LICEO DE CAGAYAN UNIVERSITY

COLLEGE OF MEDICINE
BIOCHEMISTRY 1ST BIMONTHLY
AUGUST 11, 2020

Fernandez, Ann Ross L. 20200733258

WATER, ACIDS, BASES AND BUFFERS

LEARNING OBJECTIVES:

1. Define the following:

1.1. Dipoles – A dipole is a molecule which has an electrical charge that is unequally or
assymetrically distributed.
1.2. Hydrogen bond – A hydrogen bond is “formed” when one Hydrogen atom is covalently bound
to an Oxygen or Nitrogen atom, and interacts with an Oxygen or Nitrogen atom of another
molecule. This bond is a weak noncovalent interaction.
1.3. Covalent bond – A covalent bond is formed when two atoms share electrons.
1.4. Noncovalent bond – A noncovalent “bond” involves the interaction of molecules/ions without
sharing their electrons (Raymond, 2006, p. 108). These interactions may either be attractive
or repulsive. An example of a noncovalent bond is the hydrogen bond.
1.5. Nucleophile – A nucleophile is a chemical group that is rich in electrons, and is thus attracted
to a positively charged nucleus (Lieberman & Peet, 2015, p.86).

2. Describe the properties of water that account for its surface tension, viscosity, liquid state at
ambient temperature and solvent power.
The properties of water that make it a “universal solvent” include its being a dipole and its ability to
form hydrogen bonds. Through its hydrogen bonds, water molecules are able to self-associate
into oredered arrays, contributing to its surface tension. Hydrogen bonds are also relatively weak
and transient which contributes to its high viscosity and allowing movement of water and solutes.
Because of water’s strong dipole, it also has a high dielectric constant (water decreases the force
of attraction between charged and polar species) which enables water to dissolve large quantities
of charged compounds. Aside from this,the hydrogen bonds present in water also enables water
to dissolve organic molecules which contain functional groups that can participate in hydrogen
bonding.
3. Explain the role played by entropy in the orientation, in an aqueous environment of the polar and
nonpolar regions of macromolecule.
The second law of thermodynamics states that in all natural processes, the total entropy of a
system always increases (Lieberman & Peet, 2015, p. 244). When a hydrophobic group is
adjacent to a water molecule, it decreases or restricts the degrees of freedom (entropy). To
reduce the number of water molecules (with restricted degrees of freedom), nonpolar molecules
tend to form droplets that minimize the exposed surface area. In living cells, the hydrophobic
portions of biopolymers tend to be buried inside the structure of the molecule to minimize contact
with water. Similarly to maximize enthalpy (energy) the polar regions of a biopolymer make
contact with water through hydrogen bonds.

4. Indicate the quantitative contributions of salt bridges, hydrophobic interactions and van der Waals
forces to the stability of macromolecules.
Electrostatic interactions or salt bridges contribute to the stability of macromolecules by having
interactions between oppositely charged groups over large distances. Hydrophobic interactions
refer to the tendency of nonpolar compounds to self-associate in an aqueous environment. Thus,
the polar regions come into contact with water while nonpolar regions of the compound is buried
inside the structure of the molecule (e.g. nonpolar nucleotide bases in DNA). Van der Waals
forces contribute to the stability of macromolecules through transient or temporary dipoles. As
molecules or atoms decrease their distance from each other, their attraction increases until they
reach the van der Waals contact distance and get separated due to the repulsion of their electron
clouds. These forces all contribute to the stabilization of biomolecules such as in DNA.
5. Explain the relationship of pH to acidity, alkalinity and the quantitative determinants that
characterize weak and strong acids.
When we refer to pH, it is the negative logarithm of the hydrogen ion concentration [H +]. A high pH
value corresponds to low hydrogen ion concentration (more basic; more alkaline). A low pH value
corresponds to high hydrogen ion concentration (more acidic).

The pH can also be used to look for the hydrogen ion concentration of acids. However, since
many biochemicals are weak acids, instead of using the ion product for water, we use the
dissociation constant (Ka). The result is the pKa which expresses the relative strengths of both
acids and bases (conjugates). The pKa reflects the strength of an acid. Acids with a pK a of 2 are
stronger acids than those with a pKa of 5 because, at any pH, a greater proportion is dissociated.

