Chapter 3

Cell Structure
and Taxonomy
 Learning Outcomes:
• explain what is meant by the cell theory
• state the contributions of Hooke, Schleiden and
Schwann, and Virchow to the study of cells
• describe the parts and functions of a eukaryotic cell
• differentiate the parts and functions of a bacterial cell
• compare and contrast plant, animal, and bacterial cells
• describe the five-kingdom and three-domain systems of
classification
• describe evolution and the tree of life
 What is a Cell?
• A cell is defined as the fundamental unit of any living organism.
• The cell exhibits the basic characteristics of life
• It obtains food (nutrients) from the environment to produce
energy for metabolism and other activities
• Metabolism refers to all of the chemical reactions that occur
within a cell; because of its metabolism, a cell can grow and
reproduce.
• It can respond to stimuli in its environment such as light, heat,
cold, and the presence of chemicals.
• A cell can mutate (change genetically) as a result of changes in
its genetic material – the deoxyribonucleic acid (DNA) that
makes up the genes of its chromosomes.
 What is a Cell?
• Bacterial cells exhibit all the characteristics of life, although
they do not have the complex system of membranes and
organelles.
• The less complex cells, which include Bacteria and Archaea,
are called prokaryotes or prokaryotic cells.
• The more complex cells that contain a true nucleus and many
membrane-bound organelles are called eukaryotes or
eukaryotic cells.
• Eukaryotes include organisms such as algae, protozoa, fungi,
plants, animals, and humans.
 What is a Cell?
• Viruses appear to be the result of regressive or
reverse evolution.
• They are composed of only a few genes protected
by a protein coat, and may contain one or a few
enzymes.
• They depend on the energy and metabolic
machinery of a host cell to reproduce.
• They are regarded as acellular or are not composed
of cells.
 Eukaryotic Cell Structure

• Eukaryotes (eu = true, karyo refers to a nut

or nucleus) have a true nucleus and their
DNA is enclosed by a nuclear membrane
• Most animal and plant cells are 10 to 30 μm
in diameter, about 10 times larger than
most prokaryotic cells.
 Cell Membrane
• The cell is enclosed and held intact by the cell
membrane, or also known as the plasma,
cytoplasmic, or cellular membrane.
• It is a mosaic composed of large proteins and
phospholipids.
• It regulates the passage of nutrients, waste
products, and secretions into and out of the cell.
• It is selectively permeable which means that only
certain substances may enter and leave the cell.
 Cell Membrane

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 Nucleus
• The nucleus (pl., nuclei) controls the functions of the entire cell
and can be thought of as the “command center” of the cell.
• The nucleus has three components: nucleoplasm,
chromosomes, & a nuclear membrane.
• Nucleoplasm is the gelatinous matrix or base material of the
nucleus.
• The chromosomes are embedded or suspended in the
nucleoplasm.
• The nuclear membrane contains holes (nuclear pores) through
which large molecules can enter and exit the nucleus.
• Eukaryotic chromosomes consist of linear DNA molecules and
proteins.
 Nucleus
• Genes are located along the DNA molecules
• Most gene products are proteins, but some
code for the production of two types of
ribonucleic acid (RNA): ribosomal ribonucleic
acid (rRNA) and transfer ribonucleic acid
(tRNA) molecules.
• The organism’s complete collection of genes
is referred to as the organism’s genotype
(genome)
 Cytoplasm
• Cytoplasm is a semifluid, gelatinous, nutrient matrix
• Within the cytoplasm are found insoluble storage granules and
various cytoplasmic organelles, including endoplasmic
reticulum, ribosomes, Golgi complexes, mitochondria,
centrioles, microtubules, lysosomes, and other membrane-
bound vacuoles.
• Each of these organelles has a highly specific function, and all
of the functions are interrelated to maintain the cell and allow
it to properly perform its activities.
• The cytoplasm is where most of the cell’s metabolic reactions
occur.
 Endoplasmic Reticulum
• The endoplasmic reticulum (ER) is a highly convoluted system
of membranes that are interconnected and arranged to form a
transport network of tubules and flattened sacs within the
cytoplasm.
• Much of the ER has a rough, granular appearance when
observed by transmission electron microscopy and is called as
rough endoplasmic reticulum (RER).
