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BIOCHEMISTRY
(Chem. 123)
5 Units
Course Professor:
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Republic of the Philippines
UNIVERSITY OF EASTERN PHILIPPINES
COLLEGE OF VETERINARY MEDICINE
Catarman, Northern Samar, 6400 Philippines
Module # 1 - INTRODUCTION
What is Biochemistry?
• Medicine
• Agriculture
• Industrial applications
• Environmental applications
Biochemistry defined:
By controlling information flow through biochemical signaling and the flow of chemical
energy through metabolism, biochemical processes give rise to the incredible complexity of
life.
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Over the last decades of the 20th century, biochemistry become so successful at
explaining living processes that now almost all areas of the life sciences from botany to
medicine to genetics 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.
The chemistry of the cell also depends on the reactions of smaller molecules and
ions. These can be inorganic, for example water and metal ions, or organic, for example the
amino acids which are used to synthesize proteins.
The mechanisms by which cells harness energy from their environment via chemical
reactions are known as metabolism.
• In nutrition, they study how to maintain health and study the effects of nutritional
deficiencies.
• In agriculture, biochemists investigate soil and fertilizers, and try to discover ways to
improve crop cultivation, crop storage and pest control.
Biology is the science of living organisms and chemistry is the science of atoms and
molecules, so biochemistry is the science of the atoms and molecules in living organisms. Its
domain encompasses all the living world with the unifying interest in the chemical structures
and reactions that occur in living systems.
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Biochemistry underlies ordinary life in unseen ways: For example, take a middle‐aged
man who:
• Takes a drug to lower his serum cholesterol. That drug was developed by a pharmaceutical
company's biochemists to inhibit a key enzyme involved in cholesterol biosynthesis
• Shaves with a cream containing compounds that soften his beard. These active agents
were developed after studies of the physical properties of keratin, the protein in hair.
• Eats a breakfast cereal fortified with vitamins identified through nutritional biochemistry.
• Wears a shirt made from pest‐resistant cotton. The cotton plants were bioengineered by
biochemists through the transfer of genes from a bacterium into plants.
• Goes fishing after work. The conservation agents who manage the stream use biochemical
information from the DNA (deoxyribonucleic acid) sequences to track the genetics of the
fish population.
• Drinks milk before bedtime. His sleep is helped by the amino acids in the milk, which are
converted by his brain into molecular signals that lead to a resting state in other parts of his
brain.
When you do stremous activities like basketball or at the gym, think about the fact
that all the cells in your body are working together to achieve your goals. Your muscles
would rapidly fail without your liver sending out the sugar they need to contract. You could
only last for a few minutes without your heart pumping oxygen-containing blood throughout
your body. And without your brain sending signals to mastermind it all, you wouldn‘t even
make it out of the locker room.
One of the goals of this course is to understand how all the body‘s organs work
together during exercise. This is pretty complicated, as you can imagine, so before we can
understand this cooperation between organs, we have to first discuss the building blocks of
the organs, cells. We can reduce cells even further down to their components, the basic
biological building blocks called lipids, carbohydrates, proteins, and nucleic acids. That‘s
what biochemistry is all about, trying to understand the whole from its parts.
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Findings of some famous Biochemist:
Carl Alexander Neuberg (29 July 1877 – 30 May 1956) was an early pioneer in
biochemistry, and he is often referred to as the "Father of modern biochemistry".
He elucidated the biochemical reactions of alcoholic fermentation in which he
discovered a number of different enzymes such as carboxylase and of intermediates
such as fructose-6-phosphate
Friedrich Wöhler was a renowned German chemist who is best known the synthesis
of urea, an organic compound, from ammonium cyanate, an inorganic salt, thus
disproving the theory of 'vitalism', that organic substances can only be produced from
living things.
Linus Carl Pauling - an American chemist, biochemist, chemical engineer. He was
best known for working out the nature of the chemical bond, yet he also discovered
(among many other accomplishments) the cause of sickle cell anemia, developed an
accurate oxygen meter for submarines, helped create synthetic plasma, and
determined the structure of proteins.
Carl Ferdinand Cori and Gerty Theresa Cori - American biochemists, husband-
and-wife team whose discovery of a phosphate-containing form of the simple sugar
glucose, and its universal importance to carbohydrate metabolism, led to an
understanding of hormonal influence on the interconversion of sugars and starches in
the animal organism.
Eduard Buchner - German biochemist who demonstrated the fermentation of
carbohydrates results from the action of different enzymes contained in yeast and not
the yeast cell itself. He discovered that yeast extract with no living yeast fungi can
form alcohol from a sugar solution. The conclusion was that biochemical processes
do not necessarily require living cells, but are driven by special substances,
enzymes, formed in cells.
