L1 Water and Carbohydrates PDF

Associate of Science Programme CCST4017 Molecular Biology and Biochemistry (MBB) 1  Objectives Introduces the structural and functional properties of biomolecules, the chemistry of macromolecules and thei...

Associate of Science Programme CCST4017 Molecular Biology and Biochemistry (MBB) 1  Objectives Introduces the structural and functional properties of biomolecules, the chemistry of macromolecules and their metabolic pathways (the metabolism of carbohydrates, lipid and proteins and enzymology). Provides an understanding of the molecular mechanisms fundamental to the signal transduction and gene expression processes. Tips: →HKDSE Chemistry Lv. 2 or above →Taking CCST4124 Chemistry for life Science →Supp. readings related to chemistry is provided 2  Lecture 1A Water – the Medium of Life 3  Learning Outcomes Understand the biological importance of water Explain the physical and chemical properties of water and its importance in biological system Understand noncovalent interactions in biomolecules  Biological importance of water 1. It is the medium in which all cellular events occurs. 2. It is required for enzyme action and for the transport of solutes in the body. 3. Water aids the folding of biomolecules like proteins, nucleic acids etc. 4. Water regulates body temperature. 5. Give shape of the cell and support body (hydroskeleton) 6. Water accelerates biochemical reactions by providing ions → ionization Functions of water in a cell Shape, medium, reactants, etc…… 6 Electronegativity & dipole moment 7 Electronegativity trend and order 8  Structure of water molecules Covalent bonds between oxygen and hydrogen atoms with a bond angle of 104.5 Electronegativity: Carbon 2.5, Hydrogen 2.1, Oxygen 3.5 Greater density of electrons around the nucleus of the oxygen than around the hydrogen Repulsion of lone pair electrons on oxygen → Bent shape Create a permanent dipole in the molecule H2O is polar molecule Lone pair e- = 9 9 Just a coincidence? Question: Polar or non-polar? Non-polar Non-polar 10  Physical properties of water Water expands as it freezes Ice is less dense than water, but more ordered. →Ice floats on water Structure of ice H-bond Hexagonal symmetry and near tetrahedral bonding angles 11  Permanent dipole-dipole interaction Hydrogen bonds Each water molecule can maximally form hydrogen bonds with four other water molecules. Hydrogen bonds readily form between an electronegative atom (the hydrogen acceptor, usually oxygen or nitrogen) and a hydrogen atom covalently bonded to another electronegative atom (the hydrogen donor) in the same or another molecule hydrogen bonds 23.3 kJ mol−1  High specific heat capacity & latent heat of water Hydrogen bonds contribute to water’s high specific heat capacity (Amount of energy needed to raise 1oC of 1 g of a substance) Hydrogen bonds must be broken to increase the KE (motion of molecules) and temperature of a substance → temperature fluctuation is minimal (i.e. more stable body temperature )  Aquatic organisms face less temperature variation than terrestrial organisms. Water provides cooling effect: Water has a high latent heat of vaporization - large amount of energy is needed to evaporate water because hydrogen bonds must be broken to change water from liquid to gaseous state. Sweating → cooling effect 13 High specific heat capacity of water 14 Latent heat of water 15  Hydrogen bonds give water a high melting point and boiling point 16  Strong tension between water molecules Tendency of water molecules to attract to one another by hydrogen bonds: cohesion, at the surface of any accumulation of water → Surface tension Water column cohesion-tension theory – transpiration Water Cup challenge 17 https://www.youtube.com/watch?v=_kn-LGRVcyE  Water as universal solvent Water can interact with and Polar/charged functional group dissolve other polar compounds and ionizable compounds, they are described as hydrophilic (water-loving). Solubility of molecules in water depends on polarity and the extent to form hydrogen bonds with water. Therefore:  the no. of polar groups in a molecule  hydrogen bonds  solubility in water 18  Interactions between biomolecules and water Non-polar biomolecules that do not dissolve appreciably in water are called hydrophobic. (water-fearing) Amphipathic biomolecules have significant amounts of both hydrophilic and hydrophobic structure. Like hydrophobic biomolecules they tend to associate when placed in contact with water molecules. 