Enzymes

Question 1

Enzymes definition

Answer 1

Biological catalysts that are able to speed up biochemical reaction by lowering activation energy without being themselves changed at end of reaction

Question 2

What is metabolism

Answer 2

Catabolism (breakdown of molecule eg hydrolysis) + anabolism (synthesis of molecule, eg condensation)

Question 3

Activation energy definition

Answer 3

Minimum amount of energy required to start a chemical reaction

Question 4

Catalyst

Answer 4

Substance that increases rate of chemical reaction but remains unchanged itself at the end of reaction

Question 5

Energy profile diagram ad explanation of enzyme catalyzed chemical reaction

Answer 5

1. Uphill portion: activation energy - represents initial investment of energy required t start reaction
2. Peak of energy profile: transition state - where bonds can be broken / formed
3. Downhill portion: conversion to product - molecules settle into their new bonding arrangement to form product

Question 6

Describe effect of an enzyme

Answer 6

1. Activation energy is lowered
2. More reactant molecules can surmount the energy barrier to reach transition state to be converted into product molecules

NOTE: total energy difference / free energy change or Gibbs free energy btw reactant molecules and product molecules remains the same

Question 7

Enzyme properties

Answer 7

1. effective in small amounts: they remain chemically unaltered at the end of the reaction and can be reused.
2. extremely efficient.
3. high degree of specificity: Most enzymes are specific to one type of substrate molecule. Other enzymes are specific to a group of similar substrates.
4. Enzymes can be denatured by heat, act most efficiently at an optimum temperature.
5. Enzymes are affected by pH and they act most efficiently at their optimum pH.
6. Enzymes activity can be regulated by activators and inhibitors.

Question 8

What is the structure of an enzyme?

Answer 8

1. Globular protein with specific 3D conformation (which can be denatured when bonds holding them in specific 3D conformation are disrupted)
2. 4 categories of amino acid residues:
   - catalytic amino acid residues -> The R groups of these amino acids are directly involved in the
   catalytic activity (making/breaking chemical bonds once substrate is bound)
   - Binding amino acid residues -> The R groups of these amino acids hold the substrate(s) in position via NON- COVALENT BONDS while catalysis takes place
   - Structural amino acid residues -> involved in maintaining the specific 3D conformation of the active site, as well as the enzyme as a whole
   - Non essential amino acid residues -> no specific functions, and can be removed or replaced without the loss of the enzyme’s catalytic function.

Question 9

What are cofactors and what are types of cofactors

Answer 9

Cofactors: additional non -protein component that is associated with enzymes via covalent bonds or weak interactions, that allow enzyme to function

3 types of cofactors:
1. Inorganic metal ions
* Mostly small divalent ions eg. Ca2+
* May either be component of active site or affect enzyme activity through allosteric regulation.
- Allosteric enzymes have multiple subunits and through conformational changes, bind activators of inhibitors at sites other than the active site.
* They usually bind reversibly to the enzyme and act by altering the enzyme’s active and/or allosteric sites to facilitate the catalytic reaction carried out by the enzyme.
* e.g. salivary amylase activity is increased in the presence of chloride ions.

2. Coenzymes
   * Loosely associates with the enzyme during the reaction. Coenzymes act as transient carriers of specific functional groups, hydrogen or electrons. Most coenzymes are derived
   from vitamins.
3. Prosthetic group
   * Prosthetic groups are tightly bound to the enzyme on a permanent basis.
   * Eg. the prosthetic group of enzyme catalase is an iron-containing haem group.

Question 10

mode of action of enzymes

Answer 10

1. formation of enzyme substrate complex
2. enzyme lowers activation energy
3. enzyme specificity
   - lock and key hypothesis
   - induced fit hypothesis

Question 11

How are enzyme substrate complexes formed

Answer 11

1. Enzyme and substrate collides in correct orientation, substrate is bound to enzyme at active site. This is an effective collision
2. Enzyme substrate complex is formed
3. Substrate is held in the active site by non-covalent bonds (eg. hydrogen and
   ionic bonds) between the R groups of the binding amino acids and the substrate molecule
4. R groups of the catalytic amino acid residues at the active site catalyse the conversion of the substrate to product
5. The alteration in chemical conformation results in the product molecule being released from the active site as it is no longer complementary to the active site structure.
6. enzyme active site is free for the binding of another substrate molecule

Question 12

How does enzyme Lower activation energy

Answer 12

1. Enzyme orientates substrates in close proximity, in correct orientation, to undergo chemical reactions
2. Enzyme strains critical bonds in substrate, allowing hem to attain unstable transition state
3. Enzyme provides microenvironment that favours reaction

Question 13

enzyme specificity

Answer 13

Enzymes are very specific as to which reactions they catalyse -> due to the specific 3D conformation of the active site of each enzyme, into which only specific substrate will fit.
- The physical conformation and chemical properties (due to R groups) of binding amino acids at the active site, ensures that only those substrates with a complementary physical and chemical fit will enter the enzyme’s active site and undergo the reaction.

Two mechanisms for enzyme action – the lock and key hypothesis and induced fit hypothesis.

