MIC2011 Week 4

are viruses considered cells? what does that make them?

no, viruses are acellular (not cells). they are not considered alive in the traditional sense.

what is the host dependence of viruses?

viruses are obligate intracellular parasites – they absolutely depend on a host cell for energy, ribosomes, and biosynthetic precursors. outside a host, they are inert.

what type of genetic material do viruses have?

viruses contain either DNA or RNA, never both. the genome can be single/double‑stranded, linear/circular, and for RNA, positive/negative sense, segmented or not.

how do viruses replicate, and how does this differ from cellular life?

viruses replicate by assembly – new virions self‑assemble from newly synthesised components inside a host cell. they do not grow or divide.

can viruses grow on cell‑free media (agar plates with nutrients)?

no. viruses cannot grow in cell‑free media – they require living host cells to replicate.

what is the evolutionary relationship among different viruses?

unlike cellular life (which shares a common ancestor), viruses are a collection of highly diverse groups largely unrelated to one another. they are grouped by behaviour, not genetic homology.

are viruses active or inert outside a host cell?

outside a host, viruses are inert chemical assemblies (virions) with no metabolism, no replication, and no activity. they only “come alive” inside a host cell.

do viruses possess their own protein synthesis machinery?

no. viruses lack ribosomes and a complete protein synthesis system. they must produce mRNA that is translated by host ribosomes.

what are the two phases in which viruses exist?

1. extracellular phase (the virion)
2. intracellular phase (the infected cell)

describe the extracellular phase of a virus. what is the virion?

the extracellular phase is the virion – a single, inert infectious particle. it acts as a carrier to protect and transport the viral genome from one host cell to another. it has no metabolism, no replication, and no activity on its own – essentially a “chemical assembly.”

describe the intracellular phase of a virus.

the virus “comes alive” only after entering a host cell. it becomes a replicating entity that depends on cellular factors and metabolism to produce new viral components. this is the phase where the virus replicates and assembles new virions.

True or False: in the extracellular phase, a virus can slowly grow and divide.

false. the extracellular virion has no metabolism, no replication, and no activity – it is inert.

in which phase does a virus actually replicate and assemble new virus particles?

the intracellular phase (inside the infected cell).

what is the main function of the extracellular virion?

to act as a carrier that protects and transports the viral genome from one host cell to another.

why is the virus considered “inert” in the extracellular phase?

because it has no metabolism, no replication, and no independent activity – it is essentially a chemical assembly until it enters a host cell.

in the one‑step growth curve, which phase corresponds to the flat part before the rise and which to the rising/burst part?

the flat part (before rise) represents the extracellular phase (no virus detected yet). the rising/burst part represents the intracellular phase (virus replication and release).

what is the main purpose of the Baltimore scheme for virus classification?

to group viruses based on their fundamental biology (genome type and replication strategy), overcoming the issue of their massive diversity and lack of common ancestry.

how many classes of viruses are there in the Baltimore scheme?

seven (often called the “magic number” seven).

what are the two key criteria used to classify viruses in the Baltimore scheme?

1. type of genome (dsDNA, ssRNA, positive‑sense)
2. pathway to mRNA – the mechanism by which the virus produces mRNA from its genome.

why is the “pathway to mRNA” a critical classification criterion?

because mRNA is required to make viral proteins. different virus classes use different strategies to produce mRNA from their genomes (some use host polymerases, others carry their own).

True or False: viruses in the same Baltimore class can have very different hosts, structures, or diseases, but they share the same fundamental biology of replication and gene expression.

true. that is the core principle of the Baltimore scheme.

match the Baltimore class to its genome type:
 I.   A. positive‑sense RNA
 II.   B. double‑stranded RNA
 III.   C. double‑stranded DNA
 IV.   D. single‑stranded DNA
 V.   E. retroviruses (positive‑sense RNA with DNA intermediate)
 VI.   F. negative‑sense RNA
 VII.   G. gapped double‑stranded DNA

I‑C, II‑D, III‑B, IV‑A, V‑F, VI‑E, VII‑G.

what is the fundamental difference between Baltimore classes I/II and classes III–VII in terms of the central dogma?

classes I and II have DNA genomes and generally follow the usual flow (DNA → RNA → protein). classes III–VII have RNA genomes or use reverse transcription, breaking the standard rules of cellular biology.

does the Baltimore scheme classify viruses based on their physical structure (icosahedral vs helical) or their disease symptoms?

no. it classifies them based on genome type and mRNA synthesis pathway. physical structure and disease are not used as criteria.

who developed the one‑step growth curve and in what year?

