sign in sign up
<<
Home , Deoxy sugar, Tetrose, Trisaccharide

2 Structure and Chemistry

Carbohydrates: Structure and Function (BI3.1)

Introduction

Disaccharides are major energy supplying nutrients in diet are polyhydroxy or with a namely, , , and . They contain two general formula Cn(H O)n (Fig. 2.1). 2 units attached to one another through glycosidic bonds that are formed between hydroxyl groups of one monosaccharide unit in the polymer with elimination Classification of Carbohydrates of water.

Carbohydrates are classified as , disaccha­ rides, , and (Table 2.1). Bond connecting anomeric carbon to alcohol oxygen is termed as glycosidic bond. O-glycosidic bonds are formed when anomeric carbon is linked via an oxygen atom to Monosaccharides another molecule. N-glycosidic bond is formed between anomeric carbon and an Monosaccharides are simplest form of carbohydrates and amine (or a nitrogen atom), e.g., D- is linked to purine they are aldehydes () or ketone () derivative and pyrimidine in nucleic acids. of polyhydric alcohols with at least three carbon atoms.

Monosaccharides have a general (CH2O)n (where n ≥ 3). Based on the number of carbon atoms, monosaccharides can Oligosaccharides be as mentioned below: Oligosaccharides are classified into subclasses based on the •• with three carbons. number of monosaccharide molecules that form when one •• with four carbons. molecule of the is hydrolyzed. Examples of •• with five carbons. oligosaccharides are listed below. •• •• with six carbons. Fructo-oligosaccharides (FOS) or oligofructose (Jerusalem artichokes, onions, canned foods). ••Galacto-oligosaccharides (GOS): , and verbascose (in beans, peas, lentils, cabbage, whole grains), soybean oligosaccharides in soy, and trans- Synthesis of Major source of (TOS). that are energy for brain •• important components Gluco-oligosaccharides (produced from sucrose). and RBCs of cell membrane ••Human milk oligosaccharides (HMO) (human breast milk). ••Isomalto-oligosaccharides or IOS (produced from Stored as Why we need Cell signaling ). carbohydrates? ••Lactosucrose (produced from lactose and sucrose). •• (produced from starch during digestion, Synthesis of found in liquid , brown rice syrup). Synthesis of glycolipids: mucopolysaccharides: water receptor sites binding, lubrication, shock Polysaccharides absorbing property They contain 10 or more monosaccharide units attached Fig. 2.1 Biological significance of carbohydrates. through glycosidic bonds, for examples, starch and 22 Chapter 2

Table 2.1 Classification of carbohydrates

Structure and examples Class Subclass Dietary source Aldose Ketose Monosaccharide Triose Glycerol – Tetrose Pentose Ribose Hexose Glucose (composed of Maltose Two glucose units α1 → 4 glycosidic bond Malt liquor two monosaccharide) Sucrose αD-glucose + β-D-fructose α1 → β2 bond Cane Lactose αD-glucose + βD-galactose1 → β4 bond Milk Oligosaccharide (composed Maltotriose Maltose and α1 → 6 glucose Beans of 2–10 monosaccharide Raffinose: Pea bran units, O-linked attached to - Whole grains OH group), e.g., IgA N-linked containing: (attached to protein via glucose, , N-glycosidic bond, e.g., and fructose Aspartate side chain), e.g., dolichol phosphate (10 or more – : Potato monosaccharide unit) and α1 → 4 bond, 200–20,000 glucose units highly Tubers their derivatives branched Cereal Homopolysaccharidesa : Grains (α-D glucose) 1 → 4 linkage plus α1 → 6 Legumes branching after 24–30 monomers Homopolysaccharide: Contains only one kind of monosaccharides Starch α1 → 4 linkage and α1 → 6 branching and Glycogen 12–14 monomers of D-glucose α1 → 4 linkage and α1 → 6 branching βD-glucose Similar to β1 → 4 bond amylopectin, branches more frequently Insulin βD-fructose (β2 → 1 bond) Plants Dextranb αD-glucose linked at α1 → 6 bond, with Tubers few branches aHeteropolysaccharides will be discussed under separate section. bDextran: Break down product of starch; Limit : Formed when of starch reaches a branch point.

glycogen. Polysaccharides can be linear or branched Table 2.2 Comparison of amylose and amylopectin polymers. Most starch forms in nature are 30% α-amylose and 70 to 90% amylopectin (Table 2.2) and are classified Amylose Amylopectin as homopolysaccharides or heteropolysaccharides. Common monosaccharide constituents of polysaccharides Glycosidic bond: α1–4 α1–4; α1–6 (at branch point) are D-glucose (most common), D-fructose, D-galactose, Linear Branched L-galactose, D-, L-, and D- Contains several thousand Branching occurs every 24–30 (Table 2.3). Functions of polysaccharides are as follows: glucose residues glucose residue ••Structural. No branching Contains up to 106 glucose residues ••Water binding. Structure and Chemistry 23

Table 2.3 Common monosaccharide derivatives Structure of Monosaccharides of polysaccharides

Amino sugar D-glucosamine All monosaccharides are optically active due to the presence of at least one asymmetric carbon. D-galactosamine Sugar derivatives N-acetylneuraminic acid Asymmetric Carbon Sugar acid Glucuronic acid Iduronic acid The carbon atom bonded to four different atoms or groups of atoms is termed as asymmetric carbon or chiral carbon. is the simplest monosachharide having one ••Reserve or storage. asymmetric carbon. ••Cell attachment and recognition sites. ••Generate metabolic intermediates: Isomerism {{Glucose-6-phosphate. Monosaccharide can rotate plane polarized light to right {{Fructose-6-phosphate. (dextrorotatory) or left (levorotatory). ••Biosynthesis of fatty acids (FA) and amino acids. D- and L-stereo isomers are based on the position of hydroxyl group on asymmetric carbon. Presence of asymmetric carbon Heteropolysaccharides allows the formation of isomers, and the number of isomers of a compound depends on the number of asymmetric They are composed of repeating units of more than one kind carbon atoms (n). of monosaccharides (Box 2.1). Number of isomers = 2n. For example, glucose has four asymmetric carbon atoms, thus 24 = 16 isomers. Box 2.1 Examples of heteropolysaccharides Mucopolysaccharides Mucoprotein Epimer () ()

Hyaluronic acid Sialic acid Epimers differ in position of –OH group at 1 or in more asymmetric carbon. D-glucose and D-galactose are epimers Chondroitin sulfate of each other at C-4. Similarly, D-mannose and D-glucose are Dermatan sulfate Gangliosides epimers at C-2 (Table 2.8). Keratan sulfate Heparin sulfate New carbon formed during cyclization is anomeric carbon. This carbon becomes chiral center with two possible configurations: in β-anomer, –OH group of anomeric carbon is above the plane of ring, and in α-anomer, it is opposite They are linear chains of repeating disaccharides in which as during hemiacetal and hemiketal formation (e.g., C in one of the monosaccharide unit is , and one 1 glucose). (or both) of monosaccharide unit contains sulfate or carboxylate group. Glycosaminoglycan (GAG) is present Depending on the size of ring formed, structure is designated; in extracellular matrix, cartilage, tendon, skin, and blood , if it is six-membered ring and , if it is five- vessels. The collagen and other proteins are embedded in a membered ring. A six-membered ring structure can adopt gel-like matrix, which is composed of GAG, proteoglycans, either a chair or boat configuration. and glycoproteins (Tables 2.4 and 2.5). Two of glucose have different physical and chemical properties. They are freely interconvertible in aqueous solutions, so at equilibrium, D-glucose is a mixture Derivatives (or Modified of β-anomer (63.6%) and α-anomer (36.4%). Monosaccharides) D-glucose adopts a chair conformation. Cyclic form of glucose and fructose with five- and six-membered rings are known Monosaccharides can be converted to several derivatives as glucofuranose and glucopyranose and fructofuranose and (Table 2.6). fructopyranose, respectively. Blood Group Antigens Blood group antigens are proteins or oligosaccharides Structure of Carbohydrates that differ from one individual to another. They consist of α-2-fucosylated galactose substitute with 3-N-acetyl galactosamine (A) or galactose (B) (Table 2.7). Carbohydrates can be depicted as straight chain and ring forms. Straight chain (Fischer projection) form is 24 Chapter 2

Table 2.4 Composition and functions of GAG

GAG Repeating unit Tissue distribution Function Feature Hyaluronic acid GlcUA and GlcNAc Synovial fluid Vitreous body: eye Serve as shock absorber β1 → 3 cartilage and lubricant GlcUA GlcNAc Loose connective tissue β1 → 4 GlcUA Vitreous humor form Consists of up to 25,000 clear, viscous jelly like disaccharide, molecular consistency weight up to 107 Chondroitin GlcUA Cartilage To maintain structure located at the site GalNAC and function of tissues of calcification in endochondral bone Dermatan sulfate IdUA, GalNAc Skin, valves blood Sclera: maintain shape Contribute to elasticity β1 → 3 vessels lung, sclera of eye ball of skin IdUA GalNAc Keratin sulfate GlcNAc, Gal Cornea Corneal transparency Present in bone, No uronic acid Bone, cartilage, horny cartilage horny structures, hair, nail structures, hair, and nail β1, 3 GlcNAc Gal β1 → 4 GlcNAc Linked to protein via: N-linkage (type1) Cornea Corneal transparency – O-linkage (type 2) Loose connective Ground substance – tissue Heparan sulfate GlcN Lung, muscle liver, Present on cell surface Cell surface component GlcUA component of or bound to ECM and extra- cellular synapse, glomerulus responsible for charge substance in blood GlcN α1, 4 GlcUA → GlcN vesicles selectiveness vessel wall and brain Not a constituent of connective tissues Occurs as intracellular granules of most cells inhibits clotting of blood Heparin GlcN, IUA Granules of mast Function as intracellular Has the highest negative α1, 4 cells, liver lung, skin binding site charge density of any IdUA GlcN anticoagulant, bind natural anticoagulant. to lipoproteins lipase Binds to antithrombin causing LP release Abbreviations: GAG, glycosaminoglycan.

