Eubacteria characteristics

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Geometry and mechanics dictate that the first structures we encounter in any cell -- and most multicellular organisms, for that matter -- are structures dealing with movement, sensation, and interaction with the world outside.  In our model eubacterium, these include a flagellum and a system of pili.
Geometry and mechanics dictate that the first structures we encounter in any cell -- and most multicellular organisms, for that matter -- are structures dealing with movement, sensation, and interaction with the world outside.  In our model eubacterium, these include a flagellum and a system of pili.
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The bacterial flagellum looks a bit like the eukaryotic organelle of the same name, but it is an entirely different structure.  The "tail" portion has no microtubules and consists more or less of an extended filament of a single protein, flagellin.  The tail is anchored on what amounts to a rotor.  The rotor extends through the outer layers of the cell into the cytoplasm.  The system actually works something like a  propeller, with the rotor forcing the flagellum to turn in a spiral.  The motive force is supplied by sodium or hydrogen ions flowing down a concentration gradient from the outside.   
The bacterial flagellum looks a bit like the eukaryotic organelle of the same name, but it is an entirely different structure.  The "tail" portion has no microtubules and consists more or less of an extended filament of a single protein, flagellin.  The tail is anchored on what amounts to a rotor.  The rotor extends through the outer layers of the cell into the cytoplasm.  The system actually works something like a  propeller, with the rotor forcing the flagellum to turn in a spiral.  The motive force is supplied by sodium or hydrogen ions flowing down a concentration gradient from the outside.   
This ion gradient system is the same basic mechanism which is used in a number of other well-known systems, for example in some of the "light reactions" of photosynthesis.  It is worth knowing reasonably well.  The usual currency of energy in the cell is adenosine triphosphate (ATP).  When the cell has ATP to spare, it uses ATP to pump certain ions (here, sodium) out of the cell.  Since the sodium concentration is higher outside the cell, the pumps have to pump against the gradient using the energy of ATP.  This makes the entire cell a sort of storage battery.  To use that stored energy, the cell merely allows some of that sodium to flow back in by means of specialized sodium channels.  These channels span the cell membrane and cell wall.  When the sodium channel proteins are activated by signals inside the cell and come in contact with a sodium ion outside the cell, they change shape, allowing the ion into the cell and, at the same time, performing some useful work, such as turning the "rotor" of a flagellum [[#Footnotes|[3]]].  The key concept is that the ion channel system takes small bits of energy (ATP molecules) which are all the same and are dispersed throughout the cell, and ultimately concentrates the energy for use at a time and place controlled by specific "signal" molecules that open specific ion channels linked to specific mechanical tasks -- a very elegant system!
This ion gradient system is the same basic mechanism which is used in a number of other well-known systems, for example in some of the "light reactions" of photosynthesis.  It is worth knowing reasonably well.  The usual currency of energy in the cell is adenosine triphosphate (ATP).  When the cell has ATP to spare, it uses ATP to pump certain ions (here, sodium) out of the cell.  Since the sodium concentration is higher outside the cell, the pumps have to pump against the gradient using the energy of ATP.  This makes the entire cell a sort of storage battery.  To use that stored energy, the cell merely allows some of that sodium to flow back in by means of specialized sodium channels.  These channels span the cell membrane and cell wall.  When the sodium channel proteins are activated by signals inside the cell and come in contact with a sodium ion outside the cell, they change shape, allowing the ion into the cell and, at the same time, performing some useful work, such as turning the "rotor" of a flagellum [[#Footnotes|[3]]].  The key concept is that the ion channel system takes small bits of energy (ATP molecules) which are all the same and are dispersed throughout the cell, and ultimately concentrates the energy for use at a time and place controlled by specific "signal" molecules that open specific ion channels linked to specific mechanical tasks -- a very elegant system!
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E. coli attached to phage by pilusThe bacterial pili are the bug's equivalent of hands, both as tactile, sensory structures and as tools for grabbing onto and manipulating things at a distance.  Our diagram is a bit misleading, since the pili can be quite long.  See image (~20,000X) at right from Le revêtement cellulaire des cellules procaryotes.  As this image shows, the pilus can serve as a guide for the formation of a cytoplasmic bridge, as for the exchange of DNA.  This is a rare, but important event with profound implications for bacterial evolution.  Bacteria are not terribly fastidious about who they exchange DNA with.  Thus genes can be acquired from unrelated bacteria, and even from non-bacteria.  For example, DNA is being exchanged between Escherrichia and a virus in the image. For this reason, "lateral inheritance" of genes from unrelated organisms is quite frequently observed in bacteria.  
