Download cofactorsA

Many cofactors are
derived from vitamins

We justify lumping these two
topics together because many
cofactors are vitamins or are
metabolites of vitamins.
Biochemistry: Vitamins & Cofactors
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What we’ll discuss
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Tightly-bound
metal ions as
cofactors
Activator ions as
cofactors
Cosubstrates
Prosthetic groups
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Biochemistry: Vitamins & Cofactors
Vitamins
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Water-soluble
vitamins
 Ascorbate
 Cofactors
Fat-soluble
vitamins
p. 2 of 49
Family tree of cofactors
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Cofactors, coenzymes, essential ions,
cosubstrates, prosthetic groups:
Cofactors
(apoenzyme + cofactor  holoenzyme)
Coenzymes
Essential ions
Activator ions
(loosely bound)
Ions in
metalloenzymes
Cosubstrates
(loosely bound)
Biochemistry: Vitamins & Cofactors
Prosthetic groups
(tightly bound)
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Metal-activated enzymes
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Absolute requirements for mobile ions
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Often require K+, Ca2+, Mg2+
Example: Kinases: Mg-ATP complex
Metalloenzymes: firmly bound metal
ions in active site
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Usually divalent or more
Sometimes 1e- redox changes in metal
Biochemistry: Vitamins & Cofactors
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Coenzymes
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Organic moeities that enable enzymes to
perform their function: they supply
functionalities not available from amino
acid side chains
Cosubstrates
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Enter reaction, get altered, leave
Repeated recycling within cell or organelle
Prosthetic groups
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Remain bound to enzyme throughout
Change during one phase of reaction,
eventually get restored to starting state
Biochemistry: Vitamins & Cofactors
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Major cosubstrates
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Facilitate group transfers, mostly small groups
Oxidation-reduction participants
Cosubstrate
ATP
S-adenosylMet
UDP-glucose
NAD,NADP
Coenzyme A
Tetrahydrofolate
Ubiquinone
Source
Function
Transfer P,Nucleotide
Methyl transfer
Glycosyl transfer
Niacin
2-electron redox
Pantothenate Acyl transfer
Folate
1Carbon transfer
Lipid-soluble e- carrier
Biochemistry: Vitamins & Cofactors
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Major prosthetic groups
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Transfer of larger groups
One- or two-electron redox changes
Prosth.gp.
FMN, FAD
TPP
PLP
Biotin
Adenosylcobalamin
MeCobal.
Lipoamide
Retinal
Vitamin K
Source
Riboflavin
Thiamine
Pyridoxine
Biotin
Cobalamin
Function
1e- and 2e- redox transfers
2-Carbon transfers with C=O
Amino acid group transfers
Carboxylation, COO- transfer
Intramolec. rearrangements
Cobalamin
Methyl-group transfers
Transfer from TPP
Vision
Carboxylation of glu residues
Vitamin A
Vitamin K
Biochemistry: Vitamins & Cofactors
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Adenosine triphosphate
Synthesizable in liver (chapter 18)
Building block for RNA
Participates in phosphoryl-group transfer
in kinases
Source of other coenzymes
Biochemistry: Vitamins & Cofactors
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S-adenosylmethionine
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Made from methionine and adenosine
Sulfonium group is highly reactive: can
donate methyl groups
Reaction diagram courtesy of
Eric Neeno-Eckwall, Hamline
University
Biochemistry: Vitamins & Cofactors
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UDP-glucose
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Most common donor of glucose
Formed via:
Glucose-1P + UTPUDP-glucose + PPi
Reaction driven to right by PPi hydrolysis
Structure courtesy of UIC
Pharmacy Program
Biochemistry: Vitamins & Cofactors
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NAD+ and NADP+
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Net charge isn’t really >0 ;
the + is just a reminder that the
nicotinamide ring is positively charged
Most important cosubstrates in oxidationreduction reactions in aerobic organisms
Structure courtesy of
Sergio Marchesini, U.
Brescia
Biochemistry: Vitamins & Cofactors
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Differences between them
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The chemical difference is in the
phosphorylation of the 2’ phosphate
group of the ribose moiety
The functional difference is that NAD is
usually associated with catabolic
reactions and NADP is usually
associated with anabolic reactions
Therefore often NAD+ and NADPH are
reactants and NADH and NADP+ are
products
Biochemistry: Vitamins & Cofactors
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How do we get back to the
starting point?
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NADH is often oxidized back to NAD+ as
part of the electron-transport chain
Imbalances can be addressed via
NAD Kinase (S.Kawai et al (2005),
J.Biol.Chem. 280:39200) and NADP
phosphatase
Biochemistry: Vitamins & Cofactors
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iClicker quiz: single question
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What would you expect to be the
phosphate donor in the NAD kinase
reaction?
