Term
| Characteristics of enzymes |
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Definition
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Term
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Definition
| where substrate binds and catalysis takes place |
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Term
| How do enzymes differ from metal catalysts? |
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Definition
| biological enzymes act under mild conditions and they are highly specific for their reactants |
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Term
| Doe enzymes change the equilibrium of a reaction? If not, what do they change? |
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Definition
| No, an enzyme doesn't affect the spontaneity of a reaction. All it does is lower the activation energy which speeds up the reaction. That's it. It doesn't make one side (product or reactant) more favorable to another. It stabilizes the transition state and provides an alternate reaction pathway |
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Term
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Definition
| catalyzes oxidation-reduction reactions |
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Term
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Definition
| transfer of functional groups |
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Term
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Definition
| Break bonds by adding water |
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Term
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Definition
| eliminates a group to form a double bond |
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Term
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Definition
| forms bonds coupled with ATP hydrolysis |
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Term
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Definition
| rearrangement of a structure |
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Term
| Difference between the deltaG of the reaction and deltaG of the transition state |
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Definition
deltaG of the reaction has nothing to do with the transition state
deltaG reaction is the energy difference between the products and reactants while deltaG of the transition state is the energy required to get to the transition state |
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Term
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Definition
| intermediate between substrates and products, extremely unstable, has an extremely short lifetime |
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Term
| Higher the energy of a transition state means |
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Definition
| the higher the energy hill, the fewer molecules that are willing to make it over that hill, the slower the reaction |
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Term
| Predicting spontaneity from a diagram using deltaG |
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Definition
| remember it's products - reactants so a spontaneous reaction will have a graph where the reactants are at a higher energy level than the products |
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Term
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Definition
| are inorganic and can exist in multiple oxidation states. is basically a helper molecule to an enzyme |
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Term
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Definition
enzymes that act as cofactors for other reactions, are organic
Two types:
cosubstrates: enter and exit the active site of an enzyme
Prosthetic group: remains in the active site tightly bound |
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Term
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Definition
in this mechanism, a proton is transferred between the enzyme and the substrate
With an acid catalyst:
acid donates proton to negatively charged group on the substrate which lowers the activation energy of the transition state. Will pluck this hydrogen off to return to its original form
With a basic catalyst:
base attaches to a hydrogen on the substrate which lowers the activation energy. Another H+ will come and kick off the BH to stabilize the transition state and the BH separates to reform the enzyme |
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Term
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Definition
| can either mediate redox reactions, interact directly with a substrate, or stabilize charge of transition state |
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Term
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Definition
In this kind of reaction, a covalent bond forms between an enzyme and substrate to form the transition state.
enzyme cycles between 2 states.
In first step, the enzyme attacks the substrate which forms the covalent bond
In the second step, the schiff base is formed and the bond is broken to regenerate the enzyme and final product
There is one transition hill that occurs as the substrate is binding to enzyme and there's another transition hill that occurs as the substrate and enzyme are separating. The reaction intermediate has an AE that's in between these two hills and represents the two covanlently bonded together |
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Term
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Definition
| In a covalent catalysis reaction, is the product bond to the enzyme |
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Term
| Amino acid residues mostly likely to participate in acid-base catalysis |
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Definition
| Asp, Glu, His, Lys, Cys, and Tyr can act as acid/base catalysts depending on their state of protonation |
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Term
| Amino acid residues mostly likely to participate in covalent catalysis |
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Definition
| Ser, Tyr, Cys, Lys, His in their deprotonated forms are most likely to participate in this kind of reaction because they need to act as nucleophiles to attack electrophile groups of the substrate |
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Term
| Chymotrypsin mechanism (complete steps) |
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Definition
Histidine extracts proton from serine. This puts a negative charge on serine's O
Negative O of serine attacks the carbonyl group of the substrate
Carbonyl carbon is now a tetrahedral intermediate (first hill in diagram)
Since histidine stole that proton, it now is an acid catalyst and will donate the stolen proton to the nitrogen of the siccile peptide bond which breaks the bond between histidine and serine. Serine is now attached to the N terminus side of the substrate (covalent intermediate) while the C terminus side is released into neverland.
Since histidine gave up its proton, water will come in and give a proton to it. This leaves a negative charge on the O of water which will attack the carbonyl carbon of the covalent intermediate (ser + N terminus of substrate). This forms the second tetrahedral intermediate.
