BGE,JU

Basic Biochemistry
Course # BGE 105
Ref.: Lehninger Principle of Biochemistry, David L. Nelson,
Michael M. Cox, 5th edition, and Other books.

2. The Cell
(Concept of life and living processes; Identifying
characteristics of a living matter; Historical background; Cell
theory; Cell size and structure; Structure of Prokaryotic and
Eukaryotic Cells.) 1
What is Life or Concept of Life:

The condition that distinguishes animals and plants from inorganic

matter, including the capacity for growth, reproduction, functional
activity, and continual change prior death.

Life is a characteristic distinguishing physical entities having

biological processes, such as signaling and self-sustaining processes.

Various forms of life exist, such as plants, animals, fungi, bacteria

and etc. Biology is the primary science concerned with the study of
life, although many other sciences are involved.

The definition of life is controversial. The current definition is that

organisms maintain homeostasis, are composed of cells, undergo
metabolism, can grow, adapt to their environment, respond to stimuli,
and reproduce.
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Concept of Living Processes:
Living processes are the series of actions that are essential to
determine, if an animal is alive. Living things have seven essential
processes in common: movement, respiration, sensitivity, growth,
reproduction, excretion and nutrition. The presence of all seven life
processes indicates a living thing.

Movement is simply the ability to get from one place to another.

Reproduction is the ability to create offspring.

Sensitivity refers to the ability to react to the world around them

using the five senses, hearing, sight, smell, touch and taste.

Growth means the ability to grow from birth into adulthood.

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Respiration, is a chemical reaction that takes place in our cells.
It is the creation of energy to keep you active.

Excretion refers to the ability to clear the body of waste. It is

how energy is produced from glucose and oxygen and the process
of removing water, carbon dioxide and other substances from your
body.

Nutrition means eating, which is important to sustain life.

These processes make it easy to determine if something is living,

and a good way to remember them.

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Identifying characteristics of a living matter:
Some properties of living matter that separate it from non-living
matter. These properties help scientists distinguish the living world
from the non-living world. One of the big reasons for interest in this
topic concerns the search for life of our own planet as well as other
planets.

Living matter is organized into complex structures based on

organic molecules:
While this characteristic alone is not sufficient to define life (many
non-living forms of matter, such as crystals, exhibit complex
structure), it is a prerequisite. An organism is made up of organs,
which are made up of tissues, which are made up of cells, which are
made up of organelles (at least in eukaryotic life forms; organelles
are little "organs", like the chloroplast, the nucleus, mitochondria,
Golgi bodies, endoplasmic reticulum), which are composed of
molecules made of atoms or particles. 5
Living matter maintains some type of homeostasis:
Homeostasis is the maintenance of relatively constant internal
conditions. Human bodies maintain a body temperature that is a
rather constant 98.6 degrees Fahrenheit. Our bodies accomplish
this through a series of biofeedback mechanisms, such as
shivering when it's cold or sweating when it's warm. Not all life
regulates temperature, but other properties are regulated, such as
their chemical composition, the amount of water in their bodies,
their salt content, etc.

Living matter grows and develops:

Most living things with which we are familiar start out small and
grow big. Your kid brother or sister; they all grew and developed
and changed. Your little brothers and sisters became men and
women.
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Living matter reproduces and passes on genetic material as
a blueprint for growth and subsequent reproduction:
Life duplicates. Over and over and over. Rabbits, roaches, mice,
humans, these are the more prolific members of the living
kingdom and we need no introduction to their modes of
reproduction.

Living matter acquires matter and energy from the external

environment and converts it into different forms:
Plants absorb water and minerals and create flowers and leaves.
We eat foods and create strong bodies and minds. (How we
accomplish this on that food is one of the still-yet-unsolved
mysteries of the Universe!) Life is constantly in motion,
organizing the flow of energy and matter in a beautiful celebration
of what is possible.
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Living matter responds to stimuli from the environment:
You get hit on the head with a brick, you say "Ouch." You
respond. Even simple bacteria can turn their way towards some
yummy or turn their way away from some bad. The list of stimuli
and responses goes on and on.

