bio-organic mechanism game

1

C:\Documents and Settings\psbeauchamp.WIN\My Documents\classes\316\special handouts\Bio-Org Game web version.doc

Chem 316 Name ___________________________________ Bio-Organic Mechanism Game – Simplistic Mechanisms for Biochemical Transformations. Mechanism arrows used in the “Bio-Org Game” are meant to suggest how the electrons move over a series of steps and are not meant to imply that all of the electrons and atoms transfer in one huge “domino” cascade. At an enzyme active site something approximating this may occur, though. In organic chemistry the mechanisms are more often multistep 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, 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! 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 fundamental 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. The problems that follow use several “typical” types of biochemical transformations in made-up sequences and even some real biochemical cycles in which to practice. With such practice you can study them in realistic settings and learn to recognize these important transfomations. 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

BH

C

O

CH

H

C

O

CH

H

resonance

C

O

C

H

B

The organic mechanism shows lone pairs, each individual step and resonance structures.

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

BH

B

= general base

= general acid

Quite often in biochemistry the acid and base functions are a cooperative action in the active site of an enzyme. This avoids the necessity of very strong acid or very strong base, often used by chemists in their reactions.

BH

B

C

O

C

H

keto tautomer enol tautomer

C

O

C

H

enol tautomer

C

O

CH

keto tautomer

B

BH

B

BH

BH

B

2


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.

C

O

aldehyde or ketone carbonyl hydrate

B

Forward Direction - hydration of a carbonyl group

Reverse Direction - dehydration of a carbonyl hydrate

B HO H

H

hydration

C

O

H

OH

BHB

carbonyl hydrate

C

O

H

OH

BH

B

dehydrationC

O

aldehyde or ketone

B HB

O H

H

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 (reaction # 8a) or allow a reverse aldol reaction (reaction #3b).

(addition reaction)

(elimination reaction)

3. Aldol reactions make a new carbon-carbon bond, forming a β-hydroxycarbonyl compound. A carbonyl Cα position

becomes the nucleophile (as enol or enolate) and reacts with a separate electrophilic carbonyl carbon. Reverse aldol reactions cleave the Cα-Cβ bond, leaving the electrons on a Cα position and forming a C=O at the Cβ-OH position. The aldol product can proceed on an additional step as shown in Example 5 (α,β-unsaturated carbonyl compounds)

C

O

B

carbonyl electrophile

BHB H

C

O

CH

carbonyl nucleophile at Cα position

Cβ

OH

Cα

C

O

B

β-hydroxycarbonyl

BH

Cβ

OH

Cα

C

O

B

β-hydroxycarbonyl

C

O

C

O

CH

B H B

This product also looks like a Michael reaction. See Example 5.

aldol(addition reaction)

reverse aldol(elimination reaction)

Aldol Reaction

Reverse Aldol Reaction

3


4. Claisen reactions make a new carbon-carbon bond, forming a β-ketocarbonyl compound. A carbonyl Cα 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 Cα-Cβ bond leaving the electrons on the Cα position and forming a carboxyl at the Cβ=O position.

C

O

OR

B

Carbonyl electrophile with a leaving group, (often an ester or thiol ester or a mixed anhydride).

BHBH

ORC

O

CH

Carbonyl nucleophile (often an ester or thiol ester).

Cβ

O

Cα

C

O

OR

B

β-ketocarbonyl

BH

Cβ

O

Cα

C

O

OR

BH

B

R OH B

ORC

O

CH

C

O

OR

β-ketocarbonyl

R OH

The tetrahedral intermediate (TI) is omitted.

The tetrahedral intermediate (TI) is omitted.

Carbonyl electrophile with a leaving group,(often an ester or thiol ester).

Claisen (acyl substitution)

reverse Claisen (acyl substitution)

alcohol or thiol

alcohol or thiol

ester or thiol ester

ester or thiol ester

Claisen Condensation

Reverse Claisen Condensation

5. Reverse Michael reaction (elimination / dehydration) eliminates H2O between the Cα-Cβ bonds (E1cB mechanism).

Dehydration carries the aldol (Example 3) one step farther along, forming α,β-unsaturated carbonyl compounds. Michael reaction (addition / hydration) is the reverse reaction and adds the elements of water across the Cα=Cβ, 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.

