The application of manipulating carbohydrates while preparing for a contest is done with intent on the muscle glycogen and water content. The thought is for you to have as much glycogen in your muscles as you can on the show day of the competition. From every gram of glycogen in your body, you have another three grams of water added into your muscle cells also. That means that a weight gain of two to four pounds could be predicted if you do it correctly.
Using Creatine before a contest
Loading yourself with creatine is done in an attempt to saturate and control a larger amount of creatine in your muscle cells. The creatine you take in helps you out with the creatine phosphate section of the kreb cycle to create energy for your working cells.
Side note: Kreb cycle – The kreb cycle is what is found in all plants and animals, a variety of enzymatic reactions in the mitochondria of cells, used to create a lot of energy phosphate compounds that are a main source of cellular energy.
Protocols for Creatine:
- First off, 20-25 grams per day for the period of 5-7 days
- Afterwards, 2-5 grams per day for 21-37 days
It has also been shown that creatine raises your total body water and glycogen while not using fluid distribution. A two week study was done to show the results that combining both the carbohydrate loading after you use creatine supplementation has lead to prove that it gives a super concentration of glycogen and water in your muscle cells.
Competitive Bodybuilders: Usage Suggestion
10 Days out: Only have an intake of a high carbohydrate based diet.
7 Days out: Put five grams of creatine into your body daily.
5 Days out: Start the period of carbohydrate depletion for the process of three days which is followed with a cessation of creatine.
2 Days of carbohydrate loading and gradual water intake decreases.
Another suggestion is for you to takea potassium supplement which could help out with any cramping you may be having.
While more research is needed on this topic to come to a conclusion, we all know that for certain people, certain choices will be made. While professional bodybuilders use a certain type of training and preperation to make sure their muscles are as good as possible for performing at the show they are featured in, other less competitive bodybuilders may not worry as much about this issue.
Either way, it is best for you to stick around and find out any conclusion that is discovered.
Friday, May 1, 2009
Thursday, April 30, 2009
Pharmacokinetics
Pharmacokinetics is the study of what the body does to a drug.
Pharmacodynamics is the study of what a drug does to the body.
Routes of Drug Administration:
Intravenous
Oral
Buccal
Sublingual
Rectal
Intramuscular
Transdermal
Subcutaneous
Inhalational
Topical
Of all of these routes you are most likely to be asked about the transdermal, as it is fashionable.
Otherwise, most other basic pharmacology questions tend to concern the pharmacology of intravenous agents; that is what is discussed below.
First Order Kinetics:
A constant fraction of the drug in the body is eliminated per unit time. The rate of elimination is proportional to the amount of drug in the body. The majority of drugs are eliminated in this way.
What follows concerns drugs which follow first order kinetics.
The Volume of Distribution (Vd) is the amount of drug in the body divided by the concentration in the blood. Drugs that are highly lipid soluble, such as digoxin, have a very high volume of distribution (500 litres). Drugs which are lipid insoluble, such as neuromuscular blockers, remain in the blood, and have a low Vd.
The Clearance (Cl) of a drug is the volume of plasma from which the drug is completely removed per unit time. The amount eliminated is proportional to the concentration of the drug in the blood.
The fraction of the drug in the body eliminated per unit time is determined by the elimination constant (kel). This is represented by the slope of the line of the log plasma concentration versus time.
Cl = kel x Vd
Rate of elimination = clearance x concentration in the blood.
Elimination half life (t1/2): the time taken for plasma concentration to reduce by 50%. After 4 half lives, elimination is 94% complete.
It can be shown that the kel = the log of 2 divided by the t1/2 = 0.693/t1/2.
Likewise, Cl = kel x Vd, so, Cl = 0.693Vd/t1/2.
And t1/2 = 0.693 x Vd / cl
The rate of elimination is the clearance times the concentration in the plasma
Roe = Cl x Cp
Fraction of the total drug removed per unit time = Cl/Vd.
If the volume of distribution is increased, then the kel will decrease, the t1/2 will increase, but the clearance won't change.
Confused?
Example: You have a 10ml container of orange squash. You put this into a litre (ok 990ml!) of water. The Vd of the orange squash is 1000ml. If, each minute, you empty 10ml of the orange liquid into the 10ml container, discard this, and replace it with 10ml of water. The clearance is 10 ml per minute. The elimination half life is: 70 minutes . The kel is Cl/Vd = 10/1000 = 0.01. Shown the other way, 0.693/50 = 0.01.
If the volume of the container is increased to 2000ml, then the clearance remains the same, but the Vd, and consequently the t1/2, increases (to 140 minutes).
Simple, isn't it?
What is described above is a single compartment model, what would occur if the bloodstream was the only compartment in the body (or if the Vd = the blood volume). But the human body is more complex than this: there are many compartments: muscle, fat, brain tissue etc. In order to describe this, we use multicompartment models.
Multicompartment Models:
Why does a patient wake up after 5 minutes after an injection of thiopentone when we know that it takes several hours to eliminate this drug from the body? What happens is that, initially the drug is all in the blood and this blood goes to "vessel rich" organs; principally the brain. After a few minutes the drug starts to venture off into other tissues (fat, muscle etc) it redistributes, the concentration in the brain decreases and the patient wakes up! The drug thus redistributes into other compartments.
If you were to represent this phenomenon graphically, you would follow a picture of rapid fall in blood concentration, a plateau, and then a slower gradual fall. The first part is the rapid redistribution phase, the alpha phase, the plateau is the equilibrium phase (where blood concentration = tissue concentration), and the slower phase, the beta phase, is the elimination phase where blood and tissue concentrations fall in tandem. This is a simple two compartment model and is as much as you need to know.
An couple of interesting pieces of information can be derived from the log concentration versus time graph. If you extrapolate back the elimination line to the y axis, then you get to a point called the CP0 - a theoretical point representing the concentration that would have existed at the start if the dose had been instantly distributed (dose/Vd). From this new straight line you can figure out how long it takes for the concentration to drop by 50%: the elimination half life. Likewise, a similar procedure can be performed on the α phase: the redistribution half life.
While it is very important that you understand these concepts, the reality is that most drugs are infinitely more complicated that this, and computer calculations are required to derive this data.
Bioavailability
This is the fraction of the administered dose that reaches the systemic circulation. Bioavailability is 100% for intravenous injection. It varies for other routes depending on incomplete absorption, first pass hepatic metabolism etc. Thus one plots plasma concentration against time, and the bioavailability is the area under the curve.
Zero Order Elimination
Why if I have 10 pints of beer before midnight will I fail a breathalyser test at 8 am the following morning? Either this is due to alcohol having a very long half life (which it does not) or that alcohol is cleared in a different way.
What happens is that the metabolic pathways responsible for alcohol metabolism are rapidly saturated and that clearance is determined by how fast these pathways can work. The metabolic pathways work to their limit. This is known as zero order kinetics: a constant amount of drug is eliminated per unit time. This form of kinetics occours with several important drugs at high dosage concentrations: phenytoin, salicylates, theophylline, and thiopentone (at very large doses). Because high dose thio is very slow to clear, we no longer use it in infusion for status epilepticus (as it takes ages for the patient to wake up!).
Dosage regimens
The strategy for treating patients with drugs is to give sufficient amounts that the required theraputic effect arises, but not a toxic dose.
The maintenance dose is equal to the rate of elimination at steady state (i.e.at steady state, rate of elimination = rate of administration):
Dosing rate = clearance x desired plasma concentration.
Drugs will accumulate within the body if the drug has not been fully eliminated before the next dose. Steady state concentration is thus arrived at after four half lives. This is all very well if you are willing to wait 4 half lives for the drug to be fully effective, but what if you are not? What you may need to do is to "load" the volume of distribution with the drug to achieve target plasma concentrations rapidly: the loading dose.
The loading dose = the volume of distribution x the desired concentration (i.e. the concentration at steady state).
You can figure this out by: Loading dose = usual maintenance dose / usual dosage interval x kel (t1/2/0.693).
