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y:\files\classes\Organic Hunger Games\Bio-Org Game newer.doc
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
N
NN
N
NH2
O
OHOH
HH
HH
P
O
O
OP
O
OP
O
O
O O
CH2O=
ATPOP
O
O
O
simplified structure actual structure
2. NAD+ and NADP+ - nicotinamide adenine dinucleotide (hydride acceptor)
N
NN
N
NH2
O
OHOH
HH
HH
P
O
O
OP
O
OH2C
O
CH2O
=
O
OH HO
N
CONH2
N
R
NADP+ has a phosphate here.
actual structure
simplified structure
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3. NADH and NADHP - nicotinamide adenine dinucleotide (hydride donor)
N
NN
N
NH2
O
OHOH
HH
HH
P
O
O
OP
O
OH2C
O
CH2O
O
OH HO
N
CONH2
N
R
NADPH has a phosphate here.
HHHH
=
simplified structure
4. Vitamin B-6 – pyridoxal phosphate (amino acid metabolism, transamination with -ketoacids, decarboxylation, removal of some amino acid side chains, epimerizations)
NH2
N
H
O
N
H
H
simplified structure
actual structure
1o amine version of Vit B-6 aldehyde version of Vit B-6
NH2
N
H
O3POO
H
simplified structure
actual structure
O
N
H
H
O3POO
H
-2
interconvert via imine, tautomers, hydrolysis
-2
==
5. TPP – Thiamine diphosphate (decarboxylation and enamine chemistry with proton or carbohydrates)
N
N
NH2
P
O
O
OP
O
O
O
CH2OS
N
HS
N
H
R
actual structure
simplified structure
B
S
N
R
ylid formof TPP
=
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6. Coenzyme A (acyl transfer)
O P
O
O
O P
O
O
OO
HOOH
N
N
NN
NH2
OH
O
NH
O
NH
S
Thiol esters form here.O
S
simplified structure of acetyl Co-A
All of this is "Co-A"
actual structuresimplified
structure of CoA
This is an acetyl group
H
CoAH
SCoA
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.)
N
N
NH
N
O
O
OH
HOOH
O P
O
O
O P
O
O
O
O
HOOH
N
N
NN
NH2
FAD - flavin dinucleotide (a hydride acceptor)
actual structure
simplified structures for FAD and FADH2
N
N
FAD FADH2
N
N
H
H
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N
N
FADflavin dinucleotide
(a hydride acceptor)
BH
FADH2flavin dinucleotide(a hydride donor)
Hydride transfer reduces FAD to FADH2 which can be oxidized to FAD.
BH
C CC
H
C
H
N
N
H
H
B
C
H
C
H
B
N
N
8. THF – tetrahdrofolate (transfer of one carbon units) –recycles cysteine to methionine and other 1C metabolic functions, many variations
NH
N
N
N
O
H2N
R
H
HN
O
HN
CO2
CO2
Tetrahydrofolate (THF)one carbon transfers as "CH3", "CH2".
H
One carbon groupscan bond here in various ways (see below structures.simplified
structure
actual structure
NH
HNAr
N
RV22-p762
5
10
One glutamate is shown, but severalcan be attached.=
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=
N
HNAr
N
Rdifferent forms
CH3
N5-methyl THF
N
NAr
N
R
5
10
N5,N10-methylene THF
H2C
N
NAr
N
R
5
10
N5,N10-methenyl THF
HC
NH
NAr
N
R
5
10
N10-formyl THF
O
H
N
HNAr
N
R
5
10
N5-formyl THFH O
N
HNAr
N
R
5
10
N5-formimino THF
H NH
THF
glycineor
serine
NAD+
NADH
NADP+
NADPH
+H2O
-H2O
+H2O-H2O+NH3
-NH3
histidine
THF
THF
HCO2ATP
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).
O
OH
NH2
S
CH3
O N
OHHO
N
NN
NH2
SAM = S-adenosylmethionine
RmetS
Rad
CH3
methionine
adenosinesimplified structure actual structure
SAM = S-adenosylmethionine
=
leaving group was triphosphate
Rmet = methionineRad = adenonine
O
OH
NH2
S
CH3
O N
OHHO
N
NN
NH2
OP
OP
OP
O
O O O O O O
methionineATP
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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.
Fe
N
N
N
N
HO2C
CO2H
N
N
N
N
Fe+3
simplified structure
+3
Enz
S S
Enz
N
N
N
N
Fe
heme, protoporphyrin IX, found in cytochrom P-450 oxidative enzymes
simplified structure
Oxidations in the body often use cytochrom P-450 enzymes.
simplified structure
Fe
O
+4 Fe+3
This is the structure that we will use.
11. Halogenase Enzymes (related to cytochrom P-450 enzymes, can have imidazole ligands from histadine amino acids
Cl
Fe+3
NCl
N
N
N
Fe+4
Halogenations in the body often iron halogen bonds.
simplified structure
Fe
O
+4 +3
This is the structure that we will use.
N
N
N
His
His
His
ON
N
O
Cl Fe
OH
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,
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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. Nature uses simple strategies applied to limited classes of molecules (carbohydrates, lipids, fats, steroids, amino acids, nucleic acids, neurotransmitters, alkaloids, terpenoids and more) having enormous variation of patterns. It’s amazing what you can speculate upon using these few reactions.
An example of mechanistic simplification.
An “organic” arrow pushing mechanism, showing keto enol tautomerization in acid, is shown without simplification, having all of the normal mechanistic details (lone pairs, formal charge, resonance, etc.). We won’t do it this way in the Bio-Org game.
C
O
CH C
O
CH
H
C
O
CH
H
resonance
C
O
C
H
B
A complete organic mechanism shows lone pairs, each individual step and resonance structures.
