Biological classification

Biological classification, or scientific classification in biology, is a method by which biologists group and categorize organisms by biological type, such as genus or species. Biological classification is a form of scientific taxonomy, but should be distinguished from folk taxonomy, which lacks scientific basis. Modern biological classification has its root in the work of Carolus Linnaeus, who grouped species according to shared physical characteristics. These groupings have since been revised to imp rove consistency with the Darwinian principle of common descent. Molecular phylogenetics, which uses DNA sequences as data, has driven many recent revisions and is likely to continue t o do so. Biological classification belongs to the science of biological systematics.

Taxonomic ranks:
In biological classification, rank is the level (the relative position) in a hierarchy. There are 7 main ranks defined by the international nomenclature codes: Kingdom, phylum/division, class, order, family, genus, species. "Domain", a level above kingdom, has become popular in recent years, but has not (ye t) been accepted into the codes.The most basic rank is that of species, the next most important is genus, and then family. Sometimes (but only rarely) the term "taxonomic category" is used instead of "rank".

The hierarchy of biological classification's eight major taxonomic ranks, which is an example of definition by genus and differentia . Intermediate minor rankings are not shown.
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Termi

mes

Taxa above t e enus level are often iven names based on t e t e enus, it a standard termination. The terminat ions used in forming these names depend on the ingdom, and sometimes the phylum and lass, as set out in the table below.
Rank Divisi n/Phylum Plants Al ae Fungi Animals acteria

-phyta

-mycota -mycotina -ia -idae

Subdivisi n/Subphylum -phytina Class Subclass Superorder Order Suborder Infraorder Superfamily Epifamily Family Subfamily Infrafamily Tribe Subtribe Infratribe

-opsida -phyceae -mycetes -idae -anae -ales -ineae -aria -acea -oidea -oidae -aceae -oideae -idae -inae -odd[4] -eae -inae -ini -ina -ad -phycidae -mycetidae

-ales -ineae

-aceae -oideae

-eae -inae

Table notes: In botany and mycology names at the rank of family and below are based on the name of a genus, sometimes called the type genus of that taxon, with a standard ending. For example, the rose family Rosaceae is named after the genus Rosa, with the standard ending -aceae" for a family. ames above the rank of family are formed from a family name, or are descriptive like Gymnospermae or Fungi . For animals, there are standard suffixes for taxa only up to the rank of superfamily. Forming a name based on a generic name may be not straightforward. For example, the atin "homo" has the genitive "homi is", thus the genus "Homo" human) is in the Hominidae, not "Homidae".

Kingdoms and domains:

From well before innaeus, plants and animals was considered separate Kingdoms. innaeus used this as the top rank, dividing the physical world into the plant, animal and mineral kingdoms. As advances in microscopy made classification of microorganisms possible, the number of kingdoms increased, five and six-kingdom systems being the most common. omains are a relatively new grouping. The three-domain system was first invented in 1990, but not gene rally accepted until later. ow, the majority of biologists accept the domain system, but a large minority use the five-kingdom method. One main characteristic of the three -domain method is the separation of Archaea and Bacteria, previously grouped into the single kingdom Bacteria a kingdom also sometimes called onera).

onsequently, the three domains of life are conceptuali ed as Archaea, Bacteria, and Eukaryota comprising the nuclei-bearing eukaryotes). A small minority of scientists add Archaea as a sixth kingdom, but do not accept the domain method.

Thomas avalier-Smith, who has published extensively on the classification of protists, has recently proposed that the eomura, the clade that groups together the Archaea and Eukarya, would have evolved from Bacteria, more precisely from Actinobacteria. His classification of 2004 treats the archaebacteria as part of a subkingdom of the Kingdom Bacteria, i.e. he rejects the three-domain system entirely.

Linnaeus 1735 2 kingdoms

Copeland Haeckel Whittaker 1938 Chatton 1866 1969 1925 4 3 5 2 empires kingdom kingdoms kingdoms s

Woese et al. 1977 6 kingdoms Eubacteria Archaebacteria Protista Fungi Plantae Animalia

Woese et al. Cavalier-Smith 1990 2004 6 kingdoms 3 domains Bacteria Archaea Bacteria Protozoa hromista Fungi Plantae Animalia

(not tr at d)

Protista

Protista Vegetabilia Animalia Plantae Animalia Eukaryota Plantae Animalia

Fungi Plantae Animalia

Eukarya

The Chromista are eukaryotic supergroup, probably polyphyletic, which may be treated as a separate kingdom or included among the Protista. They include all algae whose chloroplasts contain chlorophylls a and c, as well as various colorless forms that are closely related to them. These are surrounded by four membranes, and are believed to have been acquired from some red alga.
THE THREE DOMAIN SYSTEM:

The Three omain System, proposed by Woese and others, is an evolutionary model of classification based on differences in the sequences of
nucleotides in the cell's ribosomal RNAs ( rRNA), as well as the cell's membrane lipid structure and its sensitivity to antibiotics .

omparing rR A structure is especially useful. Because rRNA molecules

throughout nature carry out the same function, their structure changes very little over time. Therefore similarities and dissimilarities in rRNA nucleotide sequence are a good indication of how related or unrelated different cells and organisms are.
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Protista

Prokaryota

onera

onera

This system proposes that a common ancestor cell gave rise to three different cell types, each representing a domain. The three domains are the Archaea archaebacteria), the Bacteria eubacteria), and the Eukar a eukaryotes). The Eukar a are then divided into 4 kingdoms: Protists, Fungi, Anamalia, and Plantae. A description of the three domains follows:
1. The Archaea (archaebacteria)

The Archaea possess the following characteristics:

y y

Archaea are prokaryotic cells . Unlike the Bacteria and the Eukar a, the Archaea have membranes composed of branched hydrocarbon chains attached to glycerol by
ether linkages Fig. 1).

y y

The cell walls of Archaea contain no peptidoglycan . Archaea are not sensitive to some antibiotics that affect the Bacteria, but are sensitive to some antibiotics that affect the Eukar a.

