Cebu Doctors’ University

College of Arts and Sciences

Physical Sciences Department

Unit 1 – FOUNDATIONS OF BIOCHEMISTRY

Compiled by: Joselito R. Tumulak Jr., RChT, MS (cand.)
Biochemistry Professor

INTENDED LEARNING OUTCOMES

At the end of this unit, you will be able to:
1. Explain the interdisciplinary and multidisciplinary nature of biochemistry, and its role to the medical
profession;
2. Describe how molecules that make up life are organized in the cell;
3. Describe the different properties of the 4 major classes of biomolecules, and how these properties
reflect their fitness to living conditions;
4. Explain the functions of the different organelles of the cells;
5. Explain similarity and difference between organic chemistry and biochemistry;
6. Illustrate structure of common organic compounds using expanded, condensed, and skeletal
structures;
7. Categorize different organic compounds based on functional groups;
8. Explain the importance of functional groups in predicting the physical properties of organic
compound;
9. Explain how the physical properties of water affect its role as the major biochemical solvent;
10. Classify substances as acids and bases based on the Bronsted-Lowry definition; and
11. Relate the chemistry of buffers to the buffering capacity of the blood.

UNIT OUTLINE
Topic Page
I. The Nature of Biochemistry 1
II. Cellular Foundation
A. The Molecular Organization of Life
3
B. The Biomolecules
C. The Cell
III. Chemical Foundation
A. The Origin of Organic Chemistry
B. Chemical Bonding 8
C. Bonding in Organic Compounds
D. Classification of Organic Compounds Based on Functional Groups
IV. Water as Biochemical Solvent
A. Physical Properties of Water 21
B. Acids, Bases, and Buffers

I. THE NATURE OF BIOCHEMISTRY

Why Biochemistry?

I often ask this question to my students every beginning of the semester, and I often get the same response:

“Because it is required.”

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You most likely got the same response to the question in the preceding activity. At first glance, it may seem
to be a flippant response. But I don't generally take offense, so instead I look into the underlying meaning
of it. The phrase "required" is actually a deep word which stresses the importance of biochemistry in your
field. It is not included in by the university for no reason. As medical students, you study the enhancement
of life through disease treatment, and there is no better way to grasp this than to study life at the molecular
level. That is the essence of biochemistry. Understanding health and disease at the molecular level allows
for more effective treatment of a wide range of disorders.

But if you are going to ask me the same question, “Why do I study biochemistry?”, my answer is very simple:

Why not?

Take a look around. See everything that is alive or was once alive around you? All of the biochemical
processes that allow them to develop, proliferate, age, and die are biochemical in nature. In truth, you are
a living being. Thus, studying biochemistry is like to figuring out who you are on a molecular level. So, why
don't we study biochemistry if it means getting to know ourselves better?

Biochemistry also makes us see how marvelous life could be. Sometimes, it is better to just sit back and
marvel at the complexity of life, the myriad of chemical reactions that are taking place right now within our
bodies, instead of stressing yourself in memorizing them. Appreciate the concepts. I encourage you to step
back from the complexities of biochemistry occasionally, and marvel at the beauty of life that you’ll only
realize when you study it. For example, when learning the chemistry of starch and cellulose, you may start
thinking: “Just that little difference in bonds between the structural unit of starch and cellulose is basically
the difference between a potato and a tree?” And this kind of curiosity and sense of wonder will wat you to
learn more, to delve into the complexity of life, to try to understand.

What is Biochemistry?

Now that we have a good reason to proceed in studying biochemistry, let us now learn what biochemistry
really entails.

Biochemistry is the study of the chemical substances found in living organisms and the chemical
interactions of these substances with each other. As biochemistry seeks to describe the structure,
organization, and functions of living matter in molecular terms, its study can be divided into three principal
areas:
1. Structural Biochemistry
- looks into the relationship of the molecular structure of biochemical substances to their biological
functions.
2. Metabolism
- studies the totality of chemical reactions that occur in living organisms.

3. Molecular Genetics
- seeks to understand the chemistry of the processes and substances that store and transmit
biological information.
- aims to understand heredity and the expression of genetic information in molecular terms.
Biochemistry is both a multidisciplinary and an interdisciplinary science. As a multidisciplinary science,
it draws on many disciplines and use their results to answer the questions about the molecular nature of
life processes. For example, the magnetic resonance imaging (MRI) tests originated with physicists, but
became a vital tool for chemists in biochemical research. As an interdisciplinary science, biochemistry
nourishes other disciplines. For example, understanding how proteins behave help us in understanding the
nature of a lot of diseases, such as Alzheimer’s disease and sickle cell anemia.

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Although biochemistry overlaps other disciplines, biochemistry is largely concerned with the following
issues:
1. What are the chemical and three-dimensional structures of biomolecules?
2. How do biomolecules interact with each other?
3. How do the cells synthesize and degrade biomolecules?
4. How is energy conserved and used by cell?
5. What are the mechanisms for organizing biomolecules and coordinating their activities?
6. How is genetic information, stored, transmitted, and expressed?

II. CELLULAR FOUNDATIONS

A. The Molecular Organization of Life

Examinations of the chemical composition of the cell reveal a remarkable variety of biomolecules covering
a wide range of molecular dimensions. However,
these molecular constituents of the cell do not
reflect randomly the infinite possibilities. Instead,
only a limited set of the many possibilities is found,
and these collections share certain properties
essential to the establishment and maintenance of
the living state. The biomolecules are built
according to a structural hierarchy: Simple
molecules are the units for building complex
structures. The figure on the right allows you to
visualize the hierarchy of molecular organization in
the cell. Each level of the hierarchy is explained
below:

1. Inorganic Precursors
All biomolecules start from inorganic
precursors. The major precursors for the
formation of biomolecules are water,
carbon dioxide, and three inorganic
nitrogen compounds—ammonium
(NH4 ), nitrate (NO3-) and dinitrogen (N2).
+

Metabolic processes assimilate and

transform these inorganic precursors
through ever more complex levels of
biomolecular order.
2. Metabolites
In the first step, precursors are converted
to metabolites, which are simple organic
compounds. These are intermediates in
cellular energy transformation.
3. Building Blocks
Metabolites will also undergo biosynthesis into sets of building blocks: amino acids, sugars,
nucleotides, fatty acids, and glycerol.
4. Macromolecules
Through covalent linkage of these building blocks (polymerization), the macromolecules are
constructed: proteins, polysaccharides (carbohydrates), polynucleotides (DNA and RNA), and
lipids. All macromolecules, except lipids, are considered polymers because they are composed of
chains of their corresponding building blocks (monomers).
5. Supramolecular Complexes

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 Interactions among macromolecules lead to the next level of structural organization,
supramolecular complexes. Here, various members of one or more of the classes of
macromolecules come together to form specific assemblies that serve important subcellular
functions. Examples of these supramolecular assemblies are multifunctional enzyme complexes,
ribosomes, chromosomes, and cytoskeletal elements. These supramolecular complexes are an
interesting contrast to their components because their structural integrity is maintained by
noncovalent forces, not by covalent bonds. These noncovalent forces include hydrogen bonds,
ionic attractions, van der Waals forces, and hydrophobic interactions between
macromolecules. Such forces maintain these supramolecular assemblies in a highly ordered
functional state.
6. Organelles
In eukaryotes (higher organisms), these supramolecular complexes are further organized into what
is known as organelles. These are entities present in the cell. Organelles share two attributes: They
are cellular inclusions, usually membrane bounded, and they are dedicated to important cellular
tasks.
7. Cells
These organelles will then make up cells, which are considered to be the basic unit of life. They
are the smallest entities capable of displaying attributes associated uniquely with the living states.

