PRE-TEST:

This pre-test aims to test your previous knowledge on the topics covered by this module.

INTRUCTIONS:

Read the following questions and choose your answer from the choices provided. On the
space provided before each number, write your answer in capital letter.

______1. What is the science that deals with life at the molecular level?

A. Organic Chemistry B. Inorganic Chemistry

C. Biochemistry D. Analytical Chemistry

______2. What is the theory that suggests that life began in a pond or ocean as a result of the
combination of chemicals from the atmosphere and some form of energy to make amino acids, the
building blocks of proteins, which would then evolve into all the species?

A. Primordial Soup Theory B. Bubble Hypothesis

C. Panspermia D. RNA World Hypothesis

______3. Who is the Father of Modern Biochemistry?

A. Hans Kreb B. Fred Sanger

C. Carl Alexander Neuberg D. Antonie Van Leeuwenhoek

______4. What is considered the powerhouse of the cell?

A. Nucleus B. Mitochondria

C. Endoplasmic Reticulum D. Ribosome

______5. What is a substance that resists change in pH upon the addition of acid or base?

A. Water B. Oxide

C. Buffer D. Salt

HOW DO YOU RATE YOURSELF?

• If you got a perfect score, your level of knowledge of the topics is high.

• If you got a score of 3-4, your level of knowledge of the topics is moderate. • If

you got a score of 0-2, your level of knowledge of the topics is low.
Introduction
Biochemistry is the science concerned with the chemical basis of life. It comes from
the words “bio” meaning “life” and chemistry, thus the “chemistry of life”. Unlike other
fields, it focuses on the processes that occur at molecular level by studying how the
structure of a molecule relates to its function. It deals with the structure, properties and
chemical reactions of biomolecules that are present in a living system. As a result, it allows
the prediction on how molecules will act.
Living systems are composed of various biomolecules like carbohydrates, proteins,
lipids, vitamins, minerals, water and nucleic acid etc. Life depends on the interaction of
various biomolecules and biochemical reactions. Any abnormalities in these process may
lead to disease.
Medicine is the science or practice of the diagnosis, treatment, and prevention of
disease. And for a treatment of any medical condition or disease, one must understand the
reason behind this condition. Knowledge of chemical nature and reactions of biomolecules
(biochemistry) is essential to understand health and diseases. It can be said that all diseases
have a biochemical basis. In medicine, it is needed to understand the basis of these diseases
in order to diagnose and treat.

Objectives:
After the lesson, you are expected to learn the following
∙ Describe the scope of biochemistry and relate its central role in the life sciences
especially in the field of medicine.

∙ Explain how biochemistry integrates knowledge of the chemical processes in living

cells with strategies to maintain health, understand disease, identify potential
therapies, and enhance our understanding of the origins of life on earth.

What is Biochemistry?
Biochemistry is the systematic study of the chemical substances found in living
organisms, their organization and chemical interactions with each other, and the principles
of their participation in the processes of life. It is the study of the molecular basis of life or
the understanding of life phenomena in chemical terms. Once known as physiological
chemistry or biological chemistry, it studies chemicals and chemical processes that occur in
living organisms.
It involves investigation of the structures, functions, and syntheses of biological
substances, including proteins, DNA (deoxyribonucleic acid), RNA (ribonucleic acid),
carbohydrates, lipids, nucleotides, and amino acids. Hence, its most fundamental goal is to
determine in detail the molecular logic of the living cell and hopefully develop an increasing
insight into human disease and its alleviation, into plant life and agriculture and into the
ecological balance of the biosphere.

Importance of Biochemistry
In medical biochemistry (also known as molecular biology), biochemical techniques
are applied to human health and disease.
 The typical scope of medical biochemistry includes the following:
a. The chemical components of the human body, including carbohydrates and lipids;
amino acids and proteins; blood and plasma; biological membranes; nucleic acids (DNA and
RNA)
b. The major chemical processes in the human body, such as cell development;
enzyme activity; membrane transport mechanisms; homeostasis; blood coagulation
(clotting); oxygen transport; neurotransmitter function; ageing
c. Nutrition and mineral metabolism, including the role and function of vitamins in
the body
d. Molecular genetics
e. Heredity
f. Genomics