19 Solubility of organic molecules in water 20 Water as a reactant in biochemical reaction Nucleophilic nature of water Chemicals that are electron-rich (nucleophiles) seek electron deficient chemicals (electrophiles). Nucleophiles are negatively charged or have lone pairs of electrons attack electrophiles during substitution or addition reactions. Examples of nucleophiles: oxygen, nitrogen, sulfur, carbon, water (weak) Important in hydrolysis reactions (catalyzed by enzymes such as protease) e.g. protein → amino acids 21 NUCLEOPHILIC SUBSTITUTION REACTIONS 22  Hydrolysis in biomolecules Macromolecules are large molecules. Some of them are polymers (like proteins, nucleic acids, starch). Polymers are consisting of many repeating subunits of monomers. Monomers are joined together to form dimers (2 monomers linked together) → oligomers → polymers by condensation; a molecule of water is removed to join them (dehydration). To disassemble a polymer the water is added and the molecule separates (hydrolysis). These reactions are constantly occurring in organisms and catalyzed by enzymes. Condensation 23 Polymers in biomolecules 24  Noncovalent interactions in biomolecules 1. Hydrogen bonds More important when they occur between molecules or within molecules. → stabilize structures such as proteins and nucleic acids. 2. Charge-charge interactions or electrostatic interactions Occur between two oppositely charged particles. Strongest noncovalent force that occurs over greater distances. Can be weakened significantly by water molecules (can interfere with bonding). 3. Hydrophobic interactions Very weak Important in protein shape and membrane structure. 4. Van der Waals forces Occurs between neutral atoms. Weaker than hydrogen bonds. 25 e.g. London dispersion forces  Interactions of molecules – bond strength Video: What Are Intermolecular Forces 26 https://www.youtube.com/watch?v=9YwdeEDrfPI  Interactions within protein molecules Protein-protein interaction Noncovalent Interactions and Macromolecular Structure Noncovalent interactions are weak attractions between molecules. Their stability is relatively low because the bond strength is weak. Nonetheless, noncovalent interactions play important roles in protein and nucleic acid stabilization because they are collectively strong. 27  Hydrogen Bonding in biomolecules Molecules such as sugars and amino acids, which contain polar functional groups, commonly are quite soluble in water because of the stabilizing effects hydrogen bonds have on interactions between the solvent and solute. Biologically important hydrogen bonds between Watson-Crick A-T base pairs e.g. glucose 28 Electrostatic interactions in biomolecules 29  Hydrophobic interactions in biomolecules Nonpolar molecules are hydrophobic and are not soluble in water because water molecules interact with each other rather to nonpolar molecules → The hydrophobic effect is the observed tendency of nonpolar molecules to aggregate in aqueous solution and exclude water molecules “Like dissolves like” principle 30  Hydrophobic interactions Hydrophobic molecules, such as hexane, and the nonpolar portions of amphiphiles, such as long-chain fatty acids, lack polar functional groups that can interact with water molecules. This results in a highly ordered cage-like shell (clathrate) of water molecules immediately surrounding the nonpolar molecule. Suspension of a hydrophobic substance in water is thermodynamically unfavorable due to the decreased entropy (i.e. the level of disorder will be reduced/more ordered) of water molecules in the cage-like shell. 31 Unfavorable!  Hydrophobic interactions Nonpolar molecules are hydrophobic and are not soluble in water because water molecules interact with each other rather to nonpolar molecules → The hydrophobic effect is the observed tendency of nonpolar molecules to aggregate in aqueous solution and exclude water molecules “Like dissolves like” principle 32  Entropy – Degree of disorder The Laws of Thermodynamics, Entropy, and Gibbs Free Energy 33 https://www.youtube.com/watch?v=8N1BxHgsoOw  Hydrophobic interactions Second Law of Thermodynamics Spontaneous changes cause an increase in the entropy of the system. Non polar substance like fat molecules tend to clump up together rather to allow them to have a minimal contact of water. 