B. The Biomolecules

Living systems are made up of specialized organic compounds know as biomolecules. These
biomolecules are classified into 4 major divisions – carbohydrate, lipids, proteins, and nucleic acids -
and they differ from each other in properties and physiological roles.

As previously stated, despite their large size, these biomolecules are structurally composed of smaller units,
their building blocks. Some of them, such as carbohydrates, proteins, and nucleic acids, form long
chains of these building blocks (polymers), whereas others, such as lipids, are non-polymeric.
Nonetheless, lipids are large molecules with few building blocks.

The polymeric biomolecules are biosynthesized by identical mechanisms. It always involves the removal of
water molecule to join the building blocks (monomers) together, a process known as condensation
reaction. If a polymer comprises identical monomers, it is called a homopolymer. However, if it is
constructed from a number of different kind of monomers, it is called a heteropolymer.

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Below is a table that differentiates some properties of these biomolecules.
Building
Biomolecules Structural Characteristics Physiological Roles
Blocks
Branched or unbranched - main source of energy for the
polymer of monosaccharides body
monosaccharide
Carbohydrates connected via glycosidic - involved cell recognition
(simple sugars)
bonds (also known as - plays structural roles in
polysaccharides) plants and some animals
- long-term energy storage of
fatty acids and the body
exists in large complexes with
Lipids glycerol (most of - important component of the
no common structural features
the time) cell membrane
- gives palatability to food
- involves in almost all
Unbranched polymer of physiological processes, such
amino acids connected via as catalysis and transport, and
Proteins amino acids
peptide bonds (also known has structural functions
as polypeptides) - can also be a source of
energy
Unbranched polymer of - involved in heredity
nucleotides connected via - responsible for the synthesis
Nucleic Acids nucleotides
phosphodiester bonds (also of proteins in the cell
known as polynucleotides)

Elemental Composition of Biomolecules

Like any organic compounds, biomolecules are all carbon compounds. The prevalence of C is due to its
unparalleled versatility in forming stable covalent bonds through electron-pair sharing. Atoms commonly
found in covalent linkage to carbon in biomolecules are carbon itself, hydrogen, oxygen, and nitrogen.

D. The Cell

As mentioned, the cell is smallest entity capable of displaying attributes associated uniquely with the living
states. Although the cellular level may be considered as one of the simple levels of structures,
understanding the mechanisms involved within it may help elucidate how the higher levels of structure
works and functions.

The 2 Major Types of Cells

There are two types of cells, prokaryotic cells and eukaryotic cells. The simplest way to distinguish these
two types is that a prokaryotic cell contains no well-defined nucleus, whereas the opposite is true for a
eukaryotic cell.

Organisms comprising prokaryotic cells are considered prokaryotes. Prokaryotes are mostly bacteria.
Besides the lack of a nucleus, there are few well-defined structures inside a prokaryotic cell. The exterior
of a prokaryotic cell has three components: a cell wall, an outer membrane, and a plasma membrane.
These components allow controlled passage of material into or out of the cell. The materials necessary for
proper functioning of the cell float about inside it, in a soup known as the cytoplasm.

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The illustration below shows a simplified version of a prokaryotic cell.

Organisms comprising eukaryotic cells are considered eukaryotes. Eukaryotes are animals, plants,
fungi, and protists. You are a eukaryote. In addition to having a nucleus, eukaryotic cells have a number of
membrane-bound components known as organelles. Eukaryotic organisms may be either unicellular or
multicellular. In general, eukaryotic cells contain much more genetic material than prokaryotic cells.

The illustration below shows a labeled illustration of typical animal and plant cells, which are eukaryotes.

Listed below are the common organelles present in animal and plant cells and their functions. Some
organelles are specific to either animal cell or plant cell only.

1. Nucleus: The nucleus is the most obvious organelle in any eukaryotic cell. It is enclosed in a double
membrane and communicates with the surrounding cytosol via numerous nuclear pores. Within
each nucleus is nuclear chromatin that contains the organism’s genome. The chromatin is efficiently
packaged within the small nuclear space. Genes within the chromatin are made of deoxyribonucleic
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 acid (DNA). The DNA stores the organism’s entire encoded genetic information. The DNA is similar
in every cell of the body, but depending on the specific cell type, some genes may be turned on or
off - that's why a liver cell is different from a muscle cell, and a muscle cell is different from a fat cell.
When a cell is dividing, the nuclear chromatin (DNA and surrounding protein) condenses into
chromosomes that are easily seen by microscopy.
2. Nucleolus: The prominent structure in the nucleus is the nucleolus. The nucleolus produces
ribosomes, which move out of the nucleus and take positions on the rough endoplasmic reticulum
where they are critical in protein synthesis.
3. Cytosol: The cytosol is the "soup" within which all the other cell organelles reside and where most
of the cellular metabolism occurs. Though mostly water, the cytosol is full of proteins that control
cell metabolism including signal transduction pathways, glycolysis, intracellular receptors, and
transcription factors.
4. Cytoplasm: This is a collective term for the cytosol plus the organelles suspended within the cytosol.
5. Centrosome: The centrosome, or MICROTUBULE ORGANIZING CENTER (MTOC), is an area in
the cell where microtubules are produced. Plant and animal cell centrosomes play similar roles in
cell division, and both include collections of microtubules, but the plant cell centrosome is simpler
and does not have centrioles. During animal cell division, the centrioles replicate (make new copies)
and the centrosome divides. The result is two centrosomes, each with its own pair of centrioles. The
two centrosomes move to opposite ends of the nucleus, and from each centrosome, microtubules
grow into a "spindle" which is responsible for separating replicated chromosomes into the two
daughter cells.
6. Centriole (animal cells only): Each centriole is a ring of nine groups of fused microtubules. There
are three microtubules in each group. Microtubules (and centrioles) are part of the cytoskeleton. In
the complete animal cell centrosome, the two centrioles are arranged such that one is perpendicular
to the other.
7. Golgi Apparatus: The Golgi apparatus is a membrane-bound structure with a single membrane. It
is actually a stack of membrane-bound vesicles that are important in packaging macromolecules for
transport elsewhere in the cell. The stack of larger vesicles is surrounded by numerous smaller
vesicles containing those packaged macromolecules. The enzymatic or hormonal contents of
lysosomes, peroxisomes and secretory vesicles are packaged in membrane-bound vesicles at the
periphery of the Golgi apparatus.
8. Lysosome: Lysosomes contain hydrolytic enzymes necessary for intracellular digestion. They are
common in animal cells, but rare in plant cells. Hydrolytic enzymes of plant cells are more often
found in the vacuole.
9. Peroxisome: Peroxisomes are membrane-bound packets of oxidative enzymes. In plant cells,
peroxisomes play a variety of roles including converting fatty acids to sugar and assisting
chloroplasts in photorespiration. In animal cells, peroxisomes protect the cell from its own production
of toxic hydrogen peroxide. As an example, white blood cells produce hydrogen peroxide to kill
bacteria. The oxidative enzymes in peroxisomes break down the hydrogen peroxide into water and
oxygen.
10. Secretory Vesicle: Cell secretions - e.g. hormones, neurotransmitters - are packaged in secretory
vesicles at the Golgi apparatus. The secretory vesicles are then transported to the cell surface for
release.
11. Cell Membrane: Every cell is enclosed in a membrane, a double layer of phospholipids (lipid
bilayer). The exposed heads of the bilayer are "hydrophilic" (water loving), meaning that they are
compatible with water both within the cytosol and outside of the cell. However, the hidden tails of
the phospholipids are "hydrophobic" (water fearing), so the cell membrane acts as a protective
barrier to the uncontrolled flow of water. The membrane is made more complex by the presence of
numerous proteins that are crucial to cell activity. These proteins include receptors for odors, tastes
and hormones, as well as pores responsible for the controlled entry and exit of ions like sodium
(Na+) potassium (K+), calcium (Ca2+), and chloride (Cl-).
12. Mitochondria: Mitochondria provide the energy a cell needs to move, divide, produce secretory
products, contract - in short, they are the power centers of the cell. They are about the size of
bacteria but may have different shapes depending on the cell type. Mitochondria are membrane-