• This rough appearance is caused by the many ribosomes
attached to the outer surface of the membranes.
• ER to which ribosomes are not attached is called smooth
endoplasmic reticulum (SER).
 Ribosomes
• eukaryotic ribosomes are 18 to 22 nm in diameter
• they consist mainly of rRNA and protein and play an
important part in the synthesis of proteins.
• clusters of ribosomes (called polyribosomes or polysomes)
are held together by a molecule of mRNA
• each eukaryotic ribosome is composed of two subunits – a
large subunit (the 60S subunit) and a small subunit (the
40S subunit) that are produced in the nucleolus
• the subunits are then transported to the cytoplasm where
they remain separate until such time as they join
together with an mRNA molecule to initiate protein
synthesis.
 Ribosomes
• eukaryotic ribosomes are 18 to 22 nm in diameter
• they consist mainly of rRNA and protein and play an
important part in the synthesis of proteins.
• clusters of ribosomes (called polyribosomes or polysomes)
are held together by a molecule of mRNA
• each eukaryotic ribosome is composed of two subunits – a
large subunit (the 60S subunit) and a small subunit (the
40S subunit) that are produced in the nucleolus
• the subunits are then transported to the cytoplasm where
they remain separate until such time as they join
together with an mRNA molecule to initiate protein
synthesis.
 Ribosomes
• when united, the 40S and 60S subunits form an 80S
ribosome; the “S” refers to Svedberg units, and 40S,
60S, and 80S are sedimentation coefficients;
• a sedimentation coefficient expresses the rate at
which a particle or molecule moves in a centrifugal
field; it is determined by the size and shape of the
particle or molecule.
• most of the proteins released from the ER are not
mature.
• they must undergo further processing in an organelle
known as a Golgi complex before they are able to
perform their functions within or outside of the cell.
 Golgi Complex
• A Golgi complex connects or communicates
with the ER;
• this stack of flattened, membranous sacs
completes the transformation of newly
synthesized proteins into mature, functional
ones and packages them into small,
membrane-enclosed vesicles for storage
within the cell or export outside the cell
• also referred to as “packaging plants”
 Lysosomes and Peroxisomes
• Lysosomes are small (about 1-μm diameter) vesicles that
originate at the Golgi complex.
• they contain lysozyme and other digestive enzymes that
break down foreign material taken into the cell by
phagocytosis (the engulfing of large particles by amoebas
and certain types of white blood cells called phagocytes.
• these enzymes also aid in breaking down worn out parts
of the cell and may destroy the entire cell by a process
called autolysis if the cell is damaged or deteriorating.
• Lysosomes are found in all eukaryotic cells.
 Lysosomes and Peroxisomes
• Peroxisomes are membrane-bound vesicles in
which hydrogen peroxide is both generated and
broken down
• Peroxisomes contain the enzyme catalase,
which catalyzes (speeds up) the breakdown of
hydrogen peroxide into water and oxygen.
• They are found in most eukaryotic cells, but are
especially prominent in mammalian liver cells.
 Mitochondria
• The energy necessary for cellular function is provided
by the formation of high-energy phosphate molecules
such as adenosine triphosphate (ATP).
• ATP molecules are the major energy-carrying or
energy-storing molecules within cells.
• Mitochondria (sing., mitochondrion) are powerhouses
of the eukaryotic cell because this is where most of the
ATP molecules are formed by cellular respiration.
• During this process, energy is released from glucose
molecules and other nutrients to drive other cellular
functions.
• The number of mitochondria in a cell varies greatly
depending on the activities required of that cell.
 Plastids
• Plastids are membrane-bound structures
containing various photosynthetic pigments.
• Chloroplasts, one type of plastid, contain
green, photosynthetic pigment called
chlorophyll.
• Photosynthesis is the process by which light
energy is used to convert carbon dioxide and
water into carbohydrates and oxygen; it is
the conversion of light energy into chemical
energy.
 Cytoskeleton
• Cytoskeleton is a system of fibers present throughout
the cytoplasm.
• The three types of cytoskeletal fibers are microtubules,
microfilaments (actin filaments), and intermediate
filaments.
• All three types serve to strengthen, support, and stiffen
the cell, and give the cell its shape.
• Microtubules and microfilaments are essential for
various activities, such as cell division, contraction,
motility, and the movement of chromosomes within the
cell.
