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Bio-Organic Mechanism Game – Simplistic Biochemical Structures and Simplistic Organic Reaction Mechanisms Are Used to Explain Common Biochemical Transformations

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1 Bio-Organic Mechanism Game – Simplistic biochemical structures and simplistic organic reaction mechanisms are used to explain common biochemical transformations. Simplified biochemical molecules are presented first. Many biomolecules have a somewhat complex structure that makes it difficult to write out step by step mechanisms. However, if we simplify those structures to the essential parts necessary to explain the mechanistic chemistry of each step, it becomes much easier to consider each step through an important cycle. I have proposed possible simplified structures that are used in the later examples of biochem cycles and problems. The usual strategy in biochem cycles is to just write names, or perhaps, names and a structure. Occasionally a few mechanistic steps are suggested, but almost never is a detailed sequence of mechanistic steps provided. Since it is hard to find such detailed mechanistic steps anywhere (sometimes they are not known) our proposed steps are, of necessity, somewhat speculative. In this book we are not looking for perfection, which is not possible, but for sound organic logic that is consistent with the biochemical examples presented below. There is great satisfaction in blending organic knowledge with real life reactions that help explain how life works. In working through some of the problems, you may develop an alternative mechanism that is just as good, or even better than the one I have proposed. If you do, I hope you will share it with me and if an improved version of this book ever gets written I can include it the next edition (and give you credit). It is almost certain that I have made some errors and I would appreciate it if you would let me know about them. Biomolecules and our simplified representation. 1. ATP – adenosine triphosphate – phosphorylation, energy source NH2 N N O O O O O P O ATP O P O P O P O CH2 N = O N O O O O H H simplified structure H H actual structure OH OH 2. NAD+ and NADP+ - nicotinamide adenine dinucleotide (hydride acceptor) CONH2 NH2 N N = O O N N H2C O P O P O CH2 N O N OH HO R O O H H O simplified H H actual OH OH NADP+ has a structure structure phosphate here. y:\files\classes\Organic Hunger Games\Bio-Org Game newer.doc 2 3. NADH and NADHP - nicotinamide adenine dinucleotide (hydride donor) H CONH2 NH2 H H H N N O O = N H2C O P O P O CH2 N O N N OH HO O O H H R O H H simplified OH OH NADPH has a structure phosphate here. 4. Vitamin B-6 – pyridoxal phosphate (amino acid metabolism, transamination with -ketoacids, decarboxylation, removal of some amino acid side chains, epimerizations) 1o amine version of Vit B-6 aldehyde version of Vit B-6 NH2 NH2 H O H O H interconvert H via imine, -2 O tautomers, -2 O O PO 3 hydrolysis O3PO = N N N = N H H H H simplified actual simplified actual structure structure structure structure 5. TPP – Thiamine diphosphate (decarboxylation and enamine chemistry with proton or carbohydrates) N NH2 R R N N N B N H = H S S O O S ylid form simplified O P O P O CH2 structure of TPP actual O O structure y:\files\classes\Organic Hunger Games\Bio-Org Game newer.doc 3 6. Coenzyme A (acyl transfer) All of this is "Co-A" O O O O S O P O P O N H N N O NH H H 2 O O N OH Thiol esters form here. N O HO N H CoA OH S CoA This is an S acetyl group actual simplified simplified structure structure structure of CoA of acetyl Co-A 7. FAD / FADH2 – Flavin adenine dinucleotide (oxidation – reduction) – used to deliver hydride to C=C or take hydride from CH-CH (fatty acid metabolism, etc.) O O O P O P O N O NH2 O O N HO OH N HO N actual structure OH OH N N O FAD - flavin dinucleotide (a hydride acceptor) NH N H O N N N N FAD FADH H 2 simplified structures for FAD and FADH2 y:\files\classes\Organic Hunger Games\Bio-Org Game newer.doc 4 H B H H B N C C C C H H N FAD N N H flavin dinucleotide (a hydride acceptor) C C N N H FADH2 B B H flavin dinucleotide (a hydride donor) Hydride transfer reduces FAD to FADH2 which can be oxidized to FAD. 8. THF – tetrahdrofolate (transfer of one carbon units) –recycles cysteine to methionine and other 1C metabolic functions, many variations Tetrahydrofolate (THF) one carbon transfers as R "CH3", "CH2". 