How enzymes catalyze reactions? Organic chemistry of vitamins

1. How enzymes catalyze reactions? Organic chemistry of vitamins

2. Book: Bruice • Chapter: 17 • Pages: 506-524

3. Enzyme-catalyzed reactions • Reactant of an enzyme catalysis – substrate • Substrate + Enzyme -> Product • Substrate binds in a pocket of enzyme – active site • All bond-breaking and bon-forming steps occur in that moment • Enzymes – specific for the substrates • Specificity of enzymes – molecular recognition

4. Specificity – results from its conformation and the particularamino acid side chains (α-substituents) that are at the active site • Example: AA with negatively charged side chain associates with a positively charged group on the substrate

5. Factors • Influence catalytic ability of enzymes: • • Reacting groups are brought together at the active site in the proper orientationfor reaction. • • Some of the amino acid side chains of the enzyme serve as catalysts. These arepositioned relative to the substrate precisely where they are needed for catalysis. • • Amino acid side chains can stabilize transition states and intermediates—by vander Waals interactions, electrostatic interactions, and hydrogen bonding—which makes them easier to form.

6. Enzyme mechanism • “ase” – tells something about the reaction it catalyzes • Example: glucose-6-phosphate isomerase • catalyzes an isomerization reaction that converts glucose-6-phosphate tofructose-6-phosphate • open-chain form of glucose is an aldohexose • open-chain form of fructose is a ketohexose • glucose-6-phosphate isomerase—converts an aldose to a ketose

7. Enzyme must open the six-membered-ring sugar • convert it to the five-membered-ringsugar • This enzyme – has at least 3 catalytic groups at its active site • One functioning as an acid catalyst and two acting as base catalyst

8. 1. ring opening reaction: (base catalyst-His) removes a proton and acid catalyst aids the departure of leaving group by protonation • 2. base catalyst (Glu residue) removes aproton from α-carbon of aldehyde • 3. enol converted to a ketone • 4. conjugate acid and conjugate base from corresponding acid and base close the ring

9. The mechanism of aldolase • Involved in glycolysis • D-glucose is substrate • Final product – 2 molecules of pyruvate • six-carbon compound must be cleaved into two three-carboncompounds • Aldolase - catalyzes this cleavage • The enzyme is called aldolase because the reverse reaction is an aldol addition

10. 1. fructose-1,6-diphosphate forms an imine with a Lys residue at the active site of the enzyme • 2. A Tyr residue functions as a base catalyst in the step that cleaves the bondbetween C-3 and C-4 • 3. The enamine intermediate rearranges to an imine, with the tyrosine residue nowfunctioning as an acid catalyst • 4. Hydrolysis of the imine releases dihydroxyacetone phosphate, the other three carbonproduct

11. Coenzymes and vitamins • Coenzymes – enzyme helpers • organic molecules • assist enzymes in catalyzing certain reactions that cannotbe catalyzed by the amino acid side chains of the enzyme alone • derived from organic compounds commonly known as vitamins • Vitamin - substance needed in small amounts for normal body functionthat the body cannot synthesize • The body synthesizes the coenzyme from the vitamin

12. 2 classes: water and fat soluble • Fat soluble: A, D, E and K • Vitamin K - only water-insoluble vitamin currently known to be a precursor for a coenzyme • Vitamin A - for proper vision • Vitamin D - regulates calcium and phosphatemetabolism • Vitamin E – antioxidant • Water soluble: B complex (precursors for coenzymes) and vitamin C (no precursor) • vitamin C is a radical inhibitor - must be included in their diets

14. Niacin • For redox reactions • Needs coenzyme – AA cannot perform redox reactions • coenzyme serves as the oxidizing or reducing agent • enzyme’s role is tohold the substrate and coenzyme together so that the oxidation or reductionreaction can take place • most commonly used: nicotinamide adenine dinucleotide (NAD+)

15. composed of two nucleotides • linked together through their phosphate groups • Nucleotide - heterocyclic compound attached to C-1 of a phosphorylated ribose • Heterocycliccompound – one or more of the ring atoms is an atom other than carbon • The heterocyclic component of one of the nucleotides of NAD+ is nicotinamide,and the heterocyclic component of the other is adenine • The positive charge in the NAD+ abbreviation indicates the positively charged nitrogen of the substituted pyridine ring

17. The adenine nucleotide for the coenzyme is provided by ATP • Niacin (vitamin B3) isthe portion of the coenzyme that the body cannot synthesize and must acquire throughthe diet

18. Example: malate dehydrogenase • catalyzes an oxidation reaction • of the secondary alcohol group of malate to aketone group • Oxidizing agent: NAD+ • Number of C-H bonds decreases in an oxidation reaction

19. substrate is being oxidized, it donatesa hydride ion (H-) to the 4-position of the pyridine ring of NAD+ • The pyridine ring,therefore, is reduced • The rest of the NAD+ molecule has the job of binding the coenzymeto the proper site on the enzyme • basic amino acid side chain of the enzyme can help theoxidation reaction • removing a proton from the oxygen atom of the substrate

20. The mechanism for reduction by NADH is the reverse of the mechanism foroxidation • When a substrate is being reduced, the dihydropyridinering of NADH donates a hydride ion from its 4-position to the substrate • ring, therefore, is oxidized • An acidic amino acid side chain of the enzymeaids the reduction reaction by donating a proton to the substrate

