Microbiological Notes and Research: 5 kingdom classification along information of prokaryotic and eukaryotic call

Introduction to Prokaryotes, Eukaryotes

Microorganisms and all other living organisms are classified as prokaryotes or eukaryotes. Prokaryotes and eukaryotes are distinguished on the basis of their cellular characteristics. For example, prokaryotic cells lack a nucleus and other memorane-bound structures known as organelles, while eukaryotic cells have both a nucleus and organelles (Figure 1 ).

Figure 1

The important cellular features of (a) a prokaryotic cell (a bacterium) and (b) a eukaryotic cell.

Eukaryotic Cells

Eukaryotic cells are generally larger and more complex than prokaryotic cells. They also contain a variety of cellular bodies called organelles. The organelles function in the activities of the cell and are compartments for localizing metabolic function. Microscopic protozoa, unicellular algae, and fungi have eukaryotic cells.

Nucleus. Eukaryotic cells have a distinctive nucleus, composed primarily of protein and deoxyribonucleic acid, or DNA. The DNA is organized into linear units called chromosomes, also known as chromatin when the linear units are not obvious. Functional segments of the chromosomes are referred to as genes.
The nuclear proteins belong to a class of proteins called histones. Histones provide a supportive framework for the DNA in chromosomes. The DNA replicates in eukaryotic cells during the process of mitosis.
The nucleus of eukaryotic cells is surrounded by an outer membrane called the nuclear envelope, which is a double-membrane structure consisting of two lipid layers similar to the cell membrane. Pores exist in the nuclear membrane, and the internal nuclear environment can therefore communicate with the cytoplasm of the cell.
Within the nucleus are two or more dense masses referred to as nucleoli (singular, nucleolus). The nucleolus is an RNA-rich area where ribosomes are assembled before passing out of the nucleus into the cytoplasm.
Cellular organelles. Within the cytoplasm (also known as the cytosol) of eukaryotic cells are a number of microscopic bodies called organelles (“little organs”). Various functions of the cell go on within these organelles.
An example of an organelle is the endoplasmic reticulum (ER), a series of membranes that extend throughout the cytoplasm of eukaryotic cells. In some places the ER is studded with submicroscopic bodies called ribosomes. This type of ER is referred to as rough ER. In other places there are no ribosomes, and the ER is called smooth ER. The endoplasmic reticulum is the site of protein synthesis in the cell. Eukaryotic ribosomes are 80S bodies where the amino acids are bound together to form proteins. The spaces within the ER membranes are known as cisternae.
Another organelle is the Golgi body (also called the Golgi apparatus). The Golgi body is a series of flattened sacs, usually curled at the edges. The outermost sac often bulges away to form droplike vesicles known as secretory vesicles. It is in the Golgi body that the cell's proteins and lipids are processed and packaged before being sent to their final destination.
Another organelle, the lysosome, is derived from the Golgi body. It is a somewhat circular, droplike sac of enzymes within the cytoplasm. These enzymes are used for digestion in the cell. They break down the particles of food taken into the cell and make the products available to the cell. Enzymes are also contained in a cytoplasmic body called the peroxisome.
The organelle where much energy is released in the eukaryotic cell is the mitochondrion (plural, mitochondria). The energy released is used to form adenosine triphosphate (ATP). Because they are involved in energy release and storage, the mitochondria are called the “powerhouses of the cells.”
An organelle found in certain protozoa is a large, fluid-filled, contractile vacuole. The vacuole may occupy over 75 percent of the cell interior and is used for eliminating water. Water pressure building up within the vacuole may cause the cell to swell.
