tugas 2 biokatalisis

7/27/2019 Tugas 2 Biokatalisis

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1. Difference between catalyst and biocatalyst:No Criteria Catalyst Biocatalyst

1

Function:

Catalysts are substances that

increase or decrease the rate ofa chemical reaction but remain

unchanged.

Enzymes are proteins that

increase rate of chemicalreactions converting substrate

into product.

2Molecular weight:

Low molecular weight

compounds.

High molecular weight

globular proteins.

3

Types:

There are two types of

catalysts positive and

negative catalysts.

There are two types of

enzymes - activation enzymes

and inhibitory enzymes.

4Nature:

Catalysts are simple inorganic

molecules.Enzymes are complex proteins.

5

Alternate terms: Inorganic catalyst.

Organic catalyst or bio-

catalyst.

6Reaction rates: Typically slower Several times faster

7

Specificity:

They are not specific and

therefore end up producing

residues with errors

Enzymes are highly specific

producing large amount of

good residues

8Conditions: High temperature and pressure

Mild conditions, physiological

pH and temperature

9C-C and C-H bonds: Absent Present

10Example:

Vanadium oxide, Manganesedioxide, Sulfuric Acid, Zeolite

Hydrolase, transferase,isomerase, ligase,

oxidoreductase, lyase.

11Activation Energy: Lowers it Lowers it

12Price: Low, quite affordable High

13Endurance: High endurance Easily denaturized

2.

Difference between batch and continuous reactor:

No Criteria Batch Reactor Continuous Reactor

1 Cost of factory

equipment:

High Low

2 Rate of production: High Low

3 Shut-down times: Rare Often

4 Workforce: Few people needed Many people needed


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5 Ease of automation: Relatively easy Relatively difficult

6 Production: Product needed in a small

amount or only as needed (a

speciality chemical),

production does not go on allthe time.

Product needed in a large amount,

production goes all the time.

7 Example: Pharmaceutical drugs

(medicines)

Ammonia (Haber process).

3. What is Dalton?The unified atomic mass unit (symbol: u) or dalton (symbol: Da) is the standard

unit that is used for indicating mass on an atomic or molecular scale (atomic

mass). One unified atomic mass unit is approximately the mass of a nucleon and is

equivalent to 1 g/mol It is defined as one twelfth of the mass of an unbound

neutral atom of carbon-12 in its nuclear and electronic ground state and has a

value of 1.660538921(73)1027 kg.

1 u or Da is equal to...Kg 1.660538921(73)1027eV/c2 931.494061(21)106me 1822.88839mp 7.6293610

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4. Types of enzyme inhibitor:a. Irreversible inhibitors: Irreversible inhibitors usually covalently modify an

enzyme, and inhibition can therefore not be reversed. Irreversible inhibitors

often contain reactive functional groups such as nitrogen mustards, aldehydes,

haloalkanes, alkenes, Michael acceptors, phenyl sulfonates, or

fluorophosphonates. These electrophilic groups react with amino acid sidechains to form covalent adducts. The residues modified are those with side

chains containing nucleophiles such as hydroxyl or sulfhydryl groups; these

include the amino acids serine (as in DFP, right), cysteine, threonine or

tyrosine. Irreversible inhibition is different from irreversible enzyme

inactivation. Irreversible inhibitors are generally specific for one class of

enzyme and do not inactivate all proteins; they do not function by destroying

protein structure but by specifically altering the active site of their target. For
http://en.wikipedia.org/wiki/Covalenthttp://en.wikipedia.org/wiki/Nitrogen_mustardhttp://en.wikipedia.org/wiki/Aldehydehttp://en.wikipedia.org/wiki/Haloalkanehttp://en.wikipedia.org/wiki/Alkenehttp://en.wikipedia.org/wiki/Michael_acceptorhttp://en.wikipedia.org/wiki/Sulfonatehttp://en.wikipedia.org/wiki/Methoxy_arachidonyl_fluorophosphonatehttp://en.wikipedia.org/wiki/Electrophilehttp://en.wikipedia.org/w/index.php?title=Covalent_adducts&action=edit&redlink=1http://en.wikipedia.org/wiki/Nucleophilehttp://en.wikipedia.org/wiki/Hydroxylhttp://en.wikipedia.org/wiki/Thiolhttp://en.wikipedia.org/wiki/Serinehttp://en.wikipedia.org/wiki/Diisopropylfluorophosphatehttp://en.wikipedia.org/wiki/Cysteinehttp://en.wikipedia.org/wiki/Threoninehttp://en.wikipedia.org/wiki/Tyrosinehttp://en.wikipedia.org/wiki/Protein_structurehttp://en.wikipedia.org/wiki/Protein_structurehttp://en.wikipedia.org/wiki/Tyrosinehttp://en.wikipedia.org/wiki/Threoninehttp://en.wikipedia.org/wiki/Cysteinehttp://en.wikipedia.org/wiki/Diisopropylfluorophosphatehttp://en.wikipedia.org/wiki/Serinehttp://en.wikipedia.org/wiki/Thiolhttp://en.wikipedia.org/wiki/Hydroxylhttp://en.wikipedia.org/wiki/Nucleophilehttp://en.wikipedia.org/w/index.php?title=Covalent_adducts&action=edit&redlink=1http://en.wikipedia.org/wiki/Electrophilehttp://en.wikipedia.org/wiki/Methoxy_arachidonyl_fluorophosphonatehttp://en.wikipedia.org/wiki/Sulfonatehttp://en.wikipedia.org/wiki/Michael_acceptorhttp://en.wikipedia.org/wiki/Alkenehttp://en.wikipedia.org/wiki/Haloalkanehttp://en.wikipedia.org/wiki/Aldehydehttp://en.wikipedia.org/wiki/Nitrogen_mustardhttp://en.wikipedia.org/wiki/Covalent