Histidine is now again an acid catalyst and will donate that proton back to serine which collapses the intermediate and the N terminus side of the substrate is released into neverland.
The enzyme is now reformed |
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Term
| Catalytic triad and role of each |
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Definition
Asp, His, Ser of the chymotrypsin mechanism
Serine provides nucleophile
Histidine acts as a base catalyst to activate Serine
Asp stabilizes protonated histidine |
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Term
| Siccile bone in chymotrypsin mechanism |
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Definition
| the bond to be cleaved by hydrolysis |
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Term
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Definition
| in this model, the enzyme structure is "locked" into the perfect conformation needed to bind substrate |
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Term
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Definition
| in this model, an enzyme undergoes a conformational when a substrate is bound to fully enclose the substrate |
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Term
| Low barrier hydrogen bond of chymotrypsin |
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Definition
Hydrogen bond formed between Asp and His
hydrogen is shared equally between the two, has a shorter bond length so it's stronger and helps to stabilize the transition state |
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Term
| Role of oxyanion hole in chymotrypsin |
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Definition
| When the oxygen of serine attacks the carbonyl carbon of the substrate, it changes it into a tetrahedral geometry. At this point, the substrate's oxygen can move into the hole where it forms stabilizing hydrogen bonds with 3 enzyme back groups. This stabilizing effect is important because it lowers the energy of the transition state |
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Term
| Proximity and orientation effects of enzymes |
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Definition
| the efficiency of enzymes depend on how close they are to the substrate and the substrate's orientation |
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Term
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Definition
| the different specificities of enzymes are explained by the chemical character of their specificity pockets |
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Term
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Definition
| a pocket on the enzyme surface that at the active that accommodates the N terminus side of the substrate |
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Term
| Specificity pocket of chrymotrypsin compared to trypsin and elastase |
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Definition
| chymotrypsin prefers large, hydrophobic side chains, trypsin prefers Lys or Arg, and elastase prefers Ala, Gly, or Val |
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Term
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Definition
| are inactive precursors to enzymes that are later activated when and where they are needed. Enzymes can activate themselves which can give an amplifying effect |
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Term
| Relationship between [S] and [P] over the course of a reaction |
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Definition
| concentration of substrate decreases and the concentration of the product increases linearly |
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Term
| Velocity as it relates to [S] or [P] |
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Definition
| velocity is the negative change in substrate or the positive change of [P] |
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Term
| Relationship between enzyme concentration and velocity |
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Definition
| the more enzymes that are available, the faster the reaction proceeds |
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Term
| Relationship between velocity and substrate concentration |
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Definition
| is a hyperbolic plot because after a certain substrate concentration, all the enzymes are satisfied and can't accept any other substrate molecules |
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Term
| Difference between first order reactions and second order reactions |
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Definition
| First order depends on one (molecule) reactant while second order depends on two (molecules) of a reactant |
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Term
| First order rate equation |
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Definition
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Term
| Second order rate equation |
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Definition
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Term
| Significance of Michaelis-Menten equation |
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Definition
| gives you an idea of the overall rate of the reaction based on the rates of formation and breakdown of an enzyme-substrate complex |
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Term
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Definition
| an experimental condition in which the substrate concentration is much greater than the enzyme concentration. In this situation, the concentration of the ES complex remains constant throughout the duration of the reaction because the enzyme will always have a substrate to link up with |
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Term
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Definition
represents the turnover number, the # of substrate molecules converted to product by a single enzyme in a given period of time
basically tells you how fast the ES complex converts to product |
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Term
| kcat's relationship to Vmax |
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Definition
kcat is the Vmax/the concentration of enzymes over time
the higher the kcat, the higher the Vmax and vice versa |
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Term
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Definition
| the maximum velocity of a reaction |
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Term
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Definition
Low Km means high affinity because
Km = (k-1 + k2)/k1
since k1 represents the formation of the ES complex, the higher this number, the more the enzyme wants to bind to the substrate. Since this number is high, it will make Km smaller
