1

INTRODUCTION
Biochemistry is the systematic study of the chemicals of the living systems, their organization, and the principles of their
participation in the processes of life. Its importance is due to the increasing recognition that underlying each and every
biological function is a chemical reaction. Hundreds/thousands of chemical reactions are taking place in our cells every minute
of our lives. Biochemical investigations have been directed towards the study of the chemical composition of cells and the
chemical processes in which they participate.

Several principles are central to the understanding of living organisms:
1) Cells, the basic structural units of all living things, are highly organized.
2) Living processes consist of hundreds of chemical reactions.
3) Certain fundamental reaction pathways are found in all living organisms.
4) All organisms use the same type of molecules.
5) The instructions for growth, development, and reproduction are encoded in an organisms nucleic acids.

The life of a cell requires materials, information, and energy:
A cell in particular, and a whole organism in general, has three basic needs: materials, information, and energy.
Without the daily satisfaction of these, human life would be severely constrained.

The organic materials of life will be considered, starting with the three main classes of foodstuffs carbohydrates,
lipids, and proteins. Humans use these molecules to build and run their bodies and to try to stay in some state of repair. Plants
rely heavily on carbohydrate for cell walls, and animals obtain considerable energy from carbohydrates made by plants. Lipids
serve many purposes. They are used, both by plants and animals, as materials to make cell membranes and as sources of
chemical energy. Proteins are particularly important in both the structures and functions of cells. Because of the catalytic role
of proteins in regulating chemical events in cells, the study of proteins will be immediately followed with an examination of
enzymes, which make up a particular family of proteins.

Every cell has an information system enzymes, hormones, and neurotransmitters are components of the intricate
information system in the body. Without information, the materials and energy delivered to the body could produce only
rubbish. Although enzymes are major players in the cells information system, they do not originate the cellular script. They
only help to carry out directions that are encoded in the molecular structures of the nucleic acids, which are compounds that are
able to direct the synthesis of enzymes. Hormones & neurotransmitters, two other components of cellular information, depend
on the presence of right enzymes not only for their existence but for their functions. Thus the study of the enzyme makers, the
nucleic acids, is included in any study of the molecular basis of life.

All life processes consist of chemical reactions catalyzed by enzymes. The reactions of a living cell, which are known
collectively as metabolism, result in highly coordinated and purposeful activity. Among the most frequent reactions
encountered in biochemical processes are:
1) nucleophilic substitution 4) isomerization
2) elimination 5) oxidation reduction
3) addition 6) hydrolysis

To supply materials for any use parts, information, or energy each organism has basic nutritional needs. These
include not just organic materials, including vitamins, but also mineral, water, and oxygen. Thus, together with learning about
the materials of life and how they are processed and used, the need for vitamins, minerals, water, and oxygen will also be
considered.
2

Organelle Prokaryotes Eukaryotes
Nucleus
Cell membrane
Mitochondria
Endoplasmic
reticulum
Ribosomes
Chloroplasts
No definite nucleus; DNA
present but not separate
from the rest of the cell
Present
Present Present
None; enzymes for oxi dation
are on plasma membrane
None
Present
None; photosynthesis
localized in chromatophores
Present
Present
Present
Present in
green plants
I. CELL STRUCTURE

Based on their cell structures, organisms are divided into two main groups:
1) Prokaryote: Greek derivation meaning before the nucleus; single-celled organisms
2) Eukaryote: Greek derivation meaning true nucleus; contain a well-defined nucleus surrounded by a nuclear
membrane; can be single celled, such as yeasts and Paramecium, or multicellular, such as animals and plants
Five kingdoms:
1) Monera - only prokaryotic organisms; includes bacteria and cyanobacteria
2) Protista - includes unicellular eukaryotes: yeast, Euglena, Volvox, Amoeba, and Paramecium
3) Fungi - includes molds and mushrooms
4) Plantae Fungi, plants, and animals are multicellular eukaryotes
5) Animals (with few unicellular eukaryotes)

The main difference between prokaryotic and eukaryotic cells is the existence of organelles, especially the nucleus, in
eukaryotes. An organelle is a part of the cell that has a distinct function; it is surrounded by its own membrane within the cell.





































3

Lysosomes
Peroxi somes
Cell membrane
Cell wall
Central vacuole
Membrane-bounded sacs containing hydrolytic enzymes
Sacs that contain enzymes involved in the metabolism
of hydrogen peroxi de
Separates the cell contents from the outside world
Rigid exterior layer of plant cells
Membrane-bound sac (plant cells)
Mitochondrion
Chloroplast
Endoplasmic
reticulum
Site of energy-yi elding oxi dation reactions; has
its own DNA
Site of photosynthesis in green plants and algae;
has its own DNA
Continuous membrane throughout the cell, rough
part studded with ribosomes; sites of protein synthesis
Nucleus Location of main genome & most DNA/RNA synthesis
Organelle Function
Golgi
apparatus
Series of flattened membranes; involved in secretion
of proteins from cells and in reactions that link
sugars to other cellular components