Archaea contain rRNA that is unique to the Archaea as indicated by the presence molecular regions distin ctly different from the rR A of Bacteria and Eukar a.

Archaea often live in extreme environments and include methanogens, extreme halophiles, and hyperthermophiles. One reason for this is that the ether-containing linkages in the Archaea membranes is more stabile than the ester-containing linkages in the Bacteria and Eukar a and are better able to withstand higher temperatures and stronger acid concentrations.
2. The Bacteria (eubacteria)

The Bacteria possess the following characteristics:

y y

Bacteria are prokaryotic cells . ike the Eukar a, they have membranes composed of unbranched
fatty acid chains attached to glycerol by ester linkages Fig. 1).

The cell walls of Bacteria, unlike the Archaea and the Eukarya, contain
peptidoglycan .
5

Bacteria are sensitive to traditional antibacterial antibiotics but are resistant to most antibiotics that affect Eukar a. Bacteria contain rRNA that is unique to the Bacteria as indicated by the presence molecular regions distinctly different from the rR A of Archaea and Eukar a.
Bacteria include mycoplasmas, cyanobacteria, Gram-positive bacteria, and
Gram-negative bacteria.

3. The Eukarya (eukaryotes)

The Eukar a also spelled Eucar a) possess the following characteristics:

y y

Eukar a have eukaryotic cells . ike the Bacteria, they have membranes composed of unbranched
fatty acid chains attached to glycerol by ester linkages Fig. 1).

ot all Eukar a possess cells with a cell wall, but for those Eukar a having a cell wall, that wall contains no peptidoglycan .

Eukar a are resistant to traditional antibacterial antibiotics but are sensitive to most antibiotics that affect eukaryotic cells.

Eukar a contain rRNA that is unique to the Eukarya as indicated by the presence molecular regions distinctly different from the rR A of Archaea and Bacteria.

Fig. 1: Membrane Lipids of Archaea, Bacteria, and Eukarya

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The Eukar a are subdivided into the following kingdoms: a. Protista Kingdom Protista are simple, predominately unicellular eukaryotic organisms. Examples includes slime molds, euglenoids, algae, and protozoans. b. Fungi Kingdom Fungi are unicellular or multicellular organisms with eukaryotic cell types. The cells have cell walls but are not organized into tissues. They do not carry out photosynthesis and obtain nutrients through absorptio n. Examples include sac fungi, club fungi, yeasts, and molds. c. Plantae Kingdom Plants are multicellular organisms composed of eukaryotic cells. The cells are organized into tissues and have cell walls. They obtain nutrients by photosynthesis and absorption. Examples include mosses, ferns, conifers, and flowering plants. d. Animalia Kingdom Animals are multicellular organisms composed of eukaryotic cells. The cells are organized into tissues and lack cell walls. They do not carry out photosynthesis and obtain nutrients primarily by ingestion. Examples include sponges, worms, insects, and vertebrates.

Some features distinguishing prokaryotic and eukaryotic cells are shown in Table 1:
Characters 1. nuclear body eukaryotic cell prokaryotic cell

a. The nuclear body is bounded by a. The nuclear body is not bounded by a a nuclear membrane having pores nuclear membrane. connecting it with the endoplasmic reticulum.

b. It contains one or more paired, linear chromosomes composed

b. It usually contains one circular chromosome deoxyribonucleic acid composed of

of deoxyribonucleic acid

A)

associated with histone proteins. c. A nucleolus is present. d. The nuclear body is called a nucleus.

with histone-like proteins. c. There is no nucleolus.

d. The nuclear body is called a nucleoid.

2. cell division

a. The nucleus divides by mitosis.

a. The cell usually divides by binary fission. There is no mitosis. b. Prokaryotic cells are haploid. is not needed. eiosis

3.cytoplasmic membrane (cell membrane or plasma membrane)

b. Haploid 1 ) sex cells in diploid or 2 organisms are produced through meiosis. a. The cytoplasmic membrane is a fluid phospholipid bilayer containing sterols.

a. The cytoplasmic membrane is a fluid phospholipid bilayer usually lacking sterols any bacteria do contain sterol-like molecule called hopanoids.

b. The membrane is capable of endocytosis phagocytosis and b. The membrane is incapable of pinocytosis) and exocytosis. endocytosis and exocytosis.

 

 

A) associated

Cholesterol (A Sterol) 4.cytoplasmic structures

Diploptene (A Hopanoid)

a. The ribosomes are composed a. The ribosomes are composed of a of a 60S and a 40S subunit 50S and a 30S subunit forming an 0S forming an 80S ribosome. ribosome. b. Internal membrane-bound organelles such as mitochondria, endoplasmic reticulum, Golgi apparatus, vacuoles, and lysosomes are present. b. Internal membrane-bound organelles such as mitochondria, endoplasmic reticulum, Golgi apparatus, vacuoles, and lysosomes are absent.

c. There are no chloroplasts. c. hloroplasts serve as Photosynthesis usually takes place in organelles for photosynthesis. infoldings or extensions derived from the cytoplasmic membrane. d. A mitotic spindle involved in mitosis is present during cell division.

d. There is no mitosis and no mitotic spindle.

