College of Science, UEP

Jaymar L. Erivera
eriverajaymar@gmail.com

BIOCHEMISTRY
FOR NON-CHEMISTRY MAJOR
 OVERVIEW OF THE MODULE

Purpose and Description

Biochemistry (modular approach) is an overview of the material covered in a typical college-
level biochemistry course subject. I have made every attempt to keep the material as current
as possible, but the field is changing ever so quickly. The basics, however, stay the same,
and that is where I’ am concentrate my efforts. I’ am also include information on some of
the applications of biochemistry that you read about in your everyday life, such as
forensics, cloning, gene therapy, genetic testing, genetically modified foods, and so on.

I have organized this module in a logical progression of topics that might be used in a
biochemistry course. I have made extensive use of structures and reactions. While reading,
try to follow along in the associated figures, whether they be structures or reactions. The
icons point out things to which you should pay particular attention, for various reasons. If
you are taking a biochemistry course subject, use this rather inexpensive book to supplement
that very expensive biochemistry textbook.

This module deals with the structure and function of fundamental chemical molecules of
a cell. It starts with an overview of the module and advanced applications that depend on
the subjects covered in the module. It then covers the basic chemical building blocks of cells,
from elements to macromolecules. The structure of nucleic acids will be introduced, and its
importance to the mechanism of DNA replication. Then, the different levels of protein
structure will be defined and protein-protein interactions, covalent modification and the
nature of membrane proteins, described. The functionality of proteins as enzymes will be
discussed in detail. Following an introduction to lipids and carbohydrate structures, the
role of the various macromolecules in the context of membrane flow, cell shape, cytoskeleton,
etc. will be discussed. Energy and metabolism is introduced by discussing the important
concept of free energy and relating this to the central role of ATP and coupling of
biochemical processes. The course then surveys carbohydrate and fat metabolism,
photosynthesis and related metabolic processes in plants, and concludes with section on the
integration of metabolism.
 OVERVIEW OF THE MODULE

Note for Students

W elcome to Biochemistry!

I’ am certainly happy you have decided to delve into the fascinating world of
biochemistry. Biochemistry is a complex area of chemistry, but understanding
biochemistry isn’t really complex. It takes hard work, attention to detail, and the desire
to know and to imagine. Biochemistry, like any area of chemistry, is not a spectator
sport. You must interact with the material, try different explanations, and ask yourself
why things happen the way they do.

Work hard and you will get through your biochemistry course subject. More
importantly, you might grow to appreciate the symphony of chemical reactions that
take place within a living organism, whether it be a one-celled organism, a tree, or a
person. As each individual instrument contributes to an orchestra, each chemical
reaction is necessary, and sometimes its part is quite complex. However, when you
combine all the instruments, and each instrument functions well, the result can be a
wonder to behold and hear. If one or two instruments are a little out of tune or aren’t
being played well, the orchestra still functions — but things are a little off. The sound
isn’t quite as beautiful, or there is a nagging sensation of something being wrong. The
same is true of an organism. If all the reactions occur correctly at the right time, the
organism functions well. If a reaction or a few reactions are off in some way, the
organism may not function nearly as well. Genetic diseases, electrolyte imbalance, and
other problems may cause the organism to falter. And what happens then? Biochemistry
is often where ways of restoring the organism to health are found.

As you flip through this module you will see a lot of chemical structures and reactions.
Much of the biochemistry revolves around knowing the structures of the molecules
involved in biochemical reactions. If you are in a biochemistry course, you probably have
had at least one semester of organic chemistry. You will recognize many of the
structures, or at least the functional groups, from your study of organic chem. You will
see many of those mechanisms that you loved/hated here in biochemistry.

If you got this module just to gain general knowledge about a fascinating subject, try
not to get bogged down in the details. Skim the chapters. If you find a topic that
interests you, stop and dive in. Have fun learning something new.
 OVERVIEW OF THE MODULE

Course Requirements

Welcome to the world of Biochemistry. Biochemistry is

around you all the time and impacts everything you do.
What is necessary before you start to learn and comprehend
Biochemistry?

1. Appreciation of science/chemistry. Even if you do

not enjoy science, you need to realize that our lives
change daily with new research and developments in
chemistry.

