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
which route of administration is best for maximizing concentration at site of action and minimizing it elsewhere?
topical
which route of administration is best for prolonging drug absorption?
transdermal
immediate effects of drugs
the relationship between drug concentration and effect is not linear, so the effect will not be linearly proportional to the concentration
delayed effects of drugs
changes in drug effects are often delayed in relation to changes in plasma concentration.
Drug may need time to distribute from the plasma to the site of action, may need time to dissociate from receptors, or turnover of substance needed to express the drug.
cumulative effects of drugs
drugs may take effect as they become cumulated. Can minimize cumulative effect by giving intermittent doses rather than cumulative.
target concentration
concentration of the drug that will produce the desired therapeutic effect for the individual, individualized and determines the rational dosage that you should give
maintenance dose and equation*
drugs are administered with this to maintain a steady state of drug in the body
maintenance dose= CpCLt/ F
loading dose
used for drugs that have a long half live, because it takes a long time for them to reach steady state
loading dose quickly raises the concentration of the drug in the plasma to the target concentration
target concentration strategy
- choose target concentration TC
- predict volume of distribution (V), clearance (CL) based on standard population values, adjust for factors such as weight
- give loading dose or maintenance dose calculated
- measure pt’s response and drug concentration
- revise V and/or CL based on measured concentration
- repeat steps 3-5, adjust the predicted dose to achieve TC
pharmokinetic input
the amount of drug that enters the body
depends on the patient’s adherence to the drug and variations in bioavailability due to metabolism during absorption
maximum effect
after this point, there can’t be any increase in the drug’s response, and increased dose can be ineffective or lead to toxicity
sensitivity
sensitivity of the target organ to drug concentration. Insensitive may be when you measure drug concentrations that usually produce therapeutic effect; oversensitive may mean exaggerated response to small doses
C50
the concentration required to produce 50% of the maximum effect of the drug
how can protein binding affect drug clearance?
changes in protein binding may make it look like there have been changes in the drug clearance, when actually the drug elimination is the same
drugs can bind to proteins such as albumin, alpha1-acid glycoprotein, or red blood cells.
timing of samples for concentration measurement
drugs are usually absorbed 2 hours after taken, so this is when the drug sample should be taken
factors that can affect volume of distribution
Can be affected by the drug binding to tissues (decreases plasma concentration-> apparent volume larger), edema/swelling increases apparent volume, or plasma proteins (increases plasma concentration-> apparent volume smaller)
creatinine clearance
Some drugs are cleared by the renal route, and their clearance can be predicted from renal function. A single serum creatinine measurement can predict the creatinine production rate.
where is potassium congregated while nerve at rest?
usually K concentration greater inside nerve, so they diffuse out at rest
where is sodium congregated while nerve at rest?
Na concentration is greater outside of the nerve cell, so they diffuse to the inside
Nernst potential
describes the relation of diffusion potential to the ion concentration difference across a membrane
Greater potential means greater tendency for the ion to diffuse in one direction
meaning of the sign of the Nernst potential
negative means a positive ion is diffusing from the inside to the outside (inside cell becomes more negative)
positive if a negative ion is diffusing from inside to outside (inside cell becomes more positive)
what is the resting membrane potential of large nerve fibers?
-90 mV, inside is 90mV more negative than potential outside fiber
sodium-potassium pump*
for each 1 ATP, transports 3 Na ions to the outside of the cell (pump phosphorylated) and 2 potassium ions to the inside (pump dephosphorylated). Electrogenic pump that makes negative potential inside cell membrane.
which ions are commonly leaked through the nerve cell membrane?
channel protein/potassium channels allow potassium to leak
membrane way more permeable to potassium than sodium
action potential
rapid changes in the membrane potential that spread rapidly over the nerve fiber membrane. Makes the membrane more positive, then negative, then back to normal.
resting stage
resting membrane potential before the action potential begins; -90mV
depolarization stage
Na diffuse into the axon by sodium channels, overshoots above 0 (large fibers) and potential becomes positive.
repolarization stage
Na channels start to close and voltage-gated K channels open to a greater degree than normal. K diffuse outside, reestablishes resting membrane potential
role of impermeant anions inside the nerve axon
some anions inside the membrane can’t go through membrane channels. Make the inside of the fiber negative when there is a net deficit of cations inside.
role of calcium ions during action potential
calcium may take on the role of sodium or help play the role of sodium in some cells
calcium pump brings Ca from interior to exterior
voltage-gated calcium channels brings Ca from concentrated exterior to interior, contribute to depolarization
positive-feedback cycle to open sodium channels
membrane potential becomes more positive, causes voltage-gated sodium channels to open, Na flows in, makes more positive and creates positive-feedback cycle
threshold for initiation of action potential
number of Na entering fiber has to be greater than K leaving the fiber, usually 15-30mV rise in membrane potential needed, so -65mV membrane potential is the threshold for stimulation
propagation of the action potential
Na diffuse in during depolarization, and positive electrical charges spread several millimeters in both directions in the axon. Causes Na channels in the new areas to open, and action potential spreads.