Table 2.5 Organ- and site-specific functions of GAG

GAG Organ Site Function Heparan sulfate Liver Intracellular on cell surface Anticoagulant Heparan sulfate Kidney Renal basement membrane Charge selectivity of glomerulus Keratan sulfate Cornea In between collagen fibers Corneal transparency Dermatan Sulfate Heparin Mast cells Secretory granules Inflammatory response Heparin sulfate Vascular wall Endothelium Anticoagulant activation of lipoprotein lipase Abbreviation: GAG, glycosaminoglycan. Structure and Chemistry 25

Table 2.6 Carbohydrate derivatives

Derivatives Example Location/constituent of Amino sugar Glucosamine Galactosamine Cartilage Chondroitin sulfate Neuraminic acid Cell membrane Sugar acids Ascorbic acid Vitamin C Aldonic acid Component of GAG and proteoglycans Iduronic acid Galacturonic acid Present in plasma membrane and Glucuronic acid extracellular matrix 2- DNA Sugar alcohol D-sorbitol Minor pathway intermediates D-mannitol Xylitol Glycerol Phosphoric acid esters D-glucose 1P Minor pathway intermediates (Sugar esters) D-glucose-6-P Ribose-5-P Galactose-3-sulfate Erythritol 4 C Artificial sweetener Xylitol 5 C Natural sweetener with low glycemic index Mannitol 6 C Used in head trauma Sorbitol 6 C Artificial sweetener, laxative

Abbreviations: DNA, deoxyribonucleic acid; GAG, glycosaminoglycan.

linear representation of monosaccharides. In solution, Table 2.7 Blood group antigens monosaccharides exist as ring structures. The carbonyl Antigen Structure group during the formation of ring structure reacts with hydroxyl group of same molecule to form five- or six- O -Galactose membered ring. The hydroxyl group on anomeric carbon is  above or below the plane of the ring and is labeled as β- or N-Acetyl glucosamine α-carbon, respectively.  In three-dimensional structure, the ring usually takes a chain R conformation. By intramolecular reaction between hydroxyl A NAc Galactosamine and carbonyl group, they can form cyclic hemiacetal and  hemiketals. Alcohols react with carbonyl groups to form Fucose-Galactose hemiacetal and hemiketals:  H R–O H N-Acetyl glucosamine R – H + R' – C C hemi-acetal  O R OH R B Galactose R" R–O R” hemiketal  R – OH + R' – C C O R OH Fucose-Galactose  N-Acetyl glucosamine  In solution, hydroxyl group on anomeric carbon changes R spontaneously to from α- to β-position by the process of 26 Chapter 2

Table 2.8 Isomerism in carbohydrates

Isomerism Reasoning Example DL isomerism (stereoisomer) • Same chemical formula D-, L-glucose • Differ in position of –OH group on one or more asymmetric carbon (e.g., C-5 in glucose) • Mirror images of each other Optical isomerism (enantiomer) Presence of asymmetric carbon rotate plane Enantiomer polarized light either to right [dextrorotatory, (+) isomer (+)] or to left [levorotatory (–)] (–) isomer Epimerism Differ as a result of variation in configuration Mannose at C-2 of –OH and –H group on C-2, -3 and -4 of Galactose at C-4 glucose Anomerism Differ in configuration at carbonyl or α anomer anomeric carbon β anomer α: –OH group on anomeric carbon is below plane of ring β: –OH group is above plane of ring Aldose-ketose isomerism Same molecular formula, but different Glucose: structure due to position of carbonyl carbon C-1 is Fructose: C-2 is keto

mutarotation. The α- and β-forms of glucose equilibrate via Inversion of Sugar the straight chain aldehyde form. This occurs due to opening of hemiacetal ring. Sucrose is dextrorotatory (+66.5°) and on hydrolysis by enzyme sucrase (invertase) gets converted to glucose and Mutarotases fructose. It becomes levorotatory (–28.2°). This process of change in optical rotation from dextro (+) to levo (–) is called During metabolism of lactose, (galactosyl-β-1, 4-glucose), inversion of sugar. galactose produced by hydrolysis is carried out by the enzyme lactase is in the form of β-galactose. Reduction of Carbohydrates Aldehyde or ketone group of a sugar can be reduced to a hydroxyl group, forming a polyol. Glucose is reduced to A sugar possessing free anomeric carbon atom that is not sorbitol, and galactose is reduced to galactitol. involved in a glycosidic linkage is reducing sugar, and the end containing free anomeric carbon is the reducing end. This free aldehyde or ketone group is capable of reducing Clinical Correlation alkaline copper sulfate, e.g., lactose and maltose. Sucrose is a nonreducing sugar because the glycosidic bond Sorbitol does not readily diffuse out of cells and between anomeric carbon C-1 of α-glucose and C-2 of accumulates in cells, causing osmotic damage to neurons fructose is involved in the glycosidic bond formation, i.e., and causes diabetic cataract. both anomeric carbon atoms are substituted, and neither end has a free carbonyl group. Osazone Crystals

Homodisaccharide Phenylhydrazine Reaction

These are the disaccharides in which both the monosaccharide Take a small amount of phenylhydrazine salt (0.5 inch) in a units are the same. A few examples of homodisaccharides test tube, take 5 mL sugar solution, and shake well. are maltose, , and . Maltose contains Heat in boiling water bath for 15, 30, and 45 min. Allow only glucose. Isomaltose contains two glucose units in α-1–6 the tube to cool slowly and examine the crystals under linkage (Glc-α1-4glc), while cellobiose contains linkage as microscope. Better crystals are obtained if tubes are allowed Glcβ1 → 4 Glc. to cool in water bath. Structure and Chemistry 27

••Glucosazone: Appear immediately insoluble in hot, Glycoproteins include integral membrane proteins that needle-shaped yellow. function as receptors for hormones or other molecules. Functions of glycoproteins are listed in Table 2.9. ••Maltosazone: Appear late, yellow flower petal.

{{Glucose, mannose and fructose yield similar crystals Proteoglycans because of similarity in their molecular structure because reaction involves C1 and C2. Term proteoglycan is used to describe certain complexes {{Sucrose and galactose don’t give crystals because it of carbohydrate and proteins found in glycocalyx, synovial is difficult to precipitate them. fluid of joints, and basement membrane. Proteoglycans ••Lactosazone: Appear late (soluble in hot), yellow are a family of glycoproteins whose carbohydrate­ moieties are predominantly GAG. Proteins and aminoglycans in hedge­hog shaped (cotton puff arising from a green ECM (extracellular matrix) aggregate covalently and base). noncovalently too to form macromolecules known as Principle proteoglycans (Table 2.10).

Phenylhydrazine consists of phenylhydrazine and Na acetate in ratio 1:2. Na acetate is added to promote crystal Protein Carbohydrate Linkages formation by providing pH of 4.5. There are the following two types of protein carbohydrate Glucose + 3 phenylhydrazine → glucose phenylhydrazone linkages: → glucosazone + aniline + NH 3 ••O-linkage: Sugar is attached via –OH group of a serine or threonine residue.

Glycoproteins (Mucoproteins) ••N-linkage: Sugar is attached via amide-NH2 group of asparagine residue. Carbohydrates when found attached to many globular proteins are classified as glycoproteins. Glycoproteins O-linked and N-linked Oligosaccharides have short oligosaccharide () chains (1–20 sugar moiety in length) which are highly branched and do not Oligosaccharides linked by a glycosidic linkage between contain repeating sequences. Proteoglycans are long, linear, N-acetyl galacto­samine (GalNAc) and hydroxyl group of branched glycan with disaccharide repeating units. serine or threonine residues. O-linked saccharides are often

Table 2.9 Functions of glycoprotein

Function Example Structural Component of plasma membrane Lubrication Component of mucus Receptor Hormone, other molecules Hormone hCG, thyrotropin, and erythropoietin Immune system Immunoglobulin and complement, interferon Recognition of signal Transport of hormones in signal transduction Cell-cell interaction Mediate cell to cell interaction Stabilization of proteins Stabilize protein against denaturation, proteolysis Abbreviation: hCG, human chorionic gonadotropin.

Table 2.10 Comparison between glycoproteins, glycolipids, and proteoglycans

Glycoprotein Glycolipid Proteoglycan Composition Oligosaccharide + protein Oligosaccharide + lipid GAG + protein Location Extra cellular surface of plasma Projections on membrane: cell Connective tissue joint membrane, secreted proteins – surface Ag recognition sites lubricants Abbreviation: GAG, glycosaminoglycan. 28 Chapter 2

found in cell surface glycoproteins, mucins, and low-density Diagnosis of lysosomal degradation of heparan sulfate is lipoprotein (LDL) receptor. made by the followings: They are always attached by glycosylamine linkage of ••Urine GAG. N-acetyl glucosamine (GlcNAc) to amide nitrogen of ••Leukocyte/fibroblast assay for specific enzymes. asparagine residue. This linkage is found in immunoglobulins G and M, ribo­ nuclease B, ovalbumin, and peptide hormones.