• Microtubules are slender, hollow tubules composed of
spherical protein subunits called tubulins.
 Cell Wall
• Eukaryotic cell walls are much simpler in
structure than prokaryotic cell walls and may
contain cellulose, pectin, lignin, chitin, and
some mineral salts.
• Cellulose is found in the cell walls of plants,
algae, and other microorganisms.
• The cell walls of fungi contain a
polysaccharide, chitin, which is also found in
the exoskeletons of beetles and crabs.
 Flagella and Cilia
• Some eukaryotic cells possess relatively long, thin
structures called flagella (sing., flagellum).
• Such cells are said to be flagellated or motile;
flagellated protozoa are called flagellates
• Flagella are referred to as organelles of locomotion
(cell movement).
• Cilia (sing., cilium) tend to be shorter (more hair-like),
thinner, and more numerous than flagella.
• Cilia can be found on some species of protozoa (called
ciliates) and certain types of cells in our bodies.
• Eukaryotic flagella & cilia, which contain an internal “9
+ 2” arrangement of microtubules.
 Prokaryotic Cell Structure
• Prokaryotic cells are about 10 times smaller than
eukaryotic cells
• A typical E. coli cell is about 1μm wide and 2 to 3 μm
long
• Reproduction of prokaryotic cells is by binary fission,
the simple division of one cell into two cells after DNA
replication and the formation of a separating membrane
and cell wall.
• Embedded within the cytoplasm of prokaryotic cells are
a chromosome, ribosomes, and other cytoplasmic
particles.
• The cytoplasm of prokaryotic cells is not filled with
internal membranes.
Prokaryotic Cell Structure
 Cell Membrane
• Enclosing the cytoplasm of a prokaryotic cell
is the cell
membrane (also known as the plasma, cytoplasmic, or
cellular membrane).
• The selectively permeable membrane controls which
substances may enter or leave the cell.
• Many enzymes are attached to the cell membrane &
various metabolic reactions take place here
• The mesosomes – the inward foldings of the cell
membranes – are where cellular respiration takes place
in bacteria.
 Chromosome
• The prokaryotic chromosome usually consists of a single,
long, supercoiled circular DNA molecule which serves as
the control center of the bacterial cell.
• It is capable of duplicating itself, guiding cell division, &
directing cellular activities.
• A prokaryotic cell contains neither nucleoplasm nor a
nuclear membrane.
• The chromosome is suspended in the cytoplasm.
• The DNA-occupied space within a bacterial cell is
referred to as the bacterial nucleoid.
 Chromosome
• Small, circular molecules of double-stranded DNA
that are not part of the chromosome (referred to as
extrachromosomal DNA or plasmids) may also be
present in the cytoplasm of prokaryotic cells.
• A plasmid may contain anywhere from fewer than 10
genes to several hundred genes.
 Bacterial Cell Wall
• The main constituent of most bacterial cell walls is a complex
macromolecular polymer known as peptidoglycan (murein)
consisting of many polysaccharide chains linked together by small
peptide chains.
• The cell walls of certain bacteria, called Gram-positive bacteria,
have a thick layer of peptidoglycan combined with teichoic acid &
lipoteichoic acid molecules.
• The cell walls of Gram-negative bacteria have a much thinner layer
of peptidoglycan, but this layer is covered with a complex layer of
lipid macromolecules.
• Although most bacteria have cell walls, bacteria in the genus
Mycoplasma do not.
• Archaea have cell walls, but their cell walls do not contain
peptidoglycan.
 Bacterial Cell Wall
• Some bacteria lose their ability to produce cell walls,
transforming into tiny variants of the same species, referred to
as L-form or cell wall-deficient (CWD) bacteria.
• Over 50 different species of bacteria are capable of
transforming into CWD bacteria, some of which might be
responsible for chronic diseases such as chronic fatigue
syndrome, Lyme disease, rheumatoid arthritis, and sarcoidosis.
• Clinicians are often unaware that CWD bacteria are present in
their patients because they will not grow under standard
laboratory conditions, hence, they must be cultured in a
different medium and at a different temperature than typical
bacteria.
 Glycocalyx
(Slime Layers and Capsules)
• Some bacteria have a thick layer of material known as glycocalyx
located outside the cell wall.