5.respiratory enzymes and electron transport chains

- The electron transport system is - The electron transport system is located in the inner membrane of located in the cytoplasmic membrane. the mitochondria.

"

6. cell wall

7.locomotor organelles

a. Plant cells, algae, and fungi a.With few exceptions, members of the have cell walls, usually composed domain Bacteria have cell walls of cellulose or chitin. Eukaryotic composed of peptidoglycan. cell walls are never composed of peptidoglycan. b. embers of the domain Archae have b. Animal cells and protozoans cell walls composed of protein, a complex carbohydrate, or unique lack cell walls. molecules resembling but not the same as peptidoglycan. - Eukaryotic cells may have - any prokaryotes have flagella, each flagella or cilia. Flagella and cilia composed of a single, rotating fibril and are organelles involved in usually not surrounded by a membrane. locomotion and in eukaryotic cells There are no cilia. consist of a distinct arrangement of sliding microtubules surrounded by a membrane. The microtubule arrangement is referred to as a 2X9+2 arrangement.

Structure of Eukaryotic Flagellum

Electron Micrograph of Microtubules

8.representati -ve organisms

- The domain Eukar a: animals, - The domain Bacteria and the domain plants, algae, protozoans, and Archae. fungi.

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Structure of a Bacterial Flagellum

VIRUSES
General Characteristics of Viruses
Viruses are infectious agents with both living and nonliving characteristics. They can infect animals, plants, and even other microorganisms. Viruses that infect only bacteria are called bacteriophages and those that infect only fungi are termed mycophages .
1. Living characteristics of viruses

a. They reproduce at a fantastic rate, but only in living host cells. b. They can mutate.
2. Nonliving characteristics of viruses

a. They are acellular , that is, they contain no cytoplasm or cellular organelles. b. They carry out no metabolism on their own and must replicate using
the host cell's metabolic machinery . In other words, viruses don't grow and

divide. Instead, new viral components are synthesized and assembled within the infected host cell. c. The vast majority of viruses possess either DNA or RNA but not both .
3. Criteria used to define a virus

a. The vast majority of viruses contain only one type of nucleic acid: R A, but not both.

A or

b. They are totally dependent on a host cell for replicati on. They are strict intracellular parasites.) c. Viral components must assemble into complete viruses virions) to go from one host cell to another.
4. Laboratory cultivation of viruses

Since viruses lack metabolic machinery of their own and are totall y dependent on their host cell for replication, they cannot be grown in synthetic culture media. Animal viruses are normally grown in animals, embryonated eggs, or in

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cell cultures where in animal host cells are grown in a synthetic medium and

the viruses are then grown in these cells.

Size and Shapes of Viruses

1. Size ( Fig. 2A, Fig. 2B, and Fig. 2 ):

Fig.( 2A)

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(Figs. 2 B, 2C)

Viruses are usually much smaller than bacteria and are submicroscopic . range in size from 5
to 300 nanometers (nm)

ost

.although some

Paramyxoviruses can be up to 14,000nm long.

2. Shapes ( Fig. 2A, Fig. 2B, and Fig. 2 )

a. Helical viruses : consist of nucleic acid surrounded by a hollow protein cylinder or capsid and possessing a helical structure ( Fig.3 A).

Fig.3 A: Viral Structure (Helical Virus)

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b. Polyhedral viruses: consist of nucleic acid surrounded by a polyhedral (many-sided) shell or capsid, usually in the form of an icosahedron; ( Fig.3 B).

Fig. 3B: Viral Structure (Polyhedral Virus)

c. Enveloped viruses : consist of nucleic acid surrounded by either a helical or polyhedral core and covered by an envelope ( Fig.3 and Fig. 3 ).

Fig. 3C: Viral Structure (Enveloped Helical Virus)

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Fig. 3D: Viral Structure (Enveloped Polyhedral Virus)

d. Binal (complex) viruses: have neither helical nor polyhedral forms, are pleomorphic (irregular shaped), or have complex structures (Fig. 3E).

Fig. 3E: Viral Structure (Binal)

A. Viral Structure:
Since viruses are not cells, they are structurally much more simple than bacteria. An intact infectious viral particle is called a virion and consists of:

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1. A genome:
The viral genome is a single or segmented, circular or linear molecule of nucleic acid functioning as the genetic material of the virus. It can be single-stranded or double-stranded A or R A (but never both), and codes

for the synthesis of viral components and viral enzymes for replication.

2. A capsid:
The capsid or core , is a protein shell surrounding the genome and is usually composed of protein subunits called capsomeres . The capsid serves to protect and introduce the genome into host cells. Some viruses consist of no more than a genome surrounded by a capsid and are called nucleocapsid or
naked viruses ( Fig. 3A and Fig.3 B). Attachment proteins project out from

the capsid and bind the virus to susceptible host cells .

3. An envelope:
Most animal viruses also have an envelope surrounding a polyhedral or helical nucleocapsid, in which case they are called enveloped viruses ( Fig. 3 ,Fig. 3 ). The envelope is composed of phospholipids and glycoprote in and for most viruses, is derived from host cell membranes by a process called
budding ( Fig. 4 ). The envelope may come from the host cell's nuclear

membrane, vacuolar membranes (packaged by the Golgi apparatus), or outer cytoplasmic membrane

.
Fig. 4: Virus Obtaining Its Envelope from Host Cell Membrane by Budding
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Bacteriophages: are viruses that only infect bacteria. Some bacteriophages are structurally much more complex than typical nucleocapsid or enveloped viruses and may possess a unique tail structure composed of a

base plate, tail fibers, and a contractile sheath ( Fig.3E). Other bacteriophages, however, are simple icosahedrals or helical (see Fig. 2B).

