1. Hallmarks that distinguish a living from a nonliving system (self-feeding, self-replication, differentiation, chemical signaling, and evolution). Why are virus not considered living by some people?

2. Properties of viruses:

• chemistry- composed of a nucleic acid and protein
  • genome- viruses have either a DNA or a RNA genome.
    • DNA viruses- depending on virus, genome can be either double (ds) or a single stranded (ss) structure. DNA may be either a circular or linear molecule.
    • RNA viruses- depending on virus, RNA can be ss or ds. With one possible exception, all ds-RNA viruses are animal viruses, and all have a linear genome. In some cases, animal viruses, the genes are on different RNA molecules. These viruses are referred to as segmented viruses.
  • protein- a protective protein coat, called a capsid structure, surrounds the nucleic acid. The capsid is composed of identical protein subunits called capsomers. The nucleic acid surrounded by the capsid is called the nucleocapsid structure of the virion. In the case of some animal viruses, a lipid layer may surround the nucleocapsid. These viruses are called enveloped viruses.
• size and shape- viruses are an order of magnitude smaller than their host cell. The largest virus, the vaccinia virus, is as largest as the smallest bacterium (Chlamydia), while the smallest virus can be as small as the bacterial ribosome (10 nm). Shape- linear, spherical (polyhedral), or complex (having a linear and polyhedral component).
• lack ability for self replication- in order for viruses to replicate, they must do so at the expense of a host cell. Thus, viruses are referred to as obligate intracellular parasites. What aspect to bacteria of the genus Rickettsia and Chlamydia share with viruses?

3. General step in replication of a virus:

• attachment or adsorption to host cell.
• cell entry- in the case of all phage and some animal viruses entry is the result of the nucleic acid entering the cell. this is called penetration. With enveloped animal viruses the membrane may be removed during entry or immediately after virus enters cytoplasm. This process is called uncoating.
• synthesis of viral component parts- Following entry and/or uncoating, viral genome must be replicated, phage genome must be expressed, i.e., transcription of phage genes, and translation of phage mRNA to make phage proteins. These events are called biosynthesis of viral component parts.
• assembly of viral component parts- during the maturation step, viral component parts are assembled into infectious particles. In most cases, this occurs after all component part are made, and occurs by a self-assembly process.
• release- viral particle must be released. This can occur as a result of cell lysis, rupture, or release without damage to host cell.

  A viral infection may result in a productive infection, meaning that viral particles are produced, or a latent infection. In a latent infection the viral genome becomes part of host chromosome, and no virus particles are produced. The host cell properties may be altered in specific ways, and at some future time a latent infection can lead to a productive infection. In the case of bacteria, a cell harboring phage DNA in its chromosome is called a lysogenic cell, while the integrated phage genome is called a prophage. The process of inserting phage DNA into the bacterial chromosome is called lysogeny, and phage with this ability are referred to as temperate bacteriophage. No examples of a RNA phage that inserts itself into genome of host (into host DNA)! In the case of a group of animal viruses called retroviruses, of which the HIV is an example, the viral RNA genome, which is ss, is converted to a ssDNA copy, then to a double stranded form, the viral genome, as is the case for HIV, becomes integrated into the DNA of certain cells of the human body! Not all retroviruses do this last step.

4. Examples of how certain phage replicate:

• ds-DNA phage- phage T₄ Host cell is E. coli Fig. 13.5
  • phage receptors
  • phage typing
  • phage differential gene expression
  • latent period
  • burst size
• ss-DNA phage- fX-174 and the filamentous phage M13 (ds replicative intermediate).
• ss-RNA phage (sense or + stranded phage)- MS2 phage. See replication diagram.

5. Lysogeny: Phage l (lambda). Fig. 13.6

6. Lysogenic conversion (new cell properties acquired as a consequence of carrying or harboring a prophage)- examples See Table 13.3

7. Mechanisms to resist phage infection- lack or modify phage receptor and/or make a restriction endonucleases that recognizes specific DNA sequences of phage genome. Restriction endonucleases, have ability to recognize specific nucleotide sequences within a DNA molecule, and cut the DNA. Cells protects own DNA by modifying a nucleotide within sequence recognized by a specific restriction endonuclease. In general, only one restriction endonuclease and modifying enzyme per species.

Learning Objectives:

• What properties/characteristics allow you to distinguish between a virus and a cell?
• Describe the chemical composition of a bacteriophage.
• Describe the events in the life cycle of bacteriophage (T₄).
• Compare and contrast the replication of a ds-DNA phage with that of a ss-DNA phage.
• how do ss-RNA phage replicate?
• How does phage lambda differ in its replication cycle from phage T₄.
• What is lysogenic conversion?
• How can bacteria avoid a phage infection?
• You should be familiar with the following words: host range, lytic/ temperate bacteriophage, capsid, nucleocapsid, eclipse and latent period, burst size, a lysogenic cell, and prophage.

Examples of lysogenic conversion:

• Cells immune to further infection by a similar phage due to presence of repressor protein.
• Establishes pathogenic state in certain bacteria.
  • In Corynebacterium diphtheriae prophage carries a gene which encodes for a protein toxin, diphtheria toxin, which is deleterious to the eucaryotic cell (blocks eucaryotic protein synthesis).
  • In Clostridium botulinum the prophage encodes for a neurotoxin, which causes blurred vision and respiratory paralysis which can lead to death.
  • The erythrogenic toxins produced by strains of Streptococcus pyogenes (damages blood capillaries under the skin producing a red skin rash)
  • Staphylococcal enterotoxin ( stimulates discharge of large amounts of fluids and ions from cells lining intestinal track, diarrhea) and pyrogenic toxin produced by Staphylococcus aureus, and the capsule produced by Streptococcus pneumoniae are all phage encoded.

6/181/09