Frederick Sanger - an English biochemist and molecular biologist, 'the father of
genomics', who twice received the Nobel Prize for Chemistry; in 1958 for his
discovery on the ―structure of proteins, especially that of insulin. The other half was
awarded to Paul Berg and Walter Gilbert "for his fundamental studies of the
biochemistry of nucleic acids, with particular regard to recombinant DNA" in 1980.
James Watson - was a pioneer molecular biologist who is credited, along with
Francis Crick and Maurice Wilkins, with discovering the double helix structure of
the DNA molecule. It marked a milestone in the history of science and gave rise to
modern molecular biology, which is largely concerned with understanding how genes
control the chemical processes within.
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Sir Hans Adolf Krebs – German born Bristish biochemist who discovered in living
organisms of the series of chemical reactions known as the tricarboxylic acid cycle
(also called the citric acid cycle, or Krebs cycle). These reactions involve the
conversion—in the presence of oxygen—of substances that are formed by the
breakdown of sugars, fats, and protein components to carbon dioxide, water, and
energy-rich compounds.
Oswald Avery, Colin MacLeod, and Maclyn McCarty (1944) - showed that DNA
(not proteins) can transform the properties of cells, clarifying the chemical nature of
genes. They identified DNA as the "transforming principle" while studying
Streptococcus pneumoniae, bacteria that can cause pneumonia
Rosalind Franklin using a technique called X-ray crystallography, revealed the
helical shape of the DNA molecule that made Watson and Crick realized that DNA
was made up of two chains of nucleotide pairs that encode the genetic information
for all living thing.
Organization of Life
o elements
o simple organic compounds (monomers)
o macromolecules (polymers)
o supramolecular structures
o organelles
o Cells
o Tissues
o organisms
Range of the sizes of objects studies by Biochemist and Biologist 1
angstrom = 0.1 nm
o C, N, O, P, S, H Less abundant
o essential for all organisms : Na, Mg, K, Ca, Cl Trace levels,
o essential for all organism: Mn, Fe, Co, Cu, Zn Trace levels,
o essential for some organisms: V, Cr, Mo, B, Al, Ga, Sn, Si, As, Se, I,
Elements of Life
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Biochemistry Defined
The mechanisms by which cells harness energy from their environment via
chemical reactions and all chemical changes within the organism—either the degradation of
substances, generally to gain necessary energy, or the buildup of complex molecules
necessary for life processes—are collectively called metabolism.
Advances have continued since that time, with such landmark events as the first
chemical synthesis of a protein, the detailed mapping of the arrangement of atoms in some
enzymes, and the elucidation of intricate mechanisms of metabolic regulation, including the
molecular action of hormones.
Every living cell contains, in addition to water and salts or minerals, a large number of
organic compounds, substances composed of carbon combined with varying amounts of
hydrogen and usually also of oxygen. Nitrogen, phosphorus, and sulfur are likewise common
constituents.
(1) protein,
Proteins are fundamental to life, not only as structural elements (e.g., collagen) and
to provide defense (as antibodies) against invading destructive forces but also because the
essential biocatalysts are proteins. The chemistry of proteins is based on the researches of
the German chemist Emil Fischer, whose work from 1882 demonstrated that proteins are
very large molecules, or polymers, built up of about 24 amino acids.
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Proteins may vary in size from small (nsulin with a molecular weight of 5,700 (based
on the weight of a hydrogen atom as 1) to very large—molecules with molecular weights of
more than 1,000,000. The first complete amino acid sequence was determined for the insulin
molecule in the 1950s. The abiding interest of biochemists in the structure of proteins rests
on the fact that the arrangement of chemical groups in space yields important clues
regarding the biological activity of molecules.
Nucleic acids are large, complex compounds of very high molecular weight present
in the cells of all organisms and in viruses. They are of great importance in the synthesis of
proteins and in the transmission of hereditary information from one generation to the next.
Originally discovered as constituents of cell nuclei (hence their name), it was assumed for
many years after their isolation in 1869 that they were found nowhere else. This assumption
was not challenged seriously until the 1940s, when it was determined that two kinds of
nucleic acid exist: 1) deoxyribonucleic acid (DNA), found in the nuclei of all cells and in
some viruses; and 2) ribonucleic acid (RNA), found in the cytoplasm of all cells and in most
viruses.
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Nucleic acids and various other organic derivatives are also important constituents.
