Chemistry of Carbohydrates and Nucleic acids - An introduction

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Chemistry of Carbohydrates and Nucleic acids - An introduction

  1. 1. MSB 100: Basics of Biomedical Sciences TOPIC: •CARBOHYDRATE CHEMISTRY •NUCLEIC ACID CHEMISTRY Lecturer: Dr. G. Kattam Maiyoh 11/20/13 GKM/MSB100/LECT 02/2013
  2. 2. Introduction • Carbohydrates are one of the FOUR major classes of biological molecules. •Carbs •Proteins •Lipids •NA • Carbohydrates are also the most abundant biological molecules. • Carbohydrates derive their name from the general formula Cn(H2O)~ hydrated carbon or hydrates of carbon 11/20/13 GKM/MSB100/LECT 02/2013
  3. 3. functions • Variety of important functions in living systems: – nutritional (energy storage, fuels, metabolic intermediates) – structural (components of nucleotides, plant and bacterial cell walls, arthropod exoskeletons, animal connective tissue) 11/20/13 GKM/MSB100/LECT 02/2013
  4. 4. – Informational (cell surface of eukaryotes -- molecular recognition, cell-cell communication) – Osmotic pressure regulation (bacteria) 11/20/13 GKM/MSB100/LECT 02/2013
  5. 5. In molecular terms • Carbohydrates are carbon compounds that contain large quantities of hydroxyl groups. 11/20/13 GKM/MSB100/LECT 02/2013
  6. 6. In chemical terms Carbohydrates are chemically characterized as: • Poly hydroxy aldehydes or • Poly hydroxy ketones. 11/20/13 GKM/MSB100/LECT 02/2013
  7. 7. Aldoses vs Ketoses • Sugars that contain an aldehyde group are called Aldoses. • Sugars that contain a keto group are called Ketoses. 11/20/13 GKM/MSB100/LECT 02/2013
  8. 8. 11/20/13 GKM/MSB100/LECT 02/2013
  9. 9. classification All carbohydrates can be classified as either: – Monosaccharides – Disaccharides – Oligosaccharides – Polysaccharides. 11/20/13 GKM/MSB100/LECT 02/2013
  10. 10. • Monosaccharides - one unit of carbohydrate • Disaccharides - Two units of carbohydrates. • Anywhere from three to ten monosaccharide units, make up an oligosaccharide. • Polysaccharides are much larger, containing hundreds of monosaccharide units. 11/20/13 GKM/MSB100/LECT 02/2013
  11. 11. Complexes • Carbohydrates also can combine with lipids to form glycolipids OR • With proteins to form glycoproteins / proteoglycans. 11/20/13 GKM/MSB100/LECT 02/2013
  12. 12. Isomers • Isomers are molecules that have the same molecular formula, but have a different arrangement of the atoms in space. (different structures). • For example, a molecule with the formula AB2C2, has two ways it can be drawn: 11/20/13 GKM/MSB100/LECT 02/2013
  13. 13. Isomer 1 11/20/13 GKM/MSB100/LECT 02/2013
  14. 14. Isomer 2 11/20/13 GKM/MSB100/LECT 02/2013
  15. 15. 11/20/13 GKM/MSB100/LECT 02/2013
  16. 16. Examples of isomers: 1. 2. 3. 4. Glucose Fructose Galactose Mannose Same chemical formula C6 H12 O6 11/20/13 GKM/MSB100/LECT 02/2013
  17. 17. 11/20/13 GKM/MSB100/LECT 02/2013
  18. 18. EPIMERS • EPIMERS are sugars that differ in configuration at ONLY 1 POSITION. 11/20/13 GKM/MSB100/LECT 02/2013
  19. 19. • Examples of epimers : – D-glucose & D-galactose (epimeric at C4) – D-glucose & D-mannose (epimeric at C2) – D-idose & L-glucose (epimeric at C5) 11/20/13 GKM/MSB100/LECT 02/2013
  20. 20. Epimer set 1 11/20/13 GKM/MSB100/LECT 02/2013
  21. 21. Epimer set 2 11/20/13 GKM/MSB100/LECT 02/2013
  22. 22. ENANTIOMERS Non-Superimposable COMPLETE mirror image (differ in configuration at EVERY CHIRAL CENTER. 11/20/13 GKM/MSB100/LECT 02/2013
