1. The Genetics of Viruses and Bacteria
Chapter 18
The Genetics of Viruses and Bacteria

3. Viruses
A Virus is an infectious particle consisting of a genome enclosed in a protein coat that can only reproduce within a host cell. Contains no metabolic enzymes, no ribosomes, etc.
Structure
Viral genome can consist of double or single stranded _DNA_ or _RNA_ organized as single molecule (either linear or circular).

4. Viruses The protein coat enclosing the virus is called a CAPSID.
Some viruses have ENVELOPES (derived the membranes of host cells) that surround their capsids.
The most complex capsids are found in viruses that infect bacteria known as BACTERIOPHAGES or just PHAGES.

7. Viruses
-Each type of virus can infect a limited number of hosts and some are species specific.
Viruses are only able to reproduce in a host cell, using the host cell’s enzymes, nucleotides, molecules, etc to copy its own genome and make its own proteins.

9. Viruses
Viruses that infect bacteria are some of the most well understood viruses. Any virus, that infects a bacterium is called a bacteriophage or just phage for short.
We will take a look at their reproductive cycles (these cycles & variations on them are also common in viruses that infect animals & plants)

10. Common Reproductive Cycles (of Phages)
The Lytic Cycle: results in the death of the host cell.
Phage that reproduces only using this cycle is called a virulent phage.

11. Common Reproductive Cycles (of Phages)
Basic steps of lytic cycle:
Phage attaches to host bacteria cell.
Phage injects its GENOME into host cell.
Phage DNA is copied and phage proteins are made by the host cell’s “machinery” (enzymes, etc)

12. Common Reproductive Cycles (of Phages)
Phage proteins and nucleic acids self assemble into genome with capsid around it.
Phage produces an enzyme that breaks the bacterial cell wall, killing it and releasing all the newly formed phages.
Bacteria can defend against viral (phage) infections by using RESTRICTION enzymes that recognize and cut up foreign DNA.

14. Common Reproductive Cycles (of Phages)
The Lysogenic Cycle: replicates the phage genome without destroying the host.
Phages that use this and lytic cycle are called temperate phages.

15. Common Reproductive Cycles (of Phages)
Basics of lysogenic cycle:
Again, phage injects its DNA/RNA into host cell.
This time, phage DNA is incorporated into the host cell’s genome. When this happens, the viral DNA is called a PROPHAGE.
Every time the host cell REPLICATES its DNA, it also copies the phage DNA. This enables the virus to spread without killing its host cells.

16. Common Reproductive Cycles (of Phages)
Eventually, an environmental or chemical signal triggers the phage DNA to exit the host’s genome and initiate a LYTIC cycle.
Additional information: the presence of phage DNA in other wise harmless bacteria can be BAD. Expression of prophage DNA can alter the host bacteria’s phenotype and trigger it to make toxins which are harmful to humans (this is how diphtheria, botulism and scarlet fever are caused).

18. Viruses that Infect Animals
Structure: almost all animal viruses are equipped with outer envelopes that are derived from the host’s plasma membrane.
After the virus’ genome & capsid proteins are made, the virus “buds” from the host cell plasma membrane – which doesn’t necessarily kill the host cell.

20. Viruses that Infect Animals
Many animal viruses have RNA as genetic material. There are differences in how the RNA is translated into viral proteins
Some RNA serves directly as mRNA and can immediately be translated into viral proteins upon entering the host.
Some RNA serves as a template for transcription and a complementary mRNA strand is made (then translation proceeds).
RETROVIRUSES: transcribe DNA from an RNA template using an enzyme called REVERSE TRANSCRIPTASE.
The newly made DNA then integrates as a provirus into a chromosome within the nucleus of the host cell.

21. Viruses that Infect Animals
Then, the host transcribes and translates the viral DNA into viral proteins.
HIV is a retrovirus.
ALL RNA viruses have a high mutation rate because there is no proofreading mechanism. This is why you can ALWAYS get a cold or flu --- there are always new strains. This also means that viruses like HIV are constantly mutating.

23. Evolution of Viruses
1.) Can they evolve? Are they alive? Well, they do change based on their genetic code – which they share with all other living organisms.
2.) Most likely evolved AFTER cells since they are so dependent on them.
a.) Hypothesis: viruses originated from pieces of cellular nucleic acids that could move from one cell to another.

24. Viral Diseases
Viruses cause disease by lysing cells, causing infected cells to produce toxins or having components that are toxic (proteins in viral envelopes).
The symptoms we get from the most common viral infections are usually from our own body’s defenses.
The permanent damage inflicted by a virus usually depends on what type of cells it infects and how well they can repair themselves.