Ever since Eduard Buchner’s 1897 discovery that a cell-free extract of yeast can
ferment sugar (widely considered to be the birth of biochemistry), biochemistry has enjoyed
an intimate relationship with medicine — illuminating many aspects of human health and
diseases.
The importance of Biochemistry to the medical field:
1. Accruing sufficient biochemical knowledge is needed in order to properly
understand the metabolism, function and growth of a healthy human body especially for
theose working in medicine or a related field.
For example, if a patient complains of sudden, severe pain in one or more joints, the
physician may predict the problem to be gout — a form of arthritis caused by an excess of
uric acid in the bloodstream. By measuring uric acid levels, biochemistry can then confirm
whether gout is the root of the problem.
2. All diseases have a molecular basis, so biochemistry enables us to understand the
chemical processes involved in varied medical conditions such as diabetes,
hyperammonemia, hypo- and hyperthyroidism, jaundice, kidney dysfunction,
hypercholesterolemia, atherosclerosis, etc. With information obtained from the chemical
nature of pathologies, biochemists working in medicine are able to investigate potential
treatments for diseases.
3. In pharmacy, biochemical testing provides indispensable insights into a drug’s
mode of action, half-life, storage conditions, metabolism, and potential toxic or adverse
effects. The action of a drug almost always involves some change in the biochemical
processes taking place in the body. Therefore, pharmacologists must also be acquainted
with the biochemical aspects of the human body.
4. All life on Earth depends on biochemical reactions and processes. Medicine is just
one area that has benefited from biochemistry. By integrating this scientific knowledge with
practical strategies to maintain health, understand diseases, identify potential treatments,
and enhance our understanding of the origins of life on earth, biochemistry is and will
remain to make vital contributions to different fields of science.
Watch Introduction to Biochemistry HD https://www.youtube.com/watch?
v=tpBAmzQ_pUE
 ACTIVITY 1
Enumerate the importance of Biochemistry in other fields specifically in nutrition,
agriculture and environment.

REFERENCES
Srg. The importance of biochemistry in medical
science.https://www.srgtalent.com/blog/the-importance-of-biochemistry-in-medical
science#:~:text=Much%20of%20biochemical%20inquiry%20deals,the%20functions
%20ass ociated%20with%20life.&text=Medicine%20is%20just%20one%20area%20that
%20has%2 0benefited%20from%20biochemistry.

Lesson 2: Roots of Biochemistry The

emergence of Biochemistry as a discipline is arguable and still remains unclear, even at present.
Over the last 40 years biochemistry has become so successful at explaining living processes that
now almost all areas of the life sciences from botany to medicine are engaged in biochemical
research. Today the main focus of pure biochemistry is in understanding how biological molecules
give rise to the processes that occur within living cells which in turn relates greatly to the study and
understanding of whole organisms.

Objectives:
After the lesson, you are expected to learn the following
∙ Describe how Biochemistry has developed to the science it is today

∙ Differentiate the theories on the origin of life

A Brief History of Earth & Life

Living organisms and cells are made from non-living elements. However, Cell Theory
states that only cells can produce cells. The important question on how the first cell came
into being is one of the greatest scientific questions yet to be answered to explain the origin
of life.
 Theories on the origin of life:
1. The Primordial Soup Theory
The Primordial Soup Theory suggests that life began in a pond or ocean as a result of the
combination of chemicals from the atmosphere and some form of energy to make amino
acids, the building blocks of proteins, which would then evolve into all the species.
Since its inception in 1924, the Primordial Soup Theory has gained a firm following in
scientific circles. The theory states that a young Earth possessed a reducing atmosphere
and, following exposure to various forms of energy, basic compounds were formed. These
compounds are then said to have accumulated in a ‘soup’ from which life evolved.
In 1953, the Miller-Urey experiment was all the buzz. Commonly referred to as the
"primordial soup" concept, scientists showed how the building blocks of life, such as amino
acids, could be created with only a few inorganic "ingredients" such as water, methane,
ammonia, and electricity to simulate lightning strikes in a lab setting that was set up to
mimic the conditions of early Earth.
It was later determined that some of the "ingredients" in the "primordial soup" were
in fact not present in the atmosphere of early Earth. However, it was still important to note
that organic molecules were made relatively easily out of inorganic pieces, and this process
may have played a role in the development of life on Earth.
The big question this leaves is… How and why did life evolve from this collection of
simple elements and compounds? How did it all start? Ultimately, the question revolves
around abiogenesis, which is the process by which a living organism forms naturally from
non-living matter.
2. Beneath the Ice
Some evidence indicates that, around three billion years ago, Earth’s oceans were
covered with ice. This ice may have been hundreds of meters thick and was mainly due to
the sun being much less fierce than it is nowadays. This theory contends that the ice may
have protected the compounds, allowing them to interact and, thereby, creating life. 3.
Electricity
It has been proven that electricity can produce simple sugars and amino acids from simple
elements in the atmosphere. This leads to the theory that lightning may have been
responsible for the origins of life, primarily by striking through rich volcanic clouds.

