Chapter 4 - Enzymes

Question 1

Nomenclature and Classification

1. How are enzymes often classified?
2. What are 6 examples of enzymes?

Answer 1

1. Enzymes are often classified by placing them in categories according to the reactions that they catalyze.
2. • Oxidoreductase
     - Transferase
     - Hydrolase
     - Lyase
     - Isomerase
     - Ligase

Question 2

Oxidoreductases

1. What do oxidoreductases catalyze? What happens in both parts of the reaction?
2. What are two components of oxidoreductases?
3. What catalyst is used in the reaction to turn Lactase to Pyruvate?

Answer 2

1. Oxidoreductases catalyze redox reactions. One part is oxidized and one part is reduced.
2. Reductases and Oxidases. Oxidases is also known as dehydrogenation because you will lose hydrogen atoms in the reaction.
3. Lactate dehydrogenase.

Question 3

Transferase

1. What do transferases do? What are 3 types of transferases?
2. What do each of the 3 transferases do?
3. How is glucose catalyzed to glucose-6-phosphate?

Answer 3

1. Transferases transfer a chemical group from one molecule to another. 3 types of transferases are Transaminases, Transmethylases, and Kinases.
2. • Transaminases catalyze transfer of an amino group.
     - Transmethylases catalyze the transfer of a methyl group.
     - Kinases transfer a phosphate group.
3. Glucose catalyzed by Hexokinase (6 carbon atoms in glucose and kinase because it will catalyze the transfer of a phosphate group) one of the 3 phosphate group in ATP is transferred in position on carbon #6, causing a phosphate group to be attached to that enzyme.

Question 4

Hydrolases

1. What do hydrolases do?
2. What are 4 examples of hydrolases? What do they do?

Answer 4

1. Hydrolases cleave bonds (break down) by adding water. Best example of this is any type of digestion enzyme.
2. • Phosphatases: Break down phosphates. Work in collaboration with kinases due to kinases attaching a phosphate group to a particular molecule, whereas phosphatases detach that specific molecule group.
     - Peptidases: Breaks down peptide bonds (breaks down longer chains of Amino Acids to shorter chains)
     - Lipases: Breaks down Lipids secreted by the pancreas.
     - Glycosidases: Breaks down Carbohydrates. An example is amylase (hydrolyze starch). Sucrase (hydrolysis sugar). Lactase (hydrolyze lactose).

Question 5

Phases

1. What do Lyases do?
2. What are the two major subclasses of Lyases?
3. What is an example of a Lyase?

Answer 5

1. Lyases catalyze removal of groups to form double bonds, or break double bonds.
2. Decarboxylases enzymes involved in the removal of a carboxyl group on one specific molecule.
   Synthases are enzymes involved in synthesis reactions.
3. Fumarase is an example of a Lyase. It breaks down the double bond from Fumarate and attaches on one side a hydroxyl group and the other side a hydrogen. This causes the synthesis of a Malate.

Question 6

Isomerases

1. What do Isomerases do?
2. What are two major subclasses of Isomerases?
3. What does Phosphoglycerate mutase do?

Answer 6

1. Isomerases catalyze intramolecular rearrangements (isomerization reactions) (Found in alpha-beta, L-D, and cis-trans)
2. Epimerases and Mutases
3. Moves phosphate group from the 3 carbon (which is 3-Phosphoglycerate) and attaches it to the 2nd carbon (which is now in turn 2-phosphoglycerate)

Question 7

Ligases

1. What do Ligases do? What are ligases involved in?

Answer 7

1. Ligases catalyze a reaction in which a C-C, C-S, C-O, or C-N bond is made or broken. Ligases are part of DNA. (DNA ligases can fuse two pieces of DNA)

Question 8

Nomenclature of Enzymes
1. How are enzymes named?
2. What is the common name for a hydrolase derived from? What are the enzymes for Urea and Lactose?
3. How are other enzymes named?
4, Where is the origin of the HRP enzyme name?

