Module Overview

Module Overview
Introduction
Module Overview

Biochemistry is unimaginable without studying water. Biological molecules and the

reactions they undergo can be best understood in the context of their aqueous environment.
Not only are organisms made mostly of water (about 70% of the mass of the human body is
water), they are surrounded by water on this, the “blue planet.” Aside from its sheer
abundance, water is central to biochemistry for the following reasons:

1. Nearly all biological molecules assume their shapes (and therefore their functions) in
response to the physical and chemical properties of the surrounding water.
2. The medium for the majority of biochemical reactions is water. Reactants and products
of metabolic reactions, nutrients as well as waste products, depend on water for
transport within and between cells.
3. Water itself actively participates in many chemical reactions that support life.
Frequently, the ionic components of water, the H+ and OH− ions, are the true reactants.
In fact, the reactivity of many functional groups on biological molecules depends on
the relative concentrations of H+ and OH− in the surrounding medium.

All organisms require water, from the marine creatures who spend their entire lives in
an aqueous environment to terrestrial organisms that must guard their watery interiors with
protective skins. Not surprisingly, living organisms can be found wherever there is liquid
water—in hydrothermal vents as hot as 121°C and in the cracks and crevices between rocks
hundreds of meters beneath the surface of the earth. Organisms that survive desiccation do so
only by becoming dormant, as seeds or spores. An examination of water from a biochemical
point of view requires a look at the physical properties of water, its powers as a solvent, and
its chemical behaviour—that is, the nature of aqueous acids and bases.
Course
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 Course Packet 01

Properties of Water

(a) (b)

Figure 1. (a) Certain species of fish have special adaptations which enable them to tolerate the freezing temperatures
in some habitats (b) People living in these areas have also devised techniques on how to catch these fish, an activity
known as ice fishing

Image Credits: www.magzter.com, www.outdoorhub.com

Introduction

Have you ever wondered how fish survive in cold winter weather, or where they go
when lakes and ponds freeze over?

Like many people, fish tend to be less active in the cold. As cold-blooded creatures,
their metabolism dips when temperatures take a dive.

The layer of ice that forms on top of a lake, pond, river, or stream provides some
insulation that helps the waterbody retain its heat. Because warm water sinks in very cold
freshwater, fish in these water bodies often gather in groups near the bottom. Some species,
like koi and gobies, may burrow into soft sediments and go dormant like frogs and other
amphibians, but most fish simply school in the deepest pools and take a "winter rest."

How is water able to do its wonders? Why is it an important component of biochemical

reactions? These and more questions shall be answered in this course packet.
Delivery Mode

This course packet is to be delivered online. Pertinent materials are presented in the
module including links to additional resources compiled by the instructor through Google
drive. You may go over the course packet during your most convenient time. The schedule of
our synchronous discussions as well as their corresponding links shall be posted via our official
Google classroom.

Assessment with Rubrics

You shall be answering two short quizzes in this course packet – a pre-assessment
which shall measure your prior knowledge of the topic and a post-assessment which will
measure to what extent you have learned the topic through this material.

Requirement with Rubrics

Please make sure that you accomplish the activity sheet designed specifically for this
course packet and upload it in your personal Google drive.

Readings

Doing an advance reading on the identified topics will definitely give you an edge as
you would find it easier to grasp unfamiliar concepts to be tackled in the material. Likewise,
advance reading could also help you identify potentially confusing pieces of information for
you to further read on or raise to your instructor via the channels provided (or during the
synchronous meetings).

Kindly take time to read the identified topics from any of the electronic books
accessible through this link: https://bit.ly/3jQ2T4v

Pre-Assessment

What you see below is called a K-W-L chart. It is a strategy developed in 1986 by Donna
Ogle, intended to motivate students to think about what they already know about a topic.
Activating prior knowledge is important because it helps students make connections to the
new information they will be learning. By tapping into what students already know, teachers
can assist students with the learning process.

Source: https://www.pdst.ie/node/961

This is one strategy you may apply in your own classes in the future. For now, you
shall be trying it for yourself first. The W column is where you list down the things you want
to learn from the lesson or the questions you have in mind pertaining to the lesson. The K
column is where you list down what you currently know about those things you have listed in
the W column. Three prompts have been pre-written under the W column to serve as your
guide. Go on and add more if you have more questions. After doing so, kindly accomplish the
first column while leaving the last column blank (for now).

