Important words and concepts from Chapter 10, Black, 1999 (3/28/2003):

by Stephen T. Abedon (abedon.1@osu.edu) for Micro 509 at the Ohio State University

 

 

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Vocabulary words are found below

 

 

(1) Chapter title: Viruses

(2) Obligate intracellular parasite

(a)                    Some microorganism can only reproduce if they have entered another organism's cell

(b)                    This other cell may be one of many in an animal or plant (or fungi) or may be a free living cell (a protozoa or bacterium)

(c)                    Obligate intracellular parasites include protozoa (e.g., Plasmodium which causes malaria), bacteria (e.g., Bdellovibrio which parasitizes gram negative bacteria or Rickettsia or Chlamydia), or viruses

(d)                    [obligate intracellular parasite (Google Search)] [ebola hemorrhagic fever] [viral disease] [index]

(3) Viruses

(a)                    Viruses are obligate intracellular parasites that do not themselves possess a cell

(b)                    Thus, rather than being cells that can only replicate upon entering another cell, viruses do not even possess a cell until they enter (infect) another cell

(c)                    Viruses thus are acellular intracellular parasites

(d)                    The acellular state consists of, minimally, protein plus nucleic acid (RNA or DNA)

(i)                      the former is involved in procuring new cells while

(ii)                    the latter is responsible for taking over the cell metabolically as well as making and then dispersing new virus particles

(e)                    See Figure 10.1, The components of an animal virus (a herpesvirus) [an enveloped virus] [herpes simplex virus movies (Edward K. Wagner)]

(f)                     See Figure 10.6, Bacteriophages

(g)                    [virus and cells (Google Search)] [bacteriophage ecology group (MicroDude)] [the big picture book of viruses] [virus characteristics and properties] [index]

(4) Virion

(a)                    The virion is a virus particle consisting of its nucleic acid, capsid, and, for some viruses, its envelope

(b)                    One also refers to the virus particle as a virion particle

(c)                    [virion particle (Google Search)] [index]

(5) Capsid (capsomere)

(a)                    The capsid, along with the nucleic acid, defines the acellular stage of viruses, which in turn defines viruses

(b)                    Capsids consist of proteins that surround and protect the viral nucleic acid

(c)                    These proteins, in turn, are called capsomeres

(d)                    For simple viruses the capsid consists of only a single type of protein

(e)                    For viruses with complex morphologies, many 10s of proteins are involved in capsid morphogenesis

(f)                      See Figure 10.6, Bacteriophages [for an example of a virus with a complex morphology]

(g)                    [capsid, capsomer (Google Search)] [virus structure (BS335 Virology] [index]

(6) Nucleocapsid

(a)                    A nucleocapsid is a virus nucleic acid packaged in its capsid

(b)                    [nucleocapsid (Google Search)] [index]

(7) Enveloped viruses

(a)                    Many viruses additionally possess envelopes, which are lipid bilayers surrounding the virus capsid

(b)                    For enveloped viruses, the virion particle is not complete (nor infectious) until the envelope has been acquired

(c)                    Enveloped viruses are common among animal viruses

(d)                    [enveloped virus (Google Search)] [herpes simplex virus movies] [index]

(8) Non-enveloped (naked) viruses

(a)                    Viruses that lack envelopes (i.e., do not have nor need them) are termed non-enveloped

(b)                    In non-enveloped viruses the capsids are solely responsible for attachment of the virus to the to-be-infected cell

(c)                    [naked virus, non-enveloped virus, nonenveloped virus (Google Search)] [index]

(9) Spike

(a)                    Glycoproteins (i.e., proteins with carbohydrates attached) that project from some enveloped viruses are called spikes

(b)                    Spikes are responsible for attaching the virus to the to-be-infected cell

(c)                    [spike protein (Google Search)] [herpes simplex virus movies] [index]

(10) Virus shapes

(a)                    Various virus shapes and sizes can be observed relative to an E. coli cell in Figure 10.2

(b)                    See Figure 10.2, Viral sizes and shapes

(c)                    Viruses can be helical (e.g., the tobacco mozaic virus [images])

(d)                    Viruses can be polyhedral (e.g., the adenovirus [images])

(e)                    Viruses can be helical and enveloped (e.g., the paramyxovirurs [images] in Figure 10.2 or the rabies virus in Figure 10.3c [rabies virus images])

(f)                      Viruses can be polyhedral and enveloped (e.g., the herpesvirus [images]) [herpes simplex virus movies]

