Viruses

Question 1

Describe the basic characteristics of viruses, including shape, nucleic acid organization and
components ( think conditions for living)

Answer 1

Miniscule, acellular infectious agents having either DNA or RNA

Cause many infections of humans, animals, plants, and bacteria

NO cytoplasmic membrane, cytosol, or organelles
- Contains protein coat or may contain envelope
- Have extracellular and intracellular states
- Does Not have cellular structure

Neither grow nor respond to environment
- viral particles assemble into viron, exhibit tropism (organisms turns toward direction of stimulus), and use host actin tails

Cannot carry out metabolic pathway → can redirect host cell metabolic pathways
- No biochemical reactions going on inside

Cannot respond to environment → attach host cell receptors for entry, assemble, and exit host cell and affect others
- Does Not respond to stimuli

Cannot reproduce independently
- Do replicate in host cell, like many parasitic organisms that require a host

Viruses are NOT alive
Viruses infect all cell types
Bacteriophages ( phages)
Viruses that infect bacteria
Most are eukaryotic viruses ( plants, animals…)
Classified into families based on genome structure, life cycle, morphology, genetic relatedness

Question 2

Viral basic structural components and states
(for each structure be able to expand)

Answer 2

Virion size range is 10-400 nm in diameter and most viruses must be viewed with an electron microscope

all virions contain
- nucleocapsid composed of Nucleic acid ( DNA or RNA)
- protein coat (capsid)
- envelope
( some viruses consist only of a nucleocapsid others have other components)
- envelope proteins
- extracellular state
- intracellular state
- genetic material 9 Standedness)

Question 3

what are the two types of viruses characterized by envelopes

Answer 3

• virions having envelopes = enveloped viruses
• virions lacking envelopes = naked viruses

Question 4

characteristics of Viruses capsids

Answer 4

• Protein coats that provide protection for viral nucleic acid and means of attachment to host’s cells
• Composed of proteinaceous subunits called capsomeres (can be made by single or multiple types of proteins) or protomers
• Capsids are helical, icosahedral, or complex

Question 5

describe a helical Capsid

Answer 5

Helical: shaped like hollow tubes with protein walls, capsomers self assemble, size of capsid is a function of nucleic acid

Question 6

describe a Icosahedral capsid

Answer 6

Icosahedron: regular polyhedron with 20 equilateral faces (resembles a sphere); composed of capsomers → ring or knob-shaped units made of 5-6 protomers

Pentamers (pentons) → 5 subunit capsomers

Hexamers (hexons) → 6 subunits capsomers

Question 7

describe a complex capsid

Answer 7

Complex: viruses that don’t fit into the category of having helical or icosahedral capsids.
Ex: poxviruses (largest animal virus) and large bacteriophages (binal symmetry; head resembles icosahedral and tail is helical)

Question 8

size and morphology

Answer 8

Not sure what we need to Know but see table

Question 9

Characterize the viral envelope

Answer 9

Many viruses are bound by an outer, flexible, membranous layer called the envelope

Acquired from host cell during viral replication or release

• Envelope is portion of the membrane system from host

Composed of phospholipid bilayer and proteins
- Some proteins are virally encoded glycoproteins (spikes)

Question 10

characterize viral envelope proteins

Answer 10

Viral envelope proteins:

Envelope proteins, which are viral encoded, may project from the envelope surface as spikes or peplomers

Involved in viral attachment to host cell → ex: hemagglutinin of influenza virus

Used for identification of virus
Bc the glycoproteins generate antibodies ( ask)

May have enzymatic activity or other activity → ex: neuraminidase of influenza virus

May play a role in nucleic acid replication

Question 11

characterize the extracellular states of the viruses

Answer 11

Extracellular state:
Called virion
Protein coat (capsid) surrounding nucleic acid
Nucleic acid and capsid also called nucleocapsid
Some have phospholipid envelope
Outermost layer provides protection and recognition sites for host cells

Question 12

characterize the intracellular state of the viruses

Answer 12

Intracellular state:
- Capsid removed
- Virus exists as nucleic acid j -DNA and RNA - there is no way to differentiate between it and your DNA