What I Know What I Want to know What I Learned?

What is polarity?
Why is water polar?

How do hydrogen bonds cause

water molecules to stick
together?

How does water promote

homeostasis in the cellular
level?

Topic 1: Properties of Water

Introduction

The planet Earth is often called the "water planet," and has been given the nickname
"the blue marble." Almost three-quarters of our home planet is covered by water, and without
it, life as we know it could not exist on Earth. Water, like carbon, has a special role in living
things. It is needed by all known forms of life. Although water consists of simple molecules,
each containing just three atoms, its structure gives it unique properties that help explain why
it is vital to all living organisms.

You are probably already familiar with many of the water’s properties. For example,
you no doubt know that water is tasteless, odorless, and transparent. In small quantities, it is
also colorless. However, when a large amount of water is observed, as in a lake or the ocean, it
is actually light blue in color. The blue hue of the water is an intrinsic property and is caused
by selective absorption and scattering of white light. These and other properties of water
depend on its chemical structure.

The transparency of water is important for organisms that live in water. Because water
is transparent, sunlight can pass through it. Sunlight is needed by water plants and other water
organisms for photosynthesis.

Lesson Proper

To understand how water behaves and why it does so, it is imperative that we gain a
good understanding of its physical and chemical properties first. These are listed and explained
next.

Water is a polar molecule. Water is a bent molecule, not linear (Figure 2). The hydrogen
atoms have a partially positive charge (δ+); the oxygen atom has a partially negative charge
(δ–). This charge distribution is due to the electronegativity difference between hydrogen and
oxygen atoms (the attraction that an atom has for a bonding pair of electrons). The water
molecule in Figure 2 is shown in its bent shape with a bond angle of about 105 degrees.

Water has strong intermolecular forces. Normally,

partial charges such as those found in a water
molecule result in an intermolecular force known
as a dipole-dipole force, in which the positive end
of one molecule attracts the negative end of
another molecule. The very high electronegativity
of oxygen combined with the fact that a hydrogen
atom has only one electron results in a charge
difference significantly greater than you’d
normally expect. This charge difference leads to
stronger-than-expected intermolecular forces, and
these forces have a special name: hydrogen bonds.
Figure 2: Structure of the Water Molecule

The term hydrogen bond doesn’t refer to an actual bond to a hydrogen atom but to the
overall interaction of a hydrogen atom bonded to either oxygen, nitrogen, or fluorine atoms
with an oxygen, nitrogen, or fluorine on another molecule (intermolecular) or the same
molecule (intramolecular). Hence the term intermolecular force. (Note that although hydrogen
bonds occur when hydrogen bonds to fluorine, you don’t normally find such combinations in
biological systems.)

Hydrogen bonds in oxygen- and nitrogen-containing molecules are very important in

biochemistry because they influence reactions between such molecules and the structures of
these biological molecules. The interaction between water and other molecules in which there
may be an opportunity for hydrogen bonding explains such properties as solubility in water
and reactions that occur with water as a solvent.

One environmentally important consequence of hydrogen bonding is that, upon

freezing, water molecules are held in a solid form that’s less dense than the liquid form. The
hydrogen bonds lock the water molecules into a crystalline lattice that contains large holes,
which decreases the density of the ice. The less-dense ice — whether in the form of an ice cube
or an iceberg — floats on liquid water. In nearly all other cases where a solid interacts with
water, the reverse is true: The solid sinks in the liquid. So why is the buoyancy of ice important?
The layer of ice that forms on the surface of cold bodies of water insulates the liquid from the
cold air, protecting the organisms that live under the ice.

Figure 3: The Anomalous Expansion of Water explains how aquatic organisms could
survive in “frozen” bodies of water

The anomalous expansion of water is an abnormal property of water whereby it expands instead of contracting when
the temperature goes from 4˚C to 0˚C, and it becomes less dense. As a result during winter ice forms on top of the
water. Beneath the layer of ice there are layers of water where the temperature is more than 0˚C.This is where the fishes
live.

