Chapter 13 - Chapter 13 Prokaryote and virus models have advantages for studying genetics • • • • • • Small genomes Quickly

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Unformatted text preview: Chapter 13 Prokaryote and virus models have advantages for studying genetics: • • • • • • Small genomes Quickly produce large numbers of progeny Usually haploid (easier genetic analyses) Prokaryotes are tools for biotechnology and cell research Prokaryotes are important ecologically Some prokaryotes and viruses are pathogens How Do Viruses Reproduce and Transmit Genes? Viruses are acellular • • Most consist of only a nucleic acid and a few proteins  ­ ­ some have additional molecule types Viruses do not: • • • Perform metabolic functions Regulate transport into or out of themselves Viruses can replicate only in living cells Viruses: Reproduction and Recombination Viruses are obligate intracellular parasites • • • • replicate only within living cells of specific hosts replicate using the host’s synthetic machinery, often destroying host cell in the process host cell releases progeny viruses, which infect new host cells outside cells, individual viral particles are called virions Virion genetic material is either DNA or RNA and is surrounded by a protein capsid • • characteristic shapes determined by capsid viruses are unaffected by antibiotics because they lack the structures and biochemistry of bacteria (cell walls, ribosomes) Viruses are classified by: • • • • Genome: DNA or RNA Nucleic acid structure: single ­stranded or double ­stranded Shape: simple or complex Whether or not the virion is surrounded by a membrane • • Type of organisms it infects Manner of infection (lytic or lysogenic) Viruses that infect bacteria are bacteriophages or phages . • Like other viruses, they recognize host by specific binding between capsid proteins and host cell receptor proteins • the virions have “tail” assemblies that inject the nucleic acid into the host cell Viruses: Lytic vs. Lysogenic Two types of virus reproductive cycles: • • Lytic cycle – virus replicates immediately and releases progeny, killing host cell Lysogenic cycle – virus postpones reproduction by integrating its nucleic acid into host cell genome Lytic cycle: • • • infected bacterium lyses, releasing progeny virions viruses that only have lytic cycles are called virulent viruses virus nucleic acid takes over the host’s synthetic machinery in two stages Lytic cycle – two stages • Early stage: virus genome has promoter that attracts host RNA polymerase. - Viral genes adjacent to virus promoter are transcribed - early gene products include proteins that shut down host transcription, stimulate viral genome replication, and digest host’s chromosome • Late stage: transcribe viral genes code for protein capsid, and enzymes to lyse host and release for viral release Two viruses can infect one cell. • With two different viral genomes in the same cell, there is the possibility of genetic recombination by crossing over—producing new strains Lysogenic cycle: • • • • • host cell does not lyse, but harbors the viral nucleic acid for many generations bacteria harboring a phage that are not lytic are called lysogenic bacteria. the viruses are called temperate viruses phage DNA, called a prophage, inserts into the host cell chromosome prophage replicates during the cell’s normal reproductive cycle (often without harming the host cell) • certain conditions (host mutates or is damaged) activate prophage  initiate lytic cycle that releases of new phages Lytic bacteriophage destroy their bacterial hosts, and thus might be useful in treating diseases caused by bacteria • Rise of antibiotics reduced interest in phage therapy, but it may become useful again, as bacteria become resistant to antibiotics. Animal Viruses Animal viruses are diverse Arboviruses infect both insects and vertebrates. • Virus passes from arthropod to vertebrate via an insect bite. The arthropod is a vector (carrier) Animal viruses include: • • • those with just a protein capsid and nucleic acid Enveloped viruses are those with a membrane derived from the host animal viruses have DNA or RNA, but all have small genomes Animal viruses enter cells in 3 different ways: • • • endocytosis of a naked virion endocytosis of enveloped virus (e.g. influenza) fusion of an enveloped virus with host cell’s membrane (e.g. HIV) After reproduction, enveloped viruses escape the cell by a budding process. • An envelope is acquired from the host cell’s plasma membrane in the process. HIV is a retrovirus • • Retroviruses have an RNA genome Require reverse transcriptase , which facilitates RNA ­directed DNA synthesis - makes DNA copy of the viral RNA genome for cDNA provirus • • Plant Viruses Plant viruses can be transmitted in two ways: • • • Horizontal transmission is the spread of viruses from one plant to another Vertical transmission is transfer of viruses from parent plant to offspring cDNA provirus is produced that is integrated permanently into host’s genome When proviral DNA is activated, new virions are produced To infect a plant cell, the virus must penetrate a cell wall and plasma membrane • • Insects are possible vectors – when feeding on plant they can puncture cell wall and insert virus Another means of infection is via damaged plant tissues Vertical transmission occurs via vegetative or sexual reproduction • Once inside a cell, viruses spread by moving through plasmodesmata How Is Gene Expression Regulated in Viruses? For temperate viruses (those with lysogenic cycle), there is a crucial point • When should provirus leave host chromosome and start lytic cycle? Example: Bacteriophage Bacteriophage λ — uses two regulatory proteins to determine the state of health of the host cell • • cI and Cro proteins compete for promoters on the viral genome Phage infection is a “race” between the two regulatory proteins • • When host cell is healthy, synthesis of Cro is low, cI “wins”—lysogenic cycle When host cell is damaged or stressed, more Cro is produced—lytic cycle occurs How Do Prokaryotes Exchange Genes? Unlike viruses, prokaryotes are living cells that carry out basic cellular functions. Binary fission produces clones, individuals that are genetically identical. If cells are spread on a semisolid agar medium, individual cells give rise to readily visible colonies. Prokaryotes have several ways of recombining genes: • • • • • • Conjugation Transformation Transduction Plasmids Transposable elements Conjugation is DNA exchange between two living bacteria . • • • A conjugation pilus is a fine projection made by the donor cell. DNA transfers through the thin cytoplasmic bridge. Once inside the recipient cell, the DNA recombines with homologous