Enzymatic Function & Catalyzed Reactions

Question 1

Define bioenergetics.

Answer 1

The study of the various types of energy transformations that occur in living organisms is referred to as bioenergetics.

Question 2

What can thermodynamics tell us about the energy of the cell?

Answer 2

Thermodynamics can predict the direction that events will take and determine whether or not an input of energy is necessary to cause the event to happen. However, thermodynamics cannot tell us how rapidly a process will occur or the mechanism used by the cell to carry out the process.

Question 3

State the first law of thermodynamics.

Answer 3

Energy can neither be created nor destroyed.

Question 4

Explain how the first law of thermodynamics can be applied to a system and its surroundings.

Answer 4

A loss or gain in energy of the system must correspond to a gain or loss in energy of the surroundings (and vice versa). The energy of the system is named internal energy. Change in E = Q - W, where E = internal energy, Q = heat energy, and W = work energy.

Question 5

What two ways can a change in energy be manifested in a system?

Answer 5

A change in the heat content of the system and in the performance of work.

Question 6

Describe the second law of thermodynamics.

Answer 6

The second law of thermodynamics says that events in the universe have direction; energy proceeds from a higher state to a lower state.

Question 7

What defines a spontaneous event?

Answer 7

A spontaneous event is an event that can occur without the input of external energy.

Question 8

Define entropy.

Answer 8

The tendency for the randomness and disorder in the universe to increase with every transfer of energy.

Question 9

Describe how life manipulates the property of entropy.

Answer 9

The principle of entropy says that if the system decreases in energy, then the surroundings must increase so as S >0. When simple molecules (such as amino acids) are ordered into higher-order complex molecules (such as proteins), entropy decreases. However, there is a corresponding increase in the entropy of the environment ( such as other complex molecules being broken down).

Question 10

Describe the tradeoff between entropy and information.

Answer 10

Maintaining a state of high information content (low entropy) requires the input of energy. For example, proteins and nucleic acids, in which the specific linear sequence of the subunits is highly ordered, are low in entropy and high in information content.

Question 11

Define exergonic processes.

Answer 11

Processes that happen spontaneously and have a - change in G.

Question 12

Define endergonic processes.

Answer 12

Processes that cannot happen spontaneously and have a positive change in G. They are not thermodynamically favorable.

Question 13

What role does ATP hydrolysis play in the cell?

Answer 13

It drives most endergonic reactions. It separates charge across a membrane, concentrates solutes, moves filaments in a muscle cell, and defines the properties of proteins.

Question 14

Why can ATP be used for such a diversity of functions?

Answer 14

ATP has a terminal phosphate group that can be transferred to a variety of different types of molecules, including amino acids, sugars, lipids, and proteins. In most coupled reactions, the phosphate group is transferred in an initial step from ATP to one of these acceptors and is subsequently removed in a second step.

Question 15

As a reaction tends toward equilibrium, what happens to the free energy and entropy?

Answer 15

The free energy available to do work decreases toward a minimum and entropy increases toward a maximum. Thus, the farther a reaction is kept from its equilibrium state, the less its capacity to do work is lost to the increase in entropy.

Question 16

Why can cellular metabolism maintain itself at irreversible, nonequilibrium conditions?

Answer 16

Most systems are closed, meaning there is no exchange of matter between the system and its surroundings. This is not the case for cellular organisms. The cell is an open system. Materials and energy are constantly flowing into it.

Question 17

What is a steady state?

Answer 17

A steady state occurs when the concentrations of reactants and products remain relatively constant, even though the individual reactions are not necessarily at equilibrium.

Question 18

What does it mean that cells exist in a constant state of dynamic nonequilibrium?

Answer 18

It essentially means that the rates of forward and reverse reactions can be increased or decreased instantaneously in response to changing conditions, and the cell is able to manipulate the concentrations of metabolites.

Question 19

Define enzymes.

Answer 19

Enzymes are the mediators of metabolism, responsible for virtually every reaction that occurs in a cell. Without enzymes, metabolic reactions would proceed so slowly as to be imperceptible.