Hepatic Drug Clearance
Many drugs are extensively metabolised by the liver. The rate of elimination depends on 1) The liver's inherent ability to metabolise the drug, 2) the amount of drug presented to the liver for metabolism. This is important because drugs administered orally are delivered from the gut to the portal vein to the liver: the liver gobbles up a varying chunk of the administered drug (pre-systemic elimination) and less is available to the body for theraputic effect. This is why you have to give a higher dose of morphine, for examole, orally, than intravenously.
Hepatic drug clearance (i.e. the amount of each drug gobbled up by the liver) depends on:
1) The Intrinsic clearance (Cl int).
2) Hepatic blood flow.
These two factors are independent of one another, and their combined effect is the proportion of drug gobbled up: the extraction ratio.
For drugs that have a low intrinsic clearance, this effect can be increased by giving a second agent that boosts the effect of the liver's enzyme system; these are enzyme inducers. Examples of such drugs are cigarrettes, antiepileptics (carbamazepine & phenytoin), rifampicin, griseofulvin, alcohol and spironolactone (CAR GAS) [also barbiturates]. Consequnetly if a drug addict is given rifampicin or tuberculosis, a higher dose of heroin is required for the same effect. Enzyme inhibitors have the opposite effect: examples are flagyl, allopurinol, cimetidine, erythromycin, dextropropoxyphene, imipramine, (the) pill (FACE DIP).
Likewise, if the blood flow increases, the liver has less chance to gobble up the drug, and the extraction ratio falls. This is particularly the case, as you would expect, of the intrinsic clearance is low.
Illustration: Think of factory workers picking bad apples out of a pile on a conveyor belt, if only one person (low intrinsic clearance) is doing the picking and the speed of the conveyor belt is increased, more bad apples get through. If there are several pickers (high intrinsic clearance) then they are much more able to cope with an increase in the speed of the conveyor belt, but there will come a rate at which they will become overwhelmed, and bad apples will get through.
From this example you can take home this message: for drugs with a low extraction ratio, the kinetics (the body's ability to deal with the drug) depends on enzymatic activity (giving an enzyme inducer effectively gives the single picker 4 arms!). For high extraction ratio drugs, kinetics depends on liver blood flow - the slower the flow the higher the extraction, the higher the flow the lower the extraction ratio.
Drug distribution
When a drug is introduced into the body, where it ends up depends on a number of factors:
1) blood flow, tissues with the highest blood flow receive the drug first, 2) protein binding, drugs stuck to plasma proteins are crippled, they can only go where the proteins go (and that's not very far!), 3) lipid solubility and the degree of ionisation, this describes the ability of drugs to enter tissues (highly lipid soluble / unionised drugs can basically go anywhere).
Protein Binding
Most drugs bind to proteins, either albumin or alpha-1 acid glycoprotein (AAG), to a greater or lesser extent. Drugs prefer to be free, it is in this state that they can travel throughout the body, in and out of tissues and have their biological effect. The downside of this is that they are easy prey for metabolising enzymes.
As you would expect, more highly bound drugs have a longer duration of action and a lower volume of distribution. Generally high extraction ratio drugs' clearance is high because of low protein binding and, conversely, low extraction ratio drugs' clearance is strongly dependent on the amount of protein binding.
Why is this important? If a drug is highly protein bound, you need to give loads of it to get a theraputic effect; as so much is stuck to protein. But what happens if another agent comes along and starts to compete with the drug for the binding site on the protein? Yes, you guessed it, the amount of free drug is increased. This is really important for drugs that are highly protein bound: if a drug is 97% bound to albumin and there is a 3% reduction in binding (displaced by another drug), then the free drug concentration doubles; if a drug is 70% bound and there is a 3% reduction in binding, this will make little difference.
The drugs that you really need to keep an eye on are: warfarin, diazepam, propranolol and phenytoin. For example, a patient on warfarin is admitted with seizures, you treat the patient with phenytoin, next thing you know - his INR is 10.
The amount of albumin does not appear to be hugely relavent. In disease states such as sepsis, the serum albumin drops drastically, but the free drug concentration does not appear to increase
Degree of ionisation
This is really important with regard to local anaesthetics. The essential fact to know is that highly ionized drugs cannnot cross lipid membranes (basically they can't go anywhere) and unionised drugs can cross freely. Morphine is highly ionised, fentanyl is the opposite. Consequently the latter has a faster onset of action. The degree of ionisation depends on the pKa of the drug and the pH of the local environment. The pKa is the the pH at which the drug is 50% ionised. Most drugs are either weak acids or weak bases. Acids are most highly ionised at a high pH (i.e. in an alkaline environment). Bases are most highly ionised in an acidic environment (low pH). For a weak acid, the more acidic the environment, the less ionised the drug, and the more easily it crosses lipid membranes. If you take this acid, at pKa it is 50% ionised, if you add 2 pH points to this (more alkaline), it becomes 90% ionised, if you reduce the pH (more acidic) by two units, it becomes 10% ionised. Weak bases have the opposite effect.
Local anaesthetics are weak bases: the closer the pKa of the local anaesthetic to the local tissue pH, the more unionised the drug is. That is why lignocaine(pKa 7.7) has a faster onset of action than bupivicaine (pKa 8.3). If the local tissues are alkalinised (e.g. by adding bicarbonate to the local anaesthetic), then the tisssue pH is brought closer to the pKa, and the onset of action is hastened.
Pharmacodynamics is the study of what a drug does to the body.
Routes of Drug Administration:
Intravenous
Oral
Buccal
Sublingual
Rectal
Intramuscular
Transdermal
Subcutaneous
Inhalational
Topical
Of all of these routes you are most likely to be asked about the transdermal, as it is fashionable.
Otherwise, most other basic pharmacology questions tend to concern the pharmacology of intravenous agents; that is what is discussed below.
First Order Kinetics:
A constant fraction of the drug in the body is eliminated per unit time. The rate of elimination is proportional to the amount of drug in the body. The majority of drugs are eliminated in this way.
What follows concerns drugs which follow first order kinetics.
The Volume of Distribution (Vd) is the amount of drug in the body divided by the concentration in the blood. Drugs that are highly lipid soluble, such as digoxin, have a very high volume of distribution (500 litres). Drugs which are lipid insoluble, such as neuromuscular blockers, remain in the blood, and have a low Vd.
The Clearance (Cl) of a drug is the volume of plasma from which the drug is completely removed per unit time. The amount eliminated is proportional to the concentration of the drug in the blood.
The fraction of the drug in the body eliminated per unit time is determined by the elimination constant (kel). This is represented by the slope of the line of the log plasma concentration versus time.
Cl = kel x Vd
Rate of elimination = clearance x concentration in the blood.
Elimination half life (t1/2): the time taken for plasma concentration to reduce by 50%. After 4 half lives, elimination is 94% complete.
It can be shown that the kel = the log of 2 divided by the t1/2 = 0.693/t1/2.
Likewise, Cl = kel x Vd, so, Cl = 0.693Vd/t1/2.
And t1/2 = 0.693 x Vd / cl
The rate of elimination is the clearance times the concentration in the plasma
Roe = Cl x Cp
Fraction of the total drug removed per unit time = Cl/Vd.
If the volume of distribution is increased, then the kel will decrease, the t1/2 will increase, but the clearance won't change.
Confused?
Example: You have a 10ml container of orange squash. You put this into a litre (ok 990ml!) of water. The Vd of the orange squash is 1000ml. If, each minute, you empty 10ml of the orange liquid into the 10ml container, discard this, and replace it with 10ml of water. The clearance is 10 ml per minute. The elimination half life is: 70 minutes . The kel is Cl/Vd = 10/1000 = 0.01. Shown the other way, 0.693/50 = 0.01.
If the volume of the container is increased to 2000ml, then the clearance remains the same, but the Vd, and consequently the t1/2, increases (to 140 minutes).
Simple, isn't it?
What is described above is a single compartment model, what would occur if the bloodstream was the only compartment in the body (or if the Vd = the blood volume). But the human body is more complex than this: there are many compartments: muscle, fat, brain tissue etc. In order to describe this, we use multicompartment models.
