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Principles of metabolic controlEnzyme properties and control in cell
homeostasisIsoenzymes and coenzymes
Medical implications of enzymes
Russian National Research Medical University
Maxim A. Abakumov
Moscow, 2014
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Enzymes
• Protein molecule, which 3D structure allows it
to facilitate biochemical reactions that are
hardly to occur under phisiological conditions
• Increase rate of chemical reactions in cell up to
105 – 1015 times
• Active under mild condition under 100 °C,
P =1 atm, pH 7
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Enzymes• Contains speciall surface region, called «pocket» critical for
reaction• Pocket is called active site.• Active site shows high specifity to reactants and products.• Catalytic activity can be changed by other biomolecules
(allosteric regulation, inhibitors, activators)
http://2012books.lardbucket.org/books/introduction-to-chemistry-general-organic-and-biological/s21-06-enzyme-action.html
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Specific enzyme properties
• pH dependence
• Temperature dependence
• Substrate concentration dependence
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pH and Enzyme Activity
Lehninger 2005 Figure 6.17
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Temperature and Enzyme Activity
http://plantphys.info/plant_physiology/enzymekinetics.shtml
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Substrate concentration and Enzyme Activity
http://plantphys.info/plant_physiology/enzymekinetics.shtml
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Catalase
H2O2 H2O + O2
• 4 subunit protein
• Decompose hydrogen peroxide
• Contains four porhyrin hem groups with iron
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Inernational enzyme classification
• Consists of 4 numbers separated by periods• 1st number shows to which of the six main
divisions (classes) the enzyme belongs• 2nd number indicates the subclass• 3rd number gives the sub-subclass• 4th number is the serial number of the enzyme
in its sub-subclass
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Inernational enzyme classificationSix main divisions (classes) the enzyme
Class Type of reaction catalyzed Example
Hydrolase Hydrolysis Lipase
Isomerase Rearrangement of atoms within a molecule
Phosphogluco-isomerase
Ligase Joining two or more chemicals Acetyl-CoA synthetase
Lyase Splitting a chemical into smaller parts without water
Fructose 1,6-bisphospate aldolase
Oxidoreductase Transfer of electrons (hydrogen atoms)
Lactic acid dehydrogenase
Transferase Moving a functional group from one molecule to another
Hexokinase
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Inernational enzyme classification
• Example: glucose oxidase (1.1.3.4)
• 1 – Oxidoreductase (Class 1)
• 1 – CHOH group is oxidised
• 3 – O2 as an electron aceptor
• 4 – Glucose is oxidised
For additional information on enzyme classification: http://enzyme.expasy.org/
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Principles of enzyme catalytic activity.Reaction energy diagram
www.gcsescience.com
Transition state (X)
En
ergy Reactants
ActivationEnergy
Products
ΔH
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Principles of enzyme catalytic activity.Reaction energy diagram
X1
X2
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Stages of enzymatic reaction
1. Formation of substrate-enzyme complex (ES)
2. Catalysis
3. Formation of product-enzyme complex (EP)
4. Dissosiation
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Formation of substrate-enzyme complex (ES)
Key-lock interaction (Fisher model)
http://2012books.lardbucket.org/books/introduction-to-chemistry-general-organic-and-biological/s21-06-enzyme-action.html
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Formation of substrate-enzyme complex (ES)
Induced fit modelSubstrate
Enzyme Enzyme-substrate complex
Substrate binding changesconformation of active site for better catalytic activity
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Types of enzyme catalytic mechanisms
1. Acid-Base Catalysis
2. Covalent Catalysis
3. Metal Ion Catalysis
4. Electrostatic Catalysis
5. Proximity and Orientation Effects
6. Preferential Binding of the Transition State Complex
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Acid-base catalysis• Specific Acid-Base Catalysis: Uses only the H+ on
OH- ions present in water. (No other molecules involved) Ions are transferred between water and the intermediate faster than the intermediate breaks down to reactants
• General Acid Catalysis: A process in which partial proton transfer from an acid lowers ΔΔG‡ and accelerates the reaction
• General Base Catalysis: A process in which partial proton extraction by a base lowers ΔΔG‡ and accelerates the reaction
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Covalent Catalysis
• Boost reaction through the formation of covalent bonds between substrate and catalyst
