FR- Virology

Question 1

What is the difference between temperate and lytic bacteriophages?

Answer 1

• After the progeny phage particles reach a certain number, they cause the host to lyse, so they can be released and infect new host cells.
• Thus this process is called the lytic cycle.
• Temperate bacteriophages, on the other hand, do not immediately kill their host. Instead, the phage establishes a relationship with their host called lysogeny, and bacteria that have been lysogenized are called lysogens.
• Many temperate phages establish lysogeny by inserting their genomes into the bacterial chromosome. The inserted viral genome is called a prophage.
• The host bacterium is unharmed by this, and the phage genome is passively replicated as the host cell’s genome is replicated.
• Temperate phages can remain inactive in their hosts for many generations.
• However, they can be induced to switch to a lytic cycle under certain conditions, including UV irradiation.
• When this occurs, the prophage is excised from the bacterial genome and the lytic cycle proceeds.

Question 2

When does generalized transuction most often occur?

Answer 2

during the lytic cycle of virulent phages but sometimes happens during the lytic cycle of temperate phages

Question 3

Which part of the bacterial genome can be transferred after being partially degraded as the virus takes control of its host?

Answer 3

Any part

Question 4

Which phages are called generalized transducing particles?

Answer 4

• During general transformation, a fragment of the host genome that happens to be about the same size as the phage genome is mistakenly packaged.
• Such a phage is called a generalized transducing particle, because once it is released, it may encounter a susceptible host cell and eject the bacterial DNA it carries into that cell.
• However, because it lacks viral genes this does not initiate a lytic cycle

Question 5

What are Abortive transductants?

Answer 5

About 70 to 90% of the transferred DNA is not integrated but often is able to remain intact temporarily and be expressed. Abortive transductants are bacteria that contain this nonintegrated, transduced DNA and are partial diploids

Question 6

What must be done to preserve the transferred genes?

Answer 6

As in transformation, once the DNA fragment has been released into the recipient cell, it must be incorporated into the recipient cell’s chromosome to preserve the transferred genes

Question 7

How is specialized transduction made possible?

Answer 7

• In specialized transduction, only specific portions of the bacterial genome are carried by transducing particles. Specialized transduction is made possible by an error in the lysogenic life cycle of temperate phages that insert their genomes into a specific site in the host chromosome. When a prophage is induced to leave the host chromosome, excision is sometimes carried out improperly. The resulting phage genome contains portions of the bacterial chromosome (about 5 to 10% of the bacterial DNA) next to the integration site
• However, the transducing particle is defective because it lacks some viral genes and cannot reproduce without assistance. In spite of this, it will inject the remaining viral genome and any bacterial genes it carries into another bacterium. The bacterial genes may become stably incorporated under the proper circumstances

Question 8

What is the best-studied example of specialized transduction?

Answer 8

It is carried out by the E. coli phage lambda; it involves the lambda genome inserting into the host chromosome at specific locations known as attachment or att sites

Question 9

What is a complete virus particle called?

Answer 9

A viron

Question 10

Virion morphology has been intensely studied over the past decades because of the importance of viruses. Progress has come from the use of several different techniques:

Answer 10

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

Question 11

Describe the general structural properties of viruses

Answer 11

• Virions range in size from about 10 to 400 nm in diameter.
• The smallest are a little larger than ribosomes, whereas mimiviruses, the largest viruses known, have virions larger than some of the smallest bacteria and can be seen in the light microscope.
• However, most virus particles must be viewed with electron microscopes.
• The simplest virions consist only of a nucleocapsid, which is composed of a nucleic acid, either DNA or RNA, and a protein coat called a capsid which surrounds the viral nucleic acid, protects the viral genome, and often aids in its transfer between host cells
• Capsids self-assemble by a process that is not fully understood. Some viruses use noncapsid proteins as scaffolding upon which the capsids are assembled.

Question 12

What are protomers?

Answer 12

Among the proteins encoded by the viral genome are the capsid proteins, which are called protomers.

Question 13

Describe the generalized structure of Virions:

(a) The simplest virion
(b) Virions of enveloped viruses

Answer 13

(a) The simplest virion is that of a nonenveloped virus (nucleocapsid), consisting of a capsid assembled around its nucleic acid.
(b) Virions of enveloped viruses are composed of a nucleocapsid surrounded by a membrane called an envelope. The envelope usually has viral proteins called spikes inserted into it.

