“Foundations of Biochemistry” is a process‐oriented guided inquiry learning (POGIL) style workbook for use in upper division Biochemistry courses. The book contains 36 exercises, which could be used for an almost‐exclusively POGIL one semester course or supplemented with lectures, case studies, or student presentations for a full year course. It is intended as a supplement to a textbook, and the very modest price makes it a very cost‐effective educational resource.

1. Foundations of Biochemistry
Md. Saiful Islam
B.Pharm, M.Pharm (PCP)
North South University
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2. Biochemistry is the chemistry of living things. It is concerned with
the structure and chemical processes of Proteins, carbohydrates,
lipids, nucleic acids and other molecules found in or produced by
organisms.
The Foundations of Biochemistry
Chemical Foundations
Cellular Foundations
Physical Foundations
Genetic Foundations

3. Chemical Foundations
Biomolecules
Molecules that occur naturally in living organisms are known as
biomolecules. It include macromolecules like proteins, carbohydrates, lipids
and nucleic acids as well as small molecules like primary and secondary
metabolites and natural products. Biomolecules consists mainly of carbon
and hydrogen with nitrogen, oxygen, sulphur, and phosphorus.
About four billion years ago, life arose—simple microorganisms with the
ability to extract energy from organic compounds or from sunlight, which
they used to make more complex biomolecules from the simple elements
and compounds on the Earth’s surface.
Biochemistry deals how the remarkable properties of living organisms arise
from the thousands of different lifeless biomolecules and how the inanimate
molecules interact to maintain and perpetuate life.

4. Chemical elements in organic compounds
There are 118 different
elements currently on the
periodic table. The number of
naturally occurring elements
is actually 98. Only 30 out of
these chemical elements in
the earth’s crust have been
found to be essential
components in various living
organisms.
Elements Human body (% of total
no of atoms)
H 63
O 25.5
C 9.5
N 1.4
Ca 0.31
P 0.22
Cl 0.08
K 0.06
S 0.05
Na 0.03
Mg 0.01

5. The four most abundant elements in living organisms are H, O, C
and N which make up of about 99% of the cell mass. Therefore, it
may presume that compounds of these four elements possess
unique molecular fitness for the processes that collectively
constitute the living state.
C, H, O and N possess a common property: they
readily forms covalent bonds by electron pair sharing.

6. • The simple organic compounds from which living organisms
are constructed are unique to life and do not otherwise occur
on the earth today, except as products of biological activity.
These building-block compounds are called biomolecules.
• Biomolecules were selected during the course of biological
evolution for their fitness in performing specific cell functions.
They are identical in all organisms. For example the structure
of amino acids found in micro-organism to higher animals are
unique.
20 amino acids out of 150 fitted in the synthesis of proteins in
whole living organisms.

7. Organic macromolecules in living organisms:
Most of the chemical components of living organisms are
organic compounds of carbon, in which carbon atoms are
covalently joined with other carbon atoms and with hydrogen,
oxygen, or nitrogen.
Organic compounds in living matter are extraordinary variety
and many of them are extremely large and complex. In smallest
cells like E coli contains about 5000 different kinds of organic
compounds, including 3000 different kinds of proteins and 1000
different kinds of nucleic acids.

8. In human organism there may be 50000 different kinds of proteins.
It is unlikely that any of the protein molecules of E coli is identical
with any of the proteins found in human beings, although many
function in quite similar ways. In fact, each species of organism
has its own set of protein and nucleic acid molecules.

9. Ancestor Biomolecules:
It has been suggested that the first cells on earth may have been
built from only two or three dozen different organic molecules.
This set of biomolecules may have included 20 amino acids, 5
nitrogenous bases (thymine, adenine, guanine, cytosine, uracil),
1 or more fatty acids, 2 sugars, the alcohol glycerol and the
amine choline. This set of biomolecules are regarded as the
ancestor of all other biomolecules.
The dimensions and shape of biomolecules:
Three dimentional shape are essentially important for
macromolecules, for enzymes it is called native conformation and
can not work properly if this conformation changes.

11. Biomolecules and it’s Function
• Biomolecules are complex of organic molecules which built up
living organism and form the basis of life.
• Biochemistry is the branch of chemistry which deals with the
study of chemical composition and structure of living organism
and chemical changes take place in them.
• The energy generates during oxidation of food is coupled to the
reaction leading to formation of ATP.
• Carbohydrates are polyhydroxy aldehydes or ketones. Glucose
is a naturally occurring sugar which plays a key role in release of
energy.
• Proteins are complex nitrogenous organic molecules which are
essential for growth and maintenance of life.

