1 16.5 Levels of Protein Structure Chapter 16 Amino Acids, Proteins, and Enzymes Copyright © 2009...

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16.5 Levels of Protein Structure

Chapter 16 Amino Acids, Proteins, and Enzymes

Copyright © 2009 by Pearson Education, Inc.

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Primary Structure of Proteins

The primary structure of a protein is• the particular sequence of amino acids.• the backbone of a peptide chain or

protein.

Ala─Leu─Cys─Met

CH3

SH

CH2

CH3

S

CH2

CH2CH O

O-CCH

H

N

O

CCH

H

N

O

CCH

H

N

O

CCHH3N

CH3

CH3CH

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Primary Structures

• The nonapeptides oxytocin and vasopressin have similar primary structures.

• Only the amino acids at positions 3 and 8 differ.


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Primary Structure of Insulin

Insulin• was the first protein to have its

primary structure determined.• has a primary structure of two

polypeptide chains linked by disulfide bonds.

• has a chain A with 21 amino acids and a chain B with 30 amino acids.

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Secondary Structure–Alpha Helix

The secondary structure of analpha helix is• a three-dimensional spatial

arrangement of amino acids in a polypeptide chain.

• held by H bonds between the H of –N-H group and the O of C=O of the fourth amino acid down the chain.

• a corkscrew shape that looks like a coiled “telephone cord.”


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Secondary Structure–Beta-Pleated Sheet

The secondary structure of a beta-pleated sheet• consists of polypeptide chains arranged side by side.• has hydrogen bonds between chains.• has R groups above and below the sheet.• is typical of fibrous proteins, such as silk.

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Secondary Structure–Triple Helix

The secondary structure of a triple helix is

• three polypeptide chains woven together.

• typical of collagen, connective tissue, skin, tendons, and cartilage.

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Indicate the type of protein structure.1) primary 2) alpha helix3) beta-pleated sheet 4) triple helix

A. polypeptide chains held side by side by H bondsB. sequence of amino acids in a polypeptide chainC. corkscrew shape with H bonds between amino acidsD. three peptide chains woven like a rope

Learning Check

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Indicate the type of protein structure.

1) primary 2) alpha helix

3) beta-pleated sheet 4) triple helix

A. 3 polypeptide chains held side by side by H bonds

B. 1 sequence of amino acids in a polypeptide chain

C. 2 corkscrew shape with H bonds between amino

acids

D. 4 three peptide chains woven like a rope

Solution

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• must be obtained from the diet.

• are 10 amino acids not synthesized by the body.

• are in meat and dairy products.

• are missing (one or more) in grains and vegetables.

Essential Amino Acids

Essential amino acids

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Tertiary Structure

The tertiary structureof a protein • is an overall 3-

dimensional shape.• is determined by

attractions and repulsions between the side chains of the amino acids in a peptide chain.

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Crosslinks in Tertiary Structures

Crosslinks in tertiary structures involve attractions and repulsions between the side chains of the amino acids in the polypeptide chain.

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Select the type of tertiary interaction.

1) disulfide 2) ionic

3) H bonds 4) hydrophobic

A. leucine and valine

B. two cysteines

C. aspartic acid and lysine

D. serine and threonine

Learning check

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Select the type of tertiary interaction.

1) disulfide 2) ionic

3) H bonds 4) hydrophobic

A. 4 leucine and valine

B. 1 two cysteines

C. 2 aspartic acid and lysine

D. 3 serine and threonine

Solution

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Globular Proteins

Globular proteins • have compact, spherical

shapes.• carry out synthesis,

transport, and metabolism in the cells.

• such as myoglobin store and transport oxygen in muscle.

Copyright © 2009 by Pearson Education, Inc. Myoglobin

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Quaternary Structure

The quaternary structure • is the combination of two

or more protein units.• of hemoglobin consists

of four polypeptide chains as subunits.

• is stabilized by the same interactions found in tertiary structures.


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Fibrous Proteins

Fibrous proteins• consist of long, fiber-like shapes.• such as alpha keratins make up hair, wool, skin, and

nails.• such as feathers contain beta keratins with large

amounts of beta-pleated sheet structures.

