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Flashcards in 201 Enzymes Deck (59)
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1
Q

What is an enzyme?

A

enzymes are necessary for life, highly specialized proteins, with extraordinary catalytic power (aka speed up reactions).

-enzymes play a key role in every biochemical process including breakdown of nutrients, assembly of macromolecules, generation and transformation of chemical energy.

2
Q

What are the properties of an enzyme?

A
  • large molecules
  • accelerate reactions
  • high degree of specificity
  • work in aqueous environment, - mild temp and pH
  • may require cofactors or enzymes for their functon
3
Q

What is the practical importance of enzymes? AKA how does it relate to life and why should we care about them

A

b/c they work in every biochemical process. There are Human diseases due to inactive or overactive enzymes. Enzymes can help with development of therapeutic drugs, chemical engineering, food technology and agriculture

4
Q

Even when a reaction is spontaneous and exergonic, why would an enzyme catalyst be important?

A

b/c although spontaneous, it would occur on a time scale that would not be able to sustain life. and enzymes speeds up this reaction so that energy can be released in seconds.

E.g., bacterium can reproduce every 20 mins. unless an organism is able to conduct biochemical processes in a time scale that is practical, it will not survive.

5
Q

TRUE OR FALSE: All enzymes are proteins, with the exception of a few small catalytic RNA molecules, or ribozymes

A

TRUE

6
Q

how are enzymes calssified?

A

based on the types of reactions that the enzymes catalyze

7
Q

TRUE OR FALSE: if a reaction is exergonic it will not always require an enzyme, since it is already spontaenous

A

FALSE: biochemical reactions need to occur w/in a rapid time scale regardless of whether the reactions are exergonic and endergonic

8
Q

What contributes to the rapid time scale of an enzyme?

A

its key feature, the substrate-binding site and the active site.

9
Q

What is the active site of an enzyme comprised of ?

A

the binding site and catalytic site

10
Q

What is the binding site?

A

the binding site binds and orients substrates

11
Q

what is the catalytic site?

A

this site reduces chemical activation energy

12
Q

Why is the protein structure important when it comes to enzymes?

A

b/c it scaffolds to support and position the active site

13
Q

What is the substrate-binding site?

A

a region on the enzyme molecule where the substrate molecule is secluded/sequestered and the amino-acid residues that line the binding pocket can act upon the substrate and catalyze its chemical transformation. The enzyme-substrate complex is key to the action of enzymes

14
Q

What is the difference between the substrate-binding site and the active or catalytic site of an enzyme?

A
  • the substrate binding site is those amino acid residues directly involved in binding the substrates
  • the active or catalytic site is those amino acid residues directly involved in catalysis
15
Q

In a reaction coordinate diagram, what is the ground state for substrates and products?

A

the starting point for the forward or reverse reaction

16
Q

In a reaction coordinate diagram, what would delta G be, if the free energy of the ground state of product is lower than that of substrate?

A

the standard free energy changed would be negative, meaning that this is an exergonic reaction and that at equilibrium there will be more product than substrate

17
Q

In a reaction coordinate diagram, what would delta G be, if the free energy of the ground state of product is higher than that of substrate?

A

standard free energy would be positive, aka endergonic, aka it needs energy

18
Q

On the reaction coordinate diagram, what does the energy barrier represent?

A

-the energy required to align reacting groups, form or break bonds, form intermediate transient unstable complexes, etc.

19
Q

What is the rate of reaction?

A

how fast a reaction occurs. The rate of reaction is dependent on the activation energy ΔG‡ and this is what the enzyme alters

20
Q

What is the energy hill? What are the different components of the hill?

A

on a reaction diagram, it is the energy barrier.

-the transition state - occupies the top of the energy hill is a transient state and the possibility of the reaction going either way (to substrate or to product) is equal

21
Q

What is the difference in free energy between the ground state and the transition state?

A

it is the activation energy which is denoted byΔG‡

22
Q

FILL IN THE BLANK: The greater the activation energy ΔG‡ the _____ the reaction.

A

The greater the activation energy ΔG‡ the SLOWER the reaction.

