chapter 13

What is a virus?

• Virus is not alive on its own

 

• NONLIVING, must reproduce inside host cell

 

• Ubiquitous and ecologically important

 

• Acellular particle

  • Has no cells, no metabolism, no ribosomes, and cant make its own ATP

  • Genetic material (DNA/RNA) wrapped in a protein coat

 

• Obligate intracellular parasite

  • Virus must infect a host to reproduce

When a virus infects a cell, it...

takes over the hosts machinery to make more copies of itself (new viruses are called virions)

• Subverts the cells machinery and directs it to produce viral particles

Virions:

• complete infectious virus ; outside of host cell

  • Cant reproduce

The big three

• Coronavirus

• Respiratory syncytial virus

• Influenza virus

• Coronavirus

• (+) Ss rna

• Nucleoid capsid proteins bind to genome

  • Protects genome by binding instead of boxing it in

Respiratory syncytial virus and Influenza virus

• Respiratory syncytial virus

  • Ss rna

• Influenza virus

  • Ss rna

  • Segmented genomes

    • 8

    • Allows many mutations

  • 11 proteins encoded

  • 13,500 nt bases total

 

Discovery of Viruses

• Ivanovsky (1982) + beijerinick (1898) discovered viruses while studying Tabacco mosaic disease

 

• They realized that the disease passed through filters that trapped bacteria - so the infectious agent was smaller than bacteria

 

• Called them "non-filterable particles" -> later named viruses

Basic Virus Structure

• Every virus has at least 2 parts

• 20 - 900 nm or .02 -.90 mm

• Genetic material (Genome)

• Protein coat (capsid)

Basic Virus Structure: Genetic material (Genome)

• Can be DNA/RNA, single stranded (ss) or double stranded (ds)

  • Never both at once (DNA OR RNA)

• Carries instructions for making viral parts

 

Basic Virus Structure: Protein coat (capsid)

1. Made of repeating protein units called capsomeres

   1. Individual protein subunits

2. Protects that genetic material

3. Gives the virus shape

Basic Virus Structure: Some viruses have extra parts

1. Envelope

2. Naked (nonenveloped) viruses

3. Glycoprotein spikes

Basic Virus Structure: envelope

• A membrane layer stolen from the host cells plasma membrane when the virus exits cell

• Found mostly in animal viruses

• Contains glycoprotein spikes for host recognition & attachment

  • Think of spikes like a "key" that fits the hosts "lock"

Basic Virus Structure: naked viruses

• Have only a capsid and no envelope

• Still can have spikes directly on the capsid

Basic Virus Structure: glycoprotein spikes 

• Protein structures that project from the surface of virus (either from capsid or envelope)

• Proteins for host recognition

• Attach to host receptors

• May be present in naked viruses

Shapes of Viruses

Capsid structure

• Can vary in shape and size

; 

• Helical

  • Tube like spiral

  • Tobacco mosaic virus

 

• Polyhedral (icosahedral)

  • 20-sided shape

  • Adenovirus

 

• Complex Viruses

  • Complicated structure

  • Bacteriophage

  • Posses non capsid protein components

Viral infectivity -> host:virus relationship

• infectivity depends on virus:host recognition

 

• Interaction between viral surface proteins and host cell surface molecules

 

Viral infectivity: Tissue Specificity (tropism):

• Within a host, it may target only specific cells/tissues

 

• Host cell specificity

• Rabies virus infects nerve cell

• Influenza infects respiratory cells

• Broad

  • Ebola

  • Infect multiple cell types

 

• Narrow

  • Cold virus; HIV (infects T helper cells)

Viral infectivity: Host Range

• the spectrum of host organisms a virus can infect

 

• Broad

  • Rabies virus

  • Multiple mammal hosts

 

• Narrow range

  • Only infecting one species

  • HIV infects only humans

Steps of a General Viral Life Cycle

Every virus life cycle has 4 basic stages

1. Recognition & Attachments

2. Genome Entry

3. Synthesis & Assembly

4. Maturation

5. Exit & Transmission

Viral Life Cycle: Recognition & Attachments

• Virus binds to specific proteins on the host cell surface (like matching key to lock)

• Virion uses its surface proteins (spikes or capsid proteins) to bind to a specific receptor on the host cell surface

