ch. 3: vitamins, cofactors, coenzymes, enzymes · ch. 3: vitamins, cofactors, coenzymes, enzymes...
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Ch. 3: Vitamins, Cofactors, Coenzymes, Enzymes
Ø P. J. Bruice, Organic Chemistry, 2nd ed., Prentice-Hall, Upper SaddleRiver, New Jersey, 1998, Chapter 22.
Ø H. Dugas, Bioorganic Chemistry - A Chemical Approach to EnzymeAction, 3rd ed., Springer Verlag, New York, 1996, chapter 7.
Ø O. Isler, G. Brubacher, Vitamins I: Fat-Soluble Vitamins, ThiemeVerlag, Stuttgart, 1982.
Ø O. Isler, G. Brubacher, S. Ghisla, B. Kraeutler, Vitamins II: Water-Soluble Vitamins, Georg Thieme Verlag, Stuttgart, 1988.
Ø http://www.indstate.edu/thcme/mwking/vitamins.html
∗ Readings
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Glossary
• vitamin (water soluble vitamin, fat soluble vitamin): a substanceneeded in small amounts for normal body functions that the bodycannot synthesize in adequat amounts
• enzyme: a protein that is a catalyst• metalloenzyme: an enzyme that has a tightly bound metal ion
cofactor: an organic molecule or a metal ion that certain enzymesneed in order to catalyze a reaction or a process
• coenzyme: an organic molecule (vitamin) as cofactor• prosthetic group: a cofoctor permanently associated with the
protein, often covalently bound• holoenzyme: catalytically active enzyme-cofactor complex.• apoenzyme: an enzyme without its cofactor (enzymatically inactive
protein)
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Glossary
• metabolism: reactions that living organism carry out• catabolism: energy and simple molecules are formed from
complex molecules• anabolism: synthesis of complex biomolecules using energy
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Problems - 1
@ Vitamin C and Vitamin E are both natural radical inhibitors. Explain whythis is so.
@ Explain why vitamin C is a „strong“ acid
@ Ascorbinsäure can be methylated by diazomethane. Which functionalgroup is most sensitive towards methylation?
@ (L)-Sorbose which is an intermediate in the technical synthesis of vitaminC, forms a furanosid by reaction with aceton/H+.Discuss the mechanism of formation. Are there diastereotopic methylgroups?
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Problems - 2
@ Apply Woodward-Hoffmann-Rules for the synthesis of Vitamin D3.Sum up the WH-rules for the electrocyclic and sigmatropic reactionsunder thermal respectively photochemical conditions.a) Which stereoisomer is formed by irradiating (2E,4Z,6Z)-octatriene?
@ Stereoselective oxidoreduction of ketones and alcohols using horseliver alcohol dehydrogenase (HLADH) needs NADH as cofactor.NADH is rather expensive and has to be recycled. Recyclization canbe achieved by natrium dithionite. Formulate the reaction sequencefor the keton reduction by HLADH/NADH and the subsequentrecyclization of NAD+ by dithionite.
@ Assign the pro-R hydrogen and the pro-S hydrogen of NADH.
@ Compare typical applications of NAD+/NADH und FAD asoxidoreductases with regard to their involvements in the biochemicalprocesses.
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Problems - 3
@ Nature exploits the reactivity of C-8 methyl group of flavins in order tolink to the apoenzyme via a SH group of a cystein. The overall processis as given below. The last step is the oxidation of the cystein boundFADH2 to enzyme-FAD.
N NMe
NN
Me H
O
OR
N NCySCH2
NN
Me H
O
OR
CyS-
@ Discuus the similarity of decarboxylation of a β-keto acid andenzymatic pyruvate decarboxylation.
@ The pyrimidine-amino-group in thiamin pyrophosphate contributes inthe enzymatic TPP-dependent processes. How can this be explained?