Question 20

What are the three essential properties of enzymes?

Answer 20

1. They are required only in small amounts.
2. They are not altered irrevocably during the course of the reaction, so each enzyme molecule can participate repeatedly in individual reactions.
3. They have no effect on the thermodynamics of the reaction.

Question 21

Describe the ways in which enzymes do NOT speed up a reaction.

Answer 21

1. By adding energy (they do not determine G or whether or not a reaction is thermodynamically favorable).
2. They do not determine the ratio of products to reactants.

Question 22

What is the relationship between the change in G and the rate at which a reaction proceeds?

Answer 22

There is no relationship. The magnitude of G only tells us of the difference in free energy between the beginning state and equilibrium. Something can be kinetically stable while thermodynamically unstable.

Question 23

How do enzymes as catalysts compare to the catalysts used by chemists in the lab?

Answer 23

Catalysts in the lab increase the speed of a reaction by about 100-1000x. Enzymes speed the reaction 10^8 - 10^13 fold or greater.

Question 24

Define substrates.

Answer 24

Substrates are the reactants bound by enzymes. Each enzyme has the property of specificity, meaning it will only bind to a specific molecule, even when surrounded by others.

Question 25

How do enzymes affect the activation energy of a reaction?

Answer 25

Enzymes catalyze a reaction by decreasing the magnitude of the activation barrier. They do not speed up reactions by heating it up; that would denature the enzymes themself. Rather, enzymes cause their substrates to be very reactive without having to be raised to particularly high energy levels. Enzymes are able to lower activation energies by binding more tightly to the transition state than to the reactants, which stabilizes this activated complex, thereby decreasing its energy.

Question 26

How do compounds illustrate the importance of the transition state?

Answer 26

Compounds that resemble the transition state of a reaction tend to be very effective inhibitors of that reaction because they are able to bind tightly to the catalytic region of the enzyme.

Question 27

How do antibodies illustrate the importance of the transition state?

Answer 27

Antibodies normally do not behave like enzymes but rather, simply bind to molecules with high affinity. However, antibodies that bind to a compound that resembles a transition state for a reaction are often able to act like enzymes and catalyze the breakdown of that compound.

Question 28

Define the enzyme-substrate complex and describe what it can accomplish.

Answer 28

An ES complex is a complex formed from reactants and an enzyme. It accelerates bond-breaking and bond-forming by becoming intimately involved in the activities that are taking place among the reactants.

Question 29

Describe the relationship between a substrate and an active site.

Answer 29

The substrate and active site have complementary shapes, enabling them to bind together with precision. This bond is accomplished by the same type of bonds that determine the structure of a protein: hydrogen, van der Waals, ionic, and hydrophobic forces.

Question 30

Describe the process by which a substrate interacts with an active site.

Answer 30

The active site is usually buried in a cleft within the protein. When a substrate enters the active site cleft, it typically gives up its bound water molecules and enters a hydrophobic environment within the enzyme. The reactivity within the protein may be greater than in the aqueous environment outside of it.

Question 31

Name the three mechanisms by which enzymes accelerate reactions.

Answer 31

1. By maintaining precise substrate orientation.
2. By changing substrate reactivity by altering its electrostatic configuration.
3. By exerting physical stress on bonds in the substrate to be broken.

Question 32

How do enzymes manipulate the pH?

Answer 32

The rate of reactions can be affected by a change in pH. Although enzymes themselves cannot directly change the pH of the medium, they do contain amino acids with acidic or basic side chains. These groups are capable of donating or accepting protons to and from the substrate, thereby altering the electrostatic character of the substrate, making it more reactive.

Question 33

How do enzymes impact the electrostatic properties of substrates?

Answer 33

The active sites of many enzymes contain side chains with a partial positive or negative charge. Such groups are capable of interacting with a substrate to alter its electrostatic properties and hence its reactivity. Such groups are also capable of reacting with a substrate to produce a temporary, covalent enzyme-substrate linkage.

