Microbiology 3

01.10.14
Kairi Tammoja

What is Life?
Living entity is in a state bounded by birth and death, also it is thought to
require a degree of biochemical autonomy.

Living things can grow; that is, they can increase in size.

Reproduction - asexually or sexually with gametes.

Response to their environment or taxis.

Metabolism - cells store metabolic energy in the chemical bonds of

adenosine triphosphate (ATP).

Viruses lead a kind of borrowed life according to a modern definition.

An overview of Prokaryotic and Eukaryotic Cells

There are many different kinds of cells.

Some cells are free-living, independent organisms; others live
together in colonies or form the bodies of multicellular organisms.
Cells also exist in various sizes, from the smallest bacteria to bird
eggs, which are the largest of cells. All cells may be described as
either prokaryotes or eukaryotes.

Prokaryotes

The word prokaryote comes from Greek words meaning

before nucleus.
Electron microscopy has revealed that prokaryotes
typically lack various types of internal structures bound
with phospholipid membranes that are present in
eukaryotic cells.
Bacteria and archaea differ fundamentally in such ways
as the type of lipids in their cytoplasmic membranes and in
the chemistry of their cell walls.
In many ways, archaea are more like eukaryotes than they
are like bacteria.

Prokaryotes

Scientists categorize organisms

based on shared characterstics
into groups called taxa.
Prokaryotic is a characteristic of
organisms in two taxadomain
Archaea and domain Bacteria
but prokaryote is not itself a
taxon.

The distinctive feature of

prokaryotes is that they can make
proteins simultaneously to
reading their genetic code because
a typical prokaryote does not have
a membrane surrounding its
genetic material (DNA). In other
words, a typical prokaryote does
not have a nucleus.

Eukaryotes

Eukaryotes have a membrane

called a nuclear envelope
surrounding their DNA, forming a
nucleus, which sets eukaryotes in
domain Eukarya (Greek for true
nucleus)
Eukaryotes have numerous other
internal membranes that
compartmentalize cellular
functions. These compartments are
membrane-bound organelles specialized structures that act like
tiny organs to carry on the various
functions of the cell.
The cells of algae, protozoa,
fungi, animals, and plants are
eukaryotic.

Cell size

Eukaryotes are usually larger and

more complex than prokaryotes,
which are typically 1.0 m in
diameter or smaller, as compared
to 10100 m for eukaryotic cells
Birds eggs are the largest cells.
Note that Staphylococcus, a
bacterium, is smaller than
Giardia, a unicellular eukaryote.
A smallpox virus (Orthopoxvirus)
is shown only for comparison;
viruses are not cellular.

External features of Prakaryotes

Many cells have special external features that enable them to respond to other cells and
their environment. In bacteria, these features include glycocalyces, flagella, fimbriae,
and pili.
Some cells have a gelatinous, sticky substance that surrounds the outside of the cell.
This substance is known as a glycocalyx which may be composed of polysaccharides,
polypeptides, or both. These chemicals are produced inside the cell and are extruded
onto the cells surface.
When the glycocalyx of a bacterium is composed of organized repeating units of organic
chemicals firmly attached to the cells surface, the glycocalyx is called a capsule.
A loose, water-soluble glycocalyx is called a slime layer.

Flagella

Bacterial flagella are long structures that extend beyond the surface of a cell
and its glycocalyx and propel the cell through its environment. Not all
bacteria have flagella.
Bacterial flagella are composed of three parts: a long, thin filament, a hook,
and a basal body.
The hollow filament is a long hollow shaft, about 20 nm in diameter, that
extends out into the cells environment.
Composed of globular molecules of a protein called flagellin. The cell
secretes molecules of flagellin through the hollow core of the flagellum in a
clockwise helix at the lengthening tip.
Bacterial flagella sense external wetness, inhibiting their own growth in dry
habitats.
Differences in the proteins associated with bacterial flagella vary enough to
allow classification of species into groups (strains) called serovars.

