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11/06/2008Biochemistry: Metabolism I
General Metabolism I
Andy HowardIntroductory Biochemistry
6 November 2008
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What we’ll discuss Metabolism
Definitions Pathways Control Feedback Phosphorylation Thermodynamics Kinetics
Cofactors Tightly-bound metal
ions as cofactors Activator ions as
cofactors Cosubstrates Prosthetic groups
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Metabolism 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!
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Intermediary Metabolism 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?
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Anabolism and catabolism Anabolism: synthesis of complex
molecules from simpler ones Generally energy-requiring Involved in making small molecules and
macromolecules Catabolism:degradation of large
molecules into simpler ones Generally energy-yielding All the sources had to come from
somewhere
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Common metabolic themes 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
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Metabolism and energy
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Pathway 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: Unbranched Branched Circular
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Why multistep pathways?
Limited reaction specificity of enzymes
Control of energy input and output: Break big inputs into ATP-sized inputs Break energy output into pieces that
can be readily used elsewhere
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Regulation Organisms respond to change
Fastest: small ions move in msec Metabolites: 0.1-5 sec Enzymes: minutes to days
Flow of metabolites is flux: steady state is like a leaky bucket Addition of new material replaces the
material that leaks out the bottom
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Metabolic flux, illustrated Courtesy Jeremy Zucker’s wiki
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Feedback and Feed-forward
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
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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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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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Activation and inactivation by post-translational modification
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
Phosphatases hydrolyze phosphoester:Protein-O-P +H2O Protein-OH + Pi
… no external energy source required
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Phosphorylation’s effects
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
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Glycogen phosphorylase Reaction: extracts 1 glucose
unit from non-reducing end of glycogen & phosphorylates it:(glycogen)n + Pi (glycogen)n-1 + glucose-1-P
Activated by phosphorylationvia phosphorylase kinase
Deactivated by dephosphorylation byphosphorylase phosphatase
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Amplification
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
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Other PTMs (p. 505)
Are there other reversible PTMs that regulate enzyme activity? Yes: Adenylation of Y ADP-ribosylation of R Uridylylation of Y Oxidation of cysteine pairs to cystine
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Evolution of Pathways:How have new pathways evolved? 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
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Adding a step
A B C D E P
• 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
E1 E2 E3 E4 E5
Original pathway
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Evolving a branch Original pathway:
D A B C X
Fully evolved pathway: D A B C X
E1 E2E3
E3a
E3b
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Backward evolution
Original system has lots of E P E gets depleted over time;
need to make it from D, so we evolve enzyme E4 to do that.
Then D gets depleted; need to make it from C, so we evolve E3 to do that
And so on
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Duplicated pathways
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)
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Reversing a pathway 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 CD 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
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Many cofactors are derived from vitamins We justify lumping these two
topics together because many cofactors are vitamins or are metabolites of vitamins.
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Family tree of cofactors Cofactors, coenzymes, essential ions,
cosubstrates, prosthetic groups:
Cofactors(apoenzyme + cofactor holoenzyme)
Essential ions Coenzymes
Activator ions(loosely bound)
Ions inmetalloenzymes
Prosthetic groups(tightly bound)
Cosubstrates(loosely bound)
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Metal-activated enzymes Absolute requirements for mobile ions
Often require K+, Ca2+, Mg2+
Example: Kinases: Mg-ATP complex
Metalloenzymes: firmly bound metal ions in active site Usually divalent or more Sometimes 1e- redox changes in metal
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Coenzymes Organic moeities that enable enzymes to
perform their function: they supply functionalities not available from amino acid side chains
Cosubstrates Enter reaction, get altered, leave Repeated recycling within cell or organelle
Prosthetic groups Remain bound to enzyme throughout Change during one phase of reaction,
eventually get restored to starting state
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Major cosubstrates Facilitate group transfers, mostly small groups Oxidation-reduction participantsCosubstrate Source Function
ATP Transfer P,Nucleotide
S-adenosylMet Methyl transfer
UDP-glucose Glycosyl transfer
NAD,NADP Niacin 2-electron redox
Coenzyme A Pantothenate Acyl transfer
Tetrahydrofolate Folate 1Carbon transfer
Ubiquinone Lipid-soluble e- carrier
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Major prosthetic groups Transfer of larger groups One- or two-electron redox changesProsth.gp. Source FunctionFMN, FAD Riboflavin 1e- and 2e- redox transfersTPP Thiamine 2-Carbon transfers with C=OPLP Pyridoxine Amino acid group transfersBiotin Biotin Carboxylation, COO- transferAdenosyl- Cobalamin Intramolec. rearrangements cobalaminMeCobal. Cobalamin Methyl-group transfersLipoamide Transfer from TPPRetinal Vitamin A VisionVitamin K Vitamin K Carboxylation of glu residues
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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
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S-adenosylmethionine Made from methionine and adenosine Sulfonium group is highly reactive: can
donate methyl groups
Reaction diagram courtesy of Eric Neeno-Eckwall, Hamline University
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UDP-glucose Most common donor of glucose Formed via:
Glucose-1P + UTPUDP-glucose + PPi
Reaction driven to right by PPi hydrolysis
Structure courtesy of UIC Pharmacy Program