INTRODUCTORY PROTEOMICS

Structure and Chemistry of Amino Acids

Answer the following questions as instructed.

1. What are amino acids? Provide the two (2) organic groups shared among all amino acids.
Amino acid, any of a group of organic molecules that consist of a basic amino group
(―NH2), an acidic carboxyl group (―COOH), and an organic R group (or side chain) that is
unique to each amino acid. Amino acids are molecules that combine to form proteins. Amino
acids and proteins are the building blocks of life.

The α carbon, carboxyl, and amino groups are common to all amino acids, so the R-
group is the only unique feature in each amino acid.

2. What is the meaning of R group in an amino acid?

Every amino acid also has another atom or group of atoms bonded to the central atom known
as the R group. This R group, or side chain, gives each amino acid proteins specific characteristics,
including size, polarity, and pH.

3. Enumerate the 20 amino acids found in biological systems.

Essential amino acid: BCAA (valine, leucine and isoleucine), Lysine, Threonine, Phenylalanine,
Methionine, Histidine, Tryptophan Non-essential amino acid: Glutamine, Aspartate, Glutamate,
Arginine, Alanine, Proline, Cysteine, Asparagine, Serine, Glycine, Tyrosine.

4. Name all non-polar amino acids.

Nonpolar amino acids include alanine (Ala), leucine (Leu), isoleucine (Ile), proline (Pro),
tryptophan (Trp), valine (Val), phenylalanine (Phe), and methionine (Met).

5. Name all polar amino acids.

The polar group consist of 10 amino acids, two are negatively charged - aspartic acid and
glutamic acid, 3 have a positive charge - arginine, lysine and histidine, and 5 are uncharged -
asparagine, glutamine, serine, threonine and tyrosine.

6. Name all acidic amino acids. Why are these amino acids more acidic than the others?

Two amino acids have acidic side chains at neutral pH. These are aspartic acid or
aspartate (Asp) and glutamic acid or glutamate (Glu). Their side chains have carboxylic acid
groups whose pKa's are low enough to lose protons, becoming negatively charged in the
process.

7. Name all basic amino acids. Why are these amino acids more basic than the others?
There are three amino acids that have basic side chains at neutral pH. These are
arginine (Arg), lysine (Lys), and histidine (His). Their side chains contain nitrogen and resemble
 ammonia, which is a base. Their pKa's are high enough that they tend to bind protons, gaining a
positive charge in the process.

8. Complete the following table

Amino Acid Name Three –letter Abbreviation Single-letter Abreviation

Glycine Gly G
Glutamic Acid Glu E
Asparagine Asn N
Aspartic Acid Asp D
Arginine Arg R
Tyrosine Tyr Y
Valine Val V
Tryptophan Trp W
Leucine Leu L

9. What is a peptide bond? Provide a general chemical reaction that forms the peptide bond.
A peptide bond also sometimes called eupeptide bond, is a chemical bond that is
formed by joining the carboxyl group of one amino acid to the amino group of another. A
peptide bond is basically an amide-type of covalent chemical bond. This bond links two
consecutive alpha-amino acids from C1 (carbon number one) of one alpha-amino acid and N2
(nitrogen number two) of another. This linkage is found along a peptide or protein chain.

During the formation of this bond, there is a release of water (H2O) molecules. A
peptide bond is usually a covalent bond (CO-NH bond) and since the water molecule is
eliminated it is considered as a dehydration process. Generally, this process occurs mostly
between amino groups.

Meanwhile, a peptide is a Greek word that means “digested”. A peptide is a short polymer of
amino acid monomers linked by an amide bond.

A peptide bond is formed by a dehydration synthesis or reaction at a molecular level. This

reaction is also known as a condensation reaction which usually occurs between amino acids.

As depicted in the figure given below, two amino acids bond together to form a peptide bond by
the dehydration synthesis. During the reaction, one of the amino acids gives a carboxyl group to
the reaction and loses a hydroxyl group (hydrogen and oxygen).
 The other amino acid loses hydrogen from the NH2 group. The hydroxyl group is substituted by
nitrogen thus forming a peptide bond. This is one of the primary reasons for peptide bonds
being referred to as substituted amide linkages. Both the amino acids are covalently bonded to
each other.

The newly formed amino acids are also called a dipeptide.

During the reactions that occur, the resulting CO-NH bond is the peptide bond, and the resulting
molecule is an amide. The four-atom functional group -C(=O)NH- is called an amide group or a
peptide group.

10. Why are the series of amino acids in protein important to the protein’s function?

Proteins are made up of hundreds or thousands of smaller units called amino acids, which are
attached to one another in long chains. There are 20 different types of amino acids that can be
combined to make a protein. The sequence of amino acids determines each protein’s unique 3-
dimensional structure and its specific function. Amino acids are coded by combinations of three DNA
building blocks (nucleotides), determined by the sequence of genes.

Proteins are distinguished from each other by the sequence of amino acids comprising them.
The sequence of amino acids of a protein determines protein shape, since the chemical properties of
each amino acid are forces that give rise to intermolecular interactions to begin to create secondary
structures, such as α-helices and β-strands. The sequence also defines turns and random coils that play
important roles in the process of protein folding.

Since shape is essential for protein function, the sequence of amino acids gives rise to all of the
properties a protein has. As protein synthesis proceeds, individual components of secondary structure
start to interact with each other, giving rise to folds that bring amino acids close together that are not
near each other in primary structureAt the tertiary level of structure, interactions among the R-groups of
the amino acids in the protein, as well as between the polypeptide backbone and amino acid side groups
play a role in folding.