Each class contains a great diversity of individual compounds. Many substances that cannot
be classified in any of the above categories also occur, though usually not in large amounts.
The profound biological significance of nucleic acids came gradually to light during
the 1940s and 1950s. Attention turned to the mechanism by which protein synthesis and
genetic transmission was controlled by nucleic acids. During the 1960s, experiments were
aimed at refinements of the genetic code. Promising attempts were made during the late
1960s and early 1970s to accomplish duplication of the molecules of nucleic acids outside
the cell—i.e., in the laboratory. By the mid-1980s genetic engineering techniques had
accomplished, among other things, in vitro fertilization and the recombination of DNA (so-
called gene splicing). Genetic studies have shown that the hereditary characteristics of a
species are maintained and transmitted by the self-duplicating units known as genes, which
are composed of nucleic acids and located in the chromosomes of the nucleus.
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Republic of the Philippines
UNIVERSITY OF EASTERN PHILIPPINES
COLLEGE OF VETERINARY MEDICINE
Catarman, Northern Samar, 6400 Philippines
The cell is the site of a constant, complex, and orderly set of chemical
changes collectively called metabolism. It is the basic unit of life.
The Cell theory, first developed in 1839 by Matthias Jakob Schleiden and Theodor
Schwann. It states that “all organisms are composed of one or more cells, that cells are
the fundamental unit of structure and function in all living organisms, and that all cells
come from pre-existing cells”.
The word ―cell‖ in Latin means ―Little rooms.‖
• In 1665 Robert Hooke looked at a thin slice of cork and he saw that the cork looked like
little boxes. So he called them cells.
• Anton Van Leeuwenhoek (1673) – the first person to observe living things
• Matthias Schleiden (German Scientist) conclude that all plant parts are made of cells.
• Theodor Schwann also a German Scientist concluded that all animal parts are made of
cells.
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THE CELLS - THE BASIC UNITS OF LIFE
Cells make up the smallest level of a living organism such as yourself and
other living things. The cellular level of an organism is where the metabolic
processes occur that keep the organism alive. That is why the cell is called the
fundamental unit of life.
Cells are sacs of fluid surrounded by membranes. Inside the fluid float chemicals
and organelles. An organism contains parts that are smaller than a cell, but the cell
is the smallest part of the organism that retains characteristics of the entire organism.
o For example, a cell can take in fuel, convert it to energy, and eliminate
wastes, just like the organism as a whole can. But, the structures inside the
cell cannot perform these functions on their own, so the cell is considered the
lowest level.
Cells are found in all plants, animals, and bacteria. Many of the basic structures
found inside all types of cells, as well as the way those structures work,
fundamentally are very similar, so the cell is said to be the fundamental unit of life.
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Two types of cells: Eukaryotes and Prokaryotes.
1. Eukaryotes are organisms that contain chromosomes, including plants and animals, as
well as fungi (like mushrooms), protozoa, and most algae.
Plant cells have chloroplasts, which use energy from sunlight to create food for the
plant.
Eukaryotic cells have internal membranes, which create compartments inside the
cells that have different functions.
Plants cells have a cell membrane and a cell wall, which is rigid; animal cells have
only a cell membrane, which is soft.
The cytoskeleton, which reinforces the cytoplasm of the cell, controls cellular
movements.
2. Prokaryotes
are cellular organisms that do not have a ―true‖ nucleus.
Prokaryotes have some genetic material, but it is not as well organized as it is in
eukaryotes. Still, prokaryotes are able to reproduce.
Examples of these organisms include bacteria and blue-green algae.
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Note: Organelles not found in animal cell : Chloroplast, Central vacuole, Cell wall and
The cell theory was formulated by two scientists: Theodor Schwann and Matthias
Jakob Schleiden. In 1839, Schleiden suggested that every structural part of a plant was
made up of cells or the result of cells. The cell theory is the historic scientific theory, now
universally accepted, that living organisms are made up of cells, that they are the basic
structural/organizational unit of all organisms, and that all cells come from pre-existing cells.
Cells are the basic unit of structure in all organisms and also the basic unit of reproduction.
The three (3) beliefs to the cell theory are as described below:
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•These types of cells have no membrane
covered nucleus.
•They are bacteria cells.
Cells are the smallest units of life. They are a closed system, can self-replicate, and
are the building blocks of our bodies. In order to understand how these tiny organisms work,
we will look at a cell‘s internal structures. We will focus on eukaryotic cells, cells that
contain a nucleus. Prokaryotic cells, cells that lack a nucleus, are structured differently. An
organelle is a subcellular structure that has one or more specific jobs to perform in the cell,
much like an organ does in the body. Among the more important cell organelles are the
nuclei, which store genetic information; mitochondria, which produce chemical energy; and
ribosomes, which assemble proteins.
