Chapter 8

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What type of proteins are not enzymes?
RNA molecules
Carbonic anhydrase has a half life of how long? How fast is the catalyzed rate? What dos it hydrate?
-5 seconds
- rate is 1 x 10 ^6
-changes CO2 into carbonte
-fastest enzyme
What is substrate specificity? Are proteolytic enzymes specific? Is papain? Trypsin?
Most enzymes are very specific: such as proteolytic enzymes which will cleave the C=O in proteins and ester.
-Papain is not specific it will cleave any bond
-Trypsin cleaves the carboxylic side of Lys or Arg
-Thrombin cleaves the carboxylic bond between arg and gly.
What are cofactors and what are their 2 classes?
Co factors are small molecules that help enzymes carry out their activites. The two main classes include organic molecules (vitamins) and metals.
What are tightly bound cofactors called?
They are called prosthetic groups.
What is an enzyme with it's cofactor called?
Holoenzyme
What is an enzyme without it's enzyme?
Apoenzyme
What is the sign of delta G if a reaction does not require any input of energy? Will it be exergonic or endergonic?
-The reaction will have a negative sign
-Will be exergonic
-spontaneous
At equlibrium delta G is at...
Delta G=0
A reaction that requires energy so the delta G will be negative or positive? Spontaneous or non-spontaneous?
These would be non-spontaneous and will be positive delta G.
True or false? Delta G provides information about the rate of a reaction.
FALSE! It only provides information about the free energy difference between the reactants and products; and spontaneity.
What is the equation for free energy change? What does Delta G * symbolize? What is Delta G at equilibrium?
-The equation is:
Delta G=Delta G* + RT ln (CD/AB)
-Symblizes the standard free energy
-0
Read this statement about the function of an enzyme.
-Enzyme has the ability to accelerate attainment of equilibrium but cannot shift it.
What is the equation for the equilibrium constant K?
K=[P]/[S]
K=kf/kr
All of this is equal to 100.
What is the equation for the equilibrium constant under standard conditions (K)?
[products]/[reactants]
e^delta G*/RT
What type of energy does an enzyme allow you to achieve when producing a product?
Enzymes allow you to enter the transition state by lowering the activation energy.
Why does the energy of activation does not enter the final delta G calculation, why is this?
Because the energy that was put in was released when the transition state molecule was created.
What is another way of veiwing activation energy?
You can assume that activation energy determines the concentration of the transition state molecule. The concentration of X affects the velocity it creates product.
What is the equation of the overall rate of the reaction? What does it depend on?
The overall rate of the reaction is equal to:
v[X]=(kT/h)[S]e^-Delta G/RT
Where do enzymes bring substrates together?
Substrates are brought together in the activation site.
What is the evidence for the existence of an enzyme-substrate complex?
1) A fixed amount of enzyme displays a maximal velocity. This means that all activation sites are occupied
2) X-ray crystallography of enzymes bound to substrates or substrate analogs.
3) When the ES complex forms the spectroscopic properties of the enzyme and substrate change.
What are 5 features of active sites.
1) active site is three-dimensional cleft/crevice created by amino acids from different parts of the primary structure
2) Active site is a small part of enzyme volume
3) Have polar/nonpolar micro-environments that are unique to the activation site.
4) the interaction between the enzyme and the substrate at the active site is put together by multiple weakk interactions including: Van der Waals, hydrogen bonds, electrostatic interactions, and hydrophobic interactions.
5) Not lock and key; they change conformation when the substrate binds-Induced fit.
How can you test the velocity of a reaction?
Can measure haw quickly the reactants decrease during time or how quickly products form in time.
V=k[A]

Denoted as A-> P
What is a first order reaction? What are the units?
Reactions that have a velocity that is directly proportional to reactant concentration. The unit is s^-1
What are first order or bi-molecular reactions? What are the units?
-These are reactions that have two reactants so are denoted as:
2A-->P or A +B-->P
V=k[A]^2 and [A][B]k