Source: www.quora.com (accessible through this link: https://bit.ly/2DkkrF6)

If you wish to understand better the “anomalous expansion” of water, you may watch
a video from YouTube accessible through this link https://bit.ly/3hQm6S4.

Water has a high specific heat. Specific heat is the amount of heat required to change
the temperature of a gram of water by 1 degree Celsius. A high specific heat means that
changing the temperature of water isn’t easy. Water also has a high heat of vaporization.
Humans can rid their bodies of a great deal of heat when their sweat evaporates from their
skin, making sweat a very effective cooling method.

Because of water’s high specific heat and heat of vaporization, lakes and oceans can
absorb and release a large amount of heat without a dramatic change in temperature. This give-
and-take helps moderate the earth’s temperature and makes it easier for an organism to control
its body temperature. Warm-blooded animals can maintain a constant temperature, and
coldblooded animals can absorb enough heat during the day to last them through the night.

To summarize what you just have learned from your reading, watch this video from
YouTube on the properties of water. You may use this link https://bit.ly/h2oprops.
 Topic 2: The Biochemical Role of Water

Introduction

As previously mentioned, biochemical reactions are practically aqueous reactions i.e.

they take place with water as medium. The following are examples of the roles of water in
biochemical reactions in the human body:

• Water acts as a transport medium across membranes, carrying substances into and out
of cells.
• Water helps maintain body temperature.
• Water acts as a solvent (carrying dissolved chemicals) in the digestive and waste
excretion systems.

In this lesson, we shall further explore the roles that water play in various life
processes.

Lesson Proper

Concept 1: Water is considered as the universal solvent.

As a polar molecule, water interacts best with other polar molecules, such as itself. This
is because of the phenomenon wherein opposite charges attract one another: because each
individual water molecule has both a negative portion and a positive portion, each side is
attracted to molecules of the opposite charge. This attraction allows water to form relatively
strong connections, called bonds, with other polar molecules around it, including other water
molecules. In this case, the positive hydrogen of one water molecule will bond with the
negative oxygen of the adjacent molecule, whose own hydrogens are attracted to the next
oxygen, and so on. Importantly, this bonding makes water molecules stick together in a
property called cohesion. The cohesion of water molecules helps plants take up water at their
roots. Cohesion also contributes to water’s high boiling point, which helps animals regulate
body temperature.

Figure 4: water molecules are able to stick together

Image credit: emaze.com

 Water’s extensive capability to dissolve a variety of molecules has earned it the
designation of “universal solvent,” and it is this ability that makes water such an invaluable
life-sustaining force. On a biological level, water’s role as a solvent helps cells transport and
use substances like oxygen or nutrients. Water-based solutions like blood help carry molecules
to the necessary locations. Thus, water’s role as a solvent facilitates the transport of molecules
like oxygen for respiration and has a major impact on the ability of drugs to reach their
targets in the body.

Concept 2: Water supports cellular structure

Water also has an important structural role in biology. Visually, water fills cells to help
maintain shape and structure. The water inside many cells (including those that make up the
human body) creates pressure that opposes external forces, similar to putting air in a balloon.
However, even some plants, which can maintain their cell structure without water, still require
water to survive. Water allows everything inside cells to have the right shape at the molecular
level. As shape is critical for biochemical processes, this is also one of water’s most important
roles.

Water also contributes to the formation of membranes surrounding cells. Every cell on
Earth is surrounded by a membrane, most of which are formed by two layers of molecules
called phospholipids. The phospholipids, like water, have two distinct components: a polar
“head” and a nonpolar “tail.” Due to this, the polar heads interact with water, while the
nonpolar tails try to avoid water and interact with each other instead. Seeking these favorable
interactions, phospholipids spontaneously form bilayers with the heads facing outward
towards the surrounding water and the tails facing inward, excluding water. The bilayer
surrounds cells and selectively allows substances like salts and nutrients to enter and exit the
cell. The interactions involved in forming the membrane are strong enough that the membranes
form spontaneously and aren’t easily disrupted. Without water, cell membranes would lack
structure, and without proper membrane structure, cells would be unable to keep important
molecules inside the cell and harmful molecules outside the cell.