Life Cycle of Bacteriophages:

There are two primary types of bacteriophages: lytic bacteriophages and
temperate bacteriophages .

1. Bacteriophages that replicate through the lytic life cycle are called lytic
bacteriophages , and are so named because they lyse the host bacterium as a

normal part of their life cycle. 2. Bacteriophages capable of a lysogenic life cycle are termed temperate
phages . When a temperate phage infects a bacterium, it can either

replicate

by means of the lytic life cycle and cause lysis of the host bacterium, or, it can incorporate its prophage. A into the bacterium's A and become a noninfectious

.
Electron Micrograph of Coliphage T4

After infecting bacteria with lytic bacteriophages in the lab, plaques can be seen on the petri plates. Plaques are small clear areas on the agar surface where the host bacteria have been lysed by lytic bacteriophages.

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Plaques on an agar surface after infecting Escherichia coli with Coliphage T- 4

The lytic life cycle consists of the following steps:

1. Adsorption: Attachment sites on the phage adsorb to receptor sites on the host bacterium ( Fig.5). Most bacteriophages adsorb to the bacterial cell

wall, although some are able to adsorb to flagella or pili. Speci fic strains of bacteriophages can only adsorb to specific strain of host bacteria. This is known as viral specificity.

Fig.5: Adsorption during the Lytic Life Cycle of a Lytic Bacteriophage

2. Penetration: In the case of phages that adsorb to the bacterial cell wall, a

phage enzyme "drills" a hole in the bacterial wall and the phage injects its
genome into the bacterial cytoplasm ( Fig.6). Some phages accomplish this

by contracting a sheath which drives a hollow tube into the bacterium. This begins the eclipse period. The genome o f phages which adsorb to flagella or pili enter through these hollow organelles. In either case, only the phage genome enters the bacterium so there is no uncoating stage.

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Fig.6: Penetration during the Lytic Life Cycle of a Lytic Bacteriophage 3. Replication: Enzymes coded by the phage genome shut down the

bacterium's macromolecular (protein, R A,

A) synthesis. The phage

replicates its genome and uses the bacterium's metabolic machinery to synthesize phage enzymes and phage structural components (Fig.

and

Fig.8 ).

Figs. 7&8: Early and late Replication during the Lytic Life Cycle of a Lytic Bacteriophage 4. Maturation: The phage parts assemble around the genomes ( Fig.9).

Fig.9: Maturation during the Lytic Life Cycle of a Lytic Bacteriophage 5. Release: Usually, a phage-coded lysozyme breaks down the bacterial peptidoglycan causing osmotic lysis

and

release

of

the

intact

bacteriophages ( Fig.10).

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Fig.10: Release during the Lytic Life Cycle of a Lytic Bacteriophage 6. Reinfection: From 50 to 200 phages may be produced per infected

bacterium.

The Lysogenic Life Cycle of Temperate Bacteriophages:

Bacteriophages capable of a lysogenic life cycle are termed temperate
phages . When a temperate phage infects a bacterium, it can either replicate by means of the lytic life cycle and cause lysis of the host bacterium, or, it

can incorporate its DNA into the bacterium's DNA and become a noninfectious prophage ( Fig.11).

Fig.11: Lysogenic Life Cycle of a Temperate Bacteriophage

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In the latter case, the cycle begins by the phage adsorbing to the host bacterium or lysogen and injecting its genome as in the lytic life cycle. However, the phage does not shut down the host cell. Instead, the phage
DNA inserts or integrates into the host bacterium's DNA ( Fig.12).

Fig.12: Prophage Formation during the Lyso genic Life Cycle of a Temperate Bacteriophage

At this stage the virus is called a prophage . Expression of the phage genes controlling phage replication is blocked by a repressor protein, and the phage A replicates as a part of the bacterium's bacterium now contains the prophage ( Fig.13). A so that every daughter

Fig.13: Maintaining the Prophage during the Lysogenic Life Cycle of a Temperate Bacteriophage

The number of viruses infecting the bacterium as well as the physiological state of the bacterium appear to determine whether the temperate phage enters the lytic cycle or becomes a prophage. In about one out of every million to one out of every billion bacter ia containing a prophage, spontaneous

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induction occurs. The phage genes are activated and new phages are produced by the lytic life cycle.

Classification of Viruses:
Viruses can store their genetic information in six different types of nucleic acid which are named based on how that nucleic acid eventually becomes transcribed to the viral mR A capable of binding to host cell ribosomes and being translated into viral proteins.
Only a (+) viral mRNA strand can be translated into viral protein . These

six forms of viral nucleic acid are: a. (+/-) double-stranded DNA. b. (+) single-stranded DNA. c. (+/-) double-stranded RNA. d. (-) RNA e. (+) RNA f. (+) RNA Retroviruses Retroviruses, such as HIV-1, HIV-2, and HTLV-1 are examples.

Viroids and Prions:

Viroids: are even more simple than viruses. They are small, circular,

single-stranded molecules of infectious RNA lacking even a protein coat. They are the cause of a few plant diseases such as potato spindle -tuber disease,cucumber pale fruit, citrus exoco rtis disease, and cadang-cadang (coconuts).
Prions: are infectious protein particles thought to be responsible for a group

of transmissible and/or inherited neurodegenerative diseases . Most evidence indicates that the infectious prion proteins are modified forms of normal proteins coded for by a host gene in the brain.
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Domain: Bacteria Phylum: Cyanobacteria

Cyanobacteria (also known as blue-green algae , blue-green bacteria , and Cyanophyta ) is a phylum of bacteria that obtain their energy through

photosynthesis. The name "cyanobacteria" comes from the color of the bacteria (Greek: (kyans) = blue).