Flagella that cover the surface of the cell are termed peritrichous; in
contrast, polar flagella are only at the ends. Some cells have tufts of
polar flagella.
Spiral bacteria called Spirochetes have axial filament that wraps
around the cell between its cytoplasmic membrane and an outer
membrane

Treponema pallidum, the agent of

syphilis, and
Borrelia burgdorferi, the cause of Lyme
disease, are notable spirochetes.
Some scientists think that the corkscrew
motility of these pathogens allows them
to invade human tissues.

Flagella rotate 360 like boat propellers

rather than whipping from side to side.
The flow of hydrogen ions (H+) or of
sodium ions (Na+) through the
cytoplasmic membrane powers the
rotation, at about 60 cell lengths per
secondequivalent to a car traveling
at 670 miles per hour!
Flagella rotate at more than 100,000
rpm and can change direction from
counterclockwise to clockwise.
The presence of favorable stimuli
increases the number of runs and
decreases the number of tumbles; as a
result, the cell tends to move toward an
attractant
Movement in response to a stimulus is
termed taxis. The stimulus may be
either light (phototaxis) or a chemical
(chemotaxis).
Movement toward a favorable stimulus
is positive taxis, whereas movement
away from an unfavorable stimulus is
negative taxis.

Many bacteria have rodlike proteinaceous

extensions called fimbriae.

These sticky, bristlelike projections adhere

to one another and to substances in the
environment. There may be hundreds of
fimbriae per cell, and they are usually
shorter than flagella.
An example of a bacterium with fimbriae is
Neisseria gonorrhoeae, which causes
gonorrhea.
This bacterium is able to colonize the
mucous membrane of the reproductive tract
by attaching with fimbriae.

Fimbriae are important function in biofilms,

slimy masses of microbes adhering to a
substrate by means of fimbriae and
glycocalyces. Some act as electrical wires,
conducting electrical signals among cells in
a biofilm. It has been estimated that at least
99% of bacteria in nature exist in biofilms.
A special type of fimbria are pili which are
longer than other fimbriae and usually
shorter than flagella. Typically only one to a
few pili are present per cell in bacteria that
have them. Cells use pili to transfer DNA
from one cell to the other via a process
termed conjugation.

The outer membrane is

protective, allowing Gramnegative bacteria such as
Escherichia coli to better
survive in harsh
environments.
A dead cell releases lipid A
when the outer membrane
disintegrates, causing fever,
vasodilation, inflammation,
shock, and blood clotting in
humans.
Because the cell walls of
Gram-positive and Gramnegative bacteria differ, the
Gram stain is an important
diagnostic tool. After the
Gram staining procedure,
Gram-negative cells appear
pink, and Gram-positive
cells appear purple.
A few bacteria, such as
Mycoplasma pneumoniae
lack cell walls entirely.

Cell wall

Cytoplasmic Membrane

Cytoplasmic membranes are about 8 nm thick and composed of phospholipids and

associated proteins. Some bacterial membranes also contain sterol-like molecules,
called hopanoids, that help stabilize the membrane.
The structure of a cytoplasmic membrane is referred to as a phospholipid bilayer.
Phospholipids placed in a watery environment naturally form a bilayer because of
their bipolar nature.
About half of a bacterial cytoplasmic membrane is composed of integral proteins.
Peripheral proteins are loosely attached to the membrane on one side or the other.
Proteins of cell membranes may act as recognition proteins, enzymes, receptors,
carriers, or channels.

Cytoplasmic Membrane

Movement across the cytoplasmic

membrane occurs by either
passive or active processes.
Passive processes do not
require the expenditure of a cells
metabolic energy store, whereas
active processes require it either
directly or indirectly.
Because many of the substances
that have concentration gradients
across cell membranes are
electrically charged chemicals, a
corresponding electrical
gradient, or voltage, exists
across the membrane.

Passive movement
In passive processes, the electrochemical
gradient provides the source of energy, the
cell does not expend its energy reserve.
Passive processes include:

diffusion,

facilitated diffusion,

osmosis.

