CHAPTER 21: Amino Acids and

Peptides
General, Organic, & Biological Chemistry
Janice Gorzynski Smith

EDMAR S. AGUSTIN | MAEd-SCIENCE

 CHAPTER 21: Amino Acids and Peptides

Learning Objectives:
The 20 common, naturally occurring
Amino Acids
stereochemistry
acid/base chemistry
Peptides
Formation
N & C terminals
Smith, Janice Gorzynski. General, Organic,
2
& Biological Chemistry 2nd Ed.
Amino Acids Definition

All amino acids contain two functional groups—an

amino group (NH2) and a carboxyl group (COOH).

Amino acids differ in the R group bonded to the α carbon

Smith, Janice Gorzynski. General, Organic,

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& Biological Chemistry 2nd Ed.
Amino Acids Definition

All amino acids contain two functional groups—an

amino group (NH2) and a carboxyl group (COOH).

Amino acids differ in the R group bonded to the α carbon

Smith, Janice Gorzynski. General, Organic,

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& Biological Chemistry 2nd Ed.
Amino Acids Definition

All amino acids have common names, which are

abbreviated by a three-letter or one-letter designation.

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& Biological Chemistry 2nd Ed.
The 20 common &
naturally
occurring amino
acids in humans.

Essential Amino Acids:

Isoleucine (Ile)
Leucine (Leu)
Methionine (Met)
Phenylalanine (Phe)
Threonine (Thr)
Tryptophan (Trp)
Valine (Val)
Arginine (Arg)
Histidine (His)
Lysine (Lys)

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 Amino Acids Stereochemistry

• Carbohydrates: naturally occurring isomer is the D-

isomer (OH group on right in a Fischer projection)

• Amino Acids: most naturally occurring isomers are the L-

isomer (NH3 group on the left in a Fischer projection)
Smith, Janice Gorzynski. General, Organic,
7
& Biological Chemistry 2nd Ed.
 Amino Acids Stereochemistry

• Carbohydrates: naturally occurring isomer is the D-

isomer (OH group on right in a Fischer projection)

• Amino Acids: most naturally occurring isomers are the L-

isomer (NH3 group on the left in a Fischer projection)
Smith, Janice Gorzynski. General, Organic,
8
& Biological Chemistry 2nd Ed.
 Amino Acids Stereochemistry

• Carbohydrates: naturally occurring isomer is the D-

isomer (OH group on right in a Fischer projection)

• Amino Acids: most naturally occurring isomers are the L-

isomer (NH3 group on the left in a Fischer projection)
Smith, Janice Gorzynski. General, Organic,
9
& Biological Chemistry 2nd Ed.
 Amino Acids At isoelectric pH

• The isoelectric point for amino acids is about 6, this is

the pH at which the amino acid exists as a neutral
molecule
• The pKa of the amine group is usually about 9-11
• The pKa of the carboxylic acid group is usually about 2-3
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& Biological Chemistry 2nd Ed.
Amino Acids Acid/Base Chemistry

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& Biological Chemistry 2nd Ed.
Amino Acids Acid/Base Chemistry

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& Biological Chemistry 2nd Ed.
Peptides Definition

•Peptides and proteins are formed when amino

acids are joined together by amide bonds.

•A dipeptide has two amino acids joined together

by one amide bond.

•The amide bond is called

a peptide bond.
•Individual amino acids are
called amino acid residues.

•Polypeptides have many amino acids, while

proteins have more than 40 amino acids.
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& Biological Chemistry 2nd Ed.
Peptides Amide Bond Formation

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& Biological Chemistry 2nd Ed.
Peptides Amide Bond Formation

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& Biological Chemistry 2nd Ed.
Peptides Amide Bond Formation

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& Biological Chemistry 2nd Ed.
Peptides N & C Terminal Amino Acids

•The amino acid with the free –NH3+ group is the

N-terminal amino acid and is written on the left.

•The amino acid with the free –COO− group is the

C-terminal amino acid and is written on the right.

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& Biological Chemistry 2nd Ed.
 Peptides Naming Peptides

•Name the C-terminal amino acid using its common name.

•Name all other amino acids from left to right as
substituents of the C terminal amino acid.

•Change the –ine or –ic acid ending of amino acid

name to the suffix –yl.

Smith, Janice Gorzynski. General, Organic,

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& Biological Chemistry 2nd Ed.
Peptides Naming Peptides

• The peptide can be abbreviated by writing the one-

or three- letter symbols for the amino acid in the
chain from N-terminal to the C-terminal.