(a) free phosphate
(b) pyrophosphate
(c) ATP
(d) pyridoxal phosphate
Biochemistry: Vitamins & Cofactors
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Reduced forms of NAD(P)
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Reduction occurs on the
nicotinamide ring
Ring is no longer netpositive
Ring is still planar but
the two hydrogens on
the para carbon are not
Biochemistry: Vitamins & Cofactors
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FAD and FMN
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Flavin group based on riboflavin
Alternate participants in redox reactions
Prosthetic groups: tightly but noncovalently
bound to their enzymes
That protects against wasteful reoxidation of
reduced forms
FADH2 is weaker reducing agent than NADH
These are capable of one-electron oxidations
and reductions
Biochemistry: Vitamins & Cofactors
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FAD and FMN structures
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FAD has an AMP attached P to P
Structure courtesy
Paisley University
Biochemistry: Vitamins & Cofactors
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FMN/FAD redox forms
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Two-electron version: H+ + :H- transferred
Reaction diagram courtesy of Eric
Neeno-Eckwall, Hamline University
Biochemistry: Vitamins & Cofactors
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(ADP-3’P)
Coenzyme A
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Reactive portion
is free sulfhydryl
at one end of
the molecule
Can form
thioester with
acetate, etc.
Pantoate +
b-alanine =
pantothenate
(Pantoate)
2-mercaptoethylamine)
b-alanine)
Structure courtesy of
MPB project, George
Washington University
Biochemistry: Vitamins & Cofactors
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Thiamine Pyrophosphate
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Based on thiamine, vitamin B1
Carboxylases and oxidative
decarboxylases use this coenzyme
So do transketolases (move 2 carbons
at a time between sugars with keto
groups)
Thiazolium ring is reactive center:
pKa drops from 15 in H2O to 6 in
enzyme
Biochemistry: Vitamins & Cofactors
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TPP reactions
pyrimidine
thiazolium
Diagram courtesy of
Oklahoma State U.
Biochemistry program
Biochemistry: Vitamins & Cofactors
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Pyridoxal
phosphate
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PLP is prosthetic group for many
amino-acid-related enzymes,
particularly transaminations
Carbonyl group of PLP bound as a
Schiff base (imine) to -amino
group of lysine at active site
First step is always formation of
external aldimine; goes through
gem-diamine intermediate to
internal aldimine
Biochemistry: Vitamins & Cofactors
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Biotin
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Rarity: vitamin is the prosthetic group
Used in reactions that transfer carboxyl
groups
… and in ATP-dependent carboxylations
Biochemistry: Vitamins & Cofactors
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Biotin reactivity
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Covalently bound to active-site lysines to
form species called biocytin
Pyruvate carboxylase is characteristic
reaction:
Diagram courtesy
University of Virginia Biochemistry
Biochemistry: Vitamins & Cofactors
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Tetrahydrofolate
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Primary donor of one-carbon units
(formyl, methylene, methyl)
Supplies methyl group for thymidylate
Dihydrofolate reductase (DHFR) is an
interesting drug target
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Methotrexate as cancer chemotherapeutic:
cancer needs more thymidylate than healthy cells
Trimethoprim as antibacterial:
Bacterial DHFR is somewhat different from
eucaryotic DHFR because bacteria derive DHF
from other sources; humans get it from folate
Biochemistry: Vitamins & Cofactors
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THF structure and function
Figure courtesy
horticulture program,
Purdue
Biochemistry: Vitamins & Cofactors
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Cobalamin
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Largest B vitamin
Structure related to heme but missing
one carbon in ring structure
Cobalt bound in core of ring system
Involved in enzymatic rearrangements
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Catabolism of odd-chain fatty acids
Methylation of homocysteine
Reductive dehalogenation
Biochemistry: Vitamins & Cofactors
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AdenosylCobalamin
Reactive
Co-C bond
“Missing” carbon
Diagram courtesy of
Swiss Food News
Biochemistry: Vitamins & Cofactors
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Lipoamide
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Protein-bound form of lipoic acid
Contains five-membered disulfide ring
Covalently bound via amide to protein
lysine sidechain
Involved in swinging arm between active
sites in multienzyme complexes
Disulfides break periodically
Example: pyruvate dehydrogenase
complex
Biochemistry: Vitamins & Cofactors
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Lipoamide 2e- reduction
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Cf. Scheme 7.6: thioester starting point
Fig. Courtesy Biochem
and Biophysics
program, Rensselaer
Biochemistry: Vitamins & Cofactors
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iClicker revisited
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Which coenzyme would you expect
would be required for the reaction
oxaloacetate + glutamate 
aspartate + a-ketoglutarate?
(a) ascorbate
(b) PLP
( c) thiamine pyrophosphate
(d) NAD
(e) none of the above
Biochemistry: Vitamins & Cofactors
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Vitamins: necessary
micronutrients that cannot be
synthesized internally
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What’s a vitamin for one organism is not
for another
Primates and some rodents are the only
vertebrates that don’t synthesize
ascorbate
E.coli can make almost everything given
energy and sources of atoms
Biochemistry: Vitamins & Cofactors
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Why wouldn’t organisms
make everything?
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Complex metabolites require energy for
synthesis
Control of their synthesis is also
metabolically expensive
Cheaper in the long run to derive these
nutrients from diet
Biochemistry: Vitamins & Cofactors
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Vitamins: broad classifications
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Water-soluble vitamins
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Coenzymes or coenzyme precursors
Non-coenzymic metabolites
Fat-soluble vitamins
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Antioxidants
Other lipidic vitamins
Biochemistry: Vitamins & Cofactors
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