General organic and biological chemistry structures off life CH 20 1 enzymes and enzyme action GOB structures 5th ed

• have specific amino acid residues within the active site that interact with functional groups of the substrate to form hydrogen bonds, salt bridges, and hydrophobic interactions... • W

Chapter 20 Enzymes and Vitamins

A physician assistant (PA) helps a doctor by

examining and treating patients as well as

prescribing medications

His or her duties may include obtaining patient

medical records and histories, diagnosing

illnesses, educating and counseling patients, and

referring the patient, when needed, to a specialist

Chapter 20 Readiness

Core Chemistry Skills

• Interpreting Graphs (1.4E)

• Identifying the Primary, Secondary, Tertiary, and Quaternary Structures of Proteins (19.4, 19.5)

20.1 Enzymes and Enzyme Action

Enzymes are biological catalysts that

• increase the rate of a reaction by changing

the way a reaction

takes place

• are not changed in the process of the reaction

• lower the activation energy of the reaction

Enzymes Lower Activation Energy

Enzymes increase the rate of a chemical reaction by reducing the energy required to convert reactant molecules to products.

An enzyme in the blood called carbonic anhydrase catalyzes

• the rapid interconversion of carbon dioxide and water to bicarbonate and H+.

• the reverse reaction, converting bicarbonate and H+ to carbon dioxide and water.

Enzymes and Active Sites

Nearly all enzymes

• are globular proteins with a unique three-dimensional shape that recognizes and binds a small

group of reacting molecules, called substrates.

• have a tertiary structure that includes a region called the active site where one or more small

groups of substrates bind to create a chemical reaction.

• have specific amino acid residues within the active site that interact with functional groups of the substrate to form hydrogen bonds, salt bridges, and hydrophobic interactions.

Enzymes and Active Sites

Enzymes like lactase have an active site where the substrate fits for catalysis to occur The quaternary structure of lactase consists of four subunits The substrate, lactose (gray), is held

in place in the active site by hydrogen bonds with amino acid side chains.

Specificity of Enzymes

• Some enzymes show absolute specificity by catalyzing only one reaction for one specific substrate

• Other enzymes catalyze a reaction of two or more substrates

• Some enzymes catalyze a reaction for a specific type

of bond

Enzyme-Catalyzed Reaction

• The combination of an enzyme and a substrate forms an enzyme–substrate (ES) complex.

• The ES provides an alternative pathway for the reaction with lower activation energy.

• Within the active site, amino acid R groups catalyze the reaction to form an enzyme-product (EP) complex.

Core Chemistry Skill Describing Enzyme Action

Enzyme–Substrate Complex

A flexible active site in lactase and the

flexible substrate lactose adjust to provide

the best fit for the hydrolysis reaction Once

the disaccharide is hydrolyzed, the

monosaccharide products are released from

the enzyme, which is ready

to bind another lactose.

Models of Enzyme Action

• A lock-and-key model has a rigid substrate binding to a rigid enzyme, much like a key fitting

into a lock.

• The induced-fit model, a more dynamic model of enzyme action, states that the active site

is flexible enough to adapt to the shape of the substrate.

• The induced-fit model has the substrate and enzyme working together to acquire a

geometrical arrangement that lowers the activation energy.

Study Check

1 Which is the active site?

A the entire enzyme

B a section of the enzyme

1 Which is the active site?

B a section of the enzyme

2 In the induced-fit model, what happens to the

shape of the enzyme when the substrate binds?

B adapts to the shape of the substrate

20.2 Classification of Enzymes

Enzyme names describe the compound or the

reaction that is catalyzed.

The ribbon structure for alanine transaminase, an

aminotransferase, contains 495 amino acid

residues.

Learning Goal Classify enzymes and give their names

Names of Enzymes

The name of an enzyme

• usually ends in ase

• identifies the reacting substance; for example, sucrase catalyzes the reaction of

sucrose.

• describes the function of the enzyme; for example, oxidases catalyze oxidation.

• can be a common name, particularly for the digestive enzymes, such as pepsin and

trypsin.

Enzyme Class, Oxidoreductases

The Enzyme Commission of the International Union of Biochemistry and Molecular Biology systematically

classifies enzymes according to the six general types of reactions they catalyze (Table 20.2)

Core Chemistry Skill Classifying Enzymes

Enzyme Classes, Transferases, Hydrolases

Enzyme Classes, Lyases, Isomerases

Enzyme Classes, Ligases

Study Check

Match the type of reaction with an enzyme.

1) aminase 2) dehydrogenase

3) isomerase 4) synthetase

A converts a cis fatty acid to a trans fatty acid

B removes two H atoms to form a double bond

C combines two molecules to make a new compound

D adds NH3

Match the type of reaction with an enzyme.