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Summary of Protein Structure

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Summary of Protein Structure

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Identify the level of protein structure.

1) primary 2) secondary

3) tertiary 4) quaternary

A. beta-pleated sheet

B. order of amino acids in a protein

C. a protein with two or more peptide chains

D. the shape of a globular protein

E. disulfide bonds between R groups

Learning Check

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Identify the level of protein structure.1) primary 2) secondary3) tertiary 4) quaternary

A. 2 beta-pleated sheetB. 1 order of amino acids in a proteinC. 4 a protein with two or more peptide chainsD. 3 the shape of a globular proteinE. 3 disulfide bonds between R groups

Solution

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Denaturation involves • the disruption of bonds in the secondary, tertiary, and

quaternary protein structures.• heat and organic compounds that break apart H

bonds and disrupt hydrophobic interactions.• acids and bases that break H bonds between polar

R groups and disrupt ionic bonds.• heavy metal ions that react with S-S bonds to form

solids.• agitation such as whipping that stretches peptide

chains until bonds break.

Denaturation

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Denaturation of protein occurs when• an egg is cooked. • the skin is wiped with

alcohol.• heat is used to cauterize

blood vessels.• instruments are

sterilized in autoclaves.

Applications of Denaturation


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Tannic acid is used to form a scab on a burn. An egg is hard boiled by placing it in boiling water. What is similar about these two events?

Learning Check

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Acid and heat cause the denaturation of protein. They both break bonds in the secondary and tertiary structures of proteins.

Solution

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16.6 Enzymes

16.7 Enzyme Action

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Enzymes are Biological Catalysts

Enzymes are proteins that

• Catalyze nearly all the chemical reactions taking place in the cells of the body.

• Increase the rate of reaction by lowering the energy of activation.

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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.

• could be a common name, particularly for the digestion enzymes, such as pepsin and trypsin.

Names of Enzymes

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Enzymes are classified by the reaction they catalyze.

Class Type of Reactions CatalyzedOxidoreductases Oxidation-reductionTransferases Transfer groups of atomsHydrolases HydrolysisLyases Add atoms/remove atoms to or

from a double bondIsomerases Rearrange atomsLigases Use ATP to combine small molecules

Classification of Enzymes

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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 2 H atoms to form double bond.

C. Combines two molecules to make a new compound.

D. Adds NH3.

Learning Check

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Match the type of reaction with an enzyme

1) aminase 2) dehydrogenase

3) isomerase 4) synthetase

A. 3 Converts a cis-fatty acid to a trans-fatty acid.

B. 2 Removes 2 H atoms to form double bond.

C. 4 Combines two molecules to make a new compound.

D. 1 Adds NH3.

Solution

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The active site • is a region within an

enzyme that fits the shape of the reacting molecule called a substrate.

• contains amino acid R groups that bind the substrate.

• releases products when the reaction is complete.

Active Site

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Enzyme-Catalyzed Reaction

In an enzyme-catalyzed reaction• a substrate attaches to the

active site.• an enzyme-substrate (ES)

complex forms.• reaction occurs and products

are released. • an enzyme is used over and

over.

E + S ES E + P

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Lock-and-Key Model

In the lock-and-key model, the• active site has a rigid shape.• enzyme only binds substrates that exactly fit the

active site.• enzyme is analogous to a lock.• substrate is the key that fits that lock.


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Induced-Fit Model

In the induced-fit model• enzyme structure is flexible, not rigid.• enzyme and substrate adjust the shape of the active site

to bind substrate.• the range of substrate specificity increases.• shape changes improve catalysis during reaction.


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Example of an Enzyme-Catalyzed Reaction

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Learning Check

A. The active site is(1) the enzyme(2) a section of the enzyme(3) the substrate

B. In the induced-fit model, the shape of the enzyme when substrate binds(1) stays the same(2) adapts to the shape of the substrate

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Solution

A. The active site is

(2) a section of the enzyme

B. In the induced-fit model, the shape of the enzyme when substrate binds

(2) adapts to the shape of the substrate

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Diagnostic Enzymes

Diagnostic enzymes• determine the

amount of damage in tissues.

