Properties of Viruses

Question 1

T/F: Viruses infect bacteria.

Answer 1

-True; viruses that do so are called bacteriophages. They help move genetic info around between bacteria increasing spread of drug resistance and affecting pathogenesis
-As an aside, viruses can also infect animals,
plants, and bacteria.

Question 2

T/F: Bacteria are the most abundant biological entity on earth

Answer 2

-false; viruses are

Question 3

T/F: Viruses are generally 100-1000 times smaller than cells.

Answer 3

-True

Question 4

List 3 properties of bacteria concerning their genome, protein synthesis, and energy generation.

Answer 4

• contain DNA or RNA genome, NEVER BOTH
• have NO protein synthesis machinery (no ribosomes)
• have NO energy generating machinery

Question 5

In all viruses, nucleic acids are enclosed in a ________.

Answer 5

-protective protein shell coat called a capsid

Question 6

2 phases of viral replication

Answer 6

• outside the host: inert collect of macromolecules called a virion
• inside host: utilize host machinery to copy self and produce more virus

Question 7

Viruses are ALL obligate intracellular pathogens. How is this term more strict than its use with bacteria?

Answer 7

-viruses need to access the cell’s protein synthesis machinery IN THE CYTOPLASM, and as such, they cannot replicate within intracellular vacuoles

Question 8

Viruses do not _______ or undergo _______, but are assembled from pre-form components.

Answer 8

• grow

- division

Question 9

2 general categories of proteins that viruses can make

Answer 9

-structural and nonstructural proteins

Question 10

All virions have a protein shell (capsid) surrounding the nucleic acid genome. The full assembly is called the _________.

Answer 10

-nucleocapsid

Question 11

Enveloped viruses have what additional characteristic?

Answer 11

• lipid membrane surrounding the nucleocapsid

- not all viruses have this; those without an lipid envelope are called naked or non-enveloped

Question 12

What is located on viral surfaces that allow it to attach to host cells?

Answer 12

-projections from the surface of the virions called spikes or envelope proteins

Question 13

What are 2 practical implications of why some viruses have RNA instead of DNA?

Answer 13

1. RNA polymerases usually dont have proof-reading function; thus, RNA viruses tend to mutate more than DNA viruses
2. RNA viruses tend to replicate quickly, particularly +RNA viruses since their genome is in effect already mRNA

Question 14

Do RNA or DNA carrying viruses cause chronic infections?

Answer 14

-DNA causes chronic infections (think Herpes)

Question 15

Do RNA or DNA viruses tend to have larger genomes?

Answer 15

-DNA viruses

Question 16

How are viral genomes mainly different from human genomes?

Answer 16

-unlike the human genome, there is no wasted space in viral genomes–they are almost completely packed with genes

Question 17

What are the 4 mechanisms by which viruses conserve “genetic space”?

Answer 17

• make a polyprotein that is cleaved by viral or cellular protease
• RNA splicing
• Overlapping reading frames (and splicing): single promoter with overlapping reading frames
• Ribosomal frame-shifting: when scanning along mRNA, ribosome will slip back one base and continue which gives a frameshift and gives diff. protein production

Question 18

In addition to being divided by their nucleid acids, viruses can also be divided based on the type of capsid they have; what are the 2 main categories of capsids?

Answer 18

• icosahedral capsids

- helical capsids

Question 19

5 functions of a capsid

Answer 19

1. packaging and condensation of genome
2. protection of nucleic acid
3. transport nucleic acid from cell to cell
4. provides specificity for attachment
5. metastable: capsids undergo changes that result in delivery of genetic material into a cell

Question 20

T/F: All icosahedral capsids are membrane enveloped.

Answer 20

-False; all helical capsids are and some icosahedral are

Question 21

Describe the process of viruses acquiring an envelope

Answer 21

• occurs through a process called budding where the viruses steal membrane from the host cell
• viral capsid assembles in cytoplasm, and makes integral membrane protein (spike protein) that is transported to the host cell surface where the glycoproteins form patches
• final step involves membrane fission event when the capsid binds with the intracellular domain of the spike glycoproteins

Question 22

Enveloped viruses have one or more __________. Why are these heavily glycosylated?