2. Inorganic and Organic chemistry skills. There are some problems

that requires calculations and the manipulation
of mathematical equations. You need to review your
Inorganic and Organic chemistry skills.

3. Patience and perseverance. Some say organic chemistry

is difficult, but it is not impossible. You’ve encountered
and conquered many difficult problems in
life; organic chemistry is next!

4. Tools. You need to provide yourself with tools like calculator,

periodic table, ball pen/pencil, molecular
models, etc. Internet connectivity is also necessary if
your teacher may require you to research or submit
materials online.

5. Portfolio. You may need to prepare a folder to compile

your graded LE’s along with other materials (both
hard and soft copies) to track your progress in this
course. You may be asked to submit these at the end
of the term.

How would your performance be rated?

1. Examinations. You will submit Learning Exercises (LE’s) and take examinations
(Quizzes, Midterm Exam, Final Exam)

2. Project(s). You may need to submit assigned project(s)

Percentages may vary depending on your instructor/facilitator.
Module no. 01
INTRODUCTION TO
BIOCHEMISTRY
Jaymar L. Erivera
eriverajaymar@gmail.com
 Introduction to Biochemistry
OVERVIEW

L iving things are composed of life less molecules. When these molecules are considered

individually, they are found to comfort to all the physical and chemical laws that describe the
behavior of inanimate matter. Yet when put together in a particular manner, they start to
exhibit the different attributes of life.
The smallest collection of molecules that exhibits the attributes of life is the living cell. It feeds,
respires, digests, excretes, moves, and reproduces.
In this module, we shall acquaint ourselves with the structure and biochemical activities of
living cells. It appears to be a logical first activity in our attempt to understand the chemistry
of biomolecules and ultimately, the living state.
LEARNING OUTCOME
At the end of this module, you should be able to:

• Enumerate the attributes of living matter

• Distinguish between prokaryotes and eukaryotes
• Identify the important organelles of the cell
• Enumerate the biochemical systems present in each organelle
• Correlate each part with its function
• Name the common elements required by the living organisms
• Enumerate the building blocks of biopolymers
• Describe the four classes of biopolymers

Why Biochemistry?
We suppose the flippant answer would be “Why not?” or “Because it is required.”
That first response is not too bad an answer, actually. Look around. See all the living or once
living things around you? The processes that allow them to grow, multiply, age, and die are
all biochemical in nature. Sometimes we sit back and marvel at the complexity of life, the
myriad of chemical reactions that are taking place right now within our own bodies, how all
these biochemical reactions are working together so that we can sit and contemplate them.
When John learned about the minor structural difference between starch and cellulose he
remembers thinking: “Just that little difference in the one linkage between those units is
basically the difference between a potato and a tree?” It made him want to learn more, to
delve into the complexity of the chemistry of living things, to try to understand. We encourage
you to step back from the details occasionally and marvel at the complexity and beauty of life.
What Is Biochemistry and Where Does It Take Place?
Biochemistry is the chemistry of living organisms. Biochemists study the chemical reactions
that occur at the molecular level of organisms. Normally it is listed as a separate field of
chemistry. However, in some schools it is part of biology, and in others it is separate from
both chemistry and biology.
Biochemistry really reaches out and combines aspects of all the fields of chemistry. Because
carbon is the element of life, organic chemistry plays a large part in biochemistry. Many times
biochemists study how fast reactions occur — that’s physical chemistry. Often metals are
incorporated into biochemical structures (such as iron in hemoglobin) — that’s inorganic
chemistry. Biochemists use sophisticated instrumentation to determine amounts and
structures — that’s analytical chemistry. Biochemistry is similar to molecular biology; both
study living systems at the molecular level, but biochemists concentrate on the chemical
reactions that are occurring.

Biochemists may study individual electron transport within the cell, or they may study the
processes involved in digestion. If it’s alive, biochemists will study it.

I. IDENTIFIYING CHARACTERISTICS OF LIVING MATTER

High Degree of Organization

Living matter is complicated and highly organized. Living organisms possess intricate
internal structures and contain many types of complex molecules that play specific
functions. In contrast, inanimate matter, like clay and rocks and sea water, contains
much simpler chemical compounds of random mixtures.