4. Panspermia
Panspermia is the proposal that life on Earth didn’t actually begin on Earth at all.
Rocks, and other debris from impacts, are plentiful. In fact, rocks from Mars have been
found here on Earth, and it has been suggested that any one of these would have brought
microbes that could have kick-started life.

5. RNA
The RNA world hypothesis suggests that life on Earth began with a simple RNA
molecule that could copy itself without help from other molecules.
DNA, RNA, and proteins are central to life on Earth. DNA stores the instructions for
building living things. And proteins drive the chemical reactions needed to keep cells alive
and healthy. Until recently, RNA was thought of as little more than a messenger between
DNA and proteins, carrying instructions as messenger RNA (mRNA) to build proteins.
However, RNA can do far more. It can drive chemical reactions, like proteins, and carries
genetic information, like DNA. And because RNA can do both these jobs, most scientists
think life as we know it began in an RNA world, without DNA and proteins.

6. Simple Metabolism and Reactions

In contrast to the RNA theory, this approach suggests that the primordial soup
simply continued to react with itself over time, producing more and more complex
molecules, eventually yielding life. This is the most simple of the standing theories, and is
difficult to dismiss.
7. Clay Breeding Ground
Research at the University of Glasgow, in Scotland, has given rise to the theory that
life on Earth may have evolved in clay. It is suggested that clay may have served as an area
of concentrated chemical activity, providing a breeding ground for DNA and other
components.

8. Submarine Hydrothermal Vents

Submarine hydrothermal vents, or deep-sea vents, contain vast and diverse
ecosystems. The nutrient rich environment filled with reactive gases and catalysts, creates a
habitat teeming with life. Studies suggest that life may have originated from within these
vents, a theory that cannot be ignored, and one that may in fact tie in with the ice theory at
the beginning of this article.

9. The Bubble Hypothesis

Earth was formed about 5 billion years ago, when our solar system (formed 15 billion
years ago) took shape around the sun. A current model for the origin of life on earth is the
Bubble Hypothesis also known as the Prebiotic Origin of Organic Molecules or "Pre-BOOM"
hypothesis.
Proposed by Louis Lerman, a geophysicist , this theory asserts that a major role in the
creation of living cells was played by bubbles on the ocean surface and their atmospheric
counterparts, aerosols and precipitation droplets. Under Lerman's proposed scenario,
organic material, either from extraterrestrial objects or volcanic eruptions, was dispersed
in the sea and air, then adsorbed and concentrated during the formation of underwater
bubbles and atmospheric aerosols and droplets. When the bubbles rose to the surface and
burst, this organic material was ejected into the atmosphere and carried upward by winds.
Atmospheric chemistry, triggered by lightning or ultraviolet radiation, then altered the
material into complex organic molecules that precipitated back down to earth as rain and
snow, creating more bubbles and starting the cycle all over again.

A Brief History of Biochemistry

DURING THE 17TH CENTURY

∙ 1665
Robert Hooke had successfully invented the microscope. Because of this
discovery, Robert Hooke was the first one to have a close look of how a cell appears
to be. His description of these cells was published in Micrographia. However, the cell
 walls observed by Hooke gave no indication of the nucleus and other organelles
found in most living cells.

∙ 1674
Anton van Leeuwenhoek witnessed a live cell (plant) under a microscope.

DURING THE 18TH CENTURY

∙ 1775
Antoine Lavoisier first proposed a mechanism for photosynthesis, a process
wherein plants take in carbon dioxide and release oxygen. Lavoisier was also the first
to investigate cell respiration in animals.

∙ 1777-83
❖ Chemistry became dominated by the phlogiston theory, or the
hypothetical principle of fire wherein all the combustible material was
part composed. In this principle, burning (oxidation) was caused by
liberating phlogiston, with ash as the dephlogistigated substance.
Watch https://youtu.be/HahAGmMewLU (The Discovery of Oxygen
and Combustion)

❖ Both in theory and techniques, chemistry was wholly inadequate to

unravel the mysteries of the important functions in living systems.

❖ This period marked the onset of physiological chemistry, a sub-field of

chemistry that dealt more with extra cellular chemistry, such as the
chemistry of digestion and of body fluids.
DURING THE 19TH CENTURY

∙ 1800s
 For the first time a physiological process was explained with reference to a
nonliving mechanism. “Vitalism” was a common belief: the compounds found in
living organisms (i.e., organic molecules) can only be produced by living organisms
and could not be produced in the laboratory.
Now an obsolete scientific doctrine, vitalists argued that it was the presence
of a “vital force” (life force or spirit) that distinguished the living organic world from
the inanimate inorganic world.