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 bound organelles, and like the nucleus have a double membrane. The outer membrane is fairly
smooth. But the inner membrane is highly convoluted, forming folds (cristae) when viewed in cross-
section. The cristae greatly increase the inner membrane's surface area. It is on these cristae that
food (sugar) is combined with oxygen to produce ATP - the primary energy source for the cell.
13. Vacuole: A vacuole is a membrane-bound sac that plays roles in intracellular digestion and the
release of cellular waste products. In animal cells, vacuoles are generally small. Vacuoles tend to
be large in plant cells and play several roles: storing nutrients and waste products, helping increase
cell size during growth, and even acting much like lysosomes of animal cells. The plant cell vacuole
also regulates turgor pressure in the cell. Water collects in cell vacuoles, pressing outward against
the cell wall and producing rigidity in the plant. Without sufficient water, turgor pressure drops and
the plant wilts.
14. Cell Wall (plant cells only): Plant cells have a rigid, protective cell wall made up of polysaccharides.
In higher plant cells, that polysaccharide is usually cellulose. The cell wall provides and maintains
the shape of these cells and serves as a protective barrier. Fluid collects in the plant cell vacuole
and pushes out against the cell wall. This turgor pressure is responsible for the crispness of fresh
vegetables.
15. Chloroplast (plant cells only): Chloroplasts are specialized organelles found in all higher plant
cells. These organelles contain the plant cell's chlorophyll responsible for the plant's green color and
the ability to absorb energy from sunlight. This energy is used to convert water plus atmospheric
carbon dioxide into metabolizable sugars by the biochemical process of photosynthesis.
Chloroplasts have a double outer membrane. Within the stroma are other membrane structures -
the thylakoids. Thylakoids appear in stacks called "grana" (singular = granum).
16. Smooth Endoplasmic Reticulum: Throughout the eukaryotic cell, especially those responsible for
the production of hormones and other secretory products, is a vast network of membrane-bound
vesicles and tubules called the endoplasmic reticulum, or ER for short. The ER is a continuation of
the outer nuclear membrane and its varied functions suggest the complexity of the eukaryotic cell.
The smooth endoplasmic reticulum is so named because it appears smooth by electron microscopy.
Smooth ER plays different functions depending on the specific cell type including lipid and steroid
hormone synthesis, breakdown of lipid-soluble toxins in liver cells, and control of calcium release in
muscle cell contraction.
17. Rough Endoplasmic Reticulum: Rough endoplasmic reticulum appears "pebbled" by electron
microscopy due to the presence of numerous ribosomes on its surface. Proteins synthesized on
these ribosomes collect in the endoplasmic reticulum for transport throughout the cell.
18. Ribosomes: Ribosomes are packets of RNA and protein that play a crucial role in both prokaryotic
and eukaryotic cells. They are the site of protein synthesis. Each ribosome comprises two parts, a
large subunit and a small subunit. Messenger RNA from the cell nucleus is moved systematically
along the ribosome where transfer RNA adds individual amino acid molecules to the lengthening
protein chain.
19. Cytoskeleton: As its name implies, the cytoskeleton helps to maintain cell shape. But the primary
importance of the cytoskeleton is in cell motility. The internal movement of cell organelles, as well
as cell locomotion and muscle fiber contraction could not take place without the cytoskeleton. The
cytoskeleton is an organized network of three primary protein filaments:
 microtubules
 actin filaments (microfilaments)
 intermediate fibers

III. CHEMICAL FOUNDATIONS

Organic chemistry is a separate branch of chemistry the deals with the study of carbon compounds. The
biomolecules are made up of carbon compounds. For that reason, biomolecules can be considered as
part of the subject matter of organic chemistry. However, many carbon compounds are not found in any
organism, and many topics of importance to organic chemistry have little connection with living things. That
is why, for this portion of the unit, you are only going to concentrate on the aspects of organic chemistry
that you need in order to understand what goes on in living cells.

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A. The Origin of Organic Chemistry

Organic chemistry was singled out as a separate discipline for historical reasons. Originally, it was thought
that compounds in living things, termed organic compounds, were fundamentally different from those in
nonliving things, called inorganic compounds.

In fact, chemists believed before that organic compounds can only be synthesized inside a living thing
because only living things contain “vital force” which is necessary to create organic compounds (Vitalism
Theory). The Vitalism Theory was disproven by Friedrich Wohler when he was able to synthesize urea,
a compound found in human urine, in the laboratory, using ammonium cyanate, an inorganic compound
(See reaction below). His discovery means that organic compounds can actually be created from inorganic
and non-living substances.

Despite the demise of vitalism in science, the word organic is still used today by some people to mean
“coming from living organisms” as in the term “organic supplements” and “organic fertilizers”. But in
chemistry, when we say organic compounds or materials, these are the ones containing carbon, regardless
if it is of natural or synthetic origin.

B. Chemical Bonding

Before we proceed our study of the specific concepts I organic chemistry, you need to review a basic but
familiar concept – chemical bonds. Chemical bonds are formed when 2 or more atoms are held strongly
together. Atoms form chemical bonds to achieve stability.

The subatomic particles that are involved in chemical bonds are the electrons, more specifically the
electrons present in the outermost shell of an atom known as the valence electrons.

