Chapter 12 (viruses, viroids, prions)

virus

noncellular particle containing a genome that can replicate only inside a host cell; no cell membrane, no binary fission, no