Enzymes Flashcards
Enzyme definition
A globular protein that stabilises the transition state relative to the substrate, speeding up reactions. A biological catalyst
Catalysis definition
Lowering the energy barrier to reach the transition state, without the enzyme being used up at the end
Enzyme reaction in its simplest form
E+A ⇌ EA –> E + P. Where EA is the enzyme substrate complex.
Enzyme reaction in a more complicated form
E+A ⇌ EA ⇌ EA ⇌ EP ⇌ EP ⇌ E + P
Explain the more complicated reaction symbols and stages
Substrate A rapidly reacts with Substrate E to form a loose association enzyme substrate complex.
Interactions of the substrate with the resides of the catalytic centre yields a tight transition state complex.
This state is able to convert the tightly bound substrate into a tightly bound product.
This then turns to a loosely associated EP before dissociating into a free product and enzyme.
What is the transition state complex?
A chemical reaction undergoing when the enzyme and substrate are in contact, not simply the formation of an enzyme-substrate complex. Highest free energy and is extremely unstable due to the constant bond breaking and bond forming events.
Initial state definition
the total energy content of a system before a reaction takes place
Final state definition
Energy content after a reaction has taken place
When does a reaction occur?
If Gibb’s free energy is negative
What is Gibb’s free energy?
Fraction of energy released in a biochemical process available to do work of some kind.
6 classes of chemical reactions
Hydrolysis, condensation, ligation, group transfer, redox, isomerisation
Hydrolysis reaction + enzyme
Process of using water to break down a molecule into two parts. Hydrolase
Condensation reaction
Class of organic addition reaction with the release of a water molecule
Ligation reaction + enzyme
The joining of two nucleic acid fragments using DNA ligase.
Group transfer reaction + enzyme
Process where one or more groups of atoms is transferred from one molecule to another. Tranferase
Redox reaction + enzyme
Chemical reaction where the oxidation states of the atoms are changed. Oxidoreducatases- enzymes that are associated with coenzymes
Isomerisation reaction + enzyme
Process by which one molecule is transformed into another molecule which has exactly the same number of atoms but with different arrangements. Isomerase
How do enzymes catalyst chemical reactions in general terms?
Lower the activation energy barrier, converting a complex reaction into a number of simpler ones, where each step has a smaller activation energy barrier. Hastens the approach towards equilibrium, possibly accelerating the reactions in either directions.
Active site definition
A region of the enzyme that has both a binding and catalytic site. Substrate binds to the binding site. The position in which it binds strains the substrate, causing it to change. Often a cleft, crevice or pocket.
What play an essential role in binding?
Amino acid residues, cysteine, glutamate, aspartate, lysine, arginine, histidine, serine, threonine and hydrophobic residues.
What bonds form between the active site and substrate?
non covalent bonds: hydrogen bonds, ionic attractions, hydrophobic bonds, Van Der Waals and potentially transient covalent bonds.
What does enzyme specificity depend on?
The shape of the active site (caused by the different primary structures of polypeptides) that are only complementary to a given substrate.
Different types of specificity + explained and example
Absolutely specific- glucose oxidase. Will act on glucose alone
broad substrate specificity- hexokinase. Will act on a range of hexoses, not just glucose
Group specific enzymes- alcohol dehydrogenase. Enzyme catalyst selective in acting on specific groups. Will act on both primary and secondary alcohols.
Stereospecific enzyme- L-amino acid oxidase. Act only on one enantiomer.
Enzyme promiscuity definition
Enzymes with relaxed substrate specificity, catalyse distinctly different reactions, distinct catalytic activity under unnatural conditions (extreme temperature and pH).
What is a multimeric enzyme?
An enzyme formed of two or more polypeptide chains
Isoenzymes definition
Enzymes catalysing the same reaction from different genes. Enzymes with the same function but different structure
What differs between isoenzymes?