The central concept of bonding, as explained by G.N. Lewis and W. Kossel, is that atoms become stable
when they achieve a configuration where its valence shell contains 8 electrons. This is known as the Octet
Rule. There are 2 ways that an atom may achieve Octet, and thus, forming chemical bonds. This is either
by giving off and receiving valence electrons, or by sharing valence electrons. This difference results
to 2 types of chemical bonds which are discussed below.

1. Ionic Bond
This type of bond generally results from the interaction of metals (located on the left side of the
periodic table) with nonmetals (located on the right side), such as the bond between the sodium
and chlorine atom in table salt (sodium chloride).
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 In the formation of this bond, the metal atom gives off valence electrons resulting to an ion with a
positive charge, known as cation. The electrons given off by the metal will then be accepted by a
non-metal atom resulting to an ion with a negative charge, known as anion. The chemical bond
is then formed by the electrostatic attraction between the 2 ions with different charges. As an
example, consider the formation of sodium chloride (table salt) from sodium atom and chlorine atom:

Based on the illustration above, sodium (a metal) gives off one electron
which was then gained by the chlorine atom (a non-metal). This results
to the formation of sodium ion (a cation) and chloride ion (an anion).
The attraction between the sodium and chloride ions is now known as
ionic bond. Compounds with ionic bonds are usually crystalline with
high melting point. Their crystal is composed alternating cation and
anion, such as in the case of sodium chloride in the example below.
They are also mostly soluble in water and dissociates into ions.

2. Covalent Bond
This bond generally results between the interaction of nonmetals. The
chemical bond is formed when the 2 non-metal atoms share their electrons with each other. The
hydrogen molecule, H2, provides the simplest example of a covalent bond. When two hydrogen
atoms are close to each other, their electron clouds overlap with each other forming a covalent bond
in between.

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 To simply put it, the formation of covalent bond between hydrogen atoms can be represented by:

Most of substances with covalent bonds are usually gases, liquids, or solids with low melting points.
Many, such as gasoline, vaporize readily. Many are pliable in their solid forms—for example, plastic
bags and paraffin.

Electronegativity and Bond Polarity

As you learned earlier, covalent bonds are formed
when an atom, specifically a nonmetal, share its
electrons with another atom (also a nonmetal). This
sharing of electrons can be viewed as a game of
tug of war, where the 2 atoms involved in a covalent
bond are trying to pull the shared electrons towards
themselves. Sometimes, the pulling of the shared
electrons is not equal for each atom, that is one
atom may have a stronger pull than the other.
Electronegativity is the measure of an atom’s
attraction for the shared electrons in a bond. In
other words, it indicates how much a particular
atom “wants” electrons.

A scale has been established to represent electronegativity values of elements arbitrarily from 0 to 4 in the
periodic table, as shown in the figure above. The following trends in electronegativity are observed in a
periodic table:
 Electronegativity increases across the row of the periodic table (excluding the noble gases, the
elements found in the rightmost area of the periodic table).
 Electronegativity decreases down a column of the periodic table.
As a result of this trend, the most electronegative elements are located at the upper right-hand corner
of the periodic table, and the least electronegative elements are located in the lower left-hand corner.

Electronegativity values are used as a guideline to indicate whether the electrons in a bond are equally
shared or unequally shared between two atoms. For example, whenever two identical atoms are bonded
together, each atom attracts the electrons in the bond to the same extent. The electrons are equally shared,
and the bond is nonpolar. Thus, a carbon–carbon bond is nonpolar. The same is true whenever two
different atoms having similar electronegativity values are bonded together. C –H bonds are
considered to be nonpolar, because the electronegativity difference between C (2.5) and H (2.2) is small.

Bonding between atoms of different electronegativity values results in the unequal sharing of
electrons. For example, in a C–O bond, the electrons are pulled away from C (2.5) toward O (3.4), the
element of higher electronegativity. The bond is polar, or polar covalent. The bond is said to have a dipole;
that is, a separation of charge.

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The direction of polarity in a bond is often indicated by an arrow, with the head of the arrow pointing toward
the more electronegative element. The tail of the arrow, with a perpendicular line drawn through it, is
positioned at the less electronegative element. Alternatively, the symbols δ+ and δ– indicate this unequal
sharing of electron density, where δ– means the atom has a partial negative charge since it has a stronger
pull of electrons than the other element, i.e. more electronegative; and δ+ has a partial positive charge (less
electronegative).

Students often wonder how large an electronegativity difference must be to consider a bond polar. That’s
hard to say. We will set an arbitrary value for this difference and use it as an approximation. Usually, a
polar bond will be one in which the electronegativity difference between two atoms is greater than or
equal to 0.5 units.

C. Bonding in Organic Compounds

Aside from carbon, the other major elements present in organic compounds are hydrogen (H), oxygen
(O), nitrogen (N), sulfur (S) and halogens (F, Cl, Br, and I). These elements are all non-metals, therefore
the bonds that they form with carbons are all covalent. Based in what you have learned about the Octet
Rule, each non-metal should have 8 bonds around it, and would mean that the elements C, H, O, N, S and
halogens should form bonds as shown on the next page:

The correctness of a structural formula of an organic compound is based on the fact that each element
composing the compound should satisfy the bonds shown in the table above.

Sample Problems:
1. Is the structure below valid or not?

- Upon examining the structure above, we see that all of the hydrogens have one bond, oxygen
has two bonds, and nitrogen has 3 bonds. However, one of the carbons actually has only 3 bonds
which violates the fact that carbons should have 4 bonds. Therefore, the structure is invalid.

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 2. Two structural formulas are shown below. Which is valid and which is not?

In structure (a) each H and halogen has one bond, each C has four bonds, and each O has two
bonds; therefore A is a valid structure.

As we examine (b), we note that each H has one bond, each C has four bonds, the N has three
bonds, BUT the O has three bonds. The O should only have two bonds. Therefore, (b) is not a valid
structure.

D. Classification of Organic Compounds Based on Functional Groups

In the past few lessons you already learned about the structures of organic compounds, which is a very
important concept in describing and illustrating biomolecules in the future. At this point, you are going to
study specific organic compounds and how to classify them.

There are already more than 50 million known organic molecules, according to Chemical Abstracts, a
journal that abstracts and indexes the chemical literature. Each of these compounds has unique physical
properties as well as unique chemical reactivity. This may appear to be a major difficulty when learning
organic chemistry. Fortunately, chemists have learnt throughout the years that organic compounds can be
categorized into families based on structural features, and that members of a given family often exhibit
comparable chemical behavior.

Functional Groups
So, what structural features can be used to classify organic compounds into families?

Notice that most organic molecules have C – C and C – H single bonds. (Try looking into the various
organic compounds you have previously encountered in previous lectures again). These C – C and C – H
single bonds are strong, nonpolar, and in general inert. Some organic molecules, however, may also
have the following structural feature:
 Heteroatoms – atoms other than C and H, such as O, N, S and halogens.
 Multiple bonds – double bonds (C = C) or triple bonds (C ≡ C)

These heteroatoms and/or multiple bonds, when present in an organic molecule, confer a certain reactivity
on that molecule and can, therefore, help distinguish one organic molecule from another. These structural
features comprise what is called a functional group. Functional groups are common and specific
arrangement of atoms that impart predictable reactivity and properties to a molecule.

