Chapter 10: Introduction to Metabolism Metabolites: small molecules that are intermediates in the degradation or synthesis of biopolymers. Anabolic reactions:

Chapter 10: Introduction to MetabolismChapter 10: Introduction to Metabolism

Metabolites: small molecules that are intermediates in the degradation or synthesis of biopolymers.

Anabolic reactions: Synthesis of molecules necessary for the life of the cell.

Catabolic reactions: Degradation of molecules to smaller molecules and to produce energy.

The entire network of chemical reactions carried out by the cell

AA, carb, nucleotides, fatty acids

Animals need food for organic molProvided by biosyn pathway in another species

4 major groups of biomolecules:

Metabolic PathwaysMetabolic Pathways

Pathways are sequences of reactions:

Linear pathwayCyclic pathway

(citric acid cycle)

Spiral pathway(fatty acid synthesis)

Series of independent enzymes Intermediates are regenerated every turn

(Very few are cyclic pathways)

Same set of enzymes are used repeatedly

Product is sub for next rxnPolymerization rxns

Major Metabolic PathwaysMajor Metabolic Pathways

Catabolic Pathways

Reactions and pathways can be linked to form extended metabolic routes

Major Metabolic PathwaysMajor Metabolic Pathways

Autotrophs: can utilize inorganic sources of essential elements.

Anabolic Pathways (biosynthesis)

PhotoautotrophsChemoautotrophs

Large mol from smaller molBy adding C and N

Energy provided byLight orBreakdown of organic mol from other autotrophs

Heterotrophs: need mol such as glucose

Most biochemically complex organisms?? Autotrophs

Catabolic PathwaysNot simply reverse of anabolic rxns

AA, nucleotides, monosacc,FA are formed by hydrolysis

Then degraded in oxidative rxns and energy conserved in ATP and red coenzymes (NADH)

Eliminate unwanted mol and generate energy

CAC: main source of energy to drive ATP syn

But also important in anabolic pathways: source of precurcors for AA syn

Main role:

Metabolism Proceeds in Discrete StepsMetabolism Proceeds in Discrete Steps

Narrow conditions of the cell (pH, temperature, pressure, concentrations) require specific and efficient enzymes.

Limited reaction specificity of enzymes requires multiple steps.

Multiple steps required to control energy input and output.

Allow sharing of intermediates.

Allow more control pointsto regulate biochem process.

But why are there so manydistinct rxns involved ??

Energy carriers (ATP/NADH) are in all life forms

Metabolic Pathways are RegulatedMetabolic Pathways are Regulated

Organisms react to changing environmental conditions (avail. of nutrients) and genetically programmed instructions (during development)

Regulate synthesis/degradation of biomol and generation/ use of energy

Most pathways:

Go in single direction (in physiological conditions)Without backing up and wasting energy etc

Flux = flow through a pathway.

Flow will continue as long as A is high and P is removed

Intermediates are in steady state (B,C,D,E do not change much)

Special regulatory controls that affect particular enzymes in pathwayUsually there are multiple control points

“regulatory enzymes”

Regulation of Metabolic PathwaysRegulation of Metabolic Pathways

Feedback inhibition.

Feed-forward activation.

Controls the first committed step (the first rxn unique to pathway)

Prevent unnecessary accumulation of metabolic intermediates

Inc in metabolite B increases flux thru the pathway

Two patterns of metabolic regulation

Allosteric modulation

Regulation of GlycolysisRegulation of Glycolysis

Signals adequatesupply of energy

Intermediate of CAC

Glycolysis activity dec when its products are no longer reguired

First committed step of glycolysis

High AMPindicatesdec. ATP

Phosphofructokinase-1Phosphofructokinase-1

ATP: allosteric inhibitor

AMP: allosteric activator

It is an allosteric enzyme and a regulatory step for glycolysis

Metabolically irreversible rxn.

[ATP] > ADP / AMP

Regulation of Metabolic PathwaysRegulation of Metabolic Pathways

Regulation of pathway occurs through allosteric modulators (inhibitors and activators),

and by covalent modification (protein kinases,phosphatases).

Amplification of original signal

Kinases with multiple specificities:

Coordinated reg of many pathyways

Slow process : relative to allosteric/covalent

Anabolic pathways: phosp-inactive

Rapid and reversible

Catabolic pathways: phosp-active

Regulated rate of enzyme syn/ degradation

phosphorylated protein is active or inactive

A + B C + D

Keq = [C][D]

[A][B]

G = 0 at equilibrium, no net synthesis of products

Greaction = Go’ + RTln [C][D]

[A][B]

When Greaction > 0, the reaction is unfavorable, energy needed to make G neg..When Greaction << 0, the reaction is favorable, spontaneous and irreversible

(no external source of energy needed).