Osmosis

Prokaryotic Active Transport

Figure 3.20 Mechanisms of active transport. (a) Via a uniport. (b)

Via an antiport. (c) Via a uniport coupled with a symport. In this
example, the membrane uses aTp energy to pump one substance
out through a uniport. as this substance flows back into the cell, it
brings another substance with it through the symport

Cytoplasm

The liquid portion of the cytoplasm is called cytosol. It is mostly water, but it also contains
dissolved and suspended substances, including ions, carbohydrates, proteins (mostly
enzymes), lipids, and wastes. The cytosol of prokaryotes also contains the cells DNA in a
region called the nucleoid.
Most bacteria have a single, circular DNA molecule organized as a chromosome. Some
bacteria, such as Vibrio cholerae has two chromosomes.

Deposits, called inclusions, are often found within

bacterial cytosol. Rarely, a cell surrounds its
inclusions with a polypeptide membrane. Inclusions
may include reserve deposits of lipids, starch, or
compounds containing nitrogen, phosphate, or
sulfur.
The presence of specific inclusions is diagnostic
for several pathogenic bacteria.
Many bacteria store carbon and energy in molecules
of glycogen or as a lipid polymer called
polyhydroxybutyrate (PHB). Slight chemical
modification of PHB produces a plastic that can be
used for packaging and other application

Sporulation

Some bacteria (notably Bacillus and Clostridium) produce unique structures called
endospores, which are important for several reasons, including their durability and potential
pathogenicity - they are a strategy against hostile or unfavorable conditions.
Endospore formation is a serious concern because endospores are resistant to treatments
that inhibit other microbes, and because endospore-forming bacteria produce deadly toxins
that cause such fatal diseases as anthrax, tetanus, and gangren.

Nonmemembranous Organelles

Prokaryotic nonmembranous organelles are found in direct contact with the

cytosol in bacterial cytoplasm.
Nonmembranous organelles in bacteria include ribosomes and the cytoskeleton.
Ribosomes are the sites of protein synthesis in cells. The subunits of prokaryotic
70S ribosomes are the 30S subunit that contains polypeptides and a single rRNA
molecule, and the larger 50S subunit that has polypeptides and two rRNA molecules.
Many antibacterial drugs act on bacterial 70S ribosomes or their subunits without
deleterious effects on the larger 80S ribosomes of eukaryotic cells and without
affecting protein synthesis in a patient.
Cells have an internal scaffolding called a
cytoskeleton, which is composed of three or four
types of protein fibers.
Bacterial cytoskeletons can wrap around the equator
of a cell and constrict, dividing the cell into two.
Fiber that forms a helix down the length of the cell
play a role in determining the shape of the cell.
Other fibers keep DNA molecules to certain areas in
the cell.
Spiroplasma, which lacks flagella, uses contractile
elements of its cytoskeleton for movement

Archaea

Archaeal cells have external structures similar to those seen in bacteria.

These include glycocalyces, flagella, and fimbriae. Some archaea have another kind of
proteinaceous appendage called a hamus.
There are many differences between archaeal and bacterial flagella:

Archaeal flagella are 1014 nm in diameter, which is about half the thickness of bacterial flagella.
Archaeal flagella lack a central channel; therefore, they grow with the addition of subunits at the
base of the filament rather than at the tip.
The proteins making up archaeal flagella share common amino acid sequences across archaeal
species. These are very different from the amino acid sequences common to bacterial flagella.
Sugar molecules are attached to the filaments of many archaeal flagella, a condition that is rare
in bacteria.
Archaeal flagella are powered with energy stored in molecules of ATP, whereas the flow of
hydrogen ions across the membrane powers bacterial flagella.
Archaeal flagella rotate together as a bundle both when they rotate clockwise and when they
rotate counterclock-wise. In contrast, bacterial flagella operate independently when rotating
clockwise.

External Structures of Archaea

Many archaea have fimbriae nonmotile, rodlike, sticky

projections that anchor the cells to
one another and to environmental
surfaces.
Some archaea make structures
called hami. More than 100 hami
may radiate from the surface of a
single archaeon. Hami function to
securely attach archaea to
surfaces.