BH

C

OH

CC

O

B

β-hydroxycarbonyl

C

O

CC

B H

BH

α,β-unsaturated carbonyl (Michael acceptor)

C

O

CC

α,β-unsaturated carbonyl (Michael acceptor)

OH

HB

BH

C

O

CC

O

H

H

β-hydroxycarbonyl

reverse Michael reaction

B H

B

OH

H

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.

(elimination)

Michael reaction

(addition)

Reverse Michael Reaction

Michael Reaction

4


6. Hemiacetal (or hemiketal) formation is an addition reaction to a carbonyl by an alcohol. It’s 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 BH

OO

H

hemiacetal / hemiketalalcohol

OO

H

hemiacetal / hemiketal

BB H

C

OH

C

O

alcohol aldehyde or ketone

Forward Direction

Reverse Direction

BH

addition reaction

elimination reaction

B HB

B

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


B H

O H

HB

O

OH R

intermediate (resonance)

OO

R

acetal / ketal

B H

O

intermediate (resonance)

O H

H B

OO

H


B H

Forward Direction - forms acetal or ketal

Reverse Direction - forms hemiacetal or hemiketal

eliminate ROH

addH2O

OO

R

acetal / ketal

addROH

eliminate H2O

O R

H

5


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).

1o or 2o alcoholaldehyde or ketone

oxidation of an alcohol

BB H

C

OH

H N

H

R

NAD+

equivalent

C O

N

H H

R

NADHequivalent


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

B H

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

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.

amine imine

oxidation of an amine

BH

C

NH

H N

H

R NAD+

equivalent

C N

N

H H

R NADHequivalent

R

R

Oxidation of an amine

Hydrolysis of an imine to a C=O and a 1o amine

C

NR

imine

O H

H

B H B

C

N O

HH

R

aminal

B

B H

C

ONR

H

H

B

aldehyde or ketone

BH

Overall, this is a transformation of an amine into a carbonyl group and a primary amine.


additionreaction


B

6


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.

amineimine

reduction of an imine

BB H

C

N

H

H

N

H

R

NAD+

equivalent

C

N

N

H H

R NADHequivalent

R

R

Reduction of an imine to an amine

Formation of an imine from a 1o amine and a C=O

C

N O

HH

R

aminal

C

ONR

H

H

aldehyde or ketone

BH

BB

BH

C

NR

B H

O H

H

B

imine

additionreaction


additionreaction

10. Decarboxylation of a β-ketocarboxylic acid, forming an enol, which tautomerizes (see Example 1) to a keto group.

C

O

C

H

enol tautomer

C

O

CH

keto tautomer

B

BH

BH

BC

O

CC

BH

β-ketocarboxylic acid

O

O

C

O

O

carbon dioxide

decarboxylation tautomers

HB

7


11. Decarboxylation of an α-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. Example 13 shows another reaction of α-ketocarboxylic acids with Vit B-6.

S

N

H

R

B

pKa ≈ 18

S

N

R

TPP ylid α-ketoacid

C O

CO

OH

R S

N

C

R

OH

R

C

O O

S

N

C

R

OH

R

TPP enamine

BH

TPP reaction with an α-ketoacid, decarboxylation and formation of enamine.

decarboxylation

(-CO2)

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 R

BH

S

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

Reaction of enamine nucleophile with an acid to from a new (smaller) carbohydrate.

S

N

C

R

OH

R

BH

S

N

C

R

OH

R

B

S

N

R

CR

O

H

TPP ylid a new (smaller) carbohydrate

H

H B

TPP

TPP enamine reaction with C=O

TPP enamine reaction with a proton

elimination reaction forms a carbonyl group, similar to a reverse aldol

TPP ylid addition to a carbonyl

TPP enamine addition to a carbonyl

acid/baseprotonation of TPP enamine

elimination reaction forms a carbonyl group, similar to a reverse aldol

8


12. a. Phosphorylation of an OH with an ATP equivalent (making an inorganic phosphate ester). Known to both activate enzymes and deactivate enzymes (a signaling transformation).

