Enzymes and Metabolism

Question 1

Define:

catalyst

Answer 1

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

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

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

Answer 3

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 4

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

Answer 4

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 5

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

Answer 5

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 6

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

Answer 6

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 affect these sites, reducing enzyme activity.

Question 7

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

Answer 7

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 8

Define:

substrate

Answer 8

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 9

What is the functional significance of the active site?

Answer 9

It 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 10

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

Answer 10

it 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 11

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

Answer 11

It 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 12

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

Answer 12

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 13

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

Answer 13

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 14

Define:

allosteric site

Answer 14

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 15

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

Answer 15

It 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 16

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

Answer 16

It 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 17

What is the difference between cofactors and coenzymes?

Answer 17

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

Answer 19

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 20

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

Answer 20

phosphoanhydride bonds

These phosphoanhydride bonds 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 21

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

Answer 21

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 22

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

Answer 22

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 23

Define:

bioenergetics

Answer 23

This 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 24

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

Answer 24

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.

Question 25

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

Answer 25

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 26

Define:

metabolism

Answer 26

It collectively refers to the biological processes that occur within cells. Specifically, these processes either generate energy through the breakdown of molecules or use energy to build molecules.

Metabolism is also known as “cellular respiration.”

Question 27

Define:

catabolism

Answer 27

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

The opposite of this class of metabolic reactions is anabolism.

Question 28

Define:

anabolism

Answer 28

It is the creation of larger biomolecules from smaller units. Anabolic processes require energy input.

The opposite of this class of metabolic reactions is catabolism.

Question 29

What broad distinction separates aerobic and anaerobic respiration?

Answer 29

Aerobic respiration requires oxygen, while anaerobic respiration does not require oxygen.

As part of metabolism, both processes involve the breakdown of biological molecules and the eventual release of energy.

Question 30

What is the chemical formula of glucose?

Answer 30

C₆H₁₂O₆

Broadly, glucose is a carbohydrate; specifically, it is a monosaccharide.

Question 31

The majority of glucose molecules enter the cell via which transport method?

Answer 31

facilitated diffusion

This occurs with the assistance of a family of transport proteins.

This process is promoted by high plasma glucose levels, which creates a concentration gradient that drives glucose into the cells. It is also promoted by the activity of insulin, which increases the number of glucose transporters on the membranes of certain cell types.

Question 32

Which metabolic process occurs in the cytosol regardless of the presence or absence of oxygen?

Answer 32

Glycolysis

Glycolysis is a biochemical process that forms pyruvate from the breakdown of glucose. The pathway produces 2 NADH and a net total of 2 ATP per glucose molecule.

Question 33

Describe the net reaction of glycolysis.

Answer 33

C₆H₁₂O₆ + 2NAD⁺ + 2 P_i + 2 ADP ⇒ 2 pyruvate + 2 ATP + 2 NADH + 2 H₂O + 2 H⁺

While glycolysis only produces a net of two ATP molecules, it generates a total of four. However, two molecules of ATP are used as reactants in early glycolytic steps.

Question 34

Which reaction is the rate-limiting step of glycolysis?

Answer 34

The phosphorylation of fructose 6-phosphate.

This reaction is catalyzed by the enzyme phosphofructokinase-1 (PFK-1). For this reason, PFK-1 is sometimes called the rate-limiting enzyme of glycolysis.

Question 35

Of AMP, ATP, and citrate, which is most likely to serve as an allosteric activator of PFK-1?

Answer 35

AMP

The other two molecules are inhibitors.

You can figure this out logically: “activate” means “stimulate.” Glycolysis should be stimulated when available energy is low (to make more) and inhibited when it is high. High AMP concentrations imply that cellular ATP is low.

Question 36

Which metabolic process immediately follows glycolysis in oxygen-poor conditions?

Answer 36

Fermentation

This process takes place when O₂ is too scarce to facilitate the entry of glycolytic products into the Krebs cycle.

Fermentation can produce either ethanol or lactic acid, depending on the species.

Question 37

The conversion of pyruvate to lactic acid, often referred to simply as “fermentation,” produces no ATP. However, it is still necessary in anaerobic conditions. What purpose does this process serve?

Answer 37

Fermentation regenerates NAD⁺ by oxidizing NADH and reducing pyruvate.

NAD⁺ is necessary for glycolysis, but cannot be regenerated by the electron transport chain under anaerobic conditions. Fermentation serves to produce NAD⁺, reducing buildup of NADH and allowing glycolysis to continue.

Question 38

Which two molecules can be created by the fermentation of pyruvate?

Answer 38

• ethanol
• lactate

Alcohol fermentation, which takes place in yeast and certain bacteria, involves the reduction of pyruvate to ethanol. Lactic acid fermentation, which takes place in human muscle cells as part of anaerobic respiration, involves the reduction of pyruvate to lactate.

Question 39

Which metabolic process immediately follows glycolysis and produces acetyl-CoA?

Answer 39

Pyruvate decarboxylation

Under aerobic conditions, pyruvate (a three-carbon molecule) is converted to a two-carbon acetyl group. This group then attaches to coenzyme A.