OSO – OSO – NSO Mucopolysaccharidosis 3 3 3 1 3 5 β1 4 α1 4 Mucopolysaccharidosis are metabolic disorders caused GlcNAc IduA GlcN 2 4 by absence or malfunctioning of lysosomal enzymes 6 β1 4 (Table 2.11). 2 – Hexoaminidase GlcNAc-peptide Lysosomal degradation of heparan sulfate (Fig. 2.2) presents 5 – N-sulfatase as follows: 6 – Glucosaminidase ••Skeletal deformity. ••Mental retardation. Fig. 2.2 Lysosomal degradation of HS. HS, heparan sulfate. ••Early death in severe cases.

Table 2.11 Genetic defects of proteoglycan metabolism

Syndrome Defect Products accumulated in lysosome Hurler α-1-iduronidase HS DS Hunter Iduronate sulfatase HS, DS Sanfilippo A Heparin sulfatase HS Sanfilippo B NAc glucosaminidase Sanfilippo C NAc Gln-6-sulfatase Morquio Galactose-6-sulfatase KS Maroteaux–Lamy NAc Gal4 sulfatase DS Sly β-Glucuronidase DS, HS Abbreviations: DS, dermatan sulfate; HS, heparan sulfate; KS, keratan sulfate.

Lipid: Structure and Function (BI4.1)

•• Introduction Insulation: {{Electric insulation. Lipids of major physiologic significance are FA, their {{Thermal insulator. esters, cholesterol, and steroids. Lipids are amphipathic ••Building block: They are important component of molecules (with both polar and non-polar groups). Lipids cell membrane. Typical membrane lipids include are hydrophobic in nature. They are composed of saturated phospholipids, glycolipids, and cholesterol. or unsaturated long-chain hydrocarbons. ••Transport: Lipoproteins serve transport function. Functions of Lipids ••Storage: Stored in adipose tissue as triacylglycerol (TAG). ••Fuel: Source of energy: principal energy reserve. ••Precursor for steroid hormones. ••Nutrients: Used by cells to build membranes. ••Signaling function: They serve as hormone mediators. Structure and Chemistry 29

••Special functions: Signaling, anchor, cofactor, vision, Properties eicosanoids, phospholipids, steroids, and second messengers, e.g., phosphatidylinositol. ••FA are amphipathic. ••Anchorage: They form anchors to attached proteins of ••FA form micelle in water by orienting hydrocarbon membrane. chains in center and positioning polar carboxylic ••Cofactors: They produce cofactors for enzymatic groups to surface that form hydrogen bonding with reactions, e.g., vitamin K and ubiquinone. water. ••Role in vision: Light-sensitive lipid-retinal. ••Melting point of FA increases with chain length and decreases with degree of unsaturation. ••Digestion and absorption: They act as emulsifying •• agent in digestive tract. Important for absorption of Cis FA lower the melting point more than trans FA do. fat-soluble vitamins and indispensable components of nutrition: essential FA. General Formula

Saturated FA: CH3 – [CH2]n – COOH Fatty Acids n = number of methylene groups.

FA are composed of a long hydrogen–carbon chain and Nomenclature terminal carboxyl group. They exist as free or esterified to glycerol. Humans have FA with even number of carbon FA are named by common name or a systematic name. atoms: 16–20 carbon in length. They can be classified as Systemic name is given to FA according to the number of short chain fatty acids (SCFA, 2–4 carbons), medium chain carbon atoms. Saturated FA are named by chain length, and fatty acids (MCFA, 6–12 carbons), long chain fatty acids unsaturated FA are named by position of double bonds, e.g., (LCFA, 14–24 carbons), or very long chain fatty acids (VLCFA, octadecanoic acid (18-carbon length). Important points of >24 carbons). consideration are as follows: FA mainly occur in biological systems, but only rarely in ••Suffix: the free state. FA exist as saturated (C–C bonds are single {{For saturated FA, suffix is–anoic. bond) and unsaturated FA (with one or more double bond). Saturated FA are extremely flexible molecule due to free {{For unsaturated FA, suffix is–enoic. rotation of carbon bonds. {{For example, palmitic acid, 16 C: hexadecanoic acid. Length of FA influences their transport from the gastro­ ••Naming: intestinal tract (GIT) to various tissues and cellular compart­ {{Carbons are numbered from carboxyl carbon ments. Dietary SCFA and MCFA diffuse directly into hepatic (carbon no. 1). portal vein to be transported to liver. LCFA are insoluble in aqueous solution at physiological pH, and they bind to {{Carbon adjacent to it is carbon number 2 (α-carbon). albumin for their transport. Dietary LCFA are packaged as {{Terminal methyl carbon: ω-carbon or n-carbon. TAG in chylomicrons to enter lymphatics, then blood, and finally liver. LCFA are transported into cytosol of cells by Delta Numbering System binding to FA binding proteins. It is based on number of carbons, number of double bonds, For oxidation, SCFA and MCFA diffuse directly into and position of double bonds, e.g., linoleic acid is designated mitochondrial matrix, and LCFA cross the mitochondrial as 18: 2: ∆9, 12 (18 carbons, two double bonds, and position of membrane via carnitine shuttle. VLCFA are catabolized in double bond after C9 and C12 from carboxyl end). peroxisomes. FA in unesterified form are known as free fatty acids (FFA). ••Position of double bond: {{∆9: Double bond between C9 and 10 from carbo­ xylic end. Clinical Correlation {{ω9: Double bond on ninth carbon from omega end. In Zellweger syndrome, defective biogenesis of peroxi­ somes results in accumulation of VLCFA in peroxisomes Omega Numbering System causing demyelination of nerve axons. It is based on distance from the most distal (methyl) carbon from the carboxylic end, the ω carbon (omega), e.g., ω-3 FA Solubility have double bond between third and fourth carbon from the omega end of the molecule (Fig. 2.3). ••FA with >18 C are nearly insoluble in water. Concept of α- and β-Carbons ••FA with <16 C are too soluble. At high concentration, FA disrupts the cell membrane. The Carbons 2 and 3 are referred to as α- and β-carbons as they hydrophobic property of bilayer acts as electrical insulator. are located at α- and β-positions to carboxyl group. 30 Chapter 2

Numbering of Saturated Fatty Acids

ω terminal C terminal

COOH– CH2– CH2– CH2– CH2– CH2– CH2– CH2– CH2– CH2 ∆ numbering 1 2 3 4 5 6 7 8 9 10 ω numbering 10 9 8 7 6 5 4 3 2 1 Symbols α β γ δ ω-3 FA have final double bond located, three carbons from their omega end. ω-3 FA are essential FA, e.g., linolenic acid. ω-6 FA have their last double six carbons from the omega end, e.g., linoleic acid and arachidonic acid.

Two similar groups attached to carbon double bond can Δ12 Δ9 Carboxyl end Δ12 Δ9 be on the same side (cis) or opposite side (trans). In cis configuration, molecule is bent at 120° in double bond and

CH3 – (CH2)4 – CH = CH – CH2 – CH = CH – (CH2)7 – COOH produces a kink. In trans configuration, molecule remains straight at double bond and do not introduce kinks. Trans-FA Methyl end ω–6 ω–9 have much higher melting points than corresponding (n–6) (n–9) unsaturated cis-FA. They have straight hydrocarbon chains that reduce the fluidity and mobility of membrane. Fig. 2.3 Two systems of nomenclature. FA, fatty acid. With increase in chain length, melting point of FA increases, and it decreases with unsaturation. Various FA with their Isomerism in Unsaturated Fatty Acids structural differences are listed in Table 2.12. Biological consequence of kink The carbons flanking the double bond of unsaturated FA exhibit cis- or trans-configuration. Naturally occurring In biological membrane, saturated FA chains pack closely together to form ordered, rigid arrays under certain unsaturated FA have cis double bonds. Unsaturated FA conditions. However, unsaturated FA prevent such close exhibit geometric isomerism, and two stereoisomers are packing and produce flexible fluid aggregates. This causes possible, namely, cis and trans. Double bonds formed in FA increase in membrane fluidity. are nearly always in the cis configuration, this causes a bend or kink in the FA chain. R H R H C C Classification of Lipids || || •• Cis C C Simple lipids—Esters of FA with alcohol: R H H R Trans {{Fats—esters of FA with glycerol.

