Micro Ch 13 (exam 3)

Characteristics used in Virus Classification

- Genome structure/ Replication Strategy - Capsid symmetry - Presence of absence of lipid envelope - Dimensions of the virion and capsid

Viruses are Obligate Intracellular Parasites

- Not considered living - Do not make ATP - Do not make proteins by themselves - Dependence on living cell

titer

The number is used to determine the titer, the concentration of infectious phage particles in the original phage suspension.

Oncogenes

carry genes which are very similar in DNA sequence to proto-oncogenes. Their entry into cells can interfere with the cell's own control mechanisms, leading to tumor formation.

Plaques

circular zones of clearing, form in the lawn due to cell lysis caused by the phage.

Viroids

consist solely of a small single-stranded RNA molecule that forms a closed ring.

Virion (viral particle)

consists of nucleic acid surrounded by a protein coat.

Lysogenic conversion

is a change in the phenotype of a lysogen as a consequence of the specific prophage it carries.

Cell culture/tissue culture

is commonly used to cultivate most animal viruses. Animal cells - grown in a liquid medium contained in special screw-capped flasks - are used as host cells for the virus culture.

Chronic Infections

are characterized by the continuous production of low levels of viral particles. ○ In some cases, the infected cell survives and slowly releases viral particles. In other cases, the infected cell lyses, but only a small proportion of cells is infected at any given time, resulting in a low number of viral particles being continuously released.

Reverse Transcriptase

enzyme that reverse-transcribing viruses encode. It is an RNA-dependent DNA polymerase, which makes DNA from an RNA template.

Non-enveloped/ Naked viruses

are viruses that do not have an envelope. ----> Nearly, all phages are non-enveloped. ----->In general, enveloped viruses are more susceptible to disinfectants because these chemicals damage the envelope, making the viruses non-infectious.

M13

- M13 (for example) is a filamentous phage that initiates infection by attaching to a protein on the F pilus of E. coli. ○ Its single stranded DNA genome then enter the cytoplasm of the bacterial cell, where a host cell DNA polymerase makes the complementary strand. This double stranded DNA is referred to as the replicative form (RF). § One strand of the RF is then used as a template to make mRNA as well as multiple copies of the phage's single-stranded genome. - M13 particles are assembled as the phage DNA is extruded from the cell. In this process, phage coat protein molecules are inserted into the host cell's cytoplasmic membrane. At the same time, other phage-encoded proteins form pores that span the cytoplasmic and outer membrane. Then, as phage DNA is secreted through the pores, the coat protein molecules coat the single-stranded DNA to form the Nucleocapsid. - M13 phage is useful in certain recombinant DNA procedures because its replication cycle produces both single and double stranded DNA. *** If a researcher needs a preparation of a specific sequence of single-stranded DNA without its complement, the DNA of interest can be cloned into an RF molecule of M13.

The CRISPR system

are routinely used to quantitate phage particles in samples such as sewage, seawater, and soil. In this type of assay, a double layer of agar is used; the top layer, called soft agar, is inoculated with both a bacterial host and the phage-containing specimen.

Restriction-modification systems

protect bacteria from phage infection by quickly degrading incoming foreign DNA.

Generalized Transduction

results from a packaging error during phage assembly. Some phages degrade the bacterial chromosome into many fragments during lytic infection. Any of these short bacterial DNA fragments can be mistakenly packaged into the phage head during lytic infection. - Phage heads that contain only bacterial genes in place of phage genes cannot direct a phage replication cycle. - Because of this, they are called generalized transducing particles. - Following the release of the transducing particle from the phage-infected host, the particle binds to another bacterial cell and injects its DNA. That bacterial DNA may then integrate into the recipient cell by homologous recombination. Any gene of the donor cell can be transferred this way, which is why this mechanism is called generalized transduction.

Helical

appear cylindrical when viewed with the electron microscope. Their capsomeres are arranged in a helix, somewhat similar to a spiral staircase. Some helical viruses are short and rigid, whereas others are long and filamentous.

Icosahedral

appear spherical when viewed with the electron microscope, but their surface is actually 20 flat triangles arranged in a manner somewhat similar to a soccer ball.

Acute infections

are characterized by the sudden onset of symptoms of a relatively short duration.