Don’t think, though, that the C–C and C–H single bonds are unimportant. They form the carbon backbone
or skeleton to which the functional groups are bonded. A functional group usually behaves the same
whether it is bonded to a carbon skeleton having as few as two or as many as 20 carbons. For this reason,

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we often abbreviate the carbon and hydrogen portion of the molecule by a capital letter R, and draw the R
bonded to a particular functional group.

Let us consider the following examples to understand the significance of functional groups:
 Ethane (See figure below) has only C – C and C – H single bonds, so it has no functional group. It
has no heteroatoms or multiple bonds, so it has no reactive site.
 Ethanol (See figure below), on the other hand, has two carbons and five hydrogens in its carbon
backbone, as well as an –OH group, a functional group known as hydroxyl group. This hydroxyl
group makes the properties of ethanol very different from the properties of ethane.
 Moreover, any organic molecule containing the hydroxyl group has properties similar to ethanol. For
example, cholesterol (See figure below) also as the same chemical property of ethanol due to its
hydroxyl group.

ethane ethanol cholesterol

Families of Organic Compounds According to Functional Groups

Once again, a functional group is a common and specific arrangement of atoms that impart predictable
reactivity and properties to a molecule. This can serve as a structural feature that can be used to classify
organic molecules into families.

We can subdivide the most common families of organic compounds into three types:
 Hydrocarbons
 Compounds containing C – Z single bond, where Z is an electronegative element
 Compounds containing C = O group

Hydrocarbons
Consider first the simplest form of organic compounds containing only carbon and hydrogen – the
hydrocarbons. These compounds are subdivided into different subgroups based on the type of carbon-
carbon bond present.

1. Alkanes
These are hydrocarbons that do not have multiple bonds between carbon atoms (single bonds
only), and we can indicate this in the family name and in names for specific compounds by the –
ane ending. One example is ethane whose structure is illustrated and discussed previously. As you
can see, its carbon atoms are only involved in single bonds with one another.

ethane

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 Alkanes can also be involved in rings, and in that case, they are known as cycloalkanes, such as
the one shown below.

cyclohexane

Alkanes are considered to be a compound with no functional group due to its relative inertness. The
principal sources of alkanes are natural gas and petroleum.

2. Alkenes
These are hydrocarbons containing at least one carbon-carbon double bond, and this is indicated
in the family name and in names for specific compounds by the –ene ending. The carbon-carbon
double bond has a specific reactivity; therefore, it is considered as the functional group of alkenes.
Ethene (ethylene) is an example for this subgroup of hydrocarbons, which is the simplest alkene
(See structure below). It is used as starting material for synthesis of many industrial compounds,
such as ethanol and polyethylene. It also occurs as natural plant hormone that is involved in ripening
process.

ethene (ethylene)

Alkenes are the most abundant hydrocarbons in nature.

3. Alkynes
These are hydrocarbons containing at least one carbon-carbon triple bond, and this is indicated
in the family name and in names for specific compounds by the –yne ending. The carbon-carbon
triple bond also has a specific reactivity; therefore, it is considered as the functional group of alkynes.
The simplest alkyne is ethyne (acetylene) (See structure below). This compound is used as fuel
for welding torch.

ethyne (acetylene)
4. Arene
This is a special class of hydrocarbon containing a special type of ring, the most common example
of which is benzene ring as illustrated below. Compounds (hydrocarbons or not) containing such
rings are known as aromatic compounds. The term aromatic is historical in origin, because earliest
known aromatic compounds are derived from aromatic substances. There is no special ending for
the general family of aromatic compounds.

benzene
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 Although the structure of benzene resembles an alkene, it is not really considered to be part of that
subgroup as it has different set of properties. The alternating double bonds in its structure allow for
the movement of the carbon-carbon bond electrons around the ring, which is a process known as
electron delocalization. If a compound contains a benzene ring, then it can be its functional group
and is known as phenyl.

Generally speaking, compounds such as the alkanes, whose molecules contain only single bonds, are
referred to as saturated compounds because these compounds contain the maximum number of
hydrogen atoms that the carbon compound can possess. Compound with multiple bonds, such as alkenes
and alkynes, are considered unsaturated compounds because they possess fewer that the maximum
number of hydrogen atoms, and they are capable of reacting with hydrogen under proper conditions.
Benzene and other arenes are structurally unsaturated, but have chemical reactivity different from common
unsaturated hydrocarbons. Thus, it is strictly not considered unsaturated. We still refer benzene as
aromatic.

Compounds containing C – Z single bond

The electronegative heteroatom Z can be O, N, or S. It creates a polar bond, resulting to a partial positive
charge (δ+) on carbon atom.

1. Alkyl Halides
These are compounds in which a halogen (F, Cl, Br or I) replaces a hydrogen from a hydrocarbon.
An alkyl halide has the generic formula R – X where X = halogen. The following are examples of
alkyl halides.
H H H F H
| | | | |
H – C – C – Cl H–C–C–C–H
| | | | |
H H H H H
ethyl chloride 2-fluoropropane

Chlorofluorocarbons (CFCs), main agent in damaging the ozone layer, are alkyl halides.
2. Alcohols
These are compounds containing a hydroxyl group (–OH) attached to a saturated carbon. An
alcohol has a generic formula of R – OH, more specifically:

|
– C – OH to denote that the carbon directly attached to OH is saturated.
|
Examples of alcohols are:

H H H
| | |
H – C – OH H – C – C – OH
| | |
H H H
methanol ethanol

Methanol is known as wood alcohol and is highly toxic and flammable. Ethanol is the only ingestible
alcohol and is present in alcoholic beverages.

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 Alcohols can be classified into 3 groups: primary (1o), secondary (2o), and tertiary (3o). This
classification is based on the degree of substitution of the carbon to which the hydroxyl group is
directly attached.

a. Primary alcohol – the –OH is attached to a carbon attached directly to one carbon.
H H a carbon attached directly to one carbon
| |
H – C – C – OH
| |
H H
ethanol
b. Secondary alcohol – the –OH is attached to a carbon attached directly to 2 carbons.

H H H a carbon attached directly to 2 carbons

| | |
H–C–C–C–H
| | |
H OH H
isopropyl alcohol
c. Tertiary alcohol – the –OH is attached to a carbon attached directly to one carbon.
CH3 a carbon attached directly to 3 carbons
|
H3C – C – OH
|
CH3
tert-butyl alcohol

If the hydroxyl group (–OH) is attached to a benzene ring, it is not

considered an alcohol. It is referred to as a phenol.

3. Thiols
These compounds are known as the sulfur analogs of alcohols because the structures of thiols
replace the oxygen in the hydroxyl group (–OH) with a sulfur forming a new functional group
known as a sulfhydryl group (–SH). It has the generic formula R–SH. A common example of thiol
is:

H H
| |
H – C – C – SH
| |
H H
Ethanethiol
Ethanethiol is responsible for the characteristic smell every time you open the LPG tank. It is added
to LPG intentionally to detect leakage as the natural gas in LPG is odorless.