BH
The same mechanism in the Bio-Organic Mechanism Game is shown in the first “biochem” example, using the simplified mechanistic conventions of this game.
1. Keto / enol tautomerization (two proton transfers and a shift of pi electrons).
C
O
CH
B
= general base,possibly on enzyme
= general acid, possibly on enzyme
B
C
O
C
H
keto tautomer enol tautomer
BBH
BHBH
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C
O
C
H
enol tautomer
C
O
CH
keto tautomer
B
B
BH
BH
Quite often in biochemistry the acid and base functions are a cooperative action in the active site of an enzyme, much in the manner used in this Game. This avoids the necessity of very strong acid or very strong base, often used by chemists in their reactions. Such conditions are not tolerated by living organisms. We arbitrarily use neutral base, B: and cationic acid H-B+.
2. Carbonyl hydration – a regioselective addition reaction of H2O to a carbonyl group. This also requires some proton tranfers. A carbonyl hydrate can be dehydrated via an elimination reaction which also requires some proton transfers. These steps are very similar to hemiacetal/hemiketal reactions (Example 6), but use H-O-H instead of R-O-H. The carbonyl hydrate can be used to oxidize an aldehyde (example 8) or allow a reverse aldol reaction (example 3).
C
O
aldehyde or ketone carbonyl hydrate
B
Forward Direction
O H
H
hydration
C
O
H
OH
B
(addition reaction)
B H BH
Reverse Direction
carbonyl hydrate
C
O
H
OH
BH
B
dehydration
C
O
aldehyde or ketone
B
O H
H
(elimination reaction)
B H
3. Aldol reactions make a new carbon-carbon bond, forming a -hydroxycarbonyl compound. A
carbonyl C position becomes the nucleophile (as enol or enolate) and reacts with a separate electrophilic carbonyl carbon. Reverse aldol reactions cleave the C-C bond, leaving the electrons on a C position and forming a C=O at the C-OH position. The aldol product can proceed on an additional step as shown in Example 5 (reverse Michael ,-unsaturated carbonyl compounds)
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C
O
B
carbonyl electrophile
C
O
CH
carbonyl nucleophile at C position
C
OH
CC
O
B
-hydroxycarbonyl
This product also looks like a Michael reaction. See Example 5.
aldol(addition reaction)
B H BH
Forward Aldol
C
OH
CC
O
B
-hydroxycarbonyl
C
O
C
O
CH
B reverse aldol(elimination reaction)
BH B HReverse Aldol
4. Claisen reactions make a new carbon-carbon bond, forming -ketocarbonyl compounds. A
carbonyl C position becomes the nucleophile (as enol or enolate) and reacts with a separate electrophilic carbonyl carbon (similar to Example 3, except carbonyl substitution occurs instead of carbonyl addition). Ester groups are common in organic chemistry and thiol ester groups (acetyl Co-A) are common in biochemistry. Reverse Claisen reactions cleave the C-C bond leaving the electrons on the C position and forming a carboxyl at the C=O position. The tetrahedral intermediate is omitted in the Bio-Organic Game.
C
O
OR
B
carbonyl electrophile with a leaving group, (often and ester or thiol ester or a mixed anhydride)
ORC
O
CH
carbonyl nucleophile
C
O
CC
O
OR
B
-ketocarbonyl
R OH
Claisen (acyl substitution)
alcohol or thiol ester or
thiol ester
BHBH
Forward Claisen
C
O
CC
O
OR
B
R OH B
ORC
O
CH
C
O
OR
-ketocarbonyl
carbonyl electrophile with a leaving group,(often and ester or thiol ester)
reverse Claisen (acyl substitution)
alcohol or thiol
ester or thiol ester
BH
BH
Reverse Claisen
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5. Reverse Michael reaction (elimination = dehydration) eliminates H2O between the C-C bonds (E1cB mechanism). Dehydration carries the aldol (Example 3) one step farther along, forming ,-unsaturated carbonyl compounds. Michael reaction (addition / hydration) is the reverse reaction and adds the elements of water across the C=C, a resonance extension of the C=O. We have taken liberties with the name “Michael”. It is probably better to describe these reactions as conjugate addition and reverse conjugate addition. A close variation of this reaction eliminates alcohols instead of water. Other possibilities also exist.
C
OH
CC
O
B
-hydroxycarbonyl
C
O
CC
BH -unsaturated carbonyl
(Michael acceptor)
reverse Michael reaction
OH
H
(elimination)
B H
BH
Reverse Michael Reaction
Reverse Michael Reaction
C
O
CC
-unsaturated carbonyl (Michael acceptor)
OH
HB
C
O
CC
O
H
H
-hydroxycarbonyl B
This product looks like an aldol product. See Example 3. It is now able to do a reverse aldol, or be oxidized to a 1,3-dicarbonyl, maybe followed by decarboxylation, etc.
Michael reaction
(addition)
BH
B H
6. Hemiacetal (or hemiketal) formation is an addition reaction to a carbonyl by alcohol, similar to
carbonyl hydration and dehydration, Example 2. The reverse reaction reforms the carbonyl group and alcohol in an elimination reaction., A second alcohol can react with the hemiacetal/ketal and undergo an SN1 reaction with the OH to form an acetal or ketal (Example 7, just below). The example shown here is an intramolecular reaction and typically forms rings of 5 or 6 atoms.