Answer 8

1. In most cases, enzyme names end in -ase
2. The common name for a hydrolase is derived from the substrate. Urea: Urease (Remove -a, replace with -ase). Lactose: Lactase (Remove -ose, replace with -ase)
3. Other enzymes are named for the substrate and the reaction catalyzed. (i.e: Lactate dehydrogenase - Removes hydrogen from lactose; Pyruvate Decarboxylase - Removes carboxyl group from pyruvate).
   Some names are historical - no direct relationship to substrate or reaction type.
4. HRP comes from horse radish peroxidase. Enzyme was catalyzing a peroxidase reaction and thats why it was named this.

Question 9

The Effect of Enzymes on the Activation Energy of a Reaction

1. How does an enzyme speed a reaction?
2. What are chemical reactions characterized by?

Answer 9

1. By lowering the activation energy, changing the reaction pathway. This provides a lower energy route for conversion of substrate to product.
2. They are characterized by an equilibrium constant, K (eq), which is a reflection of the difference in energy between REACTANTS, aA, and PRODUCTS, bB. Reaction is K(eq) = product/reactant

Question 10

Diagram of Energy Difference Between Reactants and Products

1. What type of activation energy (Ea) does an uncatalyzed reaction have?
2. What type of activation energy (Ea) does a catalyzed reaction have?

Answer 10

1. Uncatalyzed reactions have a large activation energy (Ea).
2. Catalyzed reactions have a lowered activation energy (Ea). This significantly increases the rate of the reaction.

Question 11

The Effect of Substrate Concentration on Enzyme-Catalyzed Reactions
1. How are the rates of uncatalyzed reactions increased?
2, What do the two stages of enzyme-catalyzed reactions show?
3. What is Rate limited by?
4. What is the Rate of reaction (velocity) in an Uncatalyzed and Enzyme-Catalyzed reaction?
5. What is the role of enzymes within the reaction?

Answer 11

1. The rates of uncatalyzed reactions increase as the substrate concentrations increase.
2. The first stage is the formation of an enzyme-substrate complex. This is followed by slow conversion of substrate into product.
3. RATE is limited by ENZYME AVAILABILITY.
4. Uncatalyzed Reaction: Infinite (no maximum rate).
   Enzyme-Catalyzed: Reaches maximum rate dependent on substrate concentration. (Increases with enzyme availability).
5. Enzymes participate in the reaction, but are not used (consumed). They act as intermediates/matchmakers in the reaction.

Question 12

The Enzyme-Substrate Complex

1. What are the 4 steps involved in an enzyme catalyzed reaction?
2. What is the name of the part of the enzyme that combines with the substrate?
3. What characteristics can be found on the surface of the enzyme?
4. What is the shape of the active site complimentary to?
5. How does the enzyme attract and hold substrate?
6. What does conformation of the active site determine?

Answer 12

1. Step 1: Enzyme binds the substrate (Enzyme + Substrate) which forms a Enzyme-Substrate (ES) complex.
   Step 2: Enzyme-Substrate complex is then converted to a transition state.
   Step 3. Enzyme-Product Complex is formed.
   Step 4: Enzyme-Product complex separate, forming E + P.
2. The Catalytic Active Site. Characteristics include:
3. Pockets or clefts in the surface of the enzyme. (R groups at active site are called CATALYTIC GROUPS).
4. Shape of active site is complimentary to the shape of the substrate.
5. The enzyme attracts and holds the substrate using weak non-covalent interactions.
6. Conformation of the active site determines the specificity of the enzyme

Question 13

Lock and Key Enzyme Model

1. In this model, what is the enzyme and substrate assumed to be?
2. What does this model fail to take into account?
3. What happens to enzyme action in the induced-fit model?

Answer 13

1. The enzyme is assumed to be the lock and the substrate they key. The enzyme and substrate are made to fit exactly.
2. It fails to take into account proteins conformational changes to accommodate a substrate molecule.
3. Induced Fit Model: Enzyme action assumes that the enzyme active site is a more flexible pocket whose conformation changes to accommodate the substrate.

Question 14

Specificity of Enzyme-Substrate Complex

1. What is required for the surfaces of an enzyme and substrate in order for them to react?
2. What is Enzyme Specificity? What is the specificity of Urease?