Table 2.12 Different fatty acids with their structure

Name No. of carbon atom Systemic name Double Saturated FA Lauric acid 12 Dodecanoic acid – Myristic acid 14 Tetradecanoic acid – Palmitic acid 16 Hexadecanoic acid – Unsaturated FA Stearic acid 18 Octadecenoic acid – Palmitoleic acid 16 cis-Hexadecenoic acid 1:9 (ω9) Oleic acid 18 cis-Octadecenoic acid 1:9 (ω9) Elaidic acid 18 trans-Octadecenoic acid 1:9 (ω9) Linoleic acid 18 cis-9,12-Octadecoidenoic acid 2:9, 12 (ω6) Linolenic acid 18 cis-9,12,15-Octadectrienoic acid 3:9, 12, 15 (ω3) Arachidonic acid 20 cis-5,8,11,14-Eicosatetraenoic acid 4:5, 8, 11, 14 (ω6) Abbreviation: FA, fatty acid. Structure and Chemistry 31

{{Waxes—esters of FA with higher molecular weight Fatty Acid-Derived Lipids alcohols. The lipids derived from FA can be described based on their ••Complex lipids—Esters of FA with alcohol and contain head, tail groups, and backbone. Backbone molecules of an additional group: FA-derived lipids are glycerol and sphingosine. {{Phospholipids. Head group could be hydroxyl group or phosphate residue ••Phosphatidic acid: Esters of FA with alcohol and to C-3 of glycerol or sphingosine. Tail group is formed by FA phosphoric acid residue. chains attached to back bone molecules attached through ester bonds formed with glycerol or amine bonds formed ••Alcohol can be glycerol: glycerophospholipids (GPL). with sphingosine. ••Alcohol can be sphingosine: sphingophospholipids. Animal fats contain a high amount of saturated triglycerides. ••Plasmalogens: Highly reduced carbons of triglycerol yield large amount of {{Glycolipids (glycosphingolipids [GSL]): energy, i.e., 1 g yields 38 kJ of energy. It is the molecule of choice for storage because of its hydrophobic nature and –– Esters of FA, with sphingosine and a carbo- capacity to aggregate in anhydrous forms. hydrate. {{Other complex lipids: Advantages of using TAG as stored fuel over glycogen and starch –– Sulfolipids, aminolipids, and lipoproteins. • TAG is hydrophobic and unhydrated. –– Phosphatidic acid: glycerol + 2 acyl residues + • On the other hand, polysaccharides carry 2 g water per PO4. gram of carbohydrates. ••Precursor and derived lipids: They include FA, • The carbon atoms of FA in TAG are more reduced than those in . glycerol, steroids, and alcohol. in addition, derived • Oxidation of TAG yields more energy per gram (nearly lipids include ketone bodies, steroids, fatty aldehydes, double) as compared to oxidation of carbohydrates. prostaglandins, lipid soluble vitamins, and hormones. • Thus, organism carries fat as fuel, but does not carry ••Neutral Lipids. extra weight of water of hydration associated with stored polysaccharides.

Unsaturated Fatty Acids ••Monoacyl Glycerol: One FA is esterified. ••Diacyl Glycerol: Two FAs are esterified, e.g. Unsaturated FAs are slightly more abundant in nature phospholipids (Fig. 2.4). than saturated FAs are, especially in plants. Most common unsaturated FA is oleic acid or C18: 1∆9.

They may contain one or more double bonds and can be: O Monounsaturated : One double bond ||1 R1—C—O — CH2 Polyunsaturated : Two or more double bonds | Eicosanoids : Prostanoids, leukotriene, R—C — O — 2CH O prostacyclin, and thromboxane 2 | || 3 CH2 — O — P — OR3 Common unsaturated FA include oleic acid and linoleic acid. FA || O Glycerides Glycerol Alcohol Glycerides contain glycerol backbone to which one to three FA residues are esterified. Three types of glycerides exist: TAG, diacylglycerol (DAG), and monoacylglycerol (MAG). 1. FA 2. G L Trans Fatty Acids (BI11.24) FA Y C They are formed in some bacteria and ruminant animals. E R Butter, milk, cheese, and meat of these animals contains 3. PO4 4. Alcohol trans-fats. Artificial trans-fats are produced by partial O hydrogenation of polyunsaturated FA. L

Fried foods, margarine, and baked goods contain substantial Fig. 2.4 Phospholipids. 1. Fatty acid; 2. Platform backbone amount of trans-fats and can contribute to cardiovascular to which FA is attached; 3. PO4; 4. alcohol attached to risk. Diets high in trans-FA raise plasma LDL cholesterol PO . GlyceroPL, glycerophospholipids; FA, fatty acid; PL, and triglyceride levels and lower high-density lipoprotein 4 phospholipids. (HDL) levels. 32 Chapter 2

••Triacylglycerol: They are major form of dietary and sphingolipids, while Table 2.14 provides precise location stored fat. They are found primarily in adipose tissue and defects of various kinds of lipids. where they serve as depot for fat. Triglyceride (or TGA) are esters of FA and glycerol. They are principal neutral derivatives of glycerol. (Fig. 2.5). Membrane lipids (Polar) Membrane Lipids Storage lipids (neutral) Storage of lipids and membrane lipids are shown in Fig. 2.6. Table 2.13 lists various kinds of phospholipids and PL Glycolipids

O || TAG Glycerol Sphingolipids Galactolipid

CH2–O–C–R1 | G G G FA FA FA | L L L R2–C–O–CH Y Y Y || | O C FA C FA FA C FA O | || E E E R R R Mono or CH2–C–O–R3 FA PO4- PO4- disaccharide O O Alcohol choline O R1 and R3: saturated FA L L L

SO4 R2 unsaturated FA Sphingosine Fig. 2.5 Triacylglycerol. FA, fatty acid. Fig. 2.6 Storage and membrane lipids.

Table 2.13 Examples of phospholipids and sphingolipids

Functional group Type Phospholipids Choline Phosphatidylcholine (lecithin) Ethanolamine Phosphatidylethanolamine (cephalin) Serine Phosphatidylserine Inositol Phosphatidylinositol Another phosphatidic acid Cardiolipin Sphingolipids Phosphatidylcholine Sphingomyelin Galactose or glucose Cerebroside Sialic acid containing oligosaccharides Ganglioside

Table 2.14 Various lipids: location and defects

Type of lipid Location function Defect Sphingolipids Sphingomyelin Nerve tissue Lysosomal Blood signal Enzyme defects: lysosomal Transduction Storage disease1 Cerebroside Myelin sheath Cerebroside sulfatidase deficiency: metachromatic leukodystrophy Ganglioside Myelin sheath Neuraminidase deficiency: neurodegenerative disease Cholesterol Most mammalian tissues Abetalipoproteinemia: hypocholesterolemia, can be associated with Precursor of steroid hormones, increased risk of hemorrhagic stroke, cancer, respiratory disease, vitamin D and bile acids aortic dissection Eicosanoids Short term COX-1 deficiency: bleeding disorders Signaling molecule Abbreviation: COX-1, cyclooxygenase-1. Structure and Chemistry 33

Glycerophospholipids X | GPL are major class of membrane lipids. They are abundant O in all biological membranes. GPL contains phosphorylated | head, three-carbon glycerol backbone, and two-hydrocarbon O–P=O FA chains. FA components provide hydrophobic barrier and | remainder is hydrophilic. O GPL are most common phospholipids, and phosphatidic acid | is the parent compound for GPL. CH2—CH—CH2 | |

x O O | | | Polar o Head o – p – o CH C=O | 0 || | CH R2 1 2 3 |

CH2 – CH – CH2 R1 | | Hydrophilic tails O O Ethanolamine plasmalogen is abundant in nervous tissue | | and heart. Thus, GSL are amphipathic, containing a polar end R R 1 2 or head group because of charged phosphate group (PO4) and

substitution on PO4 and non-polar tail (due to hydrophobic carbohydrates chains of fatty acyl groups). Every tissue and Phospholipase cellular membrane have a distinct composition of GPL and a Phospholipase hydrolyze ester bonds of GPL. Phospho­ definite pattern of FA composition. lipase A1 (PLA1) and A2 remove FA chains from the first and second positions of GPL. Phospholipase C (PLC) and Sphingolipids phospholipase D (PLD) attack polar head group of GPL. PLC releases diacylglycerol­ and inositol triphosphate (1P3). In sphingomyelin, terminal OH group of sphingosine is Phospholipase B (PLB) removes FA from both the first and esterified to phosphorylcholine, so that its polar head second positions. GPL includes the followings: is similar to PC. It is second major class of phospholipids. ••Phosphatidylcholine (PC). They contain sphingosine backbone rather than glycerol. ••Phosphatidylcholine ethanolamine (PE). Sphingosine is linked to FA by amide bond forming ceramide, which is precursor of sphingolipids. It is the most abundant ••Phosphatidylcholine serine (PS). sphingolipid in mammalian tissues. Sphingolipids are found ••Phosphatidylglycerol (PG). in large quantities in membrane of nerve cells in brain and ••Phosphatidylcholine inositol (PI). neural tissue. ••Diphosphatidylglycerol (cardiolipin): Cardiolipin is Sphingomyelin has structural similarity to GPL and has present exclusively in inner mitochondrial membrane. many properties in common. C1, C2, and C3 of sphingosine molecule structure are analogous to three carbons of TAG. ••GPL contain two fatty acyl groups esterified to C-1 and In GPL, ceramide is structurally similar to diacylglycerol. C-2 of glycerol. There are three subclasses of sphingolipids: sphingomyelin, There is a high degree of coiling of hydrocarbon chain in neutral glycolipids, and gangliosides. All these are derivatives a GPL that is disrupted by a double bond. Usually, on C-1, of ceramide, but differing in their head groups. Functions saturated FA, e.g., palmitic acid and stearic acid are found, of GSL: and on C-2, unsaturated FA is present, e.g., oleic acid, linoleic acid, and linolenic acid. Designation of GPL does not specify ••Cell–cell recognition. which FA is present, as seen in case of PC and PE. ••Tissue immunity. Glycerol Ether Phospholipids Phospholipids and sphingolipids are degraded in lysosomes. PLA removes one of the two FA producing lysophospholipid, Plasmalogen: Structurally, the plasmalogens resemble and lysophospholipase removes the remaining FA. phosphatidylethanolamine, but possess an ether link on the Gangliosides are degraded by lysosomal enzymes that sn-1 carbon instead of the ester link. catalyze stepwise removal of sugar to yield ceramide finally. 34 Chapter 2