 

Viral Life Cycle: Genome Entry

• Virus or its genome enters the cell

  • Sometimes whole virus enters

  • Sometimes only the genome is injected

    • Like bacteriophages

Viral Life Cycle: Synthesis & Assembly

 

• The hosts enzymes, ribosomes, and nucleotides are stolen to make viral proteins and genomes

 

• New viral parts assemble to complete virions

 

• The viral genome hijacks the host cells machinery to make copies of the viral genome and transcribe/translate viral genes to produce viral proteins

  • This is where virus takes over

Viral Life Cycle: Maturation

• The newly created genomes and proteins are put together to form new, complete virions

Viral Life Cycle: Exit & Transmission

• New viruses leave the host cell:

  • Lysis

    • Cell bursts (common in bacteria)

  • Budding

    • Virus "buds off" from cell membrane (common in animal viruses w/ envelopes)

• New virions infect more cells

• Viruses mutate faster because…

• Viruses mutate faster because our cells have systems in place for mistakes RNA doesn’t 

  • RNA

  • DNA can fix mistakes; not as good

Viral Classification (Taxonomy)

• Viruses are classifies by

 

• Type of genome

  • DNA 

  • RNA

 

• Whether the genome is ss or ds

  • Single strand

  • Double strand

 

• Envelope presence

  • enveloped

  • Naked

 

• Capsid shape

  • Helical

  • Icosahedral

  • Complex

 

• Host range

  • What organisms it can infect

 

• Taxonomy

  • A viral species = a group of viruses with a similar genetic information and host range

 

Bacteriophage Life Cycles

• Viruses that infect bacteria

• 2 major life strategies

• 1. Lytic Cycle

2. Lysogenic Cycle

Lytic Cycle

• Ex: T-even phages (like T4 which is SSRNA + )

• Are virulent

  • Phage quickly replicates killing host cell

 

• Steps

  1. Attachment

     • Viruses attach to bacterial cell wall

  2. Penetration

     • Injects its DNA into the host cell

  3. Biosynthesis

     • Viral DNA takes over -> makes copies of DNA and proteins

     • Host DNA is destroyed

  4. Maturation

     • Viral parts assemble into new virions

  5. Release

     • Host cell lyses and releases new virions (50 - 500)

     •  lysosome breaks down peptidoglycan

 

• Eclipse period: time between viral entry and appearance of complete virions. Virions are not intact

Lysogenic Cycle

• Ex: lambda phage

 

• Are temperate

 

• The virus does not kill the host right away

 

1. Virus injects DNA

 

2. Viral DNA intergrates into host chromosome -> now called prophage

 

3. Every time the bacterial cell divides, the prophage "wakes up" and enters the lytic cycle, making new viruses and killing the host

 

Lysogenic Cycle part 2

• Will go into lytic cycle when host is healthy + dividing because there are many cells to infect

 

• Can also when host is not doing well like lack of nutrients because they are already in dying cells and only option is lysis 

• Lysogenic cells are immune to reinfection by the same phage

 

• Can lead to transduction (transfer of bacterial genes via phage)

 

• Environmental stress triggers switch to lytic cycle

 

lytic vs lysogenic 

 

Feature	Lytic Cycle	Lysogenic Cycle
Viral DNA activity	Takes over host immediately	Integrates into host DNA (prophage)
Host outcome	Cell bursts (dies)	Cell survives & divides
Viral replication	Fast, destructive	Dormant until activated
Example	T4 phage	Lambda (λ) phage

SSRNA+ & SSRNA -

SSRNA +

• Serves as mRNA

• = mRNA

 

SSRNA -

• Template for mRNA synthesis

 

REVIEW

 

Step	What Happens	Description
1. Attachment (Adsorption)	Virus attaches to the host cell	Virus binds to specific receptor proteins on the host’s surface.
2. Entry (Penetration)	Virus or its genome enters the cell	Can happen by fusion (envelope merges with membrane) or endocytosis (cell “eats” the virus).
3. Biosynthesis/Replication & Assembly	Virus takes over and makes copies of itself	Host machinery makes viral proteins and genomes; parts assemble into new virions.
4. Exit/Release	New viruses leave the cell	By lysis (cell bursts) or budding (virus pushes out through cell membrane).

