1 functions of proteins proteins perform many different functions in the body

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Functions of Proteins

Proteins perform many different functions in the body.

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Amino Acids

Amino acids • are the building blocks of proteins.• contain a carboxylic acid group and an amino group on

the alpha () carbon.• are ionized in solution.• each contain a different side group (R).

R side chain R │ + │H2N—C —COOH H3N—C —COO−

│ │ H H Zwitterion (ionized form)

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Examples of Amino Acids

H + │H3N—C—COO−

│ H Glycine

CH3

+ │H3N—C—COO−

│ H Alanine

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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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Types of Amino Acids

Amino acids are classified as

• nonpolar (hydrophobic) with hydrocarbon side chains.

• polar (hydrophilic) with polar or ionic side chains.

• acidic (hydrophilic) with acidic side chains.

• basic (hydrophilic) with –NH2 side chains.

Nonpolar Polar

AcidicBasic

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Nonpolar Amino Acids

An amino acid is nonpolar when the R group is H, alkyl, or aromatic.

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Polar Amino Acids

An amino acid is polar when the R group is an alcohol, thiol, or amide.

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Acidic and Basic Amino Acids

An amino acid is • acidic when the R group is a carboxylic acid.• basic when the R group is an amine.

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Solution

Identify each as (1) polar or (2) nonpolar.

+

A. H3N–CH2–COO− Glycine (2) nonpolar

CH3

| CH–OH + │

B. H3N–CH–COO − Threonine (1) polar

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A zwitterion

• has charged −NH3+ and COO– groups.

• forms when both the –NH2 and the –COOH groups in an amino acid ionize in water.

• has equal + and – charges at the isoelectric point (pI).

O O ║ + ║

NH2—CH2—C—OH H3N—CH2—C—O–

Glycine Zwitterion of glycine

Zwitterions

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In solutions more basic than the pI,

• the —NH3+ in the amino acid donates a proton.

+ OH–

H3N—CH2—COO– H2N—CH2—COO– Zwitterion Negative ion at pI pH > pI

Charge: 0 Charge: 1-

Amino Acids as Acids

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In solution more acidic than the pI,• the COO– in the amino acid accepts a proton.

+ H+ +

H3N—CH2—COO– H3N—CH2—COOH Zwitterion Positive ionat pI pH< pI

Charge: 0 Charge: 1+

Amino Acids as Bases

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pH and ionization

H+ OH–

+ +

H3N–CH2–COOH H3N–CH2–COO– H2N–CH2–COO–

Positive ion Zwitterion Negative ion

low pH pI high pH

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The Peptide Bond

A peptide bond• is an amide bond. • forms between the carboxyl group of one amino acid and

the amino group of the next amino acid.

O CH3 O

+ || + | ||H3N—CH2—C—O– + H3N—CH—C—O–

O H CH3 O + || | | ||

H3N—CH2—C—N—CH—C—O– peptide bond

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Formation of a Dipeptide

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Solution

Write the dipeptide Ser-Thr. OH CH3

| | CH2 O HCOH O + | ║ + | ║

H3N─CH─C─O– + H3N─CH─C─O– Ser Thr

OH CH3

| | CH2 O H HCOH O + | ║ | | ║

NH3─CH─C─N ─CH─ C─O– + H2O

Ser-Thr

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Naming Dipeptides

A dipeptide • is named from the free amine (NH3

+) using a -yl ending for the name.

• names the last amino acid with the free carboxyl group (COO–) by its amino acid name.

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Write the names and three-letter abbreviations of the tripeptides that could form from two glycine and one alanine.

Glycylglycylalanine Gly-Gly-Ala

Glycylalanylglycine Gly-Ala-Gly

Alanylglycylglycine Ala-Gly-Gly

Solution

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Solution

Tripeptides possible from one each of leucine, glycine, and alanine:

Leu-Gly-Ala

Leu-Ala-Gly

Ala-Leu-Gly

Ala-Gly-Leu

Gly-Ala-Leu

Gly-Leu-Ala

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Learning Check

Write the three-letter abbreviation and name for the

following tetrapeptide.

CH3

│ CH3 S │ │ CH–CH3 SH CH2

│ │ │ CH3 O H CH O H CH2 O H CH2 O + │ ║ │ │ ║ │ │ ║ │ │ ║H3N–CH–C–N–CH–C–N–CH–C–N–CH–C–O–

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Solution

Ala-Leu-Cys-Met Alanylleucylcysteinylmethionine

CH3

│ CH3 S │ │ CH–CH3 SH CH2

│ │ │ CH3 O H CH O H CH2 O H CH2 O

+ │ ║ │ │ ║ │ │ ║ │ │ ║H3N–CH–C–N–CH–C–N–CH–C–N–CH–C–O–

Ala Leu Cys Met

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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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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.

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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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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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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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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. 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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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. 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. 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