Question 14

lock and key hypothesis

Answer 14

• exact fit/complementary shape or conformation between the substrate and the active site of the enzyme, in the same way that a key fits into a lock very precisely
• The enzyme is viewed as a rigid structure, where only substrates that are exactly
  complementary to the conformation of the active site are able to bind to the active site for catalysis.
• This explains substrate specificity of enzymes.

Question 15

what is induced fit hypothesis? key ideas and itneraction

Answer 15

induced fit hypothesis further explains group specificity, where one enzyme is able to catalyse reactions for a
variety of substrates that share similar structural or chemical properties.

Key ideas in induced fit hypothesis
- Active site flexibility
1. active site does not have a rigid conformation that fits only one type of substrate
2. is rather flexible in conformation and can allow more than one type of substrate to bind
3. is not in precise complementary conformation to the substrate before binding to the substrate

Interaction between enzyme and substrate:
- Upon binding of substrate, the active site changes its conformation slightly to bind the substrate even more firmly/snugly so that the R groups of the catalytic amino acids at the active site are:
* moulded into a specific conformation
* brought into close proximity to the chemical bonds in the substrate hence facilitating catalysis where the substrate is converted to product

Question 16

how to find rate of reaction

Answer 16

rate of an enzyme-catalysed reaction is the amount of substrate which is converted to product by enzymes per unit time
It can be obtained by measuring the rate of:
1. Product formation
2. Substrate usage

Question 17

measuring rate of product formation

Answer 17

Hydrogen peroxide is converted to water and oxygen by the enzyme catalase:

               catalyse  2H2O2(aq) ---> 2H2O(l) + O2(g)

From the equation, the rate of the reaction can be measured by:
1. measuring the rate of water production or
2. measuring the rate of oxygen gas production.

• more convenient to measure the rate of oxygen production
• after finding out o2 production, draw graph, initial rate of reaction is used (measuring grad of tangent to first part of curve)

Question 18

how to measure initial rate of rxn?

Answer 18

• calculate initial gradient
• Initial rate of reaction =Initial amount of product formed or substrate used / Time duration

Question 19

measuring rate of substrate usage

Answer 19

Starch is converted to maltose by the enzyme amylase.

rate of the reaction can be measured by:
1. measuring the rate of maltose production or
2. measuring the rate of disappearance of starch.

In this case, it is more straightforward to measure the rate of disappearance of starch.

Question 20

factors affecting rate of enzymatic rxn

Answer 20

• Substrate concentration
• Enzyme concentration
• Temperature
• pH

Question 21

what is limiting factor? principle of limiting factors p

Answer 21

When a reaction is affected by more than one factor, its rate is limited by the factor which is in shortest supply -> which is the limiting factor.

The principle of limiting factors states that:
* The rate of a biochemical process, which consists of a series of reactions, is limited by the slowest reaction in the series.
* When a biochemical process is affected by several factors, its rate is limited by that
factor which is in the shortest supply, known as the limiting factor.
* When the supply of the limiting factor is increased, it will lead to an increase in the rate of reaction.

Question 22

what is Vmax

Answer 22

Vmax (maximal reaction velocity) : reflect max rate that a reaction can proceed in the presence of a specific concentration of enzyme and excess substrate.

Km (Michaelis constant): measured as substrate concentration that allows an enzyme-catalysed reaction to proceed at half the reaction velocity, 1/2 Vmax
- it measures affinity of enzyme for a particular substrate (enzymes with low Km value exhibit high affinity for their substrate, enzymes with high Km value exhibit low affinity for their substrate)
- used to compare efficiency at which two enzymes work

tips on graph drawing
y axis: initial reaction rate
x axis: concentration of substrate

Question 23

competitive inhibition

Answer 23

• competitive inhibitiors are structually similar to substrate molecule and compete with the substrate for binding to the active site
• not acted upon by the enzyme but it remains bound to active site and prevents substrate binding to active site

Describe
* The initial rate of reaction is reduced in the presence of competitive inhibitor.
* However, when [S] is very high, both reactions reach the same Vmax, but this requires a longer period of time to produce the same amount of product.

Explain
* An increase in substrate concentration reduces the effect of inhibition.
* cuz substrate and the inhibitor are in direct competition for the enzymes’ active sites -> greater the proportion of the substrate molecules, the greater the chance a substrate can out-compete the inhibitor to enter the active site.
* If so, a rate of reaction almost equivalent to Vmax can be attained.
* The final amount of product formed is the same as the substrate continues to be
converted by any enzymes molecules that are unaffected by the inhibitor.
- bigger value of Kmax

Question 24

non-competitive inhibition

Answer 24

• Non-competitive inhibitors bear no structural resemblance to the substrate.
• It does not compete with the substrate for the active site.
• However, it binds to a part of the enzyme molecule that is not the active site -> alters the 3D conformation of the enzyme molecule and active site -> enzyme molecule no longer has an active site that is complementary in conformation to the substrate.
• Hence substrate does not bind to the enzyme active site and no enzyme-substrate
  complex can be formed.

