Dexter John B.

Taguding
BS Chemical Engineering IV
Intro to Biotechnology

BASIC CONCEPT OF MICROBIOLOGY

I. Structure of Cells

The cell is the Iunctional basic unit oI liIe. It was discovered by Robert Hooke and is the Iunctional unit oI all known living
organisms. It is the smallest unit oI liIe that is classiIied as a living thing, and is oIten called the building block oI liIe. Organisms can
be classiIied as unicellular (consisting oI a single cell; including most bacteria) or multicellular (including plants and animals).
Humans contain about 100 trillion cells; a typical cell size is 10 m and a typical cell mass is 1 nanogram. The human cell extrema
are: largest - anterior horn in the spinal cord (135 vs. 120 Ior the ovum), longest - pseudounipolar cells which reach Irom
extremities, including the toes to the lower brain stem, and smallest - granule cells in the cerebellum, at 4 . The largest known cells
are unIertilised ostrich egg cells, which weigh 3.3 pounds

The word cell comes Irom the Latin cellula, meaning "a small room". The descriptive term Ior the smallest living biological
structure was coined by Robert Hooke in a book he published in 1665 when he compared the cork cells he saw through his microscope
to the small rooms monks lived in.

A. Prokaryotic Cell
The prokaryote cell is simpler, and thereIore smaller, than a eukaryote cell, lacking a nucleus and most oI the other organelles
oI eukaryotes. There are two kinds oI prokaryotes: bacteria and archaea; these share a similar structure.
Nuclear material oI prokaryotic cell consist oI a single chromosome that is in direct contact with cytoplasm. Here, the
undeIined nuclear region in the cytoplasm is called nucleoid.
A prokaryotic cell has three architectural regions:
O On the outside, Ilagella and pili project Irom the cell's surIace. These are structures (not present in all prokaryotes) made oI
proteins that Iacilitate movement and communication between cells;
O Enclosing the cell is the cell envelope generally consisting oI a cell wall covering a plasma membrane though some bacteria
also have a Iurther covering layer called a capsule. The envelope gives rigidity to the cell and separates the interior oI the cell
Irom its environment, serving as a protective Iilter. Though most prokaryotes have a cell wall, there are exceptions such as
coplasma (bacteria) and Thermoplasma (archaea). The cell wall consists oI peptidoglcan in bacteria, and acts as an
additional barrier against exterior Iorces. It also prevents the cell Irom expanding and Iinally bursting (cytolysis) Irom
osmotic pressure against a hypotonic environment. Some eukaryote cells (plant cells and Iungi cells) also have a cell wall;
O Inside the cell is the cytoplasmic region that contains the cell genome (DNA) and ribosomes and various sorts oI inclusions.
A prokaryotic chromosome is usually a circular molecule (an exception is that oI the bacterium orrelia burgdorferi, which
causes Lyme disease). Though not Iorming a nucleus, the DNA is condensed in a nucleoid. Prokaryotes can carry
extrachromosomal DNA elements called plasmids, which are usually circular. Plasmids enable additional Iunctions, such as
antibiotic resistance.
B. Eukaryotic Cell
A eukaryote whose cells contain complex structures enclosed within membranes. Eukaryotes may more Iormally be reIerred
to as the taxon Eukarya or Eukaryota. The deIining membrane-bound structure that sets eukaryotic cells apart Irom prokaryotic cells
is the nucleus, or nuclear envelope, within which the genetic material is carried. The presence oI a nucleus gives eukaryotes their
name, which comes Irom the Greek cu (eu, "good") and kupuov (karon, "nut" or "kernel"). Most eukaryotic cells also contain other
membrane-bound organelles such as mitochondria, chloroplasts and the Golgi apparatus. All species oI large complex organisms are
eukaryotes, including animals, plants and Iungi, although most species oI eukaryote are protist microorganisms.
Cell division in eukaryotes is diIIerent Irom that in organisms without a nucleus (prokaryotes). It involves separating the
duplicated chromosomes, through movements directed by microtubules. There are two types oI division processes. In mitosis, one cell
divides to produce two genetically identical cells. In meiosis, which is required in sexual reproduction, one diploid cell (having two
instances oI each chromosome, one Irom each parent) undergoes recombination oI each pair oI parental chromosomes, and then two
stages oI cell division, resulting in Iour haploid cells (gametes). Each gamete has just one complement oI chromosomes, each a unique
mix oI the corresponding pair oI parental chromosomes.
Eukaryotes appear to be monophyletic, and so make up one oI the three domains oI liIe. The two other domains, Bacteria and
Archaea, are prokaryotes and have none oI the above Ieatures. Eukaryotes represent a tiny minority oI all living things; even in a
human body there are 10 times more microbes than human cells. However, due to their much larger size their collective worldwide
biomass is estimated at about equal to that oI prokaryotes
II. Types of Cells

