Microbiology chapter 6

In experiment E. Coli mixed with T4

After short interval, the mixture was greatly diluted so that any virions released upon host cell lysis would not encounter and infect other cells. The diluted culture was then incubated, and over time samples were removed to determine the number of infectious phages particles in the culture. This was determined using plaque assay as we describe in section 6.5.

Attachment (adsorption)

All viruses, with the exception of plant viruses, must attach to a potential host cell long enough to gain entry into the cell. Attachment to host is accomplished by specific interactions between molecules on the surface of the virion (ligand) and molecules on the surface of the host cell called receptors. Binding of an animal virus particle to its receptor often causes conformational changes in virion proteins that facilitate interaction with secondary receptors, entry into the host, and nucleocapsid uncoating

Cellular genomes are

Always double stranded (ds) DNA

Influenza virions have

An RNA genome and carry an enzyme that synthesizes RNA using an RNA template. Thus although viruses lack true metabolism and cannot reproduce independently of living cells, their virions may carry one or more enzymes essential to the completion of their life cycle

Poxvirus virions

Are among largest of the animal viruses (abt 400 by 240 by 200 nm in size) and can be seen with a light microscope. Complex internal structure with an ovoid to brick-shaped exterior

Leukemias

Are composed of undifferentiated malignant white blood cells that circulate throughout the body. Indeed, dozens of kinds of cancers arise from a variety of cell types and afflict all kinds of organisms.

Some viruses use noncapsid proteins

As scaffolding upon which the capsids are assembled Most important advantage of this design strategy is the viral genome is used with maximum efficiency. I.e. tobacco mosaic virus capsid is constructed using a single type of protomer.

When MOI is high, a virulent phages would rapidly _______________ the avaible host cells in its environment. However, a prophage will be replicated as the host cell reproduces.

Destroy

Vaccinia virus

Double stranded DNA genome is associated with proteins and contained in the core, a central structure shaped like a bioconcave disk and surrounded by a membrane. Two lateral bodies lie between the core and the virion's outer envelope and contain viral enzymes.

A plot of the number of phages particles versus time shows several distinct periods in the resulting growth curve (red line). The latent period occurs immediately following addition of the phages.

During this period, no virions are released. The rise period follows and is characterized by the rapid release of infective phages. Finally, a plateau is reached and no more virions are produced.

Virion morphology progress has come from

Electron microscopy, X-ray diffraction, biochemical analysis, and immunology

Virus genomes are

Employ all four possible nucleic acid types: dsDNA, single stranded (SS) DNA, ssRNA, and dsRNA. All four types are used by animal viruses. Most plant viruses have ssRNA genomes, and most bacterial and archaeal viruses have dsDNA. The size of viral genomes also varies greatly. Some save additional space by using overlapping genes.

Some viruses have ________ within their capsids

Enzymes Usually involved in nucleic acid replication

cytopathic effect (CPE)

Eukaryotic viruses can cause microscopic or macroscopic degenerative changes or abnormalities in host cells and in tissues that are distinct from lysis. Viruses use a variety of mechanisms to cause cytopathic and cytocidal effects. One mechanism of particular note is that some viruses cause the host cell to be transformed into a malignant cell.

Viruses can exist

Extracellularly or intracellularly When extracellularly, they are inactive because they possess few, if any, enzymes and cannot reproduce outside of living cells When intracellularly, viruses exist primarily as nucleic acids that can, at some point in the viral life cycle, commander host cells and use them to synthesize viral components from which progeny virions are assembled and eventually released.

Three modes of different entry employed by animal viruses

Fusion of the viral envelope with the host cell's plasma membrane Entry by endocytosis Release of viral nucleic acid into the cytoplasm of the host cell.

Important feature of the synthesis stage is the tight regulation of

Gene expression and protein synthesis. Genes are often referred to as early, middle, or late genes based on when they are expressed. The proteins they encode are likewise referred to as early, middle, or late proteins.

Viruses have been classified into numerous families based on

Genome structure, life cycle, morphology, and genetic relatedness

Viruses

Group of infectious agents unique in their simple, a cellular organization and pattern of multiplication

Temperate phages

Have two options, upon entry into the host, they can multiply like virulent phages and lyse the host cell, or they can remain within the host without destroying it. Bacteriophage lambda is an example of this type of phages.

binal symmetry

Head that resembles an icosahedron and a tail that is helical . Icosahedron head is elongated by one or two rows of hexamers in the middle and contain the DNA genome. The tail is composed of a collar joining it to the head, a central hollow tube, a sheath surrounding the tube, and a complex baseplate. In T-even phages, the baseplate is hexagonal and has a pin and a jointed long tail fiber and a short tail fiber at each corner.