Ability to Extract, Transform and Use Energy from their Environment

• FOOD AS ENERGY SOURCE

All living things need food as their source of energy for all body activities. Plants
make their own food from water and carbon dioxide with the aid of sunlight,
while animals get their food by eating plants and other animals.

• RESPIRATION
Living organisms respire to get energy from food. Usually, this process involves
taking in oxygen and giving out carbon dioxide.

• WASTE DISPOSAL
Feeding and respiration also produce waste substance. Getting rid of them is
called excretion. Plants excrete through their leaves. Animals do it in various
ways.
 • MOVEMENT
All living things move, though some, like plants, usually move too slowly for us
to see. Most animals can move their whole bodies so that they can go from
place to place. This is called locomotion.

• GROWTH
All living things grow. Trees keep on growing throughout their lives while
others, like us, reach a certain size and then stop. Inanimate objects are not
capable of growth.

• REPRODUCTION
Perhaps the most extraordinary attribute of living organisms that
differentiates them from non-living things is their capacity to self-replicate,
that is, to produce new versions of themselves.

Self-Assessment Question 1-1

1. Why isn’t a jeep living matter?
It needs food (gasoline) and it excrete waste (form its exhaust
pipe) It turns its food to energy in its combustion chamber and it
moves as you manipulate its steering wheel. But why isn’t it alive?

II. DIVERSITY AMONG CELLS

Cells are the smallest units that are capable of life. The smallest organisms consist of
single cells, while the human body is believed to contain at least 10 14 cells, which are
grouped into tissues and organs. There are many different types of cells that are
usually highly specialized. One type may carry messages; another tenses a muscle. One
may deliver oxygen, another gobble bacterium. These specialized cells cannot
maintain themselves independently. Each cell depends on its neighbors for some of
its own needs. The miracle of the human body, or of any complex organism, is the
coordination of this fantastic number of cells.

Despite these differences, various cells have similar basic structural features. Each cell
is surrounded by a membrane wall or a cell wall which makes it self-contained and to
some extent self-sufficient. Within each cell is a nucleus or in its absence, a nuclear
zone, where the genetic materials are stored. The rest of the cell outside the nucleus
or nuclear zone is called cytoplasm.

Two Basic Types of cell

Living cells exist in two basic patterns: prokaryotes and eukaryotes. These two terms
are derived from Greek word Karyon “nut” or “Kernel”, i.e. nucleus. Prokaryotic means
“before the nucleus” while eukaryotic, “well-formed nucleus”.

The characteristic that distinguishes one cell type from the other is the complexity of
their cellular organization. The eukaryotic cell possesses a membrane-bound nucleus
while a prokaryotic cell does not.

Prokaryotes include; bacteria,

Archean (ancient bacteria)
blue-green algae, rickettsia and
spirochetes.

Eukaryotes include; green

algae, fungi, protozoa and all
other plant and animal cell.

Figure 1.1. Prokaryotes and Eukaryotes

• PROKARYOTES
are usually smaller and are considered the first type of cells to arise in
biological evolution. Within the cell membrane of prokaryotes is the cytoplasm
where the nuclear material, ribosomes, and other nutrients are indistinctly
spread out. There is, therefore, little that could be called internal structure in
prokaryotic cells.

• EUKARYOTES
Eukaryotes, on other hand, are much larger than prokaryotes. Their volume is
1,000 to 10,000 times greater. The eukaryotes include green algae, fungi,
protozoans and all other plants and animals. They exhibit a high degree of
organization by way of membrane – enclosed subcellular structures called
organelles which have distinct features, composition, and functions.
 Figure 1.2. Prokaryotic cell and Eukaryotic cell

Fig. 1.3. Eukaryote cell structure. (a) Structure of a typical animal cell, (b) structure of a typical
plant cell.