(g)                    Viruses can be complex, i.e., have complex morphologies (e.g., the poxvirus [pox virus images] or T4 bacteriophage [T4 images]) (note that no matter how complex you might consider a virus’ life cycle, the term complex refers to the morphology of the virion; thus, for example, HIV is not considered to be a complex virus)

(h)                    [virus shapes (Google Search)] [virus structures (numerous cartoons) (BS335: Virology)] [index]

(11) Host range

(a)                    Supposedly all cellular life forms have associated viruses (like all absolutes, I find this statement difficult to swallow even though authors typically state it as gospel; as a viral ecologist it would be self-serving for me to buy into this gospel—unfortunately, I simply do not)

(b)                    All existing viruses, however, are limited in their host range, i.e., they are not able to infect all possible organisms

(c)                    A virus' host range is the range of cellular organisms a virus is capable of infecting

(d)                    Many viruses are limited to only a single species or not even an entire species as hosts

(e)                    Other viruses display host ranges that include numerous species, though usually the more closely related the host species, the more likely that two host species will share a given virus

(f)                      [virus "host range" (Google Search)] [viruses multiplying in humans] [index]

(12) Viral specificity (a.k.a., tropism)

(a)                    Even within a single species, viruses typically are limited in the types of cells (i.e., tissues) that they can infect

(b)                    This limitation typically is a consequence of different cells either displaying different surface markers or having different physiologies

(c)                    Different viral specificities explain in part differences in the symptoms experienced upon infection with different kinds of viruses (e.g., if your lungs hurt, chances are the virus has a lung-cell tropism)

(d)                    As with host range, viruses of different kinds vary in both the breadth of their tropisms and in the types of cells included

(e)                    [virus tropism (Google Search)] [index]

(13) Virus classification

(a)                    Early attempts at virus classification differentiated viruses in terms of host range and tropism

(b)                    Today viruses are much more likely classified in terms of the characteristics of the virus' particle morphology (e.g., enveloped versus non-enveloped) or infection physiology, as well as host range and tropism

(c)                    [virus classification (Google Search)] [list of virus families] [list of individual viruses] [virus families grouped by genome type] [virus families grouped by the Baltimore method] [virus families grouped by host] [virus families grouped by infectious disease] [index]

(14) Nucleic acid classification

(a)                    Cell genomes may consist of one or more chromosomes and are either circular or are linear, but are always double-stranded DNA (i.e., DNA double helix)

(b)                    The genomes of viruses, on the other hand, may be

(i)                      RNA versus DNA

(ii)                    Single-stranded versus double-stranded

(iii)                   One piece or many pieces (segmented)

(c)                    ["virus classification" and "nucleic acid" (Google Search)] [virus families grouped by genome type] [index]

(15) Single-stranded RNA viruses

(a)                    Single-stranded RNA viruses additionally may be either positive (+) stranded or negative (-) stranded

(b)                    The plus and minus (or positive and negative terms) refer to whether the viral single-stranded RNA, that is packaged within the viral capsid and which is deposited in a cell cytoplasm to initiate an infection, can (+) or cannot (-) serve as a viral mRNA

(c)                    Recall that in transcription the RNA is transcribed from a DNA template strand, which is only one of the two DNA strands found within a double helix

(d)                    Thus, within a double helix section coding for a gene, only one DNA strand serves as an RNA template, while the other strand is complementary to the template (since the RNA is also complementary to the template, both the RNA and the non-template strand effectively have the same nucleotide sequence)

(e)                    Now, if the viral genome must first be transcribed in order to produce an RNA message (to be translated to produce a viral protein) then the viral genome has a sequence that is complementary to its RNA, and therefore is minus (negative) stranded

(f)                      If, on the other hand, the viral RNA can serve as an RNA messenger without first being transcribed then the RNA genome is the same sequence as the RNA message and therefore is plus (positive) stranded

(g)                    [ssRNA viruses, "ssRNA viruses" and positive, "ssRNA viruses" and negative (Google Search)] [index]

(16) Virus replication

(a)                    Virus replication requires a number of steps:

(i)                      Adsorption

(ii)                    Penetration

(iii)                   Synthesis

(iv)                  Maturation

(v)                    Release

(b)                    (note in the following discussion that Adsorption is not synonymous with Penetration and that Synthesis is not synonymous with Maturation)

(17) Adsorption

(a)                    Adsorption involves the attachment of the extracellular virus particle to the host cell

(b)                    Adsorption involves interaction between viral proteins, either capsomer or envelope proteins, and host-cell viral receptors

(c)                    [virus adsorption, phage adsorption (Google Search)] [index]

(18) Viral receptor

(a)                    The viral receptor is a protein or other molecule of the host cell that is found on its surface

