Important terms of enzymology Course 2 / 210 Vladimíra Kvasnicová
Important terms of enzymologyCourse 2 / 210
Vladimíra Kvasnicová
The figure is found at: http://fig.cox.miami.edu/~cmallery/255/255enz/enzymology.htm (December 2006)
Biochemical reactions are catalyzed by enzymes:
Enzymes are commonly called according to the:
a) type of the chemical reaction
b) type of the substrate
Laboratory order form from http://spch.cz/kliniky/kbi/laboratorni_prirucka/zadanka_biochemie.pdf (December 2006)
ENZYMES
The figure is adopted from the book: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley-Liss, Inc., New York, 1997. ISBN 0-471-15451-2
„ Cardiac enzymes“
abbreviations of enzymes
• used in a medicine
• e.g. LD, ALT, ALP
old trivial names
• no relationship to the catalyzed reaction
• suffixed by -in (pepsin, trypsin)
• used for long time known enzymes
Enzyme nomenclature
EC nomenclature http://www.chem.qmul.ac.uk/iubmb/enzyme/
* each enzyme is classified by EC number(Enzyme Commission of IUBMB) – 6 classes:
• EC 1.x.x.x oxidoreductases
• EC 2.x.x.x transferases
• EC 3.x.x.x hydrolases
• EC 4.x.x.x lyases
• EC 5.x.x.x isomerases
• EC 6.x.x.x ligases (synthetases)
→ classification by a reaction catalyzed by the enzyme
IUBMB Enzyme Nomenclature
EC 2.7.1.1Accepted name: hexokinase
Reaction: ATP + D-hexose = ADP + D-hexose 6-phosphate
Other name(s): hexokinase type IV glucokinase; hexokinase D; hexokinase type IV; hexokinase (phosphorylating); ATP-dependent hexokinase; glucose ATP phosphotransferase
Systematic name: ATP:D-hexose 6-phosphotransferase
Comments: D-Glucose, D-mannose, D-fructose, sorbitol and D-glucosamine can act as acceptors; ITP and dATP can act as donors. The liver isoenzyme has sometimes been called glucokinase.
The reference is found at http://www.chem.qmul.ac.uk/iubmb/enzyme/EC2/7/1/2.html
example:
systematic names
• are made according to special rules, they specify a reaction catalyzed by the enzyme
example:ATP : D-glucose phosphotransferase (EC 2.7.1.2)
→ transfers (2) phosphate (7) to an alcohol group (1)
ATP + D-Glc → ADP + D-Glc-6-phosphate
(Glc-6-P)
EC 2.7.1.2. = glucokinase = accepted name
oxidation / reduction (ions, organic compounds)enzymes: oxidoreductases (EC 1.x.x.x)
distinguish:
� dissociation / pH / acidity / H+ / H30+
� dehydrogenation / H / H2
• „redox equivalents“
� FADH2
� NADH+H+
� NADPH+H+
http://biochem.siuc.edu/web_lessons/bmb_vit.htm
FAD (oxidized) FADH2 (reduced)
http://dolly.biochem.arizona.edu/Bioc462b_Honors_Spring_2009/kyang/whatisnad2.html
common names (= accepted names) *
• simple, commonly used in practice
• very important!
1. oxidoreductases: Aox + Bred →→→→ Ared + Box
* dehydrogenase (H- or H)
* reductase
* oxidase
* peroxidase (various peroxides)
* oxygenase (O2)
* hydroxylase (= monoxygenase; -OH)
* desaturase (-CH2CH2- → -CH=CH-)
enzymes transferring groups = transferases (EC 2.x.x.x)
→ transfer of –NH2, phosphate, acyl, C1-fragments,...
distinguish:
� acyl of an acid
� anion of an acid
2. transferases: A-x + B →→→→ A + B-x* grouptransferase (e.g. aminotransferase)
* kinase (= phosphotransferase)* phosphorylase
* transketolase
* transaldolase
enzymes catalyzing hydrolysis = hydrolases (EC 3.x.x.x)
• reactions: condensation / hydrolysis
3. hydrolases: A-B + H2O →→→→ A-H + B-OH
„substrate“-ase
* peptidase, glycosidase, lipase, nuclease
* esterase (R1-CO-O-R2)
* phosphatase (phosphate-O-R) → Pi !!!
* phosphodiesterase
(R1-O-phosphate-O-R2)
enzymes catalyzing introduction or releasing of a small compound
= lyases (EC 4.x.x.x)
- addition or elimination of water = hydration / dehydration
- removing of CO2 = decarboxylation (not carboxylation!)