Still another organelle within the cell is the cytoskeleton, an interconnected system of fibers, threads, and interwoven molecules that give structure to the cell. The main components of the cytoskeleton are microtubules, microfilaments, and intermediate filaments. All are assembled from subunits of protein.
Many eukaryotic cells contain flagella and cilia. Eukaryotic flagella, like prokaryotic flagella, are long, hairlike organelles that extend from the cell. Eukaryotic flagella whip about and propel the cell (as in protozoa) and are composed of nine pairs of microfilaments arranged about a central pair. Cilia are shorter and more numerous than flagella. In moving cells, they wave in synchrony and move the cell. Paramecium is a well-known ciliated protozoan.
The cell wall. Many species of eukaryotes, such as fungi, contain a cell wall outside the cell membrane. In fungi, the cell wall contains a complex polysaccharide called chitin as well as some cellulose. Algal cells, by contrast, have no chitin; rather, their cell walls are composed exclusively of the polysaccharide cellulose.
Cell walls provide support for eukaryotic cells and help the cells resist mechanical pressures while giving them a boxlike appearance. The cell walls are not selective devices, as are the cell membranes.
The cell membrane. The eukaryotic cell membrane conforms to the fluid mosaic model found in the prokaryotic membrane. In eukaryotes, the membrane is a dynamic structure governing passage of dissolved molecules and particles into and out from the cytoplasm. However, it neither contains the enzymes found in the prokaryotic cell nor functions in DNA replication.
In order for the cytoplasm of prokaryotic and eukaryotic cells to communicate with the external environment, materials must be able to move through the cell membrane. There are several mechanisms by which movement can occur. One method, called diffusion, is the movement of molecules from a region of high concentration to one of low concentration. This movement occurs because the molecules are constantly colliding with one another, and the net movement of the molecules is away from the region of high concentration. Diffusion is a random movement of molecules, and the pathway the molecules take is called the concentration gradient. Molecules are said to move down the concentration gradient in diffusion.
Another method of movement across the membrane is osmosis, the movement of water from a region of high concentration to one of low concentration. Osmosis occurs across a membrane that is semipermeable, meaning that the membrane lets only certain molecules pass through while keeping other molecules out. Osmosis is a type of diffusion involving only water.
A third mechanism for movement across the membrane is facilitated diffusion, a type of diffusion assisted by certain proteins in the membrane. The proteins permit only certain molecules to pass across the membrane and encourage movement from a region of high concentration of molecules to one of low concentration.
A fourth method for passing across the membrane is active transport. When active transport is taking place, a protein moves a certain material across the membrane from a region of low concentration to one of high concentration. Because this movement is happening against the concentration gradient, it requires that energy be expended, energy usually derived from ATP.
The final mechanism for movement across the cell membrane is endocytosis, a process in which a small patch of cell membrane encloses particles or tiny volumes of fluid at or near the cell surface. The membrane enclosure then sinks into the cytoplasm and pinches off from the membrane. When the vesicle contains particulate matter, the process is called phagocytosis; when it contains droplets of fluid, the process is called pinocytosis.