Question 34

Explain how an induced fit works.

Answer 34

Once the enzyme-substrate complex has formed, often, the conformation of the protein can shift to improve the complementary fit.

Question 35

Define maximal velocity.

Answer 35

Maximal velocity is the point at which a reaction is saturated. This means that the level of enzyme and substrate available to react are perfectly balanced so as to be most efficient. If there is too much reactant, the enzyme cannot keep up. If there is too little reactant, the enzyme is idle.

Question 36

Define turnover number.

Answer 36

An enzyme’s turnover number refers to the maximum number of molecules of substrate that can be converted to produce by one enzyme molecule per unit time. A typical turnover number is about 10^3. Turnover number can also be referred to as the catalytic constant.

Question 37

Define the Michaelis constant.

Answer 37

This constant is equal to the substrate concentration when the reaction velocity is one half of the maximal velocity. It is constant for a given enzyme and is independent of substrate or enzyme concentration. The higher the Km, the greater the substrate concentration needed to reach one-half Vmax, and thus to lower the affinity of the enzyme for that substrate.

Question 38

Define enzyme inhibitors.

Answer 38

Enzyme inhibitors are molecules that are able to bind to an enzyme and decrease its activity. The cell relies on inhibitors to regular the activity of many of its enzymes. Inhibitors can be divided into two categories: reversible and irreversible.

Question 39

Define irreversible enzyme inhibitors.

Answer 39

These inhibitors bind very tightly to an enzyme, often by forming a covalent bond to one of its amino acid residues.

Question 40

Define reversible enzyme inhibitors.

Answer 40

Reversible inhibitors bind only loosely to an enzyme and thus are readily displaced. The two subtypes are competitive and noncompetitive.

Question 41

Define competitive inhibitors.

Answer 41

Competitive inhibitors are reversible inhibitors that compete with a substrate for access to the active site of an enzyme. They are similar to the substrate in that they too complement the active site, but they differ in the product that is made as a result.

Question 42

Describe how noncompetitive inhibitors work.

Answer 42

In this type of inhibition, the substrate and inhibitor do not compete for the same binding site. The level of inhibition depends on the concentration of the inhibitor and increasing the concentration of the substrate will not be able to overcome it. Essentially, the maximal velocity of the reaction cannot be reached.

Question 43

How does the equilibrium constant of a reaction relate to the favored direction of the reaction?

Answer 43

When K > 1, the reaction is favored towards the products and there is a negative free energy change.
When K < 1, the reaction is favored towards the reactants and there is a positive free energy change.

Question 44

Compare and contrast the cell’s method of “burning” glucose with burning glucose with a match.

Answer 44

If glucose were burned with a match, all of the energy stored in its bonds would be released as heat. The cell, however, releases this energy in a series of small reactions, using enzymes that favor the forward reaction in order to overcome the activation energy. This release of energy in small units is better suited for storage and use within the cell. The energy is “harvested” in carrier molecules such as ATP and NADH.

Question 45

Describe the structure of ATP.

Answer 45

Adenine is covalently linked to ribose (a five-carbon sugar). Adenosine is then formed from ribose + adenine.

Question 46

Why is ATP so well-suited for transporting energy in the cell?

Answer 46

It is easy to add and remove phosphate groups. The electrostatic forces between the four closely spaced negative charges of the phosphate groups are released when it is removed from the ATP molecule. This generates a very negative free energy charge.

Question 47

What does the breakdown of ATP look like?

Answer 47

ATP breaks down into ADP and an inorganic phosphate group. ATP can also use an alternative pathway release (which generates twice the energy as breaking down to just ADP) to break down from ATP to AMP + 2 phosphates.

Question 48

How does the concentration of ATP compare to the concentration of ADP in the cell, and what implications does this have for the free energy available?

Answer 48

The concentration of ATP is about 10 times more than that of ADP. This means that much more Gibbs free energy is released than predicted under standard conditions (without an enzyme present).