Question 13

Describe the genetic material of viruses

Answer 13

Shows more variety in nature of their genomes than do cells
Primary way scientists categorize and classify viruses
May be DNA or RNA, but never both
Can be dsDNA, ssDNA, dsRNA, ssRNA
Strandedness

May be linear and segmented or single and circular
Much smaller than genomes of cell

Question 14

what are the two types of criteria used to classify viruses

Answer 14

Classification based on numerous characteristics

Determined by ICTV (international committee on taxonomy of viruses):

David baltimore

Question 15

describe the ICTV

Answer 15

Nucleic acid type
- Presence or absence of envelop
- Capsid symmetry
-Dimension of viron and capsid

Question 16

describe the David Baltimore classification

Answer 16

Focused on viral genomes and process used to synthesize viral mRNA
7 life cycle groups based on
dsDNA
ssDNA
dsRNA
ssRNA (+ or – strand)
Retrovirus (ssRNA and dsDNA)

DNA viruses are categorized

Question 17

KNOW HOW

Answer 17

ON THE EXAM: GIVEN strand, be able to tell what kind of genetic material it is (strandedness slide)

Question 18

Describe lytic replication

Answer 18

Replication cycle that usually results in death and lysis of host cell

Stages:
1. Attachment
2. Entry
3. Synthesis
4. Assembly
5. Release

Phage injects its DNA into cytoplasm and directs the synthesis of many new phages. The cell lyses and releases the new phages. New phages can then bind to bacterial cells

Question 19

describe Lysogenic replication

Answer 19

The phage DNA injects its DNA into the cytoplasm of the bacterial cell. The phage DNA integrates into the host chromosome. Then the prophage DNA is copied when the cell divides. Exposure to stress such as UV light triggers excision from the host chromosome.

Lysogenic conversion results when phages carry genes that alter phenotype of a bacterium (lysogenic ALWAYS feeds into Lytic)

Fusion of bacteriophage DNA with that of the host genome
Typically reserved to describe bacteriophages
Prophages: inactive phages
Provirus: inactive virus

know two adv. of Lysogeny
temperature phage changes phenotype of its host

Question 20

what are the two advantages of lysogeny

Answer 20

Phage remains viable but may not replicate

Multiplicity of infection ensures survival of host cell

Question 21

understand the effects pf temperature phage changing the phenotype of its host

Answer 21

Bacteria become immune to superinfection
Phage may express pathogenic toxin or enzyme

Question 22

similarities of the lytic and lysogenic cycle

Answer 22

Both lytic and lysogenic replication cycles are mechanisms of viral reproduction, they occur within a host cell, and both cycles may produce thousands of original copies of original virus

Question 23

Describe Viral entry

Answer 23

Varies between naked or enveloped virus
Three methods:
1. Fusion of viral envelope with host membrane; nucleocapsid enters

2. Endocytosis in vesicle; endosome aids in viral uncoating
3. Injection of nucleic acid (Penetration)

3 mechanisms of entry of animal viruses
- Direct injection of nucleic acid
- Membrane diffusion
- endocytosis

Question 24

Describe Viral Exit

Answer 24

Budding
- Viral proteins are first incorporated into host membrane
- Nucleocapsid may bind to viral proteins
- Envelope derived from host cell membrane, but may be golgi, ER, or other
- Virus may use host actin tails to propel through host membrane
exocytosis

Cell death (lysis)
- Viral proteins may attack peptidoglycan or membrane
- Cell explodes

Question 25

Describe DNA viruses + their replication

Answer 25

Categorized by
- Their genomic structure
- Presence of an envelope
- Size and shape of their capsid
- The host cells they attack

3 types

• dsDNA → virus can follow normal replication flow (DNA → RNA → protein)
• ssDNA → host enzymes are used to synthesize a complementary strand to genome strand, thus producing dsDNA which can then follow normal replication flow
• dsDNA-RT (double stranded DNA retroviruses)