Multicompartment Models:
Why does a patient wake up after 5 minutes after an injection of thiopentone when we know that it takes several hours to eliminate this drug from the body? What happens is that, initially the drug is all in the blood and this blood goes to "vessel rich" organs; principally the brain. After a few minutes the drug starts to venture off into other tissues (fat, muscle etc) it redistributes, the concentration in the brain decreases and the patient wakes up! The drug thus redistributes into other compartments.
If you were to represent this phenomenon graphically, you would follow a picture of rapid fall in blood concentration, a plateau, and then a slower gradual fall. The first part is the rapid redistribution phase, the alpha phase, the plateau is the equilibrium phase (where blood concentration = tissue concentration), and the slower phase, the beta phase, is the elimination phase where blood and tissue concentrations fall in tandem. This is a simple two compartment model and is as much as you need to know.
An couple of interesting pieces of information can be derived from the log concentration versus time graph. If you extrapolate back the elimination line to the y axis, then you get to a point called the CP0 - a theoretical point representing the concentration that would have existed at the start if the dose had been instantly distributed (dose/Vd). From this new straight line you can figure out how long it takes for the concentration to drop by 50%: the elimination half life. Likewise, a similar procedure can be performed on the α phase: the redistribution half life.
While it is very important that you understand these concepts, the reality is that most drugs are infinitely more complicated that this, and computer calculations are required to derive this data.
Bioavailability
This is the fraction of the administered dose that reaches the systemic circulation. Bioavailability is 100% for intravenous injection. It varies for other routes depending on incomplete absorption, first pass hepatic metabolism etc. Thus one plots plasma concentration against time, and the bioavailability is the area under the curve.
Zero Order Elimination
Why if I have 10 pints of beer before midnight will I fail a breathalyser test at 8 am the following morning? Either this is due to alcohol having a very long half life (which it does not) or that alcohol is cleared in a different way.
What happens is that the metabolic pathways responsible for alcohol metabolism are rapidly saturated and that clearance is determined by how fast these pathways can work. The metabolic pathways work to their limit. This is known as zero order kinetics: a constant amount of drug is eliminated per unit time. This form of kinetics occours with several important drugs at high dosage concentrations: phenytoin, salicylates, theophylline, and thiopentone (at very large doses). Because high dose thio is very slow to clear, we no longer use it in infusion for status epilepticus (as it takes ages for the patient to wake up!).
Dosage regimens
The strategy for treating patients with drugs is to give sufficient amounts that the required theraputic effect arises, but not a toxic dose.
The maintenance dose is equal to the rate of elimination at steady state (i.e.at steady state, rate of elimination = rate of administration):
Dosing rate = clearance x desired plasma concentration.
Drugs will accumulate within the body if the drug has not been fully eliminated before the next dose. Steady state concentration is thus arrived at after four half lives. This is all very well if you are willing to wait 4 half lives for the drug to be fully effective, but what if you are not? What you may need to do is to "load" the volume of distribution with the drug to achieve target plasma concentrations rapidly: the loading dose.
The loading dose = the volume of distribution x the desired concentration (i.e. the concentration at steady state).
You can figure this out by: Loading dose = usual maintenance dose / usual dosage interval x kel (t1/2/0.693).
Hepatic Drug Clearance
Many drugs are extensively metabolised by the liver. The rate of elimination depends on 1) The liver's inherent ability to metabolise the drug, 2) the amount of drug presented to the liver for metabolism. This is important because drugs administered orally are delivered from the gut to the portal vein to the liver: the liver gobbles up a varying chunk of the administered drug (pre-systemic elimination) and less is available to the body for theraputic effect. This is why you have to give a higher dose of morphine, for examole, orally, than intravenously.
Hepatic drug clearance (i.e. the amount of each drug gobbled up by the liver) depends on:
1) The Intrinsic clearance (Cl int).
2) Hepatic blood flow.
These two factors are independent of one another, and their combined effect is the proportion of drug gobbled up: the extraction ratio.
For drugs that have a low intrinsic clearance, this effect can be increased by giving a second agent that boosts the effect of the liver's enzyme system; these are enzyme inducers. Examples of such drugs are cigarrettes, antiepileptics (carbamazepine & phenytoin), rifampicin, griseofulvin, alcohol and spironolactone (CAR GAS) [also barbiturates]. Consequnetly if a drug addict is given rifampicin or tuberculosis, a higher dose of heroin is required for the same effect. Enzyme inhibitors have the opposite effect: examples are flagyl, allopurinol, cimetidine, erythromycin, dextropropoxyphene, imipramine, (the) pill (FACE DIP).
Likewise, if the blood flow increases, the liver has less chance to gobble up the drug, and the extraction ratio falls. This is particularly the case, as you would expect, of the intrinsic clearance is low.
Illustration: Think of factory workers picking bad apples out of a pile on a conveyor belt, if only one person (low intrinsic clearance) is doing the picking and the speed of the conveyor belt is increased, more bad apples get through. If there are several pickers (high intrinsic clearance) then they are much more able to cope with an increase in the speed of the conveyor belt, but there will come a rate at which they will become overwhelmed, and bad apples will get through.
From this example you can take home this message: for drugs with a low extraction ratio, the kinetics (the body's ability to deal with the drug) depends on enzymatic activity (giving an enzyme inducer effectively gives the single picker 4 arms!). For high extraction ratio drugs, kinetics depends on liver blood flow - the slower the flow the higher the extraction, the higher the flow the lower the extraction ratio.
Drug distribution
When a drug is introduced into the body, where it ends up depends on a number of factors:
1) blood flow, tissues with the highest blood flow receive the drug first, 2) protein binding, drugs stuck to plasma proteins are crippled, they can only go where the proteins go (and that's not very far!), 3) lipid solubility and the degree of ionisation, this describes the ability of drugs to enter tissues (highly lipid soluble / unionised drugs can basically go anywhere).
Protein Binding
Most drugs bind to proteins, either albumin or alpha-1 acid glycoprotein (AAG), to a greater or lesser extent. Drugs prefer to be free, it is in this state that they can travel throughout the body, in and out of tissues and have their biological effect. The downside of this is that they are easy prey for metabolising enzymes.
As you would expect, more highly bound drugs have a longer duration of action and a lower volume of distribution. Generally high extraction ratio drugs' clearance is high because of low protein binding and, conversely, low extraction ratio drugs' clearance is strongly dependent on the amount of protein binding.
Why is this important? If a drug is highly protein bound, you need to give loads of it to get a theraputic effect; as so much is stuck to protein. But what happens if another agent comes along and starts to compete with the drug for the binding site on the protein? Yes, you guessed it, the amount of free drug is increased. This is really important for drugs that are highly protein bound: if a drug is 97% bound to albumin and there is a 3% reduction in binding (displaced by another drug), then the free drug concentration doubles; if a drug is 70% bound and there is a 3% reduction in binding, this will make little difference.
The drugs that you really need to keep an eye on are: warfarin, diazepam, propranolol and phenytoin. For example, a patient on warfarin is admitted with seizures, you treat the patient with phenytoin, next thing you know - his INR is 10.
The amount of albumin does not appear to be hugely relavent. In disease states such as sepsis, the serum albumin drops drastically, but the free drug concentration does not appear to increase
Degree of ionisation
This is really important with regard to local anaesthetics. The essential fact to know is that highly ionized drugs cannnot cross lipid membranes (basically they can't go anywhere) and unionised drugs can cross freely. Morphine is highly ionised, fentanyl is the opposite. Consequently the latter has a faster onset of action. The degree of ionisation depends on the pKa of the drug and the pH of the local environment. The pKa is the the pH at which the drug is 50% ionised. Most drugs are either weak acids or weak bases. Acids are most highly ionised at a high pH (i.e. in an alkaline environment). Bases are most highly ionised in an acidic environment (low pH). For a weak acid, the more acidic the environment, the less ionised the drug, and the more easily it crosses lipid membranes. If you take this acid, at pKa it is 50% ionised, if you add 2 pH points to this (more alkaline), it becomes 90% ionised, if you reduce the pH (more acidic) by two units, it becomes 10% ionised. Weak bases have the opposite effect.