4. lyases: A-x ↔↔↔↔ B + x* decarboxylase (→ CO2)
* dehydratase (→ H2O)
* hydratase (-CH=CH- + H2O → -CH(OH)CH2-)
* (synthase)
enzymes catalyzing isomerization = isomerases (EC 5.x.x.x)
isomers = chemicals having the same molecular formula but differing in their structures
e.g. C6H12O6 glucose / fructose
5. isomerases: A →→→→ iso-A
* epimerase (monosacharide → its epimer)
* mutase (rearangement of a phosphate group)
enzymes catalyzing synthetic reaction which needs energy from an energy rich compound = ligases (EC 6.x.x.x)
6. ligases: A + B + ATP →→→→ A-B + ADP + Pi
* carboxylase
* (synthetase)
examples:
• pyruvate carboxylase
• glutamine synthetase = glutamate-ammonia ligase
AST aspartate aminotransferase
ALT alanine aminotransferase
GMT gamma-glutamyl transpeptidase
ALP alkaline phosphatase
ACP acid phosphatase
AMS α-amylase
LPS lipase
CK creatine kinase
CHE cholinesterase
LD lactate dehydrogenase
Add class to which each enzyme belongs
Cofactors of
oxidoreductases:NAD+ nicotinamide adenine dinucleotideNADP+ nicotinamide aden. dinucl. phosphate
(precursor: niacin = nicotinic acid) H-
FAD flavin adenine dinucleotideFMN flavin mononucleotide
(precurzor: riboflavin = vitamin B2) 2 H
heme Fe3+ + e- ↔ Fe2+ ⇒ e-
transferases:
ATP adenosine triphosphate / phosphateGTP guanosine triphosphate / phosphate
TDP thiamine diphosphate / C-fragment(prekurzor: thiamine = vitamin B1)
PALP pyridoxal phosphate / -NH2
(prekurzor: pyridoxine = vitamin B6)
THF tetrahydrofolate / C1-fragment(prekurzor: folic acid)
CoA coenzyme A (HS-Co-A) / acyl
PAPS phosphoadenosine phosphosulfate / sulfate
http://web.indstate.edu/thcme/mwking/amino-acid-metabolism.html (Jan 2007)
3´-phosphoadenosine-5´-phosphosulfate (PAPS)
transfers sulfate group to a substrate (sulfatation)
http://lxyang.myweb.uga.edu/bcmb8010/pic/NAD+.gif and http://oregonstate.edu/instruct/bb450/stryer/ch14/Slide26.jpg (Jan 2008)
Coenzyme A = CoA-SH
http://www.dentistry.leeds.ac.uk/biochem/postgrad/thftypes.gif (Jan 2008)
Derivates of tetrahydrofolate
lyases:
PALP pyridoxal phosphate (decarboxylases)
ligases:
ATP adenosine triphosphate
→ acyl-CoA-synthetases
→ aminoacyl-tRNA-synthetases
biotin = vitamin H (carboxylases)
Enzymes
• lower an energy of activation (EA)• reduce the time to reach the reaction equilibrium• are not consumed or changed by the reaction• help the reaction proceed under a body´s T, p and pH• are specific• can be regulated
• don´t change the ∆G of the reaction• don´t change the equilibrium position of the reaction
self study
The figure is adopted from the book: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley-Liss, Inc., New York, 1997. ISBN 0-471-15451-2
The figure is found at: http://stallion.abac.peachnet.edu/sm/kmccrae/BIOL2050/Ch1-13/JpegArt1-13/05jpeg/05_jpeg_HTML/index.htm (December 2006)
Each enzyme has
temperature optimum pH optimum affinity to its substrate
Some enzymes are produced as precursors (= PROENZYMES or ZYMOGENS)
The figure is found at: http://wine1.sb.fsu.edu/bch4053/Lecture26/zymogen.jpg (December 2006)
The figure is found at: http://fig.cox.miami.edu/~cmallery/150/memb/c11x11enzyme-cascade.jpg(December 2006)
or must be activated to be active (e.g. by phosphorylation):
Isoenzymes (isozymes) are enzymes which catalyze the same reaction but differ in their primary structure and phyzico chemical properties
Isoenzymes are
• produced by different genes (= true isozymes)
• or produced by different posttranslationalmodification (= isoforms)
• found in different compartments of a cell
• found in different tissues of an organism
• can be oligomers of various subunits (monomers)
The figure is found at: http://wine1.sb.fsu.edu/bch4053/Lecture26/isozymes.jpg (December 2006)
example: 5 isozymes (various monomer ratio)
This is Figure 17.6 from Garrett, R.H.; Grisham, C.M. Biochemistry; Saunders: Orlando,1995; page 553, found at http://www.uwsp.edu/chemistry/tzamis/enzyme_complex.html (December 2006)
multienzyme complexesseparate enzymes of a mtb pathway
The figure is found at: http://faculty.uca.edu/~johnc/pdhrxns.gif (December 2006)
example: 2-oxoacid dehydrogenase multienzyme complex
The figure is adopted from the book: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley-Liss, Inc., New York, 1997. ISBN 0-471-15451-2
Allosteric enzyme : a) monomeric, b) oligomeric
The figure is adopted from the book: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley-Liss, Inc., New York, 1997. ISBN 0-471-15451-2
Allosteric enzyme in T and R conformations: modulators shift the equilibrium
