Virolgy Quiz 1

Capsid

Protein encasement/coat that surrounds the viral genomic nucleic acid

Nucleocapsid

Capsid plus the nucleic acid genome packaged inside it

Envelope

Lipid membrane some viruses acquire from a host membrane; NOT part of the nucleocapsid

Virion

The complete, fully infectious virus particle

Virus (as a particle)

A physical particle; obligate intracellular parasite consisting minimally of nucleic acid + protein coat

Why are viruses "acellular"?

They do not arise by fission/division, have no ribosomes, no energy-generating machinery, and cannot translate their own mRNAs

4 things host cells provide that viruses lack

Enzymes for building blocks (nucleotides/amino acids/lipids), enzymes for ATP/energy, ribosomes+tRNAs+translation machinery, and organizing membranes

Koch's Postulate 1

The disease-causing agent must be found/isolated in all organisms suffering from the disease

Koch's Postulate 2

The agent must be grown in pure culture

Koch's Postulate 3

The pure agent must cause disease when introduced into a new healthy host

Koch's Postulate 4

The agent must be re-isolated from the newly diseased host

Which Koch's postulate did viruses fail, leading to their discovery?

Postulate 2 (growth in pure culture) — viruses pass through bacteria-retaining filters and can't be cultured like bacteria

Who first showed the tobacco mosaic disease agent could pass through bacteria-retaining filters?

Dimitrii Ivanovski (1892) and Martinus Beijerinck (1898), independently

First virus discovered

Tobacco mosaic virus (TMV)

First animal virus discovered

Foot-and-mouth disease virus (a picornavirus), Loeffler & Frosch, 1898

First human virus discovered

Yellow fever virus (a flavivirus), Finlay & Reed, 1900

Who crystallized tobacco mosaic virus, and what did it imply?

Wendell Stanley, mid-1930s; implied viruses sit on the edge between living organisms and simple chemical compounds

What was the "phage group" and what field did it help found?

An informal network of scientists (Delbrück, Ellis, Luria) studying bacteriophages in the late 1930s-40s; helped found molecular biology

Hershey-Chase experiment (1952) showed what?

That bacteriophage DNA is injected into the host cell while the protein coat stays outside — supporting DNA (not protein) as genetic material

Who discovered reverse transcriptase, and when?

Howard Temin and David Baltimore, 1971 (in retroviruses)

Plaque assay measures what, in what units?

Infectivity/infectious titer, in plaque-forming units per mL (PFU/mL)

Plaque assay formula

PFU/mL = (number of plaques counted) x (dilution factor) / (mL of dilution plated)

Hemagglutination assay: what does it detect and how sensitive is it?

Detects virus via cross-linking of red blood cells through surface receptor-binding proteins; less sensitive than plaque assay (~10^5 virions per HA unit) but cheap and fast

Why can the ratio of physical particles to infectious particles be much greater than 1?

Damaged/denatured surface proteins, defective genomes, "empty" capsids lacking genome, and host antiviral defenses

Multiplicity of infection (m.o.i.) definition

Number of infectious virus particles added per susceptible cell

Typical experimental m.o.i. used to synchronize infection

10 to 100 PFU per cell

7 steps of the virus replication cycle

1) Bind to receptor 2) Entry & uncoating 3) Early gene expression 4) Genome replication 5) Late gene expression 6) Assembly 7) Release/exit

What two properties must a capsid have?

Metastability and genome economy

Metastability (capsid property)

Stable enough to protect the genome outside the cell, but primed to disassemble and release the genome upon receptor binding/entry (the "Jack-in-the-box" concept)

Genome economy (capsid property)

Using many copies of a small number of protein subunits, since the genome is too small to encode one giant unique capsid protein

3 capsid morphologies

Icosahedral, helical, complex

Icosahedron: faces and vertices

20 faces, 12 vertices

Icosahedral symmetry axes

2-fold, 3-fold, and 5-fold rotational axes

How many 5-fold, 3-fold, and 2-fold axes does an icosahedron have?