Glycosphingolipids estrogen, progesterone, glucocorticoid, mineralocorticoids, and bile acids are derived from cholesterol. (Refer Chapter 4 GSL are sugar-containing lipids built on backbone of for more details.) ceramide. They lack PO4 group, have sugar moiety or primary –OH group of sphingosine (in ceramide). They carry net negative charge at neutral pH, for example, Lipoproteins glucocerebroside—present in non-neuronal tissue and galactocerebroside—present in brain and nervous tissue. Lipoproteins are complexes of lipids and protein molecules. The primary function of lipoproteins is transport and Gangliosides delivery of FA, cholesterol and TAG. (Refer Chapter 4 for more details.) They are complex sphingolipids having oligosaccharide as their polar head group and one or more residues of NAc Neu, sialic acid at termini. Gangliosides are concentrated Terpenes and Polyprenoids in outer surface of cell and present points of recognition for Terpenes are a class of lipids formed by combination of two extracellular molecules. Gangliosides are present in nerve or more molecules of isoprene. Long-chain polyisoprenoid endings and are important in nerve impulse transmission. molecules with terminal alcohol moiety are polyprenoids. Polyprenoids and dolichols (16–22 isoprene units) belong Clinical Correlation to this class. Steroids are terpene-based lipids having a common structural motif of three six-membered and one Tumor formation induces synthesis of new complement five-membered rings fused altogether. of gangliosides. Absence of enzymes required for

degradation of GSL results in genetically transmitted Essential Fatty Acids

diseases, e.g., Tay Sachs disease (GM2 involved). Certain polyunsaturated FA cannot be synthesized and must be supplied in the diet. n-3 FA eicosapentaenoic acid Glycolipid (20:5, n-3) and docosahexaenoic acid (20:6, n-3; DHA) is n–3 FA, is physiologically important eicosanoid. Fish oils They are present in all tissues on the outer surface of plasma are particularly rich in these FAs. Breast milk also contains membrane. Glycolipid consists of sphingosine, FA, and an sufficient amount of DHA. oligosaccharide residue. Phosphate residue is absent in Two essential FA are linoleic acid (18:2, n-6) and α-linolenic glycolipid. acid (183, n-3). These FA have to be obtained from diet Sulfatides: They are cerebrosides in which sugar is esterified 12 15 since humans lack ∆ and ∆ desaturase enzymes. If they with sulfuric acid. are excluded from the diet, deficiency symptoms develop in the form of skin lesions and retarded growth. There is Cholesterol a competition between FA families for desaturation and elongation and predominance of one family (e.g., n-6 acids) Cholesterol is a principal component of plasma membrane in diet can limit synthesis of some of the members of n-3 and lipoproteins. Steroid hormones namely androgens, family.

Proteins: Structure and Fuction (BI5.1)

Introduction Amino Acids

Proteins are most abundant biological macromolecules, Amino acids are nitrogen-containing carboxylic acids. They occurring in cells and parts of cells and have diverse form components of lipids, e.g., serine in phospholipid and biological functions. They are found throughout the body. glycine in bile acids. They function as neurotransmitter, Over 40% of body proteins are found in skeletal muscle, and precursor of neurotransmitter, mediator, or hormone. They over 25% are in body organs. Each body protein is unique in are precursor for other metabolites, e.g., glucose in gluco­ the characteristic and sequential pattern of its constituent neogenesis, purine, and pyrimidine bases and heme. amino acids. Proteins are built from amino acids and There are about 300 amino acids present in nature, and contribute to fuel supply, structural support, and activity of only 20 α-amino acids coded by genetic code occur in the cell (Box 2.2, Tables 2.15 and 2.16). proteins. Additional amino acids occur in specific protein Structure and Chemistry 35

Box 2.2 Functions of proteins Table 2.15 Diversity of protein function

• Structural elements: They include contractile proteins, Function Protein globular proteins, and fibrous proteins. They make up Protection, shape, movement Cytoskeleton cytoskeleton to provide structure and strength to cells. • Fibrous proteins: Protective and barrier to Cell membrane chemicals {{ Collagen {{ Elastin Mucus GIT, lung cell membrane {{ Keratin Protection Immunoglobulin • Globular proteins: Catalyst Enzyme {{ Myoglobin Hormone GH {{ Calmodulin Signaling G-protein {{ Many enzymes • Contractile protein: Genetic Histone {{ Actin and myosin: Found in cardiac, skeletal, and Contractile protein Tubulin, myofilament smooth muscles. Channels Ion channel {{ Movement: Actin and myosin are responsible for Receptors, cell adhesion Hormone, integrin muscle contraction. Immunoprotection Immunoglobulin • Enzyme catalysis: {{ Transporters: Hair Keratin – Albumin Abbreviation: GIT, gastrointestinal tract. – Hemoglobin – Prealbumin – Ion channels Table 2.16 Types of amino acids – Transferrin Amino acid type Example pK – Ceruloplasmin a – Lipoprotein. Neutral Cysteine 8.3 {{ Storage: Muscle protein constitute nutrient reserve. Tyrosine 10.1 {{ Oxygen molecule: Hemoglobin. Acidic Aspartic acid 3.9 {{ Messenger: Glutamic acid 4.3 – Hormone. Basic Arginine 12.5 – Neurotransmitter. Lysine 10.5 • Blood coagulation: Histidine 6.0 {{ Immunity: Immunoglobulin. {{ Buffers: – Amino acids serve as buffer. α-Amino Acids – Fluid balancer: Plasma proteins contribute to osmotic pressure. The carbon atom next to the carboxyl group is called the • Control and regulation of gene expression: α-carbon. Amino acids containing an amino group bonded {{ Signaling: Proteins function as signaling substances directly to the α-carbon are referred to as α-amino acids. (hormones) and as function in cell adhesion, and as hormone receptors. β-Amino Acids {{ As conjugated proteins: Proteins joined to non-protein compounds, e.g., glycoproteins form connective tissue A β-amino acid is the one where the amino group is attached (collagen, elastin, and bone matrix). to the secondary carbon rather than the α-carbon. β-amino {{ Proteoglycans present in extracellular matrix. acids occur in nature in free and bound form (bound to pep­tides). Biologically important β-amino acids are Taxel, cocaine, penicillin, and nocardicin A. They are found in many biologically active natural products and drugs. by “post translational” modifications of these 20 common amino acids. For example, Peptidyl proline—4-hydroxyproline γ-Amino Acids

Peptidyl lysine—5-hydroxylysine Some gamma amino acids are also formed in living Peptidyl glutamate—ϒ-carboxy glutamate. organisms, e.g., gaba (gamma amino butyric acid). 36 Chapter 2

Various Groups in Amino Acid to form polypeptide chain. The amino acid side chains in the polypeptide account for differences among proteins. They include amino groups, acid groups. In addition, these side chains affect protein folding and determine the final form of protein molecule. E.g., insulin has two polypeptide chains. NH2 Amino group

O Secondary Structure R C C Acid group H Secondary structure is created by coiling and/or pleating of polypeptide chain. Secondary structure arises by H α-carbon conformations stabilized by hydrogen bonds within peptide chain or between neighboring chains, forming stable filaments or fibers, namely,α-helix, β-pleated sheets, and random coils. Peptide Bond Formation Importance of Secondary Structure Peptide bond formation involves removal of elements of ••α water from carbonyl group of one amino acid and α-amino -Helix forms tough insoluble protective structures group of another. It is an example of condensation reaction. with variable flexibility, e.g., keratin of hair and nail. Molecule are referred to as polypeptide when their molecular ••β-Conformation results in soft, flexible filaments, e.g., weight is below 10,000 and proteins when molecular weight silk fibroin. is higher. α-Helix This CO–NH (amide) linkage is peptide bond. Peptide chains have a direction and thus, two ends, namely amino-terminus Right-handed α-helix is the most common secondary and carboxy-terminus. structure, where each turn covers 3.6 amino acid residues with a pitch of 0.54 nm. It is stabilized by hydrogen bonds. Hydrogen bonds are formed parallel to the axis of helix. Structure of Proteins (BI5.2) Examples include ferritin, myosin, tropomyosin, and transmembrane proteins. Functional role of protein is determined by its basic structure Left-handed α-helix are rarely found in nature. Glutamic and organization. acid, methionine, and alanine are associated with α-helix The structure of proteins are divided into four namely, formation and glycine; proline and asparagine are less primary, secondary, tertiary, and quaternary structure. frequently involved. Primary structure of protein determines its spatial structures β-Pleated Sheets and biological functions. Proteins having similar amino acid sequences have functional similarity. Any change in Peptide chains are arranged like a regularly folded sheet of key amino acids in a protein can cause loss of its biological paper, and hydrogen bonds are formed between neighboring functions. Also, particular spatial structure of a protein is chains (strands) in pleated sheets. correlated with its specific biological functions. Examples: Distance between adjacent amino acids along a β-strand ••Denatured proteins: Their primary structure is retained, is 3.5 Å. This is in contrast to a distance of 1.5 Å among but, they have no biological function. α-helix. Hydrogen bonds are formed between two (or more) polypeptide chains. Amino acids with a branched or bulky ••Allosteric change of hemoglobin by O : Alterations in 2 side-chain or an aromatic ring (valine, isoleucine, tyrosine, amino acids at distant places in the primary sequence leucine, phenylalanine, and tryptophan) are commonly can result in changes in folding. Also, this can alter the found in such conformations. There are the following two enzyme activity or binding of the ligands to receptor types of sheets: proteins via changes in chemical interactions amongst amino acids at active site. ••Antiparallel: Two strands run in opposite directions. ••Protein misfolding and degenerative diseases: An error ••Parallel: When they run in the same direction. in protein conformation can lead to disease. Random coil is a third type of secondary structure of ••Hb structure and sickle cell disease proteins. Little stability exists in this structure because of presence of certain amino acids whose side chains interfere ••Qualitative hemoglobinopathy: Hereditary hemolytic with one another. disorders caused by insufficient production of subunits of Hb. Clinical Correlation Primary Structure ••Mutations in primary structure of protein: e.g. sickle cell Primary structure of protein is linear sequence of amino mutation: alters primary structure and charge by chang­ β acids. Amino acids are linked to each other by peptide bonds ing glutamate to valine in -chain structure of RBCs. Structure and Chemistry 37