2 H2N N N V2 -p762 R H N N actual H N structure One glutamate is H shown, but several 5 = O HN can be attached. N H 10 HN One carbon groups H N CO2 Ar can bond here in various ways (see simplified below structures. structure O CO2 y:\files\classes\Organic Hunger Games\Bio-Org Game newer.doc 5 different forms R R R R N N N N NAD+ NADP+ +H2O 5 5 N NADH 5 NADPH H -H2O N N N 10 O N 10 10 Ar CH3 HN N HC N H2C 10 Ar Ar Ar N -formyl THF 5 5 10 H N -methyl THF 5 10 N ,N -methenyl THF N ,N -methylene THF HCO2 ATP glycine -H2O +H2O or +NH3 R THF serine R THF -NH3 N N 5 5 histidine N N THF 10 10 HN HN H NH Ar H O Ar 5 = N5-formyl THF N -formimino THF 9. SAM = S-adenosylmethionine (methyl transfer agent), The methyl group (CH3) attached to the methionine sulfur atom in SAM is chemically reactive. This allows donation of this group to an acceptor substrate in transmethylation reactions. More than 40 metabolic reactions involve the transfer of a methyl group from SAM to various substrates, such as nucleic acids, proteins, lipids and secondary metabolites. SAM can be made from methionine and N5-methyl THF (just above). leaving group was triphosphate N SAM = S-adenosylmethionine methionine NH2 NH2 Rmet Rad O O N S S N CH = 3 OH CH3 N simplified structure actual HO OH adenosine structure SAM = S-adenosylmethionine Rmet = methionine Rad = adenonine N O O O O O O NH2 NH2 P P P O N O O O O O S N N OH methionine CH3 HO OH ATP y:\files\classes\Organic Hunger Games\Bio-Org Game newer.doc 6 10. Cytochrom P-450 enzymes are oxidizing agents in the body. They can convert inert alkane sp3 C-H bonds into C-OH bonds and they can make epoxide groups at alkenes and aromatic pi bonds. Oxidations in the body often use cytochrom P-450 enzymes. N N N +3 N N N +3 Fe simplified simplified Fe N N structure Fe structure N N N N S S Enz Enz HO2C CO2H O heme, protoporphyrin IX, found in This is the structure cytochrom P-450 oxidative enzymes that we will use. +4 +3 Fe Fe simplified structure 11. Halogenase Enzymes (related to cytochrom P-450 enzymes, can have imidazole ligands from histadine amino acids Halogenations in the body often iron halogen bonds. His N O N N O N N +3 This is the structure Fe N that we will use. His Fe+4 Cl H Cl N O O N +4 +3 N Cl Fe Fe simplified structure His Biochemical Reaction Mechanism Examples Mechanism arrows used in the “Bio-Org Game” are meant to suggest how the electrons move over a single transformation, and are not necessarily meant to imply that all of the electrons and atoms transfer in one huge “domino” cascade. Organic mechanisms are often multistep transformations, but it’s harder to pin down biochemical transformations. The symbolism used in these examples represents a concise way to show electron movement involving making and breaking bonds. Lone pairs are rarely drawn (or used). They are included on the generic base (B:) used to show proton transfers. A generic acid (H-B+) is used to provide a proton. Very occasionally a pair of electrons is used when it provides some special effect (enamine reaction, y:\files\classes\Organic Hunger Games\Bio-Org Game newer.doc 7 resonance stabilization in acetal formation or breakdown). Multiple resonance structures are not drawn. Only very occasionally is an intermediate drawn, when confusion arises from too many arrows going in too many different directions. Do not confuse these examples for real mechanisms! They are designed to show the essential how changes might occur in complex biochemical reactions. Also, at physiological pH (7) a few organic groups are ionized (RCO2H is -- + anionic as RCO2 , and RNH2 is cationic as RNH3 ). They are drawn in their neutral forms in this game. The initial examples of biochemical transformations can serve as foundational reactions in endless biochemical sequences or cycles. Knowing how these reactions work can provide insight into many biochemical aspects of anabolism and catabolism and can help improve your organic “mechanistic” logic. First, bare-bones examples are provided to show the essence of each type of reaction. The problems that follow use several “typical” types of biochemical transformations in made-up sequences and many real biochemical cycles in which to practice. With such practice using these simple model reactions you can learn to recognize where (when) and how similar transformations might be occurring in real biochemical reactions that are presented without any mechanistic detail in a book or article.
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