6. Describe what buffers do, how they do it, and the conditions under which a buffer is most effective
under physiologic or other conditions.
A buffer is a mixture of an undissociated acid and its conjugate base. It resists changes in pH
when either H+ or OH- is added. A solution of a weak acid and its conjugate base buffers most
effectively in the pH range pKa +/- 1.0 pH unit.
7. Define and illustrate how the Henderson-Hasselbalch equation can be used to calculate the net
charge on a polyelectrolyte at a given pH.
The Henderson-Hasselbalch equation defines the relationship between the pH of a solution, the
Ka of an acid, and the extent of the acid dissociation. Derived from the equilibrium constant for
dissociation, the equation is pH = pKa – log [HA]/[A-]. Using the equation, if an acid is half-
neutralized, it can be said that the pH = pKa. If we plot this in a titration curve, the the point of its
pKa also gives us the net charge. This net charge indicates the probability of a given molecule to
have a unit positive/negative charge at any given moment in time.
8. Identify the relative strengths of selected acids of biologic significance.
Normal metabolism generates metabolic acids (lactate, ketone bodies), inorganic acids (sulfuric
acid, hydrochloric acid), and carbon dioxide.

Some of these acids can donate or give more than one hydrogen ion [H + ] (e.g. diprotic acids can
donate two hydrogen ions, triprotic acids can donate three hydrogen ions). With every successive
donation of hydrogen ion by an acid, we can see that its pKa increases.

Since we know that pKa is related to Ka (dissociation constant) in a similar way as pH is related to
the hydrogen ion concentration [H+], the lower the pKa value, the stronger the acid. The reverse is
also true: the higher the pKa value, the weaker the acid.

The following table lists the pKa (expressing the relative strength of weak acids) of some of the
aforementioned acids:

1st ionization 2nd ionization 3rd ionization

Lactic acid (C3H6O3 ) pKa = 3.86
Acetic acid pKa = 4.76
(CH₃COOH)
Ammonium ion (NH₄⁺) pKa = 9.25
Carbonic acid (H2CO3 ) pKa = 6.37 pKa = 10.25
Succinic acid pKa = 4.21 pKa = 5.64
((CH₂)₂(CO₂H)₂)
Glutaric acid pKa = 4.34 pKa = 5.41
(C₃H₆(COOH)₂)
Phosphoric acid pKa = 2.15 pKa = 6.82 pKa = 12.38
(H3PO4 )
Citric acid pKa = 3.08 pKa = 4.74 pKa = 5.40

9. Analyze and interpret the components of arterial blood gases.

Some of the components of arterial blood gas include partial pressure of CO 2 (PaCO2 measured
in mmHg), bicarbonate (HCO3-), and pH. In relation to acid-buffer systems, the bicarbonate buffer
system is one important system for modulation of rapid changes in pH.

In the example in one of the references (i.e. Mark’s Essentials), the patient was diabetic and was
not able to inject the right amount of insulin. The patient’s elevated levels of ketone bodies
 (considered weak acids) resulted to an increase in [H +] and lowering of pH (becoming more
acidic).

A drop in pH elicits an increase in rate of breathing. Bicarbonate (buffer) combines with protons,
producing carbonic acid (H2CO3 ), while lowering bicarbonate levels. The H 2CO3 is converted to
CO2 and H2O, which increases the CO2 concentration (see reaction below). However, this
increase in the CO2 concentration leads to an increase in the respiratory rate, causing a fall in the
partial pressure of arterial CO2 (PaCO2). The patient’s PaCO2 was 28mmHg (reference range of 37
to 43) and her bicarbonate level was 8mEq/L (reference range of 24 to 28). Her low arterial blood
pH of 7.08 tells us that the patient’s deep breathing was unable to fully compensate for the high
rate of acidic ketone body production.

REFERENCES:
Harper’s Illustrated Biochemistry 31ST edition
Lieberman, M., & Peet, A. (2015). Marks’ Essentials of Medical Biochemistry (2nd edition).
Philadelphia, PA: Lippincott Williams & Wilkins.
Raymond, K. (2006). General, Organic, & Biological Chemistry: An integrated approach (2nd edition).
Hoboken, New Jersey: Wiley.