Viruses use _________________ that are always present on the surface of the host cell and are important for normal host cell function.

Host receptors For instance, human immunodeficiency virus (HIV) particles bind to two different proteins on human cells (e.g. CD4 & CCR5)

Most viruses have either. (Capsids of complex symmetry)

Icosahedral or helical capsids, but some viruses do not fit into either category. Pox viruses and large bacteriophages are two important examples.

Two major types of tumor growth patterns exist

If the tumor cells remain in place to form a compact mass, the tumor is benign. In contrast, cells from malignment or cancerous tumors actively spread throughout the body in a process known as metastasis. Some cancers are not solid but cell suspensions

Myc

Important proto-oncogene encodes a protein called Myc. Myc controls transcription of many genes, including some involved in DNA replication and other cell-cycle-related functions.

What is occurring during the latent period?

In a subsequent set of experiments , infected cells were artificially lysed during the latent period. This revealed that intracellular virions could not be detected early in the latent period. In essence, the phages disappeared once inside the cell. This period is called the eclipse period because the infecting virions were concealed or eclipsed within host cell. Other experiments eventually showed that a carefully orchestrated series of events occurs during the latent period.

Virions of no enveloped viruses and some enveloped viruses enter cells by one of the endocytic pathways

Including clathrindependent endocytosis and macropinocytosis. Resulting endocytic vesicle contains the virion and fuses with endosome. Endosome o enzymes can aid in virion uncoating and low pH often triggers the uncoating process.

Can continue for many generations until conditions arise that cause the prophage to initiate synthesis of phages proteins and to assemble new virions, a process called ________________

Induction Is commonly caused by changes in growth conditions or ultraviolet irradiation of the host cell.

Pandoraviruses

Infect protist. About 2.5 x 10^6 nucleotides long, exceeding some bacteria and archaea in coding capacity.

Infections of eukaryotic cells

Infection that results in cell death is a cytocidal infection. As with bacteria and archaeal viruses, this can occur by lysis of the host.

Carcinogenesis

Is a complex, multi step process caused by mutations in multiple genes. Some mutations lead to the unregulated proliferation that is a major characteristic of a cancer cell. Other mutations prevent cells from repairing DNA damage, thereby making the cells more inclined to mutate further. This leads to additional genotypes changes. Example. Mutations that may promote metastasis may occur, allowing the tumor to invade other tissues.

icosahedral capsid

Is a regular polyhedron with 20 equilateral triangular faces and 12 vertices. Most efficient way to enclose a space. Constructed from ring-or knob-shapes assemblages of five or six protomers. Assemblages are called capsomers

Cancer

Is one of the most serious medical problems in developed nations, and it is the focus of an immense amount of research

Noneveloped or naked viruses

Lacking a membrane Construct a capsid from many copies of one protein and a few minor proteins. Each subunit is termed a protomer, and thousands of protomers self-assemble to form capsid

The ends of ____________ viral genomes May be covalently closed, attached to a protein, or otherwise masked.

Linear Some DNA genomes can switch from one form to the other.

E. Coli phages lambda has a __________ genome in its capsid, but it becomes _____________ once it enters the host cell.

Linear and circular

Infection does not always result in __________ of host cells.

Lysis Some viruses (e.g. herpesvirus) can establish persistent infections lasting many years.

As a result of induction, the _____________ cycle ends and the _________ cycle commenced; the host cell lyses and progeny phages particles are released.

Lysogenic Lytic

Proto-oncogenes

Normal cellular genes Normally are expressed if cell division is to occur. However, they normally are expressed only if the cell receives an appropriate signal, such as binding of a growth factor to a receptor on the cell surface.

Envelope

Nucleocapsid a of many animal viruses, some plants viruses, and at least one bacterial virus are surrounded by an outer membranous layer called ______________. Animal virus envelopes usually arise from the plasma or nuclear membranes of the host cell. Envelope lipids and carbohydrates are therefore acquired from the host.

Fusion (of viral envelope with the host cell membrane)

Often involves viral envelope glycoproteins or phospholipids that interact with proteins in the plasma membrane of the host cell. These events allow nucleocapsid to enter. Nucleocapsid then enters host cell cytoplasm, where a viral enzyme carried within the nucleocapsid begins synthesizing viral mRNA while it is still within the capsid.