Answer 22

• spike proteins (some viruses have 1 for receptor binding and membrane fusion, other viruses have separate proteins for these functions)
• since carbs are not immunogenic, this functions as a shield to protect the protein from antibodies

Question 23

3 functions of spike proteins

Answer 23

• attach virus to cell surface
• mediate fusion with cell to get virus into cell
• targets for neutralizing antibodies

Question 24

Describe the difference in transmission of enveloped vs. nonenveloped viruses

Answer 24

• while lipid membranes are stable, they are sensitive to osmotic stress, dessication, and extremes of pH and salt; thus enveloped viruses are transmitted by transfer of body fluids
• nonenveloped are much more stable outside of the body and can be transmitted by a much wider variety of mechanisms(fluids, fomites, fecal oral, etc) (not killed by simple soaps)

Question 25

6 steps in the life cycle of a virus

Answer 25

1. Attachment: virus binds to a specific R (R determines tropism)
2. Penetration:
3. Uncoating: genome is inside capsid, so it needs to be uncoated for replication to process
4. Translation, transcription, replication
5. Assembly
6. Release

Question 26

What is a common way to measure the amount of virus in solution?

Answer 26

• plaque forming units (PFU)
• viral solution is serially diluted and placed on a monolayer of cells; as it infected cells, monolayer will develop holes or plaques

Question 27

When cells are infected with a virus, you can collect the media at different times after infection and measure the amount of PFUs present. At first the amount of virus recovered ___________ and then with time, the amount of virus will _________. The period of time between the start of infection and when the first progeny viruses emerge is called the ___________.

Answer 27

• decrease; the virus you add binds and infects cells
• increase; new viruses are made and released from infected cells and the PFU goes up again
• eclipse phase

Question 28

5 things a viral receptor may do

Answer 28

1. binds the virus to the cell
2. can just act to merely tether the virus
3. can itself initiate entry
4. can trigger conformational changes in capsid or glycoprotein needed for entry
5. may send signals to cell that in some way prepare it for infection (virus induces cell to become more permissive host)
   * *need receptor for virus to infect a cell**

Question 29

Viruses can use all sorts of different cell surface proteins as receptors. Most receptors are proteins, but some viruses bind to _______.

Answer 29

• carbs

- influenza binds to sialic acid which is common and explains the wide tropism of influenza

Question 30

Do viruses usually bind to 1 or more than 1 receptor to attach to a cell surface, initiating the entry process?

Answer 30

• usually 1

- rarely more than 1

Question 31

Define viral tropism and what determines it.

Answer 31

• spectrum of tissues and cell types infected by a given virus
• some have restricted while some have broad tropisms
• often explained by the presence of absence of the appropriate viral receptor

Question 32

What are the 3 ways viruses cross a cell’s membrane and which type of viruses use each method?

Answer 32

• membrane fusion*: ALL ENVELOPED viruses have one or more membrane proteins (spike) that catalyze fusion between the viral and cellular membranes
• pore formation: some nonenveloped viruses form pores in membrane
• Membrane lysis: some nonenveloped viruses enter cells by endocytosis, then lyse the vacuole to escape to the cytoplasm

Question 33

Because nonenveloped viruses do not have a membrane, what method of entry into a cell can they not do?

Answer 33

-membrane fusion because they have no membrane to fuse with!

Question 34

5 stages of enveloped virus entry

Answer 34

1. attachment
2. receptor engagement
3. Trigger event (pH dependent or pH independent)
4. conformational change
5. membrane fusion

Question 35

What is an added difficulty of enveloped viruses infecting cells?

Answer 35

• its genetic material must traverse both the viral and cellular membranes
• all enveloped viruses encode and express on their surface a protein or proteins that under the right conditions changes its structures in a way that mediated fusion and affords cytoplasmic access to the viral genome

Question 36

What does pH-dependent trigger event mean for an enveloped virus?

