botany

Prokaryote introduction

·      prokaryotes are the smallest, the simplest structurally, and the most abundant worldwide

·      The prokaryotes are, in evolutionary terms, the oldest

·      organisms on Earth.

·      Prokaryotes are the most dominant and successful forms of life on earth

·      They can live in extreme environments

o   Ice, dark depths, boiling waters, oxygen free zones

·      Viruses consist primarily of a genome that replicates itself within a living host cell by directing the genetic machinery of that cell to synthesize viral nucleic acids and proteins

Characteristics of prokaryotic cell

·      a single circular, or continuous, molecule of DNA associated with non-histone proteins is localized in a region of the cell called the nucleoid

·      may also contain one or more smaller extrachromosomal pieces of circular DNA called plasmids that replicate independently of cells chromosome and carry important genetic traits in addition to its chromosome

·      chromosomes are very long

·      occasionally containing inclusions, distinct granules consisting of storage material

·      cyanobacteria and prochlorophytes contain extensive systems of membranes called thylakoids

o   bear chlorophyll and other photosynthetic pigments

What defines outside of prokaryotes

·      plasma membrane is formed from a lipid bilayer

o   similar in composition to eukaryotes

·      respirating prokaryotes (aerobic or anaerobic), plasma membrane incorporates electron transport chain

o   found in mitochondrial inner membrane in eukaryotic cells

·      bacteria contain complex polymers called peptidoglycans which are responsible for the strength of cell walls

·      those whose cells retain the dye are gram positive (pink)

·      those whose cells cannot retain dye are gram negative (purple)

·      Commonly known as a “capsule,” the general term for these layers is glycocalyx.

o   Plays an important role in infection, allowing certain pathogenic bacteria to attach to specific host tissues

o   May also protect bacteria from desiccation

·      Many prokaryotes are motile, and their ability to move independently is usually due to long, slender appendages known as flagella

·      Fimbriae and pili are filamentous structures assembled from protein sub-units in much the same way as the filaments of flagella

o   Pili are generally longer than fimbriae, and only one or a few are present on the surface of an individual cell.

·      nanotubes, these tubules are composed of cell wall material, a plasma membrane, and cytoplasm, and are structurally distinguishable from pili involved in conjugation.

Diversity of Form

·      A prokaryote with a cylindrical shape is called a rod, or bacillus; spherical ones are called cocci ; and long curved, or spiral, rods are called spirilla.

o   Bacilli usually separate after cell division.

·      Nearly all prokaryotes growing on surfaces tend to form biofilms, assemblages of cells attached to the surface and enclosed in a matrix of polysaccharides, proteins, and DNA excreted by the prokaryotic cells

Reproduction and Gene Exchange

·      binary fission, which means “dividing in two”

·      Further adaptability is provided by horizontal, or lateral, gene transfer. Three mechanisms of lateral gene transfer are known for prokaryotes: conjugation, transformation, and transduction.

o   Conjugation has been characterized as the prokaryotic version of sex

o   Transformation occurs when a prokaryote takes up free, or naked, DNA from the environment.

o   Transduction occurs when viruses that attack bacteria—viruses known as bacteriophages—bring with them DNA they have acquired from their previous host.

Endospores

·      endospores, which are dormant resting cells

o   Bacillus and Clostridium

·      Endospore formation greatly increases the capacity of the bacterial cell to survive.

·      exceedingly resistant to heat, radiation, and chemical disinfectants, primarily due to their dehydrated protoplasts.

Metabolic Diversity

·      most prokaryotes are heterotrophs, requiring organic compounds as a carbon source. The vast majority of heterotrophs are saprotrophs (Gk. sap-ros, “rotten,” or “putrid”)

·      Saprotrophic bacteria and fungi are responsible for the decay and recycling of organic material in the soil; indeed, they are the recyclers of the biosphere.

World ecosystem role

·      The role of certain bacteria in fixing atmospheric nitrogen is likewise of major biological significance

·      More than 90 percent of the CO2 production in the biosphere, other than that associated with human activities, results from the metabolic activity of bacteria and fungi.