Local anaesthetics are weak bases: the closer the pKa of the local anaesthetic to the local tissue pH, the more unionised the drug is. That is why lignocaine(pKa 7.7) has a faster onset of action than bupivicaine (pKa 8.3). If the local tissues are alkalinised (e.g. by adding bicarbonate to the local anaesthetic), then the tisssue pH is brought closer to the pKa, and the onset of action is hastened.
Xenobiotic metabolism
Xenobiotic metabolism is the set of metabolic pathways that modify the chemical structure of xenobiotics, which are compounds foreign to an organism's normal biochemistry, such as drugs and poisons. These pathways are a form of biotransformation present in all major groups of organisms, and are considered to be of ancient origin. These reactions often act to detoxify poisonous compounds; however, in some cases, the intermediates in xenobiotic metabolism can themselves be the cause of toxic effects.
Xenobiotic metabolism is divided into three phases. In phase I, enzymes such as cytochrome P450 oxidases introduce reactive or polar groups into xenobiotics. These modified compounds are then conjugated to polar compounds in phase II reactions. These reactions are catalysed by transferase enzymes such as glutathione S-transferases. Finally, in phase III, the conjugated xenobiotics may be further processed, before being recognised by efflux transporters and pumped out of cells.
The reactions in these pathways are of particular interest in medicine as part of drug metabolism and as a factor contributing to multidrug resistance in infectious diseases and cancer chemotherapy. The actions of some drugs as substrates or inhibitors of enzymes involved in xenobiotic metabolism are a common reason for hazardous drug interactions. These pathways are also important in environmental science, with the xenobiotic metabolism of microorganisms determining whether a pollutant will be broken down during bioremediation, or persist in the environment.
Xenobiotic metabolism is divided into three phases. In phase I, enzymes such as cytochrome P450 oxidases introduce reactive or polar groups into xenobiotics. These modified compounds are then conjugated to polar compounds in phase II reactions. These reactions are catalysed by transferase enzymes such as glutathione S-transferases. Finally, in phase III, the conjugated xenobiotics may be further processed, before being recognised by efflux transporters and pumped out of cells.
The reactions in these pathways are of particular interest in medicine as part of drug metabolism and as a factor contributing to multidrug resistance in infectious diseases and cancer chemotherapy. The actions of some drugs as substrates or inhibitors of enzymes involved in xenobiotic metabolism are a common reason for hazardous drug interactions. These pathways are also important in environmental science, with the xenobiotic metabolism of microorganisms determining whether a pollutant will be broken down during bioremediation, or persist in the environment.
MTT assay
The MTT assay and the MTS assay are laboratory tests and standard colorimetric assays (an assay which measures changes in color) for measuring the activity of enzymes that reduce MTT or MTS + PMS to formazan, giving a purple color. It can also be used to determine cytotoxicity of potential medicinal agents and other toxic materials, since those agents would result in cell toxicity and therefore metabolic dysfunction and therefore decreased performance in the assay.
Yellow MTT (3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide, a tetrazole) is reduced to purple formazan in living cells.[1] A solubilization solution (usually either dimethyl sulfoxide, an acidified ethanol solution, or a solution of the detergent sodium dodecyl sulfate in diluted hydrochloric acid) is added to dissolve the insoluble purple formazan product into a colored solution. The absorbance of this colored solution can be quantified by measuring at a certain wavelength (usually between 500 and 600 nm) by a spectrophotometer. The absorption maximum is dependent on the solvent employed.
MTS is a more recent alternative to MTT. MTS (3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium), in the presence of phenazine methosulfate (PMS), produces a water-soluble formazan product that had an absorbance maximum at 490-500 nm in phosphate-buffered saline.[2] It is advantageous over MTT in that (1) the reagents MTS + PMS are reduced more efficiently than MTT, and (2) the product is water soluble, decreasing toxicity to cells seen with an insoluble product.
These reductions take place only when reductase enzymes are active, and therefore conversion is often used as a measure of viable (living) cells. However, it is important to keep in mind that other viability tests (such as the CASY cell counting technology) sometimes give completely different results, as many different conditions can increase or decrease metabolic activity. Changes in metabolic activity can give large changes in MTT or MTS results while the number of viable cells is constant. When the amount of purple formazan produced by cells treated with an agent is compared with the amount of formazan produced by untreated control cells, the effectiveness of the agent in causing death, or changing metabolism of cells, can be deduced through the production of a dose-response curve
Yellow MTT (3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide, a tetrazole) is reduced to purple formazan in living cells.[1] A solubilization solution (usually either dimethyl sulfoxide, an acidified ethanol solution, or a solution of the detergent sodium dodecyl sulfate in diluted hydrochloric acid) is added to dissolve the insoluble purple formazan product into a colored solution. The absorbance of this colored solution can be quantified by measuring at a certain wavelength (usually between 500 and 600 nm) by a spectrophotometer. The absorption maximum is dependent on the solvent employed.
MTS is a more recent alternative to MTT. MTS (3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium), in the presence of phenazine methosulfate (PMS), produces a water-soluble formazan product that had an absorbance maximum at 490-500 nm in phosphate-buffered saline.[2] It is advantageous over MTT in that (1) the reagents MTS + PMS are reduced more efficiently than MTT, and (2) the product is water soluble, decreasing toxicity to cells seen with an insoluble product.
These reductions take place only when reductase enzymes are active, and therefore conversion is often used as a measure of viable (living) cells. However, it is important to keep in mind that other viability tests (such as the CASY cell counting technology) sometimes give completely different results, as many different conditions can increase or decrease metabolic activity. Changes in metabolic activity can give large changes in MTT or MTS results while the number of viable cells is constant. When the amount of purple formazan produced by cells treated with an agent is compared with the amount of formazan produced by untreated control cells, the effectiveness of the agent in causing death, or changing metabolism of cells, can be deduced through the production of a dose-response curve
DNase footprinting assay
A DNase footprinting assay[1] is a DNA footprinting technique from molecular biology/biochemistry that detects DNA-protein interaction using the fact that a protein bound to DNA will often protect that DNA from enzymatic cleavage. This makes it possible to locate a protein binding site on a particular DNA molecule. The method uses an enzyme, deoxyribonuclease (DNase, for short) to cut the radioactively end-labelled DNA, followed by gel electrophoresis to detect the resulting cleavage pattern.
For example, the DNA fragment of interest may be PCR amplified using a 32P 5' labeled primer, with the end result being many DNA molecules with a radioactive label on one end of one strand of each double stranded molecule. Cleavage by DNase will produce fragments, the smaller of which will move further on the electrophoretic gel. The fragments which are smaller with respect to the 32P-labelled end will appear further on the gel than the longer fragments. The gel is then used to expose a special photographic film.
The cleavage pattern of the DNA in the absence of a DNA binding protein, typically referred to as free DNA, is compared to the cleavage pattern of DNA in the presence of a DNA binding protein. If the protein binds DNA, the binding site is protected from enzymatic cleavage. This protection will result in a clear area on the gel which is referred to as the "footprint".
By varying the concentration of the DNA-binding protein, the binding affinity of the protein can be estimated according to the minimum concentration of protein at which a footprint is observed.
This technique was developed by David Galas and Albert Schmitz at Geneva in 1977
For example, the DNA fragment of interest may be PCR amplified using a 32P 5' labeled primer, with the end result being many DNA molecules with a radioactive label on one end of one strand of each double stranded molecule. Cleavage by DNase will produce fragments, the smaller of which will move further on the electrophoretic gel. The fragments which are smaller with respect to the 32P-labelled end will appear further on the gel than the longer fragments. The gel is then used to expose a special photographic film.
The cleavage pattern of the DNA in the absence of a DNA binding protein, typically referred to as free DNA, is compared to the cleavage pattern of DNA in the presence of a DNA binding protein. If the protein binds DNA, the binding site is protected from enzymatic cleavage. This protection will result in a clear area on the gel which is referred to as the "footprint".
By varying the concentration of the DNA-binding protein, the binding affinity of the protein can be estimated according to the minimum concentration of protein at which a footprint is observed.