∙ 1828
Friedrich Wöhler disproved “vitalism” by synthesizing urea, an organic
molecule and a waste product of animal metabolism, from ammonium cyanate, an
inorganic molecule obtained from mineral (i.e., nonliving) sources. Many science
historians considered this in vitro synthesis of urea by Wöhler as the starting point of
Biochemistry.

∙ 1836
Theodore Schwann, the proponent of the cell theory in Biology, proposed that the
process of fermentation is solely limited to living yeast cells. Liebig did not agree
to this and instead, he proposed another alternative theory of fermentation.

∙ 1856
Louis Pasteur opposed Liebig’s chemical theory. In his experiment, he showed that
fermentation depends highly on the physiological functions that occur in bacteria
and in living yeast cells. This work of Pasteur received general recognition.

∙ 1810s-1830s
A major substance from animals and plants was identified, composed of C, H,
O, and N. The term “Protein”, meaning the most important thing, was first used in
1838.

∙ 1850s-1890s
Carbohydrates, lipids, and nucleic acids were recognized.

∙ 1860s
During this period, the view is that the gelatinous and homogenous form of
matter in organisms or more commonly known as the protoplasm carries out all the
intracellular processes. These include respiration, biosynthesis of molecules, and the
breakdown of matter.
∙ 1869
Friedrich Miescher first identified what he called “nuclein” inside the nuclei
of human white blood cells.
Watch Friedrich Miescher at https://youtu.be/vR2tQ2dY1Es

∙ 1893
 Many consider Eduard Buchner's first demonstration of alcoholic
fermentation in cell-free yeast extracts as the starting point for the birth of
biochemistry. This was another blow to the vitalistic thinking, showing that the
presence of living yeast cells were not needed for fermentation. Previously, scientists
believed that only living cells could catalyze such complex biological reactions.

Miller-Urey Experiment
Experiments recreating the atmosphere of primitive earth, with the energy
sources and temperatures have led to the spontaneous formation of amino acids
and other biologically significant molecules. The Miller-Urey experiment showed that
a variety of organic molecules, including the amino acids could form in an early,
reducing atmosphere. Thus, living things obey the standard laws of physics
and chemistry. And, no “vitalistic” force is required to explain life at the
molecular level.

TWENTIETH CENTURY UP TO THE PRESENT

∙ Biochemistry interfaces with biology and chemistry even before nineteenth century
with studies concerned with the chemical processes that take place within living
cells. Modern biochemistry developed out of and largely came to replace what in
the nineteenth and early twentieth centuries was called physiological chemistry,
which dealt more with extra cellular chemistry, such as the chemistry of digestion
and of body fluids. The name Biochemistry was coined in 1903 by a German
chemist named Carl Neuber. However, work in this very living aspect of chemistry
had started much earlier. Claude Bernard is accredited with the Sirehood of
Biochemistry.

https://www.facebook.com/biochemistrymolecularbiology/posts/carl-alexander-neuberg
was-an-early-pioneer-in-biochemistry-and-he-is-often-refe/1694818810645478/ ∙ 1900s
One of the most important events that happened during this period is the
experiment done by Eduard Buchner. He prepared a cell-free extract of yeast which
he called the zymase. It fermented glucose and produced carbon dioxide and
ethanol. In this way, Buchner then had introduced the concept of an “enzyme”. This
discovery of Buchner had debunked the previous theory of
 protoplasm .Furthermore, the distinction between catalysis by hydrolytic
extracellular enzymes and by intracellular enzymes disappeared.

∙ 1904
The term “Biochemistry” was officially coined by the German chemist Carl
Neuberg.

∙ 1919
Phoebus Levene, a Russian physician and chemist, first discovered the order
of the three major components of a single nucleotide (phosphate, pentose sugar, and
nitrogenous base). He was also the first to discover the carbohydrate component of
RNA (ribose), and carbohydrate component of DNA (deoxyribose). Years later, Levene
finally identified how DNA and RNA molecules are put together. ∙ 1937
Hans Krebs discovered the process of the Citric Acid Cycle (also known as Krebs
cycle, in honor of him), which a series of chemical reactions that occur during cell
respiration. Here, glucose and oxygen get converted to water, carbon dioxide, and
energy. The advancement in the field of molecular biology, a field of biology that
focuses on the physiological organization of living organisms in molecular level, is
indeed a great help in the progress of biochemistry. Somehow, it is quite difficult to
distinguish between molecular biology and biochemistry since both of them are
concerned with the intermolecular and intercellular transformations. It was then
theorized that proteins were composed of linear chains of amino acids. This,
however, happened even prior to the identification of the amino acid constituents of
amino acids.