Question 40

What are the substrates and products of pyruvate decarboxylation?

Answer 40

Pyruvate, a three-carbon molecule, is the substrate. CO₂, NADH, and acetyl-CoA are the ultimate products.

Question 41

Two glucose molecules undergo glycolysis, producing pyruvate. How many molecules of NADH will be produced simply from the decarboxylation of these pyruvate products?

Answer 41

4 NADH molecules

During glycolysis, the initial two glucose molecules will be converted into four molecules of pyruvate. For every molecule of pyruvate that is decarboxylated by pyruvate dehydrogenase, one molecule of NADH is formed.

Question 42

Which metabolic process generates both NADH and FADH₂?

Answer 42

The Krebs cycle produces the electron carriers NADH and FADH₂, as well as an ATP equivalent (either ATP or GTP).

The Krebs cycle, also known as the citric acid cycle, involves the cyclic transformation of organic molecules. It occurs in the mitochondrial matrix.

Question 43

What is the initial substrate of the Krebs cycle, and with which molecule does it first react?

Answer 43

Acetyl-CoA, a two-carbon compound, is the substrate entering the cycle. It immediately reacts with oxaloacetate to form a six-carbon compound (citrate).

Coenzyme A is released in this process and can be used again.

Question 44

How many molecules of NADH and FADH₂, respectively, are produced during one turn of the Krebs cycle?

Answer 44

One full cycle produces 3 NADH molecules and 1 FADH₂.

Other products include carbon dioxide, which is released as waste, and one molecule of GTP.

Question 45

Which metabolic process takes place along the inner mitochondrial membrane?

Answer 45

The electron transport chain (ETC) uses a series of complexes along the inner mitochondrial membrane. These molecules support a chain of oxidation-reduction reactions, ultimately resulting in the oxidization of NADH and FADH₂ and the reduction of O₂.

The transport of electrons through the chain creates a proton gradient that provides the energy to convert ADP to ATP.

Question 46

The electron transport chain functions to produce a proton gradient. Into which mitochondrial region are these protons pumped?

Answer 46

Protons are pumped from the mitochondrial matrix to the intermembrane space.

AP Biology questions may involve conditions or toxins that dissipate (remove) the proton gradient. Remember that this system relies on the impermeability of the inner mitochondrial membrane. If protons could diffuse straight back into the matrix instead of building up in the intermembrane space, ATP production would be greatly impaired.

Question 47

Which metabolic process is facilitated by the proton gradient within the mitochondria?

Answer 47

ATP synthesis

After establishment of the gradient, proton concentration in the intermembrane space is high. When possible, these protons will move down their gradient and reenter the matrix; this can only occur if they pass through ATP synthase, an enzyme. As this process occurs, ATP synthase uses this energy to convert ADP to ATP.

Question 48

Which of the following molecules are necessary substrates for the electron transport chain?

• glucose
• O₂
• NADH
• pyruvate
• CO₂

Answer 48

NADH is a required substrate, and O₂ must be present as the final electron acceptor in the chain.

Glucose and pyruvate, though linked to NADH production, are not directly necessary for the electron transport chain. CO₂ is a waste product of cellular respiration.

Question 49

Which of the following molecules are necessary substrates for fermentation?

• ethanol
• lactate
• pyruvate
• NADH
• NAD⁺

Answer 49

• Pyruvate
• NADH

Ethanol, lactate, and NAD⁺ are all products of fermentation.

Question 50

Which of the following molecules are products of glycolysis?

• glucose
• ATP
• NAD⁺
• pyruvate
• O₂

Answer 50

• ATP
• pyruvate

NADH, though not listed here, is another glycolytic product. Glucose and NAD⁺ are consumed in glycolysis, while O₂ is not involved. Remember that glycolysis is an anaerobic process.

Question 51

Which of the following molecules are products of the Krebs cycle?

• NADH
• acetyl-CoA
• pyruvate
• FADH₂
• NAD⁺

Answer 51

The Krebs cycle produces NADH and FADH₂, which are electron carriers that are later used.

Acetyl-CoA and NAD⁺ are consumed in the Krebs cycle, while pyruvate is not directly involved.

Question 52

Which two processes of cellular metabolism take place in the cytoplasm?

Answer 52

1. Glycolysis
2. Fermentation

Note that fermentation only takes place in anaerobic conditions.

All other processes take place in the mitochondria.

Question 53

Which two processes of cellular metabolism take place in the mitochondrial matrix?

Answer 53

1. The Krebs cycle
2. Pyruvate decarboxylation

The electron transport chain is also a mitochondrial process, but occurs along the inner membrane, not within the matrix itself.

Question 54

Which enzymes are responsible for the metabolism of proteins?

Answer 54

Proteases

also called peptidases

Proteins are cleaved into amino acids. Depending on their identity, these amino acids can be converted to acetyl-CoA, pyruvate, or other metabolic intermediates.

Question 55

What homeostatic change occurs in the blood when the cells are in oxygen debt?

Answer 55

Acidosis

or low pH

This is the result of excess CO₂ and the buildup of lactic acid in muscles during anaerobic respiration.

Note that normal plasma pH is 7.4.