Delbrück & Ellis, 1939 (using bacteriophage T4 and E. coli).

define the eclipse period in the one‑step growth curve.

the period after infection during which no infectious virus is detectable inside or outside cells – virions have disassembled and new components are being synthesised.

what is the latent period in the one‑step growth curve?

he period during which virus is present inside cells but has not yet been released.

define burst size.

the number of new virions produced per infected cell (can be hundreds).

what happens during the release phase of the one‑step growth curve?

cells lyse (or bud) and release many new virions, causing a sharp rise in detectable virus.

what is the principle of the plaque assay?

a single infectious particle infects one cell; progeny virus spreads to neighbouring cells, forming a visible plaque (clear area in a cell monolayer or bacterial lawn).

list the basic steps of the plaque assay procedure.

1. serially dilute the virus sample.
2. mix with host cells in a viscous medium (to limit spread).
3. incubate until plaques form.
4. count plaques.
5. calculate PFU/mL using the dilution factor.

what does PFU stand for and what does it measure?

plaque‑forming units per mL – a measure of the concentration of infectious virus particles in a sample.

True or False: each plaque in a plaque assay can arise from multiple virions infecting the same cell.

false. each plaque arises from a single infectious virion, which is why the assay allows accurate quantification.

in the one‑step growth curve, which period corresponds to the intracellular phase of the virus?

the eclipse and latent periods (virus is inside cells, either disassembled or assembled but not yet released). the release phase is the transition back to extracellular virions.

what are the two core chemical components of every virus?

1. genome (either DNA or RNA, never both)
2. capsid (protective protein coat)

what is a capsid made of?

many identical protein subunits called capsomeres.

define nucleocapsid.

the capsid plus the viral genome (nucleocapsid = capsid + genome).

what is the difference between an enveloped and a naked virus?

enveloped viruses have a lipid membrane derived from the host cell surrounding the capsid; naked viruses have no envelope.

name the three main structural forms (shapes) of viruses.

1. icosahedral
2. helical
3. complex

describe an icosahedral virus structure.

a roughly spherical shape with 20 triangular faces and ordered symmetrical arrangement of protein subunits. examples: adenovirus, poliovirus.

describe a helical virus structure.

a rod‑shaped or filamentous structure where protein subunits are arranged in a spiral around the genome (like a spiral staircase). examples: rabies virus, tobacco mosaic virus.

what is a complex virus? give examples.

viruses with no consistent symmetry; often large with mixed shapes. examples: poxviruses, bacteriophages.

True or False: all viruses have a capsid.

false. some viruses have no capsid – they are simply an RNA genome with a polymerase attached (mentioned in the first set of notes).

what are the spikes found on some viruses?

glycoproteins that protrude from the envelope of enveloped viruses. they are involved in host cell attachment.

which type of virus is generally more environmentally stable – enveloped or naked? why?

naked viruses are more stable (resistant to drying, detergents, and environmental stress). enveloped viruses are more fragile because the lipid envelope can be easily damaged.

what determines whether a virus is naked or enveloped?

whether the virus acquires a host‑derived lipid membrane during assembly and release. enveloped viruses bud through host membranes; naked viruses are released by lysis without taking a membrane.

match the virus to its structural type:
 A. adenovirus   1. helical
 B. rabies virus  2. icosahedral
 C. poxvirus    3. complex

A‑2, B‑1, C‑3.

list four functions of viral structure.

1. cell attachment mechanisms
2. entry and uncoating
3. assembly and release
4. stability / transmission

list the 5 general stages of the viral life cycle in order.

1. attachment
2. penetration & uncoating
3. synthesis
4. assembly
5. release

what happens during attachment? what determines host and tissue tropism?

a viral surface protein (capsid or envelope glycoprotein) binds to a specific receptor on the host cell. the presence/absence of that receptor determines host and tissue tropism.

what are the two key events during penetration & uncoating?