Kinetic parameters, regulatory proteins and amino acid sequence
Isozyme Example
Lactate Dehydrogenase (LDH) is a tetramer formed of two subunits, H form and M form. Exists in 5 forms. Found mostly in red blood cells and heart and indicate damage of diseased tissue
Multienzyme complex definition
Stable assemblies of more than one enzyme, generally involved in sequential catalytic transformations.
Multienzyme complex example
pyruvate dehydrogenase is a complex of three different enzymes that collectively catalyse the oxidation of pyruvate. Has two catalytic sites providing TPP and magnesium ion cofactor.
cAMP- dependent protein kinase explained
Protein kinase A activated by a rise in cAMP, causing the catalytic subunits to dissociate and become released- physical separation of catalytic and regulatory proteins in the enzyme. Dependent on allosterity (binding of cAMP.
Co-factor definition
A non-protein chemical compound or metallic ion that is required for an enzyme’s activity as a catalyst. T
Two types of co factors explained
prosthetic group- consists of a coenzyme with a permanently bound co factor.
Co-substrate- co factor is transiently bound
Two classifications of cofactor
Inorganic- metal ions and organic- vitamins and derivatives.
Holoenzyme definition
Complete enzyme with cofactor
apoenzyme definition
An inactive enzyme without a cofactor
Why are vitamins/vitamin derivatives often cofactors?
Contain an AMP structure, such as ATP, coenzyme A, FAD or NAD+.
Which vitamins act as precursors?
B1, B2, B6 and B12
Which vitamin acts as a cofactor?
Vitamin C
What trace elements act as cofactors?
Fe3+, Zn2+, Ca2+. CO3+
Metal ion functions
May determine the enzyme structure
help bind to the substrate, enhancing the action of the enzyme.
Can shield charge- such as Mg2+ which forms an Mg-ATP complex, orientating the phosphates on ATP to form the correct orientation and reduces the charge on the polyphosphate chain, preventing repulsion with the substrate
What must occur for an ES complex to form?
The molecules must be in close proximity and correct orientation for the transient bonds to form between the active site and substrate.
What is the regulator of a pathway?
The enzyme that catalyses the first step in a metabolic pathway.
Two types of regulatory enzyme
Allosteric or regulated by covalent modification
Allosteric enzyme definition
An enzyme with a different binding site (not just active site) where an effector can bind causing a conformational change which either activates or inhibits the enzyme
What is the different binding site called?
Allosteric site
Example of allosteric regulator explained
Feedback inhibition, where the final product of the metabolism pathway inhibits the enzyme, which can slow the rate of action of the enzyme if the products exceed the requirements.
Allosteric effector definition
Regulatory molecule that binds to the allosteric site and modifies the rate. Positive if they stimulate enzyme activity and negative if they depress enzyme activity
Two types of allosteric modulator explained
Homotropic- allosteric modulator is the substrate itself
heterotropic- allosteric modulator is different from the substrate.
Explain mechanism of cooperativity
Most allosteric enzymes have many subunits with many allosteric sites. Long distance interactions between the sites causes a sigmoidal dose curve, becomes easier for substrate to bind.
This is due to the initial effector causing a conformational change in the other active sites so its easier to bind.
Cooperativity rules
- Subunits of proteins are functionally related
- Each protein can exist in two functional states- T tense and R relaxed. These states are in equilibrium even if ligand is not bound
- Binding of ligand shifts the equilibrium towards either tense or relaxed changing the affinity for the ligand.
- inhibitors will bind to tense form and effectors to relaxed form.
Allosteric enzyme response curve explained
Enzyme activity plotted against increasing concentrations of substrate a sigmoidal curve is formed. Binding of ligand creates a long distance change, altering the active sites. However, hard to bind final molecules as probability of colliding with the right orientation in the right place is lowered.
Terms for binding the same/different molecule
Heterotropic- different
homotropic- same e.g oxygen in haemoglobin
Two types of inhibition
Competitive and non competitive
Competitive inhibition explained
Substrate and inhibitor occupy the same binding site on the enzyme or if binding of substrate changes the conformation of the enzyme so that the inhibitor cannot bind to an allosteric site.
