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Bacteria

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Bacteria

-          Very adaptable both in natural selection and adaptation to changes in the environment.

-          Made of one double-stranded DNA molecule arranged in a circle.

-          The bacterial chromosome (not to be confused with a eukaryotic chromosome) is so tightly packed that it does not even fill the whole cell but forms a structure something like a loop of yarn tangled into a ball.  This dense region is called the nucleoid and is not bounded by a membrane.

-          Some bacteria also have Plasmids that have a small number of genes in them.

-          Bacterial cells divide by binary fission, which is preceded by replication of the bacterial chromosome.

-          From a single point of replication, the copying of DNA progresses in both directions around the circular chromosome.

-          Bacteria may proliferate very rapidly in a favorable environment.

-          Since fission is asexual, most of the bacteria are genetically identical to the parent cell.

-          As a result of mutation, some of the offspring do differ slightly in makeup.

-          Some new mutations can have a significant impact on genetic diversity when reproduction rates are high and this diversity affects the evolution of the populations.

 Genetic Recombination

             -          Genetic recombination generates diversity within bacterial populations.

-          Recombination means combining genetic material from two individuals into the genome of one individual.

-          Genetic recombination in bacteria is different from recombination in eukaryotes.

-          The mechanisms for genetic recombination in bacteria are transformation, transduction, and conjugation.

Transformation

-          The alteration of a bacterial cellís genotype by the uptake of naked, foreign DNA from the environment.

-          The bacteria takes in this DNA and then incorporates it into its genome.  The process is like crossing over in eukaryotes.

-          The transformed cell now has a chromosome containing DNA derived from two different cells.

-          Scientists have learned that many bacterial species possess proteins on their surfaces that are specialized for the uptake of DNA from the surroundings.

-          These proteins specifically recognize and transport only DNA from closely related species of bacteria.  E.coli does not seem to have this ability.

 Transduction

-          Viruses that infect bacteria called phages transfer bacterial genes from one host cell to another. 

-          Generalized transduction takes place during the lytic cycle.  When the phage DNA is introduced, the host DNA is hydrolyzed and breaks apart.  Then when the DNA is packaged for the new phages, sometimes the hostís DNA is packaged as well.  When the released phages then attach to another bacterial cell, the hostís DNA is released into the new host and incorporated and replaces the hostís homologous region of DNA.  The cellís chromosome now has a combination of genetic material derived from two cells.

-          Specialized transduction requires infection by a temperate phage from the lysogenic cycle.  When the prophage is integrated into the bacteriumís chromosomes at a specific site and then later excised, it takes with it small regions of the bacterial DNA that were adjacent to the prophage.  A virus carrying the bacterial DNA infects another cell and passes on the original hostís DNA.  This is specific because the temperate phageís DNA is incorporated into a specific site and the genes surrounding it are then excised with the prophage.

 Conjugation

-          The direct transfer of genetic material between two bacterial cells that are temporarily joined.

-          This is referred to as the bacterial version of sex.

-          The DNA donor is referred to as the male and it uses an appendage called a sex pilli to attach to the DNA recipient (female). 

-          A cytoplasmic bridge is formed between the two cells. 

-          Maleness is the ability to form the sex pilli and donate DNA during conjugation.  It requires the presence of a specialized plasmid called an F plasmid.

 Plasmids

-          A small circular DNA molecule separate from the bacterial chromosome. 

-          Replicate independently but do so in synchrony with the chromosomes.

-          Certain Plasmids can undergo reversible incorporation into the cellís chromosome, therefore, it can replicate as an extrachromosomal molecule or as a part of the main bacterial chromosome called an episome.

-          They lack and extracellular stage and are beneficial to the bacterial cell.

-          Each has only a few genes and these genes are not required for the survival and reproduction under normal conditions but they also have advantages to bacterial in stressful conditions.

 The F Plasmid and Conjugation

-          The F plasmid consists of about 25 genes most required for the formation of the sex pilli. (Also seen as F+)

-          The F plasmid is inheritable and replicates in synchrony with the chromosomal DNA.

-          Division of an F+ cell usually gives rise to two offspring that are both F+.

-          Cells that lack the F+ are referred to as F- and act as the females during conjugation.

-          The F+ plasmid replicates in the male and then is transferred to the female converting it from an F- to an F+ cell.

-          The F plasmid is also an episome and can incorporate itself into the main chromosome.  This is now called an Hfr cell (high frequency of recombination).

-          An Hfr cell continues to function as a male during conjugation and transfers the F genes to its F- partner along with some to the chromosomal DNA.

-          The Hfr cells chromosome is replicated as the DNA is transferred so that it does not lose any DNA.

-          Recombination only occurs when the newly acquired DNA aligns with the homologous region of the cellís own chromosome and a crossover exchanges DNA.  Binary fission gives rise to a colony of recombinant bacteria.

-          If cells are interrupted during conjugation, scientists are able to sequence the genes around the episome because only parts of the DNA are recombined.

 R Plasmid and Antibiotic Resistance

-          Noticed in the 1950ís that certain strains of bacteria were resistant to different antibiotics. 

-          This resistance is not carried in the bacterial chromosome but in a plasmid called the R plasmid. (R for resistance)

-          Exposure of a bacterial population to a specific antibiotic will kill antibiotic sensitive bacteria but not those that have R Plasmids that counter the antibiotic will live. 