This technique was developed by David Galas and Albert Schmitz at Geneva in 1977
Reversible inhibitors
[edit] Enzyme activity
Enzyme activity = moles of substrate converted per unit time = rate × reaction volume. Enzyme activity is a measure of the quantity of active enzyme present and is thus dependent on conditions, which should be specified. The SI unit is the katal, 1 katal = 1 mol s-1, but this is an excessively large unit. A more practical and commonly-used value is 1 enzyme unit (EU) = 1 μmol min-1 (μ = micro, x 10-6). 1 U corresponds to 16.67 nanokatals.[1]
[edit] Specific activity
The specific activity of an enzyme is another common unit. This is the activity of an enzyme per milligram of total protein (expressed in μmol min-1mg-1). Specific activity gives a measurement of the purity of the enzyme. It is the amount of product formed by an enzyme in a given amount of time under given conditions per milligram of enzyme. Specific activity is equal to the rate of reaction multiplied by the volume of reaction divided by the mass of enzyme. The SI unit is katal kg-1, but a more practical unit is μmol mg-1 min-1. Specific activity is a measure of enzyme processivity, usually constant for a pure enzyme.
[edit] Related terminology
The rate of a reaction is the concentration of substrate disappearing (or product produced) per unit time (mol L − 1s − 1)
The % purity is 100% × (specific activity of enzyme sample / specific activity of pure enzyme). The impure sample has lower specific activity because some of the mass is not actually enzyme. If the specific activity of 100% pure enzyme is known, then an impure sample will have a lower specific activity, allowing purity to be calculated.
[edit] Types of assay
All enzyme assays measure either the consumption of substrate or production of product over time. A large number of different methods of measuring the concentrations of substrates and products exist and many enzymes can be assayed in several different ways. Biochemists usually study enzyme-catalysed reactions using four types of experiments:[2]
(1) Initial rate experiments. When an enzyme is mixed with a large excess of the substrate, the enzyme-substrate intermediate builds up in a fast initial transient. Then the reaction achieves a steady-state kinetics in which enzyme substrate intermediates remains approximately constant over time and the reaction rate changes relatively slowly. Rates are measured for a short period after the attainment of the quasi-steady state, typically by monitoring the accumulation of product with time. Because the measurements are carried out for a very short period and because of the large excess of substrate, the approximation free substrate is approximately equal to the initial substrate can be made. The initial rate experiment is the simplest to perform and analyze, being relatively free from complications such as back-reaction and enzyme degradation. It is therefore by far the most commonly used type of experiment in enzyme kinetics.
(2) Progress curve experiments. In these experiments, the kinetic parameters are determined from expressions for the species concentrations as a function of time. The concentration of the substrate or product is recorded in time after the initial fast transient and for a sufficiently long period to allow the reaction to approach equilibrium. We note in passing that, while they are less common now, progress curve experiments were widely used in the early period of enzyme kinetics.
(3) Transient kinetics experiments. In these experiments, reaction behaviour is tracked during the initial fast transient as the intermediate reaches the steady-state kinetics period. These experiments are more difficult to perform than either of the above two classes because they require rapid mixing and observation techniques.
(4) Relaxation experiments. In these experiments, an equilibrium mixture of enzyme, substrate and product is perturbed, for instance by a temperature, pressure or pH jump, and the return to equilibrium is monitored. The analysis of these experiments requires consideration of the fully reversible reaction. Moreover, relaxation experiments are relatively insensitive to mechanistic details and are thus not typically used for mechanism identification, although they can be under appropriate conditions.
Enzyme assays can be split into two groups according to their sampling method: continuous assays, where the assay gives a continuous reading of activity, and discontinuous assays, where samples are taken, the reaction stopped and then the concentration of substrates/products determined.
Temperature-controlled cuvette holder in a spectrophotometer.
[edit] Continuous assays
Continuous assays are most convenient, with one assay giving the rate of reaction with no further work necessary. There are many different types of continuous assays.
[edit] Spectrophotometric
In spectrophotometric assays, you follow the course of the reaction by measuring a change in how much light the assay solution absorbs. If this light is in the visible region you can actually see a change in the color of the assay, these are called colorimetric assays. The MTT assay, a redox assay using a tetrazolium dye as substrate is an example of a colorimetric assay.
UV light is often used, since the common coenzymes NADH and NADPH absorb UV light in their reduced forms, but do not in their oxidised forms. An oxidoreductase using NADH as a substrate could therefore be assayed by following the decrease in UV absorbance at a wavelength of 340 nm as it consumes the coenzyme.[3]
Direct versus coupled assays
Coupled assay for hexokinase using glucose-6-phosphate dehydrogenase.
Even when the enzyme reaction does not result in a change in the absorbance of light, it can still be possible to use a spectrophotometric assay for the enzyme by using a coupled assay. Here, the product of one reaction is used as the substrate of another, easily-detectable reaction. For example, figure 1 shows the coupled assay for the enzyme hexokinase, which can be assayed by coupling its production of glucose-6-phosphate to NADPH production, using glucose-6-phosphate dehydrogenase.
[edit] Fluorometric
Fluorescence is when a molecule emits light of one wavelength after absorbing light of a different wavelength. Fluorometric assays use a difference in the fluorescence of substrate from product to measure the enzyme reaction. These assays are in general much more sensitive than spectrophotometric assays, but can suffer from interference caused by impurities and the instability of many fluorescent compounds when exposed to light.
An example of these assays is again the use of the nucleotide coenzymes NADH and NADPH. Here, the reduced forms are fluorescent and the oxidised forms non-fluorescent. Oxidation reactions can therefore be followed by a decrease in fluorescence and reduction reactions by an increase.[4] Synthetic substrates that release a fluorescent dye in an enzyme-catalyzed reaction are also available, such as 4-methylumbelliferyl-β-D-galactoside for assaying β-galactosidase.
[edit] Calorimetric
Chemiluminescence of Luminol
Calorimetry is the measurement of the heat released or absorbed by chemical reactions. These assays are very general, since many reactions involve some change in heat and with use of a microcalorimeter, not much enzyme or substrate is required. These assays can be used to measure reactions that are impossible to assay in any other way.[5]
[edit] Chemiluminescent
Chemiluminescence is the emission of light by a chemical reaction. Some enzyme reactions produce light and this can be measured to detect product formation. These types of assay can be extremely sensitive, since the light produced can be captured by photographic film over days or weeks, but can be hard to quantify, because not all the light released by a reaction will be detected.
The detection of horseradish peroxidase by enzymatic chemiluminescence (ECL) is a common method of detecting antibodies in western blotting. Another example is the enzyme luciferase, this is found in fireflies and naturally produces light from its substrate luciferin.
[edit] Light Scattering
Static Light Scattering measures the product of weight-averaged molar mass and concentration of macromolecules in solution. Given a fixed total concentration of one or more species over the measurement time, the scattering signal is a direct measure of the weight-averaged molar mass of the solution, which will vary as complexes form or dissociate. Hence the measurement quantifies the stoichiometry of the complexes as well as kinetics. Light scattering assays of protein kinetics is a very general technique that does not require an enzyme.
[edit] Discontinuous assays
Discontinuous assays are when samples are taken from an enzyme reaction at intervals and the amount of product production or substrate consumption is measured in these samples.
[edit] Radiometric
Radiometric assays measure the incorporation of radioactivity into substrates or its release from substrates. The radioactive isotopes most frequently used in these assays are 14C, 32P, 35S and 125I. Since radioactive isotopes can allow the specific labelling of a single atom of a substrate, these assays are both extremely sensitive and specific. They are frequently used in biochemistry and are often the only way of measuring a specific reaction in crude extracts (the complex mixtures of enzymes produced when you lyse cells).
Radioactivity is usually measured in these procedures using a scintillation counter.
[edit] Chromatographic
Chromatographic assays measure product formation by separating the reaction mixture into its components by chromatography. This is usually done by high-performance liquid chromatography (HPLC), but can also use the simpler technique of thin layer chromatography. Although this approach can need a lot of material, its sensitivity can be increased by labelling the substrates/products with a radioactive or fluorescent tag. Assay sensitivity has also been increased by switching protocols to improved chromatographic instruments (e.g. ultra-high pressure liquid chromatography) that operate at pump pressure a few-fold higher than HPLC instruments (see HPLC#Pump_pressure).[6]
[edit] Factors to control in assays
Salt Concentration: Most enzymes cannot tolerate extremely high salt concentrations. The ions interfere with the weak ionic bonds of proteins. Typical enzymes are active in salt concentrations of 1-500 mM. As usual there are exceptions such as the halophilic (salt loving) algae and bacteria.