Living matter evolves:

Living matter improves itself. External environmental forces or
biological competition for resources favors certain individuals of a
given species. These favored individuals typically have slightly
different genetic codes than the non-favored types. (All
populations of organisms have variations in their genetic codes,
including humans.) If those selective forces continue, then the
genetic codes of the favored individuals survive and reproduce.
Eventually, after thousands, perhaps millions of years, the genetic
codes of the survivors are different enough to be considered a new
species. 8
The fossil record provides unequivocal evidence that living things
evolve (or change) over time.

It doesn't mean that you have to accept that humans came from
apes or that God doesn't exist.

That isn't what scientists (especially Darwin!) is saying at all.

What they are saying is that life changes in response to
environmental or biological factors.

Genetic characteristics that are favored survive and those that are
disfavored pass away.

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Historical background life:
The evolutionary history of life on Earth traces the processes by
which living and fossil organisms have evolved since life appeared
on the planet, until the present day.

Earth formed about 4.5 billion years ago (Ga) and there is evidence
that life appeared as early as 4.1 Ga. The similarities between all
present-day organisms indicate the presence of a common ancestor
from which all known species have diverged through the process of
evolution.

More than 99 percent of all species, amounting to over five billion

species, that ever lived on Earth are estimated to be destroyed.

Estimates on the number of Earth's current species range from 10

million to 14 million, of which about 1.9 million are estimated to
have been named and 1.6 million documented in a central database to
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date.
The earliest evidence for life on Earth is graphite found to be a
biogenic substance in 3.7 billion-year-old meta-sedimentary rocks
discovered in western Greenland and microbial mat fossils found in
3.48 billion-year-old sandstone discovered in Western Australia.

More recently, in 2015, "remains of biotic life" were found in 4.1

billion-year-old rocks in Western Australia. In March 2017,
researchers reported evidence of possibly the oldest forms of life on
Earth.

Microbial mats of coexisting bacteria and archaea were the dominant

form of life in the early Archean and many of the major steps in early
evolution.

The evolution of photosynthesis, around 3.5 Ga, eventually led to a

buildup of its waste product, oxygen, in the atmosphere, leading to
the great oxygenation event, beginning around 2.4 Ga.
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The earliest evidence of eukaryotes (complex cells with organelles)
dates from 1.85 Ga, and while they may have been present earlier,
their diversification accelerated when they started using oxygen in
their metabolism. Later, around 1.7 Ga, multicellular organisms
began to appear, with differentiated cells performing specialised
functions.

Sexual reproduction, which involves the fusion of male and female

reproductive cells (gametes) to create a zygote in a process called
fertilization is, in contrast to asexual reproduction, the primary
method of reproduction for the vast majority of macroscopic
organisms, including almost all eukaryotes (which includes animals
and plants).

However the origin and evolution of sexual reproduction remain a

puzzle for biologists though it did evolve from a common ancestor
that was a single celled eukaryotic species. Bilateria, animals with a
front and a back, appeared by 555 Ma (million years ago). 12
The earliest land plants date back to around 450 Ma, although
evidence suggests that microorganisms formed the earliest terrestrial
ecosystems, at least 2.9 Ga.

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Cell theory:
In biology, cell theory is a scientific theory which describes the
properties of cells. These cells are the basic unit of structure in all
organisms and also the basic unit of reproduction.

Cell theory was eventually formulated in 1839. Credit for developing

cell theory is usually given to two scientists: Theodor Schwann and
Matthias Jakob Schleiden. Schleiden suggested that every structural
part of a plant was made up of cells or the result of cells.

He also suggested that cells were made by a crystallization process

either within other cells or from the outside. This crystallization
process is no longer accepted with modern cell theory.

In 1839, Theodor Schwann states that along with plants, animals are
composed of cells or the product of cells in their structures. Cell
theory has become the foundation of biology and is the most widely
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accepted explanation of the function of cells.
The three belief to the cell theory are as described below:
All living organisms are composed of one or more cells. (However,
this is considered a controversy because non-cellular life such as
viruses are disputed as a life form.)
The cell is the basic unit of structure and organization in organisms.
Cells arise from pre-existing cells.