(b)                    The viral receptor is not displayed by the host cell in order to serve as a viral receptor but instead serves a role in the host physiology

(c)                    The viral receptor instead is co-opted by a virus as an adsorption target—the place that a virus attaches to begin its infection

(d)                    Differences in the ability of viruses to infect otherwise similar cells are often seen in viral receptors where infectable hosts possess the appropriate receptor whereas non-infectable cells either lack the receptor or possess a variant that the virus cannot recognize, i.e., attach to

(e)                    [virus receptor, phage receptor (Google Search)] [index]

(19) Penetration

(a)                    Penetration is the entry of the virus genome into the host cell

(b)                    [virus penetration (note how “virus penetration” is used on the web mostly to describe viral passage through man-made barriers such as filters, condoms, and latex gloves) (Google Search)] [index]

(20) Synthesis

(a)                    Synthesis involves both the synthesis of viral proteins and the replication of the viral nucleic acid

(b)                    [viral synthesis (note how viral synthesis is also used as a synonym for progeny-virus production) (Google Search)] [index]

(21) Maturation

(a)                    Virus particles are not said to be the product of replication so much as maturation

(b)                    Maturation is the combining of replicated viral nucleic acid with viral capsid proteins

(c)                    In addition, maturation involves the acquisition of an envelope (for enveloped viruses)

(d)                    [viral maturation (Google Search)] [herpes simplex virus movies] [index]

(22) Release

(a)                    Release is when intracellular virus particles exit the host cell to the extracellular environment

(b)                    The release is part of the maturation of some viruses

(c)                    Different viruses undergo release in two categorically different ways:

(i)                      Host cell lysis

(ii)                    Chronic release

(d)                    Only the former directly and immediately kills the host cell (thus terminating the infection)

(e)                    [virus release from cell (Google Search)] [herpes simplex virus movies] [index]

(23) Bacteriophages

(a)                    Bacteriophages (or phages) are viruses that infect bacteria

(b)                    A great deal is known about bacteriophages because they are easy to work with and served as model systems for the elucidation of many universally applicable principles of biology

(c)                    [bacteriophage OR phage (Google Search)] [the bacteriophage ecology group (MicroDude)] [bacteriophage images (MicroDude)] [Myoviridae] [Tectiviridae] [introduction to bacteriophages] [coliphage field kit: technical final report] [index]

(24) Replication of T4 phage

(a)                    The replication of phage T4 is typical of viral replication in at least certain respects

(b)                    Phage T4 is an example of a obligately lytic bacteriophage

(c)                    See Figure 10.7, Replication of a virulent bacteriophage

(d)                    [replication phage T4 (Google Search)] [index]

(25) Virulent virus (lytic virus)

(a)                    Viruses are termed lytic (as well as virulent) if they must destroy their host cell, to release their virus progeny, given host-cell infection

(b)                    This contrasts with temperate which are viruses capable of entering into a lysogenic relationship with their host therefore are not obligately lytic given infection (though may be obligately lytic to release progeny virus)

(c)                    This destruction occurs because they possess no mechanism for progeny-virus release except for poking holes in the host-cell's plasma membrane, plus, for lytic viruses, no mechanism to avoid making and then releasing progeny virus

(d)                    Poking holes in a plasma membrane kills the host cell and terminates the viral infection of that cell

(e)                    [lytic cycle, virulent phage (Google Search)] [index]

(26) Viral yield (burst size)

(a)                    The number of viruses released by a host cell upon lytic-virus release is called the burst size (or viral yield from that cell)

(b)                    In other words, per generation a lytic virus increases in number one burst size full

(c)                    For many viruses burst sizes can be rather substantial ranging from on the order of 100 to on the order of 1000 progeny viruses released per cell

(d)                    Compare this per-generation increase to the per-generation increase in number associated with binary fission, i.e., one cell becomes two cells (with generation durations often similar to those of viruses)

(e)                    Thus, viruses possess a capacity to increase in number at a rate that is well in excess of the rate at which their cellular hosts can increase in number

(f)                      This rapid rate of progeny production results from the very simple structure that virus particles have (that is, to make a new virus particle there is no need to make a new cell whereas to make a new cell via binary fission, the bacterial parent must make a completely new cell)

(g)                    The ability of viruses to very rapidly increase in numbers, and thereby infect many cells, is responsible, in part, for the ability of viruses to cause disease (the other side of the coin is the ability of viruses to damage the cells they infect)

(h)                    ["burst size" and virus, "burst size" and phage, vrial yield (Google Search)] [index]