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& Biological Chemistry 2nd Ed.
 Peptides/Prote
Insulin
in
Gly-Ile-Val-Glu-Gln-Cys-Cys-Thr-Ser-Ile-Cys-Ser-Leu-Tyr-Gln-Leu-Glu-Asn-Tyr-Cys-R

Phe-Val-Asn-Gln-His-Leu-Cys-Gly-Ser-His-Leu-Val-Glu-Ala-Leu-Tyr-Leu-Val-Cys-Gly-
Glu-Arg-Gly-Phe-Phe-Tyr-Thr-Pro-Lys-Thr-R’
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& Biological Chemistry 2nd Ed.
Proteins Primary Structure

The primary structure of a protein is the sequence

of amino acids joined together by peptide bonds.

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& Biological Chemistry 2nd Ed.
 Proteins Secondary Structure
•The secondary structure is the 3D arrangement of localized regions of a
protein.
•These regions arise due to hydrogen bonding between the N—H group
of one amide with the C═O group of another.

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& Biological Chemistry 2nd Ed.
Proteins Secondary Structure

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& Biological Chemistry 2nd Ed.
 Proteins Tertiary Structure

The tertiary structure is the 3D shape adopted by the entire

peptide chain:
• Maximize Hydrogen bonding with water (hydrophilic)
• Stabilize non-polar sidechains by london dispersion forces
(hydrophobic)
• Polar functional groups H-bond with each other
• Charged sidechains attracted through electrostatic interactions
• Disulfide bonds form

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& Biological Chemistry 2nd Ed.
Proteins Tertiary Structure

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& Biological Chemistry 2nd Ed.
 Proteins Quaternary Structure

The quaternary structure of the protein is the shape

adopted when two or more folded poly-peptide chains come
together into one complex. Ex: Potassium Channel:

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& Biological Chemistry 2nd Ed.
Proteins Quaternary Structure

Hemoglobin

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& Biological Chemistry 2nd Ed.
Proteins Quaternary Structure

Hemoglobin

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& Biological Chemistry 2nd Ed.
Proteins 1°, 2°, 3°, 4° Structure

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& Biological Chemistry 2nd Ed.
 Proteins Peptide Hydrolysis

Protein hydrolysis involves breaking the peptide bonds by

treatment with aqueous acid, base, or certain enzymes: Pepsin
(gastric juices), Trypsin and Chymotrypsin (intestines)

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& Biological Chemistry 2nd Ed.
 Proteins Peptide Denaturation

Denaturation is the process of altering the shape of a protein

without breaking the amide bonds that form the primary
structure: heat, acid, base, or agitation

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& Biological Chemistry 2nd Ed.
 Enzymes Definition

Enzymes are proteins that serve as biological catalysts

for reactions in all living organisms.
• They increase the rate of a reaction (106 to 1012 times faster),
but are unchanged themselves.
• Enzymes are very specific; each enzyme catalyzes a certain
reaction or type of reaction only.
• The names of most enzymes end with the suffix “-ase” like
peptidase, lipase, and hydrolase
• A cofactor is a metal ion or an organic molecule needed for an
enzyme-catalyzed reaction to occur.

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& Biological Chemistry 2nd Ed.
Enzymes Function

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http://leavingbio.net/enzymes.htm
 Enzymes Conformational Changes Upon Binding

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http://plantcellbiology.masters.grkraj.org/html/Plant_Cell_Biochemistry_And_Metabolism1-Proteins_And_Enzymes.htm
 Enzymes Inhibition

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http://o.quizlet.com/i/WRLW8kdWLDOY1YZbEdKgyA_m.jpg
 Enzymes HIV Protease Inhibitor
Protease inhibitors are designed to
mimic a peptide linkage (-NH-CO-)
but replaces the linkage with a
–CH2-CH(OH)- which binds to the
active site but the protease cannot
cleave a linkage so it stays bound.
Saquinavir:

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http://en.wikipedia.org/wiki/Discovery_and_development_of_HIV-protease_inhibitors
 Enzymes Lipoxygenase Inhibitor

Zileuton is an asthma maintenance

medication that inhibits 5-lipoxygenase,
therefore, inhibiting leukotriene
formation.

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http://en.wikipedia.org/wiki/Zileuton
 Enzymes Differences in Binding Sites

Superoxide Dismutase: SOD Superoxide Reductase: SOR

Hydrophobic Binding Pocket Hydrophilic Binding Pocket
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& Biological Chemistry 2nd Ed.
 Enzymes Mechanistic Differences: SOR vs SOD

OH
NHis

O2 - OAsp FeIII O2- H+

NHis O2
NHis
SOD Mechanism
OH OH2
NHis NHis
OAsp FeIII OAsp FeII

NHis
NHis NHis SOR Mechanism
NHis

OH2 O2 -
HOOH NHis H2O
H+ 2H+ OAsp FeII O2-
NHis
NHis
* O2- hydrogen bonds to residues in secondary
coordination sphere, positioning it near Fe(II),

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& Biological Chemistry 2nd Ed.
Enzymes Zymogens

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& Biological Chemistry 2nd Ed.