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 4. Ethers
These are compounds containing an oxygen in between an alkyl group or a phenyl ring. It has
the generic formula R–O– R’, where R and R’ can be the same or different alkyl groups.

An ether with similar alkyl groups beside its oxygen atom is referred as symmetrical ether, while
the one that has different alkyl groups are known as asymmetrical ether. Examples of ethers are:
H H H
H H H H | | |
| | | | H– C – C – O – C – H
H– C – C – O – C – C – H | | |
| | | | H H H
H diethyl
H etherH H ethyl methyl ether
(symmetrical ether) (asymmetrical ether)

Diethyl ether was previously used as a deep anesthesia before, but are now replaced with
halogenated derivatives. The addition of halogens reduces the flammability of diethyl ether which is
a disadvantage in the use as anesthesia.

5. Amines
These compounds are considered organic derivatives of ammonia, since structurally an amine is
formed when one of the hydrogens in ammonia is replaced with an alkyl group or phenyl ring. The
nitrogen in an amine is known as the amino group.
.. ..
H–N–H R–N–H
| |
H H
ammonia amine
Amines are classified as primary (1o), secondary (2o), and tertiary (3o). This classification is based
on the number of organic groups attached to the nitrogen atom.
a. Primary amine – the nitrogen is attached to 1 organic group.
H
| ..
H–C–N–H
| |
H H
Methylamine

b. Secondary amine – the nitrogen is attached to a 2 organic groups.

H H
| .. |
H–C–N–C–H
| | |
H H H
Diemthylamine

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 c. Tertiary amine – the nitrogen is attached to 3 organic groups.
..
H3C – N – CH3
|
CH3
trimethylamine

Amines usually have a foul odor of decaying matter or rotten fish.

Compounds containing C = O group

Many families of organic compounds possess a C = O group, known as the carbonyl group. The C = O
group is also a polar group, just like the C – Z bond earlier.

1. Aldehydes and Ketones

The carbonyl group of an aldehyde is bonded to one hydrogen atom and one carbon atom (except
for formaldehyde, which is the only aldehyde bearing 2 hydrogen atoms.) The carbonyl group of a
ketone is bonded to 2 carbon atoms. Their generic formulas are:
O O O
|| || ||
H–C–H R–C–H R – C – R’
formaldehyde aldehyde ketone

Some specific examples of aldehydes are:

O
O ||
|| –C–H
CH3 – C – H

acetaldehyde benzaldehyde
Some specific examples of ketones are:
O O
|| ||
CH3 – C – CH3 CH3 – C – CH2CH3
acetone ethyl methyl ketone

2. Carboxylic acids, Esters, and Amides

When a carbonyl group is attached directly to a hydroxyl group, it becomes a supra-functional
group known as carboxyl group. The reason this is considered to be a new functional group is
because this combination results to acidic properties. Compounds containing carboxyl groups are
known as carboxylic acids.
O O
|| ||
– C – OH R – C – OH
carboxyl group carboxylic acid

Esters and amides are considered derivatives of carboxylic acids. The formation of carboxylic acid
derivative is usually done by replacing the –OH of the carboxyl with a different group. An ester is

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 formed when the –OH of the carboxyl is replaced with an ether-like group (–O – R’). An amide is
formed when the –OH of the carboxyl is replaced with an amino group (–NH2). That is,
O O O
|| || ||
R – C – OH R – C – O – R’ R – C – NH2
carboxylic acid ester amide

Some common examples of carboxylic acids are: O

. ||
O O – C – OH
|| ||
CH3 – C – OH CH3CH2CH2 – C – OH
acetic acid butyric acid benzoic acid

Acetic acid is responsible for the tart taste of vinegar. Butyric acid is the cause of the characteristic
smell of old butter. Benzoic acid is used in pharmaceuticals as antimicrobial agent. Most carboxylic
acids often have irritating odor.

Some common examples of esters are:

.
O O
|| ||
CH3 – C – O – CH2CH3 CH3CH2CH2 – C – O – CH2CH3
ethyl acetate ethyl butyrate

Ethyl acetate has the characteristic smell of plastic balloon and is used as organic solvent. Ethyl
butyrate is ester responsible for the smell of pineapples. Most esters have fruity odor and are used
in flavorings and fragrances.

Some common examples of amides are:

.
O O
|| ||
H – C – NH2 CH3 – C – NH2
formamide acetamide

Proteins and plastics, such as Nylon, have amide in their structures.

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Sample Problem:
Atenolol and donepezil are examples of useful drugs that contain a variety of functional groups. Atenolol
is a β blocker, a group of drugs used to treat hypertension. Donepezil, sold under the trade name Aricept,
is used to treat mild to moderate dementia associated with Alzheimer’s disease. Identify the functional
groups of the 2 compounds.

Solution:

IV. WATER AS BIOCHEMICAL SOLVENT

A. Physical Properties of Water

Any study of the chemistry of life must include a study of water. Living organisms are mostly made up of
water, which accounts for 60-95% of living cells. In the human body, 55% of the water is intracellular fluids
(within the cell). The other remaining 45% is divided between:
 plasma (8%),
 interstitial and lymph (22%), and
 connective tissue, bone and cartilage (15%)
Normal metabolic activity can only occur only when the cells are at least 65% H2O.

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Function of Water as Solvent for Biochemical Reactions:
1. Water acts as transport medium across membranes, carrying substances in and out of cells.
2. Water helps maintain temperature of the body.
3. Water acts as solvent (carrying dissolved chemicals) in the digestive and waste excretion systems.
4. Nearly all biological molecules assume their shapes, and therefore their functions, in response to
the physical and chemical properties of water.

Water Balance in the Body

Healthy humans experience intake and loss of water every day. A water balance must be maintained within
the body. If the loss of water in the body significantly exceeds the intake, the body experiences
dehydration. If the loss of water in the body is significantly less the intake, the body experiences edema
(fluid retention in tissues).

II. PHYSICAL PROPERTIES OF WATER

Water can be considered a hydride of oxygen due to its elemental composition H2O. In comparison to
other hydrides that are its nearest neighbors in the periodic table, namely ammonia (NH3), hydrogen fluoride
(HF), and hydrogen sulfide (H2S), water has substantially higher:
 boiling point,
 melting point,
 heat of vaporization, and
 surface tension.

Indeed, all of these physical properties are anomalously high for a substance of this molecular weight that
is neither metallic nor ionic. These properties suggest that intermolecular forces of attraction between
H2O molecules are high. Furthermore, the maximum density of water is found in the in the liquid state,
not solid, unlike most matter. This is the reason why solid water (ice) floats on top of liquid water.

These eccentric properties of water are really fascinating, but should have an explanation. And the
explanation lies in its unrivaled ability to form hydrogen bonds.

A. Polarity of Water

The 2 hydrogens of water are covalently linked to the oxygen atom giving a non-linear arrangement. This
structure of water is known as bent structure (See Figure below). In the O–H bonds of H2O, oxygen is
more electronegative than hydrogen, meaning there is a higher probability that the bonding electrons are
closer to the oxygen. This gives rise to a partial negative charge in the oxygen atom and partial positive
charge in the hydrogen atom. The partial charges are usually depicted us δ+ and δ-, respectively.