The Free Energy of Metabolic ReactionsThe Free Energy of Metabolic Reactions

Gibbs free energy change: measure of energy available from a rxn

Standard Gibbs free energy: change under standard conditions(1M reactants and products)

Actual Gibbs free energy: depends on real concentrations

G = H - TS chem process)

Measure how far from equilibrium the reacting system is operating

Go’

G

Determine the spontaneity of a rxn and thus its direction

G

A + B C + D

Keq = [C][D]

[A][B]G = 0 at equilibrium, no net synthesis of products

Greaction = Go’ + RTln [C][D]

[A][B]

Gibbs free energy change

Measure how far from equilibrium the reacting system is operating

Near equilibrium rxns: small free energy changes

Rxns are readily reversible

Can accomodate flux in either directionand quickly restore levels of R and P to equil status

(Most metabolic rxns)

Not suitable control points of a pathway

Direction of rxn can be controlled by changes in [S] [P]

G

A + B C + D

Keq = [C][D]

[A][B]G = 0 at equilibrium, no net synthesis of products

Greaction = Go’ + RTln [C][D]

[A][B]

Near equilibrium rxns: small free energy changes

Metabolically irreversible rxns

Rxns are readily reversible

Rxns greatly displaced from equil

Large G

Can accomodate flux in either directionand quickly restore levels of R and P to equil status

Flux is is unaffected by changes in metabolite concthus usually controlled by modulating the enzyme

(Most metabolic rxns)

Gibbs free energy change

Measure how far from equilibrium the reacting system is operating

G

Metabolic Pathways are RegulatedMetabolic Pathways are Regulated

Most pathways:

Go in single directionWithout backing up and wasting energy etc

Regulation of unidirectional rxns (irreversible)

“regulatory enzymes”

[S] and [P] far from equilibrium

Regulatory enzyme controls flux

E6

Reverse reaction need different enzyme…….key regulatory step

unaffected by changes in metabolite conccontrolled by modulating the enzyme

Large G

Metabolically irreversible rxns : need diff enzyme for reverseMetabolically irreversible rxns : need diff enzyme for reverse

Fructose 1,6 bisphosphatase

Inhibited by AMP

Inc in AMP indicatesDec in ATPNeed ATPNeed glycolysisInhibit glc synthesis

The Free Energy of ATPThe Free Energy of ATP

ATP (and PPi) is an energy-rich compound:

Why large amt of energy released during hydrolysis?

Electrostatic repulsion of negative charges on phosphoanhydride bonds is less after hydrolysis.

Products of hydrolysis are better solvated (by H2O) than ATP.

The products of hydrolysis are more stable than ATP.

e- on terminal oxygens more delocalized

Phosphoanhydride vs Phosphoester linkage

Dec the repulsion of P groups drive the rxn

Bridging O two terminal O

The Free Energy of ATPThe Free Energy of ATP

[ATP] >> other NTP but all are called ‘energy rich compounds’

Intracellular [ATP] little fluctuation

Maintained by adenylate kinase AMP + ATP + 2Pi 2 ATP + 2 H20

[ATP] > ADP / AMP small change in [ATP]…large change in [ADP/AMP]

allosteric modulator of some energy yielding processes

Phosphoanhydride higher energy

The Metabolic Roles of ATPThe Metabolic Roles of ATP

Phosphoryl-group transfer:

Glutamate + NH4+ Glutamine; Go’ = +14 kJ mol-1

Rxn not possible (not spontaneous) in living cells:Glutamine steady state levels are highLimiting supply of ammonia

ATP hydrolysis drives the rxn

The Metabolic Roles of ATPThe Metabolic Roles of ATP

Phosphoryl-group transfer:

Glutamate + NH4+ Glutamine; Go’ = +14 kJ mol-1

Glutamate + ATP Glutamyl-P + ADPGlutamyl-P + NH4

+ Glutamine +Pi

Glutamate + NH4+ Glutamine Go’ = +14 kJ mol-1

ATP ADP + PiGo’ = -32 kJ mol-1

Glutamate + NH4+ + ATP Glutamine + ADP + Pi Go’ = -18 kJ mol-1

Carboxyl group Is activated

Coupledrxn

(Glutamine synthetase)

Phosphoryl group-transfer potentialPhosphoryl group-transfer potential

ATP: intermediate phos-group-trans potential and kinetically stable thus mediates most energy transfers

Measure of free energy required for formation of the phosp compound

Production of ATP by phosphoryl group transfer:

Phosphagens

High phosphorylgroup-transfer potential

More stableMetabolically irreversible

Energy storage in muscle

3-4 sec burst of energy

When ATP low

Allows replenishment

The Metabolic Roles of ATPThe Metabolic Roles of ATP

Nucleotidyl group transfer:

ATP AMP + PPi

Acetate + HS-CoA Acetyl-CoA PPi 2Pi

Go’ = -45 kJ mol-1

Go’ = +32 kJ mol-1

Go’ = -29 kJ mol-1

Acetate + ATP + HS-CoA Acetyl-CoA + AMP + 2PiGo’ = -42 kJ mol-1

Removal of (PPi) productdrives the rxn

AMP is transferred

Thioesters have high free energies of hydrolysisThioesters have high free energies of hydrolysis

GTP synthesis by coupling to thioester hydrolysis.

Thioesters less stable than oxygen estersunshared e- of S not effectively delocalized

Energy similar to phosphoanhydride linkage

Substrate level phosphorylation Conserves the energy used in formation