vk terms enzymology - Univerzita Karlovavyuka-data.lf3.cuni.cz/CVSE1M0001/vk_terms_en... · The figure is adopted from the book: Devlin, T. M. (editor): Textbook of Biochemistry with

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 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


Allosteric enzyme : a) monomeric, b) oligomeric


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:



Km describes an affinity of the enzyme to its substrate

! indirect proportionality !


linearization of the curve :

y = k x + q



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


• 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


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)


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

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vk terms enzymology - Univerzita Karlovavyuka-data.lf3.cuni.cz/CVSE1M0001/vk_terms_en... · The figure is adopted from the book: Devlin, T. M. (editor): Textbook of Biochemistry with