Bt 202 aug 19 2011new


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Bt 202 aug 19 2011new

  1. 1. BT-202 Netaji Subhas Institute of Technology, Dwarka, New Delhi. Dr. Amita Pandey Aug 19, 2011
  2. 2. HCl is a Polar Covalent molecule <ul><li>The difference between the electronegativities of chlorine ( EN = 3.16) and hydrogen ( EN = 2.20). </li></ul><ul><li>Covalent bond: EN < 1.2 </li></ul><ul><li>δ + δ -   </li></ul><ul><li>H Cl   </li></ul><ul><li>Only one linear bond. </li></ul>
  3. 3. Biomolecules <ul><li>Antoine-Laurent Lavoiser (1743-1794); plant and animal world were composed of compounds rich in the elements carbon, oxygen, nitrogen, and phosphorus. </li></ul><ul><li>In 1954 Jacques Monod : “what is true for E. coli is also true of the elephant.” </li></ul><ul><li>Biochemical unity. Also reinforces the fact that all organisms share a common evolutionary origin. </li></ul>
  4. 4. Elements essential to animal life and health
  5. 5. <ul><li>Fewer than 30 of the more than 90 naturally occurring chemical elements are essential to organisms. </li></ul><ul><li>99% mass of cell is made up of hydrogen, oxygen, nitrogen, and carbon. </li></ul><ul><li>Trace elements comprise a tiny fraction of the weight of human body. </li></ul>
  6. 6. <ul><li>Carbon accounts for more than half the dry weight of cells. </li></ul><ul><li>Biomolecules are compounds of carbon with a variety of functional groups. </li></ul>
  7. 7. Versatility of carbon bonding
  8. 8. <ul><li>Covalently linked carbon atoms in biomolecules can form linear chains, branched chains, and cyclic structures. </li></ul><ul><li>Most biomolecules are derivatives of hydrocarbons, where hydrogen atom is replaced by a variety of functional groups. </li></ul>
  9. 10. <ul><li>The chemical personality of a compound is determined by the chemistry of its functional groups and their disposition in 3-D space. </li></ul>
  10. 11. Several common functional groups in a single biomolecule
  11. 12. <ul><li>Central metabolites also called primary metabolites in the major pathways occurring in nearly every cell. </li></ul><ul><li>like amino-acids, nucleotides, sugars and their phosphorylated derivatives, and mono-, di-, and tricarboxylic acids. </li></ul><ul><li>polar or charged, water soluble and present in micromolar or millimolar concentrations. </li></ul>
  12. 13. <ul><li>secondary metabolites are specific to certain types of cells or organisms. For example vascular plants. </li></ul><ul><li>eg These molecules give plants their specific scents. Quinine, nicotine, and caffeine. </li></ul>
  13. 14. <ul><li>Metabolome </li></ul><ul><li>The entire collection of small molecules in a given cell is called a cell’s metabolome. </li></ul>
  14. 16. <ul><li>Many of the biological molecules are macromolecules . </li></ul><ul><li>Polymers with molecular weight above 5,000. </li></ul><ul><li>Oligomers are shorter polymers. </li></ul><ul><li>Macromolecules can also assemble into supramolecular complexes , forming functional units such as ribosomes. </li></ul>
  15. 17. <ul><li>Carbohydrates </li></ul><ul><li>These are the polymers of simple sugars such as glucose. </li></ul><ul><li>energy rich fuel stores. </li></ul><ul><li>component of cell wall. </li></ul><ul><li>extracellular recognition elements that bind to protein on other cells. </li></ul><ul><li>oligosaccharides attach to proteins or lipids on cell surface and serve as specific cellular signals. </li></ul>
  16. 18. Proteins (Proteome) <ul><li>Polymers of amino acids. </li></ul><ul><li>Constitutes the largest fraction of the cell. </li></ul><ul><li>some proteins with catalytic activity function as enzymes. </li></ul><ul><li>protein are transporters. </li></ul><ul><li>signal transduction molecules. </li></ul><ul><li>structural elements. </li></ul>
  17. 19. Nucleic acids <ul><li>Polymers of nucleotides. </li></ul><ul><li>DNA and RNA. </li></ul><ul><li>Store and transmit genetic information. </li></ul><ul><li>RNA can have catalytic activity and structural role in supramolecules. </li></ul>
  18. 20. Lipids <ul><li>Water insoluble hydrocarbon derivatives. </li></ul><ul><li>Serve as structural components of membranes. </li></ul><ul><li>Energy rich fuel stores. </li></ul><ul><li>Intracellular signals. </li></ul><ul><li>Pigments. </li></ul>
  19. 21. Informational molecules <ul><li>Proteins, nucleic acids and some oligosaccharides. </li></ul>
  20. 22. <ul><li>Stereoisomers </li></ul><ul><li>Molecules with same chemical bond but different configurations, the fixed spatial arrangement of atoms. </li></ul><ul><li>Interactions between biomolecules are invariably stereospecific. </li></ul>
  21. 23. Representation of alanine
  22. 24. Stereoisomers <ul><li>Configuration is conferred by the presence of either </li></ul><ul><li>(1) double bond. </li></ul><ul><li>(2) chiral center. </li></ul><ul><li>Stereoisomers cannot be interconverted without temporarily breaking one or more covalent bond. </li></ul>
  23. 25. Geometric isomers, or cis-trans isomers <ul><li>Differ in the arrangement of their substituent groups with respect to the nonrotating double bond. </li></ul><ul><li>Each isomer can be separated from the other and has unique chemical properties. </li></ul>
  24. 26. Configuration of geometric isomers
  25. 27. Configuration of geometric isomers
  26. 28. <ul><li>Chiral centers </li></ul><ul><li>A carbon atom with four different substituents is said to be asymmetric, and asymmetric carbons are called chiral centers. </li></ul>
  27. 29. Number of stereoisomers = 2 n Enantiomers, Diastereomers
  28. 30. The resulting stereoisomers have similar or identical chemical properties but different physical and biological properties. Enantiomers have different physical properties was first observed by Louis Pasteur (1848). Their interaction with plane polarized light.