A. Bacteria

Bacteria are a large domain oI prokaryotic microorganisms. Typically a Iew micrometres in length, bacteria have a wide
range oI shapes, ranging Irom spheres to rods and spirals. Bacteria are present in most habitats on Earth, growing in soil, acidic hot
springs, radioactive waste, water, and deep in the Earth's crust, as well as in organic matter and the live bodies oI plants and animals.
There are typically 40 million bacterial cells in a gram oI soil and a million bacterial cells in a millilitre oI Iresh water; in all, there are
approximately Iive nonillion (510
30
) bacteria on Earth, Iorming a biomass that exceeds that oI all plants and animals. Bacteria are
vital in recycling nutrients, with many steps in nutrient cycles depending on these organisms, such as the Iixation oI nitrogen Irom the
atmosphere and putreIaction. Most bacteria have not been characterised, and only about halI oI the phyla oI bacteria have species that
can be grown in the laboratory. The study oI bacteria is known as bacteriology, a branch oI microbiology.

A.1. Morphology
Bacteria display a wide diversity oI shapes and sizes, called morphologies. Bacterial cells are about one tenth the size oI
eukaryotic cells and are typically 0.55.0 micrometres in length. However, a Iew species Ior example, Thiomargarita namibiensis
and Epulopiscium fishelsoni are up to halI a millimetre long and are visible to the unaided eye; E. fishelsoni reaches 0.7 mm.
Among the smallest bacteria are members oI the genus coplasma, which measure only 0.3 micrometres, as small as the largest
viruses. Some bacteria may be even smaller, but these ultramicrobacteria are not well-studied.
Most bacterial species are either spherical, called cocci (sing. coccus, Irom Greek kokko-kokkos, grain, seed), or rod-shaped,
called bacilli (sing. bacillus, Irom Latin baculus, stick). Elongation is associated with swimming. Some rod-shaped bacteria, called
vibrio, are slightly curved or comma-shaped; others, can be spiral-shaped, called spirilla, or tightly coiled, called spirochaetes. A small
number oI species even have tetrahedral or cuboidal shapes. More recently, bacteria were discovered deep under the Earth's crust that
grow as long rods with a star-shaped cross-section. The large surIace area to volume ratio oI this morphology may give these bacteria
an advantage in nutrient-poor environments. This wide variety oI shapes is determined by the bacterial cell wall and cytoskeleton, and
is important because it can inIluence the ability oI bacteria to acquire nutrients, attach to surIaces, swim through liquids and escape
predators.
Many bacterial species exist simply as single cells, others associate in characteristic patterns: Neisseria Iorm diploids (pairs),
Streptococcus Iorm chains, and Staphlococcus group together in "bunch oI grapes" clusters. Bacteria can also be elongated to Iorm
Iilaments, Ior example the Actinobacteria. Filamentous bacteria are oIten surrounded by a sheath that contains many individual cells.
Certain types, such as species oI the genus Nocardia, even Iorm complex, branched Iilaments, similar in appearance to Iungal mycelia
B. Yeast
easts are eukaryotic micro-organisms classiIied in the kingdom Fungi, with 1,500 species currently described estimated to
be only 1 oI all Iungal species. Most reproduce asexually by mitosis, and many do so by an asymmetric division process called
budding. easts are unicellular, although some species with yeast Iorms may become multicellular through the Iormation oI a string oI
connected budding cells known as pseudohyphae, or Ialse hyphae, as seen in most molds. east size can vary greatly depending on the
species, typically measuring 34 m in diameter, although some yeasts can reach over 40 m.
By Iermentation the yeast species Saccharomces cerevisiae converts carbohydrates to carbon dioxide and alcohols - Ior
thousands oI years the carbon dioxide has been used in baking and the alcohol in alcoholic beverages. It is also extremely important as
a model organism in modern cell biology research, and is one oI the most thoroughly researched eukaryotic microorganisms.
Researchers have used it to gather inIormation about the biology oI the eukaryotic cell and ultimately human biology. Other species oI
yeast, such as Candida albicans, are opportunistic pathogens and can cause inIections in humans. easts have recently been used to
generate electricity in microbial Iuel cells, and produce ethanol Ior the bioIuel industry.
B.1 Reproduction
easts, like all Iungi, may have asexual and sexual reproductive cycles. The most common mode oI vegetative growth in
yeast is asexual reproduction by budding. Here a small bud (also known as a bleb), or daughter cell, is Iormed on the parent cell. The
nucleus oI the parent cell splits into a daughter nucleus and migrates into the daughter cell. The bud continues to grow until it
separates Irom the parent cell, Iorming a new cell. Some yeasts, including Schi:osaccharomces pombe, reproduce by Iission instead
oI budding.
Under high stress conditions, haploid cells will generally die; under the same conditions, however, diploid cells can undergo
sporulation, entering sexual reproduction (meiosis) and producing a variety oI haploid spores, which can go on to mate (conjugate),
reIorming the diploid.
Some pucciniomycete yeasts, particularly species oI Sporidiobolus and Sporobolomces produce aerially dispersed, asexual
ballistoconidia.
C. Mold
Molds are Iungi that grow in the Iorm oI multicellular Iilaments called hyphae.
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Molds are considered to be microbes but
microscopic Iungi that grow as single cells are called yeasts. A connected network oI these tubular branching hyphae has multiple,
genetically identical nuclei and is considered a single organism, reIerred to as a colony.
Molds do not Iorm a speciIic taxonomic or phylogenetic grouping, but can be Iound in the divisions Zygomycota,
Deuteromycota and Ascomycota. Some molds cause disease or Iood spoilage, others play an important role in biodegradation or in the
production oI various Ioods, beverages, antibiotics and enzymes.
D. Algae and Protozoa