(27) Phage-induced lysis

(a)                    When a lytic bacteriophage terminates its infection to release progeny phages, the mechanism of host-cell destruction is called lysis

(b)                    Usually lysis involves not just the poking of holes in the bacterial plasma membrane but also the enzymatic destruction of the bacterial cell wall

(c)                    Lysis is just one of many mechanisms different viruses use that damage their host cells

(d)                    [phage lysis (Google Search)] [index]

(28) Phage growth (replication) curve (eclipse period, latent period)

(a)                    Lytic phages may be followed in terms of progeny phage maturation as well as host-cell lysis

(b)                    Such a curve occurs over various intervals termed

(i)                      Eclipse period which spans from the point of phage adsorption to the point at which the first phage progeny have matured within an infected cell

(ii)                    Latent period which spans from the point of phage adsorption to the point at which host lysis occurs

(c)                    See Figure 10.8, Growth curve for a bacteriophage

(d)                    [one-step growth, single-step growth, "eclipse period" and phage, "eclipse period" and virus, "latent period" and phage, "latent period" and virus (Google Search)] [one step growth curve (note, various links will ask you to purchase on-line lab book)] [index]

(29) Plaque assay

(a)                    Similar to the enumeration of bacteria, bacteriophages may be enumerated using a plate-count assay

(b)                    A difference between bacteria and bacteriophages, however, is the requirement by bacteriophages for a bacterial hosts

(c)                    To enumerate bacteriophages via a plaque-count assay one must first mix bacteria and bacteriophages in melted agar

(d)                    Following plating and incubation, the bacteria-inoculated agar grows into a lawn which is a highly turbid growth of bacterial microcolonies (micro because one plates approximately one-million bacteria per petri dish and with that many bacteria each colony is very small as well as immediately adjacent to neighboring colonies)

(e)                    The regions surrounding a bacteriophage on such a lawn contain instead an absence of bacterial cells resulting from phage-induced lysis and phage replication

(f)                      These holes are termed plaques and one counts bacteriophage plaques in the same manner one counts bacteria colonies, including employing serial dilutions when bacteriophage concentrations in a given culture are excessive

(g)                    See Figure 10.9, Plaque assay

(h)                   

(i)                      Plaque assays are also employed to enumerate eukaryote viruses

(j)                      [plaque assay (Google Search)] [index]

(30) Lysogeny

(a)                    Some bacteriophages can choose, upon infecting a host cell, whether they will go through a lytic cycle (i.e., synthesis, followed by maturation, followed by lysis-associated release)

(b)                    An example of such a phage is called simply the Greek letter l (i.e., lambda phage)

(c)                    Instead of entering a lytic cycle, phage l instead integrates its dsDNA genome into the chromosome of its host

(d)                    In this way phage l ties its fate to that of its host

(e)                    In return l protects its host from l lytic infections

(f)                     See Figure 10.11, Replication of a temperate bacteriophage

(g)                    [lysogeny (Google Search)] [index]

(31) Temperate phage

(a)                    A temperate phage is one which is capable of displaying a lysogenic life cycle

(b)                    Phage l is an example of a temperate phage

(c)                    [temperate phage (Google Search)] [index]

(32) Prophage

(a)                    A temperate phage that has integrated its genome into that of its host

(b)                    A host-chromosome integrated phage l is an example of a prophage

(c)                    [prophage (Google Search)] [index]

(33) Lysogen

(a)                    A bacterium which has a prophage is called a lysogen

(b)                    A bacterium possessing an integrated phage l, for example, is called a lysogen

(c)                    [lysogen (Google Search)] [index]

(34) Lysogenic conversion

(a)                    Prophages can change bacterial properties in dramatic ways

(b)                    One way is by supplying genes coding for exotoxins, thus converting other non-pathogenic bacteria into pathogenic bacteria (example = Corynebacterium diphtheriae)

(c)                    Any phenotypic change in a bacterium resulting from the presence of a prophage is termed lysogenic conversion

(d)                    [lysogenic conversion (Google Search)] [index]

(35) Animal viruses

(a)                    Animal viruses go through the same basic steps as bacteriophages including equivalents to the bacteriophage lytic cycles and lysogenic cycles, though details do differ both between bacteriophages and animal viruses as well as between different bacteriophages and between different animal viruses

(b)                    See Figure 10.12, Replication of an enveloped dsDNA animal virus

(c)                    See Figure 10.13, Replication of RNA viruses

(d)                    Note the chronic release by the dsDNA animal virus, i.e., the release of the virus particle through the plasma membrane without membrane disruption

(e)                    For enveloped viruses, the maturation of the virus particle always involves passage through a membrane (not necessarily the plasma membrane), which is how the virus envelope is acquired

(f)                     Note the resemblance between the HIV life cycle, which involves integration into the host genome, and the lysogenic cycle of phage l.

