1. Advanced Biochemistry and Chemical Biology CHM4034 Spring 2008 Dr. Lyons office hours lyons@chem.ufl.edu 846-3392 -W 10-11 AM -T,R 4:00-5:00 PM Class website http://www.chem.ufl.edu/~lyons/

2. Monosaccharides are modified

4. Aldonic AcidAldose Uronic Acid Glucose Gluconic AcidGlucuronic Acid Oxidation reduction reactions : The aldehyde moiety in aldoses can be oxidize to yield a carboxylic acid, the resulting compounds are known as aldonic acids.

5. Monosaccharides are modified

6. Ribose Ribitol - The reduction of the carbonyl group in aldoses and ketoses yields polyols known as alditols

7. Glycerol Inositol

8. Nucleic Acids The Ultimate Building Blocks

11. Purines Adenosine NUCLEOSIDE Adenosine monophosphate NUCLEOTIDE Adenine BASE Deoxyadenosine DEOXYNUCLEOSIDE Deoxyadenosine monophosphate DEOXYNUCLEOTIDE

12. Purines Guanine BASE Guanosine NUCLEOSIDE Guanosine monophosphate NUCLEOTIDE Deoxyguanosine DEOXYNUCLEOSIDE Deoxyguanosine monophosphate DEOXYNUCLEOTIDE

13. Pyrimidines Cytosine BASE Cytidine NUCLEOSIDE Cytidine monophosphate NUCLEOTIDE Deoxycytidine DEOXYNUCLEOSIDE Deoxycytidine monophosphate DEOXYNUCLEOTIDE

14. Pyrimidines (DNA only) Thymine BASE Thymidine NUCLEOSIDE Thymidine monophosphate NUCLEOTIDE Deoxythymidine DEOXYNUCLEOSIDE Deoxythymidine monophosphate DEOXYNUCLEOTIDE

15. Pyrimidines (RNA only) Uracil BASE Uridine NUCLEOSIDE Uridine Monophosphate NUCLEOTIDE

16. Nucleotide monphosphate Nucleotide diphosphate Nucleotide triphosphate AMP/dAMP ADP/dADP ATP/dATP

17. BaseNucleosideDeoxy Nucleoside NucleotideDeoxy Nucleotide Adenine A Adenosine A Deoxyadenosine dA Adenosine mono, di, triphosphate AMP, ADP, ATP Deoxyadenosine mono, di, triphosphate dAMP, dADP, dATP Thymine T Thymidine T Deoxythymidine dT Thymidine mono, di, triphosphate TMP, TDP, TTP Deoxythymidine mono, di, triphosphate dTMP, dTDP, dTTP Cytosine C Cytidine C Deoxycytidine dC Cytidine mono, di, triphosphate CMP, CDP, CTP Deoxycytidine mono, di, triphosphate dCMP, dCDP, dCTP Guanine G Guanosine G Deoxyguanosine dG Guanosine mono, di, triphosphate GMP, GDP, GTP Deoxyguanosine mono, di, triphosphate dAMP, dADP, dATP Uracil U Uridine U Deoxyuridine dU Uridine mono, di, triphosphate UMP, UDP, UTP Deoxyuridine mono, di, triphosphate dUMP, dUDP, dUTP

20. Signaling nucleotides

22. The stability of RNA v. DNA

24. Functions for nucleotides other than for DNA/RNA Enter ATP GTP, CTP, UTP and TTP also used in this capacity

28. NADP + has a 2’ phosphate

30. Ribitol

32. Cobalamin Vitamin B 12 Becomes Coenzyme B 12

34. Fatty Acids

36. Nomenclature Saturated = -anoic acid, -anoate Unsaturated = -enoic acid, -enoate Take the example of fatty acid with 16 carbons 16 carbon hydrocarbon = hexadecane Fatty acid C16:0 hexadecanoic acid (hexadecanoate) palmitic acid (palmitate) 1 double bond = C16:1, hexadecenoic acid 2 double bonds = C16:2, hexadecadienoic acid Three systems of nomenclature symbol, systematic, common

37. SymbolCommon NameSystematic Name 12:0Lauric acidDodecanoic acid 14:0Myristic acidTetradecanoic acid 16:0Palmitic acidHexadecanoic acid 16:1 ∆9Palmitoleic acid9-Hexadecenoic acid 18:0Stearic acidOctadecanoic acid 18:1 ∆9Oleic acid9-octadecenoic acid 18:2 ∆9∆12Linoleic acid9,12-octadecadienoic acid 18:3 ∆9∆12∆15Linolenic acid9,12,14-octadecatrienoic acid 20:0Arachidic acidEicosanoic acid 20:4 ∆5∆8∆11∆14Arachidonic acid5,8,11,14-eicosatetraenoic acid 20:5 ∆5∆8∆11∆14∆17Eicospentaenoic acid5,8,11,14,17- eicosapentaenoic acid 22:0Behenic acidDocosanoic acid 24:0Lignoceric acidTetracosanoic acid 24:1 ∆15Nervonic acid15-tetracosenoic acid

38. Storage lipids/Neutral lipids Triglycerides Triacylglycerol Sterylesters

41. Structural Lipids - Membrane components Glycerolipids Sphingolipids Diphytanyl lipids

42. Signaling Lipids Ceramides Inositol containing lipids Eicosanoids Steroids

44. Thiamine pyrophosphate (TPP)

50. Phosphohexose isomerase

53. Breaking a C-C bond between  and  carbons

64. Enolase

66. Pyruvate kinase

67. Acetyl CoA Citrate Synthase Oxaloacetate Claisen condensation Ligase

68. Aconitase: lyase

69. Breaking a C-C bond between  and  carbons

70. With a  keto acid To decarboxylate you need an electron withdrawing group Use you can generate an enolate that can be stabilized by metals, Schiff’s base, etc…

71. Isocitrate dehydrogenase: oxidoreductase IsocitrateOxalosuccinate

72. Isocitrate dehydrogenase: oxidoreductase  -ketoglutarate Oxalosuccinate + CO 2 Enol intermediate

73. Breaking a C-C bond between carbonyl carbon and  carbon NEED TO STABILIZE CARBANION

75. With an  keto acid To decarboxylate you need an electron withdrawing group Use thiamine pyrophosphate to attack the  carbonyl

80. Almost the Same Reaction as pyruvate dehydrogenase/decarboxylase  -ketoglutarate dehydrogenase

82.  -ketoglutarate dehydrogenase

83. Succinyl-CoA

84. Succinyl-CoA synthetase: transferase Succinyl-CoA Succinyl-phosphateSuccinate Phosphoenzyme

85. Succinyl-CoA synthetase: transferase Phosphoenzyme

86. Succinate dehydrogenase: oxidoreductase Succinate Fumarate

87. Fumarase: lyase FumarateMalate

88. Malate dehydrogenase oxaloacetate Malate