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 H

B

acyl-like substitution reaction

inorganic ester hydrolysis

c. An elimination reaction of a phosphate leaving group to make an alkene (pi bond). Could actually be E1, E2 or E1cB.

CC

H

OP

O

O

O

B

H

CC

OP

O

O

O

H

B H

E1, E2 (anti) or E1cBmechanismsare possible

d. An acyl phosphate (inorganic anhydride) and formation of a thiol ester (like acetyl Co-A).

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

Mg+2


O

H3C

O

H3C

organic-inorganic mixed anhydride

Co-A S

HB


O

SCo-A

very reactive thiol ester(acetyl Co-A)

O P

O

O

O

ADP leaving group phosphate leaving group

9


13. Vit B-6 reactions – Many possibilities exist. a. Convert a C=O into a CHNH2 or the other way around: 1. imine formation with α-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). b. Use amine group of an amino acid with the C=O form of Vit B-6 to make an imine. Any of the 3 groups on the Cα carbon of the amino acid can be potentially cleaved (the proton (like above), loss of CO2 or the loss of the Cα branch in serine or threonine.

N

N

H vitamin B-6(1o amine version)

H

B

BHdehydration (-H2O)

B H

iminesynthesis

H

B

OH

OO

R

α-keto acid

N

N

H

H

R

OH

O

OH

N

N

H

R

OH

O

N

N

H

R

OH

O

keto / enol tautomerization, makes imine on the other side

H

HB

B H

N

N

H

R

OH

O

H

addition of water

HO

H

HO

H

B BH

hydrolysis of imine

N

N

H

R

OH

O

H

N

N

H

R

OH

O

HH

O

H

B BH

N

H2N

H

R

OH

O

H

O H

vitamin B-6(aldehyde version)

α-amino acid

Similar to Example 9b.

Similar to Example 9a.

Similar to Example 1.

Imine formation

Tautomerization

Imine hydrolysis

water + imine aminal

N

N

H

R

O

O

H

H B

N

N

H

R

C

O

- CO2

O

BH

H

Can hydrolyze to a C=O, or pick up proton viatautomerization. N

N

H

CO2H

OH

H B

N

N

H

CO2H

CH2

O

- CO2

BH

H

Loss of CO2 Loss of Cα side chain

aa = serine

Can hydrolyze to a C=O, or pick up proton viatautomerization.

10


Summary of Biochemical Topics having examples provided: 3 types of problems are possible 1. fill in details, 2. state what transformation occurred (provide details), 3. given the term, draw the step (provide details) 1. Keto/enol tautomerization (proton transfer, resonance, proton transfer).

Keto/enol tautomerization (proton transfer, resonance, proton transfer).

2. a. Carbonyl hydration (addition reaction of H2O to a C=O) b. carbonyl hydrate dehydration (elimination reaction forms a C=O and H2O).

3. a. Aldol (makes a β-hydroxy carbonyl compound). b.Reverse aldol, (makes 2 C=O from a β-hydroxy carbonyl compound).

4. Claisen (makes a β-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 β-hydroxy carbonyl compounds, an elimination reaction forms α,β-unsaturated carbonyl compounds and carries an aldol reaction one step farther. Michael reaction (addition / hydration) adds a nucleophile at the beta carbon of an α,β-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). 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. This is followed by imine hydrolysis to a C=O (opposite of 9b, below). b. Formation of an imine, C=N-R, from a C=O and a 1o amine, followed by reduction to CH(NHR) (an amine) with an NADH equivalent, which forms NAD+ (opposite of 9a, above).

10. Decarboxylation of a β-ketocarboxylic acid, liberates CO2 and forms an enol which tautomerizes to a keto group.

11. Decarboxylation of an α-ketocarboxylic acid with TPP (thiamine diphosphate). The “TPP ylid” adds to an α-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 or SN1) reaction with a phosphate leaving group is possible. d. Formation of acyl phosphates (mixed anhydrides) also allows for exothermic carbonyl substitution reactions.

13. Vit B-6 reactions – Many reactions are possible. An example shows 1. imine formation with an α-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 (-CO2), an alpha C-H proton (tautomers), and certain amino acid side groups, -CH2OH in serine, and –CH(OH)CH3 in threonine). Imines are also seen in Example 9 and α-keto acids in Example 11. There are many other biochemical reactions, but this is all I have created examples for so far. The other pages should provide simplistic mechanism examples of the reactions listed above. It is quite possible there are some mistakes, since this was put together quickly without much editing. If you notice some inconsistencies, please point them out to me.