Two of the most important tumor suppressor proteins are

Rb and p53 P52 is often referred to as "the guardian of the genome" because not only does it cause cell cycle attest, but it also initiated programmed cell death in response to DNA damage. Programmed cell death, also called apoptosis. P53 when inactivated, the cell reproduces in a n unregulated fashion, avoiding programmed cell death even when it should destroy itself. Can lead to the accumulation of additional mutations that contribute to carcinogenesis.

Plant viruses Do not have

Receptors for binding Rather, damage of host cells is required for the virus particles to enter the host.

Nonenveloped animal viruses cannot employ the membrane fusion mechanism for _____________ from the endosome . In this case, it is thought that the low pH of the endosome causes a conformational change in the capsid. The altered capsid contacts the endosome membrane and either releases the viral nucleic acid into the cytosol or ruptured the membrane to release the intact nucleocapsid

Release

What is missing from viruses?

Ribosomes for protein synthesis and a mechanism for generating ATP. Cytoplasm is absent, and while a few enzymes may be found, there are not enough to sustain cellular processes

Synthesis stage RNA viruses

Same is not true for RNA viruses. Cellular organisms lack the enzymes needed to replicate RNA or to synthesize mRNA from an RNA genome. Therefore RNA viruses must carry in their nucleocapsids the enzymes needed to complete the synthesis stage, or the enzymes must be synthesized during the infection process.

Nucleocapsid

Simplest virions. Composed of a nucleic acid, either DNA or RNA, and a protein coat called a capsid Nucleocapsid Of influenza viruses are thin and flexible and are enclosed within an envelope.

Segmented genomes

Some RNA viruses have Consist of multiple pieces (segments) of RNA. Each segment codes for one protein and may be as many as 10-12 segments. Usually all segments are enclosed in the same capsid. Genome of mosaic virus, a virus that infects certain grasses, is composed of three segments distributed among three different virions.

Capsid

Surrounds the viral nucleic acid, protects the viral genome, and often aids in its transfer between host cells Only a small fraction of the genome is used to code for the capsid

In humans, the presence of receptor molecules on a cell surface varies with the organ and tissue. Viruses have ______________.

Tropism

Viral replication complexes and viroplasms are sometimes referred to as

Virus factories

Virion

complete virus particle

Most DNA viruses use _____________ as their genetic material. However, some have ______________ genomes.

dsDNA and ssDNA In both cases genomes may be either linear or circular.

Relatively few RNA viruses have ______________ genomes. More common are viruses with ____________ genomes.

dsDNA and ssDNA Polio, tobacco virus mosaic, rabies, influenza, and human immunodeficiency (HIV) are all ssRNA viruses.

TMV is a well studied example of

helical capsid structure. Self-assembly of TMV protomers into a helical arrangement produces a rigid tube. The capsid encloses an RNA genome, which is wound in a spiral and lies within a groove formed by the protein subunit. Not all helical capsids are as rigid as the TMV capsid.

spikes

projections from outer surface Can be used to identify some virus Spikes are involved in virion attachment to the host cell surface

Middle proteins often participate in

replication of the viral genome or activation of expression of late genes

Helical capsids

shaped like hollow tubes with protein walls Size is influenced by both its protomers and the viral genome. The diameter of the capsid is a function of the size, shape, and interactions of the protomers. The length of the capsid appears to be determined by the nucleic acid because a helical capsid does not extend much beyond the end of the viral genome

Virology

study of viruses

Neoplasia

unregulated abnormal new cell growth and reproduction A tumor is a growth or lump of tissue resulting from neoplasia

Late proteins usually include

Capsid proteins and other proteins involved in self-assembly and release

bacteriophages (phages)

A virus that infects bacteria Fewer archaeal have been identified Most known viruses infect eukaryotic organisms, including plants, animals, protists, and fungi

Viral life cycle has 5 steps

1. Attachment (adsorption) to a host 2. Entry of either entire nucleocapsid or just the viral nucleic acid into the host. If nucleocapsid enters, in paying of the genome usually occurs before the life cycle continues. 3.Synthesis stage Viral genes are transcribed and translated. This allows the virus to take control of the host cell, forcing it to manufacture viral genomes and viral proteins. 4. Assembly New nucleocapsids are constructed by self-assembly of coat proteins and nucleic acids are packaged within. 5. Virion release Mature virions escape the host

To understand role viruses play in cancer, we must begin by considering _________________ when viruses are not involved.