Self-Assessment Question 1-2

a) With the help of Fig. 1.2, give the schematic comparison of prokaryotic
cell and eukaryotic cell.
b) Using the Fig. 1.3 give at least two differences between plant and
animal cells.
There are three basic component of a typical cell; cell membrane, cytoplasm, and the
nucleus.
I. Cell Membrane
The cell membrane or plasma membrane is the outer most component of the cell. The
cell membrane encloses the cytoplasm and form the boundary between material
inside the cell and material outside it. It serves as the selective barrier that determines
what substance moves into and out of the cell. It also plays a role in communication
between cells.
The plasma membrane is made up of two major molecules; the phospholipids and
protein. In addition, the membrane also contains other molecule, such as cholesterol,
carbohydrates, water, and ions. The phospholipids form a double layer molecule
forming outer and inner layer of the plasma membrane. The polar, phosphate-
containing end of the phospholipids are hydrophilic (water loving) and therefore face
the water inside and outside the cell. The non-polar, fatty acid ends of the
phospholipids are hydrophobic (water-fearing) and therefore face away from water
on either side of the membrane. The double layer of the phospholipids molecule forms
a lipid barrier between the inside and outside the cell. This arrangement of
phospholipids molecule in the cell membrane gives rise to a model of structure called
fluid-mosaic model.
The cholesterol within the phospholipids membrane gives its added strength and
flexibility. The protein molecule that floats among the phospholipids molecule and in
some case, it may extend from the inner to the outer surface of cell membrane. The
protein component of the plasma membrane function as membrane
channel/membrane pore, carrier molecule, receptors molecules, enzymes or structural
protein.
The membrane channel and the carrier protein are involved with the movement of
substance through the cell membrane. Receptor molecules are part of an intercellular
communication system that enables cell recognition and coordination of the activities
of cells. receptors cells are found in the nerve cells. A nerve cell can release a chemical
messenger that moves to a muscle cells and temporary binds to its receptor. The
binding acts as signal that triggers a response such as contraction of muscle cell.
Enzymes are protein molecules that catalyze chemical reaction within the cell. The
structural proteins provide rigidity and support to the cytoplasm.

II. Cytoplasm and Cytoplasmic Organelles

The cytoplasm is a viscous, transparent, water material surrounding the nucleus and
is enclosed by the plasma membrane. The cytoplasm contains a large percentage of
water, inorganic ions (K+, Ca2+, Na+, and Cl-), and naturally occurring organic
compounds such as protein, lipids, and carbohydrates. The viscous, semitransparent
fluid that is 70% to 90% water is called the cytosol.
The eukaryotic cytoplasm contains the functional structures of the cell called the
organelles. Organelles are the cells metabolic unit. Each organelle performs specific
function to maintain the life of the cell.
1. Mitochondria are small, bean-shaped, rod-shaped, long, threadlike organelles
with inner and outer membrane. Mitochondria is the major sites of adenosine
triphosphate (ATP) production with the cell. ATP is the major energy source for
most chemical reaction within the cell.
The number of mitochondria in a particular cell reflects the cells have abundant
number mitochondria as compared to those inactive cells.
2. Ribosomes are granular material found free in the cytoplasm or attached to a
network of membrane called the endoplasmic reticulum. They are considered to
be the sites for protein synthesis.
3. Endoplasmic reticulum is extensive network of membrane-bound tubules
extending from the outer nuclear membrane into the cytoplasm. Rough ER is the
part of endoplasmic reticulum with ribosomes attached to its membrane. Large
amount of rough ER in the cell indicate that it is synthesizing large amount of
protein for export from the cell.
On other hands, ER without ribosomes is call smooth ER. Smooth ER is a site for
lipid synthesis and also participates in detoxification of chemical within the cell.
Since the liver is involved in detoxification activity large amount of smooth ER are
found in their cells. In skeletal muscles, the smooth ER that stores calcium ions is
called sarcoplasmic reticulum.
4. Golgi apparatus are membrane bound sacs that collect, modifies, packages; and
distribute protein and lipids manufactured in the endoplasmic reticulum.
5. Secretory Vesicle is a small, membrane-bound sacs that support or stores material
within the cell. Secretory vesicle pinches off from golgi apparatus and move
towards the cell membrane. Their membrane fuse with the cell membrane and
release their content to the exterior of the cell.
6. Lysosomes are membrane bound vesicles formed from golgi apparatus. They
contain a variety of enzyme and functions as the intracellular digestive system. The
lysosomes pinch off from the golgi apparatus and move toward the phagocytic
vesicle formed from endocytosis and fused with their membrane. The enzyme
within the lysosomes is released into the phagocytic vesicle and breakdown its
content. Phagocytic cells such as the white blood cells are expected to have an
abundant number of lysosomes.
7. Peroxisomes are small, membrane bound vesicle containing oxidizing enzymes
(peroxidase) that breakdown hydrogen peroxides formed as a by-product from
breakdown of fatty acid and amino acids. Since hydrogen peroxides are toxic to
the cell, an enzyme peroxidase released from peroxisomes breakdown hydrogen
peroxide to water and oxygen.
8. Cytoskeleton consists of protein that supports the cell, hold organelles in place,
and enable the cell change shape. Cytoskeleton consists of;
a. Microtubules are hollow structure formed by tubulin protein subunits. It
helps provides support to the cytoplasm of cell, assist in the process of cell
division and form essential component of cilia and flagella.
b. Microfilaments are small fibrils formed from protein subunit that
structurally support the cytoplasm. Some microfilaments are involved with
 cell movement. Microfilament is muscle cell enable the cell to shorten or
contract to cause movement.
c. Intermediate filaments are fibrils formed form protein subunit that are
smaller in diameter than microtubules but are larger in diameter than
microfilament. They provide mechanical support to the cell.
9. Centrosomes and Centrioles is a specialized zone of the cytoplasm closed to the
nucleus that is the center of microtubule formation. The centrosomes contain two
centrioles. During cell division, the centrioles from the spindle fibers that facilitate
the movement of chromosomes towards the centrosomes at the opposite poles
of the cell.