Effects of Temperature: All enzymes work within a range of temperature specific to the organism. Increases in temperature generally lead to increases in reaction rates. There is a limit to the increase because higher temperatures lead to a sharp decrease in reaction rates. This is due to the denaturating (alteration) of protein structure resulting from the breakdown of the weak ionic and hydrogen bonding that stabilize the three dimensional structure of the enzyme. The "optimum" temperature for human enzymes is usually between 35 and 40 °C. The average temperature for humans is 37 °C. Human enzymes start to denature quickly at temperatures above 40 °C. Enzymes from thermophilic archaea found in the hot springs are stable up to 100 °C.[7] However, the idea of an "optimum" rate of an enzyme reaction is misleading, as the rate observed at any temperature is the product of two rates, the reaction rate and the denaturation rate. If you were to use an assay measuring activity for one second, it would give high activity at high temperatures, however if you were to use an assay measuring product formation over an hour, it would give you low activity at these temperatures.
Effects of pH: Most enzymes are sensitive to pH and have specific ranges of activity. All have an optimum pH. The pH can stop enzyme activity by denaturating (altering) the three dimensional shape of the enzyme by breaking ionic, and hydrogen bonds. Most enzymes function between a pH of 6 and 8; however pepsin in the stomach works best at a pH of 2 and trypsin at a pH of 8.
Substrate Saturation: Increasing the substrate concentration increases the rate of reaction (enzyme activity). However, enzyme saturation limits reaction rates. An enzyme is saturated when the active sites of all the molecules are occupied most of the time. At the saturation point, the reaction will not speed up, no matter how much additional substrate is added. The graph of the reaction rate will plateau.
Level of crowding, large amounts of macromolecules in a solution will alter the rates and equilibrium constants of enzyme reactions, through an effect called macromolecular crowding.[8]
[edit] List of enzyme assays
MTT assay
Overlay assay
Fluorescein diacetate hydrolysis
[edit] See also
Restriction enzyme
DNase footprinting assay
Enzyme kinetics
[edit] References
^ Nomenclature Committee of the International Union of Biochemistry (NC-IUB) (1979). "Units of Enzyme Activity". Eur. J. Biochem. 97: 319–20. doi:10.1111/j.1432-1033.1979.tb13116.x. http://www.blackwell-synergy.com/doi/pdf/10.1111/j.1432-1033.1979.tb13116.x.
^ Schnell, S., Chappell, M. J., Evans, N. D. and Roussel, M. R. The mechanism distinguishability problem in biochemical kinetics: The single-enzyme, single-substrate reaction as a case study. Comptes Rendus Biologies 2006; 329, 51-61. DOI: 10.1016/j.crvi.2005.09.005
^ Bergmeyer, H. U. "Methods of Enzymatic Analysis", Vol. 4, Academic Press (New York, NY:1974), pp.2066-2072.
^ Passonneau, J. V., and Lowry, O. H. "Enzymatic Analysis. A Practical Guide", Humana Press (Totowa, NJ:1993), pp.85-110.
^ Todd MJ, Gomez J. Enzyme kinetics determined using calorimetry: a general assay for enzyme activity? Anal Biochem. 2001 Sep 15;296(2):179-87.
^ Churchwella, M; Twaddlea, N; Meekerb, L; and Doergea, D. Improving Sensitivity In Liquid Chromatography-Mass Spectrometry. Journal of Chromatography B Volume 825, Issue 2, 25 October 2005, Pages 134-143
^ Cowan DA (1997). "Thermophilic proteins: stability and function in aqueous and organic solvents". Comp. Biochem. Physiol. A Physiol. 118 (3): 429–38. doi:10.1016/S0300-9629(97)00004-2. PMID 9406427.
^ Minton AP (2001). "The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media". J. Biol. Chem. 276 (14): 10577–80. doi:10.1074/jbc.R100005200. PMID 11279227. http://www.jbc.org/cgi/content/full/276/14/10577.
v • d • eMedicine: Pathology
Principles of pathology
Disease/Medical condition (Infection, Neoplasia) - Hemodynamics (Ischemia) - Inflammation - Wound healing
Cell death: Necrosis (Liquefactive necrosis, Coagulative necrosis, Caseous necrosis) - Apoptosis - Pyknosis - Karyorrhexis - Karyolysis
Cellular adaptation: Atrophy - Hypertrophy - Hyperplasia - Dysplasia - Metaplasia (Squamous, Glandular)accumulations: pigment (Hemosiderin, Lipochrome/Lipofuscin, Melanin) - Steatosis
Anatomical pathology
Surgical pathology - Cytopathology - Autopsy - Molecular pathology - Forensic pathology - Dental pathology Gross examination - Histopathology - Immunohistochemistry - Electron microscopy - Immunofluorescence - Fluorescent in situ hybridization
Clinical pathology
Clinical chemistry - Hematopathology - Transfusion medicine - Medical microbiology - Diagnostic immunology - ImmunopathologyEnzyme assay - Mass spectrometry - Chromatography - Flow cytometry - Blood bank - Microbiological culture - Serology
Specific conditions
Myocardial infarction
v • d • eProteins: key methods of study
Experimental
Protein purification - Green fluorescent protein - Western blot - Protein immunostaining - Protein sequencing - Gel electrophoresis/Protein electrophoresis - Protein immunoprecipitation - Peptide mass fingerprinting
Bioinformatics
Protein structure prediction - Protein-protein docking - Protein structural alignment - Protein ontology - Protein-protein interaction prediction
Assay
Enzyme assay - Protein assay - Secretion assay
Retrieved from "http://en.wikipedia.org/wiki/Enzyme_assay"
Categories: Protein methods Enzymes Chemical pathology
Views
Article
Discussion
Edit this page
History
Personal tools
Log in / create account
Enzyme activity = moles of substrate converted per unit time = rate × reaction volume. Enzyme activity is a measure of the quantity of active enzyme present and is thus dependent on conditions, which should be specified. The SI unit is the katal, 1 katal = 1 mol s-1, but this is an excessively large unit. A more practical and commonly-used value is 1 enzyme unit (EU) = 1 μmol min-1 (μ = micro, x 10-6). 1 U corresponds to 16.67 nanokatals.[1]
[edit] Specific activity
The specific activity of an enzyme is another common unit. This is the activity of an enzyme per milligram of total protein (expressed in μmol min-1mg-1). Specific activity gives a measurement of the purity of the enzyme. It is the amount of product formed by an enzyme in a given amount of time under given conditions per milligram of enzyme. Specific activity is equal to the rate of reaction multiplied by the volume of reaction divided by the mass of enzyme. The SI unit is katal kg-1, but a more practical unit is μmol mg-1 min-1. Specific activity is a measure of enzyme processivity, usually constant for a pure enzyme.
[edit] Related terminology
The rate of a reaction is the concentration of substrate disappearing (or product produced) per unit time (mol L − 1s − 1)
The % purity is 100% × (specific activity of enzyme sample / specific activity of pure enzyme). The impure sample has lower specific activity because some of the mass is not actually enzyme. If the specific activity of 100% pure enzyme is known, then an impure sample will have a lower specific activity, allowing purity to be calculated.
[edit] Types of assay
All enzyme assays measure either the consumption of substrate or production of product over time. A large number of different methods of measuring the concentrations of substrates and products exist and many enzymes can be assayed in several different ways. Biochemists usually study enzyme-catalysed reactions using four types of experiments:[2]
(1) Initial rate experiments. When an enzyme is mixed with a large excess of the substrate, the enzyme-substrate intermediate builds up in a fast initial transient. Then the reaction achieves a steady-state kinetics in which enzyme substrate intermediates remains approximately constant over time and the reaction rate changes relatively slowly. Rates are measured for a short period after the attainment of the quasi-steady state, typically by monitoring the accumulation of product with time. Because the measurements are carried out for a very short period and because of the large excess of substrate, the approximation free substrate is approximately equal to the initial substrate can be made. The initial rate experiment is the simplest to perform and analyze, being relatively free from complications such as back-reaction and enzyme degradation. It is therefore by far the most commonly used type of experiment in enzyme kinetics.