Carcinogenesis

Lytic and lysogenic infections are common for

Bacterial and archaeal cells Most bacteriophages are either virulent or temperate

Plant virus is often achieved

By infection by plant eating insects that carry virions from one plant to another. The virions are deposited in plant tissues as the insect devours the plant. Some viruses may alter their plant hosts to promote activity of the insects and thereby foster transmission to new plants.

Envelope proteins are coded for

By viral genes and may even project from the envelope surface as spikes, which are also called peplomers Many envelope viruses have virions with a somewhat variable shape and are called pleomorphic. Bullet shaped rabies viruses are firmly attached to the underlying nucleocapsid and endow the virion with a constant, characteristic shape.

virion size

Can be extraordinarily tiny (abt 20 nvm in diameter) to about the same size as a rod-shaped bacterial cell (1.5 x 0.5 um) Smallest little larger than ribosomes, whereas mimiviruses, among the largest viruses known, can be seen in the light microscopes.

Animal and plant virus synthesis stsge

Carry out synthesis stage and subsequent assembly step within the host's cytoplasm. To protect these processes from host defenses, some viruses bring about the reorganization of host cell membranes (e.g. membranes of the ER, Golgi apparatus, and lysosomes) to form membranous structures that enclose the machineries needed for genome replication, transcription, and protein synthesis. Structures are called viral replication complexes, and appear as vesicles, tubular structures, and other forms in electron micrograph of infected cells. These areas of concentrated viral genomes, mRNAs, and proteins are called video plasma, and they are also visible in electronicrographs if infected cells.

Corynebacterium diptheriae

Cause of diphtheria, is infected with phages b. The phages genome encodes diphtheria toxin, which is responsible for the disease. Thus only strains of C. Diptheriae that are infected by the phages cause disease.

Many archaeal viruses establish ______________ infections.

Chronic

Capsomers

Composed of five protomers are called pentamers (pentons); hexamers (hexons) are capsomers that posssess six protomers. Pentamers are usually at the vertices of the icosahedron, whereas hexamers generally form its edges and triangular faces. Virions of some RNA viruses have pentamers and hexamers constructed with only one type of subunit. Other virions have pentamers and hexamers composed of different proteins. Many icosahedral capsids contain both pentamers and hexamers, some have only pentamers.

Enveloped viruses

Covered by lipid membrane Require both nucleocapsid proteins and additional proteins to anchor the membrane

Another important outcome of lysogeny is ________________

Lysogenic conversion This occurs when a temperate phages changes the phenotype of its host. Lysogenic conversion often involves alteration in surface characteristics of the host. Example. When a member of genus salmonella is infected by epsilon phages, the phages changes activities of several enzymes involved in construction of the carbohydrate component of the bacterium's lipopolysaccharide. This eliminates the receptor for epsilon phage, so the bacteria becomes immune to infection by another epsilon phages. Gives the host pathogenic properties

Infected bacteria are called

Lysogens or lysogenic bacteria Lysogenic bacteria reproduce and in most other ways appear to be perfectly normal Two distinct characteristics First. They cannot be reinfected by the same virus; that is they have immunity to superinfection. Second.they reproduce, the prophage is replicated and inherited by progeny cells.

Relationship between a temperate phages and it's host is

Lysogeny

One step growth experiment devised in 1939 by

Max delbruck and Emory Ellis Worked with bacteriophage T4 They knew T4 lysed its host, E. coli, and released progeny phages.

Viruses serve as

Model organisms for understanding DNA replication, RNA synthesis, and protein synthesis

Virulent phages

One that has only one option; to begin multiplying immediately upon entering its bacterial host, followed by release from the host by lysis. T4 is an example of a virulent phages.

Hemagglutinin

Participate in virion attachment to host cells. Most of its envelope proteins are glycoproteins—proteins that have carbohydrates attached to them.

Tropism

Particular cell types are infected based on the distribution of surface receptors in tissues. Example poliovirus receptor are found only in human nasopharynx, gut, and anterior horn cells of the spinal cord. Therefore poliovirus infect these tissues, causing disease that range from milder forms such as gastrointestinal disease to more serious paralytic disease. In contrast measles virus receptors are present in most tissues and disease is disseminated throughout the body.

receptor specificity

Partly responsible for preference viruses have for a particular host Bacteriophages not only infect a particular bacterial species but often infect only certain strains within a given species. Animal viruses infect specific animals and, in some cases, only particular tissues within host If receptor recognized by a virus is present in numerous animas, then the virus will infect more than one animal species. Such is the case with rabies viruses.