The ability of cyanobacteria to perform oxygenic photosynthesis is thought to have converted the early reducing atmosphere into an oxidizing one, which dramatically changed the composition of life forms on Earth by stimulating biodiversity and leading to the near -extinction of oxygen-intolerant organisms. According to endosymbiotic theory(The endosymbiotic theory concerns the origins of mitochondria and plastids (e.g. chloroplasts) ,which

are organelles of eukaryotic cells. According to this theory, these organelles originated as separate prokaryotic organisms that were taken inside the cell as endosymbionts. Mitochondria close developed relatives) from proteobacteria (in and chloroplasts

particular, Rickettsiales or

from cyanobacteria), chloroplasts in plants and eukaryotic algae have evolved from cyanobacteria via endosymbiosis.

Characteristics:
yanobacteria include unicellular and colonial species. olonies may form

filaments, sheets or even hollow balls. Some filamentous colonies show t he ability to differentiate into several different cell types: vegetative cells, the normal, photosynthetic cells that are formed under favorable growing conditions; akinetes, the climate-resistant spores that may form when environmental conditions become harsh; and thick -walled heterocysts, which contain the enzyme nitrogenase, vital for nitrogen fixation. Heterocysts may also form under the appropriate environmental conditions (anoxic) when fixed nitrogen is scarce. Heterocyst-forming species are specialized for nitrogen fixation and are able to fix nitrogen gas into ammonia (NH3), nitrites (NO2) or

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nitrates (NO3) which can be absorbed by plants and converted to protei n and nucleic acids [atmospheric nitrogen cannot be used by plants directly]. Many cyanobacteria also form motile filaments, called hormogonia, that travel away from the main biomass to bud and form new colonies elsewhere. The cells in a hormogonium are often thinner than in the vegetative state, and the cells on either end of the motile chain may be tapered. In order to break away from the parent colony, a hormogonium often must tear apart a weaker cell in a filament, called a necridium. Each individual cell of a cyanobacterium typically has a thick, gelatinous cell wall.. They lack flagella, but hormogonia and some species may move about by gliding along surfaces. Many of the multi-cellular filamentous forms of Oscillatoria are capable of a waving motion.
Classification:

The cyanobacteria were traditionally classified by morphology into five sections. The first three - hroococcales, Pleurocapsales, and Oscillatoriales are not supported by phylogenetic studies. However, the latter two - Nostocales and Stigonematales - are monophyletic, and make up the heterocystous cyanobacteria. The members of hroococales are unicellular and usually

aggregate in colonies. The classic t axonomic criterion has been the cell morphology and the plane of cell division. In Pleurocapsales, the cells have the ability to form internal spores (baeocytes). The rest of the sections include filamentous species. In Oscillatoriales, the cells are unise riately arranged and do not form specialized cells (akinetes and heterocysts). In Nostocales and Stigonematales the cells have the ability to develop heterocysts in certain conditions. Stigonematales, unlike Nostocales, includes species with truly branched trichomes.

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Domain: Bacteria Phylum: Cyanobacteria Order: Nostocales

Genus: Nostoc

The Nostocales order contains most of the species of cyanobacteria. It includes filamentous forms, both simple or branched, and both those occurring as single strands or multiple strands within a sheath. Some but not all members show a decrease in width from the base. Again, some but not all have heterocysts

Domain: Phylum: Order: Genus:

Bacteria Cyanobacteria Oscillatoriales

Oscillatoria

Oscillatoria is a genus of filamentous cyanobacteria which is named for the oscillation in its movement. Filaments in the colonies can slide back and forth against each other until the whole mass is reoriented to its light source. It is commonly found in watering-troughs waters, and is mainly blue -green or brown-green. Oscillatoria is an organism that reproduces by fragmentation. Oscillatoria forms long filaments of ce lls which can break into fragments called hormogonia. The hormogonia can grow into a new, longer filament. Breaks in the filament usually occur where dead cells(necridia) are present. Oscillatoria uses photosynthesis to survive and reproduce.

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THE PROKARYOTIC CELL: BACTERIA A. SIZES, SHAPES, AND ARRANGEMENTS OF BACTERIA

Bacteria are: a.prokaryotic. b.single-celled, microscopic organisms (Exceptions have been discovered that can reach sizes just visible to the naked eye. They include Epulopiscium fishelsoni, a bacillus-shaped bacterium that is typically 80 micrometers (m) in diameter and 200-600 m long, and Thiomar arita nami iensis, a spherical bacterium between 100 and 50 m in diameter.) c.generally much smaller than eukaryotic cells. d.very complex despite their small size.

Epulopiscium fishelsoni

Thiomargarita namibiensis

Most bacteria come in one of three basic shapes : coccus, rod or bacillus, and spiral.
1. The coccus:

The

cocci

are

spherical

or

oval

bacteria

having

distinct arrangements based on their planes of division.

26

'

&

one

of

several

Arrangements of Cocci a. ivisionin one plane produces

either a diplococcus or streptococcus arrangement. diplococcus: cocci arranged in pairs streptococcus: cocci arranged in chains

b.

ivision in two planes produces a tetrad arrangement. A tetrad: cocci arranged in squares of 4

c. ivision in three planes produces a sarcina arrangement.

sarcina: cocci in arranged cubes of 8

d. ivision in random planes produces a staphylococcus arrangement.

staphylococcus: cocci arranged in irregular, often grape -like clusters. An average coccus is about 0.5-1.0 micrometer (m) in diameter. (A micrometer equals 1/1,000,000 of a meter.)
2. The rod or bacillus:

Bacilli are rod-shaped bacteria. Bacilli all divide in one plane producing iplobacillus , streptobacillus , or coccobacillus arrangement.
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Arrangements of Bacilli

a. bacillus: single bacilli. b. streptobacillus: bacilli arranged in chains. c. a coccobacillus: oval and similar to a coccus. An average bacillus is 0.5-1.0 m wide by 1.0-4.0 m long.
3. The spiral :

Spirals come in one of three forms, a vibrio, a spirillum, or a spirochete .