12. • Enzymes are biological catalysts produced by living cells which
catalyze the biochemical reactions in living organisms. All enzymes
are globular protein.
• All proteins on partial hydrolysis give peptides of varying molecular
masses and on complete hydrolysis yield amino acids.
• Nucleic acids RNA and DNA are polymers of nucleotides.
• DNA is a double helical structure while RNA is single stranded.
• DNA stores the genetic information in the form of the sequence of
bases.
• The process in which duplication of DNA takes place during cell
division is known as replication through which the genetic message
is passed on to the daughter nuclei.
• One strand of DNA acts as a template on which a complementary
strand of RNA is synthesized. This process is called transcription.
• The newly formed RNA dictates the synthesis of protein at the
ribosome. This process is known as translation.

13. • Lipids are fatty or waxy substances present in the living
organisms which are soluble in organic solvents and are
sparingly soluble in water. They are energy reservoirs of the
cell.
• Phospholipids and lipoproteins are important constituents of
cell membrane.
• Hormones are biomolecules produced from endocrine
(ductless) glands of the body. These transfer information from
one group of cells to a distant organ or tissue and thus control
the metabolism and other body systems.
• Vitamins are essential components of diet. Their deficiency
causes specific diseases.

14. Cellular Foundations
Cells are the structural and functional units of all living organisms. Cells of all
kinds share certain structural features. The plasma membrane defines the
periphery of the cell, separating its contents from the surroundings.
The cytosol is a highly concentrated solution containing enzymes and the
RNA molecules that encode them; hundreds of small organic molecules like
metabolites, coenzymes, inorganic ions. All cells have DNA where complete
set of genes locates and replicated.
Most cells are microscopic, invisible to the unaided eye. Animal and plant
cells are typically 5 to 100µm in diameter, and many bacteria are only 1 to
2µm long.
All living organisms fall into one of three large groups, archaebacteria,
eubacteria and eukaryotes. Most of the well studied bacteria, including
Escherichia coli, are eubacteria. The archaebacteria, more recently
discovered, most inhabit extreme environments—salt lakes, hot springs,
highly acidic bogs, and the ocean depths.

15. Cells Contain a Universal Set of Small Molecules
Cytosol of all cells is a collection of 100 to 200 different small organic
molecules, this collection of molecules includes the common amino acids,
nucleotides, sugars and their phosphorylated derivatives, and a number of
mono-, di-, and tricarboxylic acids. The molecules are polar or charged,
water soluble, and present in micromolar to millimolar concentrations.
The universal occurrence of the same set of compounds in living
cells is a manifestation of the universality of metabolic design.
In addition to the universal set, other metabolites include compounds that
give plants their characteristic scents, and compounds such as morphine,
quinine, nicotine, and caffeine that are valued for their physiological effects
on humans but used for other purposes by plants.
The entire collection of small molecules in a given cell has been called that
cell’s metabolome, in parallel with the term “genome”

17. Biological Cells: Prokaryotic
Molecular composition Properties and functions
Cell wall and
membrane
The cell wall contains a rigid framework
of polysaccharide chains cross-linked
with short peptide chains, outer surface
is coated with lipopolysaccharides.
The cell membrane contains about 45%
lipid, 55% protein.
Cell wall protects bacteria
against swelling in
hypotonic media. It is
porous and allows most
small molecules to pass.
Serve to transfer DNA
during conjugation.
The membrane is selectively
permeable, allows water,
certain nutrients and metal
ions to pass freely.
Nuclear zone The genetic material is a single
chromosome of double helical DNA,
2nm in diameter and 1.2mm long, tightly
coiled
DNA is the carrier of genetic
information. From one
strand of DNA, the genetic
message is transcribed to
form mRNA which dictates
protein synthesis.

18. Ribosomes Each E coli cell contains about 15000
ribosomes, each ribosome has a large
and small subunit. The size of the
ribosome is 70s (50s and 30s). Each
subunit contains about 65% RNA
and 35% protein.
Ribosomes are the sites of
protein synthesis
Storage
granules
E coli and many other bacteria
contain storage granules that are
polymers of sugars.
When needed as fuel, these
polymers are enzymatically
degraded to yield free
glucose
Cytosol The soluble proteins of the cytoplasm
is highly viscous, the protein
concentration is very high, exceeding
20%
Most of the proteins in
cytoplasm are enzymes and
required in metabolism,
also contains metabolic
intermediates and
inorganic salts