34  Formation of micelles Hydrophobic interactions, refers to the entropy-driven aggregation of nonpolar molecules in aqueous solution that occurs to minimize the ordering of water molecules with which they are in contact This is not an attractive force, but rather a thermodynamically driven process Amphiphiles (with both hydrophilic and hydrophobic portions), such as detergent, surfactants, or long-chain fatty acids form molecular assemblies know as micelles, wherein the hydrophilic portions of the molecules are in contact with water and the hydrophobic regions are sequestered away from water in the interior of the assembly → can be found in the formation of membranes, the folding of proteins and the formation of double helical DNA. 35  Van der Waals’ forces (VDW) VDW Base stacking interaction 36 Protein – tertiary structure DNA – double helix  Reference CONCEPT 2.2 Atoms Interact and Form Molecules https://www.macmillanhighered.com/BrainHoney/Resource/ 6716/digital_first_content/trunk/test/hillis2e/hillis2e_ch02_3. html 37 Lecture 1B: Carbohydrates 38  Learning outcomes Differentiate among different types of carbohydrates Understand the structure of different carbohydrates and correlated with biological function and its significance Describe the modification of sugars and their biological significance 39  Carbohydrates Functions - Serves as energy source for cells in fed state - Energy storage: starch (plant), glycogen (animal) - Regulate blood glucose level - Transport of energy molecules in dissolved form (blood glucose in human and sucrose in plant) - Facilitate digestion (fiber) - Structural materials for cells Glucose e.g. cellulose in the cell wall (plants), chitin in the exoskeleton (insects) proteoglycans, glycoproteins in extracellular matrix of all organisms. Components - composed of C, H, O - common name of carbohydrates: sugars (Latin: saccharum), some are monomers and others are polymers - contain functional groups: hydroxyl (-OH) and carbonyl (aldehyde or ketone) 40 Carbohydrates Monosaccharides Also called simple sugars, with general formula [CH2O]n where n is between 3 to 7. General formula: Cx(H2O)y Disaccharides Contain 2 monosaccharide units Oligosaccharides Contain 3–10 (or 6-10) monosaccharide units Polysaccharides Contain > 10 monosaccharide units 41  Monosaccharides Structures and Naming Classification based on number of carbon: triose (3C), pentose (5C) and hexose (6C) are most common in cells. Classification based on position of carbonyl group The carbonyl oxygen of a linear sugar may be located at the end of the carbon chain as an aldehyde group (aldose) or inside the chain as a ketone group (ketose). The remaining carbon atoms carry hydroxyl groups (-OH) and hydrogen atoms. 42  Carbon numbering The carbons of the chain are conventionally numbered from 1 to n, starting from the end which is closest to the carbonyl. If the carbonyl is at the very beginning of the chain (carbon 1), the monosaccharide is said to be an aldose, otherwise it is a ketose. 43  Fischer Projections A two-dimensional representation showing the configuration of a stereocenter horizontal lines represent bonds projecting forward from the stereocenter (towards you) vertical lines represent bonds projecting toward the rear (away from you) carbon atoms are numbered from the top downwards (Left) 3-D representation (wedge-and-dash) the vertical bonds from the stereocenter are directed away from you the horizontal bonds from it are directed toward you 44 none of the bonds to stereocenter are in the plane of the paper  Chiral carbons and molecules Video: Chirality: Basic Concept Explained 45 https://www.youtube.com/watch?v=JS-iAuCIexk  Class practice Which carbon(s) are chiral? Answer 46  Stereoisomers: Epimers 1. Epimers: Stereoisomers which differ in orientation of H and OH around only one chiral carbon, e.g. glucose and galactose. Differ only at C2 Differ only at C4 Differ only at C4 47 https://glossary.periodni.com/glossary.php?en=epimer  Stereoisomers in monosaccharides 2. Enantiomers/Optical isomers Molecules contain chiral carbon are optically active, i.e. can rotate the plane polarized light (PPL) Compound which can rotate the PPL to clockwise (prefix “+”, right) is called dextrorotatory (D) while which can rotate PPL to anticlockwise is called Levorotatory. e.g. D- and L-glucose Most monosaccharides synthesized in nature are D-sugars. D is also called R, L is also called S in some textbooks L or S D or R 48  D- and L- sugars Lowest chiral carbon -OH at right hand side → D-form 49  Optical activity and enantiomers Class Practice 1. Draw the Fischer projection for the enantiomer of D-galactose ANS 2. Determine which one is the epimer or enantiomer of D-mannose. 