Question 14

State the three types of capsid symmetry

Answer 14

• helical
• icosahedral
• complex

Question 15

What are viruses with virions having an envelope called, what are those with an envelope called?

Answer 15

Viruses with virions having an envelope are called enveloped viruses, whereas those lacking an envelope are called nonenveloped or naked viruses

Question 16

Describe the shape of helical caspids

Give an example of a virus with that caspid structure

Answer 16

• Helical capsids are shaped like hollow tubes with protein walls.
• Tobacco mosaic virus is a well-studied example of helical capsid structure
• The 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 subunits

Question 17

Describe the shape of icosahedral caspids

Answer 17

• An icosahedron is a regular polyhedron with 20 equilateral triangular faces and 12 vertices
• Icosahedral capsids are the most efficient way to enclose a space.
• They are constructed from ring- or knob-shaped assemblages of five or six protomers; the assemblages are called capsomers

Question 18

Give examples od caspids of complex symmetry

Answer 18

Most viruses have either icosahedral or helical capsids, but some viruses do not fit into either category.

Poxviruses and large bacteriophages are two important examples.

Question 19

Explain the properties of viral envelopes and enzymes

Answer 19

• The nucleocapsids of many animal viruses, some plant viruses, and at least one bacterial virus are surrounded by an outer membranous layer called an envelope
• 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. In contrast, envelope proteins are coded for by viral genes and may even project from the envelope surface as spike, which are also called peplomers
• In many cases, spikes are involved in virion attachment to the host cell surface. Because spikes differ among viruses, they also can be used to identify some viruses. Many enveloped viruses have virions with a somewhat variable shape and are called pleomorphic.
• However, the envelopes of viruses such as the bulletshaped rabies viruses are firmly attached to the underlying nucleocapsid and endow the virion with a constant, characteristic shape

Question 20

Explain the properties of the enveloped influenza virus

Answer 20

• Influenza virus is a well-studied enveloped virus with 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, so named because they bind virions to red blood cells and cause the cells to clump together—a process called hemagglutination.
• Influenza virus’s hemagglutinins participate in virion attachment to host cells.
• Most of its envelope proteins are glycoproteins— proteins that have carbohydrate attached to them.
• A nonglycosylated protein, the M (matrix) protein, is found on the inner surface of the envelope and helps stabilize it

Question 21

In addition to enzymes associated with the envelope or capsid (e.g., influenza neuraminidase), some viruses have enzymes within their capsids

Answer 21

• Such enzymes are usually involved in nucleic acid replication.
• For example, influenza virus 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 cycles

Question 22

One clear distinction between cellular organisms and viruses is the nature of their genomes. Cellular genomes are always doublestranded (ds) DNA. Viruses, on the other hand, employ all four possible nucleic acid types:

Answer 22

• dsDNA, single-stranded (ss) DNA, ssRNA, and dsRNA.
• Most plant viruses have ssRNA genomes, and most bacterial viruses have dsDNA

Question 23

Most DNA viruses use dsDNA as their genetic material. However, some have ssDNA genomes, in both cases:

Answer 23

• In both cases, the genomes may be either linear or circular. Some DNA genomes can switch from one form to the other.
• For instance, the E. coli phage lambda has a linear genome in its capsid, but it becomes circular once it enters the host cell
• Relatively few RNA viruses have dsRNA genomes. More common are viruses with ssRNA genomes.
• Polio, tobacco mosaic, SARS, rabies, mumps, measles, influenza, human immunodeficiency, and brome mosaic viruses are all ssRNA viruses.

Question 24

Some RNA viruses have segmented genomes, what is this?

Give an example of a virus with a segmented genome

Answer 24

• —genomes that consist of more than one piece (segment) of RNA. In many cases, each segment codes for one protein and there may be as many as 10 to 12 segments.
• Usually all segments are enclosed in the same capsid; however, this is not always the case. For example, the genome of brome mosaic virus, a virus that infects certain grasses, is composed of three segments distributed among three different virions.

Question 25

What must happen for a virus to give rise to new progeny viruses?