(2) Progress curve experiments. In these experiments, the kinetic parameters are determined from expressions for the species concentrations as a function of time. The concentration of the substrate or product is recorded in time after the initial fast transient and for a sufficiently long period to allow the reaction to approach equilibrium. We note in passing that, while they are less common now, progress curve experiments were widely used in the early period of enzyme kinetics.
(3) Transient kinetics experiments. In these experiments, reaction behaviour is tracked during the initial fast transient as the intermediate reaches the steady-state kinetics period. These experiments are more difficult to perform than either of the above two classes because they require rapid mixing and observation techniques.
(4) Relaxation experiments. In these experiments, an equilibrium mixture of enzyme, substrate and product is perturbed, for instance by a temperature, pressure or pH jump, and the return to equilibrium is monitored. The analysis of these experiments requires consideration of the fully reversible reaction. Moreover, relaxation experiments are relatively insensitive to mechanistic details and are thus not typically used for mechanism identification, although they can be under appropriate conditions.
Enzyme assays can be split into two groups according to their sampling method: continuous assays, where the assay gives a continuous reading of activity, and discontinuous assays, where samples are taken, the reaction stopped and then the concentration of substrates/products determined.
Temperature-controlled cuvette holder in a spectrophotometer.
[edit] Continuous assays
Continuous assays are most convenient, with one assay giving the rate of reaction with no further work necessary. There are many different types of continuous assays.
[edit] Spectrophotometric
In spectrophotometric assays, you follow the course of the reaction by measuring a change in how much light the assay solution absorbs. If this light is in the visible region you can actually see a change in the color of the assay, these are called colorimetric assays. The MTT assay, a redox assay using a tetrazolium dye as substrate is an example of a colorimetric assay.
UV light is often used, since the common coenzymes NADH and NADPH absorb UV light in their reduced forms, but do not in their oxidised forms. An oxidoreductase using NADH as a substrate could therefore be assayed by following the decrease in UV absorbance at a wavelength of 340 nm as it consumes the coenzyme.[3]
Direct versus coupled assays
Coupled assay for hexokinase using glucose-6-phosphate dehydrogenase.
Even when the enzyme reaction does not result in a change in the absorbance of light, it can still be possible to use a spectrophotometric assay for the enzyme by using a coupled assay. Here, the product of one reaction is used as the substrate of another, easily-detectable reaction. For example, figure 1 shows the coupled assay for the enzyme hexokinase, which can be assayed by coupling its production of glucose-6-phosphate to NADPH production, using glucose-6-phosphate dehydrogenase.
[edit] Fluorometric
Fluorescence is when a molecule emits light of one wavelength after absorbing light of a different wavelength. Fluorometric assays use a difference in the fluorescence of substrate from product to measure the enzyme reaction. These assays are in general much more sensitive than spectrophotometric assays, but can suffer from interference caused by impurities and the instability of many fluorescent compounds when exposed to light.
An example of these assays is again the use of the nucleotide coenzymes NADH and NADPH. Here, the reduced forms are fluorescent and the oxidised forms non-fluorescent. Oxidation reactions can therefore be followed by a decrease in fluorescence and reduction reactions by an increase.[4] Synthetic substrates that release a fluorescent dye in an enzyme-catalyzed reaction are also available, such as 4-methylumbelliferyl-β-D-galactoside for assaying β-galactosidase.
[edit] Calorimetric
Chemiluminescence of Luminol
Calorimetry is the measurement of the heat released or absorbed by chemical reactions. These assays are very general, since many reactions involve some change in heat and with use of a microcalorimeter, not much enzyme or substrate is required. These assays can be used to measure reactions that are impossible to assay in any other way.[5]
[edit] Chemiluminescent
Chemiluminescence is the emission of light by a chemical reaction. Some enzyme reactions produce light and this can be measured to detect product formation. These types of assay can be extremely sensitive, since the light produced can be captured by photographic film over days or weeks, but can be hard to quantify, because not all the light released by a reaction will be detected.
The detection of horseradish peroxidase by enzymatic chemiluminescence (ECL) is a common method of detecting antibodies in western blotting. Another example is the enzyme luciferase, this is found in fireflies and naturally produces light from its substrate luciferin.
[edit] Light Scattering
Static Light Scattering measures the product of weight-averaged molar mass and concentration of macromolecules in solution. Given a fixed total concentration of one or more species over the measurement time, the scattering signal is a direct measure of the weight-averaged molar mass of the solution, which will vary as complexes form or dissociate. Hence the measurement quantifies the stoichiometry of the complexes as well as kinetics. Light scattering assays of protein kinetics is a very general technique that does not require an enzyme.
[edit] Discontinuous assays
Discontinuous assays are when samples are taken from an enzyme reaction at intervals and the amount of product production or substrate consumption is measured in these samples.
[edit] Radiometric
Radiometric assays measure the incorporation of radioactivity into substrates or its release from substrates. The radioactive isotopes most frequently used in these assays are 14C, 32P, 35S and 125I. Since radioactive isotopes can allow the specific labelling of a single atom of a substrate, these assays are both extremely sensitive and specific. They are frequently used in biochemistry and are often the only way of measuring a specific reaction in crude extracts (the complex mixtures of enzymes produced when you lyse cells).
Radioactivity is usually measured in these procedures using a scintillation counter.
[edit] Chromatographic
Chromatographic assays measure product formation by separating the reaction mixture into its components by chromatography. This is usually done by high-performance liquid chromatography (HPLC), but can also use the simpler technique of thin layer chromatography. Although this approach can need a lot of material, its sensitivity can be increased by labelling the substrates/products with a radioactive or fluorescent tag. Assay sensitivity has also been increased by switching protocols to improved chromatographic instruments (e.g. ultra-high pressure liquid chromatography) that operate at pump pressure a few-fold higher than HPLC instruments (see HPLC#Pump_pressure).[6]
[edit] Factors to control in assays
Salt Concentration: Most enzymes cannot tolerate extremely high salt concentrations. The ions interfere with the weak ionic bonds of proteins. Typical enzymes are active in salt concentrations of 1-500 mM. As usual there are exceptions such as the halophilic (salt loving) algae and bacteria.
Effects of Temperature: All enzymes work within a range of temperature specific to the organism. Increases in temperature generally lead to increases in reaction rates. There is a limit to the increase because higher temperatures lead to a sharp decrease in reaction rates. This is due to the denaturating (alteration) of protein structure resulting from the breakdown of the weak ionic and hydrogen bonding that stabilize the three dimensional structure of the enzyme. The "optimum" temperature for human enzymes is usually between 35 and 40 °C. The average temperature for humans is 37 °C. Human enzymes start to denature quickly at temperatures above 40 °C. Enzymes from thermophilic archaea found in the hot springs are stable up to 100 °C.[7] However, the idea of an "optimum" rate of an enzyme reaction is misleading, as the rate observed at any temperature is the product of two rates, the reaction rate and the denaturation rate. If you were to use an assay measuring activity for one second, it would give high activity at high temperatures, however if you were to use an assay measuring product formation over an hour, it would give you low activity at these temperatures.
Effects of pH: Most enzymes are sensitive to pH and have specific ranges of activity. All have an optimum pH. The pH can stop enzyme activity by denaturating (altering) the three dimensional shape of the enzyme by breaking ionic, and hydrogen bonds. Most enzymes function between a pH of 6 and 8; however pepsin in the stomach works best at a pH of 2 and trypsin at a pH of 8.
Substrate Saturation: Increasing the substrate concentration increases the rate of reaction (enzyme activity). However, enzyme saturation limits reaction rates. An enzyme is saturated when the active sites of all the molecules are occupied most of the time. At the saturation point, the reaction will not speed up, no matter how much additional substrate is added. The graph of the reaction rate will plateau.