C
OH
C
O
aldehyde or ketone
B
OO
H
hemiacetal / hemiketalalcohol
Forward Direction
addition reaction
B
BHB H
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OO
H
hemiacetal / hemiketal
B
C
OH
C
O
alcohol aldehyde or ketone
Reverse Direction
elimination reaction
BB HBH
7. Acetal (or ketal) formation from a hemiacetal (or hemiketal). The “OH” becomes a water
molecule leaving group that is replaced by an “OR” in an SN1 reaction, producing an ether linkage. In the reverse reaction (acetal or ketal forming a hemiacetal or hemiketal) an alcohol leaving group is replaced by a water molecule in an SN1 reaction. These are reversible reactions that require acid catalysis. Because arrows are used in both directions on the same bonds, we show the intermediate in this example. These reactions often occur when one sugar molecule “OH” connects to another sugar molecule at its hemiacetal site (such as galactose + glucose = lactose). Such linkages can go on for hundreds of sugar molecules (glycogen in animals and cellulose in plants).
OO
H
hemiacetal / hemiketal
O H
HB
O
OH R
intermediate
Forward Direction
OO
R
acetal / ketal
addROH
eliminate H2O
B H
OO
R
acetal / ketal
O
intermediate
O H
H B
OO
H
hemiacetal / hemiketal
Reverse Direction
eliminate ROH
addH2O
B H B H
8. a. Oxidation of CH(OH) to C=O (1o ROH aldehyde, 2o ROH ketone, hydrated aldehyde
carboxylic acid) with an equivalent of NAD+. NAD+ accepts a hydride via conjugate addition, quenching the positive charge on the nitrogen and forms NADH. A base removes a proton from the adjacent oxygen atom allowing an elimination reaction to produce the C=O (or in Example 9, a C=N).
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1o or 2o alcohol aldehyde or ketone
oxidation of an alcohol
B
C
OH
H N
H
R
NAD+
equivalent
C O
N
H H
R
NADHequivalent
elimination reaction
B H
b. Reduction of C=O to CH(OH) with an NADH equivalent is the opposite of the above reaction. NADH is a hydride donor that becomes aromatic (forms NAD+) with the transfer of the nucleophilic hydride to the electrophilic C=O. A nearby acid protonates the oxygen completing the addition reaction.
aldehyde or ketone
C
O
N
H H
R
NADHequivalent
reduction of a carbonyl
N
H
R NAD+
equivalent
C
O H
H
B
1o or 2o alcohol
additionreaction
B H
9. a. Oxidation of an amine, CH(NHR), to imine (C=N-R) with an NAD+ equivalent that is reduced
to NADH, followed by hydrolysis to a C=O. This is the opposite of 9b, below. The first step is similar to reaction 8a above with an alcohol. Overall, this is a transformation of an amine into a carbonyl group and a primary amine.
amine imine
oxidation of an amine
C
NH
H N
H
R NAD+
equivalent
C NN
H H
R NADHequivalent
R
R
Oxidation of an amine
elimination reaction
B
BH
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Hydrolysis of an imine
C
NR
imine
O H
HB
C
N O
HH
R
aminal
B
C
ONR
H
H
B
aldehyde or ketone
additionreaction
elimination reaction
B HB H
BH
b. Formation of an imine, C=N-R, from a C=O, followed by reduction to CH(NHR) (an amine) with an NADH equivalent that is oxidized to NAD+. This is the opposite of 9a, above. The second step is similar to reaction 8b above with an alcohol. Overall, this is a transformation of a carbonyl group into an amine.
Formation of an imine
C
N O
HH
R
aminal
C
ONR
H
H
aldehyde or ketone
BB
C
NR
O H
H
B
imine
additionreaction
elimination reaction
BH BHBH
amineimine
reduction of an imine
B
C
N
H
H
N
H
R
NAD+
equivalent
C
N
N
H H
R NADHequivalent
R
R
Reduction of an imine
additionreaction
B H
10. Decarboxylation of a -ketocarboxylic acid, forming an enol, which tautomerizes to a keto group.
C
O
C
H
enol tautomer
C
O
CH
keto tautomer
B
BC
O
CC
-ketocarboxylic acid
O
O
C
O
O
carbon dioxide
decarboxylation tautomers
HB BH
BH
BH
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11. Decarboxylation of an -ketocarboxylic acid with TPP (thiamine diphosphate). Also includes
both “TPP ylid” and “TPP enamine” chemistry. The enamine can be protonated to form an aldehyde or it can react with another carbonyl compound to make a new carbon-carbon bond (a larger carbohydrate in this game) The TPP ylid is also regenerated, which can react again or protonate to make TPP. See another reaction of -ketocarboxylic acids with Vit B-6 in Example 13.
S
N
H
R
B
pKa 18
S
N
R
TPP ylid-ketoacid
C O
CO
OH
R
S
N
C
R
OH
R
C
O O
S
N
C
R
OH
R
TPP enamine
TPP reaction with an a-ketoacid, decarboxylation and formation of enamine.
decarboxylation(-CO2)
H B
TPP TPP ylid addition to a carbonyl
BH
Reaction of enamine nucleophile with a carbonyl electrophile followed by an E2-like reaction to from a new (larger) carbohydrate.
S
N
C
R
OH
R
C
O
H RS
N
C
R
OH
R
C
OH
R
H
B
S
N
R
CR
O
CH
OH
CH
OH
R
TPP ylid
a new (larger) carbohydrate
TPP enamine reaction with C=O
TPP enamine addition to a carbonyl
elimination reaction forms a carbonyl group, similar to a reverse aldol
BH
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Reaction of enamine nucleophile with an acid to from a new (smaller) carbohydrate.
S
N
C
R
OH
R S
N
C
R
OH
R
B
S
N
R
CR
O
H
TPP ylida new (smaller) carbohydrate
H
TPP enamine reaction with a proton
elimination reaction forms a carbonyl group, similar to a reverse aldol
acid/baseprotonation of TPP enamine
BH
12. a. Phosphorylation of an OH with an ATP equivalent (making an inorganic phosphate ester).
