1. How enzymes catalyze reactions? Organic chemistry of vitamins

2. Book: Bruice
Chapter: 17
Pages:

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 particular amino 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 orientation for reaction.
• Some of the amino acid side chains of the enzyme serve as catalysts. These are positioned relative to the substrate precisely where they are needed for catalysis.
• Amino acid side chains can stabilize transition states and intermediates—by van der 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 to fructose-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-ring sugar
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 a proton 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-carbon compounds
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 bond between C-3 and C-4
3. The enamine intermediate rearranges to an imine, with the tyrosine residue now functioning as an acid catalyst
4. Hydrolysis of the imine releases dihydroxyacetone phosphate, the other three carbon product

11. Coenzymes and vitamins
Coenzymes – enzyme helpers
organic molecules
assist enzymes in catalyzing certain reactions that cannot be 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 function that 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 phosphate metabolism
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 to hold the substrate and coenzyme together so that the oxidation or reduction reaction 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
Heterocyclic compound – 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) is the portion of the coenzyme that the body cannot synthesize and must acquire through the diet

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

19. substrate is being oxidized, it donates a 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 coenzyme to the proper site on the enzyme
basic amino acid side chain of the enzyme can help the oxidation reaction
removing a proton from the oxygen atom of the substrate

20. The mechanism for reduction by NADH is the reverse of the mechanism for oxidation
When a substrate is being reduced, the dihydropyridine ring 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 enzyme aids the reduction reaction by donating a proton to the substrate

21. Niacin deficiency Causes pellagra
Disease that begins with dermatitis and ultimately causes insanity 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 succinate dehydrogenase to oxidize succinate to fumarate
dinucleotide in which one of the heterocyclic compounds is flavin and the other is adenine
instead of ribose, the flavin nucleotide has 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-catalyzed oxidation reactions involving carbonyl compounds
alcohols being oxidized to ketones, aldehydes, or carboxylic acids
FAD - coenzyme used in other types of oxidations

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

26. Example: Pyruvate decarboxylase requires TPP
catalyzes the decarboxylation of pyruvate and transfers the remaining two-carbon fragment to a proton, resulting in the formation of acetaldehyde

27. pyruvate dehydrogenase system - group of three enzymes and five coenzymes
overall reaction catalyzes the decarboxylation of 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 converting them to thioesters
more reactive than are carboxylic acids
pKa of the conjugate acid of the thiol leaving group 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 that live in the intestine
does not have to be included in our diet and deficiencies are rare
can be found in people who maintain a diet high in raw eggs
Egg whites contain a protein that binds biotin tightly and thereby prevents it from acting as a coenzyme
When eggs are cooked, the protein is denatured, 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-CoA carboxylase converts acetyl-CoA into malonyl-CoA
Biotin-requiring enzymes use 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 an aldehyde
deficiency -causes anemia; severe deficiencies can cause seizures and death
PLP - required by enzymes that catalyze certain reactions of amino acids like decarboxylation

32. Vitamin B12 coenzyme B12 Has CN or HO- group coordinated with Cobalt
Humans must obtain all their vitamin B12 from their diet, particularly from 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 reactions that transfer a group containing a single carbon to their substrates
produced by the reduction of two double bonds of folic acid (folate)

35. required for the synthesis of the bases found in DNA and RNA and for 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, is structurally similar to p-aminobenzoic acid
Sulfanilamide acts by inhibiting the enzyme that incorporates paminobenzoic acid 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 of the γ-carbon of glutamate side chains in proteins, forming γ-carboxyglutamates

39. Warfarin (coumadin) and dicoumerol - used as anticoagulants
Prevent clotting by inhibiting the enzyme that synthesizes vitamin KH2 from vitamin K epoxide
enzyme cannot tell the difference between vitamin K epoxide and warfarin (or dicoumerol) - two compounds compete for binding at the enzyme’s active site
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