Figure 5: structure of an amphipathic molecule

Image credit: ib.bioninja.com.au
 In addition to influencing the overall shape of cells, water also impacts some
fundamental components of every cell: DNA and proteins. Proteins are produced as a long
chain of building blocks called amino acids and need to fold into a specific shape to function
correctly. Water drives the folding of amino acid chains as different types of amino acids seek
and avoid interacting with water. Proteins provide structure, receive signals, and catalyze
chemical reactions in the cell. In this way, proteins are the workhorses of cells. Ultimately
proteins drive contraction of muscles, communication, digestion of nutrients, and many other
vital functions. Without the proper shape, proteins would be unable to perform these functions
and a cell (let alone an entire human) could not survive. Similarly, DNA needs to be in a specific
shape for its instructions to be properly decoded. Proteins that read or copy DNA can only bind
DNA that has a particular shape. Water molecules surround DNA in an ordered fashion to
support its characteristic double-helix conformation. Without this shape, cells would be unable
to follow the careful instructions encoded by DNA or to pass the instructions onto future cells,
making human growth, reproduction, and, ultimately, survival infeasible.
 Activity Sheet
After going through the course packet, you are now ready to go back to your K-W-L
chart and accomplish the last column (What I Learned). Please note that it is perfectly fine if
what you just learned does not agree (partly or totally) with what you knew. Remember that
learning sometimes entails being able to unlearn.

As always, if you want to learn more, please feel free to go over the uploaded
learning materials in our shared Google drive.

What I Know What I Want to know What I Learned

What is polarity?
Why is water polar?

How do hydrogen bonds cause

water molecules to stick
together?

How does water promote

homeostasis in the cellular
level?
 Assessment
PART I – MULTIPLE CHOICE

INSTRUCTIONS: Read each item carefully. Choose the best answer from the choices and
write the CAPITAL LETTER that corresponds to your choice on the blank before each number.

_____ 1. Which of the following correctly describes the shape of the water molecule?

A. linear B. bent C. pyramidal D. circular

_____ 2. Given its shape, the bond angle of a water molecule is around…

A. 100 degrees B. 105 degrees C. 110 degrees D. 115 degrees

_____ 3. This term pertains to the overall interaction of a hydrogen atom with atoms on the
same or another molecule.

A. ionic bond B. covalent bond C. metallic bond D. hydrogen bond

_____ 4. This physical quantity is technically defined as the amount of heat required to
change the temperature of a gram of water by 1 degree Celsius.

A. specific heat B. heat of vaporization C. heat of latency D. boiling point

_____ 5. Water molecules sticking together exhibit a property known as…

A. adhesion B. cohesion C. surface tension D. evaporation

PART II – CONSTRUCTED RESPONSE TYPE

INSTRUCTIONS: Answer the questions below briefly but concisely.

1. Identify three physico-chemical properties of water and discuss how each of these properties
enable water to support life.

2. How does water maintain the structural integrity of cells? You may provide examples and/or
illustrations to further support your answer.
 Assignment

You learned from your basic sciences that around 70% of the Earth’s water is in the
oceans. Now that you learned how important water is to sustain life, some of you might ask:
What if the oceans dry up? Would its impact be limited to organisms inhabiting the oceans?
Will it create a domino effect and make this planet totally inhabitable? Watch this episode from
WHAT IF’s YouTube channel. You may access the video directly through this link:
https://bit.ly/DryOcean.

As you watch the video, kindly take note of the effects mentioned in the video. Jot
them down below. Course
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Course Packet 02
Course Packet 02

Acids, Bases, and pH

Figure 6. Urine pH may reveal internal issues even without symptoms

Urine pH test usually comes as a part of routine urinalysis in most clinical laboratories. Though ignored by some,
determining urine’s pH could actually warn you if one or more of your internal organs are not functioning properly.
For example, urine pH readings towards the extremes (too acidic or too basic) may indicate the likelihood of kidney
stone formation. Early detection of problems through simple tests such as this guides your healthcare provider in
his/her medical decisions concerning your health.

Image credit: www.tyentusa.com

Introduction

In aqueous solutions — especially in biological systems — the concentration of

hydrogen ions (H+) is very important. Biological systems often take great pains to make sure
that their hydrogen ion concentration — represented as [H+] or by the measurement of pH (the
measure of acidity in a solution) — doesn’t change.