C O
H
P
O
O
O
O P
O
O
O P
O
O
O ATP
B
BH
O P
O
O
O P
O
O
O ADP
C O P
O
O
O
Mg+2
Complexing with Mg+2 can make one phosphorous atom more electrophilic and the other one a better leaving group. The Mg+2 is not required to show this reaction. Mg+2 is not used in the other reactions below, but it could be.
Mg+2 acyl-like substitution reaction
inorganic phosphate ester
ADP = leaving group
b. Dephosphorylation of an inorganic phosphate ester to an alcohol and phosphate.
C O P
O
O
O
B
OH
H
B H
C O P
O
O
OH
O
H
B
acyl-like substitution reaction
inorganic ester hydrolysis
B H
c. An elimination reaction of a phosphate leaving group to make an alkene (pi bond). Could actually be E1 or E2.
CC
H
OP
O
O
O
B
H
CC
OP
O
O
O
H
E1 or E2 (anti) mechanismsare possible
B H
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d. acyl phosphate (inorganic anhydride) and formation of a thiol ester (like acetyl Co-A)
C O
H
P
O
O
O
O ATP
B
O P
O
O
O P
O
O
O ADP
C O P
O
O
O
Mg+2
acyl-like substitution reaction
O
H3C
O
H3C
organic-inorganic anhydride
Co-A S
HB
acyl-like substitution reaction
O
SCo-A
very reactive thiol ester(acetyl Co-A)
O P
O
O
O
ADP leaving group
phosphate leaving group
Mg+2
Mg+2
BH
13. Vit B-6 reactions – 1. imine formation with -keto acid and the amino version of Vit B-6 (similar
to Example 9b), 2. tautomerization (Example 1) and 3. imine hydrolysis to amino acid and the aldehyde version of Vit B-6 (similar to Example 9a).
N
N
H vitamin B-6(1o amine version)
H
B
BHdehydration (-H2O)
iminesynthesis
H
B
OH
OO
R
-keto acid
N
N
H
H
R
OH
O
OH
N
N
H
R
OH
O
HO
HSimilar to Example 9b.
B H
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N
N
H
R
OH
O
keto / enol tautomerization, makes imine on the other side
H
HB
N
N
H
R
OH
O
H
Similar to Example 1.
B H
addition of water
HO
H
B
hydrolysis of imine
N
N
H
R
OH
O
H
N
N
H
R
OH
O
HH
O
H
B
N
H2N
H
R
OH
O
H
O H
vitamin B-6(aldehyde version)
-amino acid
Similar to Example 9a.
BHBHH
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Three additional vit B6 reactions from aromatic imine 1. Decarboxylation
decarboxylation
N
N
H
O
O
H B
R H
N
N
H
R
H
CO O
BH
N
N
H
R
HH
HO
H
B
BHH
N
N
H
R
O
H H
BBH
N
N
H
R
O HH
H
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2. Elimination of side R group, like serine or threonine.
decarboxylation
N
N
H
O
vitamin B-6(aldehyde version)
H B
N
N
H
CO2H
H2C O
BH
N
N
H
CO2H
HO
H
B
BHH
N
N
H
CO2H
O
H H
BBH
N
N
H
CO2H
O HH
H
CO2H
serine aa
glycine aa
vitamin B-6(imine version)
also threonine aa
N
N
H
OH
CO2H
N
CO2H
H
H
glycine aa
H
O
3. Epimerize a proton at the C position of an amino acid.
N
N
H
B
N
N
H
CO2H
BH
CO2H
S amino acid
vitamin B-6(imine version)
R
H
R
N
N
H
CO2H
H
RR amino acid
vitamin B-6(imine version)
proton adds on the opposite face
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14. FAD / FADH2 reduction of C=C to CH-CH or the reverse reaction oxidation of CH-CH to a C=C, FAD can be recharged with NADH.
N
N
H
H
FADH2
BH
B
Simplified mechanism of action for reduction of C=C by FADH2 FAD and mechanism for reforming FADH2 from NADH.
N
N
FAD
R
O
SCoA
R
O
SCoA
HH
H H
B H
B
R
N
HH
R
N
N
N
FADB H
N
N
H
H
FADH2
NAD+NADH
FAD - flavin dinucleotide (a hydride acceptor) used
to reoxidize fats for energy.
CC
O
SEnzC
R
H H
HH
FADH2 - flavin dinucleotide
(a hydride donor)
B
A saturated fatty acid chain.
CC
O
SEnzC
R
H
H
An ,-unsaturated fatty acid chain.
BH
N
N
N
N
H
H
FADH2
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15. Cytochrom P-450 oxidation of sp3 C-H bonds to make sp3 C-OH groups
The free radical-like oxygen atom abstracts a hydrogen atom from a C-H bond in the enzyme cavity, forming an O-H bond and a carbon free radical.
CCO
H
Fe +4
O CH
Fe +4
OH
The carbon free radical abstracts hydroxyl (OH) from iron, making an C-OH bond where a C-H bond had been. The iron is reduced back at Fe+3 to begin the process all over again.
Fe +3
sp3 C-H bonds alcohols
89
16. Cytochrom P-450 oxidation of C=C pi bonds (alkenes and aromatics) to make epoxides, which can
be opened to diols.
The free radical-like oxygen atom adds to a C=C bond (alkene or aromatic) in the enzyme cavity, forming a O-C bond and a carbon free radical.
Fe +4
O
Fe +4
O
The carbon free radical abstracts the oxygen atom from the iron, making an epoxide ring. The iron is reduced back at Fe+3 to begin the process all over again. Reactiveepoxides can be opened up to diols (more water soluble).