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Vitamins, coenzymes, cofactors, enzymes
enzyme
protein + coenzyme (vitamin)
protein + cofactor (metal ion)
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Vitamins, coenzymes, enzymes cofactors
Vitamins that are coenzymeprecursors
Ø D. Voet, J. G. Voet, Biochemistry, second edition ed., John Wiley &Sons, New York, 1995.
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Structure of water soluble vitamins
N
OH
O
niacinnicotinic acid
S
NHHN
O
CO2H
biotinvitamin H
N
N
N S
H3C
NH2 H
H3C
OH
+
thiaminevitamin B1
S S
CO2Hn
n = 3lipoate
N CH3
OH
CH2OH
HOCH2
pyridoxinevitamin B6
NHO
Me Me
OH
O
CO2H
H
N
N N
NNH
O
H2N
H
NH
OCO2H
CO2H
O
H
HO OH
O
OHH
CH2OH
HH
H
OH
OHOH
OH
N NMe
NN
Me HO
O
pantothenatefolate
vitamin B12
vitamin Cascorbic acid
riboflavinvitamin B2
subunit of CoA-SH
BO/BBM
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Ø Discovering Nature's Diverse Pathways to Vitamin B12: A 35-Year Odyssey: A. I.Scott, J. Org. Chem. 2003, 68, 2529-2539..
Vitamin B12BO/BBM/SKB
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Fat soluble vitamins
O
CH3
HO
H3C
CH3
CH3
O
O
CH3n
HO
Me
H
Me
Me
Me
CH2OH
vitamin Eαα-tocopherol vitamin K1
n = 3
vitamin D3
vitamin A (all-trans)
BO/BBM
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Vitamin C
• mp 190-192°C• pK1 = 4.17; pK2 = 11.57• anti-scorbutically factor (essential for the synthesis of
collagen)• reducing agent in hydroxylation reactions• radical scavenger (inhibitor)
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Industrial synthesis of vitamin C (Reichstein, 1934)
Ø H. Beyer, W. Walter, Lehrbuch der Organischen Chemie, 1998.
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Vitamin D
• Metabolism of calcium and phosphorous• Deficiency impairs bone formation (rickets)• Excess causes calcification of soft tissues
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Photochemical formation of vitamin D3
∗ two step reaction- first step: conrotatory photochemical ring opening- second step: [1,7] sigmatropic antarafacial hydrogen shift (thermal)
∗ Woodward-Hoffmann rules∗ Active form 1,25-dihydroxyvitamin D3
C-25C-1
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Oxidoreduction: Pyridine nucleotide coenzymes(NAD+/NADP+) (Vitamin B3, Niacin)
∗ NAD+/NADH; NADP+/NADPH
- Structure
- Oxidation reactions
- Reduction reactions (Pyruvate → lactate; lactatedehydrogenase)
- Comparison with LiAlH4
- Mechanism and stereochemistry (Prochirality)
CH3 OH
H(R)
H(S) H(R) and H(S) enantiotopic hydrogens
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Bioactive flavins
∗ vitamin B2 – riboflavin
∗ flavin mononucleotide
(FMN)
∗ flavin adenine dinucleotide
(FAD)
O
OHHO
OH
N NMe
NN
Me H
O
O
H
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Flavin Biochemistry
∗ Dehydrogenation∗ Activation of oxygen, hydroxylation, oxygenation∗ Electron transfer, electron transport, respiration chain,
etc.∗ Light emission, bacterial luciferase
(bioluminescence)∗ Photobiology: Photolyase, phototropism,
photomorphogenesis, circadian processes(Cryptochrome, Phototropin, blue-light photoreceptors)
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Flavin structure
Ø F. Müller, Chemistry and Biochemistry of Flavoenzymes, Vol. I, CRC,Boca Raton, 1991.