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The bacterial pili are the bug's equivalent of hands, both as tactile, sensory structures and as tools for grabbing onto and manipulating things at a distance.  Our diagram is a bit misleading, since the pili can be quite long.  See image (~20,000X) at right from Le revêtement cellulaire des cellules procaryotes.  As this image shows, the pilus can serve as a guide for the formation of a cytoplasmic bridge, as for the exchange of DNA.  This is a rare, but important event with profound implications for bacterial evolution.  Bacteria are not terribly fastidious about who they exchange DNA with.  Thus genes can be acquired from unrelated bacteria, and even from non-bacteria.  For example, DNA is being exchanged between Escherrichia and a virus in the image. For this reason, "lateral inheritance" of genes from unrelated organisms is quite frequently observed in bacteria.  
Pili perform a great many functions, and consequently are structurally quite diverse.  Typically the backbone of the pilus is made up of a long chain protein or polysaccharide (sugar chain) with some type of functionally specific arrangement at the tip.  One function of considerable clinical interest is cell - to - cell recognition.  The complex array of carbohydrates in and on the pili are the method by which bacteria recognize other cells, and are recognized by them.  So, for example, one strain of a germ may be harmless to us while another, differing only in a few sites, may be a deadly pathogen if it recognizes our cells as food, or has surface features which our cells do not recognize as dangerous.  Shorter pili, usually referred to as fimbriae, are a structurally distinct group of extrusions which operate mostly in bacterial attachment to substrate or to other cells.
Pili perform a great many functions, and consequently are structurally quite diverse.  Typically the backbone of the pilus is made up of a long chain protein or polysaccharide (sugar chain) with some type of functionally specific arrangement at the tip.  One function of considerable clinical interest is cell - to - cell recognition.  The complex array of carbohydrates in and on the pili are the method by which bacteria recognize other cells, and are recognized by them.  So, for example, one strain of a germ may be harmless to us while another, differing only in a few sites, may be a deadly pathogen if it recognizes our cells as food, or has surface features which our cells do not recognize as dangerous.  Shorter pili, usually referred to as fimbriae, are a structurally distinct group of extrusions which operate mostly in bacterial attachment to substrate or to other cells.
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Within the capsule is the relatively rigid cell wall [[#Footnotes|[4]]].  The fundamental scaffolding of the cell wall is peptidoglycan.  See, generally, The Cell Wall.  Peptidoglycan is an absolutely bizarre material.  As this is not a biochemical essay, we will have to skip over much of the good stuff.   
Within the capsule is the relatively rigid cell wall [[#Footnotes|[4]]].  The fundamental scaffolding of the cell wall is peptidoglycan.  See, generally, The Cell Wall.  Peptidoglycan is an absolutely bizarre material.  As this is not a biochemical essay, we will have to skip over much of the good stuff.   
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The first element of peptidoglycan is a chain of repeating sugar molecules (a slightly modified glucose, N-acetylglucosamine).  This part of the structure is precisely the same as chitin, the material which makes up the exoskeleton of insects and, in more or less modified form, in almost all arthropods.  Significantly, it is also found in the radular "teeth" of molluscs, the setae (bristles) and jaws of annelid worms, and the cell walls of [[Fungi]].  So, this is exceedingly ancient stuff, possibly predating the split between bacteria and metazoans.   
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The first element of peptidoglycan is a chain of repeating sugar molecules (a slightly modified glucose, N-acetylglucosamine).  This part of the structure is precisely the same as [[chitin]], the material which makes up the exoskeleton of insects and, in more or less modified form, in almost all arthropods.  Significantly, it is also found in the radular "teeth" of molluscs, the setae (bristles) and jaws of annelid worms, and the cell walls of [[Fungi]].  So, this is exceedingly ancient stuff, possibly predating the split between bacteria and metazoans.   
However, in the Eubacteria, every second sugar residue is linked at the 3-position with an amino acid, threonine, which in turn leads on to a strange and unique chain of amino acids (i.e., a peptide chain).  The ordinary amino acids which make up all proteins are asymmetrical.  That is, they can occur in left-handed (L) or right -handed (D) forms (racemers).  All higher organisms use only the L-racemers.  In fact, even bacteria use only L racemers for ordinary proteins.  But they also use certain D-racemers in peptidoglycan.  Does this suggest that the bacterial cell wall is older than the standard machinery of protein synthesis and harks back to a time when life wasn't so picky about which racemers it used?  It could mean this.  Certainly some scientists have thought so.  But, since there are no similar structures in the Archaea or the Eukaryota, the more likely explanation is that this is a specialized feature of Eubacteria.  
However, in the Eubacteria, every second sugar residue is linked at the 3-position with an amino acid, threonine, which in turn leads on to a strange and unique chain of amino acids (i.e., a peptide chain).  The ordinary amino acids which make up all proteins are asymmetrical.  That is, they can occur in left-handed (L) or right -handed (D) forms (racemers).  All higher organisms use only the L-racemers.  In fact, even bacteria use only L racemers for ordinary proteins.  But they also use certain D-racemers in peptidoglycan.  Does this suggest that the bacterial cell wall is older than the standard machinery of protein synthesis and harks back to a time when life wasn't so picky about which racemers it used?  It could mean this.  Certainly some scientists have thought so.  But, since there are no similar structures in the Archaea or the Eukaryota, the more likely explanation is that this is a specialized feature of Eubacteria.  