You can estimate Vmax by multiplying the velocity associated with Km by 2
You can estimate the Km by looking at Vmax, dividing it by 2 and see where on the curve the substrate concentration represents this V |
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Term
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Definition
| a combination of 3 rate constants looking at the equation and is also the substrate concentration at which the reaction velocity is half maximal |
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Term
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Definition
indicates catalytic efficiency because an enzyme's effectiveness depends on how avidly it binds its substrates and how rapidly it converts them to products
as kcat (or Vmax) goes up or Km goes down, the efficiency goes up |
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Term
| Factors that affect catalytic efficiency |
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Definition
| electronic rearrangements of the transition state and how often it collides with its substrate |
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Term
| Significance of the Lineweaver-Burk equation |
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Definition
| an L-B plot is a linear plot of the reciprocals of the substrate and velocity concentrations. |
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Term
| How to determine Vmax and Km from a L-B plot |
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Definition
The Y intercept is 1/Vmax so just takw the reciprocal of it
-1/Km is the x intercept so take the negative reciprocal of it |
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Term
| Why do bi-bi reactions not obey michaelis-menten kinetics? |
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Definition
| has 2 substrates that violate assumption #1 |
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Term
| Why do multi-step reactions not obey michaelis-menten kinetics? |
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Definition
| based on the example in the book, has 2 substrates which violates assumption #1 |
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Term
| Why do reactions catalyzed by allosteric enzymes not obey michaelis-menten kinetics? |
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Definition
| allosteric enzymes have multiples active sites which affect each other's affinities for substrates. this leads to a sigmoidal curve so it doesn't follow michaelis-menten rates |
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Term
| Ordered sequential reaction |
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Definition
| in this type of reaction, substrates bind in a specific order first and the products are formed in this same order |
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Term
| Random sequential reaction |
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Definition
| in this type of reaction, the substrates can bind in any order |
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Term
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Definition
| in this type of reaction, one substrate bind, its product forms, the other substrate binds and then its product forms |
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Term
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Definition
| substrate is covalently bound to enzyme so tightly that it makes the enzyme irreversibly noneffective. |
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Term
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Definition
| an irreversible enzyme. it's irreversible because they enter the enzyme's active site and begin to react but can't complete thus leaving it stuck in the active site |
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Term
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Definition
| Includes competitive inhibition, noncompetitive inhibition, mixed inhibition and uncompetitive inhibition |
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Term
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Definition
in this type of inhibition, the inhibitor resembles the substrate and is able to bind to the enzyme's active site however binding of the inhibitor and substrate is mutually exclusive (both can't be bound to the substrate at the same time)
Vmax and Kcat aren't effected because you can add enough substrate to out compete the inhibitor
Increases the Km (apparent Km) because the enzyme's affinity for the substrate is decreased since the inhibitor is all up in the way
In the graph, has a hyperbolic plot that isn't as steep as a reaction without an inhibitor
On an L-B plot, the slope is waaaay steeper (since this is a reciprocal graph) which indicates that the reaction runs slower. Also, the x intercept is more positive (indicates that the reaction has a lower affinity for substrate since graph is reciprocal) |
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Term
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Definition
the factor that makes Km appear larger
alpha = 1 + ([I]/Ki) |
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Term
| What makes a good competitive inhibitor? |
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Definition
| One that obviously resembles the substrate but also one that resembles the transition state. The ones that resemble the transition rate are the ones that are the most powerful |
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Term
| How to calculate Ki from L-B plots |
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Definition
In the presence of an inhibitor, the x intercept of the plot is -1/(alpha*Km)
solve for alpha and then plug into the alpha equation |
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Term
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Definition
| represents the dissociation constant for the enzyme-inhibitor complex. The lower the Ki, the tighter the inhibitor binds to the enzyme and thus the higher degree of inhibition |
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Term
| Noncompetitive inhibition |
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Definition
inhibitor binds at a separate site than the active site so it doesn't compete with the substrate. Both inhibitor and substrate can be bound at the same time
Because there's no competition, adding more substrate won't do anything
Because the inhibitor doesn't affect the active site of the enzyme, the Km doesn't change
Because the reaction can't proceed while the inhibitor is bound (causes a conformational change to where the enzyme can't proceed), the kcat and Vmax are lowered |
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Term
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Definition
In this type of inhibition, the inhibitor affects both the kcat/Vmax and Km.