Answer 25

• If a virus is to multiply and give rise to new progeny viruses, it must find and use (and in many cases abuse) a host cell.
• To accomplish this, a virus must use 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 a host cell, a virus uses a repertoire of clever tricks to take control of cellular functions, thereby ensuring that viral genomes, mRNAs, and proteins are synthesized.
• The diversity of tricks viruses use has led to a plethora of distinctive viral life cycles (also called viral replicative cycles).
• The tricks used by a virus are often related to its virion structure, in particular the nature of its genome. Thus, viruses with a similar type of genome (e.g., dsDNA, ssRNA) often employ similar tricks.

Question 26

Despite the diversity of viral life cycles, a general pattern of viral replicative cycles can be discerned; it can be divided into five steps:

Answer 26

1. viruses need a host cell in which to multiply, the first step is usually attachment (often called adsorption) to a host.
2. This is followed by entry of either the nucleocapsid or the viral nucleic acid into the host. If the nucleocapsid enters, uncoating of the genome usually occurs before the life cycle continues.
3. Once inside the host cell, the synthesis stage begins. During this stage, viral genes are expressed. That is, the virus’s 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. Then follows the assembly stage, during which new nucleocapsids are constructed by self-assembly of coat proteins with the nucleic acids.
5. Finally, during the release step, mature virions escape the host

Question 27

Describe the attachment stage of the viral llife cycle

Answer 27

• 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 the host is accomplished by specific interactions between molecules on the surface of the virion (ligands) and molecules on the surface of the host cell called receptors.
• For instance, some bacteriophages use cell wall lipopolysaccharides and proteins as receptors, while others use teichoic acids, flagella, or pili.
• 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 uncoating.

Question 28

Describe the specificity of viral attachment (adsorption)

Answer 28

• Receptor specificity is at least partly responsible for the preferences viruses have for a particular host.
• Bacteriophages not only infect a particular bacterial species but often infect only certain strains within a given species.
• Likewise, animal viruses infect specific animals and, in some cases, only particular tissues within that host.
• However, if the receptor recognized by a virus is present in numerous animals, then the virus will infect more than one animal species. Such is the case with rabies viruses

Question 29

Why have viruses evolved such that they use host receptors that are always present on the surface of the host cell?

Answer 29

Viruses have evolved such that they use host receptors that are always present on the surface of the host cell and are important for normal host cell function.

Because the cell surface proteins are vital for cellular function, mutations that change them significantly are not tolerated, and this ensures that the virus can infect the host. In some cases, two or more host cell receptors are involved in attachment.

For instance, human immunodeficiency virus (HIV) particles bind to two different proteins on human cells (e.g., CD4 and CCR5). Both of these host molecules normally bind cytokines—signaling molecules used by the immune system

Question 30

Why are plant viruses a notable exception to attachment based on receptor binding?

Answer 30

No receptors have been identified for plant viruses. Rather, damage of host cells is required for the virus particles to access and enter the host. This is often achieved by plant-eating insects that carry virions from one plant to another.

Question 31

Explain the entry stage of the viral life cycle

Answer 31

After attachment to the host cell, 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, the nucleocapsid of many viruses of eukaryotes enters the cytoplasm with the genome still enclosed. Once inside the cytoplasm, some shed their capsid proteins in a process called uncoating, whereas others remain encapsidated

Question 32

What are the three different modes of entry usually employed by animal viruses?

Answer 32

Fusion of the viral envelope with the host cell’s plasma membrane, entry by endocytosis, and release of viral nucleic acid into the cytoplasm of the host cell

Question 33

How do virions of nonenveloped viruses and some enveloped viruses enter cells?

How do virions of most enveloped viruses enter cells?

Answer 33

• By one of the endocytic pathways, including clathrindependent endocytosis and macropinocytosis. The resulting endocytic vesicle contains the virion and fuses with an endosome.
• For some enveloped viruses, the viral envelope fuses with the endosomal membrane, and the nucleocapsid is released into the cytosol (the capsid proteins may have been partially removed by endosomal enzymes). Once in the cytosol, the viral nucleic acid may be released from the capsid upon completion of uncoating or may function while still attached to capsid components.