Spiral Forms

A. Vibrio: a curved or comma-shaped rod. B. Spirillum: a thick, rigid spiral. . Spirochete: a thin, flexible spiral. Spirals range in size from 1 m to over 100 m in length.

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4. Exceptions to the above shapes

Trichome-forming,

sheathed

stalked, filamentous,

square,

star-shaped,

spindle-shaped, lobed, and pleomorphic.

B. CELL STRUCTURE OF THE DOMAIN BACTERIA: An Overview

Structurally, a typical bacterium usually consists of:
y

a cytoplasmic membrane surrounded by a peptidoglycan cell wall and may be an outer membrane;

A fluid cytoplasm containing a nuclear region (nucleoid) and numerous ribosomes. Often various external structures such as a glycocalyx, flagella, and pili.

1. The Cytoplasmic Membrane:

The cytoplasmic membrane, also called a cell membrane or plasma membrane, is about nanometers (nm; 1/1,000,000,000 m) thick. It lies internal to the cell wall and encloses the cytoplasm of the bacterium (Fig. 1).

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Fig. 1: Prokaryotic Cell ( Bacillus megaterium)

A. Structure and Composition

Like all biological membranes in nature, the bacterial cytoplasmic membrane is composed phospholipid and protein molecules . In electron micrographs, it appears as 2 dark bands separated by a light band and is actually a fluid
phospholipid bilayer imbedded with proteins (Fig.2). With the exception of

the mycoplasmas, the only bacteria that lack a cell wall, prokaryotic membranes lack sterols (STEROLS: Complex lipids found in the membranes of eukaryotic cells.). Many bacteria, however, do contain sterol -like molecules called hopanoids. Like the sterols found in eukaryotic cell membranes, the hopanoids most likely stabilize the bacterial cytoplasmic membrane . The phospholipid bilayer i s arranged so that the polar ends of the molecules (the phosphate and glycerol portion of the phospholipid that is soluble in water) form the outermost and innermost surface of the membrane while the non-polar ends (the fatty acid portions of the phospholi pids that are insoluble in water) form the center of the membrane (Fig.2).

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Fig.2: Diagram of a Cytoplasmic Membrane B. Functions:

The cytoplasmic membrane is a selectively permeable membrane that

determines what goes in and out of the organism . C. Functions of the cytoplasmic membrane other than selective permeability:

Functions are associated with the bacterial cytoplasmic membrane include : 1. Energy production : The electron transport system for bacteria with aerobic and anaerobic respiration, as well as photosynthesis for bacteria converting light energy into chemical energy is located in the cytoplasmic membrane. 2. Motility: The motor that drives rotation of bacterial flagella is located in the cytoplasmic membrane. 3. Waste removal : Waste byproducts of metabolism within the bacterium must exit through the cytoplasmic membrane.

4. Formation of endospores (discussed later; Fig.3).

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Fig.3: Endospore stain of Bacillus megaterium

D. Binary fission

Bacteria divide by binary fission where in one bacterium splits into two. Therefore, bacteria increase their numbers by geometric

progression whereby their population doubles every generation time.

2. The Peptidoglycan Cell Wall:

The mycoplasmas are the only bacteria that naturally lack a cell wall. All other bacteria have a cell wall. The Bacteria (eubacteria), with the exception of the Chlamydias, have a semirigid cell wall containing peptidoglycan. The Archaea (archaebacteria), that are often found growing in extreme environments, also have a semirigid cell wall but it is composed of chemicals distinct from peptidoglycan such as protein or pseudomurein.
A. Function of Peptidoglycan:

Peptidoglycan prevents osmotic lysis . Without a strong cell wall, the

bacterium would burst from the osmotic pressure of the water flowing into the

cell.
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B. Structure and Composition of Peptidoglycan

Peptidoglycan, also called murein, is a vast polymer consisting of interlocking

chains of identical peptidoglycan monomers (Fig. 4A and Fig. 4B).

Fig. 4A&4B: Structure of Peptidoglycan: Staphylococcus aureus and

Escherichia coli A peptidoglycan monomer consists of two joined amino sugars,

N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM), with a pentapeptide coming off of the NAM ( Fig. 5A and Fig.5 B).

Fig. 5A&5B: The Peptidoglycan Monomer of Escherichia coli and

Staphylococcus aureus

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E. Gram-Positive and Gram-Negative Bacteria:

Most bacteria can be placed into one of two groups based on their color after specific staining procedures are performed: gram-positive, gram-negative, or acid-fast.
y

Gram-positive: retain the initial dye crystal violet during the Gram stain

procedure and appear purple when observed through the microscope. Common gram-positive bacteria of medical importance include Streptococcus pyogenes, Streptococcus pneumoniae, Staphylococcus aureus, Enterococcus faecalis, and Clostridium species.
y

Gram-negative: decolorize during the Gram stain procedure, pick up

the counterstain safranin, and appear pink when observed through the microscope. Common Gram-negative bacteria of medical importance include Salmonella species, Shigella species, Neisseria gonorrhoeae, Neisseria meningitidis, Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa. Also see gram stain of a mixture of gram-positive and gram-negative bacteria.(Fig.6)