1. virus enters the cell
2. capsid disassembles, releasing the genome into the cytoplasm or nucleus

how do bacteriophages penetrate the host cell?

direct injection of nucleic acid through the bacterial cell wall (ejection from the capsid).

how do enveloped animal viruses penetrate the host cell? (two methods)

1. fusion with the plasma membrane
2. endocytosis followed by fusion with the endosome membrane

why can’t naked animal viruses fuse with the plasma membrane, and how do they enter?

they have no envelope to fuse. they enter via endocytosis, then form pores or disrupt the endosome to release the genome into the cytoplasm.

what happens during the synthesis stage?

the viral genome directs production of viral proteins (using host ribosomes) and replication of the nucleic acid genome.

what happens during assembly?

newly synthesised viral genomes and structural proteins self‑assemble into virions.

what are the two main methods of release? which virus types use each?

1. budding – used by enveloped viruses
2. lysis – used by naked viruses and bacteriophages

True or False: during attachment, viral surface proteins bind to receptors that evolved specifically for viral entry.

false. receptors have normal cellular functions; viruses have evolved to exploit them.

which stage directly follows penetration & uncoating?

synthesis.

which stage directly precedes release?

assembly.

define viral tropism.

the specific host species and cell/tissue types a virus can infect.

what is the primary mechanism that determines viral tropism?

receptor binding – viral surface proteins (capsid or envelope glycoproteins) bind to specific receptors on the host cell. these receptors have normal cellular functions, not evolved for viruses.

how does receptor distribution affect tropism?

receptors may be present only on certain differentiated cells (blood cells, liver, neurons), which restricts the virus to those cell types.

what is a co‑receptor? give an example of a virus that requires one.

a second receptor required for viral entry. (example not specified in notes, but HIV requires CD4 and a co‑receptor like CCR5 or CXCR4.)

explain species specificity as a mechanism of tropism.

the same receptor molecule may differ slightly between species. minor differences can prevent cross‑species infection. mutations in viral surface proteins can overcome this barrier, leading to outbreaks.

how does tropism determine which tissues are damaged in a viral disease? give an example.

if a virus can only infect a specific cell type, those cells will be damaged. example: polio virus infects neurons → causes paralysis.

why do some viruses infect only humans while others are zoonotic?

due to species specificity – the viral surface protein may not recognise the receptor in other species, or the receptor differs. zoonotic viruses have the ability to cross that barrier.

how can viral evolution lead to emergence of new diseases?

mutations in viral surface proteins can allow the virus to bind to receptors in a new species or cell type, overcoming the normal species barrier (SARS‑CoV‑2).

True or False: viral receptors evolved specifically for viruses to attach to cells.

false. receptors have normal cellular functions; viruses have evolved to exploit them.

what is the relationship between attachment (first stage of viral life cycle) and tropism?

attachment – the binding of viral surface protein to a specific receptor – is the primary determinant of host and tissue tropism.

what is the central idea of the Baltimore Scheme?

classification based on:
1. type of genome nucleic acid
2. mechanism to generate mRNA (and more genome)

list the 7 Baltimore classes by number and genome type.

I – dsDNA
II – ssDNA
III – dsRNA
IV – (+)ssRNA
V – (–)ssRNA
VI – Retroviruses (positive‑sense RNA with DNA intermediate)
VII – Gapped dsDNA

which Baltimore classes use RNA‑dependent RNA polymerase (RdRP)? what rule do they break?

classes III, IV, and V. they break the rule “RNA cannot be made from RNA without a DNA intermediate” – they perform RNA → RNA replication.

which Baltimore classes use reverse transcriptase (RNA‑dependent DNA polymerase)? what rule do they break?

classes VI and VII. They break the rule “information flows only from DNA to RNA” – they perform RNA → DNA reverse transcription.

what polymerases are used for replication and transcription in Class I (dsDNA) viruses like Herpes Simplex Virus?

replication: viral or cellular DNA‑dependent DNA polymerase (DdDP)
transcription: cellular DNA‑dependent RNA polymerase (DdRP) (usually Pol II)

describe the gene expression program of Class I dsDNA viruses (Immediate Early → Early → Late).