1. Cell membrane / plasma membrane
- a semi-permeable membrane surrounding the cell separating its internal environment from the external
environment; permits and/or enhances the absorption of essential nutrients into the cell while preventing the
diffusion of needed metabolites.
- a lipid bilayer that mechanically holds cell together, composed of lipid and protein molecules. Lipids provide the
basic structure of biological membranes. Proteins are embedded in the membranes and provide channels/carriers
for the transport of ions and nutrients. Other membrane proteins act as receptors that bind certain cellular
constituents, particularly enzymes in a location apparently most advantageous for the performance of their
specific biochemical functions. Receptors also bind hormones on the external surface of the cell which interaction
initiates a programmed response by the cell. For example, binding of the hormone insulin to insulin receptors
results in a series of changes in the cells activity,
2. Nucleus
- the information center of the cell; enclosed by a nuclear membrane and contains the cells genetic information
and the machinery for converting that information into protein molecules.
- site of DNA and RNA synthesis
- contains a comparatively large amount of nucleoprotein (50% DNA and 50% proteins, histones and prolamines
located in the chromosomes, and a small amount of RNA; >95% of nucleic acids of the cell is in the nucleus
Nucleolus
- small, round dense body present within the nucleus; not surrounded by a membrane; essentially a cluster of
looped chromosomal segments; contains 10-20% of the total RNA of the cell, chiefly mRNA
- serve as a storehouse for mRNA prior to its movement into the cytoplasm by way of the nuclear pores
3. Cytoplasm
- structureless and highly viscous; the aqueous phase of the cell in which many particulate constituents like
mitochondria, ribosomes, etc. are suspended.
- contains a wide variety of solutes including proteins, enzymes, nucleic acids (RNA), a number of electrolytes,
metabolites for cellular utilization (e.g., glucose), and waste products of cellular activity (e.g., urea, creatinine,
uric acid, etc.)

4


4. Mitochondria
- the second largest organelle; usually ellipsoidal in shape; the powerhouse of the cell where carbohydrates, lipids,
and amino acids are oxidized to CO
2
and H
2
O by molecular O
2
and the energy set free is converted into the
energy of ATP
- has a double-membrane structure, an outer membrane and an inner membrane. The inner membrane, in which the
enzymes of electron transport and energy conversion are located, is convoluted to form shelves termed cristae;
site for cellular respiration.
5. Endoplasmic reticulum
- appears to be a system of interconnected tubules or canaliculi extending throughout the cell cytoplasm and is
continuous with the outer nuclear membrane; two types: rough and smooth er
- rough er is lined with a number of small, spheric, electron-dense particles called ribosomes; primarily involved in
synthesis of membrane proteins and proteins for export from the cell
- smooth er lacks ribosomes; appears to be involved in the biosynthesis of steroids, phospholipids, and complex
polysaccharides; functions also include biotransformation, a process in which water-soluble organic molecules
are prepared for excretion
6. Ribosomes
- consist of ~50% RNA (rRNA) and 50% protein; involved in protein synthesis in the cell and are sometimes
referred to as the workbench for protein synthesis
- complex structures containing two irregularly shaped subunits of unequal size; they come together to form whole
ribosomes when protein synthesis is initiated, when not in use, the ribosomal subunits separate
7. Golgi apparatus (Golgi complex)
- structures composed of flattened sacs with vesicles, located near the nucleus, probably continuous with er
- the organelles to which synthesized proteins are transported and temporarily stored before release from the cell
- the packaging stations of the cell, the primary site for packaging and distribution of cell products to internal and
external compartments
- there is a continuous flow of substances through the Golgi apparatus
- responsible for sorting and packaging several types of proteins, small molecules, and new membrane components
8. Lysosomes
- membrane-bound organelles containing a variety of hydrolytic and degradative enzymes and having an optimum
pH of 5.0
- has regulatory and defense function; function in the digestion of materials brought into the cell by phagocytosis
and pinocytosis; also serve to digest cell components after cell death; the suicide bags of the cell
- upon death of the cell or its exposure to environmental conditions, the lysosomal membrane disintegrates,
releasing its contents, which cause the self-digestion or autolysis of the cell constituents
9. Peroxisomes
- contains oxidative enzymes that oxidize amino acids, uric acid, and various 2-hydroxyamino acids using O
2
with
the formation of H
2
O
2
, which is then converted to H
2
O and O
2
by the enzyme catalase


The study of the composition of the living matter is necessary for the intelligent understanding of the chemical
processes taking place in the body. The protoplasm, the living matter, is composed of:

also present in the
peroxisomes thus the cell protects itself from the toxicity of H
2
O
2

a) bioinorganic substances that include water (70-90%) and inorganic salts (chloride, sulfate, phosphate,
carbonate, etc. salts of Na, K, Ca, Mg, NH
4
) and

b) bioorganic compounds that include proteins, lipids, carbohydrates, and nucleic acids.




5














Some importance of water in the cell:
1. the solvent
- the agency that enables water-soluble, water-miscible, or emulsifiable substances to be transferred in the body not
only in the blood but also intercellularly and intracellularly
2. in biochemical reactions
- ionization is a prerequisite to many biochemical reactions and ionization takes place in water
3. in physiologic regulation of body temperature
- high specific heat (amount of heat required to raise the temperature of 1g of H
2
O 1
o
C) enables the body to store
heat effectively without greatly raising its temperature
- high heat conductivity permits heat to be transferred readily from the interior of the body to the surface
- high latent heat of evaporation causes a great deal of heat to be used in its evaporation and thus cools the
surface of the body

























Chemical reactions occurring in vivo have the following properties:
1. mildness
- energy is taken up and released in a gentle way, nor violently as those occurring in vitro (because of high specific
heat of water which makes up a large proportion of the protoplasm)
2. speed
- glucose, for instance, is oxidized in the body with surprising speed, while in vitro, the same reaction is quite a
long and tedious process. This is due to the presence of enzymes, without which life as we know it would not be
possible
3. orderliness
- a high degree of orderliness is due to the existence of cell specialization within the different organs of the body
6