11


Practice Problems – 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. OH OH

OH OH

OH

O

OH

reverse aldol

reverse those steps, do a forward aldol

(acyl substitution reaction)


2.OH OH

OH OH

OH

O

OHhemiacetal formation6 atom ring

reverse that reactionback go a carbonyl and an alcohol

(addition reaction)


3.

OH OH

OH OH

OH

O

OH reverse Michael(dehydration)

forward Michael(hydration)


(addition reaction)

4.

OH OH

OH OH

OH

O

OH keto/enol tautomerizationto form an aldehyde

carbonyl (hydration)

(addition reaction)

5.

OH OH

OH OH

OH

O

OH keto/enol tautomerizationto form a new ketone

hemiacetal formation5 atom ring

(twice) (addition reaction)

6.

OH

OH

OH

OH

O keto/enol tautomerizationto form a beta keto acid decarboxylation

OH

NAD+

oxidation

keto/enol tautomerizationto form an aldehyde

carbonyl (hydration)

(addition reaction)


12


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 O

reverse Claisen

forward ClaisenO

R



9. OH

OH

OH O

NADH reductionH

OH

NAD+

oxidation to an aldehyde

(addition reaction)


10. acetal formation (2 steps)

O

OHHO

HO OH

intermediate overall = SN1


(addition reaction)

11. acetal hydrolysis to hemiacetal (2 steps)

O

OHO

HO OH

R


(addition reaction)

overall = SN1intermediate

12. Vit B-6 imine formation(2 steps)

O

OH

O (addition reaction)


13


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 reaction)

15.

N

H

OH

imine hydrolysisto an aldehyde (2 steps)

OH NAD+

oxidation to an imine

R H



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


14


19.

P

O

O

O

O PP ATP

formation of mixed anhydride

O

OH


20. O

SCo-AH

Claisen condensation

O

OP

OO

OH (acyl-like substitution reaction)

21. O

SCo-A

O NADH reduction of keto group

(addition reaction)

22.

O

SCo-A

Oreverse Michaelreaction

H


23. O

SCo-A

NADH hydride reduction of the conjugated C=C by a Michael reaction

(addition reaction)

15


Glycolysis – This is the real stuff, minus the complication of stereochemistry.

OH OH

O OH

OH

O

H

open chain glucose

6 atom hemiacetal

H

O

OH

OHHO

HO

HO

ATPO

O

OHHO

HO

OP

O

O

O reversehemiacetal

O OH

OH OH

OH

O

H

open chain glucose-6-phosphateO3P-2

O OH

OH OH

OH

OH

O3P

ene-diol

keto-enol tautomers

keto-enol tautomers

O OH

O OH

O

OH

O3P

open chain fructose-6-phosphate

-2-2

5 atom hemiacetal

H

OOH

OHOH

HO

OO3P

-2

ATP

OOH

OPO3OH

HO

OO3P

cyclic fructose-6-phosphatecyclic fructose-1,6-bisphosphate

cyclic glucose cyclic glucose-6-phosphate

-2

O OH

O OH

O

O

O3P

H

open chain fructose-1,6-bisphosphate

reverse aldol

PO3

-2

-2

-2

O O

O

OH

O

O

O3P

H

PO3

H

-2

-2

glyceraldehyde-3-phosphate dihydroxyacetone phosphate(made into glyceraldehyde-3-phosphate)

keto-enol tautomers

OH

OH

OPO3

ene-diol

keto-enol tautomers

OO

O

PO3

H

H H

glyceraldehyde-3-phosphate

-2

-2

SR H

O

O

PO3

H

H

-2

SR

O

H

NAD+

O

O

PO3

H

S

-2

O

R

O3P O-2

O

O

PO3

H

O

O

-2

P

O

OO

1,3-bisphosphoglycerate

acylsubstitution

PADP-PO

O

O

O

ATP

O

O

PO3

H

HO

O

-2

3-phosphoglycerate

PN

O

O

O

N

O

O

PO3

PO3

HO

O

2,3-bisphosphoglycerate

-2

-2

NN

H O

O

H

PO3

HO

O

NN

O3P

-2

-2

HO

PO3

HO

O

P OP-PDA

O

O

O

ATP

OH

HO

O

keto-enol tautomers

O

HO

O

pyruvate

NADH

OH

HO

O

lactate

TPP ylid

O

O

HO

S

N

RH

decarboxylation

S

N

R

HO

acid/base

S

N

R

O

H

H

eliminate TPP ylid

S

N

R

O

H ethanal(acetaldehyde)