-          Natural selection predicts that an increasing number of bacteria will inherit genes for antibiotic resistance and those that are resistant will become more common.

-          The problem is compounded by the F plasmid because the R plasmid can be transferred during conjugation.

 Transposons      

-          Transposable genetic elements are pieces of DNA that con move from one location to another in a cells genome.

-          In bacteria a transposon may move from one locus to another within the chromosome, from a plasmid to a chromosome or from one plasmid to another.

-          Often referred to as jumping genes.

-          The transposonís genes are not replicated before moving so the number of copies is conserved. 

-          In a replicative transposition, the transposon replicates at its original site and a copy inserts at some other location in the genome.

-          A transposon does not have a single specific target in the genome.

Insertion sequences

-          Insertion sequences are the simplest.

-          They consist of only the DNA necessary for the act of transposition.

-          The one gene found in an insertion sequence codes for transponase, which is an enzyme that catalyzes the transposition.

-          The transponase gene is bracketed by a pair of DNA sequences called inverted repeats; noncoding sequences about 20 to 40 nucleotides long.

-          They are inverted because these two regions of DNA on the ends of an insertion sequence are upside down, backward versions of each other.

-          Transponase recognizes these inverted repeats as the boundaries of the transposon. 

-          The enzyme binds to the two regions brings them close together and catalyzes the cutting and resealing required for transposition.

-          DNA polymerase helps form identical regions of DNA, which flack the transposon in its new target site.

-          The insertion causes a mutation that can increase or decrease the transcription rates.

 Complex Transposons and R Plasmids

-          Transposons are larger and more complex than insertion sequences.

-          Complex transposons include other genes that go along for the ride like the genes for antibiotic resistance.

-          These genes are sandwiched between two insertion sequences.

-          These complex transposons may help bacteria adapt to new environments.

-          Transposable genetic elements are not unique to bacteria but are important in eukaryotic genomes as well.

-          The first evidence was seen in Barbara McClintockís breeding of Indian corn that changed the colors of the kernels.

 The Control of Gene Expression

-          Individual bacteria are able to adjust their metabolism based on environmental change.  For instance, if an E.coli bacteria does not receive tryptophan from the host, it enables an enzymatic pathway that allows it to make its own tryptophan until the host intakes a meal with tryptophan.

-          Metabolic control occurs on two levels

-             Cells vary the numbers of specific enzyme molecules meaning they can control gene expression.

-             Cells can vary the activities of enzymes already present.  This mode is more immediate and depends on the sensitivity of many enzymes to chemical cues that increase or decrease their catalytic activity.

-          Many genes of the bacterial genome are switched on or off by changes int the metabolic status of the cell.

-          The method for this was first describe in 1961 by Francois Jacob and Jacques Monod.  They described this as the operon model.

 Operons

-          A promoter unit is a site where RNA polymerase can bind to DNA and begin transcribing genes. 

-          In the tryptophan unit, five genes code for the polypeptide chains that make up these enzymes that produce tryptophan.  In this unit, a single promoter serves all five genes.

-          Transcription gives rise to one long mRNA molecule representing all five genes required.  It is then translated into five different sequences due to start and stop codons.

-          Genes that code for polypeptides are called structural genes. 

-          An advantage of grouping structural genes into one transcription unit is that a single switch can control a complete cluster of functionally related genes.

-          The switch is a segment of DNA called an operator.

-          It is located within the promoter or between the promoter and the structural genes.

-          It controls the access of RNA polymerase to the structural genes.

-          The entire stretch of DNA required for enzyme production is referred to as an operon.  This includes the promoter, the operator, and the structural genes.

-          By itself, the operator is on and RNA polymerase can bind to the promoter and transcribe the structural genes.

-          The operator is switched off by a protein called the repressor.

-          The repressor binds to the operator and blocks the attachment of RNA polymerase to the promoter which stops transcription of the structural genes.

-          Repressor proteins are specific to the operator and operon.

-          The repressor is a product of a gene called a regulatory gene and is located some distance away from the operon it controls.

-          Regulatory genes are transcribe continuously but at a slow rate.

-          Binding of the repressor to the operator is reversible.

-          Repressors are synthesized in an inactive form.

-          It assumes its active conformation and attaches to the operator only if it first binds to a molecule called a corepressor which is a small molecule that cooperates with a repressor protein. 

 Repressible vs. Inducible Enzymes

-          Repressible enzymes can have their synthesis inhibited by a metabolic end-product

-          Inducible enzymes are stimulated by specific small molecules.

-          The most well known is the lac operon.

-          An inducer is used to change the active conformation of the repressor.  This may be an isomer of the end-product. 

Positive Gene Regulation           

-          To control how fast the enzymes are produced, sometimes a catabolite activator protein is used (CAP)

-          A catabolite is a molecule that can be consumed by the metabolic pathway.

-          CAP accelerates the transcription of an operon by adhering to the promoter and facilitating the binding of RNA polymerase.

-          Since CAP associates directly with the DNA to stimulate gene expression, this is referred to as positive regulation.

-          CAP may work on several operons.

-          The cellís ability to use alternative catabolites provides backup systems that enable the cell deprived of another molecule to survive.