However, the idea that all cells come from pre-existing cells had in
fact already been proposed by Robert Remak. Remak published
observations in 1852 on cell division, claiming Schleiden and
Schawnn were incorrect about generation schemes. He instead said
that binary fission, which was first introduced by Dumortier, was
how reproduction of new animal cells were made. Once this principle
was added, the classical cell theory was complete.

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Modern interpretation:
The generally accepted parts of modern cell theory include:
All known living things are made up of one or more cells.
All living cells arise from pre-existing cells by division.
The cell is the fundamental unit of structure and function in all
living organisms.
The activity of an organism depends on the total activity of
independent cells.
Energy flow (metabolism and biochemistry) occurs within cells.
Cells contain DNA which is found specifically in the chromosome
and RNA found in the cell nucleus and cytoplasm.
All cells are basically the same in chemical composition in
organisms of similar species .

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Cell Size:
Cells are of two types, eukaryotic, which contain a nucleus, and
prokaryotic, which do not. Prokaryotes are single-celled organisms,
while eukaryotes can be either single-celled or multicellular.

Prokaryotic: Prokaryotic cells were the first form of life on Earth,

characterised by having vital biological processes including cell
signaling and being self-sustaining. They are simpler and smaller
than eukaryotic cells, and lack membrane-bound organelles such as
the nucleus. Most prokaryotes are the smallest of all organisms
ranging from 0.1 to 5.0 µm in diameter.

Eukaryotic: Plants, animals, fungi, slime moulds, protozoa, and algae

are all eukaryotic. These cells are about fifteen times wider than a
typical prokaryote. Eukaryotic cells, which have diameters ranging
from 10–100 µm.
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The main distinguishing feature of eukaryotes as compared to
prokaryotes is compartmentalization: the presence of membrane-
bound organelles (compartments) in which specific metabolic
activities take place. Most important among these is a cell nucleus, an
organelle that houses the cell's DNA.

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Structural features of Cells of Living Organisms:

All Cells share certain structural features (Fig. 1-3). The plasma
membrane defines the periphery of the cell, separating its contents
from the surroundings.

The plasma membrane is composed of lipid and protein molecules that

form a thin, rough, flexible, hydrophobic barrier around the cell. The
membrane is a barrier to the free passage of inorganic ions and most
other charged or polar compounds.

Transport proteins in the plasma membrane allow the passage of

certain ions and molecules; receptor proteins transmit signals into the
cell; and membrane enzymes participate in some reaction pathways.

The individual lipids and proteins of the plasma membrane are not
covalently linked, the entire structure is remarkably flexible, allowing
changes in the shape and size of the cell. 19
As a cell grows, newly made lipid and protein molecules are inserted
into its plasma membrane; cell division produces two cells, each with
its own membrane. This growth and cell division occurs without loss
of membrane integrity.

FIGURE 1-3 The universal features of

living cells. All cells have a nucleus or
nucleoid, a plasma membrane, and
cytoplasm.

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The internal volume bounded by the plasma membrane, the
cytoplasm (Fig. 1-3), is composed of an aqueous solution, the
cytosol, and a variety of suspended particles with specific functions.

The cytosol is a highly concentrated solution containing enzymes and

the RNA molecules that encode them; the components (amino acids
and nucleotides) from which these macromolecules are assembled;
hundreds of small organic molecules called metabolites,
intermediates in biosynthetic and degradative pathways; coenzymes,
compounds essential to many enzyme-catalyzed reactions; inorganic
ions; and ribosomes, small particles (composed of protein and RNA
molecules) that are the sites of protein synthesis.

All cells have some part of their life, either a nucleus or a nucleoid, in
which the genome-the complete set of genes, composed of DNA-is
stored and replicated.

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The nucleoid, in bacteria, is not separated from the cytoplasm by a
membrane; the nucleus, in higher organisms, consists of nuclear
material enclosed within a double membrane, the nuclear envelope.

Cells with nuclear envelopes are called eukaryotes; those without

nuclear envelopes-bacterial cells-are prokaryotes.

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There Are Three Distinct Domains of Life:
All living organisms fall into one of three large groups (kingdoms, or
domains) that define three branches of evolution from a common
progenitor (Fig. 1-4).

