BIOCHEMISTRY

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What do you usually think when you hear the term “Biochemistry”? If you think that
this is boring, complicated, useless, or just another requirement, you should think again.
Biochemistry is the study of substances essential to life. This includes the study of the
composition, structure, and chemical functions of living organisms. This also deals with
the different principles and processes involving living organisms.

Biochemistry is the study of the compounds, chemical reactions, and molecular

interactions that are involved in the production, maintenance, and reproduction of living
organisms. It serves as a central component of all the health sciences, including
microbiology, genetics, physiology, nutrition, medicine, dentistry, and nursing.
Advancements in biochemical knowledge would set the foundation in the search for the
prevention and treatment of heart disease, cancer, genetic diseases, periodontal disease,
nutritional deficiencies, infectious diseases, and other health disorders. The present
knowledge about biochemistry has come up with the mechanisms on how oncogenes
convert normal cells into tumor cells, how enzymes catalyze chemical reactions, how
cholesterol contributes to heart disease, how aspirin lowers body temperature, and many
more.

The goal of biochemistry is to explain cellular metabolism in terms of

comprehensible chemical reactions at the molecular level. It is very important to
understand the biological processes of humans, animals, and plants for a healthier body
and a wholesome environment.
TOPIC 1:
Introduction to Chemical Biology

Goals/Objectives:
At the end of the session, you should be able to:
1. define biochemistry.
2. identify the different characteristics of living organisms.
3. differentiate prokaryotic and eukaryotic cells.

What makes living organisms unique? The answer is found in their organization and
regulation. The different levels of organization are the organ, the tissue, the cell, the
membrane, and the enzyme, all of which are intimately interrelated.

The most highly developed living organisms are composed of water, proteins, nucleic
acids, carbohydrates, lipids, and inorganic substances. These chemicals are the materials
from which cells, the organized sacks or compartments of life, are constructed. Each living
cell acts as a miniature chemical factory, taking in food and giving off waste materials. Thus,
the composite of all the functions of individual cells represents a major part of the chemical
functions of the organism.

Organisms are basically divided into two main groups based on their cell structures,
we have the prokaryotes and the eukaryotes. Prokaryotic cell lacks a well-defined nucleus
and internal membrane; it has only a nuclear region; the portion of the cell that contains DNA
and a cell membrane that separate it from the outside world. The other major feature of a
prokaryotic cell’s internal structure is the presence of a ribosome which is considered as the
site of protein synthesis. On the other hand, a eukaryotic cell has a well-defined nucleus,
internal membranes, cell membrane, and a more complex internal structure. The nucleus is
separated from the rest of the cell by a double membrane. The eukaryotic DNA in the nucleus
is associated with proteins. There is also a continuous membrane system called the
endoplasmic reticulum throughout the cell. Eukaryotic cells have membrane bounded
organelles which make them unique. The two most important are mitochondria; sites of
energy yielding reactions, and the chloroplasts; sites of photosynthesis for plants.
CHARACTERISTICS OF LIFE

All living organisms share several characteristics or functions that ensure survival. When
viewed together, these attributes serve to define life.

1. Adaptation - All living organisms respond to the environment. For example, if you step
on a block of wood, it will just lie there, but if you step on a dog, it may move or even
bark at you. All living things are aware of what’s going on around them, and respond
to whatever change is happening in the environment. An adaptation refers to the
process of responding to and becoming adjusted to the environment. This is what
makes living things fit to live in its habitat.
2. Growth and repair - All living organisms have the ability to grow and repair. As
children, we get taller every year. That growth happens because our bodies keep
adding new cells/tissue. Living things also sometimes suffer injury and bruises, but
they are able to repair themselves by growing new cells to replace damaged parts in
a process called mitosis.
3. Reproduction - Living organisms have the ability to reproduce. They make more
organisms like themselves. The organism may be a dog, a rabbit, a tree, or even a
bacterium. Life creates more life. What will happen if a species cannot create the next
generation? The species will go extinct. Reproduction is the ability to beget offspring;
sexual or asexual process, ensuring propagation and continuance of species.
4. Metabolism - This is the biological and chemical activities or functions that provide
energy. Constructive metabolism is called anabolism, while destructive metabolism is
catabolism. The sum of all the chemical reactions in a cell is metabolism.
5. Complexity and organization - All living things have a complex chemistry. A flower, for
example, has a complicated and beautiful structure. So does a crystal. But if you look
closely at the crystal, you see no change. The flower, on the other hand, is
transporting water through the petals, producing pigment molecules, breaking down
sugar for energy, and undergoing a large number of other biochemical reactions that
are needed for living organisms to stay alive. Complexity refers to the elaborate
structures needed to carry out laborious tasks like metabolism. Organization is
putting the different body structures into order, so that the organism can function
effectively and efficiently.
6. Regulation - Even the smallest organisms are complex and require a lot of regulatory
mechanisms to counterpart internal functions, respond to stimuli, and cope with
environmental stresses. Two examples of internal functions regulated in an organism
 are nutrient and blood flow. Regulation is the ability to keep the functions under
control through the use of substances like hormones or enzymes.
7. All living things possess a characterized size and shape.
8. Responsiveness to stimuli or sensitivity - This is the ability to respond favorably or
unfavorably to its environment. The process by which organisms respond to stimuli in
ways that keep conditions in their body capable for life is called homeostasis.
9. Locomotion - This is the ability of an organism to move on its initiative and under its
control.
10. Variation and change - They explain why no two organisms are exactly alike and no
organism remains unchanged forever. Adaptation and evolution are mechanisms of
change.
11. Stereo specificity - This refers to the ability of certain molecules present in an
organism to interact with nature in a left or right-handed manner.