••Prions are infectious proteins formed from neutral Quaternary Structure proteins through induced changes in secondary struc­ Polypeptide chains can assemble into multi subunit α ture causing secondary structure change from -helix structures, e.g., Hb tetramer with two subunits of α and β β to -structure in prions forming filamentous aggregates chains each held by noncovalent interaction and binds four that are resistant to degradation by digestion or heat. molecules by cooperative binding. This is responsible for encephalopathies in humans. Quaternary structure is the final level of protein organization ••Denatured polypeptide chains aggregate and become involving interactions among two or more polypeptide insoluble due to interaction of exposed hydrophobic chains forming an aggregate called oligomer. Interactions side chains, e.g., in glucose-6-phosphate dehydrogenase include hydrogen bond electrostatic salt bridges or (G6PD) deficiency, oxidative damage, and denaturation attractions. For example, Hb contains two α-subunits and of hemoglobin (Hb) forms Heinz bodies. two β-sub units held by non-covalent interactions and binds ••Cystic fibrosis: Membrane protein that pump chloride four molecules of oxygen (O2) by cooperative binding. It is ions out of cell is defective due to mutation in gene the arrangement of more than one protein chain (subunit) coding the membrane protein. into complex.

Super Secondary Structure Protein Modification

Motif is a recognizable folding pattern involving two or Proteins can be associated with carbohydrate molecules more elements of secondary structure that form connections (glycosylation) to form glycoproteins or lipids to form between them. Examples are as follows: lipoproteins. There are twenty proteinogenic amino acids, ••Helix-turn-helix: DNA-binding protein. out of which 11 are polar and 9 are non-polar. They are ••Strand-turn-strand: protein with antiparallel incorporated into proteins during translation. β-structure. Classification of Amino Acids ••Alternating strand turn: helix-turn-strand: many α/β-proteins. Amino acids are functional units of proteins. Amino acids

are composed of two functional groups—amino (–NH2), and Tertiary Structure carboxyl (–COOH); a hydrogen atom (–H) and a distinctive α It is a three-dimensional conformation of a polypeptide side-chain (–R), -carbon attached to a central carbon. α chain. Based on side chain (–R) attached to -carbon atom, amino acids can be divided into polar and non-polar amino acids (Table 2.17). Unstructured proteins have non-folded and partially unfolded Side chains of non-polar amino acid have a variety of shapes conformation, e.g., Scaffold proteins, hormones, and cyclin- and sizes, while side chains of polar amino acids have dependent kinases. hydroxyl amide or thiol group. They can be positively or negatively charged (Table 2.18). The polypeptide chain folds in a three-dimensional space Table 2.19 provides classification of amino acids based on with its hydrophobic side chains buried, and the polar charge. Polar amino acids are exposed on surface of proteins charged chains are on the surface. This structure results and non-polar one are buried in hydrophobic core of a from interactions among amino acid residues or side chains, protein. Functional classification of amino acids is provided e.g. myoglobin. in Table 2.20. These interactions can produce a linear, globular, or spherical structure. These interactions include clustering of Table 2.17 Classification of amino acids based on structure hydrophobic amino acids, electrostatic attractions, strong covalent bonding, and weak hydrogen bonding, to determine Polar (hydrophilic) Non-polar (hydrophilic) the particular function of protein. Glycine Alanine Importance of Tertiary Structure Serine Leucine

Trypsin contains two domains with a cleft that forms the Threonine Isoleucine substrate-binding catalytic site. Calmodulin is helix-turn- Cysteine Valine helix motifs/and addition of side chain completes the Arginine Methionine tertiary structure domain. Histidine Proline Clinical Correlation Lysine Tyrosine Aspartate Phenylalanine Alzheimer’s disease: Characteristic feature of this disease Asparagine Tryptophan is aggregates of β-amyloid in senile plaques in brains. This occurs due to conformation change of soluble α-helix to Glutamate β-sheets. Glutamine 38 Chapter 2

Based on nutritional requirement amino acids can be peptides. They are not involved in primary metabolism. classified into the followings: Rare non-proteinaceous amino acids are ornithine, ••Essential Amino acid: Amino acids that cannot citrulline, dopa, and selenocysteine. be synthesized by body and must be supplied in diet are called essential amino acids. They are 10 in number and include methionine, arginine, threonine, Table 2.18 Classification of amino acids based on side chain tryptophan, valine, isoleucine, leucine, phenylalanine, lysine, and histidine Neutral Amino acids ••Non-essential amino acids: Human can synthesize Alanine Cysteine some non-essential amino acids from glucose and Asparagine Isoleucine ammonia using Krebs cycle or from free amino acids by transamination or reductive amination. Amino Glycine Leucine acids can be synthesized by the body to meet its Glutamine Methionine demands. They include glycine, alanine, serine, Phenylalanine Tryptophan cysteine, aspartate, asparagine, glutamate, glutamine, tyrosine, and proline. Proline Tyrosine ••Facultative essential amino acids: Tyrosine and Threonine Valine cysteine are facultative essential amino acids. They are Serine synthesized from essential amino acids and become essential only if there is deficiency of their precursor amino acids. Tyrosine is derived from phenylalanine Table 2.19 Classification of amino acids based on charge and cysteine from methionine and serine. Negatively charged Positively charged Based on their metabolic fate of carbon skeletons, amino amino acid amino acid acids can be classified into glucogenic, ketogenic, or both (Table 2.21). Aspartic acid Arginine Histidine Structurally, all amino acids have a central carbon, at least one amino group, at least one carboxyl (acid) group, and Glutamic acid Lysine a side chain (R) that makes amino acid unique (Fig. 2.7, Box 2.3). The distinct characteristics of side chain of amino Table 2.20 Functional classification of amino acids acids is responsible for protein structure and its functional role in the body. Except for glycine, all acids contain at least Functional group Amino acid one asymmetric carbon atom (αcarbon atom). Asymmetry of α-carbon gives rise to two optically active (chiral) isomers Hydrophilic, polar termed D- and L-amino acids. L-form is present in proteins, Acidic Carboxylate (–COO–) Asp, Glu

and D-form appears in bacteria. Of the 20 amino acids, only + Basic Amines (–NH3 ) Lys, Arg, His proline is an imino acid (–NH–), and not an α-amino acid. Neutral Carboxyamines Asn, Gln Amino acids can be categorized as follows: (–CONH2) ••Proteinaceous amino acids: They are 20 amino acids Alcohol (–OH) Ser, Thr, Tyr that exist in nature, coded by genetic code. Thiol (–SH) Cys ••Non-proteinaceous amino (NPA) acid: NPA are also called non-coded or unnatural amino acids since they Hydrophobic, non-polar

are not naturally coded or not found in genetic code Aliphatic –CH2– Ala, Val, Leu, Ile, Met of other organisms (Table 2.22). They occur naturally Aromatic Benzene ring Phen, Tyr, Trp and can be synthesized chemically. They can arise Others – Pro, Gly during metabolic reactions, enzymatic modification of amino acid residues in peptide or proteins. They can be widely used as a tool in drug discovery. However, Table 2.21 Categories of amino acids based on their fate proteinaceous amino acids are used as therapeutic Glucogenic Ketogenic Both Ala Met Leu ILe H | Arg Pro Lys H N — C — COOH 2 Asp Ser Phe |α R Cys Thr Trp Glu Val Tyr Fig. 2.7 Structure of amino acid. Gly

Note: –NH 2: amino group (basic); –COOH: carboxyl group (acidic); –R: side chain. His Structure and Chemistry 39

Box 2.3 Structure of α-amino acids Lysine [Lys, K] – CH2 – CH2 – CH2 – CH2 – NH2

Amino acid Structure of R moiety Arginine [Arg, R] – CH2 – CH2 – CH2 – NH – C – NH2 Aliphatic amino acids:  NH Glycine [Gly, G] – H Sulfur-containing amino acid: Alanine [Ala, A] – CH3

Cysteine [Cys, C] – CH2 – SH CH3 Valine [Val, V] – CH Methionine [Met, M] – CH2 – CH2 – S – CH3 CH3 Imino acid: CH 3 Proline (Pro, P) – Leucine [Leu, L] – CH2 – CH

CH3

CH3 N COO  H 2 Isoleucine [Ile, I] – CH – CH2 – CH3

Neutral amino acids: Aromatic amino acid: Serine [Ser, S] – CH – OH 2 Phenylalanine Threonine [Thr, T] – CH – OH  – —CH2 — CH — COO CH3 | + O NH3 Asparagine [Asn, N] – CH2 – C NH2 Tyrosine O

Glutamine [Gln, Q] – CH2 – CH2 – C – NH HO— —CH2 — CH — COO 2 | Acidic amino acids: + NH3 Aspartic acid [Asp, D] – CH2 – COOH Tryptophan Glutamic acid [Glu, E] – CH2 – CH2 – COOH

– Basic amino acids: —CH2 — CH — COO Histidine [His, H] – CH | 2 + NH3 N | N NH H