The inhibitor can either bind to the free enzyme or the ES complex. Is a mixture of competitive inhibition and uncompetitive inhibition
Results in the lowering of Vmax and inrease (very rarely decrease) of Km
So its plot will have a lower Vmax and a higher Km |
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Term
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Definition
an inhibitor that binds to the ES complex (ONLY AFTER substrate has already bound)
Binds in the active site WITH the substrate therefore prevents the reaction from occurring (lowers Vmax)
It also lowers the Km (increases the affinity for the substrate) because of Le Chatelier's principle. This is because the inhibitor lowers the concentration of the ES complex and so the reaction will want to increase the concentration of the complex
It decreases Vmax and Km by the same degree |
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Term
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Definition
| the process where an enzyme can both be inhibited and activated depending on what binds to its allosteric site |
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Term
| Ways that enzyme activity can be regulated |
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Definition
| changes in enzyme concentration, location, ion concentration, and covalent modification |
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Term
| How phosphofructokinase is regulated by PEP |
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Definition
| PEP is a feedback inhibitor and so when its concentration gets significantly high, it will shut down its own synthesis by blocking the activity of phosphofructokinase |
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Term
| Triacylglycerols structure |
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Definition
| has a glycerol backbone and 3 fatty acids |
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Term
| Glycerophospholipids structure |
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Definition
| has a glycerol backbone, 2 fatty acids and the other phosphate derivative head group. This makes them amphipathic because the phosphate head group has a negative charge on it (polar) |
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Term
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Definition
sphingosine backbone which includes an alkyl chain (fatty acid) from palmitate (a bunch of carbons with a double thrown in there) and a portion from serine (has the NH3)
a fatty acid is already included as part of its backbone and a second one will be attached to the nitrogen via an amide bond.
The third component is a phosphate head group so sphingolipids are ampiphatic. |
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Term
| Cerebrosides and gangliosides structure |
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Definition
| a cerebroside is a sphingolipid with one ring structure (monosaccharide) in its head group and a ganglioside is a sphingolipid with multiple ring structures (polysaccharide) in its head group |
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Term
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Definition
constructed from isoprene units and are big, rigid ring structures (hydrophobic)
includes hormones and steroids? |
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Term
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Definition
| 3 carbon chain with each being attached to an oxygen (acyl groups) |
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Term
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Definition
| chains that have a double bond in it, has a lower melting point, is fluid at room temp |
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Term
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Definition
| chains that have no double bonds, has a higher melting point, is solid at room temp |
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Term
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Definition
| Via van der waals due to the hydrophobic effect (that's why you have the nonpolar regions associate in the tail area and the polar heads associate |
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Term
| Most lipids are amphipathic why? |
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Definition
| polar head, nonpolar tail |
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Term
| Longer fatty acid chains and melting point |
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Definition
| the longer the chain, the higher the melting point |
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Term
| How do triglycerides aggregate? |
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Definition
| form globules because their polar head groups are too small to form a proper bilayer |
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Term
| How do fatty acids aggregate? |
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Definition
| form missiles because they have a large head group attached to one tail which makes them hard to align in a bilayer |
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Term
| How do glycerophospholipids and sphingolipids aggregate? |
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Definition
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Term
| Cholesterol on membrane fluidity |
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Definition
acts as a buffer because it can either decrease on increase fluidity
will increase fluidity in low temps by inserting itself between membrane lipids, preventing their ability to pack close to each other
will decrease fluidity at high temps by restricting the movement of nearby acyl chains |
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Term
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Definition
| a region in a membrane that is nearly crystalline. Made up of cholesterol and sphingolipids |
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Term
| Lipid movements that occue in bilayer |
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Definition
| lipids move more easily laterally than flipping sides though they can do this with the help of flippases |
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Term
| Are the two leaflets of the bilayer identical? |
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Definition
| No they have different lipid compositions depending on the orientation of the lipids |
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Term
| Integral membrane protein |
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Definition
| passes through both leaflets |
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Term
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Definition
carries lipid molecule as an anchor
associates with only one of the leaflets |
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Term
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Definition
not directly attached to the membrane
may either associate with an integral protein or a lipid |
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Term
| Alpha helical structure of integral proteins |
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Definition
| if this is used, it usually spans 20 hydrophobic AAs that interact with the tail and has polar head groups that itneract with lipid head groups |
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Term
| Beta barrel structure of integral protein |