Prokaryotic Cells

The characteristics of prokaryotic cells apply to the bacteria and cyanobacteria (formerly known as blue-green algae), as well as to the rickettsiae, chlamydiae, and mycoplasmas.

Size and shape. Prokaryotes are probably the smallest living organisms, ranging in size from 0.15 μm (mycoplasmas) to 0.25 μm (chlamydiae) to 0.45 μm (rickettsiae) to about 2.0 μm (many of the bacteria). Certain prokaryotes, such as bacteria, occur in spherical forms called cocci (singular, coccus) or in rodlike forms called bacilli (singular, bacillus). Some bacteria have a comma shape ( vibrio), or a flexible, wavy shape ( spirochete), or a corkscrew shape ( spirillum).
Some prokaryotes have a variety of shapes and sizes and are said to be pleomorphic. Rickettsiae and mycoplasmas are examples of pleomorphic microorganisms.
When certain prokaryotes divide, they cling to each other in a distinct arrangement. A diplococcus, for example, consists of a pair of cocci, while a streptococcus consists of a chain of cocci, and a tetracoccus consists of four cocci arranged in a cube. A grapelike cluster of cocci is called a staphylococcus. Bacilli sometimes form long chains called streptobacilli.
The cell wall and cell membrane. With the exception of mycoplasmas, all bacteria have a semirigid cell wall. The cell wall gives shape to the organisms and prevents them from bursting, especially since materials in the cytoplasm exert osmotic pressures.
The chief component of the prokaryotic cell wall is peptidoglycan, a large polymer composed of N-acetylglucosamine and N-acetylmuramic acid. Gram-positive bacteria have more peptidoglycan in their cell wall, which may account for their ability to retain the stain in the Gram stain procedure. Gram-negative bacteria have more lipids in their cell wall. Polymers of teichoic acid are commonly associated with the peptidoglycan in Gram-positive bacteria.
In addition to the cell wall, Gram-negative bacteria have a very thin surrounding layer called the outer membrane. Lipopolysaccharides known as endotoxins are part of this outer membrane. A space called the periplasmic space separates the cell wall from the outer membrane and contains a substance called periplasm.
All prokaryotes have cytoplasm surrounded by a cell membrane, also known as the plasma membrane. The cell membrane conforms to the fluid mosaic model, which means that its proteins float within a double layer of phospholipids. Respiratory enzymes are located at the cell membrane of prokaryotes, and the membrane assists DNA replication and has attachment points for bacterial flagella.
The cytoplasm. The cytoplasm of prokaryotic cells contains ribosomes and various other granules used by the organism. The DNA is contained in the nuclear region (the nucleoid) and has no histone protein to support it. Prokaryotic cells have in their cytoplasm a single, looped chromosome, as well as numerous small loops of DNA called plasmids. Genetic information in the plasmids is apparently not essential for the continued survival of the organism.
Prokaryotic ribosomes contain protein and ribonucleic acid (RNA) and are the locations where protein is synthesized. Prokaryotic ribosomes have a sedimentation rate of 70S, and are therefore known as 70S ribosomes. (Eukaryotic cells have 80S ribosomes.) Certain antibiotics bind to these ribosomes and inhibit protein synthesis.
Some prokaryotic cells that engage in photosynthesis have internal membranes called thylakoids where their chlorophyll pigments are located. These membranes are also the sites of enzymes for photosynthesis. Certain bacteria have granules of phosphorus, starch, or glycogen. Granules called metachromatic granules stain with methylene blue and are used in diagnostic circumstances. Some bacterial species also have magnetosomes, which contain magnetic substances to help orient the organisms to hospitable environments.
External cellular structures. Many prokaryotic cells have at their surface a number of external structures that assist their functions. Among these structures are flagella. Flagella are found primarily in bacterial rods and are used for motility. A bacterium may have a single flagellum (a monotrichous bacterium), or flagella at both ends of the cell (an amphitrichous bacterium), or two or more flagella at one end of the cell (a lophotrichous bacterium), or it may be surrounded by flagella (a peritrichous bacterium).
Flagella are long, ultrathin structures, many times the length of the cell. They are composed of the protein flagellin arranged in long fibers. A hooklike structure and basal body connect the flagellum to the cell membrane. Flagella rotate and propel the bacteria.
Spirochetes lack flagella, but they possess axial filaments. The axial filaments extend beyond the cell wall and cause the spirochete to rotate in a corkscrew fashion and thereby move.
Some bacterial species have projections called pili (singular, pilus). Pili are used for attachments to surfaces such as tissues. Many pathogens possess pili, which are composed of the protein pilin. Certain pili, known as conjugation pili, unite prokaryotic cells to one another and permit the passage of DNA between the cells. The term fimbriae is often used for the attachment pili.
Many bacteria, especially pathogens, are enclosed at their surface by a layer of polysaccharides and proteins called the glycocalyx. The glycocalyx, composed of a thick, gummy material, serves as a reservoir for nutrients and protects the organism from changes in the environment. When the glycocalyx is a tightly bound structure, it is known as a capsule. When it is a poorly bound structure that flows easily, it is known as a slime layer. The material in dental plaque is composed largely of the material from the slime layer.
Endospores. Bacteria of the genera Bacillus and Clostridium are able to form highly resistant internal structures called endospores, or simply spores. Spores are formed during the normal life cycle when the environment becomes too harsh (Figure 1 ).