III. Nucleus
The nucleus is a large organelle usually located near the center of the cell.it controls
cellular activity. All cells of the body have nucleus at some point in their life cycle,
although some cells such as the red blood cells, loses their nuclei as they mature. Some
cells in the body contain only one nucleus such as smooth muscle cells while other cell
such as bone cell, heart and skeletal muscle, and nerve cell has more than one nucleus.
The nucleus is bounded by a nuclear envelope, which consist of outer and inner
membrane with a narrow space between them. At many points on the surface of the
nucleus, the inner and outer membrane come together from the nuclear pore,
through material pass in and out of the nucleus.
When the cell is not dividing its nucleus contains loosely coiled fibers called chromatin
consisting of DNA (deoxyribonucleic acid) and protein. During cell division, the
chromatin fiber shortens and becomes more tightly coiled to form the 23 pairs of
chromosomes.
A certain segment of chromosomes contains the genes, the basic unit of heredity. It is
made up of DNA molecule bound with simple protein histones. It influences the
structural and functional feature of every individual.
The nucleoli are rounded, dense, well define nuclear bodies with no surrounding
membrane. Nucleoli are the sites of ribosomes synthesis. Protein produced in the
cytoplasm move through the nuclear pore into the nucleus and into the nucleolus. The
proteins are joined with ribosomal ribonucleic acid (rRna) forming ribosomes.

CHEMICAL MAKEUP OF LIVING CELLS

The chemical makeup of all organism appears to have been determined by the
availability of raw materials in the environment and by the fitness of the atoms for
specific roles. Simple and complex living organism originate from simple elements.
Carbon, hydrogen, and oxygen combine to make up carbohydrates and fatty acids.
The addition of nitrogen, as well as sulfur forms amino acids and makes the possible
combination of different amino acid to form protein. With addition of phosphorus, it
forms a nucleotide – the building blocks for the synthesis of nucleic acid; DNA and
RNA, and complex lipid.
A. Elemental Composition of Living Cell
There are many chemical elements present in living matter. The chemical
elements present in the living organism are categorized into:
1. Major Principal element these are the elements that make up the
macromolecules of life. This includes; Carbon, Hydrogen, Oxygen, Nitrogen,
Phosphorus, and Sulfur. The first four major elements accounts for
approximately 96% of the dry mass of human body.
2. Minor/Lesser elements this are metal elements that are regularly present in
very small/minute amount in the tissue and are known to be essential in the
normal growth and development. The minor element makes up 3.9% of living
cell. The following are the minor/lesser elements present in all living organism;
Phosphorus, Potassium, Sodium, Manganese, Iron, Calcium, Chlorine,
Cupper, Iodine, and Zinc. Some organism contains the following minor
elements; Boron, Aluminum, Silicon and Molybdenum.
3. Trace element these are metallic elements required in a very minute amount.
They are important for biochemical reaction to takes place and are commonly
found as part of an enzyme (co-factor). It makes up less than 0.01% of the cell.
It includes monoatomic ions such as; Magnesium, Cupper, and Zinc.