• The more stable covalent bond is formed for the transition state the higher is reaction speed
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Metal ion catalysis
• Metaloenzymes: contain strongly bound metal ions: Zn2+, Fe2+, Fe3+,Cu2+ and etc
• Metal activated enzymes: temporally actived by metal ions: Na+, K+, Ca2+, Mg2+
Metal ions:a. Bind substrates to orient them for catalysisb. Gain or loss of electronsc. Electrostatically stabilize or shield negative charges
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Stabilization of enzyme-transition state complex
Proximity and orientation effects:• Bringing substrate into contact with catalytic groups and
multiple substrates with each other- 5 fold boost• Binding substrates in proper orientation to promote the
reaction – 100 boost
Preferential transition state binding:
• The more tightly an enzyme binds its reaction’s transition state (KT) relative to the substrate (KR) , the greater the rate of the catalyzed reaction (kE) relative to the uncatalyzed reaction (kN) - 107 fold boost
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Coenzymes and cofactors
• Some enzymes need any additional nonpeptide components (cofactors) for effective catalysis
• Cofactors can be inorganic or organic• Inorganic: metal ions, iron sulfur clusters• Organic:
1) Tightly bound to enzyme (prosthetic group)
2) Can be released during reaction (coenzymes)
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Coenzymes and cofactors• Enzymes can:
a. Carry out acid-base reactionsb. Transient covalent bondsc. Charge-charge interactions
• Enzymes can not do:d. Oxidation -Reduction reactionse. Carbon group transfers
Holoenzyme: catalytically active enzyme with cofactor.Apoenzyme: Enzyme without its cofactor
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Inorganic cofactorsInorganic Element Enzyme
Cu2+ Cytochrome oxidase
Fe2+; Fe3+ Cytochrome oxidase, catalase
K+ Pyruvate kinase
Mg2+ Hexokinase, pyruvate kinase
Mn2+ Arginase
Mo dinitrogenase
Ni2+ Urease
Se Glutathione
Zn2+ Carbonic anhydrase, alcohol dehyfrogenase
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Organic cofactors
Coenzyme Chemical groups transferred
Dietary precursors
Biotin CO2 Biotin
Coenzyme A Acyl groups Panthothenic acid
5’-Deoxyadenosylcobalamin H, alkyl groups Vitamin B12
Flavin adenine dinuclrotide Electons Riboflavine
Lipoate Electrons, acyl groups
Nicotinamide dinucleotide Hidride ion Nicotinic acid
Pyridoxal phosphate Amino groups Pyridoxine
Tetrhydrofolate One-carbon groups Folate
Thiamine pyrophosphate Aldehydes Thiamine
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Enzyme regulation
• Two main mechanisms:
1) Change in enzyme catalytic properties
(inhibition or activation)
2) Change in total amount of enzyme in cell
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Types of inhibitionInhibition
Nonspecific Specific
Irreversible Reversible
NoncompetetiveCompetetive Uncompetetive
Inhibitor - Any substance that reduces the velocity of an enzyme-catalyzed reaction
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Nonspecific inhibition
1. pH
2. Temperature
3. Heavy metal ions
4. Ionic strength
5. Red/Ox chemicals
6. Organic solvents
• Inhibits all enzyme in same way• Usually goes through denaturation of enzyme and deformation
of active site• Usually occurs under non phisiological conditions
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Types of inhibitionInhibition
Nonspecific Specific
Irreversible Reversible
NoncompetetiveCompetetive Uncompetetive
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Reversible and irreversible inhibition
• Reversible inhibition – inhibitor can bound
and unbound from enzyme
• Irreversible inhibitor is strongly attached to
enzyme (usually by covalent bondind to active
site)
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Irreversible inhibition. Suicide inhibition
• Occurs when inhibitor is transformed in active
site into reactive form
• Aspirin inhibits cyclooxigenase 1 and 2
• Allopurinol inhibits xantine oxidase in the
treatment of gout
• 5-fluorouracil acts as a suicide inhibitor of
thymidylate synthase during the synthesis of
thymine from uridine
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Michaelis-Menten equation
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Lineweaver-Burk linearization
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Lineweaver-Burk linearization
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Lineweaver-Burk linearization =0, если
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Lineweaver-Burk linearization
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Types of inhibition
Specific
Reversible
NoncompetetiveCompetetive Uncompetetive
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Competetive inhibition• Inhibitor is usually a substrate-like molecule• Competitive - where the inhibitor competes with the substrate• Can be reduced be increased concentration of substrate.