Answer 14

1. Surfaces of each must be complementary.
2. Enzyme Specificity: The ability of an enzyme to bind only one, or a very few, substrates. The enzyme Urease is VERY specific (has HIGH DEGREE OF SPECIFICITY).

Question 15

Classes of Enzyme Specificity

1. What are the 4 classes of Enzyme Specificity?

Answer 15

1. • Absolute: Enzyme reacts with only one substrate.
     - Group: Enzyme catalyzes reaction involving any molecules with the same functional group.
     - Linkage: Enzyme catalyzes the formation or break up of only certain category or type of bond.
     - Stereochemical: Enzyme recognizes only one of two enantiomers.

Question 16

The Transition State and Product Formation

1. How does the enzyme promote a faster chemical reaction? What two features does the transition state have? What does the transition state eventually disassosiate?
2. What are the 3 transition state changes?

Answer 16

1. As the substrate interacts with the enzyme, its shape changes and this new shape is energetically less stable.
   The transition state has features of both substrate and product and falls apart to yield product, which dissociates from the enzyme.
2. • 1. The enzyme might put “stress” on a bond facilitating bond breakage.
        
        • 2. The enzyme brings two reactants close to one another and in proper orientation.
        • 3. The enzyme might modify the pH of the microenvironment, donating or accepting a H+ (proton).

Question 17

Cofactors and Coenzymes

1. What is a Holoenzyme? What are two main components of a Holoenzyme?
2. Why are cofactors bound to the enzyme? What are 3 examples of these cofactors?
3. What is a coenzyme? What tends to require a coenzyme? What do coenzymes carry?

Answer 17

1. Holoenzyme is another word for “active enzyme”. 2 main components are:
   - Apoenzyme: Polypeptide portion of enzyme.
   - Cofactor: Nonprotein prosthetic group (i.e: Cu++).
2. Cofactors are bound to the enzyme for it to maintain the correct configuration of the active site. 3 examples are:
   - Organometallic compounds
   - Metal Ions
   - Organic Compounds
3. A coenzyme is an organic molecule bound to the enzyme by weak interactions/hydrogen bonds. A coenzyme is required by some enzymes. Most coenzymes carry electrons or small groups. Many have modified vitamins in their structure.

Question 18

Water-Soluble Vitamins and their Coenzymes

1. What is the function of Niacin (B3)? What are the 3 coenzymes for Niacin (B3)?
2. Oxidized coenzymes are NAD+, NADP+, and FAD. What are their Reduced forms?

Answer 18

1. Carrier of hydride ions.
   - Flavin adenine dinucleotide (FAD)
   - Nictotinamide adenine dinucletoide (NAD+)
   - Nicotinamide adenine dinucleotide (NADP+)
2. NADH, NADPH, and FADH2.

Question 19

NAD+ to NADH Mechanism

1. What does the nicotinamide part of NAD+ accept and why?
2. What is lost in this reduction?

Answer 19

1. The nicotinamide part of NAD+ accepts a hydride ion (H plus two electrons) from the alcohol to be oxidized.
2. The alcohol loses a proton (H+) to the solvent.

Question 20

Environmental Effects

1. What can the environment surrounding an enzyme have an effect on?
2. How does pH affect enzymes?
3. What are the optimal pH levels of Pepsin (stomach) and Trypsin (small intestine)?

Answer 20

1. The environment surrounding an enzyme can have a direct effect on enzyme function.
2. Enzymes work best within a particular range of pH. Extreme pH changes will denature the enzyme, destroying its catalytic ability.
3. Pepsin (stomach) has a low optimum ph. Trypsin (small intestine) has a high optimum pH.

Question 21

Temperature Effects

1. What is optimum temperature of an enzyme associated with?
2. What does the rate of an uncatalyzed reaction increase proportionally with?
3. What is optimum temperature usually close to? What happens to an enzyme if there is too much heat?

Answer 21

1. Associated with maximal function.
2. Rate increases proportionally with temperature increase.
3. Optimum temperature is usually close to the temperature at which the enzyme typically exists. (37 degrees for humans). Excessive heat can denature an enzyme, making it completely nonfunctional.

