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Flashcards in Enzymes and Metabolism Deck (55):
1

catalyst

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.

2

enzyme

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.

3

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

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.

4

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

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.

5

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

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.

6

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

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.

7

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

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.

8

substrate

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.

9

What is the functional significance of the active site?

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.

10

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

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."

11

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

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.

12

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

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.

13

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

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.

14

allosteric site

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.

15

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

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.

16

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

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.

17

What is the difference between cofactors and coenzymes?

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.

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?

Vitamins

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

19

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

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.

20

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

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).

21

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

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.

22

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

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.

23

bioenergetics

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.

24

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

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.

25

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

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.

26

metabolism

Metabolism 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."

27

catabolism

Catabolism 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.

28

anabolism

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

The opposite of this class of metabolic reactions is catabolism.

29

What broad distinction separates aerobic and anaerobic respiration?

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.

30

What is the chemical formula of glucose?

C6H12O6

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

31

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

Glucose generally enters cells via 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.

32

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

Glycolysis occurs anaerobically in the cytosol.

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.

33

Describe the net reaction of glycolysis.

C6H12O6 + 2NAD+ + 2 Pi + 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.

34

Which reaction is the rate-limiting step of glycolysis?

The rate-limiting step is 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.

35

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

AMP is an allosteric activator of phosphofructokinase-1 (PFK-1). 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.

36

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

Fermentation occurs after glycolysis in anaerobic conditions. 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.

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?

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.

38

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

Ethanol and 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.

39

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

Pyruvate dehydrogenase​ occurs between glycolysis and the Krebs cycle. This process takes place in the mitochondrial matrix.

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

40

What are the substrates and products of pyruvate decarboxylation?

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

41

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

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.

42

Which metabolic process generates both NADH and FADH2?

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.

43

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

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.

44

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

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.

45

Which metabolic process takes place along the inner mitochondrial membrane?

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.

46

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

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.

47

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

The proton gradient facilitates 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.

48

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

  • glucose
  • O2
  • NADH
  • pyruvate
  • CO2

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.

49

Which of the following molecules are necessary substrates for fermentation?

  • ethanol
  • lactate
  • pyruvate
  • NADH
  • NAD+

Pyruvate and NADH are required substrates.

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

50

Which of the following molecules are products of glycolysis?

  • glucose
  • ATP
  • NAD+
  • pyruvate
  • O2

ATP and pyruvate are produced during glycolysis.

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.

51

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

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

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.

52

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

Glycolysis and fermentation occur in the cytoplasm. Note that fermentation only takes place in anaerobic conditions.

All other processes take place in the mitochondria.

53

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

The Krebs cycle and pyruvate decarboxylation take place in the matrix.

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

54

Which enzymes are responsible for the metabolism of proteins?

Proteases, also called peptidases, break down proteins.

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

55

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

Acidosis, or low pH, occurs in the blood. 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.