Even minor changes in hydrogen ion concentration can have dire consequences to a
living organism. For example, in human blood, only a very small range of hydrogen ions allows
the body to function properly. Hydrogen ion concentrations higher or lower than this range
can cause death.

Because living organisms are so dependent on pH, we review the concepts of acids,
bases, and pH in the following sections.

Pre-Assessment

I – TRUE OR FALSE

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INSTRUCTIONS: Read each statement carefully. Guided by the words in boldface, determine
whether the statement is true or false. Write T on the blank provided if the statement is true.
Course Packet 02

Write F if false.

_____ 1. A solution with excess hydroxide ions is described as acidic.

_____ 2. Water’s ability to undergo autoionization means that it can split salts into ions.

_____ 3. In pure water, the concentration of hydronium ions is equal to that of hydroxide ions.

_____ 4. A substance with a neutral pH will have a pH value of 7.0

_____ 5. The lowest possible pH value is 1.

_____ 6. Strong acids undergo partial ionization while in an aqueous solution.

_____ 7. Buffer solutions control the pH of a solution.

_____ 8. Metabolic acidosis results from a decrease in the concentration of bicarbonate ions in

the blood.

_____ 9. A substance with a pH of 9 has a pOH of 5.

_____ 10. Buffer systems exist in the human body.

II – COMPLETION TYPE

INSTRUCTIONS: Supply the missing values using the data given in the table.

[H3O+] [OH-] pH pOH

5.62 x 10-4
5.65
9.21
4.55
1.58 x 10 -11

Lesson Proper

Subtopic 1: Achieving Equilibrium

When the concentrations of hydrogen ion (H+) and hydroxide ion (OH–) are the same,
a solution is neutral. If the hydrogen ion concentration exceeds the hydroxide ion
concentration, the solution is acidic. If the hydroxide ion concentration is greater, the solution
is basic. These chemical species are related through a chemical equilibrium.

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The equilibrium of hydrogen ions is present in all aqueous solutions. Water may or
may not be the major hydrogen ion source (usually it isn’t). Water is a contributor to the
hydrogen ion concentration because it undergoes autoionization, as shown by the following
Course Packet 02

equation:

H2O(l) ⇋ H+(aq) + OH–(aq)

The double arrow (⇋) indicates that this reaction (represented by the equation) is an
equilibrium; as such, there must be an associated equilibrium constant (K). The equilibrium
constant in the preceding equation is Kw. The value of Kw is the product of the concentrations
of the hydrogen ion and the hydroxide ion:

Kw = [H+] [OH–] = 1.0 × 10–14 (at 25°C)

The value of the constant Kw, like all K’s, is only constant if the temperature is constant.
In the human body, where T = 37°C, Kw = 2.4 × 10–14. In pure water, at 25°C, [H+] = 1.0 × 10 –7 M
(1.6 × 10–7 M at 37°C). The hydroxide ion concentration is the same as the hydrogen ion
concentration because they’re formed in equal amounts during the autoionization reaction.
Keep in mind that [H+] = [OH–] only in pure water.

Subtopic 2: pH and pOH

Expressing hydrogen ion concentrations in an exponential form, such as 1.0 × 10 –7, isn’t
always convenient. Thankfully, you have a way of simplifying the representation of the
hydrogen ion concentration: the pH. You can calculate the pH for any solution by using the
following equation:

pH = –log [H+]
For instance, in the case of a solution with a hydrogen ion concentration of 1.0 × 10–7
M, the pH would be

pH = –log (1.0 × 10–7) = 7.0

The pH scale (see figure 7) is an open-ended scale, meaning that a solution can have a
pH greater than 14 or less than 0. For example, the pH of a 1.0 × 10 1 M solution of hydrochloric
acid is –1. The 0–14 scale is a convenient part of the pH scale for most real-world solutions —
especially ones found in biochemistry. Most biological systems have a pH near 7, although
significant deviations may exist (for example, the pH in your stomach is close to 1).