23
Q

FILL IN THE BLANK: The lower the activation energy ΔG‡ the _____ the reaction.

A

The lower the activation energy ΔG‡ the FASTER the reaction.

24
Q

What is the relationship between a catalyst and the activation energy?

A

a catalyst lowers the activation energy and thus speeds up the reaction

25
Q

Raising the temperature or pressure can speed up many reactions. How does that work? Why can’t organisms speed up reactions by just raising the temperature or pressure?

A

When you raise the temp. average kinetic energy of the different molecules increases. By increasing the number of molecules that have sufficient energy to overcome the barrier, you increase the rate of the reaction. Lowering the activation barrier is equivalent to increasing the rate of the reaction. Pressure could alter a reaction if a gas (such as O2 or CO2) is a substrate or product. Most organisms are sensitive to changes in temperature and pressure. Even though some organisms have adapted to extreme environments, they are still sensitive to changes in that environment.

26
Q

On a reaction coordinate diagram, what are the Y and X axis?

A

Y is the free energy of the system, which is plotted against, X the progress of the reaction S –> P ( progressive chemical changes such as bond breakage or formation as S is converted to P)

27
Q

On a reaction coordinate diagram, the activation energy is lower when what occurs?

A

when the enzyme catalyzes the reaction

28
Q

On a reaction coordinate diagram, ΔG‡ represents what?

A

the activation energy for each of the uncatalyzed and catalyzed reactions, where the activation energy is lower for a reaction that is catalyzed by and enzyme vs a reaction that is uncatalyzed/

AKA the reaction rate can be increased in the presence of an enzyme

29
Q

TRUE OR FALSE: an enzyme alters the overall free-energy change

A

FALSE: only alters the rate of reaction but it does not alter the overall free-energy change I.e., catalysis does not alter the equilibrium constant

30
Q

enzyme kinetics quantifies what?

A

the conversion of substrate to product as a function of time

31
Q

In enzyme kinetics, velocity represents what?

A

velocity (or rate) of a reaction is the increase in concentration of Product (P) over time [ = d[S]/dt] or equivalently, the decrease of substrate concentration over time [= -d[S}/dt]

32
Q

When thinking about enzyme kinetics, what are the two main steps for enzyme and what do these steps mean?

A

1) Binding and 2) Chemistry

binding-means binding or dissociation constants and rates

chemistry means the reaction that converts the substrate to product

33
Q

What is binding?

A

Binding is where the product is enzyme substrate (EZ), to yield an association constant, KA, with the units of M-1

34
Q

What is dissociation?

A

where product is E+S, described by a dissociation constant, KD, with units of M or uM or nM. This direction is more intuitive

35
Q

The association constant KA is the reciprocal of what?

A

of the dissociation constant, KD (KA = 1/KD) and so the higher the association constant the lesser the dissociation from the enzyme = aka the enzyme binds the substrate more tightly

36
Q

What happens when the substrate is equal to the dissociation constant Kd?

A

then half of the enzyme is in the ES complex

37
Q

What are the two ways to measure the dissociation constant (KD)?

A

1) in terms of concentrations

2) in terms of rates of decay and formation of E-S complex, which is pertinent to enzyme kinetics

38
Q

What does a low dissociation constant indicate?

A

that the ES complex does not dissociate easily, there is more ES complex than free enzyme or substrate; I.e., the ES is more stable.

This means that at any given substrate concentration, there is higher likelihood of ES being formed, and the enzyme shows high affinity for S

39
Q

What is meant by the rate limiting step?

A

this is the slowest step in a multi-step reaction

40
Q

What is meant by the rate constant?

A

this describes how fast a reaction occurs

41
Q

What is meant by the half-life of a reation?

A

this is the time required for the substrates to decrease to one half of its original concentration

42
Q

What is the relaxation time?

A

the time required for a reaction to return to equilibrium following a pertubation

43
Q

What is the first order reaction?

A

the rate of the reaction depends only on the concentration of substrate A since this is a unimolecular reaction

  • Firstorder:A→B
  • v = k∙(A), where k is a rate constant
  • First order, units = s‐1
  • Instantaneous velocity, v = ‐d(A)/dt = d(B)/dt = k∙(A)
44
Q

In the first order reaction A to B what is K?