Fig.6:A Gram Stain of a Mixture of Gram-Positive and Gram-Negative Bacteria

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The gram staining procedure involves four basic steps:

1. The bacteria are first stained with the basic dye crystal violet . Both gram-positive and gram-negative bacteria become directly stained and appear purple after this step. 2. The bacteria are then treated with gram's iodine solution . This allows the stain to be retained better by forming an insoluble crystal violet -iodine complex. Both gram-positive and gram-negative bacteria remain purple after this step. 3. Gram's decolorizer , a mixture of ethyl alcohol and acetone , is then added. This is the differential step. Gram-positive bacteria retain the crystal violet-iodine complex while gram-negative are decolorized. 4. Finally, the counterstain safranin (also a basic dye) is applied. Since the gram-positive bacteria are already stained purple, they are not affected by the counterstain. Gram-negative bacteria, which are now colorless, become directly stained by the safranin. Thus, gram-positive appear purple, and gram-negative appear pink.

3. STRUCTURES LOCATED WITHIN THE CYTOPLASM

We will now look at the following structures located within the cytoplasm. a.Cytoplasm b.The nucleoid c.Ribosomes d.Endospores e. Organelles for photosynthesis

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The Cytoplasm A. Structure and Composition

In bacteria, the cytoplasm refers to everything enclosed by the cytoplasmic membrane. About 80% of the cytoplasm of bacteria is composed of water. Within the cytoplasm can be found nucleic acids (DNA and RNA), enzymes and amino acids, carbohydrates, lipids, inorganic ions, and many low molecular weight compounds.The liquid component of the cytoplasm is called the
cytosol. Some groups of bacteria produce cytoplasmic inclusion bodies that

carry out specialized cellular functions.

B. Functions

The cytoplasm is the site of most bacterial metabolism .

The Nucleoid A. Structure and Composition

The bacterial genome is composed of chromosomal deoxyribonucleic acid

or DNA and represents the bacterium's nucleoid. Unlike the eukaryotic

nucleus, the bacterial nucleoid has no nuclear membrane or nucleoli ( Fig. 1). Since bacteria are haploid, that is they have only one chromosome and there is
no meiosis in bacteria.The nucleoid is one long, single molecule of double

stranded, helical, supercoiled DNA.

Ribosomes A. Structure and Composition

Ribosomes are composed of ribosomal RNA (rRNA) and protein . Ribosomes are composed of two subunits with densities o f 50S and 30S. ("S" refers to a unit of density called the Svedberg unit.) The two subunits combine during

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protein synthesis to form a complete 0S ribosome about 25nm in diameter. A typical bacterium may have as many as 15,000 ribosomes.
B. Functions

Ribosomes function as a workbench for protein synthesis

Endospores

Endospores are dormant alternate life forms produced by the genus Bacillus, the genus Clostridium, and several other genera of bacteria.
y

Scanning electron micrograph of Clostridium botulinum with endospore.

Electron Micrograph of Clostridium botulinum

B. Endospore Structure ( Fig. )

The completed endospore consists of multiple layers of resistant coats (including a cortex, a spore coat , and sometimes an exosporium ) surrounding a nucleoid, some ribosomes, RNA molecules, and enzymes.
Exospores are heat resistant spores produced by a budding process.

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Fig.7: Endospore Structure

Different shapes of spores C. Function of Endospores

An endospore is not a reproductive structure but rather a resistant, dormant

survival form of the organism. Endospores are quite resistant to high

temperatures (including boiling), most disinfectants, low energy radiation, drying, etc. Bacterial endospores are resistant to antibiotics, most disinfectants, and physical agents such as radiation, boiling, and drying. The impermeability of the spore coat is thought to be responsible for the endospore's resistance to chemicals.

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4. STRUCTURES LOCATED OUTSIDE THE CELL WALL

a. glycocalyx (capsule) and S-layer b. flagella c. pili
The Glycocalyx and S-Layer 1. The Glycocalyx (Capsules and Slime Layers )

All bacteria secrete some sort of glycocalyx , an outer viscous covering of fibers extending from the bacterium (Fig. 1, Fig.23 , and Fig. 24). If it appears as an extensive, tightly bound accumulation of gelatinous material adhering to the cell wall, it is called a capsule as shown in the photomicrograph in Fig. 23. If the glycocalyx appears unorganized and more loos ely attached, it is referred to as a slime layer .

Fig.23: Capsule stain of Enterobacter aerogenes

Fig.24: Encapsulated Brucella

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A. Structure and Composition

The glycocalyx is usually a viscous polysaccharide or polypeptide slime . Actual production of a glycocalyx often depends on environmental conditions.
B. Functions and Significance to Bacteria Causing Infections

Although a number of functions have been associated with the glycocalyx, such as protecting bacteria against drying, trap nutrients 1, etc., for our purposes there are two very important functions. The glycocalyx enables certain bacteria to resist phagocytic engulfment 2 by white blood cells in the body or protozoans in soil and water. The glycocalyx also enables some b acteria to
adhere to environmental surfaces 3 (rocks, root hairs, teeth, etc.), colonize , and resist flushing . 2. The S-layer A. Structure and Composition

Many gram-negative and gram-positive bacteria, as well a many Archaea possess a regularly structured layer called an S-layer attached to the outermost portion of their cell wall. It consists of a single molecular layer composed of identical proteins or glycoproteins . Although they vary with the species, S-layers generally have a thickness between 5 and 25 nm.

