Chapter 1

Introduction – Cell
Structure
 Section 18.1
Biochemistry – An Overview
The Study of Living Things
• Biochemistry is the systematic
study of the chemical substances
found in living organisms, their
organization & chemical
interactions with each other, 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.
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• Biochemical investigations have
been directed towards the study of
the chemical composition of cells
and the chemical processes in
which they participate.
• A biochemical substance is a
chemical substance found within a
living organism.
• Two types of biochemical
substances:
– Bioinorganic substances :
water and inorganic salts.
– Bioorganic substances :
carbohydrates, lipids,
proteins, and nucleic acids
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 Section 18.1
Biochemistry – An Overview

Biochemical substances • As isolated compounds,

bioinorganic and bioorganic
substances have no life in
and of themselves.
• Yet when these substances
are gathered together in a
cell, their chemical
interactions are able to
sustain life.
• 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.

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 Section 18.1
Biochemistry – An Overview
Main classes of foodstuffs - Materials
• The bioorganic 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.
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• 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.
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 Section 18.1
Biochemistry – An Overview
Information system
• 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.
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• 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.
• Thus the study of the enzyme
makers, the nucleic acids, is
included in any study of the
molecular basis of life.
• Hormones & neurotransmitters,
two other components of cellular
information, depend on the
presence of right enzymes not
only for their existence but for their
functions.
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 Section 18.1
Biochemistry – An Overview

Biochemical substances
• To supply materials for • Thus, together with
any use – parts, learning about the
information, or energy – bioorganic materials of
each organism has basic life and how they are
nutritional needs. processed and used, the
• These include not just need for vitamins,
bioorganic materials, minerals, water, and
including vitamins, but oxygen will also be
also bioinorganic considered.
materials including
minerals, water, and
oxygen.
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 Section 18.1
Biochemistry – An Overview

Metabolism • The redox chemistry of

• 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:
– nucleophilic substitution
– elimination
– addition
– isomerization
– hydrolysis
– oxidation – reduction
carbohydrates is fundamental
to life.
• Glucose is the most important
carbohydrate in biochemistry.
Almost all cells derive energy
from the oxidation of glucose
through glycolysis, citric acid
cycle, and oxidative
phosphorylation
• The energy yield from the
oxidation of glucose is shown
below.

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 Section 18.1
Biochemistry – An Overview

The Study of Living Things – The CELL STRUCTURE

• Based on their cell structures,
• Five kingdoms:
organisms are divided into two
• Monera - prokaryotic organisms;
main groups:
includes bacteria and
• Prokaryote: Greek - meaning cyanobacteria
“before the nucleus”; single- • Protista - unicellular eukaryotes:
celled organisms yeast, Euglena, Volvox, Amoeba,
• Eukaryote: Greek - meaning and Paramecium
“true nucleus” • Fungi - molds and mushrooms
– contain a well-defined nucleus • Plantae
surrounded by a nuclear • Animalia
membrane • Fungi, plants, and animals are
– can be single celled, such as multicellular eukaryotes
yeasts and Paramecium, or (with few unicellular eukaryotes)
multicellular, such as animals
and plants
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 Section 18.1
Biochemistry – An Overview

The Study of Living Things – The CELL STRUCTURE

• 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.

Orga nelle Proka ryotes Eukaryo tes

Nucleus No definite nucleus; DNA Present
pres ent but no t separate
from the rest of the cell
Cell membra ne Present Present
Mitocho ndria None; enzymes for oxidation Present
are on pla sma membrane
Endo pla smic None Present
reticulum
Riboso mes Present Present
Chloro pla sts None; photo synthesis Present in
lo ca lized in chro ma to phores green pla nts

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 Section 18.1
Biochemistry – An Overview

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 Section 18.1
Biochemistry – An Overview

The CELL STRUCTURE – Functions of the organelles

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 Section 18.1
Biochemistry – An Overview

The cell membrane • Lipids provide the basic structure

of biological membranes
• a semi-permeable membrane • Proteins are embedded in the
surrounding the cell separating its membranes and provide
internal environment from the channels/carriers for the transport
external environment; of ions and nutrients
• 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
• component biomolecules:
– Lipids: phospholipids,
cholesterol
– Proteins
– Carbohydrates

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 Section 18.1
Biochemistry – An Overview

The cytoplasm
• structureless and highly • contains a wide variety of
viscous solutes including proteins,
• the aqueous phase of the enzymes, nucleic acids
cell in which many (RNA), a number of
particulate constituents electrolytes, metabolites
like mitochondria, for cellular utilization
ribosomes, etc. are (e.g., glucose), and waste
suspended products of cellular
activity (e.g., urea,
creatinine, uric acid, etc.)

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 Section 18.1
Biochemistry – An Overview
The nucleus
• the “information center” of the cell;
enclosed by a nuclear membrane
and contains the cell’s 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
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• 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
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 Section 18.1
Biochemistry – An Overview

The mitochondria • The inner membrane, in which

the enzymes of electron
• the second largest organelle transport and energy
• the powerhouse of the cell conversion are located, is
where carbohydrates, lipids, convoluted to form shelves
and amino acids are oxidized termed cristae.
to CO2 and H2O by molecular
O2 and the energy set free is
converted into the energy of
ATP
• has a double-membrane
structure, an outer membrane
and an inner membrane
• site for cellular respiration

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 Section 18.1
Biochemistry – An Overview
The 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
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• 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
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 Section 18.1
Biochemistry – An Overview

The ribosomes • they come together to

form whole ribosomes
• consist of ~50% RNA when protein synthesis is
(rRNA) and 50% protein initiated
• involved in protein • when not in use, the
synthesis in the cell and ribosomal subunits
are sometimes referred to separate
as the “workbench” for
protein synthesis
• complex structures
containing two irregularly
shaped subunits of
unequal size

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 Section 18.1
Biochemistry – An Overview
The 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
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• 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
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 Section 18.1
Biochemistry – An Overview
The 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
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• 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
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 Section 18.1
Biochemistry – An Overview

The peroxisomes

• contains oxidative • H2O2 is then converted to

enzymes that oxidize H2O and O2 by the
amino acids, uric acid, enzyme catalase also
and various 2- present in the
hydroxyamino acids using peroxisomes
O2 with the formation of • thus the cell protects itself
H2O2 from the toxicity of H2O2

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 Section 18.1
Biochemistry – An Overview

Water in the cell

• 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
• in biochemical reactions
– ionization is a prerequisite to
many biochemical reactions
and ionization takes place in
water

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 Section 18.1
Biochemistry – An Overview

Water in the cell

• in physiologic regulation of body
temperature
– high specific heat (amount of
heat required to raise the
temperature of 1g of H2O 1oC)
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

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 Section 18.1
Biochemistry – An Overview
Characteristics of biochemical reactions
• Chemical reactions occurring
in vivo have the following
properties:
• 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
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• Mildness
– energy is taken up and
released in a gentle way, not
violently as those occurring in
vitro (because of high specific
heat of water which makes up
a large proportion of the
protoplasm)
• Orderliness
– a high degree of orderliness is
due to the existence of cell
specialization within the
different organs of the body
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