Group 8/16/19 Flashcards
Learning issues and look-ups
Here are the learning issues we decided on for Monday:
Biochemistry of enzyme kinetics (Ch8 and 9 Marks’)
Introduction to pharmacokinetics (Katzung Ch3)
Physiology of action potential and membrane potential (Guyton and Hall ch 5)
catalysts
compounds that increase the rate of chemical reactions
what do enzymes do?
they bind reactants (substrates), convert products, and release them. Enzymes will return to their original form in the end, despite being modified in the process.
They increase the reaction speed, by decreasing activation energy, and regulate the rate of metabolic reactions.
enzymes bind to the ? and convert them into ?
substrates; products
where do the substrates bind to on the enzyme?
substrate-binding sites
What is important about the substrate for the enzyme?
the enzyme is selective for a substrate, and will make a specific product
region of the enzyme where the reaction occurs
active catalytic site
what is in the active catalytic site of the enzyme?
coenzymes (tightly bound metals) provide functional groups
amino acid residues of the enzyme
transition-state complex
the high-energy, unstable intermediate stage of the reaction between the enzyme and the substrate
functional groups of the active catalytic site will decrease this energy
what determines the pH the enzyme functions at?
enzymes have an optimal pH range to function; determined by the pKa of the functional groups in the active site
covalent inhibitors
compounds that form covalent bonds with the reactive group in the enzyme active site
strong inhibitors of the enzyme’s reaction
transition-state analogs
will mimic the transition-state complex and inhibit enzymatic reactions. Enzyme binds more tightly to the transition-state complex, so these analogs are preferred for binding.
what is the general enzyme-catalyzed reaction
binding of a substrate: E + S ES
conversion to product: ES EP
release of product: EP E+P
specificity
the ability of an enzyme to select just one substrate and distinguish this substrate from a group of very similar compounds; converts it into one product
active site
where the enzyme-substrate complex is formed. Usually a cleft or crevice in the enzyme.
Has functional groups that participate in reaction. Once substrate binds, undergoes conformational change
lock-and-key model
substrate-binding site recognizes the substrate and forms bonds with it, only the substrate can fit properly in the substrate-binding site
induced-fit model
substrate and binding site complement each other, but the substrate binds and the enzyme undergoes conformational change and more binding interactions occur.
activation energy
difference in energy between the substrate and the transition-state complex
what are the major strategies used by enzymes to enable catalysis?
general acid-base catalysis, covalent catalysis, metal-ion catalyis, catalysis by approximation, and cofactor catalysis
general acid-base catalysis
a functional group on the protein either donates a proton (acid catalysis) or accepts a proton (general base catalysis) during the course of the reaction
covalent catalysis
the substrate is covalently linked during the course of the reaction to an amino acid side chain at the active site of the enzyme
metal-ion catalysis
many enzymes contain required metal ions to allow catalysis to occur
catalysis by approximation
the enzyme forces (through the formation of hydrogen bonds and ionic interactions between enzyme and substrate) substrates to bind in a manner that places reactive groups in the appropriate orientation so that the reaction can take place
cofactor catalysis
a required cofactor for an enzyme usually forms a covalent bond with the substrate during the course of a reaction
enzymes involved in amino acid metabolism use ? during cofactor catalysis
pyridoxal phosphate
categories of functional groups used in catalysis
coenzymes (eg pyridoxal phosphate), metal ions, and metallocoenzymes
coenzymes
aka cofactors; complex nonprotein organic molecules that participate in catalysis by providing functional groups. Usually synthesized from vitamins,
classes of coenzymes
activation-transfer coenzymes and oxidation-reduction coenzymes
activation-transfer coenzymes
- have a specific chemical group that binds to the enzyme
- have a separate and different functional or reactive group that participates in catalysis by forming covalent bond with substrate
- depends on the enzyme for the specificity of the substrate and catalyzing the reaction
oxidation-reduction coenzymes
these are involved in oxidation-reduction reactions catalyzed by oxidoreductase enzymes
these coenzymes do NOT form covalent bonds with substrates. Has a functional group that accepts or donates electrons, and a different portion binds to the enzyme.
metal ions in catalysis
metal ions have positive charge and act as electrophiles
they can help bind the substrate, bind multiple ligands, stabilize anions developing, or accept/donate electrons
how does pH affect enzymatic reactions? why?
