Enzyme Flashcards
When is the reaction considered spontaneous
When the delta G is negative
What does the enzymes do?
They reduce the free energy of activation (delta g ++)
When is the reaction in equilibrium?
When the rate of forming the products is the same as the rate of reforming the substrate
What is the K equilibrium?
It is the number of products (divided by) the number of substrate left at equilibrium
What does K equilibrium indicate?
It indicates that the higher the k equilibrium the more spontaneous the reaction is and it has to be 1 or more in order to be considered as spontaneous
Does all reactions with a negative delta g have a k equilibrium of more than 1?
Yes
What is the induced fit model?
It is when the substrate and the active site are of different shapes but when they come close together they undergo conformational changes to become attached, as the active site is flexible, it contains a wider range of enzymes
What is an apo enzyme
The enzyme without the cofactor (nonprotein component)
What is an holoenzyme?
The enzyme with the non-protein component
What are the branches of the (non-protein) component?
1) organic (coenzymes)
2) non-organic (metals, cofactors)
What is the lock-key theory?
That each enzyme has a specific rigid shape active site that only substrates with the matching shape can fit, but it is not the case for all enzymes.
Enzymes are of which structure of protein?
Tertiary or quaternary
Why do we use enzymes?
To speed up the reaction without increasing our internal temperature as it can damage structures of our mechanism
How does enzymes increase the reaction rate?
By lowering the activation energy
What is the free energy of activation?
The amount of energy required to convert 1mole of substrate in its (low-energy) to the transition state (highest-energy/least stable)
How does the active site lowers the energy needed for the transition state?
As it optimally orient the substrate for the reaction
How does the amino group of the active site interact with the substrate?
1) ionic
2) hydrogen
3) hydrophobic
Non-covalent, Interactions
What are the major enzyme categories?
1) Oxidoreductase
2) transferase
3) Hydrolase
4) Lyase
5) Isomerase
6) Ligase
What does Oxidoreductase do, what are its subclasses, and what does it require?
It is the enzyme that catalyzes oxidation reduction reaction via transferring an electron associated with a universal electron carriers, It requires & produce NADH, FADH2 as coenzymes
Subclass: dehydrogenase, reductases
What does Transferase do, what are its subclasses and what does it require?
Enzymes that transfer a group from one molecule to another usually a (trans group) requiring ATP & the cofactor Mg+2
Subclass: amino-transferase, kinase
What does Hydrolase do and what are its subclasses?
Catalyzes a reaction forming a cleavage bond (CO, CN, OP) IS accomplished by addition or removal of water Subclass: Peptidase, esterase (lipase), phosphatazes, proteosases
What does Lyase do and what are its subclasses?
Those enzymes either introduced a double bond or removes them, Subclass: Decarboxylase
What does isomerase do and what are its subclasses?
Enzymes that converts between isomers Subclass: racemase (D/L), geometric isomerase (cis/trans), structural isomerase (aldehyde/ketones)
What does Ligase do and what are its subclasses?
Catalyzes the formation two CC bond (not mandatory cc) Subclass: carboxylase
What are the factors which contributes to enzymes mechanism?
1) Proximity & strain effect (substrate should be close to the active site)
2) Electrostatic effects (charge distribution on the active site micro-environment which can help in positioning the substrate)
3) Acid Base catalysis (the need to change the pH of the environment)
4) Covalent catalysis (the formation of unstable covalent bond due to the bond between nucleophilic side chain & electrophilic substrate)
Which amino acid can help in enzyme catalysis?
Polar and charged amino acids which create a micro environment conducive to catalysis, while the non-catalytic, which includes all of the amino acids. Orient the substrate and stabilizes the transition rate.
What is a Diaz and examples of it?
Diaz is when two amino acids are involved in a reaction,
carboxylate - carboxylate:
1) glutamate - glutamate
2) glutamate - aspartate
3) aspartate - histidine
What is the role of cofactors in enzyme catalysis?
1) alkaline metals usually of structural importance and not catalytic
2) transition metals (highly electrophilic) involved in the catalytic activity off the enzyme (zinc, iron, copper)
What are coenzymes?
A group organic molecules that provide enzymes chemical versatility
1) Contain functional groups that amino acid side chains do not
2) Can be tightly or loosely bound and their structures are often changed by the catalytic process
3) Most are derived from vitamins
4) Three groups: electron transfer (NAD+), group transfer (coenzyme A), and high-energy transfer potential (nucleotides)
From What are the coenzymes derived?
vitamins
What are the factors that can affect the catalysis of the enzymes?
1) Temperature (37)
2) pH (depends on the enzyme)
Where is chymotrypsin found, and what is its function?
It is a Peptidase in the intestine responsible for breaking down the peptide bonds (serine proteases) it cuts where it finds aromatic amino acid, in its active site it has three important catalytic amino acid (structure Asp 102, structure His 57, major Ser 195)
Which molecules can be converted into products?
Molecules that reach the transition state
From which water-soluble vitamins is the coenzyme Thiamine pyrophosphate, and which reaction does it promote?
1) Thiamine (B1)
2) Decarboxylation (lyase), aldehyde group transfer (transferase)
From which water-soluble vitamins is FAD and FMN, and which reaction does it promote?