Question 34

Explain the synthesis stage of the viral life cycle

Answer 34

• This stage of the viral life cycle differs dramatically among viruses because the genome of a virus dictates the events that occur.
• For dsDNA viruses, the synthesis stage can be very similar to the typical flow of information in cells. That is, the genetic information is stored in DNA and replicated by enzymes called DNA polymerases, recoded as mRNA (transcription), and decoded 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.
• The same is not true for RNA viruses. Cellular organisms (except for plants) 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
• Some animal and plant viruses carry out the 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 endoplasmic reticulum, Golgi apparatus, and lysosomes) to form membranous structures that enclose the machineries needed for genome replication, transcription, and protein synthesis
• The structures are called viral replication complexes, and they appear as vesicles, tubular structures, and other forms in electron micrographs of infected cells

Question 35

Explain one important feature of the synthesis stage?

Answer 35

• One 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.
• Many early proteins are involved in taking over the host cell. Middle proteins often participate in replication of the viral genome or activation of expression of late genes. Late proteins usually include capsid proteins and other proteins involved in self-assembly and release

Question 36

Explain the assembly stage of the viral life cycle

Answer 36

• Several kinds of late proteins are involved in the assembly of mature virions.
• Some are nucleocapsid proteins, some are not incorporated into the nucleocapsid but participate in its assembly, and still other late proteins are involved in virion release.
• In addition, proteins and other factors synthesized by the host may be involved in assembling mature virions.
• The assembly process can be quite complex with multiple subassembly lines functioning independently and converging in later steps to complete nucleocapsid construction.
• The baseplate, tail fibers, and head components of bacteriophage T4 are assembled separately.
• Once the baseplate is finished, the tail tube is built on it and the sheath is assembled around the tube.
• The phage prohead (procapsid) is constructed with the aid of scaffolding proteins that are degraded or removed after assembly is completed.
• DNA is incorporated into the prohead by a complex of proteins sometimes called the “packasome.”
• The packasome consists of a protein called the portal protein, which is located at the base of the prohead, and an enzyme called terminase, which moves DNA into the prohead.
• The movement of DNA consumes energy in the form of ATP, which is supplied by the metabolic activity of the host bacterium.
• After the head is completed, it spontaneously combines with the tail assembly.

Question 37

Explain the release stage of the viral life cycle

Answer 37

• Several release mechanisms have been identified. The two most common are release by lysing the host cell and release by budding. Release by lysis is especially common for bacterial viruses and some nonenveloped animal viruses. This process involves the activity of viral proteins. For instance, lysis of E. coli by T4 requires two specific proteins.
• One is lysozyme, an enzyme that attacks peptidoglycan in the host’s cell wall. The other, called holin, creates holes in E. coli’s plasma membrane, enabling T4 lysozyme to move from the cytoplasm to the peptidoglycan.

Question 38

A virulent phage is one that has only one option:

Temperate phages have two options:

Answer 38

A virulent phage is 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 phage.

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

Question 39

What is the relationship between a temperate phage and its host called?

Answer 39

lysogeny

Question 40

The form of the virus that remains within its host is called what?

Answer 40

A prophage

A prophage is simply the viral nucleic acid either integrated into the bacterial chromosome or free in the cytoplasm

Question 41

What are lysogenic bacteria?

Answer 41

The infected bacteria are called lysogens or lysogenic bacteria. Lysogenic bacteria reproduce and in most other ways appear to be perfectly normal.

Question 42

Lysogenic bacteria reproduce and in most other ways appear to be perfectly normal. However, they have two distinct characteristics:

Answer 42

• The first is that they cannot be reinfected by the same virus; that is, they have immunity to superinfection.
• The second is that as they reproduce, the prophage is replicated and inherited by progeny cells. This can continue for many generations until conditions arise that cause the prophage to initiate synthesis of phage proteins and to assemble new virions, a process called induction.

Question 43

What is induction caused by?

When does the lytic cycle begin?

Answer 43

Induction is commonly caused by changes in growth conditions or ultraviolet irradiation of the host cell. As a result of induction, the lysogenic cycle ends and the lytic cycle commences; the host cell lyses and progeny phage particles are released.

Question 44

Describe another important outcome of lysogeny

Answer 44

Lysogenic conversion.

• This occurs when a temperate phage changes the phenotype of its host.
• Lysogenic conversion often involves alteration in surface characteristics of the host.
• For example, when a member of the genus Salmonella is infected by epsilon phage, the phage changes the 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 bacterium becomes immune to infection by another epsilon phage