Archeael shapes

Archaeal cell walls are composed of specialized proteins or polysaccharides.

All archaeal walls lack peptidoglycan, which is common to all bacterial cell walls.

Gram-negative archaeal cells have an outer layer of protein rather than an outer
lipid bilayer as seen in Gram-negative bacteria. Gram-negative archaea still appear
pink when Gram stained.
Gram-positive archaea have a thick cell wall and Gram stain purple, like Grampositive bacteria.
Archaeal cells are typically spherical or rod shaped, though irregularly shaped,
needle-like, rectangular, and flattened square archaea exist
Archaeal cytoplasmic membranes are composed of lipids that lack phosphate groups
and have branched hydrocarbons linked to glycerol by ether linkages (ester in
bacteria). Ether linkages are stronger than ester linkages, allowing archaea to live
in extreme environments.

Structural Characteristics of Prokaryotes

20 min!

Eukaryotic Cell Structure

Glycocalyces
Eukaryotic glycocalyces are not as structurally organized as
prokaryotic capsules.
Glycocalyces are absent in eukaryotes that have cell walls, such
as plants and fungi.
Glycocalyces:

help to anchor animal cells to each other,

strengthen the cell surface,

providing protection against dehydration,

function in cell-to-cell recognition,

function in communication.

Eukaryotic Cell Wall

The eukaryotic cells of fungi, algae, and plants have cell walls.
The cell wall takes on one of the functions of a glycocalyx by providing protection
from the environment. The wall also provides shape and support against osmotic
pressure.
Most eukaryotic cell walls are composed of various polysaccharides but not the
peptidoglycan seen in the walls of bacteria.

The walls of plant cells are composed of

cellulose.
Fungi also have walls of polysaccharides,
including cellulose, chitin, and/or
glucomannan.
The walls of algae are composed of a
variety of polysaccharides or other
chemicals, depending on the type of alga.
These chemicals include cellulose,
proteins, agar, carrageenan, silicates,
algin, calcium carbonate, or a
combination of these substances.

Eukaryotic Cytoplasmic Membrane

A eukaryotic cytoplasmic membrane

is a fluid mosaic of phospholipids and
proteins, which act as recognition
molecules, enzymes, receptors,
carriers, or channels.
Channel proteins for facilitated
diffusion are more common in
eukaryotes than in prokaryotes.
Additionally, within multicellular
organisms some membrane proteins
serve to anchor cells to each other.

Eukaryotic membranes contain steroid

lipids (sterols), such as cholesterol in
animal cells, that help maintain
membrane fluidity.

Eukaryotic cells use membrane rafts

to localize cellular processes, including
signaling the inside of the cell,
protein sorting, and cell movement.

Some viruses, including those of AIDS,

Ebola, measles, and flu, use
membrane rafts to enter human cells or
during viral replication.
Eukaryotic cells frequently attach
chains of sugar molecules to the
outer surfaces of lipids and proteins
in their cytoplasmic membranes;
prokaryotes rarely do this. Sugar
molecules may act in intercellular
signaling, cellular attachment, and
in other roles.

Eukaryotic Cytoplasmic Membrane

Eukaryotic cytoplasmic membrane controls the movement of materials

into and out of a cell.
Eukaryotic cytoplasmic membranes use both passive processes
(diffusion, facilitated diffusion, and osmosis) and active transport.
Eukaryotic membranes do not perform group translocation, which
occurs only in some prokaryotes, but many perform another type of active
transport endocytosis.
Endocytosis is termed phagocytosis if a solid is brought into the cell and
pinocytosis if only liquid is brought into the cell. Nutrients brought into a
cell by endocytosis are enclosed in a food vesicle.
Some eukaryotes also use pseudopods for locomotion by a process
called amoeboid action.
Exocytosis, an eukaryotic process, is the reverse of endocytosis - it
enables substances to be exported from the cell.
Not all eukaryotic cells can perform endocytosis or exocytosis.