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The bacterial plasma membrane is a bit simpler than the plasma membrane of most eukaryotes.  Eukaryotic cells have, in addition to phospholipids, cholesterol and other big, flat, mostly non-polar molecules which tend to stabilize the membrane and make it stiffer.  Bacteria don't have cholesterol. Eukaryotes also frequently have a good many elaborate lipoproteins (proteins with fats attached) and glycoproteins (proteins with sugars attached).  These derivitized proteins do many of the same jobs which are performed by the cell wall and capsule in bacteria.  Eukaryotes also have an extensive internal membrane system including the Golgi apparatus, endoplasmic reticula, vesicles, mitochondria, and a nuclear membrane.  The Eubacteria have none of these.  Some bacteria have small folds in the plasma membrane, in which some specialized functions may occur -- notably the ATP-driven [[active transport]] of ions discussed above, as well as photosynthesis in the blue-green algae.  However, there are no cytoplasmic membranes.     
The bacterial plasma membrane is a bit simpler than the plasma membrane of most eukaryotes.  Eukaryotic cells have, in addition to phospholipids, cholesterol and other big, flat, mostly non-polar molecules which tend to stabilize the membrane and make it stiffer.  Bacteria don't have cholesterol. Eukaryotes also frequently have a good many elaborate lipoproteins (proteins with fats attached) and glycoproteins (proteins with sugars attached).  These derivitized proteins do many of the same jobs which are performed by the cell wall and capsule in bacteria.  Eukaryotes also have an extensive internal membrane system including the Golgi apparatus, endoplasmic reticula, vesicles, mitochondria, and a nuclear membrane.  The Eubacteria have none of these.  Some bacteria have small folds in the plasma membrane, in which some specialized functions may occur -- notably the ATP-driven [[active transport]] of ions discussed above, as well as photosynthesis in the blue-green algae.  However, there are no cytoplasmic membranes.     
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The cytoplasm itself is thus a rather uniform solution without a lot of structure.  It does contain cytoplasmic inclusions of various kinds for storage of various critical metabolites.  These include metachromatic granules of phosphate, glycogen (a polymer of glucose), grains of starch and salts, and poly(3-hydroxyalkanoate), the bacterial equivalent of fat.   
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The cytoplasm itself is thus a rather uniform solution without a lot of structure.  It does contain cytoplasmic inclusions of various kinds for storage of various critical metabolites.  These include metachromatic granules of phosphate, glycogen (a polymer of glucose), grains of [[starch]] and salts, and poly(3-hydroxyalkanoate), the bacterial equivalent of fat.   
In addition, the cytoplasm may contain plasmids.  These are small, circular pieces of DNA derived from bacterial viruses (bacteriophages), other bacteria, or perhaps even other organisms.  The genes carried on the plasmid may simply be dead weight, which continues to reproduce with the bacterium only because it happens to contain a working site for DNA polymerase.  Thus, when this enzyme is active in the cell preparing the bacterial DNA for cell division, it tends to make a copy of the plasmid as well, even though the plasmid serves no biological function.  On the other hand, plasmids can be of great practical importance, to humans as well as the bacterial host.  Antibiotic-resistant disease bacteria often carry the extra genes which confer resistance on plasmids acquired from some completely different species. Plasmids may also contain other virulence factors, genes which code for proteins which can turn a harmless symbiotic species into a lethal disease vector.   
In addition, the cytoplasm may contain plasmids.  These are small, circular pieces of DNA derived from bacterial viruses (bacteriophages), other bacteria, or perhaps even other organisms.  The genes carried on the plasmid may simply be dead weight, which continues to reproduce with the bacterium only because it happens to contain a working site for DNA polymerase.  Thus, when this enzyme is active in the cell preparing the bacterial DNA for cell division, it tends to make a copy of the plasmid as well, even though the plasmid serves no biological function.  On the other hand, plasmids can be of great practical importance, to humans as well as the bacterial host.  Antibiotic-resistant disease bacteria often carry the extra genes which confer resistance on plasmids acquired from some completely different species. Plasmids may also contain other virulence factors, genes which code for proteins which can turn a harmless symbiotic species into a lethal disease vector.   
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This more or less concludes our whirlwind tour of cell biology and the bacterial cell.  It is conventional to have lots of pictures and diagrams of transcription and translation.  We have deliberately chosen to depart from this tradition in the interests of getting these painful necessities over quickly and without visual distraction.  For good or evil, we will have plenty of opportunities for graphics later.
This more or less concludes our whirlwind tour of cell biology and the bacterial cell.  It is conventional to have lots of pictures and diagrams of transcription and translation.  We have deliberately chosen to depart from this tradition in the interests of getting these painful necessities over quickly and without visual distraction.  For good or evil, we will have plenty of opportunities for graphics later.
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== Characteristics ==
== Characteristics ==

Latest revision as of 23:41, 23 March 2010

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