• Glycocalyx is a slimy, gelatinous material produced by the cell
membrane and secreted outside of the cell wall.
• There are two types of glycocalyx.
• One type, called a slime layer, is not highly organized and is not
firmly attached to the cell wall.
• It easily detaches from the cell wall and drifts away.
• Bacteria in the genus, Pseudomonas produce a slime layer, which
sometimes plays a role in diseases caused by Pseudomonas species.
• Slime layers enable certain bacteria to glide or slide along solid
surfaces, and seem to protect bacteria from antibiotics &
desiccation.
 Glycocalyx
(Slime Layers and Capsules)
• The other type of glycocalyx, called a capsule, is highly organized and
firmly attached to the cell wall.
• Capsules usually consist of polysaccharides combined with lipids and
proteins depending on the bacterial species.
• Different strains of the bacterium H. influenza, a cause of meningitis
and ear infections in children, are identified by their capsular types.
• A vaccine, called Hib vaccine, is available for protection against disease
caused by H. infuenzae capsular type B.
• Other examples of encapsulated bacteria are Klebsiella pneumoniae,
Neisseria meningitidis, and Streptococcus pneumoniae.
• Encapsulated bacteria usually produce colonies on nutrient agar that
are smooth, mucoid, and glistening; they are referred to as S-colonies.
• Nonencapsulated bacteria tend to grow as dry, rough colonies,
called R-colonies.
 Flagella
• Flagella (sing., flagellum) are thread-like, protein appendages that
enable bacteria to move.
• Flagellated bacteria are said to be motile, whereas nonflagellated
bacteria are usually nonmotile.
• Bacterial flagella are about 10 to 20 nm thick; too thin to be seen
with the compound light microscope.
• Bacteria possessing flagella over their entire surface (perimeter) are
called peritrichous bacteria.
• Bacteria with a tuft of flagella at one end are described as being
lophotrichous bacteria, whereas those having one or more flagella at
each end are said to be amphitrichous bacteria.
• Bacteria possessing a single polar flagellum are described as
monotrichous bacteria.
• Some spirochetes (spiral-shaped bacteria) have two flagella-like
fibrils called axial filaments, one attached to each end of the
bacterium.
 Pili (Fimbriae)
• Pili (sing., pilus) or fimbriae (sing., fimbria) are hair-like
structures, most often observed on Gram-negative
bacteria.
• They are composed of polymerized protein molecules
called pilin. Pili are much thinner than flagella, have a
rigid structure, and are not associated with motility.
• These tiny appendages arise from the cytoplasm and
extend through the plasma membrane, cell wall, and
capsule (if present).
• There are two types of pili: one type merely enables
bacteria to adhere or attach to surfaces; the other type
(called a sex pilus) facilitates transfer of genetic
material from one bacterial cell to another following
attachment of the cells to each other.
 Pili (Fimbriae)
• The pili that merely enable bacteria to anchor themselves to
surfaces (e.g., tissues within the human body) are usually quite
numerous.
• In some species of bacteria, piliated strains (those possessing
pili) are able to cause diseases such as urethritis and cystitis,
whereas nonpiliated strains (those not possessing pili) of the
same organisms are unable to cause these diseases.
• A bacterial cell possessing a sex pilus (called a donor cell)— and
the cell only possesses one sex pilus—is able to attach to another
bacterial cell (called a recipient cell) by means of the sex pilus.
• Genetic material (usually in the form of a plasmid) is then
transferred from the donor cell to the recipient cell—a process
known as conjugation.
 Spores (Endospores)
• A few genera of bacteria (e.g., Bacillus and Clostridium) are
capable of forming thick-walled spores as a means of survival
when their moisture or nutrient supply is low.
• Bacterial spores are referred to as endospores, and the process
by which they are formed is called sporulation.
• During sporulation, a copy of the chromosome and some of the
surrounding cytoplasm becomes enclosed in several thick
protein coats.
• Spores are resistant to heat, cold, drying, and most chemicals.
• Spores have been shown to survive for many years in soil or
dust, and some are quite resistant to disinfectants and boiling.
• When the dried spore lands on a moist, nutrient-rich surface, it
germinates, and a new vegetative bacterial cell (a cell capable
of growing and dividing) emerges.
 Prokaryotic Cell Reproduction
• Prokaryotic cell reproduction is quite simple when
compared with eukaryotic cell division.