Eukaryotic Cytoplasmic Membrane

Cytoplasm of Eukaryotes

The cytoplasm of eukaryotic cells is more complex than that of either bacteria or archaea.

The most distinctive difference is the presence of numerous membranous organelles.

Similarly to prokaryotes, eukaryotes also have organelles for locomotion and

nonmembranous organelles.

Eukaryotic flagella are within the

cytoplasmic membrane; they are
internal structures that push the
cytoplasmic membrane out around
them. Their basal bodies are in the
cytoplasm.
The shaft consists of tubulin.
Nine pairs of microtubules surround
two microtubules in the center,this
arrangement is common to all
flagellated eukaryotic cells, whether
they are found in protozoa, algae,
animals, or plants.

Movement of Eukaryotic Flagella and Cilia

Differently from prokaryotes, eukaryotic

flagella undulate rhythmically.
Some eukaryotic flagella push the cell
through the medium (as occurs in animal
sperm),
Others pull the cell through the medium
(as occurs in many protozoa).
Positive and negative phototaxis and
chemotaxis are seen in eukaryotic cells,
but such cells do not move in runs and
tumbles.
Other eukaryotic cells move using hair-like
structures called cilia, which and are
shorter and more numerous than flagella.
No prokaryotic cells have cilia.
Like flagella, cilia are composed primarily
of tubulin.

Cilia beat rhythmically, much like a

swimmer doing a butterfly stroke such movement of cilia helps cleanse
the human respiratory tract of dust
and microorganisms.

Other Nonmembranous Organelles

Ribosomes
Eukaryotic ribosomes are 80S and are composed of 60S and 40S subunits. In addition
to the 80S ribosomes found within the cytosol, many eukaryotic ribosomes are
attached to the membranes of the endoplasmic reticulum.

Cytoskeleton

Eukaryotic cells contain an extensive

cytoskeleton.
The eukaryotic cytoskeleton acts to anchor
organelles and functions in cytoplasmic
streaming and in movement of organelles.
Cytoskeletons have a function in movement of
cells and produce the basic shapes of the cells.

The eukaryotic cytoskeleton is made up of tubulin

microtubules, thinner microfilaments composed of
actin, and intermediate filaments composed of
various proteins.

Centrioles and Centrosome

Animal cells and some fungal cells contain

two centrioles, in a region of the cytoplasm
called the centrosome.
Plants, algae, and most fungi (and
prokaryotes) lack centrioles but usually have
a region of cytoplasm corresponding to a
centrosome.
Centrioles are composed of nine triplets of
tubulin microtubules arranged in a way that
resembles the 9 + 0 arrangement seen at the
base of eukaryotic flagella and cilia.
Centrosomes play a role in mitosis,
cytokinesis (cell division), and the formation
of flagella and cilia.
Brown algal sperm and numerous one-celled
algae, are able to form flagella and undergo
mitosis and cytokinesis, without having
centriols.

Eukaryotic Organelles

Membranous Organelles
Nucleus
The nucleus is usually spherical to ovoid and is often the largest organelle in a cell.
Some cells have a single nucleus; others are multinucleate, while still others lose their nuclei.
Cells that lose their nuclei, such as mammalian red blood cells, can survive for only a few months.

Nucleus

The semiliquid matrix of the nucleus is called nucleoplasm.

The nucleoplasm contains one or more nucleoli which are
specialized regions where RNA is synthesized.
The nucleoplasm also contains chromatin - DNA associated with
histones.
During mitosis (nuclear division), chromatin becomes visible as
chromosomes.
Surrounding the nucleus is a double membrane called the nuclear
envelope, which is composed of two phospholipid bi-layers.
The nuclear envelope contains nuclear pores that function to
control the import and export of substances through the
envelope.