12 five-fold axes, 20 three-fold axes, 30 two-fold axes

Simplest possible icosahedral capsid (baseline number of subunits)

60 identical protein subunits

Shape vs Symmetry — definitions

Shape = external form/contour/outline; Symmetry = quality of parts being identical and facing each other or arranged around an axis

Triangulation number formula

T = h^2 + hk + k^2, where h and k are integers and at least one must be greater than 0

Total number of capsid subunits given T

60 x T

Equivalence (capsid subunits)

Every protein subunit has identical molecular interactions with its neighbors (true ONLY for T=1)

Quasi-equivalence (capsid subunits)

Subunits have similar, but not identical, interactions with neighbors, allowing flexibility so one protein type can occupy both 5-fold and 6-fold positions

Which T numbers show true "equivalence"?

Only T = 1

Why must any T > 1 capsid show quasi-equivalence?

Because it contains both hexons (6-fold local environment) and pentons (5-fold local environment), which are geometrically different contexts, so identical contacts everywhere are impossible

How many pentons does a true icosahedral capsid always have?

Always 12, regardless of T number

How many subunits total are always in the pentons of an icosahedral capsid?

Always 60 subunits (12 pentons x 5 subunits each)

Formula for number of hexons given T

Hexons = (60T - 60) / 6, which simplifies to 10(T-1)

T=3 capsid: total subunits, hexons, pentons

180 total subunits; 20 hexons; 12 pentons

T=4 capsid: total subunits, hexons, pentons

240 total subunits; 30 hexons; 12 pentons

T=7 capsid: total subunits, hexons, pentons

420 total subunits; 60 hexons; 12 pentons

T=25 capsid: total subunits, hexons, pentons

1500 total subunits; 240 hexons; 12 pentons

Jelly-roll beta-barrel

A common rigid, brick-like protein fold found in many icosahedral capsid proteins (parvovirus, picornavirus, polyomavirus, adenovirus hexon)

Helical symmetry parameters u and p

u = number of subunits per turn of the helix; p = axial rise (displacement) per subunit along the helix axis

Helical pitch formula

P (pitch) = u x p

Tobacco mosaic virus helical parameters

u is about 16.33 subunits/turn, p is 1.4 Angstroms (0.14 nm), P is about 2.3 nm; each subunit binds 3 nucleotides of RNA

Advantage of helical capsids for genome packaging

Can flexibly accommodate variable genome lengths (useful for segmented genomes like influenza)

Non-structural proteins that can associate with a capsid (4 categories)

Scaffold proteins, enzymes (polymerases/proteases), chaperones (often host-derived), and phosphate-backbone neutralizing proteins

Scaffolding proteins

Help assemble the procapsid during virion assembly, then are discarded/not present in the mature virion

Most common way a virion is "primed" (metastable) for genome delivery

Proteolytic cleavage (e.g., picornavirus VP0 cleaved to VP4+VP2; flavivirus PrM cleaved to M)

How are most viral envelopes acquired?

By budding from a preexisting cellular membrane (plasma membrane, ER, Golgi, or nuclear membrane)

Matrix protein (viral envelope) role

Bridges the cytoplasmic tails of envelope glycoproteins with the nucleocapsid during budding (example: influenza M protein)

6 physical classification criteria for viruses

RNA vs DNA, single- vs double-stranded, linear vs circular, segmented vs non-segmented, helical vs icosahedral, enveloped vs naked

Virus taxonomy hierarchy

Species -> Genus (genera) -> Family

Virus family and genus naming suffixes

Family names end in -viridae; genus names end in -virus

6 broad host categories used in virus taxonomy

Bacteria, Archaea, Lower eukaryotes (fungi/protozoa/algae), Plants, Invertebrates, Vertebrates

Human genome size

About 3 billion base pairs (3x10^9)

Largest known viral genome and its approximate size

Mimivirus/megavirus, about 1.2-1.3 million base pairs

Herpesvirus genome size (approximate)

About 100,000 base pairs (1x10^5)

Polyomavirus genome size (approximate)

About 5,000 base pairs (5x10^3)

Anellovirus genome size (approximate)

About 3,000 nucleotides (3x10^3)

Smallest known viral genomes belong to which group, and how big?

Circoviruses; less than 2,000 nucleotides

Smallest known virion diameter

About 20 nanometers

Largest known virion diameter (mimivirus)

About 500 nanometers

If a 100nM virus were compared to a 100uM cell, how much smaller is the virus?