1. Immediate Early (IE) – transcribed first by cellular DdRP; proteins include transcriptional activators.
2. Early (E) – encode viral DdDP (replicates genome) and other enzymes.
3. Late (L) – encode structural proteins for assembly.

why can’t Class II (ssDNA) viruses be transcribed directly? how do they replicate?

ssDNA cannot be transcribed to mRNA. it must first be converted to dsDNA by cellular repair processes, then proceed like Class I.

define positive‑sense (+) RNA and negative‑sense (–) RNA. which can be translated immediately?

positive‑sense – same sequence as mRNA → can be translated immediately by ribosomes.
negative‑sense – complement of mRNA → cannot be translated; must first be copied to +RNA.

do Class IV (+)ssRNA viruses (coronaviruses) carry their own polymerase in the virion? why or why not?

no. the (+)ssRNA genome can be translated immediately by host ribosomes to produce viral RdRP, which then replicates the genome and transcribes mRNA.

do Class V (–)ssRNA viruses (Ebola) carry their own polymerase? why?

yes. the host cell cannot transcribe (–)ssRNA, so the virus must carry RdRP in the virion to produce (+)mRNA.

describe the replication flow for Class VI retroviruses (HIV).

1. (+)ssRNA → converted to dsDNA by reverse transcriptase (carried in virion)
2. dsDNA inserted into host genome by integrase → provirus
3. proviral DNA transcribed by cellular DdRP → mRNA (protein) and new genome
Flow: RNA → DNA → RNA → Protein

what is unusual about the genome of Class VII (gapped dsDNA) viruses?

they have double‑stranded DNA with gaps. they use reverse transcriptase during replication, similar to retroviruses.

in Class I dsDNA virus T7 bacteriophage, which genes are transcribed by the host DdRP and which by the viral DdRP?

host DdRP transcribes early genes (Class I) – including the viral DdRP (T7 RNA polymerase).
viral DdRP then transcribes Class II genes (helicase, primase, DdDP) and Class III genes (structural).

for a Class IV (+)ssRNA virus, what must its genome encode? why?

it must encode RdRP because the virus needs to replicate its RNA genome and produce mRNA, but host cells do not have RdRP.

True or False: viruses in the same Baltimore class always have the same physical structure (icosahedral, helical).

false. baltimore classification is based on genome type and mRNA synthesis pathway, not physical structure. viruses in the same class can have very different structures.

define lytic infection.

productive infection; virus replicates and causes cell lysis (in many viruses).

define latent / lysogenic infection.

long‑term infection where viral genome is maintained with limited gene expression and no loss of host cell viability. enables persistence, immune evasion, and sporadic reactivation.

what is a temperate phage? give an example.

a bacteriophage that can undergo either lytic or lysogenic cycles. example: bacteriophage λ.

describe the lytic cycle of bacteriophage λ.

injects DNA → replicates → lyses host → releases progeny.

describe the lysogenic cycle of bacteriophage λ.

injects DNA → integrates into host chromosome (as a prophage) → replicates with host DNA → no lysis → can reactivate later.

what determines whether bacteriophage λ enters the lytic or lysogenic cycle?

a stochastic (random) molecular switch that depends on which repressor protein binds first to overlapping operator sequences.

what are the two key repressor proteins in the λ phage switch, and which operon does each regulate?

1. λ repressor (cI protein) – represses the right (lytic) operon.
2. right‑operon repressor – represses the left (lysogenic) operon.

what happens if λ repressor (cI) binds first to the operator?

it inhibits the right (lytic) promoter → left operon is transcribed → more λ repressor produced → positive feedback → lysogeny.

what happens if the right‑operon repressor binds first?

it inhibits the left (lysogenic) promoter → lytic genes are expressed → lytic cycle.

how does genotoxic stress (DNA damage) trigger reactivation from lysogeny?

the SOS pathway is activated, producing protease RecA which degrades λ repressor (cI). removal of λ repressor allows the right (lytic) operon to be expressed → lytic cycle reactivates.

name four human herpesviruses that establish latent infection.

HSV‑1 (cold sores), HSV‑2, VZV (chicken pox → shingles), EBV, HCMV.

after primary infection with a herpesvirus (VZV), what happens to the virus?

it becomes latent for life. periodic reactivation (shingles from VZV, cold sores from HSV‑1) enables spread and maintenance in the population.

True or False: during latent infection, the viral genome is completely silent with no gene expression.

false. latent infection involves limited gene expression (not complete silence), but no loss of host cell viability.

what is a prophage?

the viral genome when it is integrated into the host bacterial chromosome during lysogeny.

how does the molecular switch in animal virus latency (herpesviruses) compare to bacteriophage λ?

similar principles apply: two transcriptional programs (latent vs lytic), a molecular switch results in predominance of one program, and reactivation triggers differ but the concept is analogous.