H2 Biology - Notes on Enzymes

Notes on enzymes 



Describe the structure and function of enzymes o Enzymes are biological catalysts o Most are globular proteins produced in living cells and speed up chemical reactions while remaining unchanged in the process o Highly efficient in small amounts o Highly specific o Reversible reactions o Easily denatured and affected pH, temperature, [S], [E], cofactors/coenzymes and inhibitors o Types of enzyme catalysed reactions: anabolic reactions, catabolic reactions Explain the mode of action of enzymes in terms of an active site, enzyme/substrate complex, lowering of activation energy and enzyme specificity o Substrate must first bind to enzyme’s active site and form enzyme substrate complex. Once this occurs, enzyme will catalyze the reaction by lowering the activation energy promoting the breaking/forming of bonds to change substrate to products o Enzymes have unique 3D conformation Category of amino acid Catalytic residues

Function Make or break chemical bonds Basis of catalytic activity Binding residues Hold substrate in place at active site Structural residues Maintain the correct globular shape of the active site Non-essential residues Near the surface of enzymes, no specific functions o The primary sequence of these amino acide determine its subsequent folding due to specific interactions between the amino acids (H bonds, hydrophobic interactions, ionic, disulfate) determine specificity of the enzyme Lock and key hypothesis

    

Induced fit

   

1 Created by SefLRho (2012) DHS

Enzymes are rigid Have active site with fixed shape Enzyme (lock) has unique shape which is complimentary to substrate (key) Substrate fit and bind at active site Once formed, the products no longer fit into active site and are released into the surrounding medium Active site is quite flexible physically When a suitable substrate binds, conformation change is induced in the enzyme cuasing enzyme to close up and enfold substrate Induced fit may strain substrate bonds and help lower the activation energy Competitive inhibitors able to enter the active site but cannot cause the change in shape required for the catalysis

o

For reaction to occur, activation energy is required to destabilize the existing chemical bonds and to initiate a chemical reaction, often supplied in the form of heat. Enzymes help to lower the activation energy required

Proximity effect





Temporary binding of reactants next to each other on an enzyme increase the change of effective collisions Strain effect Slight distortion of the reactants as they bind to the enzyme straining the bonds which are to be broken and increase the chance of breakage Orientation effects Reactants are held by enzyme in such as away that bonds are exposed to attack Microenvironment effects Hydrophobic amino acids create a water-free zone in which non-polar reactants may react more easily Acid-base catalysis Acidic and basic amino acids in the enzyme facilitate the transfer of reactants to and from the reactants Follow the time course of an enzyme-catalyzed reaction o Measure through rate of formation of product eg amount of gas product released o Measure through the disappearance of substrate eg rate of disappearance of starch Investigate and explain the effects of temperature, pH, [E], [S] on rate of enzymatic reactions

Temperature

   

   pH

  

[E]

  

Optimum at a narrow range. At low temp., enzymes are inactive as they have very little KE for effective collision. As the temp increase, KE of enzymes increases, thus increasing the frequency of effective collisions between enzyme and substrate to form more enzyme-substrate complexes However rate of reaction can only increase up to a optimum temperature where the frequency of effective collision is at its highest and the most number of enzyme-substrate complexes are formed per unit time Beyond that optimum temp, rate of reaction decreases as the bonds of the enzymes are broken causing enzymes to lose their 3D conformation and loss of active site Enzyme is denatured Hydrogen bonds and hydrophobic interactions are especially sensitive to temperature changes At extreme pH, the excess ions in the surrounding (H+ and OH-) would neutralize the charged of R group of amino acids at the active site Binding and catalytic residues which are usually charged can be neutralized causing enzyme to not being able to interact with substrate, catalytic activity lost Extreme pH can also disrupt ionic bonds within enzymes leading to alteration to the 3D conformation shape of the enzyme Enzymes are denatured Normally reversible At low [E], when [E] increases, rate of reaction increases proportionally as more active sites are available for the substrates to collide with. Limiting factor is [E]. Frequency of effective collision increases and more enzyme-substrate complexes are formed per unit

2 Created by SefLRho (2012) DHS

time As the [E] increase, rate of reaction level off and increasing [E] would no longer have any effect as the limiting factor is [S]. There are many more empty active sites than there are substrates. [S]  At low [S], increase in [S] would result in increase proportionally with the rate of reaction as there are more substrate to collide with the empty active sites. Limiting factor is S. Frequency of effective collision increases and more enzyme-substrate complexes are formed per unit time  At high [S], the rate of reaction level off as all the active sites are saturated. Limiting factor is E  Explain the effects of competitive and non-competitive inhibitors on rate of enzymatic activity o Reversible: if only weak bonds are affected, effect is temporary and cause no permanently damage to enzyme & removal of inhibitor is possible o Irreversible: if strong bonds are formed, permanent binding to active site or changing the shape of active site eg toxins and poisons 

Type Reversible

Competitive

Allosteric

Description  Inhibitor has complimentary shape to active site  Competes with substrate for limited enzyme active sites, preventing substrate from entering

 

Irreversible aka noncompetitive inhibitors

  

Inhibitor binds to allosteric site on enzyme Alters 3D conformations causing substrate to no longer fit into active site but is reversible Usually permanently combine with sulphydryl groups Binds to allosteric site other than active site Change the conformational structure of enzyme including the active site

3 Created by SefLRho (2012) DHS

Effect of rate of reaction  Lowers rate of reaction  But can be overcome by increase [S] so that as active sites become available, more substrate molecules than inhibitors molecules are around to gain entry  Final amount of products still the same  Lowers rate of reaction  Amt of products formed would be less  

Amt of product will not reach maximum Lowers rate of reaction

4 Created by SefLRho (2012) DHS