REVIEW P2

Stage	Bacteriophages	Animal Viruses
Attachment	Tail fibers attach to cell wall proteins.	Attachment sites are plasma membrane proteins and glycoproteins.
Entry	Viral DNA is injected into the host cell. 44	The entire capsid enters the host cell by receptor-mediated endocytosis or fusion.
Uncoating	Not required (only DNA enters).	Required: Enzymatic removal of capsid proteins to release the genome.
Biosynthesis	Occurs in the cytoplasm.	Occurs in the nucleus (DNA viruses) or the cytoplasm (RNA viruses).
Chronic Infection	Lysogeny (integration into host DNA as a prophage).	Latency (dormant state), slow viral infections, or cancer.
Release	Host cell is lysed (burst open) and killed.	Enveloped viruses bud out (acquiring the envelope); nonenveloped viruses rupture the plasma membrane (lysis).

 

Animal Virus Life Cycle

1. Attachment (adsorption)

2. Entry (penetration)

3. Uncoating

4. Biosynthesis

5. Assembly and release

Animal Virus Life Cycle: Attachment (adsorption)

• Virus binds to specific receptor sites on the host cell membrane

 

• These receptors are often glycoproteins (proteins with sugar groups)

 

• Specificity:

  • The virus can only attach to cells that have the matching receptor (lock and key)

 

• The virus uses its outer structures (capsid proteins, envelope proteins, or glycoproteins [a protein with a sugar attached]) to bind to specific receptor sites (proteins or glycoproteins) on the surface of the host cell

 

• Difference from Bacteriophages:

  • Animal viruses attach to plasma membrane proteins and glycoproteins, whereas bacteriophages use tail fibers to attach to the bacterial cell wall

Animal Virus Life Cycle: Entry (penetration)

 

• Two main entry mechanisms depending on virus type

 

1. Fusion (enveloped viruses)

   • The viral envelope fuses directly with the host membrane

 

• The viral capsid and genome are released into the cytoplasm

 

• HIV and Influenza

 

2. Receptor mediated Endocytosis (enveloped or naked)

 

• The hosts cell plasma membrane folds inward to bring the virus, which is attached to a receptor, into a small vesicle called an endosome. This is how non enveloped and some enveloped viruses enter. (togavirus)

 

• The host swallows the virus by forming a vesicle (called and endosome)

 

• Inside, the virus later escapes into the cytoplasm

 

Animal Virus Life Cycle: Uncoating

• Crucial step for animal viruses; but not bacteriophages

 

• Capsid (protein coat) is removed, releasing the viral genome inside the host cell

 

• Separating the genome from the capsid

 

• The enzymatic removal of capsid proteins to separate the viral genome from its capsid

 

• Occurs

  • Cell membrane

  • Inside endosome

    • Where H+ acidifies the endosome

  • Nuclear membrane

Animal Virus Life Cycle: Biosynthesis

• Where the virus takes over hosts machinery

 

• Viruses use hosts ribosomes to make viral proteins

 

• Specific location and mechanisms depend on the viral genome type

 

1. DNA viruses

   • Location

     • Replication and assembly occur in host NUCLEUS

     • Why?

       • Need DNA polymerase to copy their genome

 

• Mechanisms

  • They use the host own replication machinery (like DNA polymerase) for DNA synthesis and transcription (making mRNA)

 

• Steps

  • Viral DNA is replicated in the nucleus

 

• A portion of viral DNA is transcribed in nucleus to produce mRNA that encodes "early" viral proteins

 

• The mRNA moves outside the nucleus (cytoplasm) to be translated into viral proteins (ex: capsid proteins) using host ribosomes

 

• These proteins return to the nucleus where virions are assembled

2. RNA Viruses

• Location

  • Replication, synthesis of viral proteins, and assembly all occur outside the nucleus (in host cells cytoplasm)

 

• Enzyme

  • Typically posses their own enzyme RNA- dependent RNA polymerase (RDRP). Bc host cells don’t have an enzyme that can copy RNA from an RNA template

 

Animal Virus Life Cycle: Assembly and release

• New viral components (capsid + genome) are assembled

 

• Enveloped viruses:

  • Instert their spike proteins into the hosts plasma membrane

 

• Virions leave by

 