50  Answer Enantiomer Ans: (A) Ans: (B) C-4 epimer of D-mannose Ans: (C) 51 http://www.edu.utsunomiya-u.ac.jp/chem/v9n1/hunsen/monocycle-072405-rev.htm  The D-family of aldoses The configuration in each case is determined by the highest numbered chiral carbon, i.e. farthest away from the carbonyl group (shown in grey). Combine: 1. no. of C 2. Functional group (-CHO or –CO) 3. D- or L- aldehyde group 52  The D-family of ketoses The configuration in each case is determined by the highest numbered chiral carbon, i.e. farthest away from the carbonyl group (shown in grey). Combine: 1. no. of C 2. Functional group (-CHO or –CO) 3. D- or L- ketone group 53 Cyclic structures of monosaccharides Hemi- Hemi- 54  Cyclic structures of monosaccharides With pentoses and hexoses, the most stable forms are actually ring structures containing five or six atoms. Pyranose Furanose (6C, aldohexose) 55 Cyclic structures of monosaccharides Ribopyranose (5C, aldopentose) Ribofuranose  Cyclic structures of monosaccharides Haworth Projections A representation to view furanose and pyranose forms of monosaccharides; the ring is drawn flat and viewed through its edge, with the anomeric carbon on the right and the oxygen atom to the rear Cyclization produces one of two anomers: alpha or beta 57  Alpha & beta form in ring structure The new carbon stereocenter created in the forming the cyclic structure is called anomeric carbon. The anomeric C of an aldose is C1; that of the most ketoses is C2. Haworth projections represent the cyclic sugars as having essentially planar rings, with the OH at the anomeric C1 (in aldose) extending either: below the ring () above the ring () These are called alpha and beta anomers. 58 Cyclic structures of ketose Anomeric carbon (ketohexose) 59  Mutarotation Mutarotation The change in specific rotation that occurs when an  or β form of a carbohydrate is converted to an equilibrium mixture of the two forms. What is happening is that each solution, initially containing only one anomeric form, undergoes equilibration to the same mixture of - and β-pyranose forms. The open-chain form is an intermediate in the process. For glucose, the dominant form is pyranose, of which 64% is β form. The most stable form! 60 Less repulsion between atoms!  Anomers Class Practice Identify the following carbohydrates as the  or β anomers α β β The standard format of this answer should be: The –OH of anomeric carbon is on the same side of the ring as from sixth carbon. So this is __β___ anomer. 61  Disaccharides Disaccharides are formed when two monosaccharides are chemically bonded together by a glycosidic linkage (via dehydration/condensation reaction) via enzyme such as glycogen synthase. Two monosaccharide rings may be five- or six-membered, but six-membered rings are much more common. The two rings are connected by an O atom that is part of an acetal, called a glycosidic linkage, which may be oriented α or β. Naming glycosidic bonds: need to specify the anomer bonded and the carbon bonded. 62  Disaccharides The three most abundant disaccharides are maltose, lactose, and sucrose. Gal1—>4Glc is lactose. Glc1—>4Glc is maltose. Glc1—>2Fru is sucrose. They are hydrolyzed by sucrase, lactase, and maltase in intestinal microvilli. Many adult humans lack lactase (lactose intolerance).  Reducing sugars The cyclization reactions are highly reversible: hemiacetals and hemiketals easily convert back to aldehydes and ketones plus alcohol. Oxidation state of carbon +3 +2 64  Benedict’s test The cyclic hemiacetal form of a sugar will produce an equilibrium amount of the open-chain aldehyde form: Aldehydes are fairly easy to oxidize to carboxylic acids (Oxidation) will then reduce the copper (II) to copper (I) and give a positive test. (Reduction) 65  Benedict’s Test and reducing sugars Maltose and lactose Glycosidic bond is →4, i.e. the anomeric C (C1) of the right glucose is not in glycosidic bond this hemiacetal is in equilibrium with free aldehyde (mutarotation) and can be oxidized to a carboxylic acid → reducing sugar Sucrose Anomeric carbons of both glucose and fructose are involved in the formation of the glycosidic bond, neither sugar unit is in equilibrium with its open-chain form → non-reducing sugar reducing sugar 66 Benedict’s Test Stachyose Verbascose Trehalose Raffinose 67 67  Polysaccharides Large numbers of monosaccharide units bonded together by glycosidic bonds. e.g. starch, glycogen, and cellulose. Starch is a plant’s way