Persistent Infections

can continue with or without symptoms for years, or even the life of the host.

Temperate Phage Infections

- Temperate Phages - have the option of either directing a lytic infection (productive infection) or incorporating their DNA into the host cell genome. - The latter situation is called a lysogenic infection, and the infected cell is a lysogen. - In a lysogenic infection, the phage DNA exists within the cell without causing damage. In this state, the integrated phage DNA, called a prophage, is replicated along with the host cell chromosome. - When the cell divides, the prophage is passed on to the cell's progeny. Later, the prophage can begin the process that leads to a productive infection.

Viruses are obligate intracellular parasites which makes them hard to study

- Unlike most bacteria and eukaryotic cells, which can be grown in pure culture, viruses require live organisms as hosts. - They are also too small to be seen with a light microscope and can be seen only with an electron microscope.

Enveloped viruses

- a lipid bilayer outside of the capsid. ----> Obtain that bilayer from the host cell. ------>Sandwiched between the Nucleocapsid and envelope is the matrix protein, which is unique to enveloped viruses.

Viral Replication

- all viruses go through the same 5 basic steps for replication: • Attachment - recognition of target surface • Entry - use of lysozyme • Synthesis - • Assembly - recognition of viral nucleic acid Release

Steps in the Replication of the Lytic Phage T4 in E. coli

1. Attachment - Phage attaches to specific receptors on the E. coli cell wall 2. Genome Entry - The tail contracts and phage DNA is injected into the bacterial cell leaving the phage coat outside 3. Synthesis - Phage genome is transcribed and phage proteins synthesized. Phage DNA is replicated, other Virion components are made, and host DNA is degraded. 4. Assembly - Phage components are assembled into mature Virions. Release - The bacterial cell lyses and many new infectious Virions are released. The burst size is the number of phage particles release- is about 200.

Animal Virus Replication

A generalized infection cycle of animal viruses can be viewed as a five-step process: attachment, genome entry, synthesis, assembly, and release.

Release

Budding - most enveloped viruses are released by budding, this is a process whereby the virus acquires its envelope. → Before budding occurs, virally encoded protein spikes insert into specific regions of the host cell's membrane. → Apoptosis - many viruses trigger a normal cellular process call apoptosis, also called programmed cell death, prior to the release of the viral particles.

Filamentous Phages

Filamentous phages are single-stranded DNA phages that look like long fibers. They cause productive infections, but the process does not kill the host cells. Infected cells, however, grow more slowly then uninfected cells.

Viruses have specific protein components that allow the Virion to attach (adsorb) to specific receptor sits on host cells.

For example, Phages have tail fibers that attach to host cells, and many animal viruses have protein structures called spikes that stick out from either the lipid bilayer of enveloped viruses or the capsid of non-enveloped viruses.

Restriction Enzymes

Not only explain why some bacteria can degrade foreign DNA, but they have also played an important role in the biotechnology revolution. The enzyme gave scientists a tool to remove genes from one DNA molecule, so that they can be joined to another, the basic for recombinant DNA technology.

Modification Enzymes

Protects the host cell's own DNA from the action of the restriction enzyme. It does this by adding methyl groups to the nucleobases recognized by the restriction enzyme.

Lytic or Virulent phages

exit the host at the end of the infection cycle by lysing the cell. These viral infections result in the formation of new viral particles and are called productive infections. An intensively studied lytic phage is T4, a double stranded DNA phage. During its infection cycle, the phage takes over a bacterial cell, directing that cell to synthesize new phage particles. The infection cycle of T4, which is similar to that of other lytic phages, can be viewed as a five-step process.

Complex

have more complicated structures. Phages are the most common examples of this, many have icosahedral Nucleocapsid, referred to as the head, with a long helical protein component, the tail.

Specialized Transduction

results from an excision mistake made by a temperate phage during its transition from a lysogenic to a lytic cycle. Following induction, the phage DNA is usually excised precisely from the bacterial chromosome. - The excised DNA containing both bacterial and phage genes -- replicates and then becomes incorporated into phage heads during assembly. - These phage particles do not carry the entire set of phage genes, so they are defective. The defective phage particles are then released as the host cells lyse. Only bacterial genes adjacent to the integrated phage DNA can be transferred, which is why the process is called specialized transduction.