1) Riboflavin (B2)
2) Redox reaction
From which water-soluble vitamins is Pyridoxal phosphate, and which reaction does it promote?
1) Pyridoxine (B6)
2) Amino group transfer reaction
From which water-soluble vitamins is NAD and NADP, and which reaction does it promote?
1) Nicotinic acid (niacin)
2) Redox reaction
From which water-soluble vitamins is Coenzyme A, and which reaction does it promote?
1) Pantothenic acid
2) Acyl transfer
From which water-soluble vitamins is Biotin, and which reaction does it promote?
1) Biotin
2) Carboxylation
From which water-soluble vitamins is Tetrahydrofolic acid, and which reaction does it promote?
1) Folic acid
2) one carbon group transfer reaction
From which water-soluble vitamins is Deoxyadenosylcobalamin, methylcobalamin, and which reaction does it promote?
1) Vitamin B12
2) intramolecular rearrangements reaction
which water-soluble vitamins promote hydrocarboxylation reaction?
1) Ascorbic acid (vitamin C)
How does a change in the pH affect the enzyme?
Catalytic activity is related to ionic state of the active site, change in pH cause changes in ionizable groups and affects structure and function of the enzyme
What is a zero order reaction?
When the rate of the reaction is not affected by the addition of substrate
What is a first order reaction?
When the reaction increases due to the increase in one substrate it is unimolecular (A WILL PRODUCE B) with a hyperbolic curve
What is a second order reaction?
(Bimolecular) When a reaction is affected by the increase of two of the reactant or when the increase of one of the reactants double the reaction it occurs in allosteric enzymes having a sigmoidal curve
What is Km (Michaelis constant)?
The concentration of the substrate which is required for the reaction to reach half of the Vmax
What does the Km indicates?
The affinity of the substrate to the enzyme, the lower the Km moles the higher the affinity
What is a multi substrate reaction and how many types are there?
A reaction which involves two or more substrate
Two types:
1) sequential
2) double displacement
What are the types and meanings of sequential reaction?
1) ordered sequential reaction, the binding of A is followed by the binding of B and then the product is formed
2) Random sequential reaction, The binding of A or B is not in order and random but both must bind for the product to be formed and released
What is a double-displacement reaction?
When the binding of one substrate release the product it forms without the need for the other substrate to bind
How many type of enzyme inhibition do we have?
1) reversible inhibition
2) non-reversible inhibition (the inhibitor must be removed)
What are the types of reversible inhibition?
1) Competitive (inhibitors compete with substrate as they share some structural similarities, it increases the Km but not the Vmax, you can overcome its effect by increasing the amount of the substrate to increase the chance of its binding) FORMS EI complex
2) Non-competitive (The inhibitor will bind to sites other than the active site, it will prevent the reaction to reach the Vmax and they wont affect the Km) forms ESI complex
3) Uncompetitive (it binds to the enzyme substrate complex, it decreases both the Vmax & Km)
4) Mixed (mixture of different types of inhibition)
When is the graph of the inhibition parallel?
In the uncompetitive inhibition
In which type of inhibition the Km is increased but the Vmax is kept the same?
Competitive inhibition
When is the Km kept the same while the Vmax is lowered?
Pure non-competitive inhibition
What type of inhibition changes the Vmax and Km but the lines intersect somewhere?
Mixed noncompetitive inhibition
Why is enzyme regulation necessary?
1) Maintenance of ordered state
2) conservation of energy
3) responsiveness to environmental changes
How are enzymes regulated?
1) genetic control
2) covalent modification
3) allosteric regulation
4) compartmentation
How can genetic control affect enzyme regulation?
It can control the synthesis of enzymes
How can enzyme be regulated by covalent modification?
1) phosphorylation
2) methylation
3) acetylation
4) nucleotidylation
(adding a functional group to the enzyme to either activate or deactivate the enzyme)
How can allosteric regulation regulate enzyme?
(binding of a molecule to a site other than the active site inhibiting or activating the enzyme (homotropic, if it was the substrate itself, & heterotropic if it different) & it can either be positive or negative cooperativity depending on whether it facilitates the binding of the substrate or not)
How can compartmentation regulate enzymes?
They are created by cellular infrastructure,
1) control several metabolic pathways at the same time
(First pathway of glucose degradation occur in the cytoplasm of liver and muscle cells, but citric acid cycle occur inside the mitochondria, Fatty acid synthesis occur in the cytoplasm, but fatty acid degradation occur inside the mitochondria)
2) specialize reaction conditions
- low pH
3) damage control as it protects the cells components from toxic species
What is the turnover number (Kcat)
It is the number of substrate molecules converted to product per unit time
What is the specificity constant?
It is the relationship between the catalytic rate and substrate binding affinity (Kcat/Km)
Which unit is used to measure enzyme activity?
International units (IU)
What is the irreversible inhibition?
It is when the inhibitor permanently impairs the enzyme via covalent interactions
How to overcome competitive inhibition?
By increasing the substrate concentration
What is meant by enzyme induction?
That enzymes are synthesized at the gene level whenever needed