B. Functions and Significance to Bacteria Causing Infections

The S-layer has been associated with a number of possible functions. These include the following: a. The S-layer may protect bacteria from harmful enzymes, from changes
in pH, from the predatory bacterium Bdellovibrio, a parasitic bacterium that

actually uses its motility to penetrate other bacteria and replicate within their cytoplasm, and from bacteriophages .

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Predatory bacterium Bdellovibrio

b. The S-layer can function as an adhesin , enabling the bacterium to adhere

to host cells and environmental surfaces, colonize, and resist flushing .

c. The S-layer may contribute to virulence by protecting the bacterium

against complement attack and phagocytosis . Flagella A. Structure and Composition

A bacterial flagellum has 3 basic parts: a filament, a hook, and a basal body. 1) The filament is the rigid, helical structure that extends from the cell surface. It is composed of the protein flagellin. With the exception of a few bacteria, such as Bdellovibrio and Vibrio cholerae, the flagellar filament is not surrounded by a sheath ( Fig.25).

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Fig.25: Structure of a Bacterial Flagellum

2) The hook is a flexible coupling between the filament and the basal body ( Fig.25). 3) The basal body consists of a rod and a series of rings that anchor the flagellum to the cell wall and the cytoplasmic membrane ( Fig.25). Unlike eukaryotic flagella, the bacterial flagellum has no internal fibrils and does not flex. Instead, the basal bo dy acts as a rotary molecular motor, enabling the
flagellum to rotate and propell the bacterium through the surrounding fluid. In

fact, the flagellar motor rotates very rapidly. Bacteria flagella (Fig. 26 and Fig. 2 ) are 10-20 m long and between 0.01 and 0.02 m in diameter and come in a number of distinct arrangements.

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Fig.

: Electron Microgra )

of Bacteria wit Flagella

B. Flagellar rrangements ( ig.

. monotrichous: a single flagellum, usually at one pole . amphitrichous: a single flagellum at both ends of the organism . lophotrichous: two or more flagella at one or both poles 4. peritrichous: flagella over the entire surface

Fig.

: Bacterial Flagellar rrangements

5. axial filaments: internal flagella found only in the spirochetes. Axial filaments are composed of from two to over a hu ndred axial fibrils (or endoflagella) that extend from both ends of the bacterium between the outer

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membrane and the cell wall, often overlapping in the center of the cell.( Fig. 29 ).

Fig.29: Spirochete Axial Filaments C. Functions

Flagella are the organelles of locomotion for most of the bacteria that are capable of motility. The bacterial flagellum can rotate both counterclockwise and clockwise. A protein switch in the molecular motor of the basal body controls rotation. Clockwise rotation results in a tumbling motion and
changes the direction of bacterial movement . On the other hand, counterclockwise rotation leads to long, straight or curved runs without a change in direction .

Pili (Fimbriae) A. Structure and Composition

Pili are thin, protein tubes originating from the cytoplasmic membrane. They are found in virtually all gram -negative bacteria but not in many gram -positive bacteria. The pilus has a shaft composed of a protein called pilin. At the end of the shaft is the adhesive tip structure having a shape corresponding to
that of specific glycoprotein or glycolipid receptors on a host cell ( Fig.

30).

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Fig.30: Adhesive Tip of Bacte rial Pili Binding to Host Cell Receptors

There are two basic types of pili: 1) short attachment pili , also known as fimbriae, that are usually quite numerous ( Fig.32).

Fig.32: Bacterial Pili

2) long conjugation pili , also called "F" or sex pili ( Fig.33), that are very few in number.

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Fig33: Conjugation (Sex) Pilus

B. Functions and Significance of Pili to Bacteria Causing Infections:

The short attachment pili or fimbriae are organelles of adhesion allowing bacteria to colonize environmental surfaces or cells and resist flushing .

Some bacteria can produce a special pilus called a conjugation or sex pilus that enables conjugation . Conjugation is the transfer of DNA from a donor or male bacterium with a sex pilus to a recipient or female bacterium to enable genetic recombination. Scanning electron micrograph E. coli with a conjugation pillus.

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C. ATYPICAL PATHOGENIC BACTERIA

These include the mycoplasmas, the rickettsias, and the chlamydias.
1. Mycoplasmas

a. Mycoplasmas are smaller than ordinary bacteria, typically being 0.15 - 0.30 micrometers (m) in size. They are the smallest microorganisms that can independently grow on a cell -free medium. b. Mycoplasmas are the only prokaryotes that lack a cell wall and contain
sterols in their cytoplasmic membrane. They are surrounded only by a

cytoplasmic membrane and are therefore highly pleomorphic, that is, their shape varies. The sterols in the cytoplasmic membrane may provide added strength. In addition, mycoplasmas are able to maintain a nearly even pressure between the outer environment and the cytoplasm by actively pumping out sodium ions. The most important mycoplasma in terms of human infections is Mycoplasma pneumoniae. This bacterium is a common cause of both upper an d lower respiratory infections, including tracheobronchitis and primary atypical pneumonia.

2. Rickettsias

a. Rickettsias are small and typically 0.3-1.0 m in size. They appear as pleomorphic bacillary or coccobacillary forms.
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b. Most are obligate intracellular parasites . The infectious form or

elementary body utilizes adhesins to adhere to the surface of the host cell. It

then uses invasins to enter the cell. c. With rare exceptions, mammals become infected with rickettsia only through the bites of infected arthropods. d. Their structure and replication are similar to gram -negative bacteria.

3. Chlamydias

a. Chlamydias are coccoid bacteria that are also quite small, typically being 0.2-0. m in size. Chlamydias also lack peptidoglycan in their cell wall. b. They are classified as a type of rickettsia that do not require arthropods for transmission to humans. c. Chlamydias are obligate intracellular parasites of vertebrates.

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