1000 times smaller

If a 20nM virus were compared to a 100uM cell, how much smaller is the virus?

5000 times smaller

3 tailed dsDNA bacteriophage families and their tail types

Myoviridae (long contractile tail), Siphoviridae (long non-contractile tail), Podoviridae (short non-contractile tail)

Baltimore Classification: what does it group viruses by?

The pathway used to generate messenger RNA (mRNA) from the packaged viral genome

Baltimore Class I

Double-stranded DNA (dsDNA); transcribed by a DNA-dependent RNA polymerase (often the host's); examples: adenovirus, herpesvirus, poxvirus

Baltimore Class II

Single-stranded DNA (ssDNA); converted to dsDNA by a host DNA polymerase before transcription; example: parvovirus

Baltimore Class III

Double-stranded RNA (dsRNA); transcribed by a virus-coded RNA-dependent RNA polymerase (RdRp) that MUST be packaged in the virion; examples: reovirus, rotavirus

Baltimore Class IV

Positive-sense single-stranded RNA (+ssRNA); the genome itself functions directly as mRNA; examples: poliovirus, coronavirus

Baltimore Class V

Negative-sense single-stranded RNA (-ssRNA); must be transcribed to positive sense by a virus-coded RdRp that MUST be packaged in the virion; examples: influenza virus, Ebola virus, rabies virus

Baltimore Class VI

Retroviruses; positive-sense ssRNA genome reverse transcribed to dsDNA by virus-coded reverse transcriptase (MUST be packaged in the virion), which integrates into the host genome; example: HIV

Baltimore Class VII

Gapped/partially double-stranded DNA; uses reverse transcriptase during replication; example: Hepatitis B virus (Hepadnavirus)

Which Baltimore classes MUST package RNA-dependent RNA polymerase (RdRp) in the virion?

Class III (dsRNA) and Class V (negative-strand RNA), because host cells have no enzyme able to make mRNA from these genome types

Which Baltimore classes MUST have reverse transcriptase associated with the virion?

Class VI (retroviruses) and Class VII (hepadnaviruses, e.g. Hepatitis B)

Which Baltimore class genome type doubles directly as mRNA with no special enzyme needed?

Class IV, positive-sense ssRNA viruses

Which genome type did the "original" Baltimore classification system miss?

The gapped/partially double-stranded DNA genome of hepadnaviruses (e.g., Hepatitis B virus) - later added as Class VII

Do dsDNA viruses (Class I) generally need to package their own RNA polymerase?

Generally no, they can use the host's DNA-dependent RNA polymerase; exception: some large DNA viruses (e.g., poxvirus) that replicate in the cytoplasm bring their own RNA polymerase

True or false: all viruses, regardless of Baltimore class, must ultimately use host ribosomes for translation

True - no virus makes its own ribosomes; translation is always carried out by host machinery

4 steps in virus entry (Chapter 4 overview)

1) Bind to specific cell surface receptors 2) Enter via vesicle or direct membrane penetration 3) Transport within the cell to site of replication 4) Genome release (uncoating)

What triggers the conformational changes in virion proteins during membrane penetration?

Interaction with a cellular receptor, or exposure to low pH inside endosomes

How do enveloped viruses penetrate cell membranes?

By fusion of the viral envelope with either the plasma membrane or the membrane of an intracellular vesicle (endosome)

How do non-enveloped viruses enter the cytosol?

By forming transmembrane channels for genome/nucleocapsid passage, or by inducing lysis of the endocytic vesicle

What cellular motor and cytoskeletal structure transport virions/nucleocapsids inside the cell?

Dynein motor protein, moving along microtubules

How do viruses that replicate in the nucleus get their genome inside?

Via the nuclear pore complex

How do plant viruses typically first enter a host, given the cell wall barrier?

Through insect bites, grafting, or other mechanical damage to the cell wall

How do plant viruses spread from cell to cell once inside a plant?

Through intercellular channels called plasmodesmata

For a naked (non-enveloped) virus, is the nucleocapsid the same thing as the virion?

Yes - for non-enveloped viruses, the nucleocapsid alone constitutes the fully infectious virion