Fe +3
CC
O
R
RRR
epoxides
C C
R
R
R
R
CR
R
C
R
R
17. Cytochrom P-450 oxidation of sulfur and nitrogen lone pairs.
R
SR
sulfursubstrate
(1e-)
R
SR
sulfursubstrate
S
RR
O
sulfoxides, further oxidation is possible, all the way to sulfate, SO4
-2
R
NR
N
RR/H
O
N-oxides, further oxidation is possible, all the way to nitrate, NO3
-1
R
NR
nitrogensubstrate
(1e-)
R/H R/H
R
Fe +4
O
Fe +4
OFe +3
Fe +4
O
Fe +4
O Fe +3nitrogensubstrate
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18. Halogenation of sp3 C-H bonds to make C-X groups (X = Cl, Br, I) using halogenase enzymes.
The free radical-like oxygen atom abstracts a hydrogen atom from a C-H bond in the enzyme cavity, forming an O-H bond and a carbon free radical.
C
C Cl
Fe +5
O CH
Fe +5
OH
The carbon free radical abstracts a halogen (Cl or Br) forming an unusal halogenated bioorganic molecule.
sp3 C-H bonds
Cl ClFe
OH
+4
19. Halogenations of aromatic rings using X-OH to make sp2 C-X bonds (like thyroxine).
OOH
HI
BH
IO
H
HO
H
B
P
O
O
O
O ATP P
O
O
O
O
I
possibly an even better leaving group
Iodide is stored in the thyroid gland. Iodoperoxidase enzyme makes it electrophilic (instead of nucleophilic iodide). It could react as hypoiodous acid, or the oxygen could be made into an even better leaving group if was a phosphate (using ATP).
a good leaving group on iodine
CO2H
OH
tyrosine
NH2
IO
H
CO2H
OH NH2
I
H
B
CO2H
OH NH2
ICO2H
OH NH2
I
repeat
I
Speculative mechanism for iodinating tyrosine and formation of thyroxine from two tyrosines.
diiodotyrosine - makes thryoxine
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20. S-adenosyl methionine (SAM-e) to methylate biomolecules.
N
N
O
NH2
H1
2
34
5
6
cytosine
Rmet
S
Rad
CH3
H
N
N
O
NH2
H
H
H3CB
N
N
O
NH2
H3C
H
5-methylcytosine
21. Anti-oxidation reactions using vit E (fat soluble), vit C (water soluble), (also possible are
glutathione, resveratrol and other bio-antioxidants).
free radical protection by vitamin E (possibly in cell membrane)
R
O
ROH
vitamin E located in cell membranes quenches radicals
OR
ROH
OR
ROH
O
O
O
O
H
H R
OR
ROH
vitamin E is recharged and still in cell membrane
O
O
O
O
H
H R
O
O
O
O
H
H
O
O
O
O
H
RR
R
Bprotects a second time
O
O
O
O R
oxidized vitamin C form washes out of the body
R R H
H B
reduced radical neutralized by body's buffer system
resonance and inductive effects stabilize radical so it does not do damage
vitamin C reduces vitamin E back to normal and ultimately washes out of the body
B
R
possible dangerous free radical reduced by vit E
R R H
H B
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other possible anti-oxidants OH
OH
HO
N
O
SH
N
O
O
OH
NH2 O
OH
glycinecysteineglutaric acid ( linkage)
glutathione
resveratrol
H
H
3 types of problems are possible 1. Fill in the missing mechanistic details. 2. State what transformation occurred (and provide the missing mechanistic details). 3. Given the term, draw the step (and provide the missing mechanistic details). Summary of Biochemical Topics having examples provided above:
1. Keto/enol tautomerization (proton transfer, resonance, proton transfer).
2. Carbonyl hydration (addition reaction of H2O to a C=O) / carbonyl hydrate dehydration (elimination reaction forms a C=O and H2O).
3. Aldol (makes a -hydroxy carbonyl compound). Reverse aldol, (makes 2 C=O from a -hydroxy carbonyl compound).
4. Claisen (makes a -keto ester). Reverse Claisen (makes two esters). Often occurs using thiol esters in biochemistry (such as acetyl Co-A).
5. Reverse Michael reaction (elimination / dehydration) of -hydroxy carbonyl compounds, an elimination reaction forms ,-unsaturated carbonyl compounds and carries an aldol reaction one step farther. Michael reaction (addition / hydration) adds a nucleophile at the beta carbon of an ,-unsaturated carbonyl compound (usually OH in this game) and adds a proton at the alpha carbon.
6. Hemiacetal (or hemiketal) formation (an addition reaction) of an alcohol to a C=O, forms an ether and an alcohol group on the same carbon. The reverse reaction reforms the carbonyl and alcohol from an elimination reaction. Typical ring sizes in the intramolecular reaction are 5-6 atoms. These transformations are very similar to carbonyl hydration / dehydration, presented in example 2 above.
7. Acetal (or Ketal) formation from a hemiacetal (or hemiketal) makes a water molecule leaving group that is replaced by an alcohol in an SN1 reaction, producing a second ether linkage. In the reverse reaction (acetal or ketal forming a hemiacetal or hemiketal) an alcohol leaving group is replaced by a water molecule in an SN1 reaction. Both are reversible reactions. Because arrows are used in both directions on the same bonds, we show the intermediate in this reaction.
8. a. Oxidation of CH(OH) to C=O with an NAD+ equivalent, which is reduced to NADH (opposite of 8b, below).
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b. Reduction of C=O to CH(OH) with an NADH equivalent, which is oxidized to NAD+ (opposite of 8a, above).