Some viruses, including Ebola, mimic damaged cells by exposing certain ____________ on their surface.

Phospholipids This display is a hallmark of dying cells targeted for phagocytosis. By camouflaging themselves as damaged cells, viruses can gain entry to wide variety of cell types.

Form of the virus that remains within its host is called

Prophage Is simply the viral genome either integrated into the bacterial chromosome or free in the cytoplasm.

Two genes that allow cancer to grow uncontrollably . Must be mutated

Proto-oncogenes and tumor suppressor genes Their names suggest that these genes are somehow abnormal.

Many Early proteins are involved in

Taking over host cell

Nonglycosylated protein

The M1 (matrix) protein, is found on the inner surface of the envelope and stabilizes both the lipid envelope and the display of both types of spike.

Two advantages of lysogeny have been recognized

The first is that lysogeny allows the viral nucleic acid to be maintained within its host. Bacteria often become dormant due to nutrient deprivation, and while in this state, they do not synthesize nucleic acids or proteins. Prophage would survive but most virulent bacteriophages would not be replicated, as they require active cellular biosynthetic machinery. Their genome would be degraded as the host cell entered dormancy. Second advantage arises when there are many more phages in an environment than there are host cells, a situation virologists refer to as a high multiplicity of infection(MOI). In these conditions lysogeny enables survivalist if infected host cells within a population that has few uninfected cells.

During carcinogenesis, mutations arise that disrupt the normal activity of these two types of genes.

The first type of mutation allows proto-onocogrnes or their protein products to function without an appropriate signal. Thus the proto-oncogene or its protein is active even when it should not be. Second type of mutation prevents expression of tumor suppressor genes, yields nonfunctional tumor suppressor proteins, or in some other way leads to inactivation of a tumor suppressor protein. Thus the Cell can continue cell division even when it shouldn't, such as in the presence of severe DNA damage.

Virions even more elaborate than poxviruses

The virions T2, T4, and T6 phages (T-even phages) that infect Escherichia coli are said to have Binal symmetry.

Entry into the host (after attachment)

The virus's genome or the entire nucleocapsid enters the cytoplasm. For many bacteriophages only their nucleic acid enters the host's cytoplasm, leaving the capsid outside and attached to the cell. In contrast to phages, many eukaryotic viral nucleocapsids enter the cytoplasm with the genome still enclosed. Once inside the cytoplasm, some shed their capsid proteins in a process called uncoating, whereas others remains encapsulated. Because penetration and uncoating are often coupled, we consider them together.

Synthesis stage

This stage of the viral cycle differs dramatically among viruses because the genome of a virus dictates the events that occur. dsDNA viruses, the synthesis stage can be very similar to the typical flow of information in cells. Genetic information is stored in DNA and replicated by enzymes called DNA polymerase, recorded as mRNA (transcription), and decided during protein synthesis (translation). Because of this similarity, some dsDNA viruses have the luxury of depending solely on their host cells' biosynthetic machinery to replicate their genomes and synthesize their proteins.

____________ cells have aberrant shapes and altered plasma membranes that may contain distinctive molecules (tumor antigens). These changes result from the tumor cells becoming less differentiated. Their unregulated proliferation and loss of differentiation result in invasive growth that forms unorganized cell masses.

Tumor

When such a signal is received, the cell initiates the cell cycle, but it cannot continue past a checkpoint controlled by the activity of proteins encoded by ____________________.

Tumor suppressor genes

Influenza virus

Two types of spikes Some spikes consist of the enzyme neuraminidase, which functions in the release of mature virions from the host cell. Other spikes are hemagglutinin proteins, named because they bind virions to red blood cells and cause the cells to clump together—a process called hemagglutination.

It is estimated that about 10 - 20% of human cancers have

Viral etiology

Viruses multiply and give rise to new progeny viruses in a new host cell by

Virus must guile and subterfuge to access an appropriate host, enter the host, and avoid any defenses the host might employ to rid itself of the virus or prevent its multiplication. Once inside host cell, a viruses uses a repertoire of clever tricks to take control of cellular functions, thereby ensuring that viral genomes, mRNAs, and proteins are synthesized using ATP generated by host. Viral strategies are often related to virion structure, in particular the nature of its genome. Viruses with similar type genome (e.g. dsDNA, ssDNA) often employ similar tactics

tumor suppressor proteins

When active, they prevent progression through the cell cycle. This for cell division to occur, proto-oncogene proteins (sometimes called protooncogene proteins) must be active, and tumor suppressor proteins must be inactive.