Two large groups of prokaryotes can be distinguished on biochemical

grounds: archaebacteria and eubacteria.

Eubacteria inhabit soils, surface waters, and the tissues of other

living or decaying organisms. Most of the well studied bacteria,
including Escherichia coli, are eubacteria.

The archaebacteria, more recently discovered, are less well

characterized biochemically; most inhabit extreme environments-salt
lakes, hot springs, highly acidic, and the ocean depths.

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FIGURE 1–4 Phylogeny of the three domains of life. Phylogenetic relationships
are often illustrated by a “family tree” of this type. The fewer the branch points
between any two organisms, the closer is their evolutionary relationship.

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The available evidence suggests that the archaebacteria and
eubacteria diverged early in evolution and constitute two separate
domains, sometimes called Archaea and Bacteria.

All eukaryotic organisms, which make up the third domain, Eukarya,

evolved from the same branch that gave rise to the Archaea;
archaebacteria are therefore more closely related to eukaryotes than
to eubacteria.

Within the domains of Archaea and Bacteria are subgroups

distinguished by the habitats in which they live. In aerobic habitats
with a plentiful supply of oxygen, some resident organisms derive
energy from the transfer of electrons from fuel molecules to oxygen.

Other environments are anaerobic, virtually lack of oxygen, and

microorganisms adapted to these environments obtain energy by
transferring electrons to nitrate, sulfate, or CO2. Many organisms that
have grown in anaerobic environments are obligate anaerobes: they
die when exposed to oxygen. 25
Classification of organisms according to the source of energy:

We can classify organisms according to how they obtain the energy and
carbon they need for synthesizing cellular material (as summarized in
Fig. 1-5).

There are two broad categories based on energy sources:

(1) Phototrophs-trap and use sunlight,
(2) Chemotrophs derive their energy from oxidation of a fuel.

All chemotrophs require a source of organic nutrients; they cannot fix

CO2 into organic compounds. The phototrophs can be further divided
into those that can obtain all needed carbon from CO2 (autotrophs) and
those that require organic nutrients (heterotrophs).

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FIGURE 1–5 Organisms can be
classified according to their source of
energy (sunlight or oxidizable
chemical compounds) and their source
of carbon for the synthesis of cellular
material. 27
No chemotroph can get its carbon atoms exclusively from CO2 (that
is, no chemotrophs are autotrophs). The chemotrophs may be further
classified according to a different criterion: whether the fuels they
oxidize are inorganic (lithotrophs) or organic (organotrophs).

Most known organisms fall within one of these four broad

categories- (1) autotrophs or (2) heterotrophs among the
photosynthesizers, (3) lithotrophs or (4) organotrophs among the
chemical oxidizers.

The prokaryotes have several general modes of obtaining carbon and

energy. Escherichia coli, is a chemoorganoheterotroph; it requires
organic compounds from its environment as fuel and as a source of
carbon. Cyanobacteria are photolithoautotrophs; they use sunlight as
an energy source and convert CO2 into biomolecules. We humans,
like E. coli, are chemoorganoheterotrophs.

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Structure of Prokaryotic Cells :
Escherichia coli (E. coli) is the most-studied prokaryotic cell:
bacterial cells share certain common structural features, but also
show group-specific specializations (Fig. 1-6). E. coli is a usually
harmless inhabitant of the human intestinal tract. The E. coli cell is
about 2 m long and a little less than 1 m in diameter.

