2024 BCH211 CHAPTER 1 Introduction to Biochemistry

A. Biochemistry as a chemical science

Biochemistry is a study of the structure, organization, and functions of living matter in molecular terms.
It can be divided into three principal areas:
1. The structural chemistry of the components of living matter and the relationship of biological
function to chemical structure.
2. Metabolism, which is all the chemical reactions that occur in living organisms.
3. The chemistry of processes and substances that store and transmit biological information.

Biochemistry draws its major themes from other disciplines, such as;
1. Organic chemistry, which describes the properties of biomolecules,
2. Microbiology, which has shown that single-celled organisms and viruses are ideally suited for the
elucidation of many metabolic pathways and regulatory mechanisms,
3. Physiology, which investigates life processes at the tissue and organism levels,

B. Unit of biological organization: The cell

Cells are the structural and functional units of living organisms. A living cell can bed defined as a self-
assembling, self-adjusting, self-perpetuating system of organic molecules which extracts free energy
and materials from its environment. There are two broad categories of cells, namely prokaryotic and
eukaryotic cells. These names refer to the absence and presence, respectively of a nucleus, but the main
distinguishing feature of these two groups of cells is that the much simpler prokaryotic cells have no
membrane enclosed organelles whereas the more complex eukaryotic cells have several such organelles.
Prokaryotes comprise of bacteria and cyanobactera, and eukaryotes are plant and animal cells (Figure
1). Prokaryotes exist as single cells although an aggregation of many single cells may occur giving a
multicellular aggregation, whilst eukaryotes may be single celled organism, such as paramecium. The
main features of the different cell types namely bacterial, animal and plant cells, are summarized in Table 1.
The distribution of biomolecules in a cell is shown in Figure 2.
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Figure 1 A graphical representation of the diffences between the prokaryotic (i.e. a bacterial cell) and
eukaryotic cells (animal and plant cells).

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Figure 2. Distribution of biomolecules in a cell.

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Table 1. Differences between prokaryotic and eukaryotic cells.
Attributes Prokaryotic Eukarpotic cells
cells Plant cells Animal cells
Size 0.2-5µm in Most are 10-50µm in diameter
diameter
Internal None Yes (See below)
compartmentali
zation
Cell wall Thick, rigid, Thick, rigid, porous and gives None
porous and shape to the cell, made up of
gives shape to cellulose fibrils.
the cell, made
up of
heteropolymer
s.
Cell membrane The cell membrane acts as a selective barrier against a lot of substances. It
contains an active transport system for specific biomolecules.
Nucleic material No definite A nucleus contains nucleolus where the genetic material
nucleus, DNA is concentrated and is bound by a nucleic membrane.
present but
not bound to
anything.
Chloroplast None Photosynthetic organelles. None
Photosynthetic reactions take
place in the laminar arrays
called chromatophores.
Mitochondrion None Found in all eukaryotic cells. They have a specific DNA.
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 They are involved in oxidation/degradation of nutrients,
thus they provide energy in the form of ATP to the cell.
They are bound by a double membrane
Vacuole None Vacuoles are particularly
prevalent in plant cells. They
segregate waste products of
the cell and remove salts and
other solutes, which gradually
increase as the cell grows
older.
Endoplasmic None They are found in all eukaryotic cells. ER is part of a
reticulum continuous membrane system thoughout the cell (Figure
6). They are usually associated with ribosomes (and are
thus called rough ER. They serve to channel protein
products through the cytoplasm.
Ribosomes These organelles are found in all eukaryotic cells, and are
usually associated with endoplasmic reticulum. They
are the site of protein synthesis.
Storage Prokaryotic None
granules cells store
some
polymers in
these vesicles.
When needed
as fuels, these
polymers are
enzymatically
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 degraded to
yield simpler
metabolites.
Lysosomes None These organelles contain
enzymes that could
cause considerable
damage to the cell, if
they were not separated
from the cells’
macromolecules such as
proteins. These enzymes
function in the digestion
of materials brought into
the cell by phagocytosis.
They also serve to digest
cell components after
cell death.
Glyoxysomes None They contain enzymes that None
catalyze the glyoxylate cycle,
a pathway that converts lipids
to carbohydrate.

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C. Distinctive properties of living organisms
1. All living things consist of lifeless molecules, yet they have unique and extraordinary properties due to
the many complex interactions that occur between these molecules.
2. Living organisms are complex and highly organized. They are made up of subunits called cells. Cells
possess subcellular structures called organelles, which are in turn made up of very large molecules
(or macromolecules).
3. Each part of a living organism has a specific function; not only the visible structures such as the
leaves, eyes, wings, etc., but also the intracellular structures such as the nucleus, mitochondria,
right down to the individual molecules.
4. Living organisms exchange energy and materials with their environments and convert it into forms that
suit their own requirements.
5. Living organisms are capable of precise self replication.