-M^-1 * s^-1
What does reaction velocity greatly depend on?
It greatly depends on substrate concentration.
There are two views of the steady-state assumption that affects the enzyme kinetics.
Draw the equatons. They can be found on page 216. the second equation is based on initial velocity or V_0 this simply means that the reaction has no products therefore the P cannot return to ES.
What does K_m stand for?
When we look at the graph with reaction velocity and substrate concentration, we can see that the V max is at the top. This is approached when the active sites are all occupied.
-Km is the concentration of substrate when the Vmax is half way.
What is Michaelis' constant?
Km=(k_-1 + K_2)/ k_1
and this is equal to [E][S]/[ES]
What is the equation for the total amount of free enzymes?
[E]_t-[ES]
What is the Michaelis-Menten equation?
How doe sthe lineweaver-Burk equation look like? This equation is the Michaelis-Menten equation that is manipulated.
Think of a line graph and how it would be represented in an equation.
Slope: Km/Vmax
Y-intercept: 1/Vmax
X-intercept: -1/Km
What does Vmax mean?
This is the position that the enzymes are fully saturated with substrate; measures product turnover.
What does Kes measure? When is this ratio important?
-measures the stability of the ES substrate
-Ratio is important only when K-1 is greater than K2
-Large means that the substrate is weak
How do you determine the fraction of enzymes bound to substrate?
This can be determined by
Fes=(V/Vmax) = ([S]/[S]+Km)
Just name the three different types of enzymatic reactions.
1)Sequential reactions
2) Double-displacement (Ping pong reactions)
What are sequential reactions. What are the 2 subdivisions.
-All substrates must bind to the enzyme to form a product. Forms a ternary (enzyme, pyruvate, NADH) or (creatine, enzyme, and ATP)
-1) Ordered: coenzyme binds first then releases lactate first.
-2) Random: what binds first or released first is not specific; Creatine-->Phosphocreatine
What are double displacement (ping pong) reactions?
-A product is released before binding all substrates bind to an enzyme.
-So from this the aspartate binds to the enzyme first then the E accepts the amino group. the first product is released forming oxalaocetate, then the amino acid is tranffered to ketoglutarate forming glutamate.
What are allosteric enzymes and what are some important characteristics of them? What is an important function of
-multiple active sites
-cooperative binding
-sigmoidal velocity/substrate curve
-they are regulated by molecules making them metabolic regulators
What are some examples of inhibitors? Name the 4 different types.
-small molecules of ions
-Irreversible inhibitors
-Reversible inhibitors
-Uncompetitive inhibitors
-Noncompetitive inhibitors
What is an irreversible inhibitor? What are some examples?
-This inhibitor dissociates very slowly from the enzyme. Binds too tightly
-Penicillin
-Aspirin
What is a reversible inhibitor? What are the three categories?
-This inhibitor dissociates very quickly
-Competitive: Binds to active sites of enzyme/ diminish by increasing substrate
-Uncompetitive: binds only to the ES/ cannot be overcome by increased substrate
-Non-copetitive: binds at a different site on enzyme and binds to the enzyme/ES. decreases turnover number. decreases concentration of functional enzyme
What is the equation to determine the dissociation constant of the inhibitor?
Ki=[E][I]/[EI]
How does the graph look like when there is competitive inhibition? the reciprocal graph?
-The Vmax does not decrease or change because substrate concentration will increase.
-The Km will increase since it will take more substrate to overcome the inhibitor
-The reciprocal shows that there is no change in Vmax but does increase Km
How does the graph look like when there is uncompetitive inhibitor? The reciprocal graph?
-No product is formed so the graph shows that the Vmax decreases since the addition of substrate does not affect the inhibition rate. Also the Km is lower
-Graph shows that the Vmax has decresed, and that the substrate needed has also
How does the graph look like when there is noncompetitive inhibitor? The reciprocal graph?
-For this the Vmax has decreased but the Km has remained unchanged.
Why is the Km for a noncomepetitive inhibitor unchanged?
It is unchanged because
Why is the Vmax for uncompetitive and uncooperative changed?
It is unchanged because there will always be a fixed about of enzymes that are not in ES. Remember if you decrease the amount of enzymes the Vmax decreases.
What is a transition state analog?
This was found that if something was made to resemble the transition state of a substrate, the enzyme would bind to it more tightly, thus this would be more effective in inhibiting the enzyme.
Read about the penicillin!
I'm almost dead!
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