NADH

OH

ethanol

acetyl Co-A(separate slide)

...or transported in blood to liver and oxidized back to pyruvate and made back into glucose via gluconeogenosis

oxidized in cell back to pyruvate

NAD+

H

reversehemiacetal same compound

hemithioacetal

hemithioacetal

oxidation

acyl-likesubstitution



2-phosphoglycerate

reverse Michael

phosphoenol pyruvate (PEP)


enol pyruvate

HETPP

TPP ylid

reduction

16


Additional Problems (older problem set) - 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”.

OH

O

OH

O

OHOH

OH

OH

1 ?O

HOH OH

O

OH

O

H

OH

OH

2 ?

11 ?

OH

O

OH

OH

OH

OH

OH

O

OH

OH

OH

OH

OH

O

OH

OH

OH

OH

3 ?

4 ?

O

OH OHOH

OH

HO

OHO

OHOH

OH

OH

OH

O

OH

OH

OH

OH

OH

O

OH OH

OH

OH

O

O OH

OH

7 ?

8 ?

OH

O

O O

OHH

9 ?

O

OH

O

H10 ?

6 ?

O

OHOH

OH

OH

5 ?O

HO

OHOH

OH

O

O

OH

H12 ?

(2 steps)

OH

O

OH

OH

OH

OH13 ?

(2 steps) OH

OH

O

OH

OH

OH

OH

O

OH

OH

OH

HOO

OH

O

H

OH two rotations15 ?

O

HOO

OH

OH

14 ?

Answers1. reverse aldol2. forward aldol3. hemi-ketal formation to 6 atom ring4. hemi-ketal formation to 5 atom ring5. reverse of hemi-ketal to form open chain6. reverse Michael reaction7. keto/enol tautomerization

10 structure

O

OH

OH

enol at both ends of the double bond, can form a carbonyl on either side,one as a ketone and one as an aldehyde

9. keto/enol tautomerization10. structure shown at right11. keto/enol tautomerization12. 2 x keto/enol tautomerization (again!)13. 2 x keto/enol tautomerization (again!)14. reverse Michael15. intramolecular Michael reaction using the OH of an alcohol group

8. reverse aldol

8.9.10.11.12.13.14.15.

1.2.3.4.5.6.7.

17


Problems (older problem set) – 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

OH

OH

OH

O

OH

OH

OH

OH

OH

OH

O

OH

OH

OH

OH

OH

OH

O

OH

OH

OH

OH

OH

OH

O

OH

OH

dehydration(reverse Michael)

keto/enol to form2,3-diketo structure

reverse aldol to 3C aldehyde and 4 carbon 2,3-diketo structure

keto/enol to form3,4-diketo structure

reverse aldol to 1C aldehyde and 6 carbon 2,3-diketo structure

dehydration(reverse Michael)

hemi-acetal formation to 5 atom ring

hemi-acetal formation to 6 atom ring

carbonyl hydration

hemi-acetalring opening

Michael addition of water (hydration)

cyclic ester ring openingaddition of water (hydration)

OH

OH

OH

OH

OH

OH

O

OHO

HOOH

OH

H

O

OHO

OH

carbonyl hydrate dehydration

keto / enol to form 2-keto structure

acetal formation with ROH

acetal formation with ROH

18


OH

OH

OH

O

OH

O

OH

H

reverse aldol forward aldol

(reverse steps)

hemiacetal formation(6 atom ring)

OH

O

OH

OH

OH

O

OH

H

reverse reactionback to carbonyl & alcohol

OH

OH

OH

OH O

OHHO H dehydration(reverse Michael)

hydration(Michael)

keto/enol tautomerization(form an aldehyde)