direction of propagation
action potential travels in all directions away from the stimulus until the entire membrane has been depolarized
all or nothing principle
once an action potential is elicited, the depolarization will travel over entire membrane if conditions are right, otherwise it does not travel at all, will stop in middle with
rhythmicity of some excitable tissues
repetitive self-induced discharges. Responsible for rhythmic heart beat, peristalsis, and neuronal events that are rhythmical like breathing
other excitable tissues can discharge repetitively if their threshold for stimulation is reduced to a low-enough level
what process is necessary for spontaneous rhythmicity
re-excitation. The membrane must be permeable to sodium (or calcium) ions to allow automatic membrane depolarization
hyperpolarization
a change in a cell’s membrane potential that makes it more negative; due to increased potassium flow out of the cell. It inhibits action potentials by increasing the stimulus required to move the membrane potential to the action potential threshold.
saltatory conduction
action potentials can flow into myelinated cells only at the nodes of ranvier, so the action potentials are conducted from node to node. Increases the velocity of nerve transmission, and conserves energy for the axon.
indentations along the myelin sheath
nodes of ranvier
name of cells that deposit myelin sheath
Schwann cells
refractory period
period after an action potential during which a new stimulus cannot be elicited
Membrane is still depolarized from preceding action potential. Sodium channels became inactivated shortly after depolarization started, will only reopen inactivation gates once resting potential reestablished
example of membrane-stabilizing factor that can inhibit excitability
high extracellular fluid calcium ion concentration decreases membrane permeability to sodium ions and reduces excitability
how local anesthetics work to decrease excitability
local anesthetics like procaine and tetracaine will make the activation gates of the sodium channels hard to open, and therefore reduce membrane excitability. Nerve impulses won’t be able to pass along nerves.
regulatory enzymes
usually catalyze the rate-limiting, or slowest, usually not reversible, step in a pathway. When their rate is increased or decreased, it affects the rate of the entire pathway
saturation kinetics*
enzymes will increase their reaction rate as the substrate concentration increases, but they’ll react a maximum velocity (Vmax)
types of reversible inhibition
competitive, noncompetitive, uncompetitive
allosteric enzymes
compounds that bind at sites other than the active catalytic site and regulate the enzyme through conformational changes that affect the catalytic site
covalent modification of enzymes
enzyme activity may be regulated by a covalent modification such as phosphorylation of serine, threonine, or tyrosine residue by a protein kinase
process that activates zymogens, inactive precursors, to synthesize enzymes
proteolysis
feedback regulation
end product of a pathway directly or indirectly controls its own rate of synthesis
feedforward regulation
substrate controls the rate of the pathway
Michaelis-Menten equation*
graph shows most enzymatic reactions follow a hyperbolic curve of [S] vs enzymatic velocity
vi (initial velocity of product formation)= Vmax[S]/ Km+ [S]
Km*
the concentration of substrate required to reach 1/2Vmax
what do the intercepts and slope of the Lineweaver-Burk transformation tell you?*
x intercept = - 1/Km
y intercept = 1/Vmax
slope= Km/Vmax
hexokinase 1 vs glucokinase Km values for glucose
hexokinase 1 is found in red blood cells, Km .05mM, dependent on glucose, lets RBCs still phosphorylate glucose even when glucose concentrations low
glucokinase is found in liver and pancreas cells, higher Km of 5-6mM, stores glycogen, promotes storage of glucose only when concentrations high
velocity and enzyme concentration
rate of a reaction is directly proportional to the concentration of the enzyme
multisubstrate reactions
most enzymes have more than one substrate, and the substrate-binding sites overlap in the active (catalytic) site
reversible inhibitor
an inhibitor that is not covalently bound to the enzyme and can dissociate at a significant rate
competitive inhibitor*
competes with the substrate for binding at the enzyme’s substrate-recognition sites; is usually a structural analog of the substrate
how could you prevent competitive inhibition in enzymes?*
increasing the substrate concentration can overcome this inhibition, because substrates will occupy the binding sites and the inhibitor won’t bind
does not work for irreversible competitive inhibition
competitive inhibitor effect on Km and Vmax*
Reversible ones increase the Km because they raise the concentration of substrate necessary to saturate the enzyme. Irreversible ones don’t change the Km.
reversible ones don’t change Vmax, irreversible ones decrease Vmax
noncompetitive inhibition, effect on vmax and kmax*
inhibitor does not compete with the substrate for the binding site, does not resemble substrate, so adding more substrate does not mitigate inhibition
makes a certain proportion of the enzyme inactive, lowers Vmax
Km is a measure of affinity of the enzyme for the substrate, so it does not change
simple product inhibition in metabolic pathways
a decrease in the rate of an enzyme caused by the accumulation of its own product. Prevents the enzyme from producing a product too fast for the next enzyme in the sequence to use.