  23. 23. Features of Enantiomers The two members of the pair are designated as D and L forms. In D form the OH group on the asymmetric carbon is on the right. In L form the OH group is on the left side. For e.g: D-glucose and L-glucose are enantiomers: 11/20/13 GKM/MSB100/LECT 02/2013
  24. 24. A pair enantiomers are mirror images of each other 11/20/13 GKM/MSB100/LECT 02/2013
  25. 25. 11/20/13 GKM/MSB100/LECT 02/2013
  26. 26. 11/20/13 GKM/MSB100/LECT 02/2013
  27. 27. 11/20/13 GKM/MSB100/LECT 02/2013
  28. 28. Asymmetric carbon in sugars • A carbon linked to four different atoms or groups farthest from the carbonyl carbon • Also called Chiral carbon 11/20/13 GKM/MSB100/LECT 02/2013
  29. 29. 11/20/13 GKM/MSB100/LECT 02/2013
  30. 30. Cyclization of sugars • Less then 1%of CHO exist in an open chain form (AKA: straight chain, fischer projection, linear form) • Predominantly found in ring form (AKA: Close, cyclic, Haworth) • For 6 Carbon sugars, involves reaction of C-5 OH group with the C-1 aldehyde group or C-2 of keto group (carbonyl carbon). 11/20/13 GKM/MSB100/LECT 02/2013
  31. 31. Ring forms • Basically 2 types • Six membered ring structures are called Pyranoses . Pyran ring • Five membered ring structures are called Furanoses . Furan ring 11/20/13 GKM/MSB100/LECT 02/2013
  32. 32. 11/20/13 GKM/MSB100/LECT 02/2013
  33. 33. Anomeric carbon • The carbonyl carbon after cyclization becomes the anomeric carbon. • This creates α and β configuration. 11/20/13 GKM/MSB100/LECT 02/2013
  34. 34. 11/20/13 GKM/MSB100/LECT 02/2013
  35. 35. • Such α and β configuration are called diastereomers and they are not mirror images. Enzymes can distinguished between these two forms: • Glycogen is synthesized from α-D glucopyranose • Cellulose is synthesized from β -D glucopyranose 11/20/13 GKM/MSB100/LECT 02/2013
  36. 36. MUTAROTATION • Unlike the other stereoisomeric forms, α and β anomers spontaneously interconvert in solution. • This is called mutarotation. 11/20/13 GKM/MSB100/LECT 02/2013
  37. 37. 11/20/13 GKM/MSB100/LECT 02/2013
  38. 38. 11/20/13 GKM/MSB100/LECT 02/2013
  39. 39. Optical Activity • When a plane polarized light is passed through a solution containing monosaccharides the light will either be rotated towards right or left. • This rotation is because of the presence of asymmetric carbon atom. • If it is rotated towards left- levorotatory (-) (L) • If it is rotated towards right- dextrorotatory (+) (D) 11/20/13 GKM/MSB100/LECT 02/2013
  40. 40. Reducing sugar • Sugars in which the oxygen of the anomeric carbon is free and not attached to any other structure, such sugars can act as reducing agents and are called reducing sugars. 11/20/13 GKM/MSB100/LECT 02/2013
  41. 41. Polysaccharides 2 types: – HOMOpolysaccharides (all 1 type of monomer), e.g., glycogen, starch, cellulose, chitin – HETEROpolysaccharides (different types of monomers), e.g., peptidoglycans, glycosaminoglycans 11/20/13 GKM/MSB100/LECT 02/2013
  42. 42. Functions of polysaccharides: – Glucose storage (glycogen in animals & bacteria, starch in plants) – Structure (cellulose, chitin, peptidoglycans, glycosaminoglycans – Information (cell surface oligo- and polysaccharides, on proteins/glycoproteins and on lipids/glycolipids) – Osmotic regulation 11/20/13 GKM/MSB100/LECT 02/2013