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Figure 7. The PH scale

Course Packet 02

Image Credit: Science ABC

You can calculate pOH (related to the concentration of the hydroxide ion) in a similar
manner to the pH calculation. That is, you can use the equation pOH = –log [OH–]. You can
calculate the hydroxide ion concentration from the hydrogen ion concentration and the K w
(equilibrium constant) relationship:

[OH–] = Kw ÷ [H+]
For example, if a solution has a [H+] = 6.2 × 10–6, its pH would be 5.21

The calculation for the pOH of that solution is pretty simple:

pOH = 14.00 – pH = 14.00 – 5.21 = 8.79

Now, if you have the pH or pOH, getting the corresponding [H+] or [OH–] is a simple
task:

[H+] = 10–pH and [OH–] = 10–pOH

For example, a solution with a pH of 7.35 has a [H +] = 10–7.35 = 2.2 × 10–7.

Concept 3: Applying the Bronsted-Lowry Theory

Because the acidity (pH) of the biological medium is so very important, here we take a
look at one of the most accepted theories concerning acids and bases — the Brønsted-Lowry
theory. According to this theory, acids are proton (H+) donors, and bases are proton acceptors.

Acids increase the hydrogen ion concentration of a solution (they lower the pH, in
other words). Some acids, known as strong acids, are very efficient at changing hydrogen ion
concentration; they essentially completely ionize in water. Most acids — particularly
biologically important acids — aren’t very efficient at generating hydrogen ions; they only
partially ionize in water. These acids are known as weak acids.

Bases accept (react with) rather than donate hydrogen ions in solutions. Bases decrease
the hydrogen ion concentration in solutions because they react with these ions. Strong bases,
although they can accept hydrogen ions very well, aren’t too important in biological systems.
The majority of biologically important bases are weak bases.

The Brønsted-Lowry theory helps to explain the behavior of acids and bases with
respect to equilibrium. A Brønsted-Lowry acid is a hydrogen ion (H+) donor, and a Brønsted-
Lowry base is a hydrogen ion acceptor. Acetic acid, a weak acid found in vinegar, partially
ionizes in solution, evidenced by the following equation:

CH3COOH ⇋ H+ + CH3COO–
The double arrow indicates that the acetic acid doesn’t completely ionize. (For a strong
acid, complete ionization would occur, indicated by a single arrow.) The equilibrium arrow

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(⇋) indicates that all three chemical species are present in the solution: the acetic acid, the
acetate ion, and the hydrogen ion, along with the water solvent.
Course Packet 02

In the Brønsted-Lowry theory, you consider the acetate ion to be a base because it can
accept a hydrogen ion to become acetic acid. According to this theory, two substances differing
by only one hydrogen ion (H+) — such as acetic acid and the acetate ion — are members of a
conjugate acid-base pair. The species with one additional hydrogen ion is the conjugate acid
(CA), and the species with one less hydrogen ion is the conjugate base (CB).

You can express the equilibrium from the acetate example, like all equilibria, by using
a mass-action expression — as long as a balance among the species is present. This expression
is also known as a reaction quotient or an equilibrium constant. For acetic acid, this expression
is as follows:

The “a” subscript means that this expression represents an acid. The square brackets
refer to the molar equilibrium concentrations of the species present. You can express the Ka as
a pKa. The calculation of pKa is similar to the calculation of pH:

pKa = –log Ka
In terms of conjugate acids and bases, every Ka expression appears as

Like an acid, a base has a Kb value (the subscript b meaning base). A weak base, like
ammonia, is part of the following equilibrium:

NH3 + H2O ⇋ OH– + NH4+

The equilibrium constant expression for this equilibrium is:

The generic form of a Kb expression is

As with a Ka expression, a Kb expression has no variations other than the actual

formulas of the conjugate acid and base.

Every acid has a Ka, and its corresponding conjugate base has a Kb. The K a and the Kb
of a conjugate acid-base pair are related by the Kw — the ionization constant for water. For a
conjugate acid-base pair, KaKb = Kw = 1.0 × 10–14. In addition, you can use the following shortcut:
pKa + pKb = 14.00.

