. ## Glycobiology - Specific oligosaccharide chains attached to components of the plasma membrane of eukaryotic cell form a carbohydrate layer (the glycocalyx) that serves as an information-rich surface that a cell shows to its surroundings. - These oligosaccharides are essential for cell-cell recognition and adhesion, cell migration during development, blood clotting, the immune response, wound healing, and other cellular processes. - The informational carbohydrate is covalently joined to a protein or a lipid to form a glycoconjugate. ### Proteoglycans - One or more sulfated glycosaminoglycan chains are joined covalently to a membrane protein or a secreted protein. ### Glycoproteins - One or several oligosaccharides of varying complexity joined covalently to a protein. Present on the exterior of cells. Synthesized on Golgi complex. Recognized by lectins. ### Glycolipids - Are membrane sphingolipids in which the hydrophilic head groups are oligosaccharides. - Proteoglycans act as tissue organizers, and they influence various cellular activities, such as growth factor activation and adhesion. The basic proteoglycan unit comprises a core protein with covalently attached glycosaminoglycan. ## Glycobiology ### Gangliosides - Are membrane lipids of eukaryotic cells in which the polar head group, the part of the lipid that forms the outer surface of the membrane, is a complex oligosaccharide containing a sialic acid and other monosaccharide residues. - Some gangliosides indicate blood group type. These are generally placed on the outer membrane. ### Lipopolysaccharides - Are predominant surface glycolipids in Gram-negative bacteria, and thus, also important determinants of the serotype of bacterial strains (based on antigenic properties). - The lipid A portion of the lipopolysaccharides of some bacteria is called endotoxin; its toxicity to humans and other animals is responsible for the dangerously lowered blood pressure that occurs in toxic shock syndrome resulting from Gram-negative bacterial infections. ## Glycolysis - In the preparatory phase of glycolysis the energy of ATP is invested, raising the free energy content of the intermediates. - The carbon chains of all the metabolized hexoses are converted to a common product, glyceraldehyde 3-phosphate. - The preparatory phase includes the following 5 steps: 1. Hexokinase 2. Phosphohexose isomerase 3. Phospho-fructokinase-1 4. Aldolase 5. Triose phosphate isomerase - In the payoff phase of glycolysis, the energy of ATP is released. - The payoff phase includes the following 5 steps: 1. Glyceraldehyde 3-phosphate dehydrogenase 2. Phospho-glycerate kinase 3. Phospho-glycerate mutase 4. Enolase 5. Pyruvate kinase ## Fates of Pyruvate ### Aerobic Fate - Pyruvate is oxidized, with loss of its carboxyl group as CO₂, to yield the acetyl group of acetyl-coenzyme A. - The acetyl group is then oxidized completely to CO₂ by the citric acid cycle. - The electrons from these oxidations are passed to O₂ through a chain of carriers in mitochondria, to form H2O. The energy from the electron-transfer reactions drives the synthesis of ATP in mitochondria. ### Lactic Acid Fermentation - Vigorously contracting skeletal muscle must function under low oxygen conditions (hypoxia). - NADH cannot be re-oxidized to NAD+, but NAD+ is required as an electron acceptor for the further oxidation of pyruvate. - Under these conditions, pyruvate is reduced to lactate, accepting electrons from NADH and thereby regenerating the NAD+ necessary for glycolysis to continue. - Certain tissues and cell types (e.g., retina and erythrocytes) convert glucose to lactate even under aerobic conditions, and lactate is also the product of glycolysis under anaerobic conditions in some microorganisms. ### Ethanol (alcohol) fermentation - Pyruvate is converted under hypoxic or anaerobic conditions to ethanol and CO2. ### Anabolic Fate - Provide the carbon skeleton for the synthesis of the amino acid alanine or for the synthesis of fatty acids. ## Feeder Pathways for Glycolysis - Many sugars can be converted into intermediates of glycolysis. ## Purpose of Gluconeogenesis - Gluconeogenesis is the synthesis of glucose from non-carbohydrate precursors. - Mammalian liver, renal cortex, epithelial cells of the intestine. - Gluconeogenesis is important for maintaining blood glucose levels during fasting. - Glucogenic glycerol, amino acids. ## Gluconeogenesis - Gluconeogenesis and glycolysis are not identical pathways running in opposite directions, although they do share several steps; 7 of the 10 enzymatic reactions of gluconeogenesis are the reverse of glycolytic reactions. - However, three reactions of glycolysis are essentially irreversible in vivo and cannot be used in gluconeogenesis: - conversion of glucose to glucose 6-phosphate by hexokinase - phosphorylation of fructose 6-phosphate to fructose 1,6-bisphosphate by phosphofructokinase-1 - conversion of phosphoenolpyruvate to pyruvate by pyruvate kinase. - In gluconeogenesis, the three irreversible steps are bypassed by a separate set of enzymes, catalyzing reactions that are sufficiently exergonic to be effectively irreversible in the direction of glucose synthesis. - Thus, both glycolysis and gluconeogenesis are irreversible processes in cells. In animals, both pathways occur largely in the cytosol, necessitating their reciprocal and coordinated regulation. ## Production of Acetyl-CoA - The first step in the pyruvate to acetyl-CoA and CO2 conversion is catalyzed by pyruvate dehydrogenase (PDH) complex, a cluster of enzymes located in the mitochondria of eukaryotic cells and in the cytosol of bacteria. - A series of chemical intermediates remain bound to the enzyme molecules as a substrate is transformed into the final product. Five cofactors, four derived from vitamins, participate in the reaction mechanism. - The overall reaction is an 'oxidative decarboxylation', an irreversible oxidation process in which the carboxyl group is removed from pyruvate as a molecule of CO2 and the two remaining carbons become the acetyl group of acetyl-CoA. ## Krebs Cycle / TCA Cycle / Citric Acid Cycle The Krebs cycle, the tricarboxylic acid (TCA) cycle, or the citric acid cycle is a series of chemical reactions used by aerobic organisms to generate energy through the oxidation of acetate derived from carbohydrates, fats, and proteins into carbon dioxide. - Acetyl-CoA is the starting point for the Krebs cycle. Acetyl-CoA is converted to citrate. - Citrate is converted to isocitrate, a-ketoglutarate, succinyl-CoA, fumarate, malate, and finally oxaloacetate. - Oxaloacetate is regenerated, and the cycle can begin again. ## Products of Krebs Cycle - The Krebs cycle produces 3 NADH, one FADH2, and one GTP (ATP) per turn. - The NADH and FADH2 are used in the electron transport chain to generate ATP. GTP is a form of energy that can be used directly by the cell. ## Lipogenic Liver (well-fed state) - In a well-fed state, the liver is primarily involved in the synthesis of fatty acids and the storage of glycogen. - Insulin is the primary hormone that regulates metabolism in a well-fed state. Insulin stimulates glucose uptake and storage as glycogen, as well as the synthesis of fatty acids. ## Glucogenic Liver (fasting state) - In a fasting state, the liver is primarily involved in the production of glucose and ketone bodies. - Glucagon is the primary hormone that regulates metabolism in a fasting state. Glucagon stimulates glycogen breakdown and gluconeogenesis, as well as the production of ketone bodies. ## Lipids - Fats and oils are derivatives of fatty acids - hydrocarbons with low oxidation state. - Fatty acids are carboxylic acids with hydrocarbon chains ranging from 4 to 36 carbons long. - They can be saturated or unsaturated. A few contain three-carbon rings, hydroxyl groups, or methyl group branches. ### Nomenclature for unbranched fatty acids: - Chain length and number of double bonds, separated by a colon. - Positions of any double bonds are specified relative to the carboxyl carbon, numbered 1, by superscript numbers following ∆ (delta). - A 20-carbon fatty acid with one double bond between C-9 and C-10 (C-1 being the carboxyl carbon) and another between C-12 and C-13 is designated as 20:2(Δ9,12). ## Lipids - In unsaturated fatty acids, double bonds generally between C-9 and C-10 or C-12 and C-15. - Double bonds are never conjugated (alternating single and double), but are separated by a methylene (-CH2) group. - The double bonds are generally in cis configuration. Trans fatty acids are produced by fermentation in the rumen of dairy animals and are obtained from dairy and meat products. - The family of polyunsaturated fatty acids (PUFAs) with a double bond between the third and fourth carbon from the methyl end of the chain are important in human nutrition. The physiological role of PUFAs is related to the position of the first double bond near the methyl end of the chain than to the carboxyl end. Thus, an alternative nomenclature is used for these fatty acids. - The carbon of the methyl group-that is, the carbon most distant from the carboxyl group-is called the w (omega) carbon and is given the number 1. In this convention, PUFAs with a double bond between C-3 and C-4 are called omega-3 (ω-3) fatty acids, and those with a double bond between C-6 and C-7 are omega-6 (w-6) fatty acids. ## Lipids - Triacylglycerols – three fatty acid chains covalently linked via ester linkage to a glycerol. - Simple triacylglycerols – same fatty acid (tripalmitin, 16:0); and mixed - The polar hydroxyls of glycerol and polar carboxylates of the fatty acids are bound in ester linkages; thus, triacylglycerols are nonpolar, hydrophobic molecules. - Lipids float on the surface of water due to low specific gravity. ## Lipids - In vertebrates, specialized cells called adipocytes (fat cells) store large amounts of triacylglycerols as fat droplets that nearly fill the cell. Triacylglycerols are also stored as oils in the seeds of many plants, providing energy and biosynthetic precursors during seed germination. Adipocytes and germinating seeds contain lipases that hydrolyze triacylglycerol. - Why store triacylglycerols when polysaccharides are available? - The carbon atoms of fatty acids are more reduced than those of sugars. - Oxidation of triacylglycerols yields more than twice as much energy, gram for gram, as the oxidation of carbohydrates. - Being hydrophobic, fats do not carry additional weight of water of hydration. ## Lipids - Triacylglycerols stored under the skin also confer insulating property to animals living in low temp. Walruses, seals, penguins. - The low density of triacylglycerols allows sperm whale to match the buoyancy of their bodies to that of surrounding cold water during deep dives. - Vegetable oils such as corn (maize) and olive oil are composed largely of triacylglycerols with unsaturated fatty acids and thus are liquids at room temperature. - Lipid-rich foods turn rancid due to oxidative cleavage of double bonds in unsaturated fatty acids, producing aldehydes and carboxylic acids of shorter chain length and higher volatility. - To improve the shelf life of vegetable oils used in cooking, and to increase their stability at the high temperatures used in deep-frying, commercial vegetable oils are subjected to partial hydrogenation. This process converts many of the cis double bonds in the fatty acids to single bonds and increases the melting temperature of the oils so that they are more nearly solid at room temperature. - But, some cis double bonds are converted to trans double bonds. Dietary intake of trans fats increases the risk of cardiovascular disease. They raise levels of low-density lipoprotein (LDL) cholesterol. Trans fats also increase inflammatory responses in body. - Fast foods (burgers, pizzas, etc.) and ready-made packed food items contain high levels of trans fats. ## Lipids - Storage and structural lipids have a passive role in cells – enzyme-mediated oxidation and barrier formation in membrane. - Some others function as signaling molecules (hormones or intracellular messengers/growth factors), enzyme cofactors in electron-transfer chain, for transfer of sugar moieties for glycosylation, or pigment molecules that absorb light (due to presence of conjugated double bonds). - Phosphatidylinositol 4,5-bisphosphate in the cytoplasmic (inner) face of