·      cleaning up dangerous spills and toxic dumps, when the techniques of using these bacteria are better developed.

Diseases

·      Human diseases caused by bacteria include tuberculosis, cholera, anthrax, gonorrhea, whooping cough, bacterial pneumonia, Legionnaires’ disease, typhoid fever, botulism, syphilis, diphtheria, and tetanus.

Anthropogenic Uses

·      Bacteria are also widely used commercially for the production of drugs and other substances, such as vinegar, various amino acids, and enzymes.

o   Efforts are under way to reengineer E. coli and other easily grown microorganisms to produce biofuels essentially similar to existing fossil fuels.

Bacteria/cyanobacteria

·      Photosynthetic cyanobacteria have chlorophyll a, together with carotenoids and other, unusual accessory pigments known as phycobilins.

o    There are two kinds of phycobilins: phycocyanin, a blue pigment, and phycoerythrin, a red one.

·      The main storage product of cyanobacteria is glycogen.

·      not algae.

·      Cyanobacteria often form filaments and may grow in large masses 1 meter or more in length.

o   Some cyanobacteria are uni-cellular, a few form branched filaments, and a very few form plates or irregular colonies

·      cyanobacteria sometimes grow under extremely inhospitable conditions

·      Cyanobacteria are absent in acidic waters, where eukaryotic algae are often abundant.

·      Layered chalk deposits called stromatolites which have a continuous geologic record covering 2.7 billion years, are produced when colonies of cyanobacteria bind calcium-rich sediments

·      Many genera of cyanobacteria can fix nitrogen, converting nitrogen gas to ammonium, a form in which the nitrogen is available for biological reactions.

o    In filamentous cyanobacteria, this nitrogen fixation often occurs within heterocysts, which are specialized, enlarged cells

·      Here, the cyanobacteria, especially members of the genus Anabaena, often occur in association with the small, floating water fern Azolla, which forms masses on the paddies.

Prochlorophytes

·      The prochlorophytes are a group of photosynthetic bacteria that contain chlorophylls a and b, as well as carotenoids, but do not contain phycobilins

·      Prochlorococcus is the smallest known photosynthetic organism (about 0.6 micrometer in diameter), has the smallest genome of any photosynthetic cell, and is thought to be the most numerous photosynthetic organism on Earth.

o   Prochlorococci represents 40 to 50 per-cent of the biomass of the phytoplankton, which produces half the oxygen on Earth, making Prochlorococcus of great ecological importance

Purple and Green Bacteria

·      The purple and green bacteria together represent the second major group of photosynthetic bacteria, after the cyanobacteria.

·      In fact, purple and green bacteria can grow in light only under anaerobic conditions, because pigment synthesis in these organisms is repressed by oxygen

·      By contrast, purple and green bacteria use several different types of bacteriochlorophyll, which differ in certain respects from chlorophyll, and have only one photosystem

·      photosynthetic autotrophs such as plants and algae, as well as the cyanobacteria and pro-chlorophytes, have both photosystems.

·      In the purple sulfur and green sulfur bacteria, sulfur compounds play the same role in photosynthesis that water plays in organisms containing chlorophyll a (page 124).

Mycoplasmas

·      Mycoplasmas are bacteria that lack cell walls.

·      Because they lack a cell wall and consequently lack rigidity, mycoplasmas can assume various forms

·      spiroplasmas, long spiral or corkscrew-shaped cells less than 0.2 micrometer in diameter, which are motile even though they lack flagella

Phytoplasmas

·      Like the mycoplasmas, phytoplasmas lack a cell wall and are very small.

·      In flowering plants, phytoplasmas are generally confined to the conducting elements of the phloem known as sieve tubes.

Archaea

·      archaea are present in less hostile environments such as soil. Archaea also constitute a major component of the oceanic picoplankton, possibly outnumbering all other oceanic organisms.