Bonds such as this are called polar bonds. Molecules with polar bonds are polar molecules, that is why
water molecule is polar. In the case where the electronegativity difference is quite small, such as in the

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C–H bond in hydrocarbons, the sharing of electrons is very nearly equal, and the bond is essentially
nonpolar.

B. The Ability of Water Molecule to Form Hydrogen Bonds

One of the important consequences of the polarity of water molecule is that water molecules attract one
another through the formation of hydrogen bonds. Hydrogen bond is a non-covalent interaction
(intermolecular force). It is a special case of a dipole-dipole interaction formed between a hydrogen
donor and a hydrogen acceptor. A hydrogen donor is a hydrogen atom covalently bonded to an
electronegative atom, specifically fluorine (F), oxygen (O), or nitrogen (N). A hydrogen acceptor is a
lone pair of electrons on any of those mentioned electronegative atoms (F, O, and N).

Water can then be both hydrogen donors and hydrogen acceptors (See figure below). The H2O molecule
has 2 hydrogen atoms bonded to an electronegative oxygen atom which can potentially be hydrogen
donors. The oxygen atom of H2O, on the other hand, has 2 lone pairs of electrons which can potentially
be hydrogen acceptors. In total, a water molecule has the potential to form 4 hydrogen bonds (2 donors
and 2 acceptors).

Hydrogen acceptor
Hydrogen donors

Hydrogen acceptor

It must also be pointed out that hydrogen bonding in water is cooperative. That is, a hydrogen bonded
water molecule serving as an acceptor is a better hydrogen donor that an unbonded molecule. A hydrogen
bonded water molecule serving as a donor is also a better hydrogen acceptor. Thus, participation in
hydrogen binding by H2O molecule is a phenomenon of mutual reinforcement.

Consequence of Hydrogen Bonding in Water

This ability of water for hydrogen bonding is the source of the strong intermolecular attractions that
endow this substance with its anomalously high boiling point, melting point, heat of vaporization, and
surface tension. Hydrogen bonding also enables water to dissolve many organic biomolecules that
contain functional groups that can participate in hydrogen bonding. For example:
1. The oxygen atoms of aldehydes, ketones, and amides provides lone pairs of electrons that can
serve as hydrogen acceptor.
2. Alcohols, carboxylic acids, and amines can serve both as hydrogen acceptors and donors for
formation of hydrogen bonds.

C. Solvent Properties of Water

1. Ionic and polar substances dissolve in water.

Substances, such as ionic substances and polar substances, that can be dissolved in
water, are known as hydrophilic.

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 Why does ionic substances dissolve in water?
 Due to the polarity of water molecule, they can align themselves around ionic substances so
that the partially negative oxygen atoms of the water molecules are oriented towards the
cations (positively charged ions) of the ionic substances and the partially positive hydrogen
atoms are oriented towards the anions (negatively charged ions). This intermolecular
interaction is known as ion-dipole interaction.
 As an example, consider what happens when a crystal of sodium chloride (NaCl) dissolves
in water. The polar water molecules are attracted to the charged ions in the crystal. The
attraction results in sodium and chloride ion on the surface of the crystal dissociating from
another and the crystal begins to dissolve. Because there are many polar water molecules
surrounding each dissolved sodium and chloride ion, the interactions between the opposite
electric charges of theses ions become much weaker that the they in an intact crystal. As a
result, more and more ions are dissociated from the crystal.

Why does polar substances dissolve in water?

 Polar substances can also be hydrated by water in the
same manner as ionic substances. The
interaction between water and another polar
molecule is known as dipole-dipole
interaction. Some polar substances may also
participate in hydrogen bonding, which
enhances solubility.
 However, they do not dissociate into ions, rather the
solution formed contains intact molecules
disperse in water. As an example, intact polar
methanol molecules are dispersed in water when
dissolved.
 An increase in number of polar groups in an organic molecule increases its solubility in water.

2. Non-polar substances do not dissolve in water.

Non-polar substances are known as hydrophobic because of their inability to be dissolved in water.

Why do non-polar substances and water mix together separate into layers?
 Non-polar substances are incapable of forming dipole-dipole interaction or hydrogen bond
with water, but can interact with each other through hydrophobic interaction. When non-
polar substances are mixed with water are mixed, water molecules tend to interact with other
water molecules rather than with non-polar molecules. Consequently, water molecules
exclude non-polar substances forcing them to associate with each other. This is known as
hydrophobic effect.
 The hydrophobic effect is critical for folding of proteins and the self-assembly of biological
membranes.

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 3. Amphipathic molecules form micelles and bilayers.
- There are molecules, such as fatty acids (right) and phospholipids (left), that are both hydrophilic
and hydrophobic. They usually have a non-polar hydrocarbon tail and an ionic or polar end. These
substances are said to be amphipathic, and are known as amphiphiles.

When amphiphiles are dispersed in water, the hydrophilic

head (polar) tends to be hydrated, while the hydrophobic
tail (non-polar) tends to be excluded. This results to the
formation of structurally ordered aggregates.

An example of these aggregates are micelles, which are

globules of up to several thousand amphipathic
substances arranged so that hydrophilic head at the globule
surface can interact with the aqueous environment, while the
non-polar tails associate with one another in the center of the
structure minimizing contact with water. Alternatively,
amphipathic molecules may arrange themselves to form
bilayer, which are sheets in which the polar groups face the
aqueous phase. In both micelles and bilayers, the aggregate is stabilized by hydrophobic effect.

B. Acids, Bases, and Buffers

Biological molecules, such as proteins and nucleic acids, have numerous functional groups that acts as
acids or bases – for example, carboxylic acids and amines, respectively. How exactly are these functional
groups considered to be acidic and basic?

There are plenty of theories that can be used to describe the nature of acids and bases. For describing
functional groups in organic compounds and biomolecules, the most important is the one formulated by
Johannes Bronsted and Thomas Lowry in 1923 known as the Bronsted-Lowry definition. This states
that an acid is a substance that can donate a proton (H+), and a base is a substance that can accept a
proton (H+). Under this definition, an acid base reaction can be written as:
HA (acid) + B (base) ↔ A- + BH+
In the previous general reaction, an acid (HA) reacts with a base (B) to form the conjugate base of the
acid (A-) and the conjugate acid of the base (BH+). A conjugate base is the one that is left when a H+
leaves an acid, and conjugate acid is the one that is formed when a base accepts a H+.

Specific examples:

1. CH3COOH + H2O ↔ CH3COO- + H3O+

acetic acid water acetate hydronium ion
o Acetic acid donates H+ to water; thus, it’s an acid. Conversely, water accepts H+ and is
therefore a base.
o Acetate is what is left when H+ leaves acetic acid; thus it is the conjugate base. On the other
hand, the hydronium ion is formed when water accepts H+ and is therefore the conjugate
acid.