• that are elevated may indicate damage or disease in a particular organ.

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Diagnostic Enzymes

Levels of enzymes CK, LDH, and AST

• are elevated following a heart attack.

• are used to determine the severity of the attack.


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Isoenzymes

Isoenzymes• catalyze the same reaction in different tissues in the

body.• can be used to identify the organ or tissue involved

in damage or disease.• such as lactate dehydrogenase (LDH), which

converts lactate to pyruvate, consists of five isoenzymes.

• such as LDH have one form more prevalent in heart muscle and another form in skeletal muscle and liver.

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Isoenzymes


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16.8 Factors Affecting Enzyme Activity

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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 Action

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Enzymes• are most active at

optimum pH.• contain R groups of

amino acids with proper charges at optimum pH.

• lose activity in low or high pH as tertiary structure is disrupted.

pH and Enzyme Action

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Optimum pH Values

Enzymes in• the body have an optimum pH of about 7.4.• certain organs operate at lower and higher optimum pH

values.

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Substrate Concentration

As substrate concentration increases, • the rate of reaction

increases (at constant enzyme concentration).

• the enzyme eventually becomes saturated, giving maximum activity.

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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.1) no change 2) increase 3) decrease

A. Increasing the concentration of sucroseB. Changing the pH to 4C. Running the reaction at 70 °C

Learning Check

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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.

1) no change 2) increase 3) decrease

A. 2 Increasing the concentration of sucrase

B. 3 Changing the pH to 4

C. 3 Running the reaction at 70 °C

Solution

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Inhibitors• are molecules that cause a loss of catalytic activity.• prevent substrates from fitting into the active sites.

E + S ES E + P

E + I EI no P

Enzyme Inhibition

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Competitive Inhibition

A competitive inhibitor• has a structure that is

similar to that of the substrate.

• competes with the substrate for the active site.

• has its effect reversed by increasing substrate concentration.

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A noncompetitive inhibitor• has a structure that is much

different than the substrate.• distorts the shape of the

enzyme, which alters the shape of the active site.

• prevents the binding of the substrate.

• cannot have its effect reversed by adding more substrate.

Noncompetitive Inhibition


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Identify each description as an inhibitor that is

1) competitive or 2) noncompetitive.

A. Increasing substrate reverses inhibition.B. Binds to enzyme surface, but not to the active site.C. Structure is similar to substrate.D. Inhibition is not reversed by adding more substrate.

Learning Check

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Identify each description as an inhibitor that is

1) competitive or 2) noncompetitive.

A. 1 Increasing substrate reverses inhibition.B. 2 Binds to enzyme surface, but not to the active site.C. 1 Structure is similar to substrate.D. 2 Inhibition is not reversed by adding more

substrate.

Solution

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16.9 Enzyme Cofactors


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Function of Coenzymes

A coenzyme prepares the active site for catalytic activity.

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Water-Soluble Vitamins

Water-soluble vitamins are• soluble in aqueous solutions.• cofactors for many enzymes.• not stored in the body.


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Fat-Soluble Vitamins

Fat-soluble vitamins• are A, D, E, and K. • are soluble in lipids, but not in aqueous solutions.• are important in vision, bone formation, antioxidants,

and blood clotting.• are stored in the body.

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Learning Check

Identify each compound as a1) water-soluble vitamin or 2) fat-soluble vitamin. A. Folic acidB. Retinol (vitamin A)C. Vitamin CD. Vitamin EE. Niacin

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Solution

Identify each compound as a1) water-soluble vitamin or 2) fat-soluble vitamin.

A. 1 Folic acidB. 2 Retinol (vitamin A)C. 1 Vitamin CD. 2 Vitamin EE. 1 Niacin

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Thiamin (Vitamin B1)

Thiamin • was the first B vitamin identified.• is part of the coenzyme thiamin pyrophosphate (TPP), required in the decarboxylation of -keto carboxylic acids.

• deficiency results in beriberi (fatigue, weight loss, and nerve degeneration).