Table 2.22 Non-protein amino acids

Alpha Non-alpha Urea cycle: Biosynthesis of polyamines Beta alanine formed during catabolism of uracil. Ornithine S-adenosyl methionine Catabolized by transamination to malonate semialdehyde Citrulline Homocysteine with subsequent CoA transfer from succinyl CoA to form malonyl-CoA which gets decarboxylated to acetyl CoA. Argininosuccinate Beta amino isobutyric acid—Catabolism of thymine: • GABA From tyrosine: Dopa ALA Thyroxine Creatinine Taurine Triiodothyronine Azaserine Ovothiol Abbreviations: ALA, amino levulinic acid; CoA, coenzyme A; GABA, gamma-aminobutyric acid. 40 Chapter 2

Importance of NPA Clinical Correlation ••They are intermediates in biosynthesis. ••In β-thalassemia, defect is impaired synthesis of one ••They are post translationally incorporated into protein. of the polypeptide sub units of Hb, absence of α-Hb ••They have a physiological role, e.g., bacterial cell wall stabilizing protein (AHSP)—a chaperone that binds component, neurotransmitter, or toxin. free Hb sub units, so free α-Hb subunits aggregate. ••They can occur naturally and can be a pharmacological ••Coagulation is irreversible denaturation, and floccu­ compound. lation is precipitation of proteins at isoelectric pH. ••They are present in meteorites. ••They include cysteine, homocysteine, S-adenosyl methionine (SAM), taurine, selenocysteine, ornithine, Amino Acid Functions citrulline, and L-dopa. They are intermediates in biosynthesis and get post- translationally incorporated Amino acids differ only in their side chains, and the sequence into protein. of side chains determines the native (tertiary structure) of proteins. Free amino acids have biological functions in intermediary energy metabolism, endocrine system, and Clinical Correlation neuronal functions (Fig. 2.8). Amino acids based on functions are as follows: Non-proteinaceous amino acids that are close analogs of any of the 20 protein amino acids can bind amino acids ••Biogenic amines: transfer ribonucleic acid (tRNA) synthetase and become {{Glycine (neurotransmitter). mistakenly bonded to polypeptide chain. This results in {{Ethanolamine. protein misfolding, dysfunctional protein, and toxicity. Some non-protein amino acids and their metabolites {{β-Alanine (coenzyme A). can be toxic to humans, e.g., Lathyrus species contain {{Thyroxine. neurotoxic oxalyldiaminopropionic acid. Homoarginine ••Neurotransmitter: is present in lentil and can be toxic. They have been speculated to be related to autoimmune disease and {{γ-Amino butyrate (GABA). aging. {{Dopamine. {{Catecholamine. {{Serotonin. Physical Dynamics of Proteins {{Histamine. Protein Folding {{Glutathione.

A unique native secondary, tertiary, or quaternary structure is essential for folding of proteins and their subsequent Nitrogen containing molecules: functions. Protein folding can occur spontaneously and may heme, Biogenic amines (dopamine, require chaperones (or heat shock proteins). Chaperones epinephrine, norepinephrine, interact with proteins and prevent their misfolding into serotonin) Component of: incorrect structures or aggregates. Skin pigment: melanin Peptide Genetic material (purine, pyrimidines) Protein Clinical Correlation Phospholipids Creatine

Aggregation of improperly folded proteins and amyloid results in a disorder termed as amyloidosis, where these proteins get deposited in various organs and tissues. Neurotransmitter Glycine L-Amino Acid Glutamine Denaturation of Protein Aspartate

Following denaturation, protein loses its secondary, tertiary, Metabolically relevant and quaternary structure and its functions. Peptide bonds Transport molecule molecules: Acetyl CoA, pyruvate, αKG, Succinyl remain intact, and primary structure is retained. This can for NH4 groups be caused by altering pH, ionic strength, heating addition of CoA, OAA, fumarate can be salts of heavy metals, denaturing agents (such as urea and generated from amino acids guanidine salts), detergents (sodium dodecyl sulfate [SDS]), Fig. 2.8 Functions of amino acids. and organic solvents. Structure and Chemistry 41

••D-Amino acids: Present in bacterial cell wall, e.g., chemical properties of free amino acids and amino acids in D-alanine, D-glutamate, D-lysine, and D-serine. In protein. animals, D-amino acids are neurotransmitters. Amino acids have two ionizable weak acid groups, –COOH ••Not an amino acid: Taurine is amino sulfonic acid and and an amino group. In aqueous solution at neutral pH, not an amino acid. amino acids exist as zwitterions or dipolar ions, i.e., they α ••Uncommon amino acids: In addition to 20 common have both positive and negative charges. The -carboxyl α amino acids, proteins may contain amino acids group is negatively charged; -amino group is positively created by modification, e.g., hydroxyproline and charged, and overall molecule is electrically neutral. At hydroxylysine are present in collagen; methyl lysine low pH, amino acid is positively charged (cation), and at is constituent of lysine; γ-carboxyglutamate is found high pH, amino acid is negatively charged (anion). The in prothrombin; desmosine is derivative of four lysine pH at which a molecule exists as a zwitterion (electrically α residues; and selenocysteine, ornithine and citrulline neutral) is termed isoelectric pH. pKa of ionizable -carboxyl α are key intermediates in arginine synthesis and urea and -amino groups are in the range of 1.8 to 2.8 and 9.1 cycle. They are also termed as non-protein amino to 9.7, respectively, i.e., when pH is higher than pKa of their acids. ionizable groups, these groups lose a proton. Side chains of some amino acids contain additional ionizable groups. Amino acids are classified by their hydrophobicity and Properties of Amino Acids charge properties. Hydrophobic amino acids have non-polar side chains and are located in the interior of a protein or at lipid protein interface. Optical Activity Non-polar amino acids are hydrophobic since their side chains are insoluble in water. They are found in hydrophobic α-Carbon atom is a chiral center, and amino acids have two interior of globular spherical proteins or on surface of possible stereoisomers. Glycine is not chiral in nature. It is proteins that interact with hydrophobic layer of cellular due to tetrahedral orientation of four different groups about membrane. They have only two pK values due to their α-carbon atom; amino acids exhibit optical isomerism (i.e., a α-carboxyl group and α-amino groups and at neutral pH; ability to rotate plane-polarized light), and the optically the net charge of these amino acid is zero. active molecules are asymmetric. These isomers are non-superimposable mirror images and referred to as Polar amino acids are hydrophilic due to their water-soluble enantiomers. side chains. They are present in cytosol or extracellular environment. They are further classified as uncharged Configuration (neutral), negatively charged (acidic), and positively charged (basic). Configuration is geometrical relationship between a Bonds formed by neutral amino acids are as follows: given set of atoms that distinguish L- from D-amino acids ••Covalent bond. conformation. There is spatial rearrangement of atoms in a ••Hydrogen bond: Formed by asparagine, glutamic acid, protein, and it is stabilized by weak interactions (Fig. 2.9). tyrosine, serine, threonine. The two amino acid configuration (based on configuration ••Disulfide bonds: cysteine. of D- and L-glyceraldehyde) are D (dextro or right) and L (levo or left) forms. Only L-α-amino acids occur in proteins. ••Phosphoester bond: Formed by hydroxyl containing In humans, most amino acids are in L-form, exception, amino acids and phosphate. D-serine (acts as neurotransmitters). D-amino acids are ••Glycosidic bond oligosaccharide attaches to hydroxyl found in bacterial cell wall and peptide antibiotics. group of serine and threonine or amide group of asparagine. Amphoteric Properties of Amino Acids

Amino acids are more soluble in polar solvents, and ionic Biogenic Amines properties of side chains influence physical and chemical properties of side chains. This influences the physical and Several amino acids are broken down by decarboxylation to form biogenic amines. Biogenic amines have various functions in the body. Some of them are components of , such as ethanolamine in phospholipids. Cl Cl Cysteamine (degradation product of cysteine) and β-alanine are components of coenzyme A and pantotheine. Other H – C – P P – C – H biogenic amines function as signaling substances. For example, GABA is neurotransmitter; dopa is a neurotrans­ Br Br mitter and precursor for catecholamines: epinephrine and non-epinephrine. Biogenic amine serotonin is synthesized Fig. 2.9 Mirror image of enantiomer from tryptophan (Table 2.23). 42 Chapter 2

Table 2.23 Various biogenic amines

Amino acid Biogenic amine Function Serine Ethanolamine Glutamate Cysteine Cysteamine Component of CoA Aspartate β-alanine Component of CoA Glutamate γ-amino butyrate GABA (neurotransmitter) Histidine Histamine Mediator, neurotransmitter L-dopa Dopamine, norepinephrine, and Neurotransmitter epinephrine

Threonine Amino propanol Component of vitamin B12 5-Hydrotryptophan Serotonin Neurotransmitter Lysine and methionine Carnitine FA transport into mitochondria Arginine, glycine, and methionine Creatine Phosphocreatine serves as energy store Abbreviations: CoA, coenzyme A; GABA, gamma-aminobutyric acid; FA, fatty acid.

Nucleic Acid: Structure and Function (BI6.2)

(NAD), nicotinamide adenine dinucleotide phosphate Introduction (NADP), coenzyme A (CoA), and SAM.

