Prokaryotes

The term prokaryotes applies to two Domains – the Bacteria and Archaea Both have simple cellular structure, Archaea. structure with no membrane bound organelles. Archaeans have more characteristics in common with eukaryotes than with bacteria but like bacteria have a simple cellular structure. Both groups are ecologically important. Some bacteria cause diseases in plants and animals. 1

Prokaryotes were likely the first forms of life on Earth. Fossilized inclusions in rock datingg to 3.8 billion yyears ago g resemble some prokaryotes alive today in bacterial communiiteis called stromatolites.

Living things accumulate carbon isotopes differentially. Analysis of carbon in rock containingg likelyy earlyy cells have life’s carbon fingerprint. 2

Prokaryotes are the most abundant forms of life. life They live in virtually every habitat on Earth and many live deep beneath the Earth’s surface. f Th diversity The di it off prokaryotes is immense and far from fully described. It is likely that less than 10% of bacterial species have been discovered. Archaeans live in some of the most extreme environments on Earth and many are referred to as extremophiles. extremophiles (See Tree of Life lecture.) This may be the product of their evolution in the extreme conditions that were likely common early in Earth’s hi history. 3

Although the Bacteria and Archaea are very different in many ways they share many features • Unicellularity U i ll l i – most exist i are single i l independent i d d cells, ll but b some can form filaments. • Cell size – most are much smaller (< 1 μm) than eukaryotic cells (>10 μm) • Genetic material – most have a single circular DNA molecule located in a region of the cell called the nucleoid. The nucleoid does not have a membrane like a eukaryotic nucleus. • Cell division is by binary fission. This mode of reproduction is asexual but they do have several mechanisms for gene transfer between cells. • Organization – they are not compartmentalized. Enzyme systems are commonlyy associated with the plasma p membrane. • Flagella – are simpler than those of eukaryotes with a single central fiber and move via a rotary motor at their base. • Metabolic diversityy – theyy can do pphotosynthesis y in a diversity y of ways and some can utilize inorganic compounds as a source of 4 energy.

Archaens and Bacteria differ in many ways: • Plasma membranes – Archaeans have membranes composed of lipids that are not found in other organisms Archaeans have ether bonds between glycerol and fatty acids.

Ether bound lipids can be linked together to form a lipid monolayer y with ppolar heads on both ends of the lipid.

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Archaens and Bacteria differ in many ways: • Cell walls – Bacterial have cell walls containing peptidoglycan – carbohydrates arranged in a mesh and linked together by amino i acids. id Archaeans A h can have h cell ll walls ll composedd off a similar compound (pseudomurein) but do not have peptidoglycan. • DNA replication – both have a single origin of replication but the process in Archaeans is more similar to the DNA replication of Eukaryotes. Eukaryotes • Gene expression – Bacteria have a single RNA polymerase used for all transcription. Archaeans have multiple RNA polymerases l that th t are more similar i il to t those th off Eukaryotes. E k t Archaeans have introns within some genes. Bacteria do not have introns. 6

Analysis y of DNA sequences q of a diversityy of prokaryotes p y and eukaryotes suggests that Archaeans share a more recent common ancestor with Eukaryotes than with Bacteria.

In spite of many similarities and both being called prokaryotes, k t Bacteria B t i andd Archaeans A h are nott closely l l related. l t d They diverged very early in the history of life.

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Molecular data have provided an estimate of the evolutionary history and relationships of prokaryotes. prokaryotes Prokaryotes are highly diverse.

The diversity among prokaryotes includes size, shape, ecology, andd bi biochemistry. h it 8

Within all bacterial diversity there are three basic cell shapes

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Bacteria have two different types of cell walls that can be differentiated using the Gram Stain Stain. Gram-positive bacteria have a thick peptidoglycan id l layer l in i their h i cell ll wall ll and stain darkly. Some antibiotics like ppenicillin easily y kill Gram+ cells byy interfering with cell wall formation.

Gram-negative bacterial have a thin peptidoglycan layer covered with a layer of lipopolysaccharides. They do not stain darkly. They are also resistant to the antibiotics that interfere with cell wall formation. 10

Many bacteria have one or more flagella In bacterial flagella there is a flagella. single central protein filament made of a protein called flagellin. Flagella move by spinning which produces a corkscrew like motion in the filament. The spinning p g is ppowered by y a rotaryy motor powered by a proton gradient (similar to ATP synthase).

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IIn Eukaryotes, E k respiration i i depends d d on creating proton gradients across the inner mitochondrial membrane. Photosynthesis in Eukaryotes also depends on creating a proton gradient across the thylakoid membranes of chloroplasts. Prokaryotes P k create proton gradients di on either side of a highly folded plasma membrane. This allows for respiration p and photosynthesis without specialized membrane-enclosed organelles. 12

Sex is the combination of genetic information from two different sources. In Eukaryotes, sex is usually associated with gamete formation and creation of new generations. In Bacteria, sex involves incorporation of new genetic information into a cell. There are at least three different ways this can occur in different bacteria: • Conjugation – many bacteria have an extra small circular DNA molecule called a plasmid that can be transferred between cells • Transduction T d ti – cellular ll l DNA bbecomes associated i d with i h a phage h and gets transferred between cells • Transformation – the uptake of DNA directly from the environment

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Conjugation j g occurs between cells with and cells without an F plasmid. F+ cells contain a plasmid that encodes the genes that promote its transfer between cells. One set of genes encodes proteins that form a pilus, or tube, between F+ cells and F- cells. The completed p tube is called a conjugation bridge.