Question 22

Regulation of Enzyme Activity

1. What is one of the major ways that enzymes differ from nonbiological catalysts?
2. What are 5 methods that organisms use to regulate enzyme activity?

Answer 22

1. Differs in the regulation of biological catalysts.
2. • Produce the enzyme only when the substrate is present - common in bacteria
     - Allosteric enzymes
     - Feedback inhibition
     - Zymogens
     - Protein modification

Question 23

Allosteric Enzymes

1. What do effector molecules change the activity of?
2. What is the difference between Positive and Negative Allosterism?
3. What occurs during the third reaction of glycolysis?
4. What type of effectors are ATP and AMP of the enzyme phosphofructokinase?

Answer 23

1. They change the activity of an enzyme by binding at a second site.
2. Positive Allosterism: (Also known as Activation) Effector binding converts the active site to an active configuration.
   Negative Allosterism: (Also known as Inhibition) Effector binding converts the active site to an inactive configuration.
3. The third reaction of glycolysis places a second phosphate on fructose-6-phosphate.
4. ATP is a negative effector and AMP is a positive effector of the enzyme phosphofructokinase.

Question 24

Feedback Inhibition

1. What is the basis for feedback inhibition?
2. In feedback inhibition, what does a product late in a series of enzyme-catalyzed reactions serve as?

Answer 24

1. Allosteric enzymes are the basis for feedback inhibition.
2. A product late in a series of enzyme-catalyzed reactions serves as an inhibitor for a previous allosteric enzyme earlier in the series. (i.e: Product F serves to inhibit the activity of enzyme E1)

Question 25

Proenzyme (zymogens)

1. What is a proenzyme (zymogen)?
2. When are proenzymes converted and to what?
3. What 2 things can cause this conversion? How is pepsinogen converted?

Answer 25

1. A proenzyme (zymogen) is an enzyme that is produced in an inactive form.
2. It is converted to its active form upon reaching the location of the reaction.
3. It is converted via Proteolysis (hydrolysis of the enzyme). It is also converted when needed at the active site in the cell. Pepsinogen is synthesized and transported to the stomach where it is converted to pepsin.

Question 26

Proenzymes of the Digestive Tract
1. If the name of a enzyme begins with “pro” or ends in “gen”, what does this mean? Applying this logic, what can be said for “Procarboxypeptidases”?

Answer 26

1. This means it is a proeznzyme and will be the inactive form (a zymogen) of the respective enzyme. Procarboxypeptidase is the inactive form of carboxypeptidase.

Question 27

Protein Modification

1. What occurs during protein modification? What occurs during Covalent Modification?
2. What is the most common form of protein modification? Where is this modification located and with what (3 things)?

Answer 27

1. A chemical group is covalently added to or removed from the protein. Covalent modification either activates or turns off the enzyme.
2. The addition or removal of a phosphate group. This group is located at the R group (with a free –OH) of: Serine, Threonine, Tyrosine (These 3 have a hydroxyl group attached to their side chain so that they can be phosphorylated)

Question 28

Inhibition of Enzyme Activity

1. What can occur when chemicals bind to enzymes?
2. On what 2 basis’ are inhibitors classified?
3. What are the two types of inhibitors?

Answer 28

1. Chemicals binding to enzymes can eliminate or drastically reduce catalytic activity.
2. Classified on the basis of reversibility and competition.
3. 1. Irreversible inhibitors: Bind tightly to the enzyme and thereby prevent the formation of the E-S complex.
4. Reversible inhibitors: (Competitive or noncompetitive) may be removed from the enzyme and this will restore enzyme activity.

Question 29

Irreversible Inhibitors

1. What does the binding of an irreversible inhibitor consist of?
2. What may this binding block?
3. What may an inhibitor interfere with?
4. What are 3 deadly examples of irreversible inhibitors?

