1. Microbial Models I: Genetics of Viruses and Bacteria 7 November, 2005 Text Chapter 18

2. Viruses are genetic parasites that are smaller than living cells. They are much more complex than molecules, but clearly not alive, since they lack their own metabolism and reproductive capacity. Viruses replicate by invading cells and using the metabolic and reproductive capacity of the cell to make hundreds or thousands of new virus particles. Viruses cause disease because the genetic takeover impairs the normal function of the cell. Virus Basics - part I

3. Viruses consist of a protein capsid and DNA or RNA genome.

5. Viruses are specialized. Each recognizes and invades a narrow range of cell types in one or a few closely related species. The protein coat functions in recognition of the host cell, invasion, and protection of the viral genome outside the host cell. The viral genetic material can be DNA or RNA. Virus usually have only a few genes (usually 10-20). These commonly specify coat and structural proteins, regulatory proteins used to take over host gene expression systems, and proteins that process or assemble completed virus. Virus Basics - part II

6. A viral infection begins when a virus recognizes a host cell. The viral genome is then replicated and transcribed by host enzymes. Viral coat and structural proteins are translated and processed. Viral components self-assemble into new virus particles. These particles exit the cell and can infect new cells. Often, the cell is destroyed in the process. Viral Reproduction

7. Phage T4 is a structurally complex phage with a simple life cycle.

8. Phage lambda can use the lytic or lysogenic cycle.

9. Animal viruses sometimes incorporate parts of the host cell membrane, including viral proteins that are processed and inserted in the membrane during viral replication. These viruses usually do not lyse the host cell but may severely impair its function, as the metabolic resources of the cell are diverted to viral replication. The membrane helps the virus evade detection by the host immune system. Enveloped Animal Virus:

10. The HIV virus is an enveloped virus. Its genome is single stranded RNA that encodes an efficient and complex life cycle with only five major genes. Two of these genes code for the structure of the virus. One gene codes for reverse transcriptase and integrase activities. Two genes code for transcription factors. HIV

11.  Because viral infections occur inside cells, they are often not accessible to the immune system. The virus is only vulnerable when it is between cells.  At this time, the three dimensional shape of proteins on the outside of the virus can be recognized as foreign and destroyed. Vaccines against viral diseases train the immune system to recognize and destroy viral coat proteins.  Viruses that target vulnerable cell populations like polio and HIV are especially damaging.  Some viruses can cause cancer by introducing or activating oncogenes.  Analysis of viral sequence indicates that viruses are escaped genes that become mobile with the help of transposable elements.

12. Escherichia coli is the best-studied organism. It is still far from completely understood. It makes an excellent model organism because it is Small Readily Cultured (Fast-Growing) Haploid Small Genome (4300 genes) Mobile Genetic Elements (Plasmids and Phages) Asexual Reproduction Rapid Evolution (10 -7 mutations per gene per replication.) Bacterial Model Systems

13. Bacteria can exchange genetic material.

14. Transformation occurs when bacteria take up DNA from their surroundings. (Think of the R to S transformation that introduced us to the idea of DNA as the genetic material.) You will take advantage of this bacterial property in lab this week. When you mix plasmid DNA with calcium chloride- treated E. coli cells, some of the cells will be transformed when they take up the plasmid. Transduction is the movement of DNA from one bacterium to another by bacteriophages. Conjugation is the direct transfer of genes between joined bacteria. Transformation, Transduction, and Conjugation

15. Transduction

17. The order of gene transfer during Hfr conjugation is the basis for the construction of bacterial gene maps. Conjugation

18. Insertion sequences, the simplest transposons, contain only a transposase gene flanked by two inverted repeats. Transposable elements (transposons) can move from one location to another in the genome.

19. In transposition, transposase cuts DNA at the target site. Then, it catalyzes the movement of the transposon to the new site. This movement can cause mutations in it moves the transposon into the coding sequence or regulatory regions of a gene.

20. Biochemical pathways are often regulated by feedback inhibition. Usually, the synthesis of the enzymes in the pathway is also regulated. This regulation is at the level of transcription. Regulation of Gene Expression

22. The trp operon is a biosynthetic operon - it codes for the enzymes that make the amino acid tryptophan. This pathway should be kept in the “off” state when tryptophan is present. When tryptophan is absent, the bacteria need to make it from scratch. Now the pathway needs to be turned on. The lac operon is a catabolic operon - it codes for the enzymes that burn the sugar lactose for fuel. This pathway should be kept in the “off” state when lactose is absent. When lactose is present, the bacteria can burn it for fuel. Now the pathway needs to be turned on.

24. Furthermore, the bacterium does not burn lactose for fuel if its preferred carbon source (glucose) is available. The decision about the presence or absence of glucose is independent of the decision about the presence or absence of lactose, and is made by the CAP protein and the nucleotide cAMP. The cell only expresses the lac operon when lactose is present and glucose is absent.