Organelles are small structures within the cytoplasm that carry out functions
necessary to maintain homeostasis in the cell. They are involved in many processes, for
example energy production, building proteins and secretions, destroying toxins, and
responding to external signals.
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1. Cell membrane (Plasma membrane/ Plasmalemma)
A plasma membrane is composed of lipids and proteins where the composition might
fluctuate based on fluidity, external environment, and the different stages of development of
the cell.
Functions:
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1. The cell membrane provides mechanical support that facilities the shape of the cell
while enclosing the cell and its components from the external environment.
2. It regulates what can be allowed to enter and exit the cell through channels, acting as
a semi-permeable membrane, which facilities the exchange of essential compounds
required for the survival of the cell.
3. It generates and distributes signals in and outside of the cell for the proper
functioning of the cell and all the organelles.
4. It allows the interaction between cells required during tissue formation and cell
fusion.
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3. Nucleus
The nucleus is a double-membraned organelle found in all eukaryotic cells. It is the
largest organelle, which functions as the control centre of the cellular activities and is
the storehouse of the cell‘s DNA.
By structure, the nucleus is dark, round, surrounded by a nuclear membrane. It is a
porous membrane (like cell membrane) and forms a wall between cytoplasm and
nucleus.
Within the nucleus, there are tiny spherical bodies called nucleolus. It also carries
another essential structure called chromosomes.
o Chromosomes are thin and thread-like structures which carry another
important structure called a gene.
4. Endoplasmic Reticulum
The Endoplasmic Reticulum is a network of membranous canals filled with fluid.
They are the transport system of the cell, involved in transporting materials
throughout the cell.
There are two different types of Endoplasmic Reticulum:
o Rough Endoplasmic Reticulum – They are composed of cisternae, tubules,
and vesicles, which are found throughout the cell and are involved with
protein manufacture.
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o Smooth Endoplasmic Reticulum – They are the storage organelle,
associated with the production of lipids, steroids, and also responsible for
detoxifying the cell.
5. Mitochondria
Mitochondria are called the powerhouses of the cell as they produce energy-rich
molecules for the cell. The mitochondrial genome is inherited maternally in several
organisms. It is a double membrane-bound, sausage-shaped organelle, found in
almost all eukaryotic cells.
The double membranes divide its lumen into two distinct aqueous compartments.
The inner compartment is called ‗matrix‘ which is folded into cristae whereas the
outer membrane forms a continuous boundary with the cytoplasm. They usually vary
in their size and are found either round or oval in shape.
Mitochondria are the sites of aerobic respiration in the cell, produces energy in the
form of ATP and helps in the transformation of the molecules.
For instance, glucose is converted into adenosine triphosphate – ATP. Mitochondria
have their own circular DNA, RNA molecules, ribosomes (the 70s), and a few other
molecules that help in protein synthesis.
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6. Ribosomes
Ribosomes are nonmembrane-bound and important cytoplasmic organelles found in
close association with the endoplasmic reticulum.
Ribosomes are found in the form of tiny particles in a large number of cells and are
mainly composed of 2/3rd of RNA and 1/3rd of protein. They are named as the 70s
(found in prokaryotes) or 80s (found in eukaryotes).
The letter S refers to the density and the size, known as Svedberg‘s Unit. Both 70S
and 80S ribosomes are composed of two sub-units.
Ribosomes are either encompassed within the endoplasmic reticulum or are freely
traced in the cell‘s cytoplasm.
Ribosomal RNA and Ribosomal proteins are the two components that together
constitute ribosomes.
The primary function of the ribosomes includes protein synthesis (Make protein)
in all living cells that ensure the survival of the cell.
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7. Golgi Apparatus - Make, process and package proteins
Golgi Apparatus also termed as Golgi Complex. It is a membrane-bound organelle,
which is mainly composed of a series of flattened, stacked pouches called cisternae.
This cell organelle is primarily responsible for transporting, modifying, and
packaging proteins and lipid to targeted destinations.
Golgi Apparatus is found within the cytoplasm of a cell and are present in both plant
and animal cells.
8. Lysosomes –
Lysosomes ontains digestive enzymes to help break food down.
They are called the suicidal bags because they are capable of breaking down or
digesting all the wastes, dead and damaged cells
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A Brief Summary on Cell Organelles
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organelle present in the of lipids and catabolism of
cytoplasm, which contains the long-chain fatty acids.
reducing enzyme.
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Biochemistry !
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