Title: Jack Sparrow Biochem / Biochemistry / Biochemistry Chapter 2
Tags: #JackSparrow::#B/B::#Biochemistry::#Chapter.2

Q: What is an enzyme?
A: An enzyme is a biological catalyst.

What are the 7 key features of enzymes?

Q: What is meant by the term enzyme specificity?
A: Enzyme specificity refers to the fact that enzymes will always only catalyze a single reaction or a single class of reactions.  In other words, enzymes are specific!

Q: What are the 6 classes of Enzymes?
A: 1.  Ligase
2.  Isomerase
3.  Lyase
4.  Hydrolyase
5.  Oxioreductase
6.  Transferase
MNEMONIC:  LIL HOT

Q: What is a ligase?
A: A ligase is an enzyme that catalyzes the building of things through addition or synthesis reactions.  Generally, ligases use ATP to conduct synthesis reactions between large molecules.  Ligases are most closely associated with nucleic acid synthesis.

Q: What is an Isomerase?
A: An isomerase catalyzes the rearrangement of bonds within a molecule.  An isomerase, depending on how it accomplishes this, can also be considered an oxioreductase, transferase, etc.
Note: Isomerase are important for catalzying reactions between stereoisomers as well as constitutional isomers.

Q: What is a Lyase?
A: A lyase catalyzes the cleavage of a single molecule into two products.
Note: When an enzyme can catalyze the reverse of its reaction to since all reactions are just equilibria.  Lyases that catalyze the reverse of a cleavage reaction are usually called synthases.  When fulfilling this role, lyases generally only combine very small molecules.  The combination of larger molecules is handled by ligases.

Q: What is a Hydrolase?
A: A hydrolase catalyzes the breaking of a compound into two molecules by using water to perform a hydrolysis reaction.

Q: What is an Oxioreductase?
A: An Oxioreductase catalyzes oxidation reduction reaction.  These enzymes usually have "dehydrogenase" Or "Reductase" in their name.

Q: What is a Transferase?
A: A transferase catalyzes the movement of a functional group from one molecule to another.  One specific example of transferases are kinases, which catalyze the transfer of a phosphate group, generally from ATP to another molecule.

Q: What is an endergonic reaction?
A: An endergonic reaction is a reaction that has a positive Delta G and therefore needs energy input to happen.

Q: What is an exergonic reaction?
A: An exergonic reaction is a reaction in which Delta G is negative, and energy is spontaneously given off.

Q: Do enzymes alter the free energy change (Delta G) of a reaction?
A: No!  All the same rules that apply to catalysts apply to enzymes, because enyzmes are catalysts!  Enzymes only lower the activation energy of a reaction.

Q: How do enzymes lower the activation energy of a reaction?
A: Enzymes lower the activation energy of a reaction by stabilizing the transition state.  This is usually accomplished by the enzyme's structure which will create a microenviroment that is favorable to the transition state and stabilizes it.

Q: What is a substrate?
A: Substrate is the term used to refer to the specific molecule upon which an enzyme acts.

Q: What is the enzyme-substrate complex?
A: The enzyme-substrate is the physically locked together enzyme and substrate.

Q: What is an active site?
A: The active site is where the enzyme holds the substrate while it catalyzes the reaction.

Q: Describe the lock and key theory of enzyme activity?
A: The lock and key theory states that enzymes are like locks and substrates are like keys, and an appropriate match allows them to interact.

Q: Describe the induced fit theory of enzyme activity?
A: The induced fit theory states that an enzyme is usually in a relaxed form, and that the binding of the substrate to the enzyme causes the enzyme to change its shape and accomodate the substrate.

Q: What is a cofactor or coenzyme?
A: A cofactor or coenzyme is any nonprotein molecule that is required for the enzyme to function properly.

Q: What is an apoenzyme?
A: An apoenzyme is an enzyme without its cofactor.

Q: What is a holoenzyme?
A: A holoenzyme is an enzyme with its necessary cofactor.

Q: What is the difference between a coenzyme/cofactor and a prosthetic group?
A: A prosthetic group is just a cofactor or coenzyme that is very tightly bound to the enzyme and is critical for its function.

Q: Generally speaking, cofactors are [organic molecules or inorganic and metal ions?]
A: inorganic or metal ions

Q: Generally speaking, coenzymes are [organic molecules or inorganic and metal ions?]
A: organic molecules

Q: How does the rate of a reaction relate to the amount of enzyme and substrate?
A: If you have 10 Enzyme molecule and 1 substrate molecule, that means only 1 enzyme is actually interacting with the substrate and speeding up the reaction, and so there will be a small increase in the speed of the reaction.
Conversely, if you have 10 enzyme molecules and 10 substrate molecules, that means all 10 enzymes are speeding up the reaction, which translates to an increased rate.
However, if you have 10 enzymes and 11 substrate molecules, that means all 10 enzymes are already speeding up the reaction, and adding more substrate will not affect the speed of the reaction.