In order to understand the impact of biochemistry on biology, one must understand the chemical elements
of living matter and the complete structures of many biological compounds - amino acids, sugars, lipids,
nucleotides, vitamins, and hormones - and their behavior during metabolic reactions. Essential
understanding of biochemistry requires knowledge of the stoichiometry (i.e. branch of chemistry that
deals with quantities of substances) and mechanisms of a large number of reactions occurring within
living organisms. In addition, an understanding of the basic thermodynamic principles is essential for
learning how plants derive energy from sunlight (photosynthesis) and how animals derive energy from
food (catabolism).

Living organisms consist mostly of water (about 70 to 80%), organic molecules (about 20 to 30%) and
minerals (about 1%). Organic molecules are composed mainly of a very few elements, principally carbon,
hydrogen, oxygen, and nitrogen (C, H, O, and N).

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D. The suitability of C, H, 0, and N to form organic compounds
These four elements form covalent bonds by electron-pair sharing. C needs four electrons, H one, 0 two,
and N three, to complete their outer shell electrons and thus they form stable covalent bonds. The
following features make these four elements to be the most suitable to form the many diverse
biomolecules found in nature:
1. They can react with each other to form a large variety of different covalently linked compounds. Four
of them (C, H, O and N) can share one electron pair to form single bonds. Three of them (C, O and N) can
share either one or two electron pairs to form single or double bonds of them, C and N, can also form
triple bonds.
2. C, H, O and N are the four lightest elements capable of forming covalent bonds and, because the
strength of a covalent bond is inversely related to the atomic mass of the bonded atoms, they form
very strong bonds.
3. These atoms can combine in very large arrays to make the many macromolecules of living organisms
possible.

In addition to the properties which are general to the four atoms, carbon displays some other attributes,
such as;
1. Carbon atoms can covalently bind each other, i.e. one C atom can bind to one, two, or three other carbon
atoms to form linear, branched or cyclic molecular structures, a fact that further increases its
versatility in forming variable and complex structures.
2. The configuration of the electron pairs around a single carbon atom is tetrahedral, which means that for
many carbon compounds, different (and almost limitless number of) configurations and
conformations are possible.

Life is not built on these four elements alone. Many other elements are necessary for living organisms
(Table 2). A "second tier" of essential elements includes sulfur and phosphorus, which form covalent
bonds, and the ions Na+, K+, Mg2+, Ca2+, and Cl-.
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Table 2. Elements that are constituents of molecules of living organisms.
Element Comment
First Tier Most abundant in all organisms
Carbon (C), Hydrogen (H), Nitrogen (N), Oxygen (O)
Second Tier Much less abundant in all
Calcium (Ca), Chlorine (Cl), Magnesium (Mg), organisms
Phosphorus (P), Potassium (K), Sodium (Na), Sulphur
(S)
Third Tier Metals present in small
Cobalt (Co), Copper (Cu), Iron (Fe), Manganese (Mn), amounts in all organisms and
Zinc (Zn) essential to life
Fourth Tier Found in or required by some
Aluminium (Al), Arsenic (As), Boron B), Bromine (Br), organisms in trace amounts
Chromium (Cr), Fluorine (F), Gallium (Ga), Iodine (I),
Molybdenum (Mo), Nickel (Ni), Selenium (Se), Silicon
(Si), Tungsten (W), Vanadium (V)

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E. Biological Molecules
The complexity of life processes Table 3. How big or heavy are atoms or molecules
requires that many of the (see also Figure 3)?
molecules that participate in these Atom/  Dalton size  Mass (kg)
processes be enormous. The Molecule (Da)
most extreme example is 1H 1 1.7 x 10-27
deoxyribonucleic acid (DNA). H2O 18 3.1 x 10-26
Consider, for instance, DNA Typical protein 3 x 106 5.1 x 10-22
molecules released from one Typical cell 4 x 1015 8 x 10-12
human chromosome. It is a long,
looped thread corresponds to just
two enormous molecules, each
with a molecular weight of about
20 x 109 Da (Table 3). Protein
molecules are generally much
smaller, but they are still large,
with a typical protein having a
mass of 3 x 106 Da.

All large macromolecules in the cell are polymers, made by joining prefabricated units, or monomers. The
monomers of a given type of macromolecule are of limited diversity and are linked together, or
polymerized, by identical mechanisms.