plasma membranes serves as a reservoir of messenger molecules that are released inside the cell in response to extracellular signals interacting with specific surface receptors. - Extracellular signals, such as the hormone vasopressin, activate a specific phospholipase C in the membrane that hydrolyzes phosphatidylinositol 4,5-bisphosphate. This releases inositol 1,4,5- trisphosphate (IP3) that is water-soluble, and diacylglycerol that remains associated with the plasma membrane. - IP3 triggers release of Ca2+ from the endoplasmic reticulum, and the combination of diacylglycerol and elevated cytosolic Ca2+ activates the enzyme protein kinase C. By phosphorylating specific proteins, this enzyme brings about the cell's response to the extracellular signal. - Certain signaling proteins bind specifically to phosphatidylinositol 3,4,5-trisphosphate in the plasma membrane, initiating the formation of multienzyme complexes at the membrane's cytosolic surface. ## Lipids - Steroid hormones - Oxidized derivatives of sterols. More polar than cholesterol. E.g., estrogen, cortisol, testosterone. - Steroid hormones move through the bloodstream (on protein carriers) from their site of production to target tissues, where they enter cells, bind to highly specific receptor proteins in the nucleus, and trigger changes in gene expression and thus metabolism. - A very low concentration of hormones is sufficient to induce very high effects due to their high affinity for receptors. - Vitamins A and D serve as hormone precursors. - Plant-based lipids, like jasmonate, are volatile substances that are used to attract pollinators, to repel herbivores, to attract organisms that defend the plant against herbivores, and to communicate with other plants. ## Lipid Catabolism - Fatty acids undergo oxidative removal of successive two-carbon units in the form of acetyl-CoA, starting from the carboxyl end of the fatty acyl chain. - For example, the 16-carbon palmitic acid (palmitate at pH 7) undergoes seven passes through the oxidative sequence, in each pass losing two carbons as acetyl-CoA. At the end of seven cycles the last two carbons of palmitate (originally C-15 and C-16) remain as acetyl-CoA. - The overall result is the conversion of the 16-carbon chain of palmitate to eight two-carbon acetyl groups of acetyl-CoA molecules. - Formation of each acetyl-CoA requires removal of four hydrogen atoms (two pairs of electrons and four H+) from the fatty acyl moiety by dehydrogenases. - Acetyl group of acetyl-CoA is oxidized to CO₂ in the citric acid cycle in the mitochondrial matrix. - This is a classical example of 'convergence' of biochemical pathways. ## ẞ-Oxidation of Fatty Acids - The first two stages of fatty acid oxidation produce the reduced electron carriers NADH and FADH2. These donate electrons to the mitochondrial respiratory chain for phosphorylation of ADP to ATP. - Four enzyme-catalyzed reactions make up the first stage of fatty acid oxidation. First, dehydrogenation of fatty acyl-CoA produces a double bond between the a and ẞ carbon atoms (C-2 and C-3), yielding a trans-∆²-enoyl-CoA. - The double bond has the trans configuration, whereas the double bonds in naturally occurring unsaturated fatty acids are normally in the cis configuration. - In one pass through the ẞ-oxidation sequence, one molecule of acetyl-CoA, two pairs of electrons, and four protons (H+) are removed from the long-chain fatty acyl-CoA, shortening it by two carbon atoms. - Palmitoyl – myristoyl - lauroyl - ... derivatives are formed in 7 steps. Palmitoyl-CoA + 7C0A + 7FAD + 7NAD+ + 7H2O 8 acetyl-CoA + 7FADH2 + 7NADH + 7H+ ## ẞ-Oxidation of Fatty Acids - In hibernating animals, fatty acid oxidation provides metabolic energy, heat, and water-all essential for survival of an animal that neither eats nor drinks for long periods. - Camels obtain water to supplement the meager supply available to them by oxidation of fats stored in their hump. - The acetyl-CoA produced from the oxidation of fatty acids can be oxidized to CO2 and H2O by the citric acid cycle. Palmitoyl-CoA + 23O2 + 108P; + 108ADP → CoA + 108ATP + 16CO2 + 23H2O