• Prokaryotic cells reproduce by a process known as
binary fission, in which one cell (the parent cell)
splits in half to become two daughter cells.
• Before a prokaryotic cell can divide in half, its
chromosome must be duplicated (a process known
as DNA replication, so that each daughter cell will
possess the same genetic information as the parent
cell.
 Prokaryotic Cell Reproduction
• The time it takes for binary fission to occur (i.e., the
time it takes for one prokaryotic cell to become two
cells) is called the generation time.
• The generation time varies from one bacterial species
to another and also depends on the growth conditions
(e.g., pH, temperature, and availability of nutrients).
• In the laboratory (in vitro), under ideal conditions, E.
coli has a generation time of about 20 minutes—the
number of cells will double every 20 minutes.
• Bacterial generation times range from as short as 10
minutes to as long as 24 hours, or even longer in some
cases
 Taxonomy
• According to Bergey’s Manual of Systematic Bacteriology, taxonomy
(the science of classification of living organisms) consists of three
separate but interrelated areas: classification, nomenclature, and
identification.
• Classification is the arrangement of organisms into taxonomic groups
(known as taxa [sing., taxon]) on the basis of similarities or
relationships.
• Taxa include kingdoms or domains, divisions or phyla, classes, orders,
families, genera, and species. Closely related organisms (i.e., organisms
having similar characteristics) are placed into the same taxon.
• Nomenclature is the assignment of names to the various taxa
according to international rules.
• Identification is the process of determining whether an isolate belongs
to one of the established, named taxa or represents a previously
unidentified species.
 Microbial Classification
• The science of taxonomy was established, based on the
binomial system of nomenclature developed in the 18th
century by the Swedish scientist Carolus Linnaeus.
• In the binomial system, each organism is given two names
(e.g., Homo sapiens for humans). The first name is the genus
(pl., genera), and the second name is the specific epithet. The
first and second names together are referred to as the species.
• In addition to the proper scientific names for bacteria,
acceptable terms such as staphylococci (for Staphylococcus
spp.), streptococci (for Streptococcus spp.), clostridia (for
Clostridium spp.), pseudomonads (for Pseudomonas spp.),
mycoplasmas (for Mycoplasma spp.), rickettsias (for Rickettsia
spp.), and chlamydias (for Chlamydia spp.) are commonly
used.
 Microbial Classification
• In 1969, Robert H. Whittaker proposed a Five Kingdom
System of Classification, in which all organisms are placed
into five kingdoms:
• Bacteria and archaea are in the Kingdom Prokaryotae (or
Monera)
• Algae and protozoa are in the Kingdom Protista (organisms
in this kingdom are referred to as protists)
• Fungi are in the Kingdom Fungi
• Plants are in the Kingdom Plantae
• Animals are in the Kingdom Animalia
 Evolution and the Tree of Life
• Although evolutionary biology is a complex and
controversial topic, many scientists believe that life
on Earth originated and then evolved from what is
commonly referred to as the last universal
common ancestor (LUCA) approximately 3.5 to 3.9
billion years ago.
• A popular theory is that highly energetic chemical
reactions produced self-replicating molecules (such
as RNA) around 4 billion years ago, which led to the
assembly of simple cells, and then about a half
billion years later, the LUCA existed.
 Evolution and the Tree of Life
• Prokaryotes inhabited Earth from approximately 3 to
4 billion years ago, and eukaryotic cells emerged
between 1.6 and 2.7 billion years ago.
• It is thought that certain bacterial cells were
engulfed by eukaryotic cells, leading to a
cooperative association known as endosymbiosis.
• Some endosymbiotic bacteria evolved into
mitochondria, whereas others (the photosynthetic
cyanobacteria) evolved into chloroplasts.
 Determining Relatedness among
Organisms
• How do scientists determine how closely related one
organism is to another?
• The most widely used technique for gauging diversity
or relatedness is called ribosomal RNA sequencing.
• Ribosomes are made up of two subunits: a small
subunit and a large subunit.
• The small subunit contains only one RNA molecule,
which is referred to as the “small subunit rRNA or
SSUrRNA.
• The SSUrRNA in prokaryotic ribosomes is a 16S rRNA
molecule, whereas the SSUrRNA in eukaryotes is an 18S
rRNA molecule.