25. Viral Diseases
Treating viruses is HARD. Antibiotics kill bacteria because they destroy bacterial proteins/enzymes. Viruses do not have many enzymes of their own and it is hard to develop antiviral drugs.
a.) Most antiviral drugs are designed to interfere with the synthesis of the virus’ genetic material.

26. Viroids + Prions = WEIRD!
Viroids: naked, circular RNA that infects plants (so this is an infectious molecule).
RNA replicates in host cells using their enzymes and disrupts plant cell metabolism, stunting plant growth.
Prions: infectious proteins
Leading Hypothesis: prions are misfolded forms of proteins that are normally present in brain cells and once inside brain cells can actually convert the normal proteins into the misfolded form.
This damages/destroys brain cells.
Example: Mad Cow Disease

27. The Genetics of Bacteria
most bacteria have one, circular chromosome composed of double stranded DNA.

28. The Genetics of Bacteria
In addition to chromosome, many bacteria also have smaller, self – replicating circles of DNA in the cytoplasm called PLASMIDS.
Bacteria reproduce by replicating their chromosome and dividing by BINARY FISSION.

30. Since this is an asexual process, most bacteria in a colony are genetically identical. However, mutations and recombination are possible:
TRANSFORMATION: The uptake of naked, foreign DNA from the environment which is then incorporated into the bacterial chromosome.

31. TRANSDUCTION: phages carry bacterial genes from one host cell to another (so a virus does the dirty work of transferring DNA). This can happen by chance packaging of host’s DNA into a viral capsid or when a prophage leaves a host’s genome it may take a piece of the host’s DNA with it.

32. Bacteia sex! Also known as CONJUGATION: the direct transfer of genetic material between temporarily joined bacteria.
One cell donates DNA and extends a SEX PILUS (OH MY!) which joins to a recipient cell and DNA is transferred from donor to recipient.
The ability to grow a sex pilus and transfer DNA is determined by the presence of a piece of DNA known as the F factor.
This factor can be part of the bacterial chromosome or can be part of plasmid (the F plasmid) in the bacteria.

34. A single strand of the F plasmid is transferred and is used as a template in both the donor and recipient cells to make the complementary DNA strand.

35. Plasmids
generally beneficial to bacteria, not required for survival of bacteria under normal conditions, can be transferred from one bacteria to another (through conjugation, transformation), are self replicating (so when a bacterium divides, its plasmid has usually replicated and is passed to the two resulting daughter cells).

36. R plasmids: contain genes that make bacteria resistant to antibiotics.
Many of these also have genes encoding for sex pili so they are transferred between bacteria.

37. Some contain genes that make them resistant to many antibiotics.
This is most likely the result of genes that can actually move from one location to another in a genome (in a single cell) – called TRANSPOSONS.
These genes can move within a bacterial chromosome, between the chromosome and plasmid or from one plasmid to another.

38. Simplest type of transposons are called INSERTION sequences
Simplest type of transposons are called INSERTION sequences. They code for only one enzyme, TRANSPOSASE which is the enzyme that catalyzes their movement. When these are inserted into other regions of coding DNA, they can cause mutations

39. Other transposons have more than one gene (maybe genes for antibiotic resistance). So when these are inserted into plasmids or bacterial chromosomes, you can end up with bacteria that is resistant to multiple antibiotics.
Eukaryotes also have mobile genetic elements like transposons!

40. Bacterial Control of Gene Expression
The Operon Model
Genes that code for proteins/enzymes that are functionally related are all grouped together in the genome (forming one big transcription unit) and have a single PROMOTER region.
Ex.) All the genes that produce enzymes needed to digest lactose are grouped together in the genome of bacteria.

42. Within the promoter region is a segment of DNA called the OPERATOR - this functions like an on/off switch for the transcription unit – controls the access of RNA polymerase to the transcription unit.
We call the promoter, operator and group of related genes an OPERON.

43. By itself, the operator (of some operons) is always switched “on” and RNA polymerase binds to the DNA and transcribes all the related genes at once.
Operator can be switched off by a protein called a REPRESSOR which binds to the operator and blocks the binding of RNA polymerase. The repressor is a product of a REGULATORY gene.

45. Repressors are constantly produced in low concentrations and in inactive forms. The binding of another molecule activates repressor which can then bind to operator. (This is a type negative feedback pathway).
This can also work the other way. Some repressors are made in their active form and are always binding to the operator and keeping a transcription unit off. They must be inactivated by the binding of another molecule. (An example of this is the lac operon which is involved in lactose metabolism in E. coli – read about it!)