All nucleic acids are made up from nucleotide components, ••They have regulatory function: signal transduction, which in turn consist of a base, a sugar, and a phosphate second messenger (cyclic adenosine monophosphate residue. They play an important role in cellular processes and [cAMP] and cyclic guanosine monophosphate [cGMP]). are components of RNA and DNA. They serve as cofactors, ••Numbering of sugars is primed (as 1′, 2′, and 3′) to regulatory agents, and constituent of biomolecules. distinguish them from rings of nucleic acid. The bases of nucleotides and nucleic acid are derivatives of Nucleoside purine or pyrimidine. Purine consists of two heterocyclic rings numbered in anticlockwise direction. Pyrimidine ring Nucleosides are formed when a base is linked to a is six-membered with two nitrogen atoms, numbered in pentose sugar at carbon 1’ position (anomeric carbon). clockwise direction. Ribonucleoside contains ribose and deoxyribonucleoside Commonly occurring pyrimidines are cytosine, uracil, and contains a deoxyribose. Common nucleosides are cytidine, thymine. Adenine and guanine are two common purines. uridine, thymidine, adenine, and guanosine. Pentose sugar Hypoxanthine, xanthine, and uric acid are other purine is added to N9 or N1 by β N-glycosidic bond. derivatives. Hypoxanthine and xanthine are rarely found in nucleic acids, and uric acid is never found in nucleic acids. Nucleic Acid Nucleotides Characteristic features of nucleic acid are as follows: ••They are essential for cellular metabolism and genetic The bases that occur in nucleic acids are compounds information storage and expression. containing nitrogen bases: aromatic/cyclic ring structures with nitrogen. They can be either purine or pyrimidine. ••They are essential intermediates in virtually all aspects Nucleotides are phosphate esters of nucleosides and are of cellular metabolism and are energy currency of components of both RNA and DNA. Thus all nucleotides have metabolism. three components: a nitrogen heterocyclic base, pentose ••They are combination of heterocyclic amine, a pentose, sugar, and phosphate residue (Table 2.24). phosphoric acid, and nucleic acid, i.e., linear polymers of nucleotides: monomeric unit of nucleic acids Nomenclature ••Purines and pyrimidines supply building blocks of nucleic acid. When a ribose attaches to a purine base, it generates ••They are high-energy intermediates. nucleoside. ••They form part of coenzymes: flavin adenine Purines end in ‘sine’: adenosine and guanosine, and dinucleotide (FAD), nicotinamide adenine dinucleotide pyrimidines end in ‘dine’: thymidine, cytidine, and uridine. Structure and Chemistry 43

Table 2.24 Nucleotides and nucleosides Isomerism in nucleotides: Naming start with nucleotide name Base Nucleoside Nucleotide Present in and add mono-, di-, or triphosphate to it, e.g., adenosine monophosphate and deoxythymidine diphosphate. Purine Adenine Adenosine (A) AMP RNA, DNA Guanine Guanosine (G) GMP RNA, DNA Pseudouridine Hypoxanthine Inosine (I) IMP – Pseudouridine is an isomer of the nucleoside uridine in Xanthine Xanthosine (X) XMP – which the uracil is attached via a carbon–carbon instead of a Pyrimidine nitrogen–carbon glycosidic bond. Cytosine Cytidine (C) CMP RNA, DNA Thymine Thymidine (T) TMP DNA Thymidine Monophosphate (TMP) Uracil Uridine (U) UMP RNA ••It contains ribose rather than deoxyribose. Abbreviations: AMP, adenosine 5’-monophosphate; CMP, cytidine monophosphate; DNA, deoxyribonucleic acid, GMP, guanosine ••It arises when uridine monophosphate (UMP) of monophosphate; IMP, inosine-5’-monophosphate; RNA, ribonucleic preformed tRNA is methylated by SAM. acid; TMP, thymidine monophosphate; UMP, uridine monophosphate; XMP, xanthosine monophosphate. Unusual Bases or Minor Bases

Isomerism: Keto-Enol Tautomerism ••5-methylcytosine.

Purine and pyrimidine exist as tautomeric pairs. Keto ••Others in tRNA: tautomers of uracil, thymine, and guanine predominate at {{N6-methyl adenine. neutral pH. Enol form of cytosine exists at neutral pH. {{N6, N6-dimethyl adenine. Hydrogen bonding between purine and pyrimidine is {{N6, N7-methyl guanine. fundamental to biological functions of nucleic acids, e.g., DNA double-helix formation. ••In bacteriophage DNA: {{5-hydroxy cytosine. Syn-Anti Conformation ••Methyl cytosine methylated purines: {{1,3,7-trimethyl xanthine: caffeine. The plane of the bases is almost perpendicular to that of sugar and bases occupy either of two principal orientations: {{1,3-dimethyl xanthine: theophylline. anti and syn. Anti-conformer has H-6 atom (pyrimidine) or {{3,7-dimethyl xanthine: theobromine. H-8 (purine) atom above the sugar ring. Syn-conformation •• has O-2 (pyrimidine) or N-3 (purine) in that position. Both Free nucleotides: Xanthine, hypoxanthine, and uric the forms exist in nature, but anti-conformers predominate. acid.

Deoxynucleotides Energy Metabolism and Purines They possess purine (A and G) or pyrimidine (C and T) bases and a 5’ phosphate group on deoxyribose (D-ribose ring Division of Labor in Nucleotides lacking a 2′ hydroxyl). Small “d” specifies loss of 2′-hydroxyl group, and deoxynucleotides are named identical to ••It directs ATP to serve as primary nucleotide in central nucleotides except for prefix ‘deoxy’ is inserted in the name. pathway of metabolism. Nucleoside diphosphates (ADP, guanosine diphosphate ••GTP is used to drive protein synthesis. [GDP], and cytidine diphosphate [CDP]) attach to their deoxy forms (dADP, dGDP, and dCDP) and require reduced ••Channeling of various nucleotides in appropriate thioredoxin as cofactors and enzyme ribonucleotide metabolic directions, e.g., CTP in phosphoglycerate reductase. synthesis; cAMP, cGMP: second messenger. ••ATP is high-energy phosphoanhydride product of Participating functional groups are as follows: and oxidative phosphorylation. ATP is main ••Amino group of C, A, and G. source of energy for metabolic work, biosynthesis, ••Ring ‘N’ at position 3 of pyrimidine, position 1 of active ion transport, muscle contraction, and purine. detoxification of xenobiotics. ••Oxygen atoms at position 4 of uracil, thymine; position ••GTP also participates in metabolic pathways namely, 2 of cytosine, position 6 of guanine. Krebs cycle, and provides energy for protein synthesis, 44 Chapter 2

(phosphoenolpyruvate [PEP] carboxykinase). Functions of Nucleotides

••UDP activated monosaccharides (UDP glucose and 1. They serve as building blocks for synthesis of nucleic UDP glucuronic acid) are involved in synthesis of acids DNA and RNA. polysaccharides, lactose and oligosaccharide chains 2. They are components of several co-enzymes and ATP. of glycoproteins and glucuronidation reaction of detoxification of xenobiotics, respectively. 3. They control rate of enzyme-catalyzed reactions by feedback allosteric regulation. ••CTP: Intermediate in GPL synthesis. 4. cAMP and cGMP serve critical roles in cellular signaling mechanisms (Table 2.25).

Table 2.25 Functions of nucleotides A. Function Example Energy metabolism ATP, muscle contraction, active transport, ion gradient, and phosphate donor Monomeric unit NTP, dNTP (for RNA, DNA) Physiological mediators cAMP, cGMP (second messenger) Signal transduction (GTP-binding protein) Adenosine: Coronary blood flow, neurotransmitter Activate G protein Precursor function GTP (mRNA capping) Activated intermediates UDP-Glucose (glycogen) CDP-choline (phospholipid) SAM (methylation) PAPS (sulfation) Allosteric affects ATP (negative for PFK) AMP (positive for phosphorylase B) dATP (negative effective RNP reductase)

Cofactors NADP/NADPH, FAD/FADH2, FMN/FMNH2, CoA, SAM B. Nucleotide Function Adenosine nucleotides ATP Source of energy cAMP Second messenger Active sulfate Sulfur donor (proteoglycans) (adenosine 3′ phosphate 5′phospho sulfate, PAPS) Sulfur conjugation of drugs Active methionine (5-adenosyl methionine SAM) Methyl donor, source of propylamine, in polyamines Guanosine derivative GDP Coupled to substrate level phosphorylation GTP Allosteric regulation, energy source cGMP Intracellular signal second messenger (NO) Hypoxanthine derivative Purine salvage pathway IMP Uracil UDP-G Glycogen synthesis UDP-Gln Glycoprotein synthesis Glucuronide conjugation reaction of bilirubin, drugs I. Cytosine CTP Phosphoglycerate synthesis CDP CDP choline: formation of sphingomyelin with ceramide II. Coenzyme NAD, FAD, NADP, CoA, SAM III. Monomeric precursors Monomeric unit of RNA, DNA Abbreviations: ATP, adenosine triphosphate; cAMP, cyclic adenosine monophosphate; CDP, cytidine diphosphate; cGMP, guanosine 3′,5′-cyclic monophosphate; CoA, coenzyme A; CTP, cytidine triphosphate, DNA, deoxyribonucleic acid; dNTP, deoxyribonucleotide triphosphate; FAD, flavin

adenine dinucleotide; FADH2, flavin adenine dinucleotide reduced, FMN/FMNH2, flavin mononucleotide/flavin mononucleotide reduced, GTP, guanosine triphosphate; IMP, inosine-5’-monophosphate; mRNA, messenger ribonucleic acid; NAD, nicotinamide adenine dinucleotide; NADP, nicotinamide adenine dinucleotide phosphate; NTP, nucleoside triphosphate; PAPS, 3-phosphoadenosine-5’-phosphosulfate; PFK, phosphofructokinase; RNA, ribonucleic acid; SAM, S-adenosyl methionine; UDP, uridine diphosphate.