Protozoans and algae are general names given to the complex single celled liIe one Iinds in ponds and wetlands. They are
cells that have a nucleus and cellular organelles.

E. Animal and Plant Cells

E.1. Plant Cell

A plant cell is bounded by a cell wall and the living portion oI the cell is within the walls and is divided into two portions: the
nucleus, or central control center; and the cytoplasm, a Iluid in which membrane bound organelles are Iound. Between the primary cell
walls oI adjacent plant cells, lies a pectic middle lamella. There can be a secondary cell wall which would be located just to the inside
oI the primary wall. Both walls consist mainly oI cellulose, but the secondary cell wall may contain lignin and other substances. The
outer boundary oI the protoplasm (cytoplasm and nucleus) is a sandwich-like, Ilexible plasma membrane. This membrane regulates
what enters and leaves the plant cell. Plant cell organelles include: endoplasmic reticulum, with and without ribosomes attached; Golgi
bodies, mitochondria, and plastids. Plastids are chloroplasts, chromoplasts or leucoplastsdepending on the color and likewise the
Iunction. Chloroplasts are oI speciIic interest to those studying plants. A plant cell also, obviously, contains a nucleus which is
bounded by a nuclear envelope with pores. The pores in the nuclear envelope allow Ior movement oI substances in and out oI the
nucleus. Within the nucleus is a number oI chromosomes. The number present is speciIic to the organism and it will be later noted
how sex cells contain one-halI the number oI chromosomes, and restore chromosome number upon Iertilization. All oI these
organelles and the nucleus are suspended in the cytoplasm. The cytoplasm has movements that are reIerred to as cytoplasmic
streaming or cyclosis.