B. Biochemical System
The different chemical elements in the living cell joints together to form the
biochemical system. The biochemical system in the living cell could be categorized
into two: the inorganic and organic biochemical system.

1. Inorganic Biochemical System

• Water
• Mineral ions
• Buffers

2. Organic Biochemical System (Macromolecules)

• Carbohydrates
• Lipids
• Proteins
• Enzymes
• Nucleic acids
 Summary
Cells are the simplest structural and functional units of living organism. The two basic classes
of cell are called prokaryotic and eukaryotic. The characteristic distinguishing the two cell
types is the complexity of their cellular organization, with the prokaryote having simpler
features.
Living matter requires only a few of the common chemical elements. The four element
carbon, hydrogen, nitrogen, and oxygen make up 99 percent of the total mass of most living
organisms. These four elements together with phosphorus and sulfur are the constituents of
the building block molecules such as amino acids, nucleotides, sugars, and also fatty acids.
They in turn are linked together to form various macromolecules, the protein, nucleic acid,
carbohydrates and lipids.

Suggested Readings

A tour of the cell. Campbell N.A. and Reece J.B. (2002). Biology (6th edition), p. 108-135.
Chemical make-up of Living cells. Harvey R.A. and Ferrier D.R. (2011). Lippincott’s Illustrated
Reviews: Biochemistry (5th edition), p. 101-127.
Biochemistry and the Organization of Cells. Campbell M.K. and Farrell S.O. (2009).
Biochemistry (6th edition), p. 23.

ANSWER TO SELF ASSESSMENT QUESTIONS (SAA)

You may now check your answers of self-assessment activities.

SAQ 1-1. A car is not a living thing because it cannot grow or reproduce.
SAQ 1-2.
a. Prokaryotes are mostly bacteria. Besides the lack of a nucleus, there are few well-
defined structures inside a prokaryotic cell. The prison wall has three components: a
cell wall, an outer membrane, and a plasma membrane. This wall allows a controlled
passage of material into or out of the cell. The materials necessary for proper
functioning of the cell float about inside it known as the cytoplasm while Eukaryotes
are animals, plants, fungi, and protists. In addition to having a nucleus, eukaryotic cells
have a number of membrane enclosed components known as organelles. Eukaryotic
organisms may be either unicellular or multicellular. In general, eukaryotic cells
contain much more genetic material than prokaryotic cells.
b. Plant cells contain the same components as animal cells plus a cell wall, a large
vacuole, and, in the case of green plants, chloroplasts compare to animal cells have a
number of components, most of which are considered to be organelles.
REFFERENCES

Campbell Neil A., and Jane B. Reece (2002), Biology, 6th edition, Pearson Education, Inc., San
Francisco, CA 94111

Campbell Mary K., and Shawn O. Farrell (2009), Biochemistry, 6th edition, Thomson Higher
Education, 10 Davis Drive Belmont, CA 94002-3098 USA

Hames David and Nigel Hooper (2005), Biochemistry, 3rd edition, Taylor & Francis Group, 270
Madison Avenue New York, NY 10016

Harvey Richard A., and Denice R. Ferrier (2011), Lippincott’s Illustrated Reviews: Biochemistry,
5th edition, Lippincott Williams & Wilkins, a Wolters Kluwer business, 351 West Camden
Street, Baltimore, MD 21201

Moore, John and Richard Langley (2008), Biochemistry for Dummies, Wiley Publishing, Inc.
111 River St. Hoboken, NJ 07030-5774, www.wiley.com