Term
| what makes enzymes so useful and versatile |
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Definition
proteins don't always act alone, so enzymes use cofactors (metals) that are good for making coordination bonds
coenzymes are organic molecules
prosthetic group is not part of the amino acid and is not covalently bonded |
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Term
| when discussing the anatomy of an enzyme, how can the active site be characterized |
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Definition
the active site is made up of key amino acids with, likewise, a specific charge and hydrophobicity due to hydrogen bonding
the active site is also where the chemistry of the reaction is done
where substrate binds to enzyme |
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Term
| when discussing the binding of substrate to enzyme, what can be a simple assumption made |
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Definition
| that the enzyme and substrate are in equilibrium |
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Term
| what is the difference in free energy of substrate and product |
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Definition
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Term
| it is known that the substrate and enzyme bind to form a complex together, how would you describe the conformation of the enzyme's active site |
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Definition
| the active site of the enzyme would likely resemble the conformation of the transition state, that is, the product formed in the reaction |
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Term
| how does the binding of substrate and enzyme occur |
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Definition
| the enzyme and substrate conform to one another, by molding and this effectively speeds up the reaction |
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Term
| what is the rate determining step when discussing the reaction of substrate and enzyme |
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Definition
| the rate determining step is the release of product after it's formation, because when a reaction is in equilibrium, there is the possibility to move back to substrate |
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Term
| what do enzymes use to get substrate to bind |
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Definition
| use their charge, hydrogen bonds between amino acids, and van der Waals interactions that affect the geometry |
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Term
| it is known how enzymes can make themselves attractive towards substrate so it will want to bind, but how do these two get even remotely close to one another |
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Definition
water-remember when we learned about how substrate and enzyme function when in solution, or more so, how water is involved in enzyme-substrate binding
water would like soluble substrate to bind to enzyme so that water can reduce its overall order |
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Term
| the delta G bind (free energy of binding) and delta G are mathematically _______ to each other |
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Definition
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Term
| mathematically, how can we determine how favorable a reaction is |
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Definition
delta G= -RTlnKeq
but this is no indication of the rate of reaction |
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Term
| how can you determine the rate of a reaction |
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Definition
velocity= k[S]
units: s-1 |
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Term
| when determining the rate of a reaction, what should be the ratio of substrate to enzyme |
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Definition
enzyme must be present, if enzyme is zero, there is no binding
the set up must have more [S] than enzyme |
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Term
| when an experimental set up is done, there are three major indications that can be made from a graph with velocity vs [S] plot |
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Definition
when [S] is low, there is a linear relationship
when [S] gets higher, the relationship begins to curve-the point where the linear line turns to a curve is (1/2) Vmax
when [S] is highest, a plateu is reached and this is our maximum velocity |
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Term
| what can the (1/2) Vmax tell us |
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Definition
at this point on the velocity vs. [S] plot graph, if a line is drawn down to the [S] or x-axis this is called the Km
the Km is what our Vmax of substrate is |
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Term
| when discussing the binding of enzyme and substrate, there are three equations that you must know, and also, be able to determine which is the rate determining, the fastest and slowest |
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Definition
the linear illustration is the binding of enzyme and substrate and is the slowest step because it is dependent on the solvent
the curve illustration is the formation of EP from ES and is the fastest step because it is thermodynamically unstable
the plateu illustration is the formation of P and is the rate determining step because when in equilibrium we can always move back to substrate except when we reach product |
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Term
| what is the michaelis-menton equation |
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Definition
Vmax [S]/ Km + [S]
the reaction is dependent on the concentration of the substrate |
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Term
| how do you get a lineweaver-burk plot from the michaelis-menton equation |
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Definition
| if you take the double reciprocal plot of the michaelis-menton equation you can get a linear line |
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Term
| what does the lineweaver-burk plot allow you to get |
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Definition
the Kcat= turnover number
# of P/time
units: s-1 |
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Term
| once you've gone through the michaelis-menton equation, than taken the double reciprocal of it to form a linear line (lineweaver-burk), then used this line to determine the Kcat, what can you do to determine the specificity constant |
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Definition
specificity constant= Kcat/ Km
units: s-1 M-1 |
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Term
| what does the specificity constant tell us, if anything at all |
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Definition
| tells me how efficiently the enzyme is able to bind substrate, form product, kick product out and get ready to bind substrate again |
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Term
| how fast is the fastest an enzyme can bind substrate |
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Definition
| this is solely dependent on how fast diffusion is |
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Term
| how can you increase diffusion |
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Definition
| heat, and shaking up a reaction |
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Term
| in essense, what does a competative inhibitor do and how are its properties, like geometry and charge, beneficial to its inhibiton abilities |
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Definition
the presence of a competative inhibitor provides direct competition for substrate (more inhibitor present means less substrate can bind)
a competative inhibitor looks similar in geometry and has similar charge as a substrate but more so the active site
the inhibitor doesn't bind covalently either |
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Term
| how does an uncompetative inhibitor work |
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Definition
| substrate can bind either first or second, but upon the binding of an inhibitor, the enzyme goes through a conformational change (example of allostery) |
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Term
| how does a mixed inhibition work |
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Definition
like the uncompetative inhibitor, substrate can bind either first or second, then the inhibitor binds very close to either the substrate or active site
this is a non-allosteric response, and the presence of the inhibitor affects the substrate binding or releasing |
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Term
| what defines an irreversible inhibitor |
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Definition
| an irreversible inhibitor is one that covalently binds to an active site and either alters or destroys the site |
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Term
| when discussing irreversible inhibitors, there are both positive and negative effects, how could there possibly be both |
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Definition
positive effects: could be used to turn off a metabolic pathway, and can be used to determine the order of an enzymatic pathway (isolate and identify, then move onto the next one)
Negative effects: remember when we discussed carbon monoxide-it covalently binds to hemoglobin-these effects and more, like sarin nerve gas, are toxic because they are irreversible inhibitors |
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Term
| why doesnt the acid from our lower stomach and upper intestines burn our lower intestines |
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Definition
| enzymes released in our stomach have an optimal pH ~ 1.7, when they reach our lower intestines the pH is ~6 so it is no longer enzymatically active |
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Term
| when discussing enzyme regulation, what are the reasons why we don't want enzymes (proteins) to come off the ribosome in an active form |
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Definition
| enzymes like chymotrypsin breaks apart covalent bonds of other proteins, so if enzymes like this came off the ribosome in an active form, they would instantly begin to destroy the cell that synthesized it. |
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Term
| it is understood that enzymes don't come off the ribosome in an active form, so then how has nature programmed a cell to make inactive forms of enzymes |
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Definition
| these immature enzymes are called zymogens and give the synthesizing cell the opportunity to relocate the zymogen before it becomes active |
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Term
| what is a regulatory enzyme |
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Definition
| is an enzyme in a biochemical pathway which, through response to the presence of other biomolecules, regulates the activity of the pathway |
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Term
| when discussing regulatory enzymes, what is the end product's job |
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Definition
the end product of a metabolic pathway is the regulator for the initial regulator enzyme
that is, the presence of the final product acts as an inhibitor of the regulatory enzyme |
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Term
| when discussing equilibrium, what can be said about metabolic pathways |
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Definition
| nothing is ever on/off it is either more active or less active |
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Term
| enzymes have many regulation sites, what does this mean in terms of its ability to communicate |
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Definition
the more regulation sites it has, the more able it is to adapt to the environment it is in
That is one regulation site could be buried in the enzyme, or on the surface or somewher in between-this gives the enzyme the ability to communicate multiple environmental situations simultaneously |
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