Endoplasmatic Reticulum

The outer membrane of the nuclear

envelope is a netlike arrangement of
flattened hollow tubules called
endoplasmic reticulum (ER)
The ER traverses the cytoplasm of
eukaryotic cells.
Endoplasmic reticulum functions as a
transport system and is found in two
forms: smooth endoplasmic
reticulum (SER) and rough
endoplasmic reticulum (RER).
SER plays a role in lipid synthesis
as well as transport.
RER is rough because ribosomes
adhere to its outer surface. Proteins
produced by ribosomes on the RER
are inserted into the lumen (central
canal) of the RER and transported
throughout the cell.

Golgi Apparatus

A Golgi body is like the shipping

department of a cell: it receives,
processes, and packages large
molecules for export from the cell
The Golgi body packages secretions in
sacs called secretory vesicles, which
then fuse with the cytoplasmic
membrane before dumping their
contents outside the cell via
exocytosis.
Golgi bodies are composed of a series
of flattened hollow sacs that are
circumscribed by a phospholipid
bilayer.
Not all eukaryotic cells contain Golgi
bodies.

Lysosomes, Peroxisomes, Vacuoles, and

Vesicles

Membranous sacs that function

to store and transfer chemicals
within eukaryotic cells.
Large vacuoles are found in
plant and algal cells that store
starch, lipids, and other
substances in the center of the
cell. Often a central vacuole is
so large that the rest of the
cytoplasm is pressed against
the cell wall in a thin layer..

Lysosomes, Peroxisomes, Vacuoles, and

Vesicles

Peroxisomes are vesicles derived

from
ER. They contain oxidase and
catalase, which are enzymes that
degrade poisonous metabolic wastes
(such as free radicals and hydrogen
peroxide) resulting from some
oxygen-dependent reactions.
Peroxisomes are found in all types of
eukaryotic cells but are especially
prominent in the kidney and liver cells
of mammals.

Mitochondria

Mitochondria are spherical to elongated structures

found in most eukaryotic cells.
They have two membranes, each composed of a
phospholipid bilayer. The inner membrane
forms numerous folds called cristae that increase
the inner membranes surface area.
Mitochondria are often called the powerhouses of
the cell because their cristae produce most of the
ATP in many eukaryotic cells.
The interior matrix of a mitochondrion contains
(pro- karyotic) 70S ribosomes and a circular
DNA.
This DNA contains genes for some RNA
molecules and for a few mitochondrial
polypeptides that are manufactured by
mitochondrial ribosomes; however, most
mitochondrial proteins are coded by nuclear DNA
and synthesized by cytoplasmic ribosomes.

Chloroplasts are light-harvesting structures found

in photosynthetic eukaryotes.
Like mitochondria and the nucleus, chloroplasts
have two phospholipid bilayer membranes and
DNA.
Further, like mitochondria, chloroplasts can
synthesize a few polypeptides with their own 70S
ribosomes.
The pigments of chloroplasts gather light energy
to produce ATP and form sugar from carbon
dioxide.
Numerous membranous sacs called thylakoids
form an extensive surface area for the biochemical and photochemical reactions of
chloroplasts. The fluid between the thylakoids and
the inner membrane is called the stroma. The
space enclosed by the thylakoids is called the
thylakoid space.
Photosynthetic prokaryotes lack chloroplasts and
instead have infoldings of their cytoplasmic
membranes called photosynthetic lamellae.

Chloroplasts

Endosymbotic Theory

This theory suggests that eukaryotes formed from the union of small
aerobic prokaryotes with larger cells.

The smaller prokaryotes were not destroyed by the larger cells but instead
became internal parasites that remained surrounded by a vesicular
membrane of the host.
According to the theory, the parasites eventually lost the ability to exist
independently, but they retained a portion of their DNA, some ribosomes,
and their cytoplasmic membranes.
During the same time, the larger cell became dependent on the parasites for
aerobic ATP production.
According to the theory, the aerobic prokaryotes eventually evolved into
mitochondria (Proteobacteria), and their cytoplasmic membranes became
cristae.
A similar scenario explains the origin of chloroplasts from phagocytized
photosynthetic prokaryotes (Cyanobacteria).

Comparison between Eukaryotes and

Prokaryotes