Ionization of Biological Molecules

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Ionization of Biological Molecules
This tutorial extends the concepts of
acid-base chemistry by showing that H, i.e.,
the pH of a solution, affects biological
functions by regulating the ionization of
biological molecules. Ionization of organic
molecules feeds into many aspects of biological
phenomena. Amino acids must have a neutral
charge in order to penetrate cell membranes.
Protein structure is stabilized by close
proximity of positive and negative charges on
neighboring amino acid side chains. Nucleic
acids derive their acid character from ionized
phosphate groups. Fatty acids acquire their
property as detergents by ionization of carboxyl
groups. The concept of ionization is vast and
encompasses all the categories of biomolecules.
In this tutorial we will focus on molecules whose
positive or negative character, indeed
biochemical properties, depend on pH.
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What is Ionization?
Ionization refers to creating positive and
negative charges on molecules. Negative charges
arise by dissociating protons from groups bearing
oxygen or sulfur atoms (click 1). Positive
charges are created by acquiring protons on
groups containing nitrogen (click 1). With the
exception of phosphate, all the groups shown are
present in amino acids. It will be to your
advantage to know these groups for future
reference.
Click to go on
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pK and Ionization
The pK of an acid or ionizable group gauges when
a proton will be picked up or released by the
group. By definition, the pK is the value for the
pH when half of the total are protonated, which
of course, infers half-ionized. To illustrate,
consider the ionization of a carboxyl group
(click 1). When pH pK, half the molecules are
R-COOH and the other half are R-COO-. Acidic
protons are displaced by water molecules. Because
the reaction is reversible, dissociation will
depend on the H in solution (click 1).
Enhancing H suppresses dissociation by forcing
the equilibrium to the left, which essentially
cancels the ionization of the acid. A strong acid
requires a very high H concentration to shift
the equilibria, whereas a weak acid (strong base)
requires a relatively low proton environment
(click 1). Remember, the greater the H the
greater the hydrogen ion pressure, the more the
proton is on. This explains why strong acids have
pK values well into the acidic range and weak
acids have very high (basic) pK values (click 1)
Dont mistake the meaning. Of this diagram. It
is intended to show that a greater H environment
is needed to suppress the negative charge on a
strong acid, less so for a weak acid. Spoken
this way helps you see how values for pK are
derived. Click to go on
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Basic Groups
The ionization of a basic group is basically the
same with the exception that when a proton
associates with the group, the group acquires a
() charge. Typical of this are when protons
associate to ionize amino groups (click 1).
Because amine groups tend to be strong bases
(weak acids), to dissociate a proton from a
charged amine, i.e., force the equilibrium above
to the left, requires a very low hydrogen ion
pressure (click 1). As the proton dissociates
the group loses its () charge. As before, H2O
and the amine group compete for the proton (click
1). Dissociation will occur only when H
(H3O)is practically nil, i.e., at very high pH.
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pH and Ionization
In the discussion of pK, you may have noticed
the words half-protonated, half-ionized in the
description. What do we mean by half. The
answer is of the total population of molecules
only one-half bear a charge not that all the
molecules are charged to half power. This is
important because (1) a single molecule has
either a full charge or no charge and (2) the
degree of ionization is a function of numbers of
charged molecules. To appreciate how numbers
change, consider the reaction of a weak acid with
NaOH (click 1). Changes are best seen as a
titration curve that is generated for the
reaction (click 1). Important points to note on
the curve are the midpoint and the extremes. As
the curve goes from left to right, more ionized
molecules appear.
Ionized
Non-ionized
Half Ionized 50
At the start of the titration, no molecules are
ionized. At the midpoint half are, and at the
end all molecules are ionized. Note that for a
given pH it is possible to determine the ratio of
ionized to non-ionized (click 1), in essence the
ratio of salt to acid. Click to go on
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Multiple Ionizable Groups
Molecules with more than one ionizable group are
common in biochemistry. A typical amino acid at
pH 7, for example, has two charged groups a ()
amine group and a () carboxyl group (click 1).
Molecules with multiple groups are handled as if
each group acts independently. For example, an
amino acid with an ?-carboxyl and ?-amino group
has 2 plateaus in a titration curve (click 1).
On a pH scale, they are 7.5 units apart. There
are 3 ionized species present as 2 conjugate
pairs (click 1). Note that the middle component
is both an acid and a base.
Review the lessons in this tutorial as often as
necessary to understand ionization or click to
test and extend your knowledge.
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Test and Extend Your Knowledge of Ionization
Q What structural feature is common to positive
charged nitrogen groups?
A All have 4 bonds to the nitrogen.
Q Based on the discussion of ionization as a
function of numbers, what would be the net charge
on acetate when the pH pK? pH 10 x pK?
A The net charge would be negative. At 10
times pK the charge will still be negative, but
instead of half, 90.9 of the total number of
molecules would bear this charge.
Q How does knowledge of a pK value allow one to
tell if a group is ionized?
A For a monoprotic (one proton) acid, you may
consider the pK as the point of neutrality. When
the value for pK equals the pH there are equal
numbers of charged and uncharged molecules. Any
pH above the pK is conducive to removing protons,
any below favors more molecules with protons on.
Q How does one evaluate the charges on a
molecule when there is more than one ionizable
group?
A More than one ionizable group means more than
one pK. The net charge will depend on what is
called the isoelectric point or pI. The pI
must be calculated by taking the sum of 2 pKs and
dividing by 2. Any pH above pI is conducive to
giving a majority of the molecules a negative
character pH below pI gives a positive
character. (See you textbook for a more detailed
discussion of isoelectric point).