COOH
CH2
CH2
COOH
succinate dehydrogenase HOOCCH
CHCOOH
COOH
CH2
COOH
succinate dehydrogenase
Succinate
Malonate
Fumarate
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Competetive inhibitionSubstrate
Enzyme
Active Site
Inhibitor
Enzyme
Active Site
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Competetive inhibitionVmax remains the same, but Km is increased
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Competetive inhibition
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Competetive inhibitionDrug Enzyme inhibited Clinical use
DicoumarolVitamin K Epoxide Reductase
Anticoagulant
Sulphonamide Pteroid Synthase Antibiotic
Trimethoprim Dihydrofolate reductaseAntibiotic
Pyrimethamine Dihydrofolate reductase Antimalarial
Methotrexate Dihydrofolate reductase Anticancer
Lovastin HMG-CoA-reductaseCholesterol lowering drug
Alpha Methyl Dopa Dopa decarboxylase Antihypertensive
Neostigmine Acetyl Cholinesterase Myastenia Gravis
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HIV protease inhibitors
http://aac.asm.org/content/55/4/1377/F1.expansion.html
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Noncompetitive inhibition
Substrate
Enzyme
Inhibitorsite
Active Site
EnzymeInhibitorsite
Active Site
Inhibitor
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Noncompetitive inhibitionVmax is decreased, but Km is the same
Normal Enzyme
Competitive Inhibitor, same Vmax, increased KM
Vmax
Vi
KM
[ S ]
Noncompetitive Inhibitor, same KM, dicreased Vmax
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Noncompetitive inhibitionVmax is decreased, but Km is the same
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Noncompetitive inhibition
• Inhibition of cytochrome oxidase by cyanide
• Inhibition of SH-grous by Iodoacetate
• Inhibition of PFK by ATP
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Uncompetetive inhibitiona) Reaction
a) Inhibition
Substrate
Substrate
Enzyme
Enzyme
Active site
Active site
Inhibitor
Inhibition site
Inhibition site
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Uncompetetive inhibition
• Inhibitor binds only to ES complex• Binding might occur in active site, but prior
substrate bindind is reguired• High concentration of substrate can not
overcome inhibition
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Uncompetitive inhibitionVmax is decreased, and Km is increased
Normal Enzyme
Competitive Inhibitor, same Vmax, increased KM
Vmax
Vi
KM
[ S ]
Noncompetitive Inhibitor, same KM, dicreased Vmax
Uncompetetive Inhibitor,Km is increased and Vmax is decreased
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Uncompetitive inhibition
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Inhibition
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Enzyme regulation
• Genetic regulation• Covalent modification• Allosteric regulation• Rate depends on substrate availability • Zymogens, isozymes and modulator proteins
may play a role
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Genetic regulation
• Affects on total amount of enzyme in cell• Controlled by gen expression• Hormone controlled • Feedback inhibition or activation• Long term mechanism
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Genetic regulation• Increase in enzyme production by increase in gene
expression is called induction.
• Decrease in enzyme production by decrease in gene
expression is called repression
• Induction and repression is used only for gene
expression
• Protein degradation process always occurs in cell
• Total amount of protein is defined by equlibrium
between degradation and synthesid
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Genetic regulation. Estrogen receptors
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Covalent modification. Controlled proteolysis (zymogens)
• Zymogens (proenzymes) – inactive form of enzyme,
that might be activated
• Zymogens usually are storage form of active enzyme
• Used for rapid regulation of amount of active enzyme
• Usually are activated by proteolysis
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Zymogens (proenzymes)
Examples:
• Activation of trypsin and chymotrypsin from
trypsinogen and chymotrypsin by proteolisys
in intestine
• Most proteins in coagulation system are
zymogens
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Covalent modification. Phosphorylation/dephosphorylation
• Covalent addition/removal of inorganic phosphate
• Can both increase and decrease reaction speed• Usually catalized by enzyme called kinase
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Allosteric regulation
• Key enzymes are regulated by allosteric regulators
• These allosteric effectors usually are located elsewhere in pathway
• Regulators might be activators or inhibitors• Tipicall S-shape (sigmoid) curve• Multisubunit enzymes structure provides
cooperative effect
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Allosteric Effect
http://www.tutorvista.com/content/biology/biology-iii/cellular-macromolecules/enzymes-classification.php
Schematic representation of allosteric enzyme activity
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Allosteric Effect
0.4 mM
2.0 mM
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Allosteric Effect
http://bcs.whfreeman.com/thelifewire/content/chp06/0602002.html
001.swf
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Feedback inhibition
• The product of a metabolic pathway inhibits is own synthesis at the beginning or first committed step in the pathway
ATCaseCarbamoyl phospate+
Aspartate
N-carbamoylaspartate
INHIBITION
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Feedback inhibition
http://highered.mheducation.com/olcweb/cgi/pluginpop.cgi?it=swf::535::535::/sites/dl/free/0072437316/120070/bio10.swf::Feedback%20Inhibition%20of%20Biochemical%20Pathways
002.swf
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Glycogen Phosphorylase
• Pi is a positive homotropic effector
• Pyridoxale phosphate is needed as a cofactor• ATP is a feedback inhibitor, and a negative
heterotropic effector (inhibitor)• Glucose-6-P is a negative heterotropic effector
(inhibitor)• AMP is a positive heterotrophic effector (activator)• Activated by phosphorylation• Deactivated by dephosphorylation
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Isozymes
• Isozymes – isoforms or different enzymes that catalise
same reaction
• These enzymes usually display different kinetic
parameters (e.g. different KM values), or different
regulatory properties
• Usually they are coded by homologous genes that
have diverged over time
• Provides adaptation of different organs and tissues
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Isozymes
Examples:
• Cytochrome P450 family proteins
• Phosphodiesterases
• Hexokinases
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IsozymesThe enzyme Lactate Dehydrogenase is made of two(B-form and A-Form) different sub units