Enzymes and Bioenergetics

Question 1

Define:

catalyst

Answer 1

A catalyst is a molecule that increases the rate of a reaction without being consumed itself.

Catalysts change the kinetics of a reaction, not the thermodynamics. In other words, they lower the activation energy without altering the equilibrium or free energy change of a reaction.

Question 2

Define:

enzyme

Answer 2

An enzyme is a biological catalyst that structurally facilitates a chemical reaction. Like all catalysts, enzymes increase the rate of a chemical reaction without being consumed.

Most enzymes are proteins, but RNA molecules called ribozymes also have enzymatic activity.

Question 3

Why are enzymes generally ineffective catalysts over a broad temperature range?

Answer 3

Enzymes must be at a certain optimal temperature to maintain their structure.

The structure of an enzyme, especially in relation to its active site, is essential to its function as a catalyst. Like other proteins, enzymes denature, or lose their original conformations, above a certain temperature. However, reactions generally progress more slowly at low temperatures, further narrowing the range of optimal activity.

Question 4

How will the free energy diagram of a catalyzed reaction differ from that of an uncatalyzed reaction?

Answer 4

The catalyzed reaction will have a lower activation energy.

Note that the overall change in free energy will be the same for the catalyzed and uncatalyzed reactions.

Question 5

What effect does a reduced activation energy have on reaction kinetics?

Answer 5

A lowered activation energy increases the reaction rate.

Each reaction must overcome an activation energy barrier to progress from reactants to products. When this barrier is lower, reactants are more likely to collide with sufficient energy, speeding up the reaction.

Question 6

What happens to the equilibrium constant (K_eq) when an enzyme is added to a reaction?

Answer 6

The equilibrium constant doesn’t change.

Catalysts only impact reaction rate and have no effect on reaction equilibrium or free energy. K_eq is only altered by changes in temperature.

Question 7

Why are enzymes generally ineffective catalysts over a broad pH range?

Answer 7

Enzymes can only maintain their functional structure at a certain optimal pH.

The structure of an enzyme, especially in relation to its active site, is essential to its function as a catalyst. The active site often contains positively or negatively charged groups, which contribute to the specificity of the site. Changes in pH can protonate or deprotonate these sites, reducing enzyme activity.

Question 8

At the molecular level, why are prolonged, high fevers dangerous to human health?

Answer 8

At higher-than-optimal temperatures, most human enzymes lose function and cannot support necessary biological processes.

Most human enzymes function most efficiently at an optimal temperature of 37 ºC. While these enzymes can remain active at slightly higher temperatures, their function is impaired.

Question 9

Why is pepsin, a key digestive enzyme of the stomach, inactive in the small intestine?

Answer 9

The optimal pH for pepsin is far below that of the small intestine.

Pepsin functions most efficiently at a pH near 2, like that of the stomach. The small intestine is much more basic. This deviation from the optimal pH alters the structure of pepsin, inactivating it.

Question 10

Define:

substrate

Answer 10

A substrate is a specific molecule that an enzyme acts upon, usually via interactions with the enzyme’s active site.

For example, starch is the substrate of salivary amylase. This means that amylase, an enzyme, catalyzes a reaction involving starch as a reactant.

Question 11

What is the functional significance of the active site?

Answer 11

The active site of an enzyme is the structural component where enzyme-substrate interactions take place.

In other words, the active site is the catalytic region of an enzyme. It is structured to facilitate the binding of its substrate, often through the presence of certain amino acid residues.

Question 12

Enzymes are usually limited to acting on a single substrate or class of substrate molecules. What term describes this quality?

Answer 12

Specificity

The substrate(s) that can be accommodated by an enzyme are determined by the shape of its active site. For example, proteases are specific to protein substrates, while lipases act on lipid-based substrates.

Question 13

How does the lock-and-key model explain enzyme-substrate specificity?

Answer 13

The lock-and-key model posits that a substrate will fit perfectly into the active site of its corresponding enzyme, without any conformational changes taking place.

In this model, the active site is the “lock” and its complementary substrate is the “key.”

Question 14

How does the induced fit model explain enzyme-substrate specificity?

Answer 14

The induced fit model posits that active sites are flexible. When a substrate approaches the enzyme, the conformation of the active site will change to better fit the substrate.

The induced fit model is a more recent adaptation of the lock-and-key model.

Question 15

What major limitation prevents the lock-and-key model from being fully accurate?

Answer 15

It wrongly portrays all enzymes as being rigid and inflexible.

In reality, the active site of an enzyme can change its conformation to facilitate binding to the substrate.

Question 16

What is the difference between cofactors and coenzymes?

Answer 16

Cofactors are a broad group of compounds that are required for the proper functioning of enzymes. Coenzymes are a class of small, organic cofactors.