Question 26

Describe RNA viruses+ their replication

Answer 26

Only infective agents that store genetic information in RNA molecules
Categorized by
- Their genomic sequence
- Presence of envelope
- Size and shape of their capsid

4 types:
- +ssRNA → acts like mRNA, can be translated directly to make viral proteins
- RNA retroviruses (+ssRNA that convert their genome to DNA)
- (–ssRNA) → cannot translate until replicated into +ssRNA by RNA dependent RNA polymerase (RdRP)
- dsRNA → uses –ssRNA as template to replicate +ssRNA
- Positive RNA acts like mRNA
(can be used by a ribosome to translate protein)
- Negative RNA must first be transcribed as mRNA to be processed by a ribosome
(Requires viral RNA-dependent RNA polymerase)

Question 27

Describe animal viruses

Answer 27

• Zoonoses (learning objective in itself so know this)
  Diseases naturally spread from animal host to humans
  EX: rabies, black plague, lyme disease, west nile virus
  Acquire zoonoses through various routes
  Direct contact with animal or its waste
  Eating animals
  Bloodsucking arthropods
  Humans are usually dead-end host to zoonotic pathogens

Question 28

Compare and contrast lytic and lysogenic replication cycles:

Answer 28

Lytic is where the viral proteins are being produced and then the lyse and rupture. lysogenic is just replication of genetic material and it later excises itself once it goes into the lytic

Lytic replication:
-Replication cycle that usually results in death and lysis of host cell
Stages:
- Attachment
- Entry
- Synthesis
- Assembly
- Release

(Phage injects its DNA into cytoplasm and directs the synthesis of many new phages. THe cell lyses and releases the new phages. New phages can then bind to bacterial cells)

Lysogenic replication:

The phage DNA injects its DNA into the cytoplasm of the bacterial cell. The phage DNA integrates into the host chromosome. Then the prophage DNA is copied when the cell divides. Exposure to stress such as UV light triggers excision from the host chromosome.
(viral proteins are not being replicated in bacteriophages???)
Infected host cells grow and reproduce normally for generations before it lyses
Viral genetic material is integrated into the chromosome

Question 29

RNA vs DNA viruses and replication of both

Answer 29

DNA viruses
Categorized by
Their genomic structure
Presence of an envelope
Size and shape of their capsid
The host cells they attack
3 types:
dsDNA → virus can follow normal replication flow (DNA → RNA → protein)
ssDNA → host enzymes are used to synthesize a complementary strand to genome strand, thus producing dsDNA which can then follow normal replication flow
dsDNA-RT (double stranded DNA retroviruses)

RNA viruses
Only infective agents that store genetic information in RNA molecules
Categorized by
Their genomic sequence
Presence of envelope
Size and shape of their capsid

4 types:
dsRNA → uses –ssRNA as template to replicate +ssRNA
+ssRNA → acts like mRNA, can be translated directly to make viral proteins
–ssRNA → cannot translate until replicated into +ssRNA by RNA dependent RNA polymerase (RdRP)
RNA retroviruses (+ssRNA that convert their genome to DNA)

Question 30

Differentiate between animal viruses and bacteriophages

Answer 30

( be able to expand on each step this is only the skeletal structure)

Animal Viruses
- Replication
- Attachment
- Synthesis
- Assembly and release
Latency of animal viruses

bacteriophages
- attachment
- replication
- synthesis
- assembly and release

Question 31

Describe potential effects of viral infection on host cells, including latency, inclusions and oncogenesis

Answer 31

Latency:
- Viruses remain hidden or dormant inside host cell which cause latent infections
- May cause an acute infection before becoming dormant
- Ex: varicella zoster virus causes chickenpox (affects many areas of the body) but 10-12 days later becomes dormant and stops replicating → after many years of dormancy the virus is reactivated and causes shingles (nerve cell specific)
- Latent viruses may remain dormant by existing as circular viral genome molecules outside of host chromosome or by becoming proviruses by integrating into host genome

Inclusions and oncogenesis:
Inclusions:
- Aggregates of proteins found in neurons
- Caused by the presence of viruses
- Represent sites of viral multiplication
- Occur in the cytoplasm

Oncogenesis:
- Process of normal cells turning into cancer cells
- Activation of oncogenes
- Series of genetic and cellular changes
- Cells divide in uncontrolled manner
- Cancer causing

Question 32

Describe the role of oncogenesis in viruses. Discuss the functioning of oncogenes.