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The Kb for the acetate ion, the conjugate base of acetic acid, would be associated with
the following equilibrium expression:
Course Packet 02

CH3COO– + H2O ⇋ OH– + CH3COOH

The Ka for the ammonium ion, the conjugate acid of ammonia, would be associated
with the following equilibrium expression:

NH4+ ⇋ H+ + NH3
An acid may be capable of donating more than one hydrogen ion. A biologically
important example of this type of acid is phosphoric acid (H 3PO4), which is a triprotic acid
(meaning it can donate three hydrogen ions, one at a time). The equilibria for this acid are:

The subscripts are modified to indicate the loss of hydrogen 1, hydrogen 2, or hydrogen
3. The associated Ka expressions are all of the form

Here’s the breakdown for each Ka

The value for each successive equilibrium constant often is significantly lower than the
preceding value. Table 1 below illustrates some biologically important acids. You can refer to
this table when working buffer problems or determining which acid is stronger.

Table 1
The Ka values for Biologically Important Acids

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Course Packet 02 013

Source: Biochemistry for Dummies 2nd Ed. (by Moore and Langley) p.26

Concept 4: Buffers and pH Control

A solution that contains the conjugate acid-base pair of any weak acid or base in
relative proportions to resist pH change when small amounts of either an acid or a base are
added is a buffer solution. Therefore, buffers control the pH of the solution. Buffer solutions
are important in most biological systems. Many biological processes proceed effectively only
within a limited pH range. The presence of buffer systems keeps the pH within this limited
range.

In the human body, the pH of various body fluids is important. The pH of blood is 7.4,
the pH of stomach acid is 1–2, and the pH in the intestinal tract is 8–9. If the pH of blood is
more than 0.2 pH units lower than normal, a condition known as acidosis results; a
corresponding increase in pH of about the same magnitude is alkalosis. Acidosis and alkalosis,
which may lead to serious health problems, each have two general causes:

• Respiratory acidosis is the result of many diseases that impair respiration, including
pneumonia, emphysema, and asthma. These diseases are marked by inefficient
expulsion of carbon dioxide, leading to an increase in the concentration of carbonic
acid, H2CO3.

• Metabolic acidosis is due to a decrease in the concentration of HCO3– (the bicarbonate

ion). This decrease may be the result of certain kidney diseases, uncontrolled diabetes,
and cases of vomiting involving nonacid fluids. Poisoning by an acid salt may also lead
to metabolic acidosis.

• Respiratory alkalosis may result from hyperventilation, because this excessive

removal of carbon dioxide can lead to a decrease in the H 2CO3 concentration.
Immediate treatment includes breathing into a paper bag, which increases the carbon
dioxide concentration in the inhaled air and, therefore, in the blood.

• Metabolic alkalosis may result from excessive vomiting of stomach acid.

To resist these pH problems, the blood has a number of buffer systems — systems that
resist a change in pH by reacting with either added acids or bases. In general, buffers may be
amphiprotic substances or mixtures of weak acids and weak bases. In the body these include
several proteins in blood plasma and the bicarbonate buffer system.

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The bicarbonate buffer system is the main extracellular buffer system. This system also
provides a means of eliminating carbon dioxide. The dissolution of carbon dioxide in aqueous
systems sets up the following equilibrium:
Course Packet 02

The presence of the conjugate acid-base pair (H2CO3 and HCO3–) means that this is a
buffer system. The conjugate acid-base ratio is about 20:1 at a pH of 7.4 in the bloodstream.
This buffer system is coupled with the following equilibrium (instrumental in the removal of
carbon dioxide in the lungs):

The second ionization of phosphoric acid, Ka2, is the primary intracellular buffer
system. The pH of this conjugate acid-base pair (H2PO4– and HPO42–) is 7.21 for a solution with
equal concentrations of these two species.

How do we calculate a buffer’s pH?

To determine a buffer’s pH, you may use a Ka or Kb calculation, as we discussed earlier

or you may use the Henderson-Hasselbalch equation, which is a shortcut.

The Henderson-Hasselbalch equation takes two forms:

and

The terms in either form are the same as those defined earlier. For example, suppose
you want to calculate the pH of a buffer composed of 0.15 M pyruvic acid and 0.25 M sodium
pyruvate. Referring back to Table 1, you see that the Ka of pyruvic acid is 3.2 × 10–3.

