Chapter 20 Amino Acids and Proteins

20.1 Functions of Proteins 20.2 Amino Acids 20.3 Amino Acids as Acids and Bases

Functions of Proteins
Proteins perform many different functions.

Amino Acids
Amino acids: Are the building blocks of proteins. Contain a carboxylic acid group and an amino group on the alpha () carbon. Have different side groups R that give each amino acid unique characteristics. R side chain | H2NC COOH General structure of an | -amino acid H
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Nonpolar Amino Acids

Amino acids are classified as nonpolar when the R groups are H, alkyl, or aromatic.

Polar Amino Acids

Amino acids are classified as polar when the R groups are alcohols, thiols, or amides.

Acidic and Basic Amino Acids

Amino acids are classified as acidic when the R group is a carboxylic acid. Amino acids are classified as basic when the R group is an amine.

Fischer Projections of Amino Acids

All amino acids except glycine are chiral. Amino acids have stereoisomers. In biological systems, only L amino acids are used in proteins.
COOH H2N H CH3 H COOH NH2 CH3 H2N COOH H CH2SH H COOH NH2 CH2SH

Learning Check
Identify each as (1) polar or (2) nonpolar A. NH2CH2COOH (Glycine) CH3 | CHOH | B. NH2CHCOOH

(Threonine)

L-Alanine D-Alanine

L-Cysteine

D-Cysteine
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Solution
A. NH2CH2COOH (Glycine) (2) nonpolar

Zwitterions
Both the NH2 and the COOH groups in an amino acid undergo ionization in water. A zwitterion forms that has + and charge. At the isoelectric point (pI), the + and charges in the zwitterion are equal. NH2CH2COOH Glycine
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CH3 | CHOH (1) polar | B. NH2CHCOOH (Threonine)

H3NCH2COO Zwitterion of glycine

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Amino Acids as Acids

In solutions more basic than the pI, the NH3+ in the amino acid donates a proton.
+

Amino Acids as Bases

In solution more acidic than the pI, the COO- in the amino acid accepts a proton. H+

OH COO H2NCH2COO Negative ion Higher pH

+

H3NCH2 Zwitterion at pI

H3NCH2COO Zwitterion at pI

H3NCH2COOH Positive ion Low pH

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pH and Ionization
Acidic amino acids such as aspartic acid have a second carboxyl group that can donate and accept protons. The pI for aspartic acid occurs at a pH of 2.8.

Electrophoresis
Electrophoresis separates amino acids according to their isoelectric points. The positively charged amino acids move towards the negative electrode. The negatively charged amino acids move toward the positive electrode. An amino acid at its pI will not migrate in either direction.
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Separation of Amino Acids

When electrophoresis is completed, the amino acids are identified as separate bands on the filter paper or thin layer plate.

Learning Check
CH3 | H3NCHCOOH
+

CH3 | H2NCH2COO (2)

(1) Which structure represents:

A. Alanine at a pH above its pI? B. Alanine at a pH below its pI?

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Solution
CH3 | H3NCHCOOH
+

Chapter 20 Amino Acids and Proteins

CH3 | H2NCH2COO (2)

(1) Which structure represents:

20.4 Formation of Peptides 20.5 Protein Structure: Primary and Secondary Levels

A. Alanine at a pH above its pI? (2) B. Alanine at a pH below its pI? (1)

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The Peptide Bond

A peptide bond is an amide bond between the carboxyl group of one amino acid and the amino group of the next amino acid. O CH3 O || | || + + H3NCH2COH + H3NCHCO O H CH3 O || | | || H3NCH2CNCHCO
+

A Dipeptide
A peptide is named from the free amine (NH3+) using -yl endings for the names of the amino acids. The last amino acid with the free carboxyl group (COO-) uses its amino acid name.

peptide bond
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Learning Check
Write the names and three-letter abbreviations of the amino acids in the tripeptides that could form from two glycine and one alanine.

Solution
Write the names and three-letter abbreviations of the amino acids in the tripeptides that could form from two glycine and one alanine. Gly-Gly-Ala Glycylglycylalanine Gly-Ala-Gly Glycylalanylglycine Ala-Gly-Gly Alanylglycylglycine

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Learning Check
Write the name of the following tetrapeptide using amino acid names and three-letter abbreviations.
CH3 CH3 CH CH3 CH3 O H3N CH C N H CH O CH C N H SH CH2 O CH C N H
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Solution
CH3 CH3 CH CH3 CH3 O H3N CH C N H CH O CH C N H SH CH2 O CH C N H S CH2 CH2 O CH C O
-

S CH2 CH2 O
CH C O

Ala

Leu

Cys

Met

Ala-Leu-Cys-Met Alanylleucylcysteinylmethionine
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Primary Structure
A polypeptide containing 50 or more amino acids is called a protein. The primary structure of a protein is the sequence of amino acids in the peptide chain. CH
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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.