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 2. NH3 + H2O ↔ NH4+ + OH-
ammonia water ammonium ion hydroxide ion
o Ammonia accepts H+ from water; thus, it’s a base. Conversely, water donates the H+ and is
therefore an acid.
o Ammonium is formed when ammonia accepts H+; thus it is the conjugate acid. On the other
hand, the hydroxide is what is left when H+ leaves water and is therefore the conjugate base.

Notice how water can act as acid or base in the examples above. Substances, such as water, that
can act as an acid in the presence of a base or act as a base in the presence of an acid are
referred to as amphoteric substances.

The pH Scale
The acidity of a solution is often expressed in terms of pH. The pH (power of hydrogen) is defined as the
negative logarithm of the hydrogen ion concentration or:

pH = − log[H + ]
This equation tells us that since neutral solution, like pure water, has a [H+] of 1 × 10−7 M, then its pH is 7.
It follows that solution with pH below 7 are acidic and solution with pH above 7 are basic.

Sample Problems:
1. What is the pH of the solution comprising 1.3 × 10-4 M? Is it acidic or basic?
Solution:
o pH = -log [H+] = -log[1.3 × 10-4] = 3.9
o The pH of the solution is below 7; therefore, it is acidic.

2. What is the pH of the solution comprising [OH-] = 1.9 × 10-5 M? Is it acidic or basic?
Solution:
o We cannot input the given value directly to the pH equation, as it is [OH-] not [H+]. However,
we can use another expression, the pOH which is:

pOH = − log[OH − ]

o After getting the pOH, use the expression below to get the pH:
pH + pOH = 14

o Therefore:
pOH = - log [= 1.9 × 10-5] = 4.7
pH = 14 – pOH = 14 – 4.7 = 9.3

The solution is basic.

Buffers
Adding a droplet (~0.01 mL) of hydrochloric acid to 1 L of pure water changes the pH of the water from 7 to
5, which represent a 100-fold increase in hydrogen ion concentration ([H+]). Such a huge change in pH
would be intolerable to most biological systems, since even small changes in pH can dramatically affect
the structures and functions of biological molecules. Maintaining a relatively constant pH is therefore
of paramount importance for living systems.

In living systems and in the laboratories, buffers are used to resist pH changes. These are solutions that
can maintain its pH even after the addition of small amount of acid or base. Typically, a buffer system is
composed of a mixture of a weak acid and its conjugate base.

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Example:
1. Mixture of acetic acid (CH3COOH) and acetate (CH3COO-),
2. Mixture of formic acid (HCOOH) and formate (HCOO-)
3. Mixture of carbonic acid (H2CO3) and bicarbonate (HCO3-)
4. Mixture of phosphoric acid (H3PO4) and dihydrogen phosphate (H2PO4-)

How can buffer resist pH change?

 Buffers work based on the nature of weak acids and their conjugate bases that compose the
buffer. If acid (H+) is added to a buffer solution, it reacts with the conjugate base to form the
weak acid.
H+ + A- (conjugate base of the buffer) → HA
 Similarly, if a base (OH ) is added to the buffer, it reacts with the weak acid to form water and
-

the conjugate base.

OH- + HA (weak acid of the buffer) → A- + H2O
 In this way, either added acid or based is “used up” by adding it to a buffer. This keeps the pH
much more stable than if the same acid or base had been added to an unbuffered system.

Bicarbonate Buffer System of Blood Plasma: A Case of Physiological Buffers

As said, maintaining a fairly constant pH is very important in living systems. There’s plenty of physiological
buffers that can be used for this purpose. In this portion, we will specifically discuss the most important type
of buffer present in the plasma of the blood – the Bicarbonate Buffer System.

The normal pH range of the blood is between 7.35-7.45. Below this range means there’s abundant
hydrogen ions (H+) in the blood and is therefore acidic. Conversely, above this pH means there’s little H+
and is therefore basic. Conditions when the blood pH is low is known as acidosis, while condition when
pH is high is known as alkalosis.

Acidosis and alkalosis are prevented from occurring through the Bicarbonate Buffer System which is
represented by the equation:
CO2 + H2O ↔ H2CO3 ↔ H+ + HCO3-
carbon dioxide carbonic acid bicarbonate

Important Features of the Buffer System:

 There are 2 key organs involved in this specific buffer system – the lungs and the kidneys.
The leftmost side of the equation (interaction between CO2 and H2O) occurs in the lungs,
while the rightmost side of the equation (interaction between H+ and HCO3-) occurs in the
kidneys.
 The buffer system responds to changes in the H+ concentration of the blood by changing the
partial pressure of CO2.
o When the pH of blood falls due to a metabolic process that produces excess H+
(acidosis), the concentration of H2CO3 increases. But this is momentarily, as the
reactions in the buffer shift to the left side. H2CO3 rapidly loses water (H2O) to form CO2
which enters the lungs and is expired as by exhalation. An increase in the partial
pressure of CO2 (pCO2) in the air expired from the lungs thus compensates for the
increased hydrogen ions.
o Conversely, when the pH of the blood rises (alkalosis), the concentration of HCO3-
increases. But the pH is rapidly restored as the reactions in the buffer shift to the right
side. Breathing rate changes and the CO2 in the lungs is converted to H2CO3 in the
capillaries of the lungs. Increase in H2CO3 will then cause an increase in the H+
concentration. Again, the equilibrium of the blood buffer system is rapidly restored by
changing the partial pressure of CO2 in the lungs.

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 Types of Acidosis and Alkalosis:
 Recall:
o Acidosis is when there is a decrease in blood pH (increase in H+). The compensation
of the body is to expel more CO2.
o Alkalosis is when there is an increase in blood pH (decreases in H+). The
compensation of the body is to keep more CO2 in the lungs.
 Acidosis and alkalosis can be classified as either respiratory or metabolic. To help us
determine which is which, we consider again the Bicarbonate Buffer System:
CO2 + H2O ↔ H2CO3 ↔ H+ + HCO3-
carbon dioxide carbonic acid bicarbonate
 The bicarbonate buffer equation can be viewed as a see-saw, wherein increase in one area can
cause a decrease on the other.

Respiratory Side of the Buffer

Let’s consider the leftmost side of the buffer first (interaction between CO2 and H2O). Recall, that
this occurs in the lungs. Acidosis or alkalosis caused by disturbance of this side of buffer is
considered respiratory.
o Respiratory acidosis
 Increase of CO2 resulting to a shift of the buffer reaction to the right which
produces more H+ and lowers blood pH.
o Respiratory alkalosis
 Decrease of CO2 resulting to a shift of the buffer reaction to the left which lowers
H+ and increases blood pH.

Metabolic Side of the Buffer

 Let’s consider the rightmost side of the buffer first (interaction between H+ and HCO3). Recall,
that this occurs in the kidneys. Acidosis or alkalosis caused by disturbance of this side of buffer
is considered metabolic.
o Metabolic acidosis
 Decrease of HCO3- resulting to a shift of the buffer reaction to the right which
produces more H+ and lowers blood pH.
o Metabolic alkalosis
 Increase of HCO3- resulting to a shift of the buffer reaction to the left which
lowers H+ and increases blood pH.

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