Week 4 - Enzymes Flashcards
What are enzymes
Enzymes are biological catalysts (protein)
- nearly all enzymes are globular proteins
What is the function of enzymes
- increase the rate of a reaction
- some catalyze the reaction of only one compound e.g. urease
- some catalyze reactions of specific types of compounds or bonds
- some change a particular functional group into another functional group
they stabilise the transition state for the reaction, lowering activation energy and increasing the rate of reaction.
Example of enzymes in dentistry
Pellicle Proteins:
- a-amylase lysozyme - protect enamel surfaces
Saliva Proteins:
- carbonic anhydrase VI isoenzyme - regulates pH in oral environment
- a-Amylase
- lysozyme
- lipase
What are cofactors
Only some enzymes require them but they are any non protein component of an enzyme which are either
coenzymes such as Coenzyme A (CoA) or
Metal ions such as Zn 2+, Mg2+ (or metal complexes
What are coenzymes
cofactors made from organic molecules
e.g. Coenzyme A (CoA)
What are apoenzymes
The protein component of an enzyme that requires a cofactor
What are holoenzymes
The combination of the apoenzyme (protein part) and cofactor (non protein part)
What is a substrate
the reactant that is going to be catalysed
e.g. phosphoenol pyruvate, ADP substrates for pyruvate kinase
What is an active site
A molecular crevice on the surface of the enzyme where the substrate (reactant to be catalysed) will fit during the reaction
What is a transition state
The intermediate stage of a reaction where the substance is neither the reactant or product
Describe the lock and key models
When the substrate (key) fits the active site (lock) catalysis can occur
Describe the induced fit model
the substrate approaches the enzyme, the enzyme senses the incoming substrate, and it adapts the active site to achieve a perfect fit with the substrate to the active site. So it’s not an inflexible lock, it creates an induced fit, which optimises the interaction with the active site upon bonding to form.
How do substrates bind to the active sight
intermolecular forces (h-bonds, salt-bridges) to AA side chains of the active site (enzymes are proteins)
What are the 6 major enzyme classification classes
- Oxidoreductases
- Transferases
- Hydrolases
- Lyases
- Ligases
- Isomerases
(Over The HILL)
What does a oxidoreductases do
oxidation - reduction reaction
What does a transferases do
group transfer reactions
they catalyse the transfer of functional groups from one molecule to another
What does a hydrolases do
hydrolysis reactions: that is the addition of a water molecule to a bond, resulting in bond breakage.
What do lyases do
addition of a group to a double bond or the removal of a group to form a double bond.
What do ligases do
Enzyme which uses ATP to form bonds
enzymes which catalyse a reaction in which a C-C, C-S, C-O or C-N bond is made or broken. This is accompanied by an ATP-ADP interconversion.
Joining of two substrates using ATP
What do Isomerases do
Isomerization reaction
Isomerases rearrange the functional groups within a molecule and catalyze the conversion of one isomer into another.
Example of a oxidoreductase enzyme
lactate dehydrogenase
Example of a transferases enzyme
pyruvate kinase
or Hexokinase (step 1 glycolysis) - transfers phosphate group
Example of a hydrolase enzyme
Lipase - hydrolysis of triglycerides into glycerol and FA
Example of a lyases enzyme
carbonic anhydrase
takes CO2 which has a double bond in it, adding water to it and turning it into carbonic acid
adolase (step 4 glycolysis) - breaks down F-6,1-P into DHAP and GAP
Example of a ligases
DNA ligase (DNA rep step 6)
Example of a isomerases enzyme
GAP triose phosphate isomerase (glycolysis step 5)
Phosphoglucoisomerase - step 2 glycolysis (G-6-P into F-6-P)
What is the enzyme catalyzed Reaction
What are Michaelis-Menten Kinetics
??
What are the main 5 amino acids which participate in the active sites in more than 65% of the enzymes
His > Cys > Asp > Arg > Glu
- Histidine
- Cysteine
- Aspartate
- Arginine
- Glutamate
4 out 5 have either acidic or basic side chains
What are the active site functions? (3)
- brings the reacting atoms of the substrate (s) together
- Moving reacting parts apart to stretch a bond to be broken
- adding H+ to increase the speed of acid catalysed reaction
Explain pyruvate kinase as a enzyme
Pyruvate kinase catalyses the transfer of PO4 3- to ADP in glycolysis
Coenzyme = ADP
2 cofactors = Mg2+ and K+ are found in the active site where catalysis occurs.