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Definition
made up of several beta sheets to satisfy hydrogen bonding
exterior surface has hydrophobic side chains and the interior may not necessarily be hydrophobic which makes sense because it's essentially shielded from the hydrophobic tails |
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Term
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Definition
according to this model, membrane proteins float randomly in a sea of lipids
is not 100% accurate because some proteins don't move as freely as was described because their movements are hindered either by cytoskeleton elements or other membrane proteins |
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Term
| Negative membrane potential |
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Definition
if [Na+]out > [Na+]in, this contributes to a negative membrane potential
a negative membrane potential means inside of cell is more negative than the outside of the cell |
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Term
| Movement of ions result in membrane potential |
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Definition
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Term
| How the axon potential works |
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Definition
so the potential starts at -70 mV
Stimulation from a signal opens Na+ channels and Na+ rushes in making the membrane more positive (depolarization)
Depolarization triggers the opening of K+ channels and they leave the cell restoring the potential back to -70 (repolarization) |
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Term
| Initial gradients before an action potential |
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Definition
concentration of Na is less inside the cell than out
concentration of K is less outside the cell than in |
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Term
| Why do signals travel in only one direction during an action potential? |
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Definition
| once a channel opens, it remains closed so the ions can't move in the opposite direction changing the potential. Thus the signal only has one direction to go |
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Term
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Definition
| wraps around axon and prevents ion movements except at nodes |
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Term
| Difference between passive and facilitated diffusion |
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Definition
| facilitated uses transporters to help molecules move down concentration gradient |
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Term
| You can determine if transport into the cell is spontaneous or not by |
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Definition
| looking at the concentrations outside the cell vs inside |
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Term
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Definition
| a trimer of 3 beta barrels, each with an even number (16 or 18) strands |
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Term
| Why are porins weakly selective? |
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Definition
| in the example of the OmpF barrel in E. coli, there is a loop that folds down in each the barrels which restrict larger molecules (over 600 Da) and it is weakly selective to cationic substances since the side chains of the loops have negative charges. They aren't highly selective though because the porin is always open and anything that can fit can get through |
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Term
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Definition
| the general structure is a multimer of alpha helices |
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Term
| Potassium channel structure |
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Definition
| is a tetramer of 4 subunits where each subunit is made up of 3 helices: 2 large and 1 small |
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Term
| Why is the potassium channel 10,000 times more selective to K than Na? |
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Definition
| the channel has 4 backbones that project carbonyl groups into the core and Na+ is too small to coordinate with the carbonyls. However, it can contract to fit Na but this is prevented by Tyr |
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Term
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Definition
helps transport a large volume of water across membrane
the hydrophobic environment of aquaporins prevents
the creation of hydronium ions which will lower the PH and Asn residues hydrogen bond with one water molecule at a time |
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Term
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Definition
helices like a drawstring move which opens and closes the channel
neuronal potassium channel opens in response to depolarization
neuronal sodium channels opens in response to a signal |
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Term
| Why can't gated channels immediately reopen? |
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Definition
| The N-terminal segment blocks the pore so the signal can go in one direction |
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Term
| Mechanosensitive channels |
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Definition
opens in response to membrane tension
helices move pass each other to open and close pores
in the smallest configuration, there's still a small pore that exists but hydrophobic residues block anything from going through it so the pore is still "closed" |
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Term
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Definition
| moves one molecule at a time, is passive |
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Term
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Definition
| moves two molecules at a time in the same direction, is active because one of the solutes moves against its gradient |
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Term
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Definition
| moves two molecules at a time in the opposite direction, is active because one of the solutes moves against its gradient |
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Term
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Definition
works by a "rocker" mechanism
glucose binds on one side
a conformational change occurs
this change forces glucose to the other side |
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Term
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Definition
requires ATP
Steps:
So the pore opening is initially facing the interior of the cell
3 sodium ions bind to the pore
This binding triggers ATP binding
A phosphate group is transferred from ATP to the channel
This causes a conformational channel which spits out the 3 Na+ ions to the extracellular side
So now the pore opening is facing the exterior of the cell
2 K+ ions bind to the pore
This causes that attached phosphate group to be released
This causes a conformational change which forces the 2 K+ ions into the cell |
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Term
| How ABC transporters work |
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Definition
requires ATP
Steps:
a solute binding protein binds solute
the complex binds to the transporter