Answer 29

1. Binding of the inhibitor to one of the R groups of a amino acid in the active site.
2. This binding may block the active site binding groups so that the enzyme-substrate complex cannot form.
3. May interfere with the catalytic group of the active site eliminating catalysis.
4. Arsenic, snake venom, nerve gas

Question 30

Reversible, Competitive Inhibitors

1. What is another name for reversible, competitive inhibitors? What are they?
2. What does resemblance permit?
3. What happens once the inhibitor is at the active site?
4. Why is inhibition competitive? What does the degree of inhibition depend on?
5. What happens if the normal substrate binds to the enzyme? What happens if competitive inhibitor (with similar shape) binds to enzyme?

Answer 30

1. Structural analogs. These are molecules that resemble the structure and charge distribution of a natural substrate for an enzyme.
2. Resemblance permits the inhibitor to occupy the enzyme active site.
3. No reaction can occur and the enzyme activity is inhibited.
4. Competitive because the inhibitor and the substrate compete for binding to the active site. Depends on the relative concentrations of enzyme and inhibitor.
5. Both molecules compete for active site. If normal substrate binds, reaction proceeds. If competitive inhibitor binds, reaction is blocked because competitive inhibitor is bound in the active site.

Question 31

Reversible, NONcompetitive Inhibitors

1. What do Reversible, noncompetitve enzymes bind to?
2. What type of effector is an example of a reversible, noncompetitve inhibitor?
3. What is the strength for binding for reversible, noncompetitive inhibitors?
4. How is enzyme activity restored?
5. Do reversible noncompetitive inhibtors bind to the active site? What do they modify?

Answer 31

1. Bind to R groups of amino acids or to the metal ion cofactors.
2. Negative allosteric effectors
3. Binding is weak.
4. Enzyme activity is restored when the inhibitor dissociates from the enzyme-inhibitor complex.
5. Does not bind to the active site. Does modify the shape of the active site once bound elsewhere in the structure.

Question 32

Proteolytic Enzymes

1. What do proteolytic enzymes do? What does their function have an effect on?
2. What does the specificity of proteolytic enzymes depend on?
3. What is a hydrophobic pocket?

Answer 32

1. Proteolytic enzymes cleave the peptide bond in proteins. They break the peptide bonds that maintain to the primary protein structure.
2. Proteolytic enzyme specificity depends on a hydrophobic pocket.
3. Hydrophobic pocket: A cluster of hydrophobic amino acids brought together by the 3-D folding of the protein chain.

Question 33

Chymotrypsin

1. What is the function of chymotrypsin and to what 4 things?

Answer 33

1. Chymotrypsin cleaves the peptide bond at the carboxylic end of: Methionine, Tyrosine, Tryptophan, and Phenylalanine.

Question 34

Proteolyic Enzymes and Evolution

1. What are pancreatic serine proteases a category of? How did they arise?
2. What kind of structures are they similar to? What’s different?
3. Why does each enzyme have a different pocket?
4. What does Chymotrypsin, Trypsin, and Elastase each cleave?

Answer 34

1. Pancreatic serine proteases are a category of enzymes which all hydrolyze peptide bonds. Appear to have arisen through divergent evolution from a common ancestor.
2. Primary, secondary, and tertiary structures. Different specificities.
3. To fit the specificity for the side chains of their substrates. (Different keys fit different locks).
4. Chymotrypsin: Cleaves peptide bonds on the carbonyl side of AROMATIC amino acids and large, hydrophobic amino acids.
   Trypsin: Cleaves on the carbonyl side of basic amino acids.
   Elastase: Cleaves on the carbyonl side of small amino acids (Gly and Ala).

Question 35

Uses of Enzymes in Medicine

1. What is the Diagnostic use of enzymes?
2. What are 3 enzymes that are an indicator of Acute myocardial infarction? 2 enzymes that are indicators of pancreatitis?
3. What are Analytical reagents? What are the two types?
4. What is replacement therapy?

Answer 35

1. Biomarker levels are altered with disease.
2. Acute myocardian infarction: Creatine kinase - MB, Amylase, and Lipase
   Pancreatitis: Amylase and Lipase
3. Analytical reagents: Enzyme used tomeasure another substance.
   - Urea is converted to NH3 via urease.
   - Blood urea nitrogen (BUN) measured
4. Replacement therapy: The administering of synthetically produced functional enzyme to patients that have non-functional enzyme due to genetic mutations.