A

the rate constant which is in units of sec‐1 (or min‐1 or years‐ 1 or centuries‐1 or …) because the equation describes (conc./time)/conc., which is 1/second (although minutes are also often used by biochemists)

the rate constant, K, provides a direct measure of how fast the reaction occurs.

45
Q

what does a high K value (rate constant) suggest?

A

a high K value suggest a fast reaction

46
Q

What is an example of 1st order reaction?

A

the decay of radioactive isotopes/

47
Q

What is a higher order reaction?

A

one in which rate is proportional to the concentration of the substrates and second order reactions involves 2 molecule that come together to form products.

The exponents a and b in the equation describe the dependence of the observed rate on the concentration of A and B. In a second order reaction a and b are each equal to 1.

The rate constant will have units of M-1 sec-1. This is b/c it is molarity/sec divided by molarity to the power of 2

[=v/(S1)*(S2)]

48
Q

How can transient covalent bonds lower the activation energy?

A

Transient covalent bonds might form between enzyme and substrate, thereby activating the reaction; or groups might be transferred from substrate to enzyme. These covalent interactions can lower the activation energy.

49
Q

What role do non-covalent interactions (like hydrogen bonds), hydrophobic, and ionic interactions play in activation energy?

A

weak non‐covalent interactions like hydrogen bonds as well as hydrophobic and ionic interactions can help stabilize protein structures.
All of this energy from enzyme‐substrate interaction contributes towards the binding energy, which is the primary source of energy that an enzyme uses to lower the activation energy.

50
Q

When is the only time an enzyme can catalyze a reaction?

A

only if it is chemically complementary to the transition state, i.e., the largest number of interactions occur in between the transition state and the enzyme

51
Q

When do maximum interactions occur? What does this create?

A

some interactions occur in the ES complex, but the max interactions occur only when the substrate is in the transition state.

The energy released from these interactions offsets some of the activation energy. This is a cumulative effect; despite the fact that each interaction may not contribute much to reducing the activation energy, a multitude of these interactions can substantially affect the activation energy. This requirement for multiple weak interactions to drive catalysis partially explains the large size of enzymes.

52
Q

What are the two models for substrate binding and catalysis?

A

1) the lock and key theory

2) active site (induced form) induced fit model

53
Q

What is the lock and key hypothesis?

A

this states that a specific substrate fits into the active site of an enzyme just as a key fits into a lock

This hypothesis explains enzyme specificity but it does not help explain catalysis itself.

54
Q

What is the induced-fit model?

A

this model states that the binding of a substrate to the substrate-binding site of an enzyme induces a change in conformation of the enzyme so that the enzyme now best fits the transition state.

this means that an enzyme just does not accept a substrate molecules as is but rather causes the substrate to alter its conformation to something close to the transition state. This is the accepted model and there is abundance evidence that this model helps explain the enzyme-catalysis

55
Q

What is an uncatalyzed bi-molecular reaction? is it entropically favored?

A
  • Two free reactants –> single restricted transition state

* Conversion is entropically unfavorable

56
Q

What is an uncatalyzed unimolecular reaction?

Is it entropically favored?

A

• Flexible reactant –> rigid transition state conversion is entropically unfavorable for flexible reactants

57
Q

catalyzed reactions and enzymes do what to binding energy of substrates? is this reaction entropically favored?

A

Enzyme uses the binding energy of substrates to organize the reactants to a fairly rigid ES complex
• Entropy cost is paid during binding
• Rigid reactant complex –> transition state conversion is entropically OK

58
Q

Enzymes bind which state best?

A

transition states better than substrates

59
Q

What information tells us that enzymes bind transition states best?

A

• Enzyme active sites are complementary to the transition state of the reaction
• Enzymes bind transition states better than substrates
• Stronger/additional interactions with the transition state as compared to
the ground state lower the activation barrier
• Largely ΔH‡ effect (i.e., chemical bonds are stabilized)