1.5 Enzymes Flashcards
Definition of enzymes
Biological catalysts that increase the rate of reaction and are chemically unaltered at the end of the reaction and thus can be reused. They are effective in small amounts
What are the 4 general characteristics of enzymes?
- Enzymes are mostly globular proteins
They consist of one or more polypeptide chains coiled and folded to form a globular unit with a 3-dimensional structure which determines its action - Enzymes increase the rate of reaction
- Enzymes operate at milder reaction conditions i.e. temp below 100, atm pressure, nearly neutral pH
- Enzymes exhibit specificity
An enzyme or a particular type of enzyme will usually catalyse a specific chemical reaction/ chemical bond
Describe the active site of enzymes and the 4 types of residues that form it
The primary structure of the enzyme will determine it’s secondary and tertiary structure that determines the overall 3D conformation of the enzyme
The precise 3D groove on the enzyme at the active site gives it a specific conformation
The specificity of an enzyme is attributed to the complementary conformation/shape and charge between the substrate and active site
- Contact/binding residues: bind reversibly to the substrate while positioning it in the correct orientation; the substrate is held in the active site by weak interactions like H bonds and ionic bonds
- Catalytic residues: act on the bonds in the substrate molecule, and the side chains/R-groups of a few of the amino acid residues catalyse the conversion of substrate to product
- Structural residues: interact to maintain the overall 3D conformation of the protein for the proper functioning of the protein [maintained by R group interactions]
- Non-essential residues
Describe and compare the two models of enzyme action
- The Lock and Key hypothesis:
Substrate= Key
complementary in conformation and charge to
Enzyme active site= Lock
E and S collide in the correct orientation to form ES complex after which catalysis occurs and products no longer fit in the active site and are released - Induced fit model
As S enters E active site, it induces a change in the shape of the protein allowing more weak bonds to form, causing the active site to enfold the substrate and hold it in place
The active site of enzymes is complementary in conformation/shape but not a perfect fit to the substrate
However, when S binds to E, it induces a change in the conformation/shape of the enzyme and its active site which allows the active site to be moulded into a more precise fit for the substrate, enabling the enzyme to perform its catalytic function most effectively
Define “Activation energy”
Activation energy is the amount of energy that reactants must absorb before a chemical reaction will start
How do enzymes increase the rate of a reaction?
Enzymes provide an alternative pathway of lower activation energy
Describe the molecular basis of enzyme action
- Proximity effect
Temporary binding of reactants next to each other in the enzyme active site increases the chance of a reaction. Uncatalysed reactions depend on random collisions between reactant molecules - Strain effect
Slight distortion of the reactants as they bind to the enzyme strains the bonds which are to be broken and increases the chance of breakage - Orientation effects
Reactants are held such that bonds are exposed to chemical attack - Microenvironment effect
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 catalysis
Describe the 3 types of enzyme cofactors
- Inorganic ions
Metal ions to change non-functioning active site to functioning one
Attachment of ion with the main enzyme (apoenzyme) changes the shape of the enzyme so as to allow the ES complex to form more easily - Coenzymes
Organic in nature - Prosthetic group
permanently bound
Describe how the rate of enzyme-catalysed reaction changes with increasing temperature
@low temp:
Increase in temp increases KE of E and S which increases the frequency of effective collisions between S and E active site resulting in an increase in the rate of formation of ES complexes
Increased KE also increases the number of molecules having sufficient energy to overcome the Ea barrier
Rate doubles for each 10 rise
Reaction rate increases with temp only until the optimal temp
Each enzyme has an optimal temp at which the rate of enzyme reaction proceeds at max
@high temp:
Increase in KE at temp beyond the optimum temp causes intramolecular vibrations to increase which breaks H, ionic bonds and other weak interactions such as hydrophobic interactions that stabilises the conformation
DENATURATION
S no longer complementary to conformation of E active site
Fewer ES complexes
Lower rate of reaction
Describe how the rate of enzyme-catalysed reaction changes with changing pH
Each enzyme has an optimal pH at which it is most active
Excess [H+] or [OH-] ions may affect the ionisation of R-groups of charged amino acids
excess H+ results in COO- becoming COOH and excess OH- results in NH3+ becoming NH2
Change in pH to extremes beyond optimum pH denatures the enzyme, reducing rate of reaction
What is Km and how does it indicate ES affinity?
Michaelis constant Km is the [S] needed to make the reaction attain half its max rate (1/2 Vmax)
Km is always the same for a particular enzyme but varies from one enzyme to the other
Low Km= High affinity ( low [S] needed to attain 1/2 Vmax )
High Km= low affinity ( High [S] needed to attain 1/2 Vmax )
Describe and compare the action of competitive inhibitors and non-competitive inhibitors
- Competitive inhibitors
Competitive inhibitors bear similar conformation to S and competes with S for the active site by binding reversibly to the active site (bonds are weak, non-covalent bonds)
They reduce the availability of the active site for substrate binding and reduces the rate of reaction
Inhibition can be overcome by increasing [S] as that increases chances of S binding to the active site instead of inhibitor; At sufficiently high [S], same Vmax - Non-competitive inhibition
Bears no structural similarity to S so it binds to a site other than active site (forming inactive enzyme-inhibitor complex)
It alters the conformation of the specific enzyme active site and thus S cannot bind in the correct orientation and rate of reaction is decreased
Cannot be overcome by increasing [S]; lower Vmax
What are the two molecules that regulate allosteric enzymes?
Inhibitors and activators
Describe the structure of an allosteric enzyme
Allosteric enzymes usually consist of 2 or more subunits where each subunit has its own:
Active site that binds substrates
Allosteric sites that bind to activators/ inhibitors
Describe the characteristics of allosteric enzymes
- Exist in 2 conformational states: activator stabilises functionally active conformation; inhibitor stabilises the functionally inactive conformation
- A single activator/ inhibitor is sufficient to activate/ inhibit enzyme activity
- The binding of substrates exhibit cooperativity where binding of the first substrate changes the conformation of the other subunits such that it becomes easier to accept subsequent substrates
- In a rate against [S] plot, S-shaped sigmoid curve often indicates cooperative binding
- Note the effect of an inhibitor on rate is opposite to that of increasing [S]; in presence of inhibitor, same Vmax can be reached at higher [S]