regulation of enzymes through conformational changes
most rate-limiting enzymes are controlled through regulatory mechanisms that change the conformation of the enzyme in a way that affects the catalytic site
types: allosteric activation/inhibition, phosphorylation or other covalent modification, protein-protein interactions, proteolytic cleavage
allosteric activators and inhibitors
compounds that bind to the allosteric site (a site separate from the catalytic site) and cause a conformational change in the active site that affects the affinity of the enzyme for the substrate
cooperativity in substrate binding to allosteric enzymes
in allosteric enzymes, they usually have multiple subunits. Binding of a substrate to one subunit facilitates the binding of substrate to another subunit.
allosteric activators vs inhibitors binding
allosteric activators bind to the enzyme in its active relaxed R conformation
allosteric inhibitors binds when the enzyme is in its T state
phosphorylation effect on enzymes
enzyme activity can be affected by phosphorylation (via protein kinases) or dephosphorylation (protein phosphatase)
phosphate is bulky, negatively chraged, interacts with other amino acid residues of protein to cause conformational change at catalytic site; makes more/less reactive
muscle glycogen phosphorylase and regulation
rate-limiting enzyme in the glycogen degradation pathway, degrades glycogen to glucose 1-phosphate
regulated by allosteric activator AMP, which increases as cells use ATP; and activated through phosphorylation by glycogen phosphorylation kinase
protein kinase A
a serine/threonine protein kinase that phosphorylates several enzymes that regulate different metabolic pathways, such as hormonal ones
what allosteric regulator is necessary to activate protein kinase A?
cAMP
calcium-calmodulin family of modulator proteins
Ca-calmodulin binds to several different proteins and regulates their functions, and it can dissociate. Also in the cytoplasm as a Ca-binding protein.
G proteins
G proteins bind to GTP, then their conformation changes so that they can bind to a target protein, and then activate or inhibit it. GTP hydrolyzes, G protein dissociates.
proteolytic cleavage
a type of enzyme regulation that is irreversible
some enzymes are synthesized as proenzymes (precursor proteins, sometimes zymogens), and must undergo proteolytic cleavage to become fully functional
regulation through changes in amount of enzyme
the rate of enzyme synthesis is regulated by increasing (induction) or decreasing (repression) the rate of gene transcription
enzymes can also undergo selective regulated degradation
substrate channeling through compartmentation
cells may have compartmentation of enzymes into multienzyme complexes or organelles, with unique conditions, and this limits the substrates’ access to enzymes. Organelles usually have enzymes with common functions, or that are a part of a sequential reaction.
proteolysis will change the ? structure of the protein
primary
what side of the cell membrane is the ATP site in the sodium potassium pump?*
cytosolic side
kinase
enzyme that catalyzes transfer of a phosphate group from a high-energy molecule (usually ATP) to a substrate
phosphorylase
enzyme that adds an inorganic phosphate onto substrate without using ATP
phosphatase
enzyme that removes a phosphate group from the substrate
dehydrogenase
enzyme that catalyzes oxidation-reduction reactions
hydroxylase
an enzyme that adds a hydroxal group onto the substrate
carboxylase
an enzyme that transfers CO2 groups with the help of biotin
mutase
an enzyme that relocates a functional group in the molecule
synthase/synthetase
an enzyme that joins two molecules using a source of energy (e.g. ATP, acetyl CoA, nucleotide sugar)
how does Km relate to the affinity of the enzyme for its substrate?*
Km is inversely related to the affinity of the enzyme for its substrate
what type of curve on the Michaelis-Menten plot would indicate cooperative kinetics?*
a sigmoidal curve, like for hemoglobin
what kinds of drug types have low volume of distribution and where are they located?*
large/charged molecules, plasma protein bound
located intravascular
what kinds of drug types have medium volume of distribution and where are they located?*
small hydrophilic molecules; ECF (extracellular fluid)
what kinds of drug types have high volume of distribution and where are they located?*
small lipophilic molecules, especially if bound to tissue protein; all tissues including fat
for first-order kinetics, how many half lives does it take for a drug to reach steady state?*
4-5
how many half lives does it take to reach 90% of the steady state level?*
3.3
how to calculate fraction remaining from half life*
(1/2)^ number of half lives
loading dose equation*
Cp (target plasma concentration at steady state) x Vd /F (bioavailability)
maintenance dose equation*
Cp (target plasma concentration at steady state) x CL x t (dosage interval, time between doses, if not administered continuously) all over F
nonsurgical distal radius fracture treatment
Displaced fracture needs to be anatomically aligned. Local anesthesia may be used for the reduction. If in good position, splint or cast is applied, wear for about 6 weeks, physical therapy. Take xray at 3 and 6 weeks if fracture was reduced or thought to be unstable.
surgical distal radius fracture treatment
for fractures that are unstable and can’t be treated with a cast
pieces of the break are put together and held in place with one or more plates or screws. Wear splint for 6 weeks, physical therapy.
what happens to the maintenance and loading dose when the person has renal or liver disease?*
maintenance dose decreases; loading dose usually unchanged
what do inhibitors affect pharmacologically?*
competitive reversible inhibitors decrease potency
irreversible competitive inhibitors and noncompetitive inhibitors decrease efficacy
