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General Metabolism I
Andy Howard
Introductory Biochemistry
6 November 2008
Biochemistry: Metabolism I
11/06/2008
What we’ll discuss
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Metabolism
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Definitions
Pathways
Control
Feedback
Phosphorylation
Thermodynamics
Kinetics
Biochemistry: Metabolism I
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Cofactors
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Tightly-bound metal
ions as cofactors
Activator ions as
cofactors
Cosubstrates
Prosthetic groups
11/06/2008
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Metabolism
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Almost ready to start the specifics
(chapter 18)
Define it!
Metabolism is the network of chemical
reactions that occur in biological
systems, including the ways in which
they are controlled.
So it covers most of what we do here!
Biochemistry: Metabolism I
11/06/2008
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Intermediary Metabolism
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Metabolism involving small molecules
Describing it this way is a matter of
perspective:
Do the small molecules exist to give the
proteins something to do, or do the
proteins exist to get the metabolites
interconverted?
Biochemistry: Metabolism I
11/06/2008
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Anabolism and catabolism
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Anabolism: synthesis of complex
molecules from simpler ones
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Generally energy-requiring
Involved in making small molecules and
macromolecules
Catabolism:degradation of large
molecules into simpler ones
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Generally energy-yielding
All the sources had to come from
somewhere
Biochemistry: Metabolism I
11/06/2008
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Common metabolic themes
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Maintenance of internal concentrations
of ions, metabolites, enzymes
Extraction of energy from external
sources
Pathways specified genetically
Organisms & cells interact with their
environment
Constant degradation & synthesis of
metabolites and macromolecules to
produce steady state
Biochemistry: Metabolism I
11/06/2008
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Metabolism and energy
Biochemistry: Metabolism I
11/06/2008
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Pathway
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A sequence of reactions such that
the product of one is the substrate
for the next
Similar to an organic synthesis
scheme
(but with better yields!)
May be:
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Unbranched
Branched
Circular
Biochemistry: Metabolism I
11/06/2008
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Why multistep pathways?
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Limited reaction specificity of
enzymes
Control of energy input and output:
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Break big inputs into ATP-sized inputs
Break energy output into pieces that
can be readily used elsewhere
Biochemistry: Metabolism I
11/06/2008
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Regulation
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Organisms respond to change
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Fastest: small ions move in msec
Metabolites: 0.1-5 sec
Enzymes: minutes to days
Flow of metabolites is flux:
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steady state is like a leaky bucket
Addition of new material replaces the
material that leaks out the bottom
Biochemistry: Metabolism I
11/06/2008
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Metabolic flux, illustrated
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Courtesy Jeremy Zucker’s wiki
Biochemistry: Metabolism I
11/06/2008
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Feedback and
Feed-forward
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Mechanisms by which
the concentration of a
metabolite that is
involved in one
reaction influences the
rate of some other
reaction in the same
pathway
Biochemistry: Metabolism I
11/06/2008
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Feedback realities
Control usually exerted at first
committed step (i.e., the first
reaction that is unique to the
pathway)
 Controlling element is usually the
last element in the path
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Biochemistry: Metabolism I
11/06/2008
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Feed-forward
Early metabolite activates a reaction
farther down the pathway
 Has the potential for instabilities,
just as in electrical feed-forward
 Usually modulated by feedback
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Biochemistry: Metabolism I
11/06/2008
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Activation and inactivation by
post-translational modification
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Most common:
covalent phosphorylation of protein
usually S, T, Y, sometimes H
Kinases add phosphate
Protein-OH + ATP 
Protein-O-P + ADP
… ATP is source of energy and Pi
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Phosphatases hydrolyze phosphoester:
Protein-O-P +H2O Protein-OH + Pi
… no external energy source required
Biochemistry: Metabolism I
11/06/2008
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Phosphorylation’s effects
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Phosphorylation of an enzyme can either
activate it or deactivate it
Usually catabolic enzymes are activated
by phosphorylation and anabolic enzymes
are inactivated
Example:
glycogen phosphorylase is activated by
phosphorylation; it’s a catabolic enzyme
Biochemistry: Metabolism I
11/06/2008
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Glycogen phosphorylase
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Reaction: extracts 1 glucose
unit from non-reducing end of
glycogen & phosphorylates it:
(glycogen)n + Pi 
(glycogen)n-1 + glucose-1-P
Activated by phosphorylation
via phosphorylase kinase
Deactivated by
dephosphorylation by
phosphorylase phosphatase
Biochemistry: Metabolism I
11/06/2008
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Amplification
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Activation of a single molecule of a
protein kinase can enable the
activation (or inactivation) of many
molecules per sec of target proteins
Thus a single activation event at the
kinase level can trigger many events
at the target level
Biochemistry: Metabolism I
11/06/2008
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Other PTMs (p. 505)
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Are there other reversible PTMs that
regulate enzyme activity? Yes:
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Adenylation of Y
ADP-ribosylation of R
Uridylylation of Y
Oxidation of cysteine pairs to cystine
Biochemistry: Metabolism I
11/06/2008
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Evolution of Pathways:
How have new pathways evolved?
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Add a step to an existing pathway
Evolve a branch on an existing pathway
Backward evolution
Duplication of existing pathway to create
related reactions
Reversing an entire pathway
Biochemistry: Metabolism I
11/06/2008
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Adding a step
E1
E2
E3
E4
E5
ABCDEP
Original pathway
• When the organism makes lots of E,
there’s good reason to evolve an
enzyme E5 to make P from E.
• This is how asn and gln pathways
(from asp & glu) work
Biochemistry: Metabolism I
11/06/2008
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Evolving a branch
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Original pathway:
D
E1 E2
A  B  C E3
X
Fully evolved pathway:
E3a D
ABC
E3b X
Biochemistry: Metabolism I
11/06/2008
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Backward evolution
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Original system has lots of E  P
E gets depleted over time;
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Then D gets depleted;
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need to make it from D,
so we evolve enzyme E4 to do that.
need to make it from C,
so we evolve E3 to do that
And so on
Biochemistry: Metabolism I
11/06/2008
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Duplicated pathways
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Homologous enzymes catalyze related
reactions;
this is how trp and his biosynthesis
enzymes seem to have evolved
Variant: recruit some enzymes from
another pathway without duplicating the
whole thing (example: ubiquitination)
Biochemistry: Metabolism I
11/06/2008
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Reversing a pathway
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We’d like to think that lots of pathways are fully
reversible
Usually at least one step in any pathway is
irreversible (Go’ < -15 kJ mol-1)
Say CD is irreversible so E3 only works in the
forward direction
Then D + ATP C + ADP + Pi allows us to
reverse that one step with help
The other steps can be in common
This is how glycolysis evolved from
gluconeogenesis
Biochemistry: Metabolism I
11/06/2008
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Many cofactors are
derived from vitamins
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We justify lumping these two
topics together because many
cofactors are vitamins or are
metabolites of vitamins.
Biochemistry: Metabolism I
11/06/2008
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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: Metabolism I
11/06/2008
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: Metabolism I
11/06/2008
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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: Metabolism I
11/06/2008
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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: Metabolism I
11/06/2008
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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: Metabolism I
11/06/2008
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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: Metabolism I
11/06/2008
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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: Metabolism I
11/06/2008
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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: Metabolism I
11/06/2008
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