Nucleocapsid

the capsid together with the nucleic acid it encloses They are composed of identical protein subunits, called capsomeres, arranged in a precise manner to form the capsid.

Transmissible spongiform encephalopathies

the characteristic sponge-like appearance of the brain tissues gave rise to the general term, which refers to all prion diseases.

Attachment

the process of attachment (adsorption) is basically the same in all virus-cell interactions. Animal viruses have attachment proteins or spikes on their surfaces. → The receptors to which these proteins bind are usually glycoproteins on the host cell cytoplasmic membrane, and often more than one receptor is required for effective attachment. → Because a Virion must bind to specific receptors, a particular virus may be able to infect only a single or a limited number of cell types and tissues called tropism, and most viruses can infect only a single species (the viral host range). → This accounts for the resistance that some animals have to certain diseases. As with receptors used by phages, the normal function of these receptors is completely unrelated to their role in virus attachment.

Uncoating

the process when the nucleic acid separates from its protein coat before the start of replication. → Most DNA viruses replicate in the nucleus of the host cell and use the host cell machinery for DNA synthesis as well as gene expression. → These viruses often encode their own DNA polymerase; this allows them to replicate even if the host cell is not actively replicating its own chromosome. → Replication of double-stranded DNA viruses is fairly simple because it follows the central dogma of molecular biology. → Replication of single-stranded DNA viruses is quite similar to that of double-stranded DNA viruses, except that a complement to the single-stranded DNA molecule must be synthesized.

Capsid

the protein coat, protects the nucleic acid from enzymes and toxic chemicals in the environment.

Provirus

the silent viral genome The fact that a provirus cannot be eliminated from the body means that the disease can recur even after an extended period without symptoms.

Prions

are composed solely of protein, which is reflected in the name.

Latent infections

the viral genome remains silent within a host cell, yet can reactivate to cause a productive infection Some viruses do not integrate into the host cell chromosome; rather, they replicate independently of the host genome, much like a plasmid.

Retroviruses

which include the human immunodeficiency virus (HIV), have a (+) strand RNA genome, and carry reverse transcriptase within the virion.

Viruses contain only a single type of nucleic acid --> either RNA or DNA but never both.

This provides a useful method for classifying viruses, which are frequently referred to as either RNA or DNA viruses. The genome may be linear or circular, either double-stranded or single-stranded.

Fusion with the host membrane

→ In the case of fusion: the lipid envelope of the virion fuses with the cytoplasmic membrane of the host cell after the virion attaches to the host cell receptor, much as drops of oil in an aqueous medium can fuse together. As a result of the fusion, the nucleocapsid is released directly into the cytoplasm.

Assembly and Maturation

→ It involves bringing together newly formed viral nucleic acid with capsid proteins and packaging them to form the nucleocapsid. → Assembly often involves modification of the newly made viral proteins, which may occur within the host cell, or after the new virions leave the host cell. Non-enveloped viruses mature fully in the host cell cytoplasm. In the case of enveloped viruses, some maturation steps occur as the virion leaves the host cell.

Penetration and Uncoating

→ The mechanism an animal virus uses to enter its host cell depends in part on whether the virion is enveloped or non-enveloped. → In all cases, the entire virion is taken into the cell. → Enveloped viruses enter the host cell by one of two mechanisms: ○ Fusion with the host membrane Endocytosis

uncoating cont

→ Their replication always requires a virally encoded RNA polymerase, often called a replicase. → Antigenic Drift - influenza viruses exhibit a type of antigenic variation → This occurs as mutations accumulate in genes encoding key viral surface proteins that are recognized by the immune system. → Antigenic Shift - when a new subtype of a virus is formed by reassortment between different strains of a virus or even between different viruses, the phenomenon is known as antigenic shift.

Endocytosis

→ Viruses that enter by endocytosis take advantage of receptor-mediated endocytosis, a normal mechanism by which cells bring certain extracellular material into the cell. → After a virion is taken into the cell, the viral envelope fuses with the membrane of the endosome, releasing the nucleocapsid into the cytoplasm. → Non-enveloped viruses, which have no lipid envelope, cannot fuse to host membranes to enter cells. Therefore, the virions enter only via endocytosis. Once in the endosome, the nucleocapsid is released into the cytoplasm.