• Lysis ( usually non enveloped)

  • Host cell burst

 

• Budding (usually enveloped)

  • Viral glycoproteins are first inserted into host cells plasma membrane

    • Golgi

 

• Capsid and genome push forward, wrapping the modifies host membrane around itself as it buds off, which gives the new virion its viral envelope

 

Viral Genome Functions

DNA VS RNA Viruses

Feature	DNA Viruses	RNA Viruses
Where genome replicates	In nucleus	In cytoplasm
Main enzyme used	Host DNA polymerase	Viral RNA-dependent RNA polymerase (RDRP)
Where proteins are made	Cytoplasm (translation)	Cytoplasm
Where virions assemble	Nucleus	Cytoplasm

 

DNA Virus

 Nucleus → copy genome, transcribe → cytoplasm → translate → return to nucleus → assemble → exit.

RNA Virus

• Everything happens outside nucleus

• Use RDRP

  • Makes new RNA strands using RNA as a template

 

 

 

1. + ssRNA Viruses

 

• Genome acts like mRNA, so it can be immediately translated by ribosomes into viral proteins

 

• RDRP makes more copies of + RNA through a - intermediate strand

 

1. (-) ssRNA Viruses

   • The RNA genome cannot be directly translated

   • The virus must use RDRO to first make a complementary + RNA strand, which acts as mRNA

   • Influenza , rabies

 

1. ds RNA

   • Have both + and - strands

   • The - strand serves as a template to make more + strands

   • Rotavirus

 

Retroviruses

• Enveloped RNA viruses that have a unique, backward replication process

 

• Infects T-helper cells of the immune system

 

 

• Key enzymes

 

• Reverse transcriptase (RT)

  • Converts viral RNA -> double-stranded DNA

 

• Integrase

  • Inserts that viral DNA into the hosts DNA -> forms provirus

Retroviruses: process

1. Entry

   • Virus enters host by fusion (bc its enveloped)

 

2. Uncoating

• RNA genome and viral enzymes are released

 

3. Reverse transcription

• RT enzyme copies viral RNA -> DNA

 

4. Integration

• The new viral DNA integrates into the host genome (becomes provirus)

 

5. Latency

• Provirus may remain inactive (persistent) for a long time

 

6. Activation

• When active, the provirus makes RNA -> which makes viral proteins

 

7. Assembly & exit:

• New viruses assemble and leave cell by budding

 

 

Ex: HIV (infects T-helped cells in the immune system)

 

• Has 2 identical + RNA strands

 

RetroVirus: Key facts

• Enveloped RNA virus

• Contains reverse transcriptase (NOT RDRP)

• Converts RNA -> DNA -> integrates into host genome

• Exits by budding

Multiplication of Animal Viruses

VIRIODS

• Not viruses, but infectious RNA molecules

 

• Lack a capsid (protein shell)

  • No structure

 

• Infect plants only

 

• Replicated by the hosts RNA polymerase

 

• RNA does not code for proteins

 

• Very small

  • 300 - 400 nucleotides long

 

• Some have catalytic activity

  • Can speed up reactions themselves, "ribozyme" function

 

• Sits on plant mRNA so that it cant be transcripted

 

PRIONS

• Infectious proteins (no DNA/RNA)

  • No nucleic acid components

 

• Cause degenerative brain diseases in animals and humans

 

• Spread through infected food

  • Like contaminated meat

 

• Extremely resistant to heat, chemicals, and radiation

 

How Prions Work

1. The normal brain protein (PrPᶜ) is converted into an abnormal misfolded form (PrPˢᶜ)

   • Prp^sc binds to normal brain protein

 

1. The abnormal proteins accumulate in the brain -> forming plaques and cavities

 

1. The brain tissue becomes spongy

 

1. Disease progresses very slowly but is always fatal

Latent infections

• Latent

  • Virus infects host but lies dormant for long periods

  • Can reactivate later due to stress or weak immunity

  • Virus "sleeps" and can "wake up"

  • Oncogenic virus; herpesvirus; chicken pox (shingles

 infections

• Acute

• Rapid onset

• Short duration

• Host clears virus quickly

infections

• Persistent (chronic)

• Virus replicates slowly and continuously; may last for years and often fatal

• Virus stays active the whole time

codons