Level of crowding, large amounts of macromolecules in a solution will alter the rates and equilibrium constants of enzyme reactions, through an effect called macromolecular crowding.[8]
[edit] List of enzyme assays
MTT assay
Overlay assay
Fluorescein diacetate hydrolysis
[edit] See also
Restriction enzyme
DNase footprinting assay
Enzyme kinetics
[edit] References
^ Nomenclature Committee of the International Union of Biochemistry (NC-IUB) (1979). "Units of Enzyme Activity". Eur. J. Biochem. 97: 319–20. doi:10.1111/j.1432-1033.1979.tb13116.x. http://www.blackwell-synergy.com/doi/pdf/10.1111/j.1432-1033.1979.tb13116.x.
^ Schnell, S., Chappell, M. J., Evans, N. D. and Roussel, M. R. The mechanism distinguishability problem in biochemical kinetics: The single-enzyme, single-substrate reaction as a case study. Comptes Rendus Biologies 2006; 329, 51-61. DOI: 10.1016/j.crvi.2005.09.005
^ Bergmeyer, H. U. "Methods of Enzymatic Analysis", Vol. 4, Academic Press (New York, NY:1974), pp.2066-2072.
^ Passonneau, J. V., and Lowry, O. H. "Enzymatic Analysis. A Practical Guide", Humana Press (Totowa, NJ:1993), pp.85-110.
^ Todd MJ, Gomez J. Enzyme kinetics determined using calorimetry: a general assay for enzyme activity? Anal Biochem. 2001 Sep 15;296(2):179-87.
^ Churchwella, M; Twaddlea, N; Meekerb, L; and Doergea, D. Improving Sensitivity In Liquid Chromatography-Mass Spectrometry. Journal of Chromatography B Volume 825, Issue 2, 25 October 2005, Pages 134-143
^ Cowan DA (1997). "Thermophilic proteins: stability and function in aqueous and organic solvents". Comp. Biochem. Physiol. A Physiol. 118 (3): 429–38. doi:10.1016/S0300-9629(97)00004-2. PMID 9406427.
^ Minton AP (2001). "The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media". J. Biol. Chem. 276 (14): 10577–80. doi:10.1074/jbc.R100005200. PMID 11279227. http://www.jbc.org/cgi/content/full/276/14/10577.
v • d • eMedicine: Pathology
Principles of pathology
Disease/Medical condition (Infection, Neoplasia) - Hemodynamics (Ischemia) - Inflammation - Wound healing
Cell death: Necrosis (Liquefactive necrosis, Coagulative necrosis, Caseous necrosis) - Apoptosis - Pyknosis - Karyorrhexis - Karyolysis
Cellular adaptation: Atrophy - Hypertrophy - Hyperplasia - Dysplasia - Metaplasia (Squamous, Glandular)accumulations: pigment (Hemosiderin, Lipochrome/Lipofuscin, Melanin) - Steatosis
Anatomical pathology
Surgical pathology - Cytopathology - Autopsy - Molecular pathology - Forensic pathology - Dental pathology Gross examination - Histopathology - Immunohistochemistry - Electron microscopy - Immunofluorescence - Fluorescent in situ hybridization
Clinical pathology
Clinical chemistry - Hematopathology - Transfusion medicine - Medical microbiology - Diagnostic immunology - ImmunopathologyEnzyme assay - Mass spectrometry - Chromatography - Flow cytometry - Blood bank - Microbiological culture - Serology
Specific conditions
Myocardial infarction
v • d • eProteins: key methods of study
Experimental
Protein purification - Green fluorescent protein - Western blot - Protein immunostaining - Protein sequencing - Gel electrophoresis/Protein electrophoresis - Protein immunoprecipitation - Peptide mass fingerprinting
Bioinformatics
Protein structure prediction - Protein-protein docking - Protein structural alignment - Protein ontology - Protein-protein interaction prediction
Assay
Enzyme assay - Protein assay - Secretion assay
Retrieved from "http://en.wikipedia.org/wiki/Enzyme_assay"
Categories: Protein methods Enzymes Chemical pathology
Views
Article
Discussion
Edit this page
History
Personal tools
Log in / create account
Sunday, April 26, 2009
Enzyme inhibitor
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HIV protease in a complex with the protease inhibitor ritonavir. The structure of the protease is shown by the red, blue and yellow ribbons. The inhibitor is shown as the smaller ball-and-stick structure near the centre. Created from PDB 1HXW.
Enzyme inhibitors are molecules that bind to enzymes and decrease their activity. Since blocking an enzyme's activity can kill a pathogen or correct a metabolic imbalance, many drugs are enzyme inhibitors. They are also used as herbicides and pesticides. Not all molecules that bind to enzymes are inhibitors; enzyme activators bind to enzymes and increase their enzymatic activity.
The binding of an inhibitor can stop a substrate from entering the enzyme's active site and/or hinder the enzyme from catalysing its reaction. Inhibitor binding is either reversible or irreversible. Irreversible inhibitors usually react with the enzyme and change it chemically. These inhibitors modify key amino acid residues needed for enzymatic activity. In contrast, reversible inhibitors bind non-covalently and different types of inhibition are produced depending on whether these inhibitors bind the enzyme, the enzyme-substrate complex, or both.
Many drug molecules are enzyme inhibitors, so their discovery and improvement is an active area of research in biochemistry and pharmacology. A medicinal enzyme inhibitor is often judged by its specificity (its lack of binding to other proteins) and its potency (its dissociation constant, which indicates the concentration needed to inhibit the enzyme). A high specificity and potency ensure that a drug will have few side effects and thus low toxicity.
Enzyme inhibitors also occur naturally and are involved in the regulation of metabolism. For example, enzymes in a metabolic pathway can be inhibited by downstream products. This type of negative feedback slows flux through a pathway when the products begin to build up and is an important way to maintain homeostasis in a cell. Other cellular enzyme inhibitors are proteins that specifically bind to and inhibit an enzyme target. This can help control enzymes that may be damaging to a cell, such as proteases or nucleases; a well-characterised example is the ribonuclease inhibitor, which binds to ribonucleases in one of the tightest known protein–protein interactions.[1] Natural enzyme inhibitors can also be poisons and are used as defenses against predators or as ways of killing prey.
From Wikipedia, the free encyclopedia
Jump to: navigation, search
HIV protease in a complex with the protease inhibitor ritonavir. The structure of the protease is shown by the red, blue and yellow ribbons. The inhibitor is shown as the smaller ball-and-stick structure near the centre. Created from PDB 1HXW.
Enzyme inhibitors are molecules that bind to enzymes and decrease their activity. Since blocking an enzyme's activity can kill a pathogen or correct a metabolic imbalance, many drugs are enzyme inhibitors. They are also used as herbicides and pesticides. Not all molecules that bind to enzymes are inhibitors; enzyme activators bind to enzymes and increase their enzymatic activity.
The binding of an inhibitor can stop a substrate from entering the enzyme's active site and/or hinder the enzyme from catalysing its reaction. Inhibitor binding is either reversible or irreversible. Irreversible inhibitors usually react with the enzyme and change it chemically. These inhibitors modify key amino acid residues needed for enzymatic activity. In contrast, reversible inhibitors bind non-covalently and different types of inhibition are produced depending on whether these inhibitors bind the enzyme, the enzyme-substrate complex, or both.
Many drug molecules are enzyme inhibitors, so their discovery and improvement is an active area of research in biochemistry and pharmacology. A medicinal enzyme inhibitor is often judged by its specificity (its lack of binding to other proteins) and its potency (its dissociation constant, which indicates the concentration needed to inhibit the enzyme). A high specificity and potency ensure that a drug will have few side effects and thus low toxicity.
Enzyme inhibitors also occur naturally and are involved in the regulation of metabolism. For example, enzymes in a metabolic pathway can be inhibited by downstream products. This type of negative feedback slows flux through a pathway when the products begin to build up and is an important way to maintain homeostasis in a cell. Other cellular enzyme inhibitors are proteins that specifically bind to and inhibit an enzyme target. This can help control enzymes that may be damaging to a cell, such as proteases or nucleases; a well-characterised example is the ribonuclease inhibitor, which binds to ribonucleases in one of the tightest known protein–protein interactions.[1] Natural enzyme inhibitors can also be poisons and are used as defenses against predators or as ways of killing prey.
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