Describe
* The initial rate of reaction is reduced in the presence of non-competitive inhibitor.
* Even when [S] is very high, the initial rate of reaction in the presence of inhibitor does not
reach the same Vmax as the reaction that is uninhibited.

Explain
* The binding of non-competitive inhibitor to a site other than the enzyme’s active site
causes a change in 3D conformation of the enzyme’s active site -> prevents substrate molecules from binding.
* A certain proportion of the enzyme molecules are rendered inactive, Vmax is lower.
* As the substrate and the inhibitor are not in direct competition for the same site, an
increase in substrate concentration has no effect on the inhibition.
*Km remains unchanged, as the affinity of the enzyme for substrate remains unaffected.
* The final amount of product formed is the same as the substrate continues to be
converted by any enzymes molecules that are unaffected by the inhibitor.

Question 25

what is allosteric regulation, mechanism

Answer 25

allosteric regulation: regulation of an enzyme by binding of molecules at an allosteric site (site other than active site) molecules - regulators (classified into activators / inhibitors) most allosterically regulated enzymes r composed of two / more polypeptide chains (multi-subnit enzyme, each subunit has own active site, allosteric sites located where subunits are classified) mechanism - allosteric enzyme alternates between active and inactive forms (only active form catalyses reactions) - inactive form of the enzyme has an active site that does not fit the substrate. For the enzyme to be active, its shape must be altered so that the substrate will fit into the active site.

Question 26

allosteric activation vs inhibition

Answer 26

Allosteric activation - When an activator binds, it **stabilizes the active form of the enzyme and increases the affinity of the enzyme for its substrate** Allosteric inhibition - When an inhibitor binds to the same region, it **stabilises the inactive form** of the enzyme and **decreases the affinity of the enzyme for its substrate** graph of allosterically activated enzyme rxn - sigmoidal in shape - start of curve, less steep grad: binding of activator to allosteric site induces favourable conformation change in active sites of all subunits of the enzyme - grad gets steeper: this significantly amplifies the response of the enzyme to substrate -> results in sudden steep rise in rate of rxn graph of cooperativity - same, sigmoidal - start of curve less steep: binding of one substrate molecule to an active site of a multimeric enzyme triggers the same favourable conformation change in the active sites of all other subunits of the enzyme. - grad steeper: cooperativity amplifies the response of enzyme to substrate. One substrate molecule primes an enzyme to accept additional substrate molecules.

Question 27

reversible vs irreversible inhibiotn

Answer 27

1. Reversible inhibition * The inhibitor binds to the enzyme via weak non-covalent bonds such as hydrogen bonds, hydrophobic interactions. * The effect of inhibitor is temporary, inhibitor can be easily removed and cause no permanent damage to the enzyme. * When the inhibitor leaves, activity of the enzyme will be restored to normal 2. Irreversible inhibition * The inhibitor binds to the enzyme via covalent bonds. * The inhibition causes permanent damage to the enzyme molecule so that it is unable to carry out catalytic activity.

Question 28

why are metabolic pathways impt

Answer 28

metabolism: totality of an organism / cell's chemical reaxctions. it involves thousands of chemical reactions arrranged as intersecting metabolic pathways impt to have structured system of control, which is provided by enzyme metabolic pathway -> beigns w specific, starting molecule, which is altered in series of defined steps, resulting in a certain product, D advantages of metabolic pathways catalysed by enzymes 1. Biochemical reactions may proceed with no accumulation of products in the cells. Products become substrates of subsequent reactions. 2. Reactants may be modified in a series of small steps, enabling: * energy to be released in controlled amounts or * minor adjustments to be made to the structure of molecules or * coupling of exergonic reactions to endergonic reactions 3. Each step is catalysed by a specific enzyme -> allowing for regulation and control of metabolism as each enzyme is a point for control of the overall pathway. Enzymes specific to the reaction are regulated by different inhibitors/activators, hence allowing for a finely balanced portioning of cell metabolites among different pathways. 4. The steps in the pathway may be spatially arranged so that the product of one reaction is ideally located to become the substrate of the next enzyme -> permits the build- up of high local concentrations of substrate molecules and biochemical reactions can proceed rapidly. A pathway arranged in this way may be catalysed by a multi-enzyme complex 5. A multi-enzyme complex is made up of a team of enzymes for several steps of a metabolic pathway. The arrangement orders the sequence of reactions, as the product from the first enzyme becomes substrate of the adjacent enzyme in the complex, and so on until the end-product is released -> increases efficiency of enzyme pathway

Question 29

where are enzymes located

Answer 29

1. Intracellular Enzymes Enzymes can be located in various compartments within the cell: * In the cytosol or nucleus (nucleoplasm) * Inside membrane-bound organelles e.g. mitochondria, chloroplast, lysosomes * Attached to the plasma membrane. * Attached to membranes of organelles e.g. mitochondria (cristae) and chloroplast (thylakoid) 2. Extracellular Enzymes * Some enzymes are produced in the cell but packaged to be secreted out of the cell, and exert their effect(s) externally.