The particular Iunction oI the other organelles contained in plant cells can be reviewed below:
1. The nucleus is in the center oI most cells. Some cells contain multiple nuclei, such as skeletal muscle, while some do not
have any, such as red blood cells. The nucleus is the largest membrane-bound organelle. SpeciIically, it is responsible Ior
storing and transmitting genetic inIormation. The nucleus is surrounded by a selective nuclear envelope. The nuclear
envelope is composed oI two membranes joined at regular intervals to Iorm circular openings called nuclear pores. The pores
allow RNA molecules and proteins modulating DNA expression to move through the pores and into the cytosol. The
selection process is controlled by an energy-dependent process that alters the diameter oI the pores in response to signals.
Inside the nucleus, DNA and proteins associate to Iorm a network oI threads called chromatin. The chromatin becomes vital
at the time oI cell division as it becomes tightly condensed thus Iorming the rodlike chromosomes with the enmeshed DNA.
Inside the nucleus is a Iilamentous region called the nucleolus. This serves as a site where the RNA and protein components
oI ribosomes are assembled. The nucleolus is not membrane bound, but rather just a region.
2. Ribosomes are the sites where protein molecules are synthesized Irom amino acids. They are composed oI proteins and
RNA. Some ribosomes are Iound bound to granular endoplasmic reticulum, while others are Iree in the cytoplasm. The
proteins synthesized on ribosomes bound to granular endoplasmic reticulum are transIerred Irom the lumen (open space
inside endoplasmic reticulum) to the golgi apparatus Ior secretion outside the cell or distribution to other organelles. The
proteins that are synthesized oI Iree ribosomes are released into the cytosol.
3. The endoplasmic reticulum (ER) is collectively a network oI membranes enclosing a singular continuous space. As
mentioned earlier, granular endoplasmic reticulum is associated with ribosomes (giving the exterior surIace a rough, or
granular appearance). Sometimes granular endoplasmic reticulum is reIerred to as rough ER. The granular ER is involved in
packaging proteins Ior the golgi apparatus. The agranular, or smooth, ER lacks ribosomes and is the site oI lipid synthesis. In
addition, the agranular ER stores and releases calcium ions (Ca
2
).
4. The golgi apparatus is a membranous sac that serves to modiIy and sort proteins into secretory/transport vesicles. The
vesicles are then delivered to other cell organelles and the plasma membrane. Most cells have at least one golgi apparatus,
although some may have multiple. The apparatus is usually located near the nucleus.
5. Endosomes are membrane-bound tubular and vesicular structures located between the plasma membrane and the golgi
apparatus. They serve to sort and direct vesicular traIIic by pinching oII vesicles or Iusing with them.
6. Mitochondria are some oI the most important structures in the cell. They are site oI various chemical processes involved in
the synthesis oI energy packets called ATP (adenosine triphosphate). Each mitochondrion is surrounded by two membranes.
The outer membrane is smooth, while the inner one is Iolded into tubule structures called cristae. Mitochondria are unique in
that they contain small amounts oI DNA containing the genes Ior the synthesis oI some mitochondrial proteins. The DNA is
inherited solely Irom the mother. Cells with greater activity have more mitochondria, while those that are less active have
less need Ior energy producing mitochondria.
7. Lysosomes are bound by a single membrane and contain highly acidic Iluid. The Iluid acts as digesting enzymes Ior breaking
down bacteria and cell debris. They play an important Irom in the cells oI the immune system.
8. Peroxisomes are also bound by a single membrane. They consume oxygen and work to drive reactions that remove hydrogen
Irom various molecules in the Iorm oI hydrogen peroxide. They are important in maintaining the chemical balances within
the cell.
9. The cytoskeleton is a Iilamentous network oI proteins that are associated with the processes that maintain and change cell
shape and produce cell movements in animal and bacteria cells. In plants, it is responsible Ior maintaining structures within
the plant cell, rather then whole cell movement. The cytoskeleton also Iorms tracks along which cell organelles move
propelled by contractile proteins attached to their various surIaces. Like a little highway inIrastructure inside the cell. Three
types of filaments make up the cytoskeleton.
1. Microfilaments are the thinnest and most abundant oI the cytoskeleton proteins. They are composed oI actin, a
contractile protein, and can be assembled and disassembled quickly according to the needs oI the cell or organelle
structure.
2. Intermediate filaments are slightly larger in diameter and are Iound most extensively in regions oI cells that are
going to be subjected to stress. Once these Iilaments are assembled they are not capable oI rapid disassembly.
3. Microtubules are hollow tubes composed oI a protein called tubulin. They are the thickest and most rigid oI the
Iilaments. Microtubules are present in the axons and long dendrite projections oI nerve cells. They are capable oI
rapid assembly and disassembly according to need. Microtubules are structured around a cell region called the
centrosome, which surrounds two centrioles composed oI 9 sets oI Iused microtubules. These are important in cell
division when the centrosome generates the microtubluar spindle Iibers necessary Ior chromosome separation.
10. Chloroplasts
It is necessary to note a bit about the Iorm oI chloroplasts, as you will encounter them throughout this tutorial. Inside a
chloroplast is a matrix called the stroma. Enzymes are Iound in the stroma as well as granastacks oI coin-shaped discs,
called thylakoids. It is within the thylakoids that photosynthesis takes place. Note that chloroplasts, like mitochondria contain
their own DNA. They do rely on proteins Irom the nucleus, and are considered semi-autonomous organelles. Photosynthesis
will be discussed in greater detail in the Plant Metabolism tutorial.
11. 'acuoles
Plant cells are also notorious Ior having huge vacuoles. Up to 90 oI the volume oI a mature cell may be taken up by a single
large vacuole or several vacuoles. The vacuole is bound by a special membrane, called the tonoplast, and contains cell sap
which is composed oI dissolved substances and may include pigments.
E.2. Animal Cell

Animal cells do not have a cell wall. Instead oI a cell wall, the plasma membrane (usually called cell membrane when
discussing animal cells) is the outer boundary oI animal cells. Animal tissues thereIore require either external or internal support Irom
some kind oI skeleton. Frameworks oI rigid cellulose Iibrils thicken and strengthen the cell walls oI higher plants. Plasmodesmata
that connect the protoplasts oI higher plant cells do not have a counterpart in the animal cell model. During telophase oI mitosis, a cell
plate is Iormed as the plant cell begins its division. In animal cells, the cell pinches in the center to Iorm two cells; no cell plate is laid
down. Centrioles are generally not Iound in higher plant cells, while they are Iound in animal cells. Animal cells do not have plastids,
which are common in plant cells (chloroplasts). Both cell types have vacuoles, however, in animal cells vacuoles are very tiny or
absent, while in plant cells vacuoles are generally quite large.