·       There are no known pathogens in this domain of prokaryotes.

Halophiles

·      The extreme halophilic archaea are a diverse group of prokaryotes that occur everywhere in nature where the salt concentration is very high

·      In addition, certain species of extreme halophiles exhibit a light-mediated synthesis of ATP that does not involve any chlorophyll pigments.

Methanogens

·      The methanogens are a unique group of prokaryotes, the only ones that produce methane gas

·      All methanogens are strictly anaerobic and will not tolerate even the slightest exposure to oxygen. Methanogens can produce methane (CH4) from hydrogen (H2) and carbon dioxide (CO2); the needed electrons are derived from the H2, and CO2 serves as both carbon source and electron acceptor.

·      Methanogens are common in sewage treatment plants, in bogs, and in the ocean depths.

o   most of the natural gas reserves now used as fuel were produced by the activities of methane-producing prokaryotes in the past

Thermophiles

·      The membranes and enzymes of these archaea are unusually stable at high temperatures: all have temperature optima above 80°C, and some grow at temperatures over 110°C.

o   Thermoplasma resembles the mycoplasmas in lacking a cell wall and being very small; individuals vary from spherical (0.3 to 2 micrometers in diameter) to filamentous.

Viruses

·      Outside its host cells, the entire infectious virus particle (genome plus coat)—also called a virion—is metabolically inert.

·      Practically every kind of organism can be infected by distinct viruses, and it is clear that a tremendous diversity of viruses exists.

·      degrees of dwarfing or stunting are symptoms of viruses in plants

·      Mosaics and ring spots are the most common symptoms produced by systemic viruses, which are those viruses that move throughout the plant

·      The transmission, or spread, of viruses from diseased to healthy plants most commonly involves insect vectors, such as aphids, leafhoppers, or whiteflies, with piercing and sucking mouthparts.

·      wounds made mechanically by nematodes or during harvest operations, or by transmission into an ovule via a pollen tube of an infected pollen grain.

·      virion sheds its coat, freeing its nucleic acid. Within the cell, the viral RNA or DNA then multiples by redirecting the cell’s biosynthetic machinery, thus producing the nucleic acids and proteins to assemble additional viral particles synthesizes a complementary (negative) strand of RNA, using the positive strand as a template. New positive RNA strands then are synthesized from the negative-strand template. Replication of the positive strand is generally assumed to involve association with cellular membranes such as the endoplasmic reticulum, outer chloroplast membrane, and tonoplast (the membrane surrounding the vacuole).

·      whereas others move throughout the plant body, resulting in a systemic infection

·      The movement of many viruses throughout the plant can be divided into two phases: (1) cell-to-cell, or short-distance, movement between parenchymatous cells, and (2) long-distance movement in the conducting channels, or sieve tubes, of the phloem tissue

·      Once in the phloem, the viruses move systemically toward growing regions, such as shoot tips and root tips, and regions of storage, such as rhizomes and tubers, where the virus reenters the parenchyma cells adjacent to the phloem.

·      hypersensitive response (HR). Activation of the hypersensitive response is dependent on recognition of the pathogen by a specific, dominant resistance gene (the host gene that determines resistance).

·      Many pathogens can elicit a mechanism known as systemic acquired resistance (SAR), which develops in response to a localized attack by a pathogen. Induction of SAR requires formation of necrotic lesions in the plant, either as part of the hypersensitive response or as a disease symptom.

·      posttranscriptional gene silencing (PTGS). Many viruses induce PTGS upon infection of the host plant. Genes silenced by PTGS continue to be transcribed, but the levels of messenger RNA are low to undetectable, because a sequence-specific mechanism is activated that degrades RNA molecules.

Viroids

·      Viroids are the smallest known agents of infectious disease. They consist of small, circular, single-stranded molecules of RNA and lack capsids of any kind

·      The viroid RNA molecule appears to be replicated in the nucleus of the host cell, where it apparently mimics DNA and allows the host cell RNA polymerase to replicate it.