inhibitorshave a greater
affinity forT-state
activators and
substrateshave a greater
affinity for R-state
Determination of enzyme activity for
diagnostic purposes
most often blood is investigated (serum, plasma)
→ evaluation of presence and seriousness of a tissue damage
units : µkat/L (= catalytical concentration of enzyme)
kat = katal1 katal = 1 mole of a substrate transformed per 1 sec
1 µkat = 10-6 kat
Enzymes found in plasma:a) plasma-specific enzymes (e.g. clotting factors)
b) secretory enzymes (e.g. digestive enzymes)c) cellular enzymes
Important knowledge:
1) intracellular localization of enzymes2) organ and tissue distribution of enzymes
3) sources of enzymes found in plasma4) way of enzyme elimination from blood
Enzyme kinetics
• activity, units�1 katal = 1 mole of a substrate transformed per 1 sec�1 IU = 1 µmole of a substrate transformed per 1 minute
1 katal = 1 mole / 1 sec= 106 µmole / 1 sec= 60 x 106 µmole / 1 min (= 60 sec)
1 katal = 6 x 10 7 IU
The figure is found at: http://www.steve.gb.com/science/enzymes.html (December 2006)
The activity is related to a constant concentration of an enzyme :
[E] = constant
The figure is found at: http://fig.cox.miami.edu/~cmallery/255/255enz/gk3x15.gif (December 2006)
! REMEMBER !
Michaelis-Menten kinetics
• the curve can be described by the equation:
The figure is found at: http://www.steve.gb.com/science/enzymes.html (December 2006)
The figure is found at: http://fig.cox.miami.edu/~cmallery/255/255enz/gk3x15.gif (December 2006)
Km describes an affinity of the enzyme to its substrate
! indirect proportionality !
The figure is found at: http://www.steve.gb.com/science/enzymes.html (December 2006)
linearization of the curve :
y = k x + q
The figure is found at: http://fig.cox.miami.edu/~cmallery/255/255enz/gk3x15.gif (December 2006)
The figure is found at: http://stallion.abac.peachnet.edu/sm/kmccrae/BIOL2050/Ch1-13/JpegArt1-13/05jpeg/05_jpeg_HTML/index.htm (December 2006)
Inhibition of enzymes
1) Competitive inhibition
• inhibitor resembles substrate
• it is bound to an active site but not converted by the enzyme
• increases K m (↓afinity of enzyme to its S)
• if concentration of a substrate is increased the inhibition is decreased
• the inhibition is reversible
The figure is found at: http://www.steve.gb.com/science/enzymes.html (December 2006)
• inhibitor binds at a site other than the substrate-bindingsite
• inhibition is not reversed by increasingconcentration of substrate(no Km change)
• Vmax is decreased (it is related to decreasing of active enzyme concentration)
• reversible only if the inhibitor is not bound by covalent bond
The figure is found at: http://www.steve.gb.com/science/enzymes.html (December 2006)
2) Noncompetitive inhibition
The figure is found at: http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/E/EnzymeKinetics.html(December 2006)
Summary of the inhibition
Some enzymes can be inhibited also byan excess of their substrate
The figure is found at: http://www-biol.paisley.ac.uk/Kinetics/chapter_3/chapter3_6_1.html (December 2006)
Inhibition by drugs and poisons
a) reversible
b) irreversible
→ inhibitor is bound covalently into the active site of enzyme
Inhibition as a regulation of metabolic pathways:
inhibition by products or intermediates:a) feedback regulation
b) cross-regulation c) feedforword regulation
inhibition byd) reversible covalent modification
(e.g. phosphorylation / dephosphorylation)
The figure is found at: http://stallion.abac.peachnet.edu/sm/kmccrae/BIOL2050/Ch1-13/JpegArt1-13/05jpeg/05_jpeg_HTML/index.htm (December 2006)
Reversible covalent modification :
A)
• phosphorylation bya protein kinase
• dephosphorylation bya protein phosphatase
B)
• phosphorylated enzymeis either active or inactive(different enzymes areinfluenced differently)
Inhibition of enzymes used in the regulation is eith er
• competitive(Km is increased above substrate concentration within a cell)
or• allosteric
(by conformational changes affecting the catalytic site)
Allostericregulation
• activator is „a positive modulator“
• inhibitor is „a negative modulator“
The figure is found at: http://www-biol.paisley.ac.uk/Kinetics/Chapter_5/chapter5_2_2.html (December 2006)
! the curve of allosteric enzymes is sigmoidal not hyperbolic !
SUMMARY
Regulation of enzyme activity
• availability of a substrate and its concentration• induction of synthesis of a regulatory enzyme• activation of enzyme precursors• covalent modification of enzymes• competitive inhibition• allosteric regulation