1) aminase 2) dehydrogenase

3) isomerase 4) synthetase

3 A converts a cis fatty acid to a trans fatty acid

2 B removes two H atoms to form a double bond

4 C combines two molecules to make a new compound

1 D adds NH3

Chemistry Link to Health:

Isoenzymes As Diagnostic Tools

Isoenzymes

• are different forms of an enzyme that catalyze the same reaction in different cells or tissues of the body.

• have quaternary structures with slight variations in the amino acids in the polypeptide subunits.

There are five isoenzymes of lactate dehydrogenase (LDH) that catalyze the conversion between lactate and pyruvate

Chemistry Link to Health:

Isoenzymes As Diagnostic Tools

Myocardial infarction may be indicated by an

increase in the levels of creatine kinase (CK) and

lactate dehydrogenase (LDH)

The different forms of an enzyme allow a medical

diagnosis of damage or disease to a particular

organ or tissue

Chemistry Link to Health:

Isoenzymes As Diagnostic Tools

The different isoenzymes of lactate

dehydrogenase (LDH) indicate damage to

different organs in the body.

20.3 Factors Affecting Enzyme Activity

The activity of an enzyme describes how fast an enzyme

catalyzes the reaction and is strongly affected by reaction

conditions, such as

• temperature

• pH

• concentration of the enzyme and substrate

Learning Goal Describe the effect of changes of

temperature, pH, concentration of enzyme, and concentration

of substrate on enzyme activity Thermophiles survive in the high

temperatures (50°C to 120°C) of

a hot spring.

Temperature and Enzyme Activity

Enzymes

• are most active at an optimum temperature

(usually 37°C in humans)

• show little activity at low temperatures

• lose activity at high temperatures as

denaturation occurs

Temperature and Enzyme Activity

Thermophiles

• live in environments where temperatures

range from 50°C to 120°C.

• have enzymes with tertiary structures that

are not destroyed by such high

temperatures.

pH and Enzyme Activity

Enzymes

• are most active at optimum pH, where proper

tertiary structure of the protein is maintained

• contain R groups of amino acids with proper

charges at optimum pH

• lose activity in low or high pH as tertiary structure

is disrupted

Optimum pH Values

Enzymes in

• the body have an optimum pH of about 7.4

• certain organs operate at lower or higher optimum

pH values

Enzyme Concentration

An increase in enzyme concentration

• increases the rate

of reaction (at

constant substrate concentration).

• binds more substrate with enzyme.

Study Check

Sucrase has an optimum temperature of 37°C and an optimum pH of 6.2

Determine the effect of the following on its rate of reaction:

A increasing the concentration of sucrase

B changing the pH to 4.0

C running the reaction at 70°C

1) no change 2) increase 3) decrease

Sucrase has an optimum temperature of 37°C and an optimum pH of 6.2

Determine the effect of the following on its rate of reaction:

A increasing the concentration of sucrase 2) increase

B changing the pH to 4.0 3) decrease

C running the reaction at 70°C 3) decrease

1) no change 2) increase 3) decrease

20.4 Regulation of Enzyme Activity

Phosphorylation is a type of covalent modification that

activates or deactivates an enzyme

a) A kinase activates an inactive enzyme by

Enzyme Regulation

The rates of enzyme-catalyzed reactions are controlled by regulatory enzymes that

• increase the reaction rate when more of a particular substance is needed.

• decrease the reaction rate when that substance is not needed.

Enzyme activity can be regulated by allosteric enzymes, feedback control, and covalent

modifications.

Allosteric Enzymes

Allosteric enzymes

• bind with a regulator molecule at the allosteric site that is different from the active site

• change the shape of the enzyme, which causes a change in the shape of the active site

• can be a positive regulator that changes the shape of the active site to allow the substrate to bind more effectively

• can be a negative regulator that changes the shape of the active site to prevent the proper binding of the substrate, which decreases the rate of the catalyzed reaction

Regulation by Allosteric Enzymes

A positive regulator changes the shape of the active site allowing the substrate to bind more effectively and increasing

• the substrate cannot bind to the active site, and production of all of the intermediate

compounds in the subsequent reaction sequence stops.

Feedback Control

In feedback control, when the level of end product is low,

• the regulator dissociates from the allosteric site on the enzyme, unblocking the active site.

• the initial substrate is allowed to bind to the active site again.

In feedback control, the end product binds to a regulatory site on the allosteric (first) enzyme

in the reaction sequence, which prevents the formation of all intermediate compounds needed in the synthesis of the end product.

Covalent Modification

Covalent modification is another way in which enzymes are modified

• Enzyme activity is modified by covalent bonds to a group on the polypeptide chain that are formed or broken.