genes. • • Transformation occurs when bacteria take up extracellular DNA and incorporate it. Plasmids – small, circular pieces of DNA in many bacteria. • Each plasmid replicates separately from primary chromosome. • • • Plasmids move between bacterial cells during conjugation. Plasmids are classified by the kinds of genes they carry. Some plasmids carry genes for unusual metabolic functions, such as degrading oils from oil spills. Fertility factors (F factors) are plasmids that carry genes for conjugation. • • • An F factor plasmid carries about 25 genes, including those responsible for the pilus. Bacteria with this plasmid are called F+. (Those without are “F ­”) The plasmid may insert into the main chromosome. When this occurs, chromosomal genes can be transferred during conjugation. Resistance factors (R factors) are plasmids with genes coding for proteins that protect the bacteria. • • • Antibiotic resistance genes interfere with antibiotic function. Resistance to multiple types of antibiotics can be transferred by conjugation. Known as “multidrug resistance” (MDR) Transposable elements are chromosome segments or plastids that can move into other genes within a cell. • • Moving into other genes can disrupt normal function. Transposons are long transposable elements (~ 5000 base pairs), that include one or more genes (“jumping genes”). • Transposons have contributed to plasmid evolution. Regulation of Gene Expression in Prokaryotes Cells conserve energy and resources by making proteins only when needed. Cells regulate protein synthesis by several methods: • • • • • Block transcription of the gene Hydrolyze the mRNA after it is made Prevent translation of mRNA at the ribosome Hydrolyze the protein after it is made Inhibit the function of the protein E. coli prefers glucose as an energy source, but can use lactose if glucose is low. • • • 3 enzymes are required for lactose metabolism presence of lactose stimulates production of these enzymes lactose is an inducer • enzymes that are produced in the presence of an inducer are said to be inducible • enzymes that are made all the time are said to be constitutive The rate of a metabolic pathway can be regulated by: • • Allosteric regulation of enzyme activity Regulation of protein synthesis—slower, but produces greater energy savings Structural genes specify primary protein structure — the amino acid sequence • • The three structural genes for lactose enzymes are adjacent on chromosome They share a promoter, and are transcribed together Regulation of Gene Expression  ­ the lac operon Operon is the whole unit • • promoter, operator, and one or more structural genes Operon containing genes for lactose metabolism: lac operon Prokaryotes shut down transcription by placing obstacle ( operator) between promoter and structural gene • Operator binds to a protein called a repressor —blocks transcription of mRNA The repressor protein has two binding sites • • one for the operator one for inducer (lactose) Binding inducer to repressor, changes repressor shape  allows promoter to bind RNA polymerase • When lactose concentration drops, inducers separate from repressors — repressor again binds operator, transcriptions stops A repressor protein is coded by a regulatory gene. • • • • The regulatory gene that codes for the lac repressor is the i (inducibility) gene i gene is near lac structural genes, but not all regulatory genes are near their operons Regulatory genes like i have their own promoter, called pi The i gene is expressed constitutively (expression is constant). Regulation of Gene Expression – the trp operon A protein is repressible if synthesis can be turned off by a biochemical cue (e.g., ample supply of that protein) • • • The trp operon controls synthesis of tryptophan — it is a repressible system Gene is normally “on”, transcribing mRNA and synthesizing structural proteins The repressor must first bind with a corepressor , in this case tryptophan (when its abundant), activating repressor • Active repressor turns gene “off”, blocking transcription Regulation of Gene Expression in Prokaryotes – Summary Inducible systems ( lac operon) • • Substrate of a metabolic pathway (inducer) interacts with a regulatory protein (repressor) — repressor cannot bind to operator —allowing transcription Control catabolic pathways (turned on when substrate is present) Repressible system (trp operon) • • Product of a metabolic pathway (corepressor) interacts with a regulatory protein (repressor) allowing it to bind to operator, blocking transcription Control anabolic pathways (turned on when product is not present). Catabolite repression • • • • • • • • lac operon can increase efficiency of the promoter A regulatory protein CRP binds cAMP This complex binds to DNA just upstream of promoter. Allows more efficient binding of RNA polymerase to promoter Presence of glucose lowers concentration of cAMP thus less CRP binding to promoter, resulting in less efficient transcription of lactose ­metabolizing enzymes The lac and trp systems are negative control of transcription — the regulatory protein prevents transcription Catabolite repression is positive control—the regulatory CRP ­cAMP complex activates transcription when needed to metabolize lactose What Have We Learned from the Sequencing of Prokaryotic Genomes? Automated techniques have allowed sequencing of prokaryote and eukaryote genomes. Three types of information can be obtained from a genomic sequence. • • • Open reading frames (ORFs) can be recognized by their promoter regions and start and stop codons Amino acid sequences can be predicted from DNA sequence Regulatory sequences of promoters and terminators can be identified Functional genomics is the assignment of roles to gene products described by genomic sequencing. • • Haemophilus influenzae has a circular chromosome of 1,830,137 base pairs and 1,743 protein ­ coding regions. When sequenced, 42% of the genes coded for proteins with unknown functions. • • • • • • Roles for most of the unknown proteins have now been identified (the genes have been annotated). Comparative genomics involves the comparison of genome sequences of different organisms. Many genes have sequence and function similarities across species. Scientists are discovering genes for proteins in prokaryotes that cause infectious diseases. These are potential targets for new drugs. There are some universal genes needed by all organisms (such as those coding for some ATP functions). ...
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This note was uploaded on 12/03/2010 for the course BSC 2010 taught by Professor Bowes during the Spring '08 term at University of Florida.

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