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example, extremes of pH or temperature usually cause denaturation of all

protein structure, but this is a non-specific effect.

Figure 1. Kinetic scheme for irreversible inhibitors

Examples: nerve gases and pesticides, containing organophosphorus, combine

with serine residues in the enzyme acetylcholine esterase.

b. Reversible inhibitors: Reversible inhibitors bind to enzymes with non-covalent interactions such as hydrogen bonds, hydrophobic interactions and

ionic bonds. Multiple weak bonds between the inhibitor and the active site

combine to produce strong and specific binding. In contrast to substrates andirreversible inhibitors, reversible inhibitors generally do not undergo chemical

reactions when bound to the enzyme and can be easily removed by dilution or

dialysis. There are four kinds of reversible enzyme inhibitors. They are

classified according to the effect of varying the concentration of the enzyme's

substrate on the inhibitor.

Competitive inhibition, the substrate and inhibitor cannot bind to theenzyme at the same time, as shown in the figure on the left. This usually

results from the inhibitor having an affinity for the active site of an enzyme

where the substrate also binds; the substrate and inhibitor compete for

access to the enzyme's active site. This type of inhibition can be overcome

by sufficiently high concentrations of substrate (Vmax remains constant),

i.e., by out-competing the inhibitor. However, the apparent Km will

increase as it takes a higher concentration of the substrate to reach the Km

point, or half the Vmax. Competitive inhibitors are often similar in

structure to the real substrate (see examples below).
http://en.wikipedia.org/wiki/Denaturation_(biochemistry)http://en.wikipedia.org/wiki/Protein_structurehttp://en.wikipedia.org/wiki/Hydrogen_bondhttp://en.wikipedia.org/wiki/Hydrophobic_interactionhttp://en.wikipedia.org/wiki/Ionic_bondhttp://en.wikipedia.org/wiki/Substrate_(biochemistry)http://en.wikipedia.org/wiki/Competitive_inhibitionhttp://en.wikipedia.org/wiki/Active_sitehttp://en.wikipedia.org/wiki/File:Irreversible_inactivation2.svghttp://en.wikipedia.org/wiki/Active_sitehttp://en.wikipedia.org/wiki/Competitive_inhibitionhttp://en.wikipedia.org/wiki/Substrate_(biochemistry)http://en.wikipedia.org/wiki/Ionic_bondhttp://en.wikipedia.org/wiki/Hydrophobic_interactionhttp://en.wikipedia.org/wiki/Hydrogen_bondhttp://en.wikipedia.org/wiki/Protein_structurehttp://en.wikipedia.org/wiki/Denaturation_(biochemistry)


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Competitive inhibition increases the apparent value of the Michaelis-

Menten constant, , such that initial rate of reaction, , is given

by

where , is the inhibitor's

dissociation constant and is the inhibitor concentration.

remains the same because the presence of the inhibitor can be

overcome by higher substrate concentrations. , the substrate

concentration that is needed to reach , increases with the

presence of a competitive inhibitor. This is because the concentration of

substrate needed to reach with an inhibitor is greater than the

concentration of substrate needed to reach without an

inhibitor.

Uncompetitive inhibition, the inhibitor binds only to the substrate-enzymecomplex, it should not be confused with non-competitive inhibitors. This
http://en.wikipedia.org/wiki/Michaelis-Mentenhttp://en.wikipedia.org/wiki/Michaelis-Mentenhttp://en.wikipedia.org/wiki/Uncompetitive_inhibitionhttp://en.wikipedia.org/wiki/Uncompetitive_inhibitionhttp://en.wikipedia.org/wiki/Michaelis-Mentenhttp://en.wikipedia.org/wiki/Michaelis-Menten


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type of inhibition causes Vmax to decrease (maximum velocity decreases

as a result of removing activated complex) and Km to decrease (due to

better binding efficiency as a result of Le Chatelier's principle and the

effective elimination of the ES complex thus decreasing the Km which

indicates a higher binding affinity).