Question 49

How do cells turn thermodynamically unfavorable reactions into favorable ones?

Answer 49

Cells couple reactions together. The change in the standard free energy of coupled reactions (those sharing products/reactants) are additive.

Question 50

Describe how the formation of sucrose is an example of two reactions coupled together to be more thermodynamically favorable.

Answer 50

The change in G of glucose + fructose to make sucrose is 5.5 kcal/mol. This is not favorable. The change in G of ATP –> ADP + P = -7.3 kcal/mol. When these two reactions are combined, it occurs in two steps with a common intermediate. Step 1: the phosphate group is transferred from ATP to the reactant. Step 2: Cleavage of the phosphate bond to generate the product.

Question 51

What are the five roles of ATP hydrolysis?

Answer 51

1. Separate charge (ions) across a membrane.
2. Concentrate a particular solute within the cell.
3. Drive an otherwise unfavorable reaction.
4. Drive movement, such as filament sliding in muscle.
5. Regulate the kinetic activity (heat) of a cell.

Question 52

Define oxidation.

Answer 52

The loss of electrons (gain O or lose H)

Question 53

Define reduction.

Answer 53

Gaining electrons (gain H or lose O)

Question 54

How is NADH used in the cell’s metabolism?

Answer 54

NADH is used as an electron source/storage molecule for reduction/oxidation reactions. NAD+ can act as an electron acceptor for two electrons, and they are stored in the nicotinamide part of the molecule. The reduced form of NAD+ is NADH.

Question 55

Give the quantity by which enzymes increase the rate of reactions.

Answer 55

10^8 - 10^13 fold.

Question 56

How do enzymes lower activation energy?

Answer 56

Enzymes drive the transition state. The active site generates a micro-environment highly favorable to the catalyzed forward reaction. Enzymes bind more tightly to the transition state than to reactants. This stabilizes the activated complex, reducing activation cost.

Question 57

How do the side chains of amino acids affect the substrates of an enzyme reaction?

Answer 57

Side chains of a protein project into the active site. The ionic interactions caused there between the bound substrates and the amino acid side chains determine substrate specificity, and alter the substrate in ways that favor the products (accelerating the conversion reaction).

Question 58

How does substrate orientation work to lower the activation energy of a reaction?

Answer 58

Enzymes hold and align substrates. They also mediate proximity and orientation of substrates to enhance the frequency of “successful” collisions.

Question 59

What are the ways in which an enzyme increases substrate reactivity in order to decrease the activation energy of the reaction?

Answer 59

The enzyme can change the distribution of charge, act as an acid/base catalysis (a proton carrier), covalent catalysis (electron carrier) electrostatic catalysis (stabilizes charge separation in the substrate), and induces strain in substrate.

Question 60

Define maximal velocity and describe what it is limited by.

Answer 60

Maximal velocity is a saturation point in the rate of a reaction which limits the enzyme turnover number.

Question 61

How is the Michaelis constant derived and how does it impact the reaction?

Answer 61

The Michaelis constant is 1/2 the maximal velocity of substrate concentration. The higher the Km, the lower the affinity the enzyme has for the substrate, thus the greater the concentration of substrate needed to propel the reaction forward.

Question 62

Describe synthase enzymes.

Answer 62

These enzymes are involved in molecular synthesis reactions. They are involved in generating covalent bonds.

Question 63

Describe hydrolase enzymes.

Answer 63

This is a general term for enzymes that cleave macromolecules by adding water (hydrolysis).

Question 64

Describe protein kinase enzymes.

Answer 64

Protein kinase enzymes covalently add phosphate (from ATP) to the side chains of proteins. Kinase means it facilitates the addition of a phosphate group, usually from ATP to a protein.

Question 65

Describe protein phosphatase enzymes.

Answer 65

These enzymes remove covalently-bound phosphate from proteins (reverse of protein kinase).

Question 66

Describe ATPase enzymes.

Answer 66

These enzymes are just a general term for enzymes that use the energy of ATP.