OH

OH

OH

OH O

OHOHH

H

hydration of carbonyl

reverse reactiondehydration ofdiol

OH

OH

OH

OH O

OHOH

keto/enol tautomerization(form a new ketone)

OH

OH

OH

OH O

OHHO H

19


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

OHO OH

HB 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

OH

OH

B BH

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

OHOH

OH

B

BH

OH

OH

OH

OH

OHO

OH

20


Biomolecules and our simplified representation. 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=

PP-ATPOP

O

O

O

simplified structure

actual structure

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


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

RNADPH has a phosphate here.

HH

HH

Vitamin B-6 – pyridoxal phosphate (amino acid metabolism, transamination with α-ketoacids)

NH2

N

H

O

N

H

H


actual structure

1o amine version of Vit B-6 aldehyde version of Vit B-6

NH2

N

H

O3POO

H

-2


actual structure

O

N

H

H

O3POO

H

-2

= =

interconvert via imine, tautomers, hydrolysis

21


TPP – Thiamine diphosphate (decarboxylation and enamine chemistry) N

N

NH2

P

O

O

OP

O

O

O

CH2O

=

S

N

HS

N

H

R

actual TPP structure


B

S

N

R

ylidstructure

Coenzyme A (acyl transfer)

O P

O

O

O P

O

O

O

O

HOOH

N

N

NN

NH2

OH

O

NH

O

NH

HS

Thiol esters form here.

H3CC

O

S CoAAcetyl Co-A =

All of this is "Co-A"

actual structuresimplified

structure

Co-AHS

This is an acetyl group

FAD / FADH2 – Flavin adenine dinucleotide (oxidation – reduction) – not used at this time

N

N

NH

N

O

O

OH

HOOH

O P

O

O

O P

O

O

O

O

HOOH

N

N

NN

NH2FAD - flavin dinucleotide (a hydride acceptor)

N

N

NH

N

O

O

R

N

N

NH

N

O

O

R

H

H

BHH

FAD - flavin dinucleotide (a hydride acceptor)

FADH2 - flavin dinucleotide (a hydride donor)

HRHydride transfer reduces FAD to FADH2.

=

simplified structures for FAD and FADH2

actual structure

THF – tetrahdrofolate (transfer of one carbon units) – not used at this time

NH

N

N

N

O

H2N

RH

H

HN

O

HN

CO2

CO2

Tetrahydrofolate (THF) - one carbon transfers as "CH3", "CH2".

H

One carbon groupscan bond here in various ways.

NH

R

HNR

=

simplified structure actual

structure

22


List of reactions Biochemical Topics having examples provided: 1. Keto/enol

enol/keto

2. Carbonyl hydration carbonyl hydrate dehydration

3. Aldol Reverse aldol

4. Claisen Reverse Claisen

5. Reverse Michael reaction Michael reaction

6. Hemiacetal / hemiketal open hemiacetal / hemiketal

7. Acetal /or Ketal reverse Acetal /or Ketal

8. a. Oxidation of CH(OH) to C=O with an NAD+ b. Reduction of C=O to CH(OH) with an NADH.

9. a. Oxidation of an amine, with NAD+, imine hydrolysis b. Form imine, C=N-R, then reduce to amine with NADH

10. Decarboxylation of a β-ketocarboxylic acid, enol tautomerizes

11. Decarboxylation of an α-ketocarboxylic acid with TPP adds to α-keto group, becomes a “TPP enamine”, a. can protonate, becomes aldehyde upon elimination of TPP or b. reacts with a C=O of another carbohydrate to make a larger carbohydrate after elimination of TPP.

12. a. Phosphorylation of an OH with an ATP equivalent b. Dephosphorylation of a phosphate ester c. An elimination (E1 or E2) or substitution (SN2 or SN1) reaction d. Formation of mixed anhydrides, carbonyl (acyl) substitution

13. Vit B-6 reactions – 1. imine formation with an α-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 a. the acid part, CO2H (-CO2), b. an alpha C-H proton (discussed just in 13), and c. certain amino acid side groups, -CH2OH in serine, and –CH(OH)CH3 in threonine.