Enzymes Flashcards
What are enzymes?
Protein catalyst that increase the rate of reactions without themselves being changed in the overall process
What are the six classes of enzymes?
Oxidoreductases, transferase, hydrolases, isomerase, lyases, ligases
Oxidoreductases enzymes are responsible for?
Oxidation reduction reactions such as lactate to pyruvate
Lactate dehydrogenase
Transferase
Catalyses the reaction of C, N, P containing groups
Serine to glycine
Serine hydroxy methyl transferase
Hydrolases
Catalyses the cleavage of bonds by addition water.
Example of hydrolases reaction
The catalytic reaction of urease to urea and water
Lyases
Catalyses cleavage of C-C, C-S, and certain C-N bonds
Example of lyases
Pyruvate to acetaldehyde in the presence of pyruvate decarboxylase.
Isomerase
Catalyses racemization of optical or geometric isomers
Examples of isomerase
Methylmalony CoA to succinyl CoA in the presence of methylmalo ny Co A mutase
Ligases
Catalyses formation of bonds between carbon and O,S,N coupled to hydrolysis of high energy phosphates
Example of ligases
Pyruvate and co2 in the presence of pyruvate carboxylate to oxaloactate.
What is an active site ?
It a cleft or special pocket in the enzyme that the substrate binds to.
What does the active site contain?
Amino acids side chains that create a 3D surface complementary to the substrate.
Describe catalytic efficiency? What is turnover?
The number of substrate molecules converted to product per enzyme molecule per second . Enzyme catalytic reactions are fast er than uncatalysed reactions.
Describe enzyme specificity?
Enzymes are specific for a single molecule or a structurally related group of substrates . Usually only 1 enzyme per reaction type.
What is a cofactor?
Inorganic component need for enzyme function
Cu2+ is a cofactor for which enzyme?
Cytochrome oxidase
Fe2+ or fe3+ is a cofactor for which enzyme?
Cytochrome oxidase , peroxidase and catalase
K+ is a cofactor for which enzyme?
Pyruvate kinase
Mg2+ is a cofactor for which enzyme?
Hexokinase, glucose 6 phosphatase, pyruvate kinase
Mn2+ is a cofactor for which enzyme?
Arginase, ribonucleotide reductase
Mo is a cofactor for which enzyme?
Dinitrogenase
Ni 2+
Urease
Se is a cofactor for which enzyme?
Glutathionate peroxidase
zn2+ is a cofactor for which enzyme?
Carbonic anhydrase, alcohol dehydrogenase carboxypeptidase a and B
What is a holoenzyme?
The enzyme plus it’s cofactor. Entire complex
What is an apoenzyme?
Enzyme protein without its cofactor. Protein part
What is a prosthetic group?
A coenzyme that’s very tightly ( covalently bonded ) attached to the protein . A non protein part.
Describe simple proteins?
Composed solely of protein, single or multiple subunits .
Describe enzyme regulation ?
The enzymes can be activated or inhibited so that the rate of product formation responds to the needs of the cell.
Describe allosteric binding sites?
Binding to a receptor site on the enzyme and not the active site. Allosteric effectors are bounded non covalently at a site other than the active site.
What effect does allosteric enzymes have on the enzymes?
Alters the affinity of the enzyme for its substrate or modify the maximum catalytic activity of the enzyme or both.
There are two types of effectors in allosteric binding. What are they?
Negative effectors and positive effectors
Describe negative effectors?
Effectors that inhibit enzyme activity
Positive effectors
Increase enzyme activity
Homotropic effectors
When the substate itself serves as an effector.
Heterotrophic effectors
Different from the substate .see figure 4.18 in lippincott
Three ways in which enzymes can be regulated
Allosteric binding site
Regulation of enzymes by covalent modification
Induction and repression of enzyme synthesis
Allosteric can be divided into two segments.
Homotropic and heterotrophic
Regulation of enzymes by covalent modification
Most enzymes can be regulated by the frequent removal or addition of phosphate groups from specifically serine, threonine residues of the enzyme .
Phosphorylation and devphosphorylation
Phosphorylation is catalalysed by enzymes protein kinase, which uses ATP as a proton donor.
Phosphate groups are cleaves from phosphorylates enzymes by the action of
Phosphoprotein
Response of enzyme to phosphorylation
Depending on the specific enzyme, the phosphorylated form may be less or more active than the unphosphorylated enzyme.
Induction
Up regulation or increase in gene expression, synthesis of more enzyme molecules.
Repression
Down regulation , decrease gene expression, decrease in synthesis of enzyme molecules
Sequestration.
Enzyme forms inactive polymers.
Susbstrate availability typically effects?
Substrate and there is a change in velocity and the time change is immediate.
Product inhibition
Typical effector is the product. Results in Vm and of Km.