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Redox processes of flavins (electron transfer/protonation)
N
N
N
N
R1
O
O
H
R2
R1
N
N
N
N
R1
O
O
H
R2
R1
N
N
N
N
R1
O
O
H
R2
R1H
N
N
N
N
R1
O
O
H
R2R1
H
N
N
N
N
R1
O
O
H
R2R1
H
H
Flox Fl-red
H+red
FlHrad
FlH-red
red
FlH2
H+
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Some enzymatic processes of flavin nucleotides
• dihydrolipoyl dehydrogenase
• L-amino acid oxidase
• succinate dehydrogenase
• NADH dehydrogenase
• luciferase catalyzed bioluminescence
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SH SH
O
OS S
O
O+ FAD
dihydrolipoyldehydrogenase + FADH2
N N O
NN
O
R
H
Me
Me
H+
S RS
H+
SS
R
FAD-dehydrogenase – oxidation of a dithiol
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Bioluminescence
• Photoluminescence
• Chemoluminescence
• Bioluminescence
• Triboluminescence
• Electroluminescence
• Lyoluminescence
• Aquoluminescence
• Sonoluminescence
• Galvanoluminescence
• …
• …
• XYZ-Luminescence
νh
Population of excited state bysome process XYZ
Electronicallyexcited state
Ground state
ge EEh −=ν
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Bacterial bioluminescence
AA
• enzyme catalyzedreaction: luciferase
• reaction cascadeultimately leads to theformation of theexcited state (S1) of 4a-hydroxyflavin
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LOV domain of Phototropin
• Genetic informationtranslated into proteinstructure
• Enzymatic synthesis ofFMN
• Molecular self-assembly• Input light, output
morphogenesis
∆ S. Crosson, K. Moffat, 2001.∆ See also: http://www.uni-
regensburg.de/Fakultaeten/nat_Fak_III/GK/SP/download/Kottke_Phototropins.pdf
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Pyruvate decarboxylase – cofactor thiaminepyrophosphate (TPP)
CH3
O
O
OCH3 H
O
+ CO2
N
N
N S
H3C
NH2 H
H3C
O P O P O
O
OO
O
+
thiamine pyrophosphateTPP
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Benzoin-type condensation – compare its mechanismto TPP catalyzed processes (transketolase)
O
HR
O
O H
H RR2
CN-
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∗ carboxylationofactivatedcarbon
Biotin – catalyzes carboxylation as a CO2 carrier
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Pyridoxal phosphate (PLP)
N CH3
OH
CH2OH
HOCH2
N CH3
OHO
P
O O
O
OH
N CH3
OO
P
O O
O
NH
Enzyme
H
H
pyridoxinevitamin B6
pyridoxal phosphatePLP
enzyme covalently bound to the
cofactor
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PLP-catalyzed processes of amino acids in Nature
N CH3
OO
P
O O
O
NH
Enzyme
H
H
enzyme covalently bound to the PLP cofactor
+
∗ transimination
∗ decarboxylation
∗ transamination
∗ racemization∗ Cα-Cβ bond cleavage
(„β-elimination“)∗ α,β-elimination
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Decarboxylation of an amino acid
∗ First step: Synthesis of amino acid-bound PLP from enzyme-
bound PLP
∗ Second step: Decarboxylation
∗ Third step: Transimination leading to enzyme-bound PLP
and „free“ decarboxylated amino acid
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Vitamin B12
∆ Discovering Nature's Diverse Pathways to Vitamin B12:A 35-Year Odyssey, A. I. Scott, J. Org. Chem. 2003, 68,2529-2539.
∆ Total synthesis of cobyric acid: historical developmentand recent synthetic innovations, D. Riether, J. Mulzer,European Journal of Organic Chemistry 2003, 30-45.
∆ W. Kaim, B. Schwederski, Bioanorganische Chemie,Teubner, Stuttgart, 1991.
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General scheme for the structure interconversioncataylyzed by B12
C1 C2
H X
YC1 C2
X H
Y
1,2 shift process
• radical mechanism