Non competitive inhibition explained
Both the free enzyme and enzyme-substrate complex can bind the inhibitor.
Substrate binding does not change the conformation of the enzyme that would change the affinity for the inhibitor.
affinity for the inhibitor is smaller than that of the substrate
Binding of the substrate reduces the affinity for binding the inhibitor
What is the Monod-Wyman-Changeux model?
Formulated for oligomeric proteins with identical subunits, each with a ligand binding site.
Equilibrium of conformational states terminal relaxed and tense, which differ in affinity for ligand molecules.
T state has low affinity and R state has high affinity.
If an allosteric protein binds a target that has a higher affinity for R, the target binding further stabilises the R state, increasing that ligand’s affinity.
What is ATCase?
Aspartate trans-carbamylase, catalyses the first step In the pyrimidine biosynthetic pathway.
ATCase structure
Contains catalytic subunits that catalyse the carbamylation of the amino group of aspartate. Also has regulatory subunits containing allosteric sites. Formed of two catalytic dimers held together by three regulatory dimers.
Inhibitors and activators OF ATCase
ATP binds to allosteric sites and activates the enzyme. (ASP and CP binding domains need to be together to work)
CTP binds to allosteric sites and inhibits the enzymes. CTP prevents the required conformational change for the enzyme to be activated
Haemoglobin cooperativity explained
When oxygen binds to iron complex, the iron atom moves back into the centre of the porphyrin ring. Other conformational changes occur to expose the oxygen binding sites.
Binding of oxygen to one monomer also shifts the conformation from tense state to relaxed
Inhibitors of haemoglobin
Competitive- carbon monoxide, cyanide and hydrogen sulfide.
Non-competitive- carbon dioxide (Bohr effect)
Myoglobin cooperativity explained
Does not exhibit cooperativity as it is a monomeric protein with one binding site, therefore follows hyperbolic binding curves
Lock and Key model explained
Proposed by E.Fischer who claimed that it is a direct fit between the rigid enzyme and substrate- very similar to strict specificity
Induced fit model explained
Proposed by Koshland- enzyme structure is plastic. Enzyme modifies its conformation when in contact with a substrate, adapting to it and orientating essential residues to obtain maximal conformational change for catalysis.
Where does the energy come from to form the ES complex assuming the induced fit model?
Activation energy derived from the binding energy between the enzyme and transition state.
Drugs as allosteric ligands explained
Bind to allosteric site and can either upregulate the enzyme, such as those involved in immune responses that can target rapidly dividing cancer cells, or down regulate (shift sites to tense) such as those involved in the cell cycle, preventing neoplasia.
How do covalent modifications regulate enzymes?
Post-translational covalent modification alters the activity of the enzymes, potentially for active or active.
Main covalent modification?
Phosphorylation
Explain phosphorylation cascade
OH functional group on serine, threonine or tyrosine of enzyme can undergo an addition of a phosphate from a protein kinase.
This forms a large negatively charged moiety which then undergoes a large conformational change, which in turn alters another protein and so forth
Coagulation cascade
Zymogen of a serine protease and its glycoprotein cofactor are activated and catalyse the next reaction in the cascade, eventually forming cross linked fibrin.
Zymogen definition
proenzymes that become catalytically active by hydrolysis.
Function of HMG-CoA reductase
catalyses the conversion of HMG-CoA into mevalonic acid, in the biosynthesis of cholesterol
What drug lowers cholesterol and how do they work?
HMG-CoA reductase inhibitors, known as statins. Prevent the formation of mevalonic acid, which thus lowers cholesterol levels. competitive inhibitor
Explain how salt concentrations effect enzyme action
At 0mM of salt, enzymes bind to one another, thus do not function
As the salt increases, the solubility of the enzyme improves, so works faster
After the salt concentration exceeds a certain value, salting out occurs
This is where the alts bind to the enzyme, neutralising all the charges, preventing the enzyme from interacting with water- forming a precipitate containing enzyme
What balances out the negative charge across the cell membrane?
Negative charge from DNA and RNA