  43. 43. Key examples of polysaccs; • Starch and glycogen – Function: glucose storage Starch -- 2 forms: • amylose: linear polymer of a(1-> 4) linked glucose residues • amylopectin: branched polymer of a(1-> 4) linked glucose residues with a(1-> 6) linked branches 11/20/13 GKM/MSB100/LECT 02/2013
  44. 44. – Glycogen: • branched polymer of a(1-> 4) linked glucose residues with a(1-> 6) linked branches • like amylopectin but even more highly branched and more compact • branches increase H2O-solubility – Branched structures: many nonreducing ends, but only ONE REDUCING END (only 1 free anomeric C, not tied up in glycosidic bond) 11/20/13 GKM/MSB100/LECT 02/2013
  45. 45. • Each molecule, including all the branches, has only ONE free anomeric C – single free anomeric C = "reducing end" of polymer – the only end capable of equilibrating with straight chain form of its sugar residue, which has free carbonyl C. 11/20/13 GKM/MSB100/LECT 02/2013
  46. 46. Which can then: – REDUCE (be oxidized by) an oxidizing agent like Cu2+ 11/20/13 GKM/MSB100/LECT 02/2013
  47. 47. 11/20/13 GKM/MSB100/LECT 02/2013
  48. 48. • Cellulose and chitin – Function: STRUCTURAL, rigidity important Cellulose: • Homopolymer, b(1-> 4) linked glucose residues • Cell walls of plants 11/20/13 GKM/MSB100/LECT 02/2013
  49. 49. Chitin: • Homopolymer, b(1-> 4) linked Nacetylglucosamine residues • hard exoskeletons (shells) of arthropods (e.g., insects, lobsters and crabs) 11/20/13 GKM/MSB100/LECT 02/2013
  50. 50. Nucleic acids • Nucleic acids are polymeric macromolecules, or large biological molecules, essential for all known forms of life. • Nucleic acids, which include DNA (deoxyribonucleic acid) and RNA (ribonucleic acid), are made from monomers known as nucleotides. • Each nucleotide has three components: a 5-carbon sugar, a phosphate group, and a nitrogenous base. • If the sugar is deoxyribose, the polymer is DNA. • If the sugar is ribose, the polymer is RNA. 11/20/13 GKM/MSB100/LECT 02/2013
  51. 51. Nucleic Acids DNA –deoxyribonucleic acid – Polymer of deoxyribonucleotide triphosphate (dNTP) – 4 types of dNTP (ATP, CTP, TTP, GTP) NB: All made of a base + sugar + triphosphate 11/20/13 GKM/MSB100/LECT 02/2013
  52. 52. RNA –ribonucleic acid – Polymer of ribonucleotide triphosphates (NTP) – 4 types of NTP (ATP, CTP, UTP, GTP) NB: All made of a base + sugar + triphosphate So what’s the difference? • The sugar (ribose vs. deoxyribose) and one base (UTP vs. TTP) 11/20/13 GKM/MSB100/LECT 02/2013
  53. 53. Deoxyribose (like ribose) is a sugar with 5 carbon atoms  in a ring Oxygen is one of the ring members In Deoxyribose, one of the OH groups is missing and  replaced with hydrogen, Thus deoxy = - 1 oxygen 11/20/13 GKM/MSB100/LECT 02/2013
  54. 54. Phosphate groups are important because they link the sugar on one nucleotide onto the phosphate of the next nucleotide to make a polynucleotide. 11/20/13 GKM/MSB100/LECT 02/2013
  55. 55. Base - pairing • Nitrogenous bases • In DNA the four bases are: – – – – Thymine Adenine Cytosine Guanine • In RNA the four bases are: – – – – Uracil Adenine Cytosine Guanine 11/20/13 GKM/MSB100/LECT 02/2013
  56. 56. DNA and RNA are polynucleotides • Both DNA and RNA are polynucleotides. • They are made up of smaller molecules called nucleotides. Nucleotide • DNA is made of two polynucleotide strands: Nucleotide Nucleotide Nucleotide Nucleotide Nucleotide Nucleotide Nucleotide Nucleotide Nucleotide Nucleotide Nucleotide Nucleotide Nucleotide Nucleotide Nucleotide • RNA is made of a single polynucleotide strand: 11/20/13 GKM/MSB100/LECT 02/2013