(g)                    [animal viruses, animal virus (Google Search)] [HIV life cycle] [strategies for antiviral therapy based on the retroviral life cycle] [index]

(36) Uncoating

(a)                    One of many detail differences between bacteriophages and animal viruses is the means by which virus nucleic acid enters the host cell

(b)                    Specifically, viral nucleic acid typical enters the animal cell still complexed with its capsid

(c)                    Uncoating is an intracellular step during which viral nucleic acid and capsid are separated

(d)                    [virus uncoating (Google Search)] [index]

(37) Latent viral infection

(a)                    Some viruses are able to hide from a host’s immune system by entering cells and not producing new viruses

(b)                    Such infections are termed latent

(c)                    The many different herpes viruses are examples of viruses capable of entering latent infections

(d)                    This is why herpes virus infections (including those that cause cold sores, genital herpes, and chickenpox/shingles) once acquired, never completely go away (e.g., chickenpox may be followed, years later, with shingles, with both the result of the same viral infection)

(e)                    [latent viral infection (Google Search)] [herpes simplex virus movies] [index]

(38) Culturing animal viruses

(a)                    Animal viruses may be cultured using a variety of means

(b)                    Listed in order of increasing modernity:

(i)                      Whole animals (this can be expensive as well as is a relatively uncontrolled environment in terms of doing scientific experiments)

(ii)                    Embryonated eggs (this are less expensive but still are relatively complex environments which therefore are difficult to control)

(iii)                   Tissue culture

(c)                    Much modern experimental virology is done using tissue culture

(d)                    This involves growing animal cells in flasks using various broth media and then infecting these cells with virus

(e)                    ["embryonated eggs" and virus, "tissue culture" and "animal virus" (Google Search)] [index]

(39) Cytopathic effects

(a)                    Non-lytic damage that viruses may do to cells are termed cytopathic effects

(b)                    These effects vary both in terms of how the damage is manifest and how damaging the effects are to the affected cells

(c)                    [cytopathic effects, CPE and virus (Google Search)] [index]

(40) Syncytia

(a)                    One form of specific cytopathic effect is termed syncytia formation

(b)                    Syncytia are giant cells that form when viral-infected cells fuse with other cells

(c)                    These giant cells are unwieldy and easily damaged and killed

(d)                    HIV (human immunodeficiency virus) is one type of virus, some strains of which readily form syncytia (in tissue culture, at least)

(i)                      This occurs when virus-infected cells display viral envelope proteins on their surface (which are then acquired by progeny virus during their budding through the host-cell plasma membrane)

(ii)                    These envelope proteins are capable of fusing infected-cell membranes to the membranes of uninfected cells (just as virus particles fuse their envelopes with cells they are adsorbing/infecting)

(iii)                   This fusion results in the fusion of the plasma membranes of the two cell together, thus forming a syncytia

(e)                    [syncitia (Google Search)] [index]

(41) Vocabulary [index]

(a)                    Adsorption

(b)                    Animal viruses

(c)                    Bacteriophages

(d)                    Burst size

(e)                    Capsid

(f)                      Capsomere

(g)                    Culturing animal viruses

(h)                    Cytopathic effects

(i)                      Eclipse period

(j)                      Enveloped viruses

(k)                    Host range

(l)                      Latent period

(m)                  Latent viral infection

(n)                    Lysogen

(o)                    Lysogenic conversion

(p)                    Lysogeny

(q)                    Lytic

(r)                     Maturation

(s)                     Naked virus

(t)                      Non-enveloped viruses

(u)                    Nucleic acid classification

(v)                    Nucleocapsid

(w)                  Obligate intracellular parasite

(x)                    Penetration

(y)                    Phage growth (replication) curve

(z)                     Phage-induced lysis

(aa)                 Plaque assay

(bb)                Prophage

(cc)                 Release

(dd)                Replication

(ee)                 Replication of T4 phage

(ff)                    Single-stranded RNA viruses

(gg)                 Spike

(hh)                 Syncytia

(ii)                     Synthesis

(jj)                    Temperate phage

(kk)                Tropism

(ll)                     Uncoating

(mm)             Viral receptor

(nn)                 Viral specificity

(oo)                Viral yield

(pp)                Virion

(qq)                Virulent (lytic) virus

(rr)                   Virus classification

(ss)                  Virus replication

(tt)                    Virus shapes

(uu)                 Viruses