Q: What is saturation?
A: Saturation is the point at which every enzyme has a substrate bound.  Adding substrate at this point will not increase the speed of the reaction.

Q: What is vmax?
A: Vmax is the theoretical maximum velocity at which the reaction can run based on the number of enzymes present.  This is the velocity at which every single enzyme is bound to a substrate molecule.

Q: What is the only way to increase vmax?
A: Adding more enzymes for substrate molecules to bind to.

Q: What is K_m
A: K_m (AKA the Michaelis Constant) is the concentration at which half of the enzyme's active sites are in use and the velocity of the reaction is half of the Vmax.
K_m can be used to compare the affinities of different enzymes for specific substrates.  For example, an enzyme with a K_m of .5M needs .5M of substrate to occupy half of its active sites.  However, an enzyme with a K_m of .25M only needs .25M of substrate to occupy half of its active sites.

Q: What is kcat?
A: kcat is the equilibrium constant for a reaction that is being catalyzed by an enzyme.

Q: What is the catalytic efficiency of an enzyme?
A: The catalytic efficiency of an enzyme is defined as kcat/Km.  It makes sense, because this term increases as the equilibrium constant forward increases and the amount of substrate necessary to get to half of the max velocity decreases.  An enzyme that makes the reaction even faster with less substrate is definitely more efficient.

Q: What is a Line-Weaver Burke Plot?
A: A Line-Weaver Burke Plot is a modified Michaelis-Menten equation.  It measures 1/v and 1/s instead of v and s.  For this reason, Line-Weaver Burke Plots are often called double reciprocal graphs.  These plots are used because they represent the equation behind enzyme kinetics in the form of a straight line.

Q: The x-intercept of the Lineweaver Burke Plot gives us the [-1/Km or 1/vmax?]
A: -1/Km

Q: The y-intercept of the Lineweaver Burke Plot gives us the [-1/Km or 1/vmax?]
A: 1/vmax

Q: What is a cooperative enzyme?
A: A copperative enzyme is an enzyme with multiple active sites that affect one another.  Generally speaking, these active sites are either in the low-affinity tense state (T) or the high affinity relaxed state (R).
Cooperativity is a lot like a good party.  When there is only one person (substrate bound) the party isn't fun (low affinity and vmax).  However, once 5 people show up, the party is a little more fun.  Now that there is 6 people, more people are down to come over, and so another 15 show up.  Then, 100 people show up because the 21 person party looks pretty fun.
Conversely, when those 100 people pass out or leave, the 21 people that are closer to the host of the party won't be as likely to stay.  At this point, another 15 might leave so there's only 6 people left.  Those last 6 are pretty dedicated to the host, but even they are more likely to want to leave with no one else around.

Q: What shape does the michaelis-menten graph of a cooperative enzyme take?
A: Sigmoidal (S-like Shape)

Q: What is the Hill's coefficient?
A: The Hill's coefficient is a mathematical representation of the cooperativeness of an enzyme.
If the Hill's coefficient is greater than 1, then the binding of one ligand increases the affinity of the enzyme for more ligands, and positive cooperative binding is occuring.
If the Hill's coefficient is less than 1, then the binding of one ligand decreases the affinity of the enzyme for more ligands, and negative cooperative binding is occuring.
If the Hill's coefficient is equal to 1, then the binding of one ligand does not affect the affinity of the enzyme for more ligands, and no cooperation is occuring.

Q: How do enzymes respond to the environment?
A: Enzymes are very sensitive to their environment!  Enzymes are, fundamentally, just big molecules, and so messing with the salinity, temperature, ph, etc. of the environment can affect the way they operate.

Q: How do increases in temperature affect enzyme kinetics?
A: Generally speaking, the velocity of an enzyme catalyzed reaction will double for every 10C° increase in temperature (more energy to react!) until the optimum temperature for the enzyme is reached (body temperature for most enzymes in the body).  After this temperature, there is so much energy that the bonds holding the enzymes together break, which causes a sharp decrease in the velocity of the reaction.

Q: How do changes in pH affect enzyme kinetics?
A: Enzymes have a specific pH at which they function most effectively.  Any deviations from this pH will cause the enzyme to lose functionality.  For most enzymes in the human body, this is equal to the blood's pH of 7.4, but there are notable exceptions such as digestive enzymes.

