Yuan Provido

Chem 2065 AY2022-23

03 Amino Acids and Peptides

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 amino acids has four different groups bonded to it’s a-
carbon, this conveys the three-dimensional structure of the amino acids, or the
stereochemistry. The R group, within the structure, determines the identity of the particular
amino acid, except when the R group is also a hydrogen group, like in the case of glycine.
Since there are four different groups connected to a tetrahedral carbon, then the particular
carbon atom is chiral, nonsuperimposable mirror images are said to be chiral. In the case
of glycine, it is not chiral, it is however achiral, the R group of glycine is also a hydrogen
group, it is differentiated through the placement of the hydrogen group, and labelled as l-
glyceraldehyde if placed the left, and d-glyceraldehyde if placed on the right. The chain of
amino acids determines the shape of protein, The sequence of amino acids defines the turns
and random coils that play important roles in the process of protein folding.

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)

Each of the common amino acids are similar in the way that it has four groups
connected to it’s a-carbon, the amino group, the carboxyl group, the hydrogen group, and
the side chain group or R group. Each common amino acid has a different compound for
their side chain group or R group.
Amino acids with
non-polar side chain
group
Alanine Small Aliphatic

Isoleucine Large Aliphatic

Leucine Large Aliphatic

Valine Medium Aliphatic

Proline Medium Aliphatic

Phenylalanine Large Aromatic

Tryptophan Large Aromatic

Methionine Large Aromatic

Amino acids with

electrically neutral
polar side chain
group
Cysteine Medium

Glutamine Large

Tyrosine Large Aromatic

Serine Small Aliphatic

Threonine Medium Aliphatic

Asparagine Medium Aliphatic

Glycine Small Aliphatic

Amino acids with

carboxyl groups in
their side chain
group
Aspartic acid Medium

Glutamic acid Large

 Amino acids with
basic side chain
group
Arginine Large Aliphatic

Histidine Large Aromatic

Lysine Large Aliphatic

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?)

Uncommon amino acids are uncommon because of their side chain group, or R
group, they are not constituents of proteins. For example, hydroxyproline and
hydroxylysine differ from the parent amino acids in that they have hydroxyl groups on their
side chains, while Thyroxine differs from tyrosine in that it has an extra iodine-containing
aromatic group on its side chain.
The relationship between the common and the uncommon amino acids is that
uncommon amino acids are derived from the 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 modification, just like hydroxyproline and hydroxylysine
they are found in a few connective-tissue proteins, such as collagen.

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 chemical structure and properties of amino acid’s side chains is vital to protein
structure because the side chains are able to bond with one another to hold a length of
protein in certain shapes and conformations.
The intermolecular force of attraction that each individual amino acid would most
likely to participate in are the following: Ionic bonding - Ionic bonds can be important to
 protein structure because they are potent electrostatic attractions. Hydrogen bonding - A
hydrogen bond is mainly formed between a donor atom such as an amine, which acts as a
ligand, or a Lewis base and acceptor atom like carboxylic acid. Van der Waals forces - Van
der Waals forces are also similar to electrostatic bonds. The formation of Van der Waals
forces depends on the shape of the side-chain; if the atoms within the side-chains of
neighboring amino acids fit well, then Van der Waals force is formed.

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?)

In the neutral form the pH levels are not low and high, this gives the amino acid a
net charge of 0, this means that it has a combination of a positive and a negative charge.
While in the cationic form the pH levels are low, the carboxylate group receives a hydrogen
ion.
The 2.34 pKa indicates an equilibrium within the carboxylic acid group, this then
shows the presence of a carboxylic acid group and an ammonium group. While the 2.3 pH
shows that there are equal concentrations of acid and base form.

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

Peptide bonds are formed by a dehydration reaction or synthesis because when a

carboxyl group of one molecule reacts with an amino acid and releases a molecule of water,
 this is how a peptide bond is formed between amino acids. This reaction is also known as
a condensation reaction which usually occurs between amino acids.

7. Illustrate how polypeptides are formed (Be able to draw oligopeptides of a specified
sequence from N-terminal to C-terminal)

8. Cite properties of amino acids aside from being peptides or proteins (neurotransmitters and
others)

One of the properties of amino acids aside from being peptides or proteins is it
serves as a neurotransmitter. Amino acids function as precursors of neurotransmitters,
especially in the brain. We hypothesized that a low protein diet (LPD) leads to low
concentrations of EAAs in the plasma and brain, resulting in a depletion of
neurotransmitters in the brain.

9. Showcase the functions of some small peptides with physiological activity (hormones and
others)
 Oxytocin which is a peptide hormone help induces labor in pregnant women and
controls contraction of uterine muscle. During pregnancy, the number of receptors for
oxytocin in the uterine wall increases. Oxytocin plays a significant role in stimulating the
flow of milk of a nursing mother. During the suckling oxytocin is then released and carried
by the blood to the mammary glands, The presence of oxytocin causes the smooth muscle
in the mammary glands to contract, forcing out the milk that is in them.
There is also the vasopressin which is in charge of the control of blood pressure by
regulating contraction of smooth muscle.