A.

IONIZATION OF AMINO ACIDS AND PEPTIDES

- Amino acids

​The Standard Amino Acids have both carboxyl group (-COOH) and amino group
(-NH2) in one molecule. We learned in organic chemistry that –COOH is an
acidic group while –NH2 is a basic group.

Here in this image, we can see the difference between a non-ionized and ionized
form of an amino acid. To be able to differentiate both non ionized and ionized, is
that in non ionized shows or has negative and positive charges on the structure.

(Gen structure for both ionized and non…makita kay theres is negative and
positive charges on the structure)

Each amino acid has at least one ionizable amine group (a- amine) and one
ionizable carboxyl group (a- carboxyl). When these are bound in a peptide bond,
they no longer ionize. Some, but not all amino acids have R-groups that can
ionize.
 Ionization of Peptides
(remember these terms…)
Protonation- accept
Deprotonation - removes or removal

Each peptide will exist in different protonated forms, depending on the pH and its
amino acid composition.
- Terminal amino and carboxyl groups can be protonated/ionized as in the
free amino acid;
- The side chain can also be ionized, if an appropriate group is present;
- The NH2 and COOH groups that are part of the peptide bond are NOT
ionized.

A peptide is a chain of amino acids that is formed when the carboxyl group of the
α-carbon of an amino acid reacts with the amino group of the α-carbon of the
second amino acid.

The bond formed in this reaction is generally an amide bond. However, for
peptide proteins, the bond is called a peptide bond.

So let’s have an example:

Alanine
 This is an example of Alanine which is a type of non essential amino acids.

Kanang middle keike: as you can see in the middle it's what we call zwitterion,

Both left and right we can see a structured form of alanine once placed in
different environments.
On the left, this is alanine on an acidic solution
On the right is alanine in a basic solution.

(before we proceed to the 2nd objective ill be giving or briefly discussing terms or units that will
be used, and so that it will be easier to understand.)
Ionization of amino acids usually involves protonation or deprotonation to be able
to convert a neutral ionizable group into its ionic form.
● pKa - acid dissociation constant; pH at which the acid/acidic
group/ionizable undergo deprotonation.
● IF : pH < pKa : ionizable group is in protonated form
● pH ≥ pKa: ionizable is deprotonated form (deprotonation since pH is larger)

B. DISCUSS HOW TO DETERMINE THE pl, NET CHARGE IN A SPECIFIC pH

CONDITION, AND pH RANGE GIVEN THE CHARGE OR THE STRUCTURE OF
AMINO ACID OR PEPTIDE.
Next slide

● pH
○ Quantitative measure of the acidity or basicity of a liquid solution

● Net Charge
○ The net charge on the molecule is affected by the pH of its environment
○ Can become more positive or negative from the gain or loss of protons

● Isoelectric Point (pI)

○ The pH wherein a particular molecule carries no net electrical charge
○ pH where the net charge=0

● pKa
○ pKa is a number that describes the acidity of a particular molecule
 ○ The lower the value of pKa, the stronger the acid and the greater its ability
to donate its protons.
Next slide

At physiological pH (near neutral), carboxyl group (-COOH) has the tendency to lose a proton
(H+), producing a negatively charged conjugate base known as carboxylate.

In the same manner, amino group (-NH2) have the tendency to accept a proton (H+), producing
a positively charged conjugate acid known as quaternary ammonium ion.

Because of this acid-base property of the carboxyl and amino groups, in aqueous solutions, the
–COOH of the Standard Amino Acids is deprotonated while the –NH2 is protonated. We can
characterize this as an intramolecular acid-base reaction. When this happens, the
Standard Amino Acid assumes the structure:

This structure is known as the zwitterion form of a Standard Amino Acid. A zwitterion or
dipolar ion is a molecule having a positive charge on one side and negative charge on the
other. Take note that while a zwitterion has charged groups it is neutral molecule because the
number of groups with positive charge is equal to the number of groups with negative charge
resulting to zero net charge. In solid state, the standard amino acids exist as zwitterions.
Finding the Net Charge in a specific pH condition
Finding the pH range