9. a. Oxidation of an amine, CH(NHR), to C=N-R (an imine) with an NAD+ equivalent which forms NADH, followed by imine hydrolysis to a C=O (opposite of 9b, below). b. Formation of an imine, C=N-R, from a C=O, followed by reduction to CH(NHR) (an amine) with an NADH equivalent which forms NAD+ (opposite of 9a, above).
10. Decarboxylation of a -ketocarboxylic acid, liberates CO2 and forms an enol which tautomerizes to a keto group.
11. Decarboxylation of an -ketocarboxylic acid with TPP (thiamine pyrophosphate = diphosphate). The “TPP ylid” adds to an -keto group, liberates CO2 and becomes a “TPP enamine”, which can protonate or react with a C=O of another carbohydrate.
12. a. Phosphorylation of an OH with an ATP equivalent (making a phosphate ester) – common in enzyme signaling b. Dephosphorylation of a phosphate ester to an alcohol and phosphate – common in enzyme signaling c. Making an alcohol OH into a phosphate ester makes it a better leaving group. An elimination (E1 or E2) or substitution (SN2) reaction with a phosphate leaving group is possible. d. Formation of acyl phosphates (mixed anhydrides) also allows for exothermic carbonyl substitution reactions (can make thiol esters).
13. Vit B-6 reactions – Many reactions are possible. The only example shown is 1. imine formation with an -keto acid and the primary amine version of Vit B-6, 2. tautomerization to a different imine, and 3. imine hydrolysis to an amino acid and the aldehyde version of Vit B-6. The imine complex also allows for the loss of various groups on amino acids (the acid part, CO2H, an alpha C-H proton, and certain amino acid side groups, -CH2OH in serine, and -CHCH3OH in threonine). Imines are also seen in Example 9 and -keto acids in Example 11.
14. FAD / FADH2 reduction of C=C to CH-CH or the reverse reaction oxidation of CH-CH to a C=C, FAD can be recharged with NADH.
15. Cytochrom P-450 oxidation of sp3 C-H bonds to make sp3 C-OH groups.
16. Cytochrom P-450 oxidation of C=C pi bonds (alkenes and aromatics) to make epoxides, which can be opened to diols.
17. Cytochrom P-450 oxidation of sulfur and nitrogen lone pairs.
18. Halogenation of sp3 C-H bonds to make C-X groups (X = Cl, Br, I) using Fe halogenase enzymes.
19. Halogenations of aromatic rings using X-OH to make sp2 C-X bonds (X = Cl, Br, I) (thyroxine).
20. S-adenosyl methionine (SAM-e) to methylate biomolecules.
21. Anti-oxidation reactions using vit C, vit E, resveratrol, glutathione, and other bio-antioxidants.
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Many of the steps of biochemical cycles can be explained with the above reactions. Problem – Use B-H+ / B: and any necessary cofactors to accomplish the following transformations using simplistic mechanisms (you do not need to show lone pairs of electrons and you can combine multiple steps using several arrows). 1.
O O
O O
O
O
O
reverse aldol
reverse those steps, do a forward aldol
(acyl substitution reaction)
(acyl substitution reaction)
HHHH
H H
2.
O O
O O
O
O
OHHHH
H H
hemiacetal formation6 atom ring
reverse that reactionback go a carbonyl and an alcohol
(addition reaction)
(elimination reaction)
3.
O O
O O
O
O
OHHHH
H H
reverse Michael(dehydration)
forward Michael(hydration)
(elimination reaction)
(addition reaction)
4.
O O
O O
O
O
OHHHH
H H
keto/enol tautomerizationto form an aldehyde
carbonyl (hydration)
(addition reaction)
(twice)
5.
O O
O O
O
O
OHHHH
H H
keto/enol tautomerizationto form a new ketone
hemiacetal formation5 atom ring
(twice) (addition reaction)
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6. OH
OH
OH
OH
O keto/enol tautomerizationto form a beta keto acid
decarboxylationOH
NAD+
oxidation
keto/enol tautomerizationto form an aldehyde
carbonyl (hydration)
(addition reaction)
(elimination reaction)
7. OH
OH
OH
OH
O keto/enol tautomerizationto form an alpha keto acid
reaction with TPP ylid
OH
elimination reaction to form new 6C carbohdrate and TPP ylid
decarboxylationto TPP enamine
TPP enamine reaction with 2C carbohydrate
O
H
OH
(addition reaction)
(addition reaction)
8. OH
OH
O Oreverse Claisen
forward Claisen
OR
(acyl substitution reaction)
(acyl substitution reaction)
9. OH
OH
OH ONADH reduction
H
OH
NAD+
oxidation to an aldehyde
(addition reaction) (elimination
reaction)
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10. acetal formation (2 steps)
O
OHO
HO OH intermediate overall = SN1
(elimination reaction)
(addition reaction)
H
OH R
11. O
OHO
HO OH intermediate overall = SN1
(elimination reaction)
(addition reaction)
R
OH H
acetal hydrolysis to hemiacetal (2 steps)
12. Vit B-6 imine formation(2 steps)
O
OH
O
(addition reaction)
(elimination reaction)
13.
keto/enoltautomerization to new imine
O
OH
N
N
H
hydrolysis of imine to amino acid and the aldehyde version of Vit B-6 (2 steps)
(addition and elimination reactions)
14.
O
H
OH
imine formation (2 steps)
OHN R
H
H NADH reduction to an amine
(addition and elimination reactions)
(addition reaction)
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15.
N
H
OH
imine hydrolysisto an aldehyde (2 steps)
OH NAD+
oxidation to an imine
R H
(elimination reaction)
(addition and elimination reactions)
16.