Allosteric
End product and change in Vm and or Km
Covalent modification
Another enzyme, change in Vm and Km
Synthesis or degeneration of enzyme
Hormone or metabolite , change in the amount of enzyme , hours to days
Alteration of plasma enzyme levels in diseases states.
The levels of specific enzyme activity in the plasma frequently correlates with the extent of tissue damage. The degree of elevation is often useful in the evaluating the prognosis for the patient .
What does an increase in tissue damage indicates?
Reflects damage to the corresponding tissues.
What are the enzymes involved in identifying myocardi al infarction?
Creatine kinase, lactate dehydrogenase, (ldh), glutamate oxaloactate transaminase (GOT)
Quaternary structure of isoenzymes.
Many isoenzymes contain different subunits in various combinations.
Example of the quaternary structure of creative kinase
Occurs are 3 isoenzymes.
Each isoenzyme is a dimer composed of two polypeptides (b and m) associated in one of the three combinations.
CK1
BB
CK2
MB
Ck3
Mm
Diagnosis of MI
The appearance of CK2 marks an MI, after an MI, this isoenzyme occurs 4-8hours after onset of chest chain and reaches a peak in activity at approximately 24 hours.
In addition to CK2 hat other enzyme is found elevated after an MI?
lactate dehydrogenase, peaks after 3-6 days after MI
What is an inhibitor?
Any substance that can diminish the velocity of an enzyme catalyst reaction.
Describe reversible inhibitor
Binds non covalently to the receptor site.
Irreversible inhibitors.
Occurs when inhibited enzyme does not regain activity upon dilution of the enzyme inhibitor complex. And form covalent bonds.
Competive inhibition
Inhibitors binds reversibility to the same site that the substate binding.
Effect on Vmax
The effect of inhibitors is reversed by increased (s).
Effect on KM in competitive inhibition
a competitive inhibitor increases the apparent Km for a given substrate.
Enzymatic reactions in the cytosol
Glycolysis
HMP pathway
Fatty acid synthesis
Enzymatic pathways occurring in the mitochondria
TCA cycle, fatty acid oxidation , oxidation of pyruvate.
How enzymes work have no perspectives
A) energy changes occurring during the reaction
The chemistry of active site
Free energy of activation
Is the energy difference between that of the reactants and high energy difference intermediate that occurs during the formation of product.
Free energy of activation
This peak of energy represents the transition state in which a high energy intermediate is formed during the conversion of reactant to product.
Rate of reaction
For molecules to react they must have sufficient energy . In the absence of an enzyme , only a small proportion of the population of molecules may possess enough energy to achieve the transition state between reactants and products.
True or false, the higher the activation rate the faster the reaction.
False
Alternate reaction pathway
An enzyme provides an alternative pathway that lowers the rate of reactions. The enzyme does not change the free energies of the reactants or products and therefore does not change equilibrium of the reaction .
Steps in enzymatic activity
- Enzyme and substrate combine to form a complex.
- Complex goes through a transition state – not quite substrate or product
- A complex of the enzyme and the product is produced.
- Finally, the enzyme and product separate.
What are the two types active sites.
Catalytic site
Binding site
Catalytic site
Is where the reaction actually takes place
Active site
• area that holds the substrate in proper place
• enzymes use weak, non-covalent interactions to
hold the substrate in place based on R groups of
amino acids
• shape is complementary to the substrate and
determines the specificity of the enzyme
• sites are pockets or clefts on the enzyme surface
Two types of enzyme mechanisms
Lock and key
Induced fit model
What is key and lock.
1.Lock and key model - 1890
•assumes only a substrate of the proper shape could fit with the enzyme
What is the purpose of induced fit?
- assumes continuous changes in active site structure as a substrate binds
- more widely-accepted
List factors that affect enzymes?
Environmental factors
• temperature, pH
Cofactors
• metal ions
Effectors
• species that alter enzyme activity
What is the optimum ph of pepsin ?
Environmental factors
• temperature, pH
Cofactors
• metal ions
Effectors
• species that alter enzyme activity
What is the optimum ph of catalase
7
What is the optimum temperature of enzymes?
• optimum temperature is usually 25 - 40 ºC (but
not always)
What is kinetics?
• Kinetics is the study of the rate of change of reactants to products
What is velocity?
Velocity (v) refers to the change in conc. of substrate or product per unit time
What is velocity?
• Rate (k) refers to the change in total quantity (of reactant or product) per unit time
Initial velocity
• Initial velocity (v0) is the change in reactant or product conc. during the linear phase of a reaction
Michaelis-Menten Kinetics 3 basic assumptions
1: ES complex is in a steady state, i.e.
remains constant during the initial phase of a
reaction
2: when enzyme is saturated all enzyme is in the
form of ES complex
3: if all enzyme in ES then rate of product
formation is maximal:
Examples of compounds that inhibit compounds?
substrate analogs
toxins
drugs
metal complexes