  29. 31. <ul><li>Racemic mixture </li></ul><ul><li>In separate solution the two enantiomers rotate the plane of plane polarized light in opposite directions. But equimolar solution show no optical rotation. </li></ul>
  30. 32. Nomenclature of stereoisomers
  31. 33. <ul><li>Another system for naming is D and L system </li></ul>
  32. 34. Conformations
  33. 35. Complementary fit between a macromolecule and a small molecule
  34. 36. Carbohydrates <ul><li>Carbohydrates are polyhydroxy aldehydes and ketones or substances that yield such compounds on hydrolysis. </li></ul><ul><li>(CH 2 O) n </li></ul><ul><li>some also contain nitrogen, phosphorous, and sulfur. </li></ul><ul><li>Monosaccharides, oligosaccharides, and polysaccharides. </li></ul>
  35. 37. Monosaccharides <ul><li>Simple sugars with single polyhydroxy aldehyde or ketone unit. </li></ul><ul><li>D-glucose (dextrose) </li></ul>
  36. 38. Monosaccharides <ul><li>Aldoses (e.g., glucose) have an aldehyde group at one end. </li></ul>Ketoses (e.g., fructose) have a keto group, usually at C2.
  37. 39. The simplest monosaccharides
  38. 40. Hexoses Pentoses
  39. 41. D vs L Designation D & L designations are based on the configuration about the single asymmetric C in glyceraldehyde. The lower representations are Fischer Projections.
  40. 42. For sugars with more than one chiral center, D or L refers to the asymmetric C farthest from the aldehyde or keto group. Most naturally occurring sugars are D isomers.
  41. 43. They have the same name, e.g., D-glucose & L-glucose. Other stereoisomers have unique names, e.g., glucose, mannose, galactose, etc. The number of stereoisomers is 2 n , where n is the number of asymmetric centers. The 6-C aldoses have 4 asymmetric centers. Thus there are 16 stereoisomers (8 D-sugars and 8 L-sugars).
  42. 44. D-Aldoses
  43. 45. D-Aldoses
  44. 46. D-Ketoses
  45. 47. D-Ketoses
  46. 48. Epimers
  47. 49. Hemiacetal & hemiketal formation
  48. 50. Glucose forms an intra-molecular hemiacetal, as the C1 Aldehyde & C5 OH react, to form a 6-member pyranose ring, named after pyran.
  49. 51. <ul><li>Cyclization of glucose produces a new asymmetric center at C1. The 2 stereoisomers are called anomers, α & β . </li></ul><ul><li>Haworth projections represent the cyclic sugars as having essentially planar rings, with the OH at the anomeric C1: </li></ul><ul><ul><li>α (OH below the ring) </li></ul></ul><ul><ul><li>β (OH above the ring). </li></ul></ul>
  50. 52. Pentoses and hexoses can cyclize as the ketone or aldehyde reacts with a distal OH.
