Download Compartmentalisation of metabolic pathways

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 FA
synthesis of ketone bodies
synthesis of cholesterol
synthesis of glucose !!!
aerobic glycolysis
oxidation of lactate (LD)
degradation of some amino acids
pyruvate
acetyl-CoA (PDH)
lactate (lactate dehydrogenase)
alanine (alanine aminotransferase)
oxaloacetate (pyruvate carboxylase)
glucose (gluconeogenesis)
aerobic glycolysis
PDH reaction
β-oxidation
citrate 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