enzymatic activity increases as pH goes from acidic to physiological level; and decreases as goes from physiological pH to basic
best at physiological pH because functional groups usually get ionized, or H bonds are formed
how does temperature affect enzymatic reactions?
ideal temperature is usually 37 C. Higher can cause denaturation, and reaction rate will increase as temp increased from 0-37 C
inhibitors
compounds that decrease the rate of an enzymatic reaction
covalent inhibitors
form covalent or extremely tight bonds with functional groups in the active catalytic site
penicillin
a transition-state analog that binds tightly to glycopeptidyl transferase, an enzyme required by bacteria for synthesis of the cell wall
penicillin will attach to its own active site, becomes an irreversible inhibitor (sometimes called a suicide inhibitor)
allopurinal
a drug used to treat gout; decreases urate production by inhibiting xanthine oxidase
example of a transition-state analog because it creates a product that binds to its own active site; suicide inhibitor
heavy metal toxicity
caused by the tight binding of a metal to a functional group in an enzyme
dehydrogenases
reactions that accept or donate electrons in the form of hydride ions (H-) or hydrogen atoms
hydroxylases/oxidases
reactions where O2 donates either one or both of its oxygen atoms, makes something oxidized
transferases
catalyze group transfer reactions; the transfer of a functional group from one molecule to another (kinases transfer phosphates, glycosyltransferases transfers carbohydrates, acyltransferases transfer fatty acyl groups, transaminases transfer nitrogen groups)
hydrolases
CO, CN, or CS bonds are cleaved by the addition of water in the form of OH- and H+
lyases
cleave CC, CO, and CN bonds by means other than hydrolysis or oxidation
isomerases
rearrange the existing atoms of a molecule; create isomers of the starting material
ligases
synthesize CC, CS, CO, and CN bonds in reactions coupled to the cleavage of a high-energy phosphate bond in ATP to another molecule
input in pharmokinetics
dose of the drug administered
distribution in pharmokinetics
drug in the tissues distributed
elimination in pharmokinetics
drug metabolized or excreted
clearance*
measure of how quickly the organs of elimination clear the body of the drug. Measure of the volume of plasma cleared of drug per unit time.
may be compromised if impairment to the kidney, heart, or liver
volume of distribution*
Considered an apparent volume because it’s body volume apparently needed to contain the amount of drug homogenously at the concentration in the blood/plasma/water.
volume of distribution equation*
V= amount of drug in body/ Concentration of drug in blood/plasma
how does volume of distribution value relate to a drug’s spread across tissues?
higher volume of distribution means the drug may be concentrated in extravascular tissue instead of being in the vascular component; NOT homogenously distributed
clearance equation*
CLb, CLp (defined with respect to blood, plasma, etc.) = rate of elimination/ C (drug concentration)
= Vd x Ke (elimination constant)
additive character of clearance
elimination of the drug may involve different organs, e.g. kidney, liver, lung
Divide the specific organ’s rate of elimination by the concentration of the drug present in that organ, then add all them up to get systemic clearance
what are the two major sites of drug elimination?
kidneys and liver
rate of elimination equation and how to tell from a graph
rate of elimination = CL x C
if clearance is first-order, can calculate the area under the curve of a time-concentration profile after a dose
capacity-limited elimination
Some drugs become saturated when dose and concentration are high enough. These will have clearance that depends on the concentration of the drug that is achieved.
flow-dependent elimination
Some drugs are cleared rapidly by the organ of elimination; “high extraction drugs”. Drug concentration depends mostly on the rate of drug delivery.
half-life*
the time required to change the amount of the drug in the body to one-half during elimination (or constant infusion).
Can be influenced by disease states
half-life equation for first order kinetics*
t1/2= .7 * V (volume of distribution)/ CL (clearance)
drug accumulation
whenever drug doses are repeated, the drug will accumulate in the body until dosing stops
accumulation factor equation
accumulation factor= 1/ fraction lost in one dosing interval
bioavailability*
(F) the fraction of unchanged drug reaching the systemic circulation following administration by any route
Will be 100% for IV and less than 100% for oral because of incomplete absorption and first-pass metabolism
first-pass elimination
drug gets absorbed into the gut wall, to the liver, may get metabolized, get secreted into bile
these events may reduce the bioavailabilty of the drug
extraction ratio
ratio between the concentration of drug entering and exiting an extraction organ like the liver
which route of administration is best for convenience?
oral