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F plasmids use a special mode of DNA replication called rolling circle replication to transfer their code to F- cells.

F plasmids are not necessary for cells to live but they often carry genes that provide antibiotic resistance to cells. 15

Plasmids can insert themselves into the cell’s genome as insertion i ti sequences (IS) bby recombination. Recombination involves the same mechanisms that eukaryotes y use for crossing-over and recombination in meiosis. Incorporated plasmids can result in the transfer of l large portions i off the h cell’s ll genome between b cells ll during conjugation by rolling circle replication of the entire genome. g Plasmids can also use recombination for excision. Errors in excision can result in the plasmid containing genes from the cell’s genome. Plasmids containing portions of the cell’s genome can also be transferred by conjugation. conjugation 16

Transduction – the transfer of cellular DNA by viruses In generalized transduction cellular DNA accidentall gets packaged into a viral accidentally iral capside. When the capsid coat attaches to another cell it can then transfer the original cell’s DNA. Specialized transduction occurs with t temperate t phages h (those (th with ith a lysogenic l i life cycle). An error in the excision of a lysogenic phage can result in a piece of the cell’s DNA becoming incorporated into the phage genome and then packaged into a capsid. capsid (See lecture on viruses.) viruses ) 17

Transformation – the uptake of DNA from the environment and incorporation into the cell’s genome.

Conjugation, transduction, and transformation can result in the transfer of antibiotic resistance between bacterial cells of the same species or in some cases between different species. This can result in bacteria having resistance genes to antibiotics to p which theyy have never been exposed. 18

Prokaryotes are metabolically diverse. There are four ways that pprokaryotes y can acquire q energy: gy 1. Photoautotrophs capture energy from sunlight – photosynthesis. Cyanobacteria capture light energy with chlorophyll a and use H20 as a source of electrons and produce O2 as a byproduct byproduct. Purple and green sulfur bacteria capture light energy using bacteriochlorophyll and use H2S as a source of electrons and l leave S as a byproduct. b d Some Archaeans are also photosynthetic and use p or pproteorhodopsin p to capture p light g energy. gy bacteriorhodopsin The energy is used to create a proton gradient to be used for ATP formation. 2 Chemolithotrophs obtain energy by oxidizing inorganic 2. compounds. Nitrifiers oxidize ammonia or nitrite. Others oxidize other substances such as sulfur or hydrogen. Deep sea ocean vent communities iti depend d d on bacteria b t i that th t capture t energy from f sulfur lf as it escapes from deep in the Earth through the vents. 19

3. Photoheterotrophs are the purple and green nonsulfur bacteria. These capture energy from sunlight but instead of trapping CO2 as a source of carbon they use carbohydrates or alcohols produced by other organisms as a carbon source. 4. Chemoheterotrophs are the most common bacteria. They obtain energy by using compounds produced by other organisms. They can be decomposers of organic material. Theyy can also be ppathogens g and feed directly y on other livingg things.

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Bacteria are pathogens of plants and animals. The development of antibiotics and immunization has helped to decrease the damage causedd bby bbacteria. i Before f antibiotics ibi i andd immunization, i i i one in i five children in the United States died of a bacterial disease before the age g of five. Bacterial diseases of children and adults include cholera, leprosy, tetanus, pneumonia, whooping cough, diphtheria, and tuberculosis. Bacteria cause tooth decay by producing acids that erode tooth enamel. Sugars are easily metabolized by such bacteria and are y thus associated with tooth decay. Bacteria are one cause of ulcers. They cause lesions and bleeding of the lining of the stomach. Many STDs are caused by bacteria. Syphilis, chlamydia, and gonorrhea are spread by sexual contact and cause many secondary h lth problems health bl suchh as nerve damage d andd heart h t disease. di 21

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Some prokaryotes are ecologically important and beneficial •Decomposition Decomposition returns the chemicals trapped in one living organisms to the ecosystem •Fixation captures important chemicals and incorporates them into i important t t biological bi l i l molecules. l l Carbon is fixed by photosynthetic prokaryotes Nitrogen as N2 gas is abundant but is not useful to living things. N2 can be captured by bacteria as ammonia (NH3). Ammonia can be used to make amino acids and nitrogenous bases. Conversion of ammonia to nitrates makes nitrogen available to plants. •Bacteria have beneficial symbiotic relationships with many other organisms. organisms Nitrogen fixers live in association with the roots of some plants and make N available to those plants. Bacteria live within the guts of most animals and help with digestion and provide some essential vitamins to their hosts.23

Bacteria have become increasing important economically • Genetically engineered bacteria are being used to produce many beneficial products such as hormones, enzymes, vitamins, antibiotics, and other pharmaceutical products. • Bacteria are bioremediators. They naturally degrade many chemicals h i l that th t eukaryotes k t can’t ’t andd many are now being b i usedd to clean up human sewage, the waste of other organisms, and toxic chemicals produced by industries.

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