THE CHEMICALS OF LIFE

All living things are mainly constructed from carbon, oxygen, and hydrogen, together
with some inorganic elements like nitrogen, sulfur, and phosphorus.
1. Water
All life forms, from the simplest bacteria to the most complex multicellular
plants and animals contain water. Human cells are composed of about 70% water,
over 80% in blood, and 60-70% of the body as a whole. The structure of water makes
it an ideal medium for sustaining life.

2. Organic Compounds
a. Nucleic Acids (DNA and RNA)
b. Proteins
c. Carbohydrates
d. Fats and Lipids

3. Inorganic Elements
a. Bulk elements such as Nitrogen, Sodium, Magnesium, Phosphorus, Sulfur,
Chlorine, Potassium, and Calcium are required in relatively large quantities.
b. Trace elements such as Iron, Zinc, and Iodine.
THE CELLULAR BASIS OF LIFE

The Morphology of Cells

All cells are surrounded by a cell membrane (plasma membrane) which is about 7nm
thick. Some cells are further encapsulated by a cell wall which serves as a cell coat or some
other protective barrier. Cells may be described as prokaryotic or eukaryotic, based on their
structural and functional properties.

Prokaryotes
They are single-celled organisms ranging in size from 1 to 10 micrometer. Biologists
classify them under Monera (bacteria) and Archaea; a new domain of organisms that are
morphologically prokaryotic but their molecular characteristics are more eukaryotic than
prokaryotic. Most prokaryotes lack any detectable internal compartments, and many are
surrounded by a rigid cell wall. The plasma membrane may fold into a multilayered structure
called mesosome. The contents of the cell, the cytoplasm, contain multiple types of particles
including a packaged form of DNA (called nucleoid) and ribosomes (factories for the
assembly of proteins. The prokaryote, Escherichia coli, is the most thoroughly studied
organism on Earth. It is a rod-shaped bacterium that is about 2 micrometer long and 1
micrometer in diameter. It is part of the intestinal flora of the human intestine and is capable
of dividing once every 20 minutes. It also possesses a single, large DNA molecule with the
blueprint of about 4000 different proteins. Some E.coli has one or more smaller DNA known
as plasmids.

What is the importance of studying prokaryotes for Biochemistry students?

1. Prokaryotes are normal beneficial inhabitants of our bodies, and
2. Others cause tooth decay, illnesses, and even death.

Eukaryotes

Animal Eukaryotes
Most eukaryotic cells range from 10 to 100 micrometer long with infinitely more
genetic information than a prokaryotic cell.
The following are some eukaryotic organelles and their major functions:
 Organelle Major Functions in Eukaryotic Cells

Nucleus Information and administrative center of the cell. It stores DNA. It

is involved in the expression of genetic information and ribosome
assembly. Contains nucleolus which is involved in the assembly of
ribosomes. Nucleus is surrounded by a double membrane called
the nuclear envelope, which is breached by numerous nuclear
pore complexes that rivet the two membranes together. The
content of the cell outside the nucleus is called the cytoplasm.

Mitochondrion This is a specialized structure unique to the cells of animals,

plants, and fungi. This is known as the powerhouse of the cell.
Mitochondria serve as batteries which powers various functions
of the cell and the organisms as a whole.

Golgi apparatus Contains stacks of flattened membrane-enclosed bodies, called

cristae. This receives proteins and lipids from the rough
endoplasmic reticulum and is responsible for packaging proteins
into vesicles prior to secretion.

Endoplasmic This is an intricate winding membrane that forms a series of

Reticulum (ER) flattened sacs within the cytoplasm.
Smooth ER: synthesis of lipids, metabolism of carbohydrates,
 detoxification of drugs and poisons.
Rough ER: aids in synthesis of secretory and other proteins from
bound ribosomes; adds carbohydrates to proteins to make
glycoproteins; produces new membrane.

Lysosome This is a membranous sac of hydrolytic enzymes, which is

responsible for the breakdown of ingested substances, cell
macromolecules, and damaged organelles for recycling.

Plant Eukaryotes
Plant cells differ from animal cells on several points:
1. Plant cells have a cell wall for protection and support.
2. They contain unique double-membrane organelles called plastids which are used for
photosynthesis and the assembly and storage of starch. Plastids used for
photosynthesis are called chloroplasts. Plastids, like the mitochondria and nucleus,
contain their own DNA.
3. They contain one or more conspicuous membrane-enclosed vacuoles which are filled
with fluid. This is for the creation and maintenance of osmotic pressure, which forces
the host cell against the surrounding cell wall. In a mature plant, vacuoles may
occupy over 90% of the total volume of the cell.

Differences between the prokaryotes and eukaryotes:

Prokaryotes Eukaryotes

No cytoskeleton There is a presence of cytoskeleton, which

is an internal network of proteins
constructed from a variety of specific
proteins, including actin, tubulin, and
keratin, thus providing structural stability.

Less DNA content They have hundreds of thousand times

more DNA

Do not contain membrane-bound There is a presence of organelles

organelles

Smaller About 5-10 times larger

 Activity 1:
Biochemistry and the Organization of Cells

1. Define the following terms:

a. catalysis
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b. cytoskeleton
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c. organelle
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d. vacuole
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e. polymer
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f. genetic code
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2. List five (5) differences between prokaryotic and eukaryotic.

PROKARYOTES EUKARYOTES
3. Which organelles contain DNA?

Which organelles are sites of energy yielding reactions?

Which organelles are surrounded by a double membrane?

4. What are the advantages of being eukaryotic?

5. Assume that a scientist claims to have discovered mitochondria in bacteria. Is such a

claim likely to prove valid? Explain your answer in not more than five sentences.