It has a protective outer membrane and an inner plasma membrane

that encloses the cytoplasm and the nucleoid. Between the inner and
outer membranes is a thin but strong layer of polymers called
peptidoglycans, which gives the cell its shape and rigidity. The
plasma membrane and the layers outside it constitute the cell
envelope. In the Archaea, rigidity is conferred by a different type of
polymer (pseudopeptidoglycan). The plasma membranes of
eubacteria consist of a thin bilayer of lipid molecules penetrated by
proteins. Archaebacterial membranes have a similar architecture,
although their lipids differ remarkably from those of the eubacteria.29
FIGURE 1–6 Common structural features of bacterial cells. Because of differences in the cell
envelope structure, some eubacteria (grampositive bacteria) retain Gram’s stain, and others
(gram-negative bacteria) do not. E. coli is gram-negative. Cyanobacteria are also eubacteria
but are distinguished by their extensive internal membrane system, in which photosynthetic
pigments are localized. Although the cell envelopes of archaebacteria and gram-positive
eubacteria look similar under the electron microscope, the structures of the membrane lipids
and the polysaccharides of the cell envelope are distinctly different in these organisms..
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The cytoplasm of E. coli contains about 15,000 ribosomes, thousands
of copies each of about 1,000 different enzymes, numerous
metabolites and cofactors, and a variety of inorganic ions. The
nucleoid contains a single, circular molecule of DNA, and the
cytoplasm (like that of most bacteria) contains one or more smaller,
circular segments of DNA called plasmids. In nature, some plasmids
confer resistance to toxins and antibiotics in the environment. In the
laboratory, these DNA segments are especially amenable to
experimental manipulation and are extremely useful to molecular
geneticists. Most bacteria (including E. coli) lead existences as
individual cells, but in some bacterial species cells tend to associate
in clusters or filaments, and a few demonstrate simple social
behavior.

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Structure of Eukaryotic Cells :
Eukaryotic cells have a variety of membranous organelles. Typical
eukaryotic cells (Fig. 1-7) are much larger than prokaryotic cells-
commonly 10 to 100 m in diameter.

The distinguishing characteristics of eukaryotes are the nucleus and a

variety of membrane bounded organelles with specific functions:
mitochondria, endoplasmic reticulum, Golgi complexes, and
lysosomes.

Plant cells also contain vacuoles and chloroplasts (Fig. 1-7). Also
present in the cytoplasm of many cells are granules or droplets
containing stored nutrients such as starch and fat.

Eukaryotes can reproduce both asexually through mitosis and sexually

through meiosis and gamete fusion. In mitosis, one cell divides to
produce two genetically identical cells.
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FIGURE 1–7
Eukaryotic cell
structure. Schematic
illustrations of the two
major types of
eukaryotic cell: (a) a
representative animal
cell and (b) a
representative plant cell.
Plant cells are usually
10 to 100 m in
diameter—larger than
animal cells, which
typically range from 5
to 30 m. Structures
labeled in red are
unique to either animal
or plant cells.
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In meiosis, DNA replication is followed by two rounds of cell division
to produce four daughter cells (haploid cells) each with half the
number of chromosomes as the original parent cell. These act as sex
cells (gametes) Each gamete has just one complement of
chromosomes, each a unique mix of the corresponding pair of parental
chromosomes resulting from genetic recombination during meiosis.

Prokaryotes cell membrane:

Gram-negative bacteria have both a plasma membrane and an outer
membrane separated by periplasm. The periplasm is a concentrated
gel-like matrix in the space between the inner cytoplasmic membrane
and the bacterial outer membrane called the periplasmic space in gram-
negative bacteria.

Other prokaryotes have only a plasma membrane. Bacteria are also

surrounded by a cell wall composed of peptidoglycan (amino acids and
sugars).
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Some eukaryotic cells also have cell walls, but none that are made of
peptidoglycan. The outer membrane of gram negative bacteria is rich in
lipopolysaccharides. The outer membrane can bleb (a small bubble) out
into periplasmic protrusions under stress conditions or upon virulence
requirements while encountering a host target cell, and thus such blebs
may work as virulence organelles.

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Difference between Prokaryotic and Eukaryotic cell:
Sl. No. Characteristic Prokaryotic Cell Eukaryotic Cell

01 Nucleus Absent Present

02 Membrane bound organelles Absent Present

(Such as Mitochondria,
Chloroplast, Endoplasmic
reticulum, & Golgi apparatus)
03 Size of ribosome 70 S 80 S

04 Cell wall composition Peptidoglycan is present No Peptidoglycan

05 Cell division Binary fission Mitosis and Meiosis

06 DNA associated with histone Absent Present

07 Number of Chromosome One More than one

08 Cell membrane composition No sterols Sterols present

09 Number of cells Usually unicellular Usually multicellular

10 Size of cells Smaller ( 1 - 5 m) Larger ( 10 - 100 m)

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