19. Eukaryotic Cell

20. Cytoskelton
The Cytoplasm Is Organized by the Cytoskeleton and Is Highly Dynamic.
Electron microscopy reveals several types of protein filaments crisscrossing the
eukaryotic cell, forming an interlocking three-dimensional meshwork, the
cytoskeleton. There are three general types of cytoplasmic filaments—actin
filaments, microtubules, and intermediate filaments. All types provide structure
and organization to the cytoplasm and shape to the cell. Each type of cytoskeletal
component is composed of simple protein subunits that polymerize to form
filaments of uniform thickness. These filaments are not permanent structures;
they undergo constant disassembly into their protein subunits and reassembly
into filaments.
Their locations in cells are not rigidly fixed but may change dramatically with
mitosis, cytokinesis, amoeboid motion, or changes in cell shape. The filaments
disassemble and then reassemble elsewhere. Organelles move through the
cytoplasm along protein filaments, their motion powered by energy dependent
motor proteins.

21. Biological Cells: Eukaryotic
Cell
membrane
The cell coat is flexible and sticky,
composed of mucopolysaccharides,
glycolipids and glycoproteins.
The plasma membrane is about 9nm
thick and contains about equal amounts
of proteins and lipids, lipids are arranged
in a bilayer, contains greater variety of
lipids than bacterial membrane.
The adhesive properties of cell
coats are specific and play an
important role in cell-cell
recognition and thus tissue
organization.
The plasma membrane is
selectively permeable. It contains
active-transport systems for Na
and K, glucose, amino acids and
other nutrients, as well as a
number of important enzymes.
Nucleus About 4-6µm in diameter, surrounded by
a perinuclear envelope, the DNA is
combined with histones and organized
into chromosomes,
During mitosis, chromosomes
undergo replication of their DNA
and separation into daughter
chromosomes, thus identical
genetic information transfers from
progeny to progeny.

22. Mitochondria There are about 800 mitochondria in
each hepatocytes, they are globular
and a little over 1µm in diameter,
occupying about 20% of the
cytoplasmic volume, outer and inner
membrane differ in lipid composition
and in enzymatic activity, the matrix is
rich in enzymes
The mitochondria are the
power plants of the cell where
carbohydrate, amino acids and
lipids are oxidized to CO2 and
H2O by molecular O2 and
produces ATP as energy. The
enzymes of electron transport
and energy conversion are
located in the inner
membrane.
Golgi complex Single membrane vesicles, small
vesicles arise peripherally, some
become vacuoles where secretory
products are concentrated.
Functions in the secretion of
cell products, helps to form
plasma membrane and
membranes of the lysosomes.

23. Peroxysome Single membrane vesicles,
about 0.5µm in diameter,
contain catalase, urate
oxidase and other oxidative
enzymes
Participate in the
oxidation of certain
nutrients
Lysosome Lysosomes are single
membrane vesicles, 0.25-
0.5µm in diameter, contains
ribonuclease and
phosphatase.
Functions in the digestion
of materials brought into
the cells through
phagocytosis, also serve
to digest cell components
after cell death
Endoplasmic reticulum
and ribosomes
Single membrane vesicles,
size of the ribosome is 80s
(60s & 40s), ribosome
composed of 65% RNA and
35% protein.
Protein synthesized by
the adhering of
ribosomes with mRNA
and tRNA

24. Lysosomal enzymes and Gout
The catabolism of purine (nitrogen containing heterocyclic
compounds found in nucleic acids) leads to the formation of uric
acids which is normally excretes in urine.
Gout is an abnormality in which there is an overproduction of
purines leading to excessive production of uric acid. In
consequences increase in uric acid concentration in blood and
deposition of urate crystals in joints (uric acid is not very soluble).
The crystal causes physical damage to the cells, lysosomes
breakdown, lysosomal enzymes come out and causes digestion of
the cellular components, the consequences are clinical
manifestations in the joints, including inflammations, pain, swelling
and increase temperature.

25. Subcellular fractionation of tissue
A tissue such as liver is first mechanically homogenized to break
cells and disperse their contents in an aqueous buffer. The sucrose
medium has an osmotic pressure similar to that in organelles, thus
preventing diffusion of water into the organelles, which would swell
and burst. (a) The large and small particles in the suspension can be
separated by centrifugation at different speeds,

26. Differential centrifugation

27. (b) particles of different density can be separated
by isopycnic centrifugation. In isopycnic centrifugation, a centrifuge
tube is filled with a solution, the density of which increases from top to
bottom; a solute such as sucrose is dissolved at different
concentrations to produce the density gradient. When a mixture of
organelles is layered on top of the density gradient and the tube is
centrifuged at high speed, individual organelles sediment until their
buoyant density exactly matches that in the gradient. Each layer can
be collected separately.

28. Isopycnic (sucrose-density)
centrifugation