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A simple example is the carbohydrate (mainly
composed of C, H, and O), cellulose (Figure 3a), a
major constituent of the cell walls of plants. Cellulose
is a polymer made by joining thousands of molecules
of glucose, a simple sugar. In this polymer all the
chemical linkages (bonds) between the monomers
are identical (1-4). Covalent links between glucose
units are formed by removing a water molecule
(dehydration) between two adjoining molecules; the
portion of a glucose molecule remaining in the chain
is called a glucose residue. Cellulose is called a
polysaccharide because cellulose is a polymer of a
simple sugar, or a saccharide. This polymer is
constructed from identical monomeric units, so it is
called a homopolymer. In contrast, many
polysaccharides and all nucleic acids and proteins are
heteropolymers, polymers constructed from several
different kinds of monomer units.
Nucleic acids (Figure 3b) are polymers of four
nucleotides (mainly composed of C, H, O, N, and P),
so nucleic acids are also called polynucleotides.
Proteins (Figure 3c) are assembled from
combinations of 20 different amino acids (mainly
composed of C, H, O, N, and S). Protein chains are
called polypeptides, a term derived from the peptide
bond that joins two amino acids together.
Figure 3. Various biomolecules.

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Figure 4. Sizes of various objects.

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F. The hierarchy of biological organization
In living organisms there is an organizational hierarchy of increasing complexity, starting with;
1. Atoms
2. Common inorganic precursors from the environment (water (H2O), nitrogen gas (N2), nitrate (NO3-),
carbon dioxide (CO2))
3. Metabolites (pyruvate, citrate, succinate, glyceraldehydes-3-phosphate, Fructose-1,6-phosphate,
3-phosphoglyceric acid)
4. Building block molecules (monosaccharides, amino acids, nucleotides, fatty acids, glycerol)
5. Macromolecules (proteins, nucleic acids, polysaccharides, lipids)
6. Supramolecular assemblies (membranes, ribosomes, microtubules, enzyme complexes,
contractile systems)
7. Organelles (nuclei, mitochondria, Golgi bodies, chloroplasts)
8. Cells
9. Organs
10. Multicellular organisms

G. Viruses
Viruses are nonliving entities, which usually consist of one molecule of nucleic acid (either DNA or
RNA) wrapped in an envelope made largely or completely of protein. The envelope is specialized to
allow the virus particle to enter particular plant, animal, or bacterial cells. Once inside the host cell or
system, they grow as intracellular parasites.

Most viruses contain virtually no metabolic machinery of their own, so they use that of the host cell to
reproduce. Viruses thus provide useful insights into the cellular functions that they co-opt during
infection. For example, the smallest DNA-containing viruses replicate their DNA using only host-cell
enzymes. Because of their small size, these viral DNA molecules can be isolated and characterized
much more easily than the nucleic giant DNA molecules in cellular chromosomes.
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H. Uses of biochemistry
The results of biochemical research are used extensively in the world outside the laboratory - in
agriculture, medical sciences, nutrition, and many other fields.
1. In clinical chemistry, biochemical measurements on people help diagnose illnesses and monitor
responses to treatment. Liver disease is now routinely diagnosed and monitored by measurements of
blood levels of enzymes called transaminases and of a hemoglobin breakdown product called bilirubin.
2. Pharmacology and toxicology are concerned with the effects of external chemical substances on
metabolism. Drugs and poisons usually act by interfering with specific metabolic pathways. A good
example is the antibiotic penicillin, which kills bacteria by inhibiting an enzyme that synthesizes an
essential polysaccharide of the bacterial cell wall. Because animal cells do not synthesize these
polysaccharides, they are not harmed by this inhibitor, which can therefore be used therapeutically.
3. A particularly exciting prospect in Biochemistry is that of creating so-called designer drugs. If the target
site for action of a drug is a protein enzyme or receptor, determining the detailed molecular structure of
that target allows us to design inhibitors that bind to it with great selectivity. Early products of this drug
architecture are then tested.
4. Herbicides and pesticides, in many instances, act in similar ways - by blocking enzymes or receptors in
the target organism. The first generations of these toxic agents (such as DDT) were nonspecific in their
effects that organisms other than the target populations were often affected, resulting in unforeseen and
often severe damage to the environment. Furthermore, the indiscriminate use of these agents gave rise to
resistant target populations, so that an ever-increasing number of toxins needed to be used.
Biochemistry is involved in understanding the actions of herbicides and pesticides, in increasing their
selectivity, and in understanding and dealing with mechanisms by which target organisms become
resistant to them. Thus, biochemistry has become an important component of environmental science.

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