of storing carbohydrates to meet its energy needs. It is stored in amyloplasts of plant cells. Two types of starch: Amylose has a straight chain structure while; Amylopectin has a branched structure. Animals can digest starchy foods and, with the aid of their -glycosidase and - amylase, hydrolyze the starch to glucose. Glycogen is the major form in which polysaccharides are stored in animals. Glycogen, a polymer of glucose containing -glycosidic bonds, has a more branched structure. They are highly abundant in liver cells and muscle cells. Cellulose is found in the cell walls of nearly all plants, where it gives support and rigidity to wood and plant stems. Humans and most carnivores cannot use cellulose as food because digestive systems do not contain β-glucosidases, enzymes that catalyze the hydrolysis of β-glucosidic bonds. 68 Linear or branched More branched Linear 69 α vs β glycosidic bonds 70  α vs β glycosidic bonds /starch 71  Glycosidic bonds in Polysaccharides Starch or glycogen structure Amylose β-1, 4- glycosidic bond 72 -glycosidic bonds vs β-glycosidic bonds Bent shape Linear shape Spiral structure with branches linear structure without branches73  Digestion of carbohydrates Symbiotic bacteria and protozoans: β-glucosidases -glycosidase -amylase 74  Modified Monosaccharides A hemiacetal can react with an alcohol or an amine to form an adduct with the removal of H2O. The resulting bond is an O-glycosidic linkage. Reaction with an amine results in a N-glycosidic bond. 75  Glycoproteins Primarily protein + some CHO As structural components, eg. found on cell membrane (extracellular side and extracellular matrix) How to attach sugars on membrane proteins? O-glycoside: sugar attached to an OH group (of Ser, Thr, hydroxylysine) N-glycoside: sugar attached to an NH2 in amide group (of Asn, Gln) Amino acids on protein  Glycoproteins Amino acids on protein The predominant sugars found in glycoproteins are glucose, galactose, mannose, fucose, N-acetylgalactosamine (GalNAc), N-acetylglucosamine (GlcNAc) and NANA (N-Acetylneuraminic acid). 77  Modified Monosaccharides Glucosamine/Galactosamine 葡萄糖胺 -OH on C2 is replaced by –NH2 and the amines are usually esterified with methanol to form N-acetylglucosamine (GluNAc) and N-acetylgalactosamine (GalNAc). Sulfated polysaccharides: The –OH on C2, C4 or C6 may be sulfated (-OH to -OSO3-) on several glycosaminoglycans. 78  Function of glycoprotein Antigen Cell surface marker 79  Proteoglycans Primarily CHO + some protein Made up of glycosaminoglycans (GAGs) linked to peptide chain Long unbranched polysaccharides containing a repeating disaccharide unit. The repeating units contain either of two modified sugars, sulfonated N- acetylgalactosamine (GalNAc) or N-acetylglucosamine (GlcNAc), and a uronic acid such as glucuronate or iduronate. The GAGs extend perpendicularly from the core in a brush-like structure. GAGs are highly negatively charged molecules, with extended conformation that imparts high viscosity to the solution. GAGs are located primarily on the surface of cells or in the extracellular matrix (ECM). Allow the cells to be attached to each other. Along with the high viscosity of GAGs comes low compressibility, which makes these molecules ideal for a synovial fluid, the lubricant of joints and collagen. At the same time, their rigidity provides structural integrity to cells. 80  Repeating unit of different GAGs Function: ECM for cell adhesion and growth ─ ─ ─ Function: Synovial fluid ─ ─ ─ ─ ─ ─ Function: anticoagulants Function: maintain the shape of eye 81  Hyaluronic acid Hyaluronic acid is the simplest acidic polysaccharide present in connective tissue. It contains from 300 to 100,000 repeating units, depending on the organ in which it occurs. It is most abundant in specialized connective tissues such as synovial fluid, the lubricant of joints in the body, and the vitreous of the eye, where it provides a clear, elastic gel that holds the retina in its proper position. Hyaluronic acid is also a common ingredient in lotions, moisturizers, and cosmetics. 82 Extracellular Matrix (ECM) - cell attachment 83 Heparin as anticoagulants 84  Differences between proteoglycans and glycoproteins 85  References Smith J. G. (2011) Organic Chemistry 3rd ed. McGraw Hill, NY, USA. Bettelheim F.A. et al. (2010) Introduction to General, Organic, and Biochemistry. 9th ed. Cengage. Boston, USA. Frost L. and Deal T. (2017) General, Organic, and Biological Chemistry. 3rd ed. Pearson, New Jersey, USA. 86