this stimulates the 2 ATP binding domains which binds ATP and ONLY hyrolyzes them (doesn't transfer them)
This causes a conformational change which opens the transporter allowing ONLY the solute to pass through |
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Term
| Secondary active transport |
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Definition
"piggy-back transport using established gradient
example is a sodium-glucose transporter
This transporter relies on the Na+ gradient that builds up in the cell due to the sodium potassium pump pumping Na+ ions out of the cell
The transporter will be able to move Na+ ions from outside the cell to the inside pretty easily since it's going down its concentration gradient due to Na+ being constantly pumped out by the sodium potassium pump. |
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Term
| Acetylcholine and Membrane Fusion mechanism |
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Definition
When an action potential reaches the axon terminus (depolarization), it causes voltage-gated calcium channels to open
Calcium flows inside the cell and the increase in the gradient triggers the fusion of the vesicles to the plasma membrane which releases the acetylcholine into the synaptic cleft |
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Term
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Definition
proteins that fuse the vesicle and plasma membrane together
2 SNAREs from the plasma membrane and 1 from the vesicle form a complex
Acts as an addressing system to make sure that the correct membranes are fused |
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Term
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Definition
| proteins, lipids, amino acid derivatives hormones |
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Term
| Difference between GPCR and receptor tyrosine kinases |
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Definition
| kinases phosphorylates itself to activate itself and can activate or inhibit another protein or enzyme while GPCR only activates G proteins |
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Term
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Definition
| have 7 transmembrane domain (7 alpha helices) |
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Term
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Definition
Ligand binds
Induces conformational change in receptor activating it
The conformational change causes the attached G protein to have a conformational change
The G protein will release GDP and bind GTP activating it
The g protein will now interact with adenylate cyclate which produces the second messenger cAMP |
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Term
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Definition
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Term
| Structure and activation/deactivation of G protein |
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Definition
is a trimer
starts out with the alpha subunit bound to GDP (inactive)
When it is activated by the receptor, the alpha subunit binds to GTP which causes the alpha subunit to dissociate from beta/gamma
The G protein is now activated
Has the ability to deactivate itself with its inherent GTPase activity
It will hydrolyze the GTP to GDP, reassociating the 3 subunits and deactivating it |
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Term
| What can a G protein do once its activated? |
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Definition
Can either activate adenylate cyclase to produce the second messenger cAMP in liver and muscle
Or it can activate phospholipase C which breaks PIP2 into the second messengers IP3 (cytoplasm) and DAG (membrane) |
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Term
| phospholipase C signal cascade |
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Definition
When it is activated by G protein, it breaks PIP2 into IP3 and DAG
IP3 is soluble in the cytoplasm and open calcium channels
DAG is soluble in the membrane and docks protein kinase C at membrane and activates it (activation requires calcium |
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Term
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Definition
How we can reverse the effects of the signal and get everything back into a pre-signal state
Examples are simply the ligand becoming unbound to the receptor, the GTPase activity of a G protein, deactivating GCPR by phosphorylating it and letting it bind to arrestin |
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Term
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Definition
| a protein that binds to a phosphorlyated GPCR which prevents it from interacting with G protein, and the short lifetime of a second messenger |
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Term
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Definition
| removes phosphate groups from side chains which can deactivate stuff? |
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Term
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Definition
| a protein that binds to calcium when it is released when IP3 in the cytoplasm is activated thus mediating its effect |
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Term
| Structure of receptor tyrosine kinase |
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Definition
| Is a transmembrane protein that has 2 cytoplasmic domains where it autophosphorylates itself |
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Term
| Activation of receptor tyrosine kinase |
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Definition
When a ligand binds, conformation change occurs which allows it to become a dimer
This allows the kinase to snatch a phosphate off of ATP and start phosphorylating itself at its 2 cytoplasmic domains. The phosphate group is attached to a tyrosine residue. Now the kinase is activated |
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Term
| How can a receptor tyrosine kinase initiate a series of kinase activation events? |
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Definition
| Once activated, a kinase can activate other kinases, which in turn can activate other kinases and so on |
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Term
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Definition
has 2 ligand binding sites, is a type of receptor tyrosine kinase so it possesses two domains where it phosphorylates itself
also indirectly interacts with G protein by binding to adapter protein |
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Term
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Definition
hormones can diffuse straight through membrane because they are very hydrophobic
They bind to receptors inside the cell which causes the dimerization of receptors
The hormone receptor complex moves to the nucleus where it binds to sequence elements in DNA ( Hormone Response Elements)
Function as transcription factor |
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Term
| Hormone Response Elements |
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Definition
| sequence elements in DNA where the hormone receptor complex binds |
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Term
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Definition
hormones that are only made in response to a signal so they are made as needed
Regulate blood pressure, coacgulation, pain,,
they degrade really quicky |
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