Cofactors can also be inorganic substances, such as ions.

Question 17

Trace amounts of copper, zinc, and magnesium are essential for human protein function. What term describes the relationship of these metals to enzymes?

Answer 17

These metals, in their ion forms, act as cofactors.

Ions are common examples of inorganic cofactors, meaning that they are required for the proper functioning of certain enzymes.

Question 18

Many coenzymes are derived from molecules like niacin and riboflavin, which must be consumed as part of the diet. What category describes these molecules?

Answer 18

Vitamins

Vitamins are often used to synthesize coenzymes, which are non-protein organic compounds that are essential for proper enzyme function.

Question 19

What happens to the rate of an enzyme-catalyzed reaction as substrate concentration increases?

Answer 19

Reaction rate initially increases, but levels off as the enzyme becomes saturated with substrate.

The maximum rate of such a reaction is called V_max. Once this rate is reached, added substrate has no effect.

Question 20

An experimenter notes that the rate of an enzyme-catalyzed reaction remains constant, even after doubling the substrate concentration. Why might this occur?

Answer 20

The enzyme is already at V_max.

Above a certain substrate concentration, an enzyme will function at a maximum rate. Increasing the substrate concentration beyond this point will not affect the reaction kinetics.

Question 21

What value is defined as the substrate concentration present when the reaction velocity is one-half of V_max?

Answer 21

K_m

In other words, K_m is the amount of substrate required to bind to half of an enzyme’s active sites. An alternative term for this value is the Michaelis constant.

Question 22

The K_m of a certain reaction is calculated when the substrate concentration is 1.5 M. How will K_m change when this concentration is doubled?

Answer 22

K_m will not change.

K_m, or the Michaelis constant, refers to the exact concentration of substrate that allows a reaction to reach one-half of V_max. Changing substrate concentration may increase or decrease the reaction rate, but it cannot alter this value.

Question 23

With regard to enzyme kinetics, what name is given to this type of plot (pictured below)?

Answer 23

This is a Michaelis-Menten graph. It shows the effect of substrate concentration ([S]) on reaction velocity (V).

Question 24

With regard to enzyme kinetics, what name is given to this type of plot (pictured below)?

Answer 24

This is a Lineweaver-Burk plot, which is a linear method of depicting enzyme activity. The x-axis is 1/[S], while the y-axis is 1/v.

Question 25

Define:

allosteric site

Answer 25

An allosteric site is a region of an enzyme, separate from the active site, where molecules can bind and affect enzyme function.

Allosteric binding can either facilitate or inhibit the binding of substrate to the active site.

Question 26

How does a competitive inhibitor alter an enzyme-catalyzed reaction?

Answer 26

A competitive inhibitor binds to an enzyme on its active site, inhibiting the reaction.

Specifically, these inhibitors compete with the substrate and block it from binding the active site.

Question 27

How does a noncompetitive inhibitor alter an enzyme-catalyzed reaction?

Answer 27

A noncompetitive inhibitor binds to an enzyme on a region outside of its active site, inhibiting the reaction.

Specifically, these inhibitors bind an allosteric site, inducing a structural change in the enzyme that decreases its efficiency. Substrates can still enter the enzyme’s active site.

Question 28

How do competitive inhibitors alter V_max and K_m?

Answer 28

Competitive inhibitors increase K_m but do not change V_max.

Since competitive inhibition can be overcome by adding substrate, the maximum reaction velocity is not lowered; reaching it simply requires more substrate. As a result, K_m (the amount of substrate needed to reach one-half of V_max) is raised in these cases.

Question 29

How do noncompetitive inhibitors alter V_max and K_m?

Answer 29

Noncompetitive inhibitors decrease V_max but do not change K_m.

Since noncompetitive inhibition acts regardless of substrate concentration, it permanently lowers V_max. However, K_m is not changed; the same substrate concentration is still required to reach one-half of the new maximum velocity.

Question 30

How can competitive inhibition be overcome?

Answer 30

Competitive inhibition can be overcome by increasing substrate concentration.

Substrates and competitive inhibitors both bind the same region of the enzyme: the active site. Increasing substrate concentration ensures that more substrate, as opposed to inhibitor, binds at that position.

Question 31

How will the action of a noncompetitive inhibitor be affected by increasing substrate concentration?

Answer 31

Adding substrate will have no effect.

A noncompetitive inhibitor binds at an allosteric site, changing the overall conformation of the enzyme. The substrate can still bind, but cannot be converted to product, regardless of its concentration.

Question 32

Which type of inhibitor is represented by the green line below?

Answer 32

Since the line representing the inhibitor shows an altered V_max, this must be a noncompetitive inhibitor.