Answer 36

• the virus engages the receptor, is taken up by endocytosis into an endosome, which is a highly acidic prelysosome, and this low pH activates the virus to fuse with the lysosome and release its contents into the cytoplasm
• others do the same thing, but with out pH being a factor (pH-independent)

Question 37

Describe how non-enveloped viruses enter and infect cells.

Answer 37

• usually enter by endocytosis
• low pH in endosomes induces conformational changes in capsid proteins
• hydrophobic domains are exposed and insert into endosomal membrane, forming a pore (or lysing endosome)
• viral DNA or RNA enters cell via pore

Question 38

Describe how large DNA vs. small DNA vs. RNA vs. retroviruses replicate their genomes

Answer 38

1. large DNA: encode many of the enzymes required (DNA pol) and are more “autonomous”
2. small viruses use host cell DNA polymerase and other enzymes
3. RNA: encode their own RNA-dependent RNA pol which uses a complementary RNA as template
4. Retroviruses: copy a ss+ RNA genome into dsDNA which is template for new genome synthesis

Question 39

Where and when does small DNA viruse DNA replication take place?

Answer 39

-in the nucleus during S phase because they rely on host cell DNA polymerase

Question 40

T/F: RNA dependent polymerase lacks proofreading, and so RNA viruses mutate quickly and often replicate faster.

Answer 40

-true

Question 41

General replication strategy of negative-stranded RNA viruses

Answer 41

• (-)RNA viruses have to carry with them their own polymerase, because this is the only way they can make a + RNA copy of their -RNA genome and a +RNA stand is needed for replication
  1. turn -RNA into + RNA with RNA-dependent RNA Pol
  2. RNA+ (mRNA) is turned into viral proteins and viral RNA polymerase or turned back into -RNA to be packed with RNA pol

Question 42

General replication strategy if positive-stranded RNA viruses

Answer 42

• +RNA can be turned directly into viral proteins, not dependent on transcription into +RNA like -RNA viruses are

Question 43

Compaire +RNA vs. -RNA on presence of viral polymerase in virion, if viral RNA is alone infectious, and the initial event in the cell they infect

Answer 43

• RNA+: no polymerase in virion, infectious alone, translation
• RNA-: have polymerase, not infectious alone (need polymerase), transcription

Question 44

Why is it beneficial for viruses (RNA viruses) to mutate quickly?

Answer 44

-enables them to evolve and adapt to new conditions, including immune escape

Question 45

3 major mechanisms by which viruses mutate

Answer 45

1. simple mutation: during replication, wrong base pair is used–point mutation
2. recombination: when 2 viruses infect same cell their genomes can recombine
3. reassortment: restricted to viruses with segmented genomes; if 2 viruses infect the same cell and replicate, their genetic segments mix and result in new generation of new virus; non classical recombination, very efficient

Question 46

Recombination occurs most frequently is what viral types? What about reassortment?

Answer 46

• recombination is common in DNA viruses

- reassortment is for segmented viruses only

Question 47

Fundamental steps of virus assembly

Answer 47

1. formation of individual structural units of the protein shell form one or several viral proteins
2. assembly of the protein shell by appropriate and sometimes variable interactions among structural units; self assembly
3. selective packaging of nucleic acid and other viral components
4. acquire envelope is needed
5. release for host cell

Question 48

How does the virus selective package its own RNA or DNA and not cellular molecules?

Answer 48

• viral genomes have packaging signals that are recognized by viral proteins
• packaging signals are usually a particular secondary structure like a stem-loop
• useful for gene therapy vectors by placing signal upstream of drug of choice

Question 49

2 general mechanisms of virus release for cells

Answer 49

1. enveloped viruses bud from a cellular membrane; this can be the PM or the ER, if the ER they are then secreted
2. Nonenveloped viruses accumulate in the cell, and are released when the cell dies and is lysed; cell may die from immune system, apoptosis, cytotoxic effects, etc

Question 50

Define burst size

Answer 50

-average number of virus particles released from an infected cell