The pKa would be 2.50. Therefore:

The greater the values of [CA] and [CB], the greater the buffer capacity of the solution.
The buffer capacity indicates how much acid or base may be added to a buffer before the buffer
ceases to function. A buffer in which the [CA] = [CB] = 1.0 would have a much higher buffer
capacity for adding either acids or bases than a buffer in which the [CA] = [CB] = 0.1. If there
were a buffer in which [CA] = 1.0 and its [CB] = 0.1, the buffer would have a higher buffer
capacity for additions of a base than for additions of an acid because the buffer contains more

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acid than base. For the buffer to be as flexible as possible, the concentrations of the conjugate
acid-base pair should be as close to equal as possible and as high as possible.
Course Packet 02

Instructor’s Note:

This topic requires you to apply your mathematical skills to solve problems on involving acids,
bases, and pH. Hence, practice is necessary towards mastery of the concepts. For this purpose, practice
problems (and their solutions) have been uploaded to our LMS. There are a number of good tutorials in
YouTube that you could watch and learn from. Nevertheless, we shall be going over these problems in
one of our synchronous sessions.

To access the problem set, kindly use this link https://bit.ly/probsets and open the file
named “pH and Buffers.”

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Activity Sheet
Activity Sheet

For this activity, we shall be having fun while learning about pH/pOH using a free
simulation accessible from phet.colorado.edu. As science teachers, an effective strategy that
you could use to teach abstract ideas in class is to use animations and this website has a lot of
them, downloadable for FREE. Use this link to access this simulation: https://bit.ly/PHactivity.

Measuring the pH of common substances 2

3
1

Instructions:

1. Select “Macro” from the options at the bottom of the page (#1 in the picture above)
2. Use the dropper to place samples inside the container just below it. Clicking the arrow (#2 in
the picture) shows a drop-down menu where you could see a list of common solutions found
at home.
3. Drag the pH meter’s probe (#3 in the picture) into the container and check the pH reading.
Record your answers in the table in the next page.

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Substance Tested pH reading Acid / Base

hand soap
Activity Sheet

Orange juice
Spit
coffee
milk
Chicken soup
blood
Drain cleaner

4. Using the same simulation, place battery acid into the container until the ½ L mark. Using
the water faucet, add water to the container until full, making sure that you are looking at the
pH reading while doing so. Repeat the same procedure this time starting with drain cleaner in
place of battery acid. What did you observe about the pH reading in the:

a. battery acid solution

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___________________________________________________________________________________

b. drain cleaner

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What could be the reason behind such observation?

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5. Choose any of the common substances and place it in the container until the ½ L mark. Pour
in some water until the container is full. Note the pH reading.

6. Open the container’s valve to release some of the solution and note if there is a change in the
solution’s pH.

What did you observe?

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What could explain this observation?

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Note: Feel free to explore the other features of this simulation.

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Assessment
I – SHORT RESPONSE TYPE
Assessment

INSTRUCTIONS: Provide brief but concise answers to each of the questions below.

1. Using the Bronsted-Lowry concept, how do you differentiate an acid from a base?

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___________________________________________________________________________________

2. What is pH? Why is this concept relevant in biochemistry?

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___________________________________________________________________________________
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3. What is the difference between strong acids/bases and weak acids/bases? Which ones are
more relevant in our study of living things? Justify your answer.
___________________________________________________________________________________
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___________________________________________________________________________________

4. How is the normal acidity in the blood maintained? Explain using the concept of
physiological buffers.
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II – PROBLEM SOLVING

INSTRUCTIONS: Provide logical and valid solutions to the problems below. Show your
computations.

1. Determine the [H3O+] concentration of a substance with a pH of 7.65.

2. What is the pOH of a 0.000901 M solution of magnesium hydroxide?
3. Calculate the [OH-] of a substance with a pH of 2.25.

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Assignment
Assignment

Image credit: SciShow

I’m sure you have heard about alkaline water from someone. You might even be one
who prefers drinking alkaline water over its counterparts in the market. Some people advance
the idea that various diseases in the human body are linked with low blood pH level. Hence,
they assert that consuming acidic water does more harm than good as it would, in effect, make
the blood more acidic and eventually lead to a myriad of diseases including osteoporosis and
cancer.

For your assignment, kindly do a quick research on the effects of consuming water of
different pH levels to the human body. You may also want to look into references supporting
or refuting the claims pertaining to the health benefits of a particular type of water and let us
discuss them in class next meeting.

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