On a Lineweaver-Burk plot, the y-intercept denotes 1/Vmax. The value of the x-intercept is equal to -1/Km.

Question 33

What type of inhibitor is represented by the orange line below?

Answer 33

Since the line representing the inhibitor shows an altered K_m with the same V_max, this must be a competitive inhibitor.

On a Lineweaver-Burk plot, the y-intercept denotes 1/V_max. The value of the x-intercept is equal to -1/K_m.

Question 34

Phosphofructokinase, a glycolytic enzyme, is allosterically inhibited by ATP. What common homeostatic process does this example demonstrate?

Answer 34

This is an example of negative feedback. In such processes, increased concentration of a product decreases the rate of the reaction that forms that product.

Glycolysis involves the breakdown of glucose to form ATP, among other products. If increased amounts of ATP are already present, glycolysis will slow.

Question 35

Define:

zymogen

Answer 35

A zymogen is an inactive precursor to a functional enzyme. Generally, zymogens must be cleaved into their active form.

Zymogens are commonly found in the digestive system. Examples include pepsinogen, trypsinogen, and chymotrypsinogen.

Question 36

What is the difference between a zymogen and a proenzyme?

Answer 36

Nothing. Zymogen and proenzyme are interchangeable terms.

Both terms refer to nonfunctional enzyme precursors that must be altered to produce their active enzyme forms.

Question 37

Enterokinase is an enzyme that converts trypsinogen to trypsin, an active digestive enzyme. Trypsinogen itself does not catalyze any reactions. What is trypsinogen an example of?

Answer 37

Trypsinogen is a zymogen.

Trypsinogen is the storage form and precursor of trypsin. Trypsinogen will not function as an enzyme until it is converted to trypsin.

Question 38

What class of substrate is common to maltase, sucrase and lactase?

Answer 38

The substrates of these enzymes are all disaccharides.

Maltase breaks down maltose into two glucose molecules. Sucrase cleaves sucrose into glucose and fructose, and lactase breaks down lactose into glucose and galactose.

Question 39

What classes of substrate are acted upon by lipases and proteases, respectively?

Answer 39

Lipases catalyze the breakdown of lipids (fats), while proteases cleave proteins.

In biology, the “-ase” ending generally denotes an enzyme. With digestive enzymes, the part of the word that precedes “-ase” often refers to the substance that is broken down.

Question 40

How does a reaction catalyzed by a kinase differ from one catalyzed by a phosphatase?

Answer 40

• A kinase catalyzes the addition of a phosphate group to a protein.
• A phosphatase catalyzes the removal of a phosphate group from a protein.

One classic example of a kinase is protein kinase A, which is involved in G-protein coupled receptor cascades. It phosphorylates a variety of molecules.

Question 41

Define:

bioenergetics

Answer 41

Bioenergetics is the study of energy transformations within organisms. Specifically, it concerns the energy released and used during the formation and breaking of chemical bonds.

Bioenergetics is closely related to thermodynamics, especially Gibbs free energy.

Question 42

What is the difference between anabolic and catabolic processes?

Answer 42

Catabolic processes involve the biological breakdown of molecules into smaller units. Catabolism is accompanied by the generation of energy.

Anabolic processes involve the creation of larger biomolecules from smaller units. Anabolism requires energy input.

Question 43

What single comparison between reactants and products can be made to determine whether a reaction will proceed?

Answer 43

The change in Gibbs free energy, or ΔG, determines reaction spontaneity.

A negative ΔG means the reaction will be spontaneous, while a positive ΔG denotes a nonspontaneous reaction.

To calculate ΔG, use the equation ΔG = ΔH - TΔS. Note that while reactions are favored when ΔH (enthalpy change) is negative and when ΔS (entropy change) is positive, neither of these quantities alone can guarantee spontaneity.

Question 44

What term can be used to describe a thermodynamically favorable reaction?

Answer 44

Thermodynamically favorable reactions are termed exergonic. In such reactions, ΔG is always negative, meaning that free energy is released.

The opposite type of reactions are endergonic. In these processes, ΔG is positive and the reaction will not proceed spontaneously.

Question 45

A student is analyzing a particular physiological reaction and finds that ΔGº = +1.6 kJ/mol. From this, he determines that the reaction will not proceed spontaneously in the body. What is the flaw in this student’s reasoning?

Answer 45

The student is using the standard ΔG value (ΔGº). This value only determines if a reaction is favorable in standard state conditions, which may not be applicable.

Standard state dictates that the temperature must be 25 ºC, gases must be under a pressure of 1 atm, and all reactants must be present in 1 M concentrations. In the human body, temperature is roughly 37 ºC, so we already know that standard state does not apply.