Q: After an enzyme is denatured due to heat, is it possible to cool it back down and renature it?
A: Sometimes!  It really just depends on the enzyme.  Some can regain their original function.  Others, once denatured, are permanently non-functional.

Q: What is feedback regulation?
A: Feedback regulation is when products or reactants later or earlier in a chain of reactions regulate enzymes involved in other reacctions in the chain.

Q: What is negative feedback?
A: Negative feedback is when a product further down in the chain of reactions inhibits a previous reaction in the chain.

Q: What is feedforward regulation?
A: Feedforward regulation is a relatively rare phenomenon in which enzymes further down in a chain of reactions are regulated by products produced earlier in the pathway.

Q: What are the 4 types of reversible inhibition?
A: 1.  Competitive Inhibition
2.  Noncompetitive Inhibition
3.  Uncompetitive Inhibition
4.  Mixed Inhibition
MNEMONIC: Cats Never Undress Men

Q: What is reversible inhibition?
A: Reversible inhibition means that the inhibition of the enzyme is accomplished through weak interactions that can be relatively easily displaced, and therefore the inhibition of the enzyme can be reversed.

Q: What is irreversible inhibition?
A: Irreversible inhibition means that the inhibition of the enzyme is accomplished through covalent bonds that permanently inhibit the activity of the enzyme.

Q: What is competitive inhibition?
A: Competitive Inhibition is when an inhibitor competes with the substrate for the enzyme's active site.

Q: How does a competitive inhibitor affect Vmax, Km, and the lineweaver burke plot?
A: Competitive inhibitors compete with the substrate, which increases the amount of substrate you need to get equal catalysis, which increases Km.
Competitive inhibitors are out-competed so hard at high substrate concentrations, that they do not affect the enzyme, which means that competitive inhibitors do not change v max.
The lineweaver Burke Plot for a competitive inhibitor will have a right shifted x-intercept with no change in the y-intercept.

Q: How does a non-competitive inhibitor affect Vmax, Km, and the lineweaver burke plot?
A: Non-competitive inhibitors bind allosteric sites far away from the active site, which means that substrate binding is not disrupted, which means Km is unaffected.
At high concentrations of substrate, the non-competitive inhibitor will still occupy its allosteric site and inhibit the enzyme, which means vmax is lowered.
The lineweaver Burke Plot for a non-competitive inhibitor will have a higher y-intercept with no change in the x-intercept.

Q: What is noncompetitive inhibition?
A: Noncompetitive inhibition is when an inhibitor binds to an allosteric site somewhere on the enzyme that causes it to change its shape and reduce its function.  Because the noncompetitive inhibitor is not competing with the substrate, increasing the concentration of substrate will reverse the inhibition.

Q: What is uncompetitive inhibition?
A: Uncompetitive inhibition is when the inhibitor only binds to the enzyme-substrate complex and locks it up, preventing the release of products.

Q: How does an uncompetitive inhibitor affect Vmax, Km, and the lineweaver burke plot?
A: Uncompetitive inhibitors make the enzyme substrate complex so stable that it won't release the substrate.  This means you need less substrate to reach half of vmax, which means Km is lowered.
Uncompetitive Inhibitors cannot be outcompeted at high concentrations of substrate, which means that the vmax of the enzyme is lowered.
The lineweaver Burke Plot for an uncompetitive inhibitor will have a higher y-intercept with a left shift of the x-intercept.  The decrease in km and vmax is proportional, so the new inhibition line will have the same slope as the uninhibited one.

Q: What is mixed inhibition?
A: Mixed inhibition is when an inhibitor can bind to the enzyme or the enzyme substrate complex, but with different affinity.  One must know the relative affinities of the inhibitor to know how the Km will be affected.  However, the Vmax is always lowered in mixed inhibition.

Q: What is an allosteric site?
A: An allosteric site is a portion of the enzyme that can be bound by allosteric molecules to inhibit or activate the enzyme.

Q: What is an allosteric inhibitor?
A: An allsoteric inhibitor is an allosteric molecule that inhibits the activity of the enzyme

Q: What is an allosteric activator?
A: An allsoteric inhibitor is an allosteric molecule that increases the activity of the enzyme.

Q: What are two common covalent modifications made to enzymes for regulatory or functional purposes?
A: 1.  Phosphorylation and dephosphorylation
2.  Glycosylation

Q: What is a zymogen?
A: A zymogen is an inactive form of an enzyme that must be modified to activate it.  The creations of zymogens is a way to further regulate and control the activity of enzymes in the body.  Most zymogens have the suffix -ogen.