  51. 53. Because of the tetrahedral nature of carbon bonds, pyranose sugars actually assume a &quot;chair&quot; or &quot;boat&quot; configuration, depending on the sugar. The representation above reflects the chair configuration of the glucopyranose ring. Haworth perspective formula
  52. 54. Organisms contain variety of sugar derivatives <ul><li>Hydroxyl at C2 is replaced with an amino group. </li></ul><ul><li>Glucosamine, galactosamine, and mannosamine. </li></ul>
  53. 55. <ul><li>Amino group at C2 </li></ul><ul><li>is condensed with </li></ul><ul><li>acetic acid. </li></ul><ul><li>N-acetylglucosamine. </li></ul><ul><li>present in cell </li></ul><ul><li>wall of bacteria. </li></ul>
  54. 56. <ul><li>Lactic acid is ether linked to oxygen at C-3 of N-acetylglucosamine. </li></ul><ul><li>N-acetylmuramic acid. </li></ul><ul><li>Component of bacterial cell wall. </li></ul>
  55. 57. <ul><li>L-fucose or L-rhamnose </li></ul><ul><li>Substitution of hydrogen for hydroxyl group at C-6 of L-galactose or L-mannose. </li></ul><ul><li>Glycoproteins, and </li></ul><ul><li>glycolipids. Later is </li></ul><ul><li>found in plant </li></ul><ul><li>polysaccharides </li></ul>
  56. 58. <ul><li>N-acetylneuraminic acid </li></ul><ul><li>Nine carbon acidic sugar derived from N-acetylmannosamine. It is a component of many glycoproteins and glycolipids. </li></ul>
  57. 59. <ul><li>Sugar phosphates </li></ul><ul><li>condensation of phosphoric acid with one of the hydroxyl groups of sugar. </li></ul><ul><li>These are intermediates during synthesis and metabolism of carbohydrates. </li></ul><ul><li>These cannot be transported out. </li></ul>
  58. 60. Fehling’s Reaction <ul><li>Test for presence of reducing sugars. By measuring the amount of oxidizing agent reduced by solution of a sugar. </li></ul>
  59. 61. Disaccharides contain a glycosidic bond <ul><li>Disaccharides have two monosaccharides joined covalently by an O-glycosidic bond. Eg. Maltose, lactose, and sucrose. </li></ul>
  60. 63. <ul><li>Glycosidic bonds are readily hydrolyzed by acid. </li></ul><ul><li>the end of the chain with free anomeric carbon is called reducing end. </li></ul><ul><li>The configuration of the anomeric carbon in the glycosidic linkage is α . </li></ul>
  61. 64. Nomenclature of Di- or oligosaccharides <ul><li>Specifies the order of monosaccharides units. </li></ul><ul><li>Configuration at each anomeric carbon. </li></ul><ul><li>Carbon atoms involved in the glycosidic linkage. </li></ul>
  62. 65. <ul><li>Lactose on hydrolysis yield D-galactose and D-glucose. Naturally occurs in milk </li></ul>
  63. 66. <ul><li>Sucrose is a disaccharide of glucose and fructose. It is a non-reducing sugar. major intermediate product of photosynthesis. Principal form in which sugar is transported in plants </li></ul>
  64. 67. <ul><li>Trehalose is a disaccharide of glucose and is non-reducing sugar. Constituent of hemolymph of insects, fungi also contain trehalose. </li></ul>
  65. 68. Polysaccharides <ul><li>Most abundantly found carbohydrates are in form of polysaccharides also called glycans. </li></ul><ul><li>Polysaccharides differ from each other </li></ul><ul><li>-identity of the recurring monosaccharide units. </li></ul><ul><li>-length of their chains. </li></ul><ul><li>-degree of branching. </li></ul>
  66. 71. <ul><li>Fig7-13 </li></ul>
  67. 72. Homopolysaccharides as stored fuel <ul><li>Starch contains two types of glucose polymer, amylose and amylopectin. </li></ul>
  68. 73. <ul><li>Starch is the most important storage polysaccharide in plants. </li></ul><ul><li>It is especially abundant in tubers (underground stems) and seeds. </li></ul>
  69. 74. <ul><li>Glycogen is a polymer of ( α 1 4)-linked subunits of glucose, with ( α 1 6)-linked branches. Glycogen is more extensively branched (branch on average at every 8-12 residues). </li></ul><ul><li>Liver </li></ul><ul><li>Skeletal muscles </li></ul>
  70. 75. <ul><li>Why not store glucose in its monomeric form? </li></ul>
  71. 77. <ul><li>1. Which of the following elements is not one of the six most abundant elements found in all living cells? </li></ul><ul><li>Oxygen </li></ul><ul><li>Nitrogen </li></ul><ul><li>Sulfur </li></ul><ul><li>Potassium </li></ul><ul><li>carbon </li></ul>
  72. 78. <ul><li>5. Which functional group(s) are basic (accept H + ions)? </li></ul><ul><li>carboxyl groups </li></ul><ul><li>hydroxyl groups </li></ul><ul><li>keto groups </li></ul><ul><li>amino groups </li></ul><ul><li>sulfhydryl groups </li></ul>