Substrates = PEP (PhosphoEnolPyuvate) and ADP
What are the characteristics of the active site
- lot of acidic and basic side chains around the enzyme
- Hydrophobic pockets
- Both a specific shape and polarity to fit the substrate
We are packing substrate/s and cofactors into the active site (so a very busy environment)
What are Isoenzyme/Isozymes
An enzyme that occurs in multiple forms, each catalyses the same reaction but in different environments
Example of an Isoenzyme/Isozyme
Lactate dehydrogenase (LDH) which catalyses the oxidation of lactate to pyruvate
It has H4 isoform which is in the heart and a M4 isoform which is in the liver and skeletal muscle
What is the turn over number
The number of catalytic reaction events/s at the active site
- the number of catalytic reaction events at the active site and the enzyme per second
What can the maximum speed of an enzyme be describe as
Maximum velocity which has the units of micro moles per litre of product per second
Vmax
REFERS TO PRODUCTS
What does enzyme activity mean
Catalytic ability to convert substrate to product expressed in catalytic units (U)
1U = 1 micro mole substrate/min
REFERS TO REACTANTS
What is the activity of an enzyme-catalyzed reaction influenced by ( 5 factors)
- enzyme concentration
- substrate concentration
- temperature
- pH
- presence of cofactors
What does this graph represent
substrate concentration vs enzyme rate
What does this graph represent
Enzyme concentration vs enzyme rate
What does this graph represent
Temperature vs enzyme rate
- peak = optimal temperature
- low trough has no activity due to insufficient energy to reaction
- second low trough, temperature is too high and the protein denatures, or enzyme is too flexible and the induced fit doesn’t work well so the activity falls off
What does this graph represent
pH vs enzyme rate
- peak = optimum pH
What are proenzymes (zymogens)
An inactive form of an enzyme that must have part of protein chain cleaved(removed) to become the active enzyme.
e.g. trypsin
Example of a proenzyme (zymogen)
Trypsin (active enzyme), trypsinogen (proenzyme)
A digestive protease is synthesized and stored as the proenzyme trypsinogen, which has no enzyme activity until its hydrolyzed from the N-terminal.
What is protein modification
A process of changing enzyme activity by covalently modifying it
Example of protein modification
Pyruvate kinase (PK)
PK is the active form of the enzyme and when it is phosphorylated by protein kinase A (PKA) it forms PK-Pi which is an inactive enzyme.
PK-Pi can then be activated by phosphatase.
What is activation in enzymes
Any process that initiates or increases the activity of an enzyme
What is inhibition in enzymes
Any process that makes an enzyme less active or inactive. Slows the rate of an enzyme catalyzed reaction.
What are the types of enzyme inhibition
- competitive inhibitor (reversible)
- competitive inhibitor (irreversible)
- non- competitive inhibitor (reversible)
- Non-competitive inhibitor (irreversible)
What are competitive inhibitors (reversible)
Substance that binds to the active site of an enzyme thus preventing the substrate to bind to it. This substance can be removed
Example of a competitive inhibitor (reversible)
Methotrexate which inhibits the metabolism of dihydrofolate. Used in chemotherapy.
What is competitive inhibitor (irreversible)
A substance that binds to the active site and blocks substrate entry. Cannot be removed
Example of a competitive inhibitor (irreversible)
Penicillin
An antibacterial drug which works as a transpeptidase inhibitor. It binds irreversible to the active site.
Transpeptidase catalyzes the last step of cell wall synthesis for bacteria.
What are non competitive inhibitors
Substance that changes the shape of the active site but isn’t attached to the active site.
Example of a non competitive inhibitor (reversible)
ATP inhibits citrate synthase (TCA S1)
Example of a non competitive inhibitor (irreversible)
- Propecia
What is allosteric control
The inhibition or activation of enzymes by a regulatory molecule which binds to a site other than the active site - regulating the activity of the enzyme
A type of enzyme regulation based on an event occurring on the enzyme not at the active site which create change in the active site.
What is an allosteric enzyme
An enzyme which undergoes allosteric regulation, and they often have multiple polypeptide chains (quaternary structure)
What are the types of allosteric control
- negative modulation
- positive modulation
What is negative modulation
Allosteric control which the active site is changed to inhibit an allosteric enzyme
What is positive modulation
Allosteric control where the active site is changed to activate an allosteric enzyme
What is a regulator (ligand)
The substance which binds to an allosteric enzyme which causes the change in the active site structure