The LineweaverBurk equation states that:

Where v is the initial reaction velocity, Km is the MichaelisMenten

constant, Vmax is the maximum reaction velocity, and [S] is the

concentration of the substrate.

The LineweaverBurk plot for an uncompetitive inhibitor produces a line

parallel to the original enzyme-substrate plot, but with a highery-intercept,

due to the presence of an inhibition term :
http://en.wikipedia.org/wiki/Lineweaver%E2%80%93Burk_plothttp://en.wikipedia.org/wiki/Lineweaver%E2%80%93Burk_plothttp://en.wikipedia.org/wiki/Lineweaver%E2%80%93Burk_plothttp://en.wikipedia.org/wiki/Reaction_ratehttp://en.wikipedia.org/wiki/Michaelis%E2%80%93Menten_constanthttp://en.wikipedia.org/wiki/Michaelis%E2%80%93Menten_constanthttp://en.wikipedia.org/wiki/Michaelis%E2%80%93Menten_constanthttp://en.wikipedia.org/wiki/Michaelis%E2%80%93Menten_constanthttp://en.wikipedia.org/wiki/Concentrationhttp://en.wikipedia.org/wiki/Y-intercepthttp://en.wikipedia.org/wiki/Y-intercepthttp://en.wikipedia.org/wiki/Concentrationhttp://en.wikipedia.org/wiki/Michaelis%E2%80%93Menten_constanthttp://en.wikipedia.org/wiki/Michaelis%E2%80%93Menten_constanthttp://en.wikipedia.org/wiki/Reaction_ratehttp://en.wikipedia.org/wiki/Lineweaver%E2%80%93Burk_plot


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Where [I] is the concentration of the inhibitor and Ki is an inhibition

constant characteristic of the inhibitor.

Mixed inhibition, the inhibitor can bind to the enzyme at the same time asthe enzyme's substrate. However, the binding of the inhibitor affects the

binding of the substrate, and vice versa. This type of inhibition can be

reduced, but not overcome by increasing concentrations of substrate.

Although it is possible for mixed-type inhibitors to bind in the active site,

this type of inhibition generally results from an allosteric effect where the

inhibitor binds to a different site on an enzyme. Inhibitor binding to this

allosteric site changes the conformation (i.e., tertiary structure or three-

dimensional shape) of the enzyme so that the affinity of the substrate for

the active site is reduced.

Non-competitive inhibition is a form of mixed inhibition where the bindingof the inhibitor to the enzyme reduces its activity but does not affect the

binding of substrate. As a result, the extent of inhibition depends only on

the concentration of the inhibitor. Vmax will decrease due to the inability

for the reaction to proceed as efficiently, but Km will remain the same as

the actual binding of the substrate, by definition, will still function

properly.

In the presence of a non-competitive inhibitor, the apparent enzyme affinity

is equivalent to the actual affinity. In terms of Michaelis-Menten kinetics,

Kmapp = Km. This can be seen as a consequence of Le Chatelier's

Principlebecause the inhibitor binds to both the enzyme and the enzyme-

substrate complex equally so that the equilibrium is maintained. However,

since some enzyme is always inhibited from converting the substrate to

product, the effective enzyme concentration is lowered. Mathematically,
http://en.wikipedia.org/wiki/Mixed_inhibitionhttp://en.wikipedia.org/wiki/Allosterichttp://en.wikipedia.org/wiki/Allosteric_sitehttp://en.wikipedia.org/wiki/Conformational_isomerismhttp://en.wikipedia.org/wiki/Tertiary_structurehttp://en.wikipedia.org/wiki/Non-competitive_inhibitionhttp://en.wikipedia.org/wiki/Enzyme_activityhttp://en.wikipedia.org/wiki/Michaelis-Menten_kineticshttp://en.wikipedia.org/wiki/Michaelis%E2%80%93Menten_kinetics#Michaelis_constant_KMhttp://en.wikipedia.org/wiki/Le_Chatelier%27s_Principlehttp://en.wikipedia.org/wiki/Le_Chatelier%27s_Principlehttp://en.wikipedia.org/wiki/Le_Chatelier%27s_Principlehttp://en.wikipedia.org/wiki/Le_Chatelier%27s_Principlehttp://en.wikipedia.org/wiki/Michaelis%E2%80%93Menten_kinetics#Michaelis_constant_KMhttp://en.wikipedia.org/wiki/Michaelis-Menten_kineticshttp://en.wikipedia.org/wiki/Enzyme_activityhttp://en.wikipedia.org/wiki/Non-competitive_inhibitionhttp://en.wikipedia.org/wiki/Tertiary_structurehttp://en.wikipedia.org/wiki/Conformational_isomerismhttp://en.wikipedia.org/wiki/Allosteric_sitehttp://en.wikipedia.org/wiki/Allosterichttp://en.wikipedia.org/wiki/Mixed_inhibition


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