Figure 1

The process of spore formation as it occurs in species of Bacillus and Clostridium.

One vegetative (multiplying) cell produces one spore. Spores are able to withstand extremely high temperatures, long periods of drying, and other harsh environments. When conditions are favorable, the spore germinates and releases a new vegetative cell, which multiplies and reforms the colony. Sporeformers include the agents of anthrax, tetanus, botulism, and gas gangrene. Spores contain dipicolinic acid and calcium ions, both of which contribute to their resistance.

Taxonomy

The Science of Classification
Download Student guided note pages (word document)

Classification: The process of putting similar things into groups.

Taxonomy: Is the science of classifying organisms.

History of Classification

384-322 B.C.
- Aristotle (Greek Philosopher)
- Created first written classification scheme
1500's - 1700's
- Many different classification systems created
  - Many of them really complicated
  - Names based on common names - This created confusion
  - Names also based on long scientific definitions
1700's - Carols Linnaeus - Swedish Biologist
- established a simple system for classifying and naming organisms

Based on structural similarities of organism
Binomial Nomenclature - 2 name naming system - still in use today.
Created a system of groups called TAXA or TAXON
Each Taxon is a category into which related organisms are placed
- Approximantly 2.5 million kinds of organisms identified

Modern Day Levels of Classification

Kids

Playing

Catch

Freeway

Get

Squashed

Kingdom

Phylum

Class

Order

Family

Genus

Species

	Man	Box Elder Tree	Bobcat	Canadian lynx
Kingdom	Animalia	Plantea	Animalia	Animalia
Phylum/Division	Chordata	Anthophyta	Chordata	Chordata
Class	Mammalian	Dicotyledonae	Mammalia	Mammalia
Order	Primates	Sapindales	Carnivora	Carnivora
Family	Hominidae	Aceracae	Felidae	Felidae
Genus	Homo	Acer	Lynx	Lynx
Species	sapiens	nugundo	rufus	canadensis

Modern Taxonomy
The Evidence used to classify into taxon groups
	1) Embryology
	2) Chromosomes / DNA
	3) Biochemistry
	4) Physiology
	5) Evolution
	6) Behavior

Binomial Nomenclature

Is a system of Scientific Naming using TWO NAMES FOR EVERY ORGANISM:
The GENUS and the SPECIES name.

The system follows certain rules:

The scientific name must be in Greek or Latin language.
This helps to accurate communicate information to other biologist around the world who use many different languages. This is done by assigning a unique two-word scientific name to each organism. (BINOMIAL NOMENCLATURE)
The first part of the name is called the Genus and the second part of the name is called the species.
The Genus name refers to the relatively small group of organisms to which a particular type of organism belongs.
The SECOND part of the name is the SPECIES.
(SPECIES means IDENTIFIER) The Species name is usually a Latin description of some important characteristic of the organism.

IDENTIFYING ORGANISMS BY THEIR GENUS AND SPECIES NAMES IS CALLED
THE BINOMIAL SYSTEM, OR BINOMIAL NOMENCLATURE. ("TWO-NAME NAMING)

Advantages of using a universal taxonomic system:

Organization
Common Language
Economics

Inferring Phylogeny

Study of evolutionary relationships

Phylogenic tree (Family Tree)

Biosystematics

Study of the evolution of one species into two reproductive compatibility

gene flow

Five-Kingdom System
Evolved from Aristotle's 2 Kingdoms
to the Present day 5 Kingdoms

Kingdom Monera Bacteria Monera

Characteristics of the Monera Kingdom:

Prokaryotes
Heterotrophic and autotrophic
(Heterotrophic - Organism that can't synthesize (make) it's own food)
(Autotrophic - Organism that CAN make it's own foon - photosynthesis)
Anaerobic and aerobic
aquatic, terrestrial and in the air
mostly asexual
mostly non motile (1 form does move)

Things like: bacteria - both eubacteria (True bacteria) and archebacteria (ancient bacteria)