Question 46

What name is given to the promotion of a thermodynamically unfavorable reaction by pairing it with a second, favorable process?

Answer 46

This pairing is known as coupling. If the sum of the reactions’ ΔG values is negative, they will proceed.

Often, an unfavorable reaction is paired with the hydrolysis of adenosine triphosphate (ATP), which is extremely exergonic.

Question 47

The phosphorylation of glucose into glucose-6-phosphate has a ΔGº of +13.8 kJ/mol. However, this reaction proceeds as the initial step of glycolysis. What process is responsible?

Answer 47

This situation is the result of coupling the reaction with another, more favorable, process. Specifically, this reaction is coupled with the hydrolysis of ATP.

glucose + P_i → glucose-6-phosphate + H₂O ΔGº = +13.8 kJ / mol

ATP + H₂O → ADP + P_i ΔGº = -30.8 kJ / mol

Together, these coupled reactions have a ΔGº of (+13.8 kJ / mol) + (-30.5 kJ / mol) = -16.7 kJ / mol. With such a negative value, this process will be spontaneous.

Question 48

What molecule is shown below, and what is its biological role?

Answer 48

This molecule is adenosine triphosphate (ATP), the major form of cellular energy.

ATP consists of three phosphate groups bound to the ribonucleoside adenosine. The cleavage of the third phosphate bond facilitates the release of energy, which the cell harnesses to drive biological processes.

Question 49

What name is given to the bonds circled in the structure below?

Answer 49

These are phosphoanhydride bonds, which exist between phosphate groups on molecules like ATP (shown) and ADP.

The name of these bonds comes from the reaction that forms them: dehydration (removal of H₂O). Predictably, they can be broken by the reverse reaction, hydrolysis (addition of H₂O).

Question 50

While the breaking of bonds usually requires energy, hydrolysis of a phosphoanhydride bond in ATP is extremely exergonic. What structural features of ATP explain this phenomenon?

Answer 50

• At a pH of 7.4, the phosphate groups on ATP have four negative charges, creating large amounts of repulsion. This is minimized when the molecule is hydrolyzed.
• The products of hydrolysis are ADP and P_i, which are highly stabilized by resonance. ATP has less resonance stabilization overall.
• Similarly, ADP and P_i are more stabilized than ATP by surrounding water molecules, due to their additional negative charges.

Question 51

Name two methods of phosphoryl group transfer that form ATP.

Answer 51

• Oxidative phosphorylation is the production of ATP from ADP by ATP synthase. This occurs immediately after the electron transport chain.
• Substrate-level phosphorylation is the transfer of a phosphoryl group from a substrate directly to ADP. An example of such a substrate is 1,3-bisphosphoglycerate.

Question 52

In what part(s) of a eukaryotic cell do oxidative and substrate-level phosphorylation occur, respectively?

Answer 52

• Oxidative phosphorylation occurs only in the mitochondria. Specifically, ATP synthase is located along the inner mitochondrial membrane.
• Substrate-level phosphorylation can occur in the cytosol (as in glycolysis) or the mitochondrial matrix (as in the Krebs cycle).

Question 53

What type of chemical reaction most closely relates to the biological molecules FAD and NAD⁺?

Answer 53

These molecules are involved in oxidation-reduction (redox) reactions.

Note that the full name of FAD is flavin adenine dinucleotide, while that of NAD⁺ is nicotinamide adenine dinucleotide. Both molecules are common electron carriers.

Question 54

For a biological oxidation-reduction reaction to proceed spontaneously, what should be the signs of its ΔG and E values?

Answer 54

Its ΔG value should be negative, while its E value, or reaction potential, should be positive.

Note that, as in most biological reactions, nonspontaneous reactions can occur if coupled with spontaneous processes. In that case, the sum of their ΔG values must still be negative.

Question 55

Is FADH₂ the reduced or oxidized form of flavin adenine dinucleotide?

Answer 55

FADH₂ is the reduced form, meaning that it is currently carrying electrons. FAD⁺ is the oxidized form.

When FADH₂ donates its electrons to another molecule, as in the electron transport chain, it is acting as a reducing agent.

Question 56

Is NAD⁺ the reduced or oxidized form of nicotinamide adenine dinucleotide?

Answer 56

NAD+ is the oxidized form, meaning that it is not currently carrying electrons. NADH is the reduced form.

When NAD⁺ accepts electrons to become NADH, it is acting as an oxidizing agent.

Question 57

How many total electrons can be accepted by eight molecules of NAD⁺?

Answer 57

Eight molecules of NAD⁺, if reduced to NADH, would hold a total of sixteen electrons.

Remember that both common electron carriers (NAD⁺ and FAD) can accept two electrons per molecule.