11/06/2008biochemistry: metabolism i general metabolism i andy howard introductory biochemistry 6...

11/06/2008Biochemistry: Metabolism I

General Metabolism I

Andy HowardIntroductory Biochemistry

6 November 2008

11/06/2008Biochemistry: Metabolism I of 34

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


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!


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?


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


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


Metabolism and energy


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


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


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


Metabolic flux, illustrated Courtesy Jeremy Zucker’s wiki


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


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


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


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


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


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


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


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


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


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


Evolving a branch Original pathway:

D A B C X

Fully evolved pathway: D A B C X

E1 E2E3

E3a

E3b


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


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)


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


Many cofactors are derived from vitamins We justify lumping these two

topics together because many cofactors are vitamins or are metabolites of vitamins.


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)


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


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


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


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


Adenosine triphosphate Synthesizable in liver (chapter 18) Building block for RNA Participates in phosphoryl-group transfer

in kinases Source of other coenzymes


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


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

11/06/2008biochemistry: metabolism i general metabolism i andy howard introductory biochemistry 6...

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