• Covalent modification is reversible.

• Zymogens, or proenzymes, are produced in their inactive form and can be activated at a

later time when they are needed

Zymogens, Proenzymes

Zymogens include

• digestive enzymes; protein hormones, such as insulin; and blood clotting enzymes

• proteases, or digestive enzymes that hydrolyze protein, produced as larger, inactive forms

Zymogens, Proenzymes

Once a zymogen is formed, it is

• transported to where the active form is needed

• converted to its active form by a covalent modification

Zymogens such as the proteases trypsinogen and chymotrypsinogen

• are stored in the pancreas until after food is ingested

• are released when triggered by hormones from the pancreas

Once formed, trypsin catalyzes the removal of dipeptides from inactive chymotrypsinogen and trypsinogen to give the active proteases chymotrypsin and trypsin.

Zymogens, Insulin

The protein hormone insulin

• is synthesized in the pancreas as a zymogen called proinsulin

• becomes biologically active when the polypeptide chain of 33 amino acids is removed by peptidases

The removal of a polypeptide chain from proinsulin produces the active form of insulin.

Phosphorylation is a type of covalent modification in which an enzyme is

deactivated or activated (a) A kinase can activate an inactive enzyme by

phosphorylation (b) A phosphatase can activate an inactive enzyme by

removal of

phosphate.

Study Check

Indicate whether the following statements describe enzyme regulation by an allosteric enzyme, a zymogen,

or covalent modification:

A. An end product attaches to the regulatory site of the first enzyme in the reaction sequence

B. Proinsulin forms in the pancreas

C. Phosphorylase kinase deactivates pyruvate

dehydrogenase

B. Proinsulin forms in the pancreas zymogen

C. Phosphorylase kinase deactivates pyruvate

Inhibitors

• are molecules that cause a loss of catalytic activity.

• prevent substrates from fitting into the active sites.

• can be classified as either reversible inhibitors or irreversible inhibitors.

Reversible Inhibition

Reversible inhibitors

• cause a loss of enzyme activity that can be restored.

• can act in different ways but do not form covalent bonds with the enzyme.

Reversible inhibition can be competitive or noncompetitive.

• Competitive inhibitors compete for the active site.

• Noncompetitive inhibitors act on another site that is not the active site.

Competitive Inhibitors

A competitive inhibitor

• has a chemical structure and polarity similar to the substrate

• competes with the substrate for the active site

• has its effect reversed by increasing substrate concentration

• Some bacterial infections are treated with competitive

inhibitors called antimetabolites

• Sulfanilamide competes with

p-aminobenzoic acid (PABA), an essential metabolite in the

growth cycle of bacteria.

Antimetabolites: Competitive Inhibitors in Medicine

Noncompetitive Inhibitors

Anoncompetitive inhibitor

• has a structure that is much different from that of the substrate

• does not compete for the active site

• distorts the shape of the enzyme, which prevents the binding of the substrate at the active site

• cannot have its effect reversed by adding more substrate

Irreversible Inhibition

In irreversible inhibition, enzyme activity is destroyed when

• the inhibitor covalently bonds with R groups of an amino acid that may be near the active site

• the inhibitor changes the shape of the enzyme, which prevents the substrate from entering the active site

Irreversible Enzyme Inhibitors

Enzyme Inhibition Summary

Study Check

Identify each description of an inhibitor that is either competitive or noncompetitive

A. Increasing substrate reverses inhibition

B. It binds to the enzyme’s surface

but not to the active site

C. Its structure is similar to that of

the substrate

D. Inhibition is not reversed by adding

more substrate

Identify each description of an inhibitor that is either competitive or noncompetitive

A. Increasing substrate reverses inhibition competitive

B. It binds to the enzyme’s surface

but not to the active site noncompetitive

C. Its structure is similar to that of

D. Inhibition is not reversed by adding

more substrate noncompetitive

20.6 Enzyme Cofactors and Vitamins

The ribbon representation of

carboxypeptidase shows a Zn2+ cofactor

(orange sphere) in the center of the active

site, held in place by amino acid residues in

the

active site.

Learning Goal Describe the types of cofactors found in enzymes

Enzyme Cofactors

• Asimple enzyme is an active enzyme that

consists only of protein

• Many enzymes are active only when they

combine with cofactors such as metal ions or

small molecules

• Acoenzyme is a cofactor that is a small organic

molecule such as a vitamin

Metal Ions as Cofactors

Many active enzymes require a metal ion

For example,

carboxypeptidase requires a Zn2+ cofactor for

the hydrolysis of the peptide bond of a

C-terminal aromatic amino acid.