Answer 32

• Oncogenesis allows viruses to encode for proteins that break down the host cell genome and prevent cell death which leads to uncontrolled cell growth.
• Oncogenes are a gene that when activated have the potential to cause cancer because they are pleiotropic and can regulate growth, apoptosis, differentiation, cell cycle, and cell proliferation.
  —-Metastasis: spread of cancerous cells throughout the body
  —-Benign: tumor remains in place
  —–Malignant: abnormal growth of neoplastic cells - form lump of tissue

( look at blue on the doc for more info)

Question 33

Discuss ways to culture and visualize viruses

Answer 33

Culturing viruses in mature organisms:
1. In bacteria
2. In Plants and animals

In embryonic chicken eggs:
1. Inexpensive
2. among the largest of cells
3. Free of contaminating microbes
4. Contain nourishing yolk

In cell tissue culture:
1. Consists of cells isolated from an organism and grown on a medium or in a broth
2. Two types of cell cultures:
a. Diploid cell cultures
b. Continuous cell cultures

Visualize Cells
1. Plaque assays:
a. Dilutions of virus preparation made and plated on lawn of host cells
b. Number of plaques counted
c. Results expressed as plaque-forming units (PFU) / mL

2. Viral plaques:
   a. Viral plaques in a lawn of bacterial growth

Question 34

Define Viroid, virusoid, and prion. Compare these subviral agents to viruses and other living organisms.

Answer 34

Viroid: A subviral particle lacking a capsid and consist solely as RNA
a. extremely small, circular pieces of RNA that are infectious and pathogenic in plants
b. Similar to RNA viruses, but lack capsid
c. Do not encode gene products
d. May appear linear due to H bonding

Virusoid: A subviral particle lacking a capsid, consist solely as RNA, and requires a virus for replication
a. Infectious agents composed only of closed, circular ssRNAs
b. Do not encode gene products
c. Requires virus helper
d. Requires host cell DNA-dependent RNA polymerase to replicate
e. Cause plant diseases → found in nucleolus or chloroplasts; disease caused by RNA silencing

Prion: A misfolded, infectious protein, only affecting the brain
- Proteinaceous infectious agents ( interacts with another protein and causes it to misfold which then interacts with another protein causing it to misfold = domino effect) changes in weak chemical interactions through protein protein interactions)
- Cellular PrP protein
a. Made by all mammals
b. Function unknown
c. Normal structure with a-helices called
cellular PrP
Prion PrP
-Disease-causing form with B-sheets called
prion PrP

Prion PrP converts cellular PrP into prion PrP by inducing conformational change

These compare to viruses and other organisms in the way that they only consist of either RNA or proteins whereas viruses and other organisms can consist of DNA and RNA and proteins all in one.

Question 35

Are viruses alive? Discuss why the status of the virus as a living organism is controversial. How does viral infection lead to morbidity and mortality?

Answer 35

No viruses are not alive because they do not meet all the requirements (cannot carry out metabolic pathways and cannot reproduce independently and require a host)

Others consider them to be the least complex living entities because they:
a. Use sophisticated methods to invade cells
b. Have the ability to take control of their host cells
c. Are able to replicate themselves

Others think it’s a complex pathogenic chemical that lacks characteristics of life
Characterics of life:
Growth
Metabolism
Responsiveness
Reproduction
Cell Structure

Viral infection leads to morbidity and mortality:
Viruses cause 20-25% of human cancers
Some carry copies of oncogenes as part of their genomes
Some promote oncogenes already present in host
Some interfere with tumor repression when inserted into hosts repressor gene
Specific viruses are known to cause 15% of human cancer

Once viral infections invade a host cell they can begin to replicate and destroy more and more cells

They can also activate oncogene which could cause uncontrolled cell growth.