Compartmentalisation of metabolic pathways

Josef Fontana

EC - 41

Overview of the seminar• Introduction to the topic: energy metabolism

– revision of the energy metabolism

• Compartmentalization of metabolic pathways• General principles of regulation of the metabolism• Regulation on the cell level

– 1) compartmentalization of metabolic pathways– 2) change of enzyme concentration (on the level of

synthesis of new enzyme)– 3) change of enzyme activity (an existing enzyme is

activated or inactivated)– A) in relation to an enzyme kinetics– B) activation or inactivation of the enzyme

Introduction to the topic: energy metabolism

Revision of the energy metabolism

The main pathways of the EM

• Catabolic reactions– glycolysis

– glycogenolysis (degradation of glycogen)

– lipolysis

– beta-oxidation

– ketone bodies degradation

– degradation of AA, proteolysis

The main pathways of the EM

• Anabolic reactions:– glycogenesis

– gluconeogenesis

– lipogenesis (synthesis of TAG), synthesis of FA

– ketogenesis

– proteosynthesis

– synthesis of AA

– urea synthesis

The main pathways of the EM

• Main reactions:– pyruvate dehydrogenase reaction

– Krebs cycle

– respiratory chain

Major intermediates are

acetyl-CoA

pyruvate

NADH

The figure is found at http://www.elmhurst.edu/~chm/vchembook/images/590metabolism.gif (December 2006)

pyruvate (PDH) – i.e. from glucose

amino acids (degrad.) – from proteins

fatty acids (β-oxidation) – from TAG

ketone bodies (degrad.) – from FA

acetyl-CoA

citrate cycle, RCH → CO2, H2O, ATP

synthesis of FAsynthesis of ketone bodies

synthesis of cholesterol synthesis of glucose !!!

aerobic glycolysisoxidation of lactate (LD)

degradation of some amino acids

pyruvate

acetyl-CoA (PDH)lactate (lactate dehydrogenase)

alanine (alanine aminotransferase)

oxaloacetate (pyruvate carboxylase)

glucose (gluconeogenesis)

aerobic glycolysisPDH reactionβ-oxidationcitrate cycle

oxidation of ethanol

NADH pyruvate → lactate

respiratory chain → reoxidation to NAD+

energy storage in ATP! OXYGEN SUPPLY IS NECESSARY !

The most important is to answer these questions

• What ?• Where ?• When ?• How ?• Why ?

The most important is to answer these questions

• Where ?

• Compartmentalization of the pathways

• Regulation of the processes

Compartmentalization of metabolic pathways

Compartmentalization

The figure is found at http://fig.cox.miami.edu/~cmallery/150/proceuc/c7x7metazoan.jpg (May 2007)

Cytoplasm• Glycolysis• Gluconeogenesis (from oxaloacetate or glycerol)• Metabolism of glycogen• Pentose cycle• Synthesis of fatty acids• Synthesis of nonessential amino acids• Transamination reactions • Synthesis of urea (a part; only in the liver!)• Synthesis of heme (a part)• Metabolism of purine and pyrimidine nucleotides

Mitochondria• Pyruvate dehydrogenase complex (PDH)• Initiation of gluconeogenesis• β-oxidation of fatty acids• Synthesis of ketone bodies (only in the liver!) • Oxidation deamination of glutamate • Transamination reactions• Citrate cycle• Respiratory chain (inner mitochondrial membrane)• Aerobic phosphorylation (inner mitoch. membrane) • Synthesis of heme (a part)• Synthesis of urea (a part)

Endoplasmic Reticulum

• Rough ER– proteosynthesis (translation and

posttranslational modifications)• Smooth ER

– synthesis of triacylglycerols and phospholipids

– elongation and desaturation of fatty acids– synthesis of steroids– biotransformation of xenobiotics– glucose-6-phosphatase

Other organels

• Golgi Apparatus– posttranslational modification of proteins– protein sorting – export of proteins (formation of vesicules)

• Ribosomes – proteosynthesis

• Nucleus– replication and transcription of DNA– synthesis of RNA

Other organels

• Lysosomes– hydrolysis of proteins, saccharides, lipids

and nucleic acids

• Peroxisomes– oxidative reactions involving O2

– use of hydrogen peroxide

– degradation of long chain FA (from C20)

General principles of regulation of the metabolism

General principles of regulation of the metabolism

• Catabolic / anabolic processes• Last step of each regulation mechanism:

change of a concentration of an active enzyme (= regulatory or key enzyme)

• Regulatory enzymes– often allosteric enzymes– catalyze highly exergonic reactions

(irreverzible)– low concentration within a cell

Regulation on the cell level

Regulation on the cell level

• 1) Compartmentalization of metabolic pathways

• 2) Change of enzyme concentration (on the level of synthesis of new enzyme)

• 3) Change of enzyme activity (an existing enzyme is activated or inactivated)

Regulation on the cell level

1) Compartmentalization of metabolic pathways

Compartmentalization of metabolic patways

• Transport processes between compartments

• Various enzyme distribution• Various distribution of substrates and

products (∼ transport)• Transport of coenzymes• Subsequent processes are close to each

other

Regulation on the cell level

2) Change of enzyme concentration (on the level of synthesis of new enzyme)

Synthesis of new enzyme molecule

• Enzyme concentration is much lower than the substrate concentration

• The rate of an enzyme-catalyzed reaction is directly dependent upon the enzyme concentration

• Induction by substrate or repression by product (on the level of transcription)– xenobiotics → induction of cyt P450

– heme → repression of delta-aminolevulate synthase

Synthesis of new enzyme molecule

• Change in the rate of synthesis or degradation of the enzyme - hormonal and nutritional factors– well-fed state: the liver improves its

capacity to synthesize fat

– fasting: ↓in quantity of lipogenetic enzymes; enzymes of gluconeogenesis are induced (↑synthesis)

Regulation on the cell level

3) Change of enzyme activity (an existing enzyme is activated or inactivated)

A) In relation to an enzyme kinetics

Enzyme kinetics

The figure is found at: http://fig.cox.miami.edu/~cmallery/255/255enz/gk3x15.gif (December 2006)

Enzyme kinetics - the curve can be described by the equation:

• Michaelis constant KM corresponds to the substrate concentration [S] at which velocity V is half of the maximum velocity Vmax (when v = ½ Vmax). An enzyme with a high affinity for its substrate has a low KM value.

• KM = mol/L

Change of activity of an existing enzyme

• A) In relation to an enzyme kinetics:– concentration of substrates (< Km)

– pH and temperature changes

– availability of coenzymes

– consumption of products

– substrate specificity - different Km

Regulation on the cell level

3) Change of enzyme activity (an existing enzyme is activated or inactivated)

B) Activation or inactivation of the enzyme

Change of activity of an existing enzyme

• B) Activation or inactivation of the enzyme:• Covalent modification of the enzyme molecule

– cleavage of an precursore (proenzyme, zymogen)

– reversible phosphorylation and dephosphorylation (interconversion of enzymes by protein kinase or protein phosphatase respectively)

• Modulation of activity by modulators (ligands):– feed back inhibition

– cross regulation

– feed forward activation