CH3 CH CH3 CH3 O H3N CH C N H CH O CH C N H SH CH2 O CH C N H

S CH2 CH2 O CH C O
-

Ala-Leu-Cys-Met

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Insulin
Insulin: Was the first protein to have its primary structure determined. Of humans has a primary structure that is similar to the insulin of pigs and cows.
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Secondary Structure: Alpha Helix

The secondary structures of proteins indicate the arrangement of the polypeptide chains in space. The alpha helix is a three-dimensional arrangement of the polypeptide chain that gives a corkscrew shape like a coiled telephone cord.

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Alpha Helix
The coiled shape of the alpha helix is held in place by hydrogen bonds between the amide groups and the carbonyl groups of the amino acids along the chain.
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Secondary Structure: Pleated Sheet

The pleated sheet: Holds proteins in a parallel arrangement with hydrogen bonds. Has R groups that extend above and below the sheet. Is typical of fibrous proteins such as silk.
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Secondary Structure: Triple Helix

A triple helix: Consists of three alpha helix chains. Contains large amounts glycine, proline, hydroxy proline and hydroxylysine that contain OH groups for hydrogen bonding. Is found in collagen, connective tissue, skin, tendons, and cartilage.

Essential Amino Acids

Essential amino acids: Are the ten amino acids that are not synthesized by the body. Must be obtained from the diet.

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Essential Amino Acids

Essential amino acids are: Found in milk and eggs (complete proteins). Not all found in grains and vegetables (incomplete proteins). Obtained by combining two or more vegetables that provide complementary proteins.
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Learning Check
Indicate the type of structure as: 1) primary 2) alpha helix 3) beta pleated sheet 4) triple helix A. Polypeptide chains held side by side by H bonds. B. Sequence of amino acids in a polypeptide chain. C. Corkscrew shape with H bonds between amino acids. D. Three peptide chains woven like a rope.
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Solution
Indicate the type of structure as: 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.
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Chapter 20 Amino Acids and Proteins

20.6 Protein Structure: Tertiary and Quaternary Structure 20.7 Protein Hydrolysis and Denaturation

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Tertiary Structure
The tertiary structure: Gives a specific overall shape to a protein. Involves interactions and cross links between different parts of the peptide chain. Is stabilized by Hydrophobic and hydrophilic interactions Salt bridges Hydrogen bonds Disulfide bonds
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Tertiary Structure

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Tertiary Structure
The interactions of the R groups give a protein its specific threedimensional tertiary structure.

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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Myoglobin
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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.

Learning check
Select the type of tertiary interaction as: 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

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Solution
Select the type of tertiary interaction as: 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

Quaternary Structure
The quaternary structure contains two or more tertiary subunits. Hemoglobin contains two alpha chains and two beta chains. The heme group in each subunit picks up oxygen for transport in the blood to the tissues.
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Summary of Structural Levels

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Learning Check
Identify the level of protein structure as: 1) Primary 2) Secondary 3) Tertiary 4) Quaternary A. B. C. D. E. Beta pleated sheet Order of amino acids in a protein A protein with two or more peptide chains The shape of a globular protein Disulfide bonds between R groups
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Solution
Identify the level of protein structure 1. Primary 2. Secondary 3. Tertiary 4. Quaternary A. 2 Beta pleated sheet B. 1 Order of amino acids in a protein C. 4 A protein with two or more peptide chains D. 3 The shape of a globular protein E. 3 Disulfide bonds between R groups
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Protein Hydrolysis
Protein hydrolysis: Splits the peptide bonds to give smaller peptides and amino acids. Occurs in the digestion of proteins. Occurs in cells when amino acids are needed to synthesize new proteins and repair tissues.

Hydrolysis of a Dipeptide
In the lab, the hydrolysis of a peptide requires acid or base, water and heat. In the body, enzymes catalyze the hydrolysis of proteins.
OH CH3 O CH2 O + H3N CH C N CH C OH H + H3N
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heat, + H2O, H OH

CH3 O CH COH

CH2 O + + H3N CH C OH
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Denaturation
Denaturation involves the disruption of bonds in the secondary, tertiary and quaternary protein structures. Heat and organic compounds break apart H bonds and disrupt hydrophobic interactions. Acids and bases break H bonds between polar R groups and disrupt ionic bonds. Heavy metal ions react with S-S bonds to form solids. Agitation such as whipping stretches chains until bonds break.
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Applications of Denaturation
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.
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Learning Check
What are the products of the complete hydrolysis of the peptide Ala-Ser-Val?

Solution
The products of the complete hydrolysis of the peptide Ala-Ser-Val are: alanine serine valine

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Learning check
Tannic acid is used to form a scab on a burn. An egg becomes hard boiled when placed in hot water. What is similar about these two events?

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

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