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Riboflavin (Vitamin B2)

Riboflavin is• made of the sugar alcohol ribitol and flavin.• part of the coenzymes flavin adenine dinucleotide (FAD)

and flavin mononucleotide (FMN).• needed for good vision and healthy skin.

N

N N

NHH3C

H3C

CH2 CH CH CH CH2 OH

OHOHOH

O

O

D-Ribitol

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Niacin (Vitamin B3)

Niacin• is part of the coenzyme

nicotinamide adenine dinucleotide (NAD+) involved in oxidation-reduction reactions.

• deficiency can result in dermatitis, muscle fatigue, and loss of appetite.

• is found in meats, rice, and whole grains.

N

C

O

OH


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Pantothenic Acid (Vitamin B5)

Pantothenic acid• is part of coenzyme A needed for energy production,

as well as glucose and cholesterol synthesis.

• deficiency can result in fatigue, retarded growth, cramps, and anemia.

• is found in salmon, meat, eggs, whole grains, and vegetables.

HO CH2 C CH C N CH2 CH2 C OH

O

H

OH OCH3

CH3

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Cobalamin (Vitamin B12)

Cobalamin• consists of four pyrrole

rings with a Co2+.• is a coenzyme for

enzymes that transfer methyl groups and produce red blood cells.

• deficiency can lead to pernicious anemia and nerve damage.


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Ascorbic Acid (Vitamin C)

Vitamin C• is required in collagen

synthesis.• deficiency can lead to

weakened connective tissue, slow-healing wounds, and anemia.

• is found in blueberries, citrus fruits, tomatoes, broccoli, red and green vegetables.

O CHOH

CH2OH

OHHO

O


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Folic Acid (Folate)

Folic acid (folate)• consists of pyrimidine,

p-aminobenzoic acid, and glutamate.

• forms the coenzyme THF used in the transfer of carbon groups and the synthesis of nucleic acids.

• deficiency can lead to abnormal red blood cells, anemia, and poor growth.


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Vitamin A

Vitamin A• is obtained from meats and beta-carotenes in plants.• has beta-carotenes that are converted by liver

enzymes to vitamin A (retinol).

H3C CH3

CH3

CH3 CH3

CH3 CH3H3C CH3

H3C

CH3 CH3

CH2OHH3C CH3

CH3

Beta-carotene

Retinol (vitamin A)


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Vitamin D

Vitamin D (D3)• is synthesized in skin

exposed to sunlight. • regulates the absorption of

phosphorus and calcium during bone growth.

• deficiency can result in weakened bones.

• sources include cod liver oil, egg yolk, and enriched milk.


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Vitamin E

Vitamin E• is an antioxidant in cells.• may prevent the oxidation of unsaturated fatty acids.• is found in vegetable oils, whole grains, and

vegetables.

O

CH3

HO

H3C

CH3

CH3

CH3

CH3 CH3 CH3

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Vitamin K

• Vitamin K1 in plants has a saturated side chain.• Vitamin K2 in animals has a long unsaturated side

chain.• Vitamin K2 is needed for the synthesis of zymogens for

blood clotting.

3n

CH3

CH3

O

O CH3 CH3

Vitamin K2 (menaquinone)

CH3

CH3

O

O CH3 CH3

Vitamin K1 (phylloquinone)

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Learning Check

Identify the vitamin associated with each:1) Thiamin (B1) 2) Vitamin A

3) Vitamin K 4) Vitamin D5) Ascorbic acid

A. Collagen formationB. BeriberiC. Absorption of phosphorus and calcium in bone D. VisionE. Blood clotting

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Solution

Identify the vitamin associated with each:

1) Thiamin (B1) 2) Vitamin A

3) Vitamin K 4) Vitamin D

5) Ascorbic acid

A. 5 Collagen formation

B. 1 Beriberi

C. 4 Absorption of phosphorus and calcium in bone

D. 2 Vision

E. 3 Blood clotting

1 16.5 Levels of Protein Structure Chapter 16 Amino Acids, Proteins, and Enzymes Copyright © 2009...

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