LICYAYO, MICHEL PAULETTE

Chem 2065 AY2022-23

03 Amino Acids and Peptides

The objectives of this chapter are to

1. Correlate the three-dimensional structure of amino acids to its interactions to its

chiral environment ( Be sure to be able to visualize the three-dimensional picture
of the amino acids. Recall the Fischer projection structure from your organic
chemistry)

The general structure of an amino acid includes an AMINO GROUP and a CARBOXYL
group (which are bonded to an α-carbon), HYDROGEN, and a SIDE CHAIN GROUP
(R). Fischer projection is a projection of a three-dimensional organic molecule into a
two-dimensional form. The most important properties of amino acids is their 3-D shape,
or stereochemistry.

Chiral – a type of molecule having non-superimposable mirror images or not mirror

images of one another.
Achiral –molecules having superimposable with their mirror images.

All amino acids discussed in the chapter have a chiral center except for glycine. The
chiral center allows stereoisomerism, meaning that there are two non-superimposable
mirror images of each other. The mirror-image forms are termed L (Left) and D (Right)
amino acids where the amino group’s position with respect to the α-carbon determines
the L and D designation.

L- amino acids are the ones that occur in all proteins while D-amino acids occur in
nature.

2. Classify the twenty (20) common amino acids according to their polarity and acid-
base properties (What makes the 20 common amino acids 'common'? Be sure to
be able to visualize the three-dimensional picture of the amino acids. In addition
to the four classic classifications, be sure to know which ones are large, small,
aromatic)

The twenty (20) common amino acids according to their polarity and acid-base
properties are:

A. NONPOLAR (HYDROPHOBIC)
- group of amino acids that has non-polar side chains.
- side chains are usually aliphatic or aromatic hydrocarbons
LICYAYO, MICHEL PAULETTE
Chem 2065 AY2022-23

• Methionine
• Leucine
• Tryptophan
• Proline
• Phenylalanine
• Alanine
• Isoleucine
• Valine
• Glycine
B. POLAR, UNCHARGED
- amino acids have polar side chains that are electrically neutral or uncharged at
neutral pH.
- have side chains that contain electronegative atoms such as O, N, and S.
- side chain group is hydrophilic.
• Threonine
• Serine
• Cysteine
• Asparagine
• Tyrosine
• Glutamine
C. ACIDIC
- have carboxyl groups in their side chains
• Aspartic acid
• Glutamic acid
D. BASIC
- have basic side chains , and their side chain is positively charged at or nearly
neutral pH level.
• Histidine
• Lysine
• Arginine

The 20 common amino acids are "common" because they are proteinogenic in
nature. This indicates that they are "protein generating" or that during translation, they
are biosynthesized into proteins. These amino acids are naturally found in the genetic
code.
LICYAYO, MICHEL PAULETTE
Chem 2065 AY2022-23

3. Point out some of the uncommon amino acids (What makes them uncommon?
What's the relationship between the common and the uncommon amino acids?)

Some examples of uncommon amino acids are hydroxylysine and hydroxyproline.

Uncommon amino acids occur in some, not all, proteins. They are derived from
common amino acids and are produced by modification of the parent amino acid
after the protein is synthesized by the organism in a process called posttranslational.
Hydroxylysine and hydroxyproline differ from their parent amino acid as they have
hydroxyl groups on their side chain.

4. Emphasize the importance of the properties of the side-chains of the amino acids
(Be able to point out the most likely intermolecular force of attraction that each
individual amino acid would participate in)

The identities of amino acids are based on its side chain or R group. As
discussed in no. 2, amino acids that contain hydrocarbon as their side chain are
non-polar, while those with hydrophilic side chains such as hydroxyl, sulfhydryl,
or phenolic groups are polar. Amino acids can be acidic when their side chains
contain carboxyl group, and basic when their side chains contain an amine group
respectively.

5. Illustrate the acidic and the basic properties of amino acids (Be able to write the
acid-base reactions of individual amino acids. (Account for the charges of the
amino acids as a function of the pH. What is the significance when the pH of the
solution is equal to the pKa of that amino acid?)
LICYAYO, MICHEL PAULETTE
Chem 2065 AY2022-23

• The basis to identify whether an amino acid is acidic or basic is the pKa of the R
group or the side chain and the chemical nature of the group. When in neutral pH
of free amino acid, the carboxylate group is negatively charged (acidic) while the
amino group is positively charged (basic).
• When the pH is higher than pKa (pH > pKa), it means that the functional group of
the amino acid is deprotonated, and when pH is lower than pKa (pH < pKa), the
functional group is protonated. But when pH of the solution and the pKa of amino
acid is equal (pH = pKa), it means the functional group is 50% protonated and
deprotonated.

6. Describe the nature of the peptide bond as it is formed from amino acids

When an α-carboxyl group of one amino acid and the α-amino group of the other
amino acid covalently bonds, it forms a peptide bond or also called an amide bond.
During this process, water is lost, and residues of the linked amino acid remain. A
bond formed in this way is called peptide bond.
LICYAYO, MICHEL PAULETTE
Chem 2065 AY2022-23

The peptide bond has partial double bond characteristics. As a result, the peptide
group that forms the link between the two amino acids is planar. Because of this
resonance stabilization, the peptide bond is also stronger than an ordinary single
bond.

7. Illustrate how polypeptides are formed (Be able to draw oligopeptides of a

specified sequence from N-terminal to C-terminal)

Polypeptides - A peptide consisting of 2 or more amino acids. Amino acids make

up polypeptides, which in turn make up proteins.
LICYAYO, MICHEL PAULETTE
Chem 2065 AY2022-23

8. Cite properties of amino acids aside from being peptides or proteins

(neurotransmitters and others)

The acidic amino acid glutamate plays a significant role in mediating excitatory
transmission (the generation of EPSPs). Gamma-aminobutyric acid (GABA), a
metabolite of glutamate, and glycine in the spinal cord and brain are the main
mediators of inhibitory neurotransmission (IPSPs).

9. Showcase the functions of some small peptides with physiological activity

(hormones and others)

Some functions of some small peptides with physiological activity are oxytocin
and vasopressin. Oxytocin induces labor in pregnant women and controls
contraction of uterine wall, and it also plays a role in stimulating the flow of milk in
lactating mothers. Vasopressin plays a role in controlling blood pressure. Another
example is insulin which maintains the glucose level in the body by converting it
into energy.