  57. 57. DNA •Information for all proteins stored in DNA in the form of chromosomes or plasmids. •Chromosomes (both circular and linear) consist of two strands of DNA wrapped together in a left handed helix.(imagine screwing inwards) •The strands of the helix are held together by hydrogen bonds between the individual bases. •The “outside” of the helix consists of sugar and phosphate groups, giving the DNA molecule a negative charge. 11/20/13 GKM/MSB100/LECT 02/2013
  58. 58. BASES 11/20/13 GKM/MSB100/LECT 02/2013
  59. 59. The Rule: Complimentarity • Adenine always base pairs with Thymine (or Uracil if RNA) • Cytosine always base pairs with Guanine. • This is because there is only exactly enough room for one purine and one pyrimidine base between the two polynucleotide strands of DNA/RNA (see next slide). • These bases are said to be complimentary to each other 11/20/13 GKM/MSB100/LECT 02/2013
  60. 60. Complimentary Base Pairs A-T Base pairing 11/20/13 GKM/MSB100/LECT 02/2013 G-C Base Pairing
  61. 61. DNA Structure – The DNA helix is “anti-parallel” – Each strand of the helix has a 5’ (5 prime) end and a 3’ (3 prime) end. 11/20/13 GKM/MSB100/LECT 02/2013
  62. 62. 11/20/13 GKM/MSB100/LECT 02/2013
  63. 63. Central Dogma • Replication – DNA making a copy of itself • Making a replica • Transcription – DNA being made into RNA • Still in nucleotide language • Translation – RNA being made into protein • Change to amino acid language 11/20/13 GKM/MSB100/LECT 02/2013
  64. 64. Replication • Remember that DNA is self complementary • Replication is semiconservative – One strand goes to next generation – Other is new • Each strand is a template for the other – If one strand is 5’ AGCT 3’ – Other is: 3’ TCGA 5’ 11/20/13 GKM/MSB100/LECT 02/2013
  65. 65. Replica – Learning check • Write the strand complementary to: 3’ ACTAGCCTAAGTCG 5’ Answer 11/20/13 GKM/MSB100/LECT 02/2013
  66. 66. Similarity between replication and transcription • Both processes use DNA as the template. • Phosphodiester bonds are formed in both cases. • Both synthesis directions are from 5´ to 3´. 11/20/13 GKM/MSB100/LECT 02/2013
  67. 67. Differences between replication and transcription replication transcription template double strands single strand substrate dNTP NTP primer yes no Enzyme DNA polymerase RNA polymerase product dsDNA ssRNA base pair A-T, G-C A-U, T-A, G-C 11/20/13 GKM/MSB100/LECT 02/2013
  68. 68. Ribonucleic acid (RNA) • Almost all single stranded (exception is RNAi). • In some RNA molecules (tRNA) many of the bases are modified (e.g. psudouridine). • Has capacity for enzymatic function -ribozymes • One school of thought holds that early organisms were based on RNA instead of DNA (RNA world). 11/20/13 GKM/MSB100/LECT 02/2013
  69. 69. RNA • Several different “types” which reflect different functions – mRNA (messenger RNA) – tRNA (transfer RNA) – rRNA (ribosomal RNA) – snRNA (small nuclear RNA) – RNAi (RNA interference) 11/20/13 GKM/MSB100/LECT 02/2013
  70. 70. RNA function • mRNA – transfers information from DNA to ribosome (site where proteins are made) • tRNA – “decodes” genetic code in mRNA, inserts correct A.A. in response to genetic code. • rRNA-structural component of ribosome • snRNA-involved in processing of mRNA • RNAi-double stranded RNA, may be component of antiviral defense mechanism. 11/20/13 GKM/MSB100/LECT 02/2013
  71. 71. 11/20/13 GKM/MSB100/LECT 02/2013

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