P
O
O
O
O PP ATPO
OH
phosphorylation of 3o alcohol withATP
H
(acyl-like substitution reaction)
17.
O
OH
P
O O
O
H
elimination reaction to form an alkenealcohol (show as an E2 reaction)
18.
O
OH
P
O O
O
H
hydrolysis of phosphate ester to di-alcohol
(acyl-like substitution reaction)
19.
P
O
O
O
O PP ATP
formation of mixed anhydride
O
OH
(acyl-like substitution reaction)
20. O
SCo-AH
Claisen condensation
O
OP
OO
OH (acyl-like substitution reaction)
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21. O
SCo-A
O NADH reduction of keto group
(addition reaction)
22.
O
SCo-A
Oreverse Michaelreaction
H
(elimination reaction)
23.
O
SCo-A
NADH hydride reduction of the conjugated C=C by a Michael reaction
(addition reaction)
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Methylates choline, norepinephrine, DNA (epigenetics) Biotin (carboxylations) Lipoic acid (acyl transfer) Possible reactions Aldol reverse Aldol
Hemi-acetal formation reverse hemi-acetal reaction (includes ketal reactions)
Acetal formation reverse acetal reaction (includes ketal reactions)
Michael reaction reverse Michael reaction
Carbonyl hydration reaction carbonyl dehydration reaction
Tautomeric changes (keto enol and/or enol keto) (enamine chem.?)
DNA / RNA base synthesis and degradation
Additional possibilities???
Enamine chemistry
Imine chemistry
Amine oxidation to carbonyl
Phosphate ester / anhydride synthesis and hydrolysis (tyrosine, serine, ATP, throxine, etc.)
xxxxxxxxxx
Lipid chemistry – glycerol esters, ethers, phosphates, carbohydrates
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C
OH
C
OB
aldehyde or ketone
B BH
OO
H
hemiacetal / hemiketalalcohol
B H
O H
HB
O
OH R
intermediate
OO
R
acetal / ketal
B H B
O
intermediate
O H
H B
OO
H
hemiacetal / hemiketal
BB H
C
OH
C
O
alcohol aldehyde or ketone
Forward Direction
Reverse Direction
loseROH
addH2O
BH
OO
R
acetal / ketal
addROH
loseH2O
C
OH
C
OB
aldehyde or ketone
B BH
OO
H
hemiacetal / hemiketalalcohol
B H
O H
HB
O
OH R
intermediate
OO
R
acetal / ketal
B H B
O
intermediate
O H
H B
OO
H
hemiacetal / hemiketal
B
B H
C
OH
C
O
alcohol aldehyde or ketone
Forward Direction
Reverse Direction
loseROH
addH2O
BH
OO
R
acetal / ketal
addROH
loseH2O
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Problem - What kind of reaction occurred in each part? Use a simplistic mechanism to show how the reaction could have proceeded. The following problems are more limited questions from the original “carbohydrate game” and do not include many of the biochemical “co-factors”.
O
OH OHOH
OH
1 ?
O
OH OHOH
O
H
O
OH OH OH
O
H
OH
2 ?
O
OHOH OH
OH OH
O
OHOH OH
OH OH
3 ?
OOH
OH
OHHO
HO
O
OHOH OH
OH OH
4 ?
O
OH
OH
OHHO
HO
O
OH
OHHO
HO 5 ?
O
OH OHOH
OH
O
OHOH OH
OH OH O
OHOH OH
OH
6 ? 7 ?
O
OOH OH
OH O
OOH O
OH
H8 ?
9 ?
10 ?11 ?
OH
OO
H12 ?
O
OHO
H
(2 steps)
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O
OHOH OH
OH OH
13 ?
OH
OOH OH
OH OH
(2 steps)
14 ?
OH
O OH
OH OH
2rotations
O
H
OH
O
HO
15 ?
OOH
OH
O
HO
O
H
HO
O
OH
OH
O
H
HO
O
O
OHO
H
HO
O
O
16 ?17 ?18 ?
1. reverse aldol
2. forward aldol
3. hemi-ketal formation to 6 atom ring
4. reverse of hemi-ketal to 5 atom ring
5. reverse of hemi-ketal to form open chain
6. reverse Michael reaction
7. keto/enol tautomerization
8. reverse aldol
9. keto/enol tautomerization
10. structure shown below
11. keto/enol tautomerization
12. 2 x keto/enol tautomerization
13. 2 x keto/enol tautomerization
14. reverse Michael reaction
15. intramolecular Michael reaction using the OH of an alcohol group16. reverse Michael on the other side of the ring17. keto/enol tautomerization
18. reverse Michael reaction
OH
OH O
enol at both ends of the double bond, can form a carbonyl on either side, one as a ketone and one as an aldehyde
Problem – Use B-H+ / B: to accomplish the following transformation using simplistic mechanisms (you do not need to show lone pairs of electrons and you can combine multiple steps using several arrows).