Sir Hans Kreb (1900-1981)

http://www.deconstructingthetour.group.shef.ac.uk/krebs-cycle/

∙ 1944
While working on bacterial samples, Oswald Avery first suggested that the
genetic material of the cell was possibly the deoxyribonucleic acid.
 ∙ 1950
A scientist named Erwin Chargaff began to challenge Levene’s previous conclusions.
He noted that the nucleotide composition of DNA differs among species and do not
repeat in the same order reached two major conclusions . Chargaff concluded that
almost all DNA, no matter what organism or tissue type it comes from, still
maintains certain properties, even as its composition varies.
He postulated the “Chargaff’s Rule” which says that the amount of cytosine is
equal to the amount of guanine, and the amount of thymine is equal to the amount
of adenine. In short, the total amount of pyrimidines (thymine and cytosine)
approximates the number of purines (adenine and guanine). Utilizing all discoveries
prior to James Watson and Francis Crick was able to derive the three-dimensional
and double-helical model of the DNA in 1953. After that, the process of replicating
the DNA was suggested.
∙ 1958
The theory of Chargaff was only confirmed after Frederick Sanger discovered
the first and complete protein structure in 1958. The protein that was first identified
is insulin.

∙ 1961
After the discovery of the genetic material, the next achieved milestone was
the cracking of the genetic code. It was discovered in this year that the genetic code
is made up of specific triplets of DNA bases that encodes for particular amino acids.

∙ 1977
Sixteen years after the discovery of the triplets of the DNA, Fred Sanger had
successfully sequenced the genome of a bacteriophage which contained more than
5000 nucleotides. Not long after, he was able to sequence the DNA of the human
mitochondrial genome which consisted of more than 16, 000 nucleotides. In the
present time, Biochemistry has promises to the world of science in development of
new path-breaking research and coming times would surely prove these promises to
be fulfilled.The development of new technology such as X-ray diffraction,
chromatography, radioisotopic labelling, electron microscopy and molecular
dynamics had paved the way for many other discoveries in the field of Biochemistry.
Such technologies will also further open other new endeavors in the future.

Frederick Sanger (1918-2013)

https://www.theguardian.com/science/2013/nov/20/frederick-sanger

ACTIVITY 2
Answer the activity without looking at the lessons above. It shall test your understanding
and memory on what you have learned. Goodluck!

1. Who is the father of biochemistry?

_______________________

2. Who discovered the process of the Citric Acid Cycle

_______________________

3. What is the title of the book where Robert Hooke published his discoveries about the
cell?

_______________________

4. What is the common belief that compounds found in living organisms (i.e., organic
molecules) can only be produced by living organisms and could not be produced in the
laboratory?

_______________________

5. Who introduced the concept of an enzyme?

_______________________

6. What is the theory which states that the amount of cytosine is equal to the amount of
guanine, and the amount of thymine is equal to the amount of adenine?

_______________________

7. Frederick Sanger discovered the first and complete protein structure, what was this
protein?

_______________________

8. What is the theory stating that a young Earth possessed a reducing atmosphere and,
following exposure to various forms of energy, basic compounds were formed?
_________________________
9. What is the proposal that life on Earth didn’t actually begin on Earth at
all? _________________________
10. What is the theory which asserts that a major role in the creation of living cells was
played by bubbles on the ocean surface and their atmospheric counterparts, aerosols and
precipitation droplets?
_________________________

REFERENCES
Singh, P., Batra, H.S., Naithani, M. History of biochemistry nih. 2004. (accessed July 20,
2016).
Society, Biochemical. What is biochemistry? Biochemistry (accessed July 21, 2016). Helvoort,
Ton van. “History of Biochemistry.” Reader’s Guide to the History of Science, 2000: 81.
Coley, N. “History of Biochemistry.” History of Biochemistry, 2016: 9.
Advameg. History of Biology: Biochemistry Biology reference. (accessed July 21, 2016).
Pray, L. “Discovery of DNA Structure and Function: Watson and Crick.” Nature Education,
2009: 100-101.
https://www.bioexplorer.net/history_of_biology/biochemistry/#TWENTIETH_CENTURY_U
P _TO_THE_PRESENT
Periscope Film. ( 2016, January 15) . The discovery of oxygen & combustion 1946 educational
film 76244 [Video file]. Retrieved from
https://www.youtube.com/watch?v=HahAGmMewLU&feature=youtu.be