21. Niacin deficiency • Causes pellagra • Diseasethat begins with dermatitis and ultimately causesinsanity and death • Reported in 1927 in USA (120,000 cases) • among poor people with unvaried diets

22. Vitamin B2 • Flavin adenine dinucleotide (FAD) is another coenzyme used to oxidize substrates • Example: FAD is the coenzyme used by succinatedehydrogenase to oxidize succinateto fumarate • dinucleotide in which one of the heterocyclic compoundsis flavin and the other is adenine • instead of ribose, the flavin nucleotidehas a reduced ribose (a ribitol group) – riboflavin or B2 • Deficiency - inflammation of the skin

23. When FAD oxidizes a compound (S), FAD is reduced to FADH2

24. NAD+ or FAD? • NAD+ - in enzyme-catalyzedoxidation reactions involving carbonyl compounds • alcohols being oxidizedto ketones, aldehydes, or carboxylic acids • FAD - coenzyme used in othertypes of oxidations

25. Vitamin B1 • Thiamine • Absence in the diet - disease called beriberi • damages the heart, impairs nerve reflexes, and in extreme cases causesparalysis • As vitamin - used to form the coenzyme thiamine pyrophosphate (TPP) • required by enzymes that catalyze the transfer of a two-carbon fragmentfrom one species to another

26. Example: Pyruvatedecarboxylase requires TPP • catalyzes the decarboxylation of pyruvate and transfersthe remaining two-carbon fragment to a proton, resulting in the formation ofacetaldehyde

27. pyruvatedehydrogenase system - group of three enzymes and five coenzymes • overall reaction catalyzes the decarboxylationof pyruvate and transfers the remaining two-carbon fragment to coenzyme A - resulting in the formation of acetyl-CoA

28. Coenzyme A • activates carboxylic acids by convertingthem to thioesters • more reactive than are carboxylic acids • pKaof the conjugate acid of the thiol leavinggroup of a thioester is approx.10 • The vitamin needed to make CoASH is pantothenate

29. Vitamin H • Biotin • unusual vitamin because it can be synthesized by bacteria thatlive in the intestine • does not have to be included in our diet anddeficiencies are rare • can be found in people who maintaina diet high in raw eggs • Egg whites contain a protein that binds biotin tightly andthereby prevents it from acting as a coenzyme • When eggs are cooked, the protein isdenatured, and the denatured protein does not bind biotin

30. required by enzymes that catalyze carboxylation of an α-carbon (a carbon adjacent to a carbonyl group) • Carboxylases • Example: acetyl-CoAcarboxylaseconverts acetyl-CoA into malonyl-CoA • Biotin-requiring enzymesuse bicarbonate and also require ATP and Mg2+

31. Vitamin B6 • pyridoxine or vitamin B6 • coenzyme - pyridoxal phosphate (PLP) • “al” suffix indicates that the coenzyme is analdehyde • deficiency -causes anemia; severe deficiencies can causeseizures and death • PLP - required by enzymes that catalyze certain reactions of amino acids likedecarboxylation

32. Vitamin B12 • coenzyme B12 • Has CN or HO- group coordinated with Cobalt • Humans must obtain all their vitamin B12 from their diet, particularlyfrom meat • deficiency - pernicious anemia • Most deficiencies are caused by the intestines’ inability to absorb the vitamin

33. Enzymes that catalyze certain rearrangement reactions

34. Folic acid • Tetrahydrofolate (THF) – coenzyme • used by enzymes that catalyze reactionsthat transfer a group containing a single carbon to their substrates • produced by the reduction of two double bonds offolic acid (folate)

35. required for the synthesis of the bases found in DNA and RNA andfor the synthesis of aromatic amino acids • Three THF-coenzymes • Methyl group transfer, methylene group transfer and formyl group transfer

36. Chemistry link: First antibiotics • Sulfonamides—commonly known as sulfa drugs • 1936 as the first effective antibiotics • sulfanilamide, the first sulfonamide, isstructurally similar to p-aminobenzoic acid • Sulfanilamide acts by inhibiting the enzyme that incorporates paminobenzoicacid into folate • Both structures compete for the active site of the enzyme

37. Vitamin K • for proper clotting of blood • K – koagulation (German word for clotting) • Process requires Ca2+ • Vitamin K needed for proper Ca2+ binding • found in the leaves of green plants • Deficiencies in the vitamin are rare because it is synthesized by intestinal bacteria • Vitamin KH2 is the coenzyme form of the vitamin

38. Vitamin KH2- coenzyme for the enzyme that catalyzes the carboxylation ofthe γ-carbon of glutamate side chains in proteins, forming γ-carboxyglutamates

39. Warfarin (coumadin) and dicoumerol- used as anticoagulants • Preventclotting by inhibiting the enzyme that synthesizes vitamin KH2 from vitamin Kepoxide • enzyme cannot tell the difference between vitamin K epoxide and warfarin (or dicoumerol) - two compounds compete for binding at the enzyme’s activesite • Warfarin – common rat poison

40. Problems to solve • Page 524

41. Summary • Enzymes • Substrate • Active site • Coenzyme • Vitamins • NAD+ and NADH • FAD and FADH2 • TPP • Biotin • PLP • Coenzyme B12 • THF • Vitamin KH2