OH
OHOH O
OH OH
OH
dehydration (reverse Michael)
keto/enol to form1,2-diketo structure
reverse aldol to 3C aldehyde and 4 carbon
2,3-diketo structure
OH
OHOH O
OH OH
OH
dehydration (reverse Michael)
keto/enol to form3,4-diketo structure
reverse aldol to 1C aldehyde and 6 carbon
2,3-diketo structure
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OH
OHOH O
OH OH
OH
hemi-acetal formation to 5 atom ring
acetal formationwith ROH
OH
OHOH O
OH OH
OH
hemi-acetal formation to 6 atom ring
acetal formationwith ROH
OH
OHOH O
OH
OH
H
dehydration to form carbonyl
keto/enol to form2-keto structure
carbonylhydration
O
O
HO
HO
OH
OH
H
hemi-acetalring opening
O
O
HO
OH
Michael addition of water (hydration)
cyclic ester ring opening addition of water (hydration)
OH OH
OH OH
OH
O
OH
reversealdol
forward aldol(reverse step)
OH OH
O OH
OH
O
OH
hemi-ketal formation to 6 atom ring
reverse reaction back tocarbonyl and alcohol
H
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OH OH
O OH O
OH
dehydration (reverse Michael)
hydration(Michael)
H
HO H
OH OH
OH OH O
OHketo/enol
tautomerization(form an aldehyde)
(2 steps)
reversealdol
OH
H
H
OH OH
OH OH O
OHreverse aldol to form a 3 carbon ketone and
4 carbon aldehyde
HO H keto/enoltautomerization(form a ketone)
(2 steps)
OH OH
OH OH O
OH
dehydration of carbonyl hydrate
hydration ofcarbonyl
OH
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A few possible answers OH
OH
OH
O
OH
O
OH
H
reverse aldol
forward aldol(reverse steps)
B BH
OH
OH
OH
O
H
OH
O
OH
H
H
BB H
OH
OH
OH
O
OH
O
OH
H
hemiacetal formation(6 atom ring)
OH
O
OH
OH
OH
O
OH
HO
OH OH
OH
OH
O OHH
B BH
reverse reactionback to carbonyl & alcohol
B
B H
OH
O
OH
OH
OH
O
OH
H
OH
OH
OH
OH O
OHHO H dehydration(reverse Michael)
B
BH
hydration(Michael)
OH
OH
OH
O
OHOH
H OHB
BHOH
OH
OH
OH O
OHHO H
keto/enol tautomerization(form an aldehyde)
OH
OH
OH
OH O
OHOHH
HB
B H
OH
OH
OH
OH O
OOH
H
HB
B H
OH
OH
OH
OH O
OOH
H
HH
hydration of carbonyl
reverse reactiondehydration ofdiol
OH
OH
OH
OH O
OHOH
H OHBB H
OH
OH
OH
OH
OHOH
O
H
OH
BBH
OH
OH
OH
OH O
OHOH
keto/enol tautomerization(form a new ketone)
OH
OH
OH
OH O
OHHO H
B H
B
OH
OH
OH
OH
OHO
H
OH
B
BH
OH
OH
OH
OH
OHO
OH
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Problem - State what type of transformation occurred and show a simplistic arrow pushing mechanism for how it occurred, adding in any B: and/or B-H+ that is necessary. (an older problem set) a.
H
O
OH
OH
OH
OH
H
O
OH OH
OH
H
O
O OH
OH
H
O
O O
OH
H
b.
O
OH OH
OH
OH
O
OH OH
OH
OH
OH OOH
OH
OHHO
HO
c.O
OHOH
OH
OH
OH OH
OHOH
OH
OH
OH
OHOH
OH
O
OH OH
H
d.
e.
f.
g.
h.
OOH
O
OHHO
HOOH
OH
O
OHHO
OH
OH
O
OHHO
OO
O
OHHO
O
O
OH OH
O
OH
H
OHO
HO
OH
OHHO
OH
H
O OOH
OH
OHOH
O
OHOH
OH
OH
OH
O
HOOH
HO OH
HO
O
OHOH
OH
OH
OH
O
HOOH
OH
HO
HO
O
OH
HO OH
HO
OR
OH H
O
OH
HO OH
HOO
R H
intermediate
OH H
OR HO
OH
OH
HO
HO
O
OOH
OH
HO
HO
R
intermediate
O
HOOH
OH
HO
HOO
OOH
OH
HO
HO
R
OR H
O
OH
OH
HO
HO
intermediate
OH H
O
OHOH
OH
OH
OH
O
HO
OH
OH
i.
O O
H
OHOH
OH H
O
H
OHOH
OHHOO O
H
OHOH
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a.
H
O
OH
OH
OH
OH
H
O
OH OH
OH
H
O
O OH
OH
H
O
O O
OH
H reverseMichael tautomerism reverse
aldol
b.
O
OH OH
OH
OH
Michael O
OH OH
OH
OH
OH OOH
OH
OHHO
HOhemi-acetal formation
c.O
OHOH
OH
OH
OH
tautomerism
OH
OHOH
OH
OH
OH
tautomerismOHOH
OH
O
OH OH
H
d.
e.
f.
g.
h.
OOH
O
OHHO
HOOH
OH
O
OHHO
OH
OH
O
OHHO
OO
O
OHHO
O reverseMichael
dehydration tautomerism
O
OH OH
O
OH
H
OHO
HO
OH
OHHO
OH
aldol reverse aldol
H
O OOH
OH
OHOH
O
OHOH
OH
OH
OH
hemi-acetal formation
O
HOOH
HO OH
HO
O
OHOH
OH
OH
OH
hemi-acetal formation
O
HOOH
OH
HO
HO
O
OH
HO OH
HO
OR
OH H
O
OH
HO OH
HOO
R H
intermediate
OH H
OR HO
OH
OH
HO
HO
O
OOH
OH
HO
HO
R
intermediate
acetal formation (2 steps)
acetal formation (2 steps)
acetal formation (2 steps)
acetal formation (2 steps)
O
HOOH
OH
HO
HO
reverse acetal formation (2 steps)
O
OOH
OH
HO
HO
R
OR H
O
OH
OH
HO
HO
intermediate
reverse acetal formation (2 steps)
OH H
reverse hemi-acetal formation
O
OHOH
OH
OH
OH
O
HO
OH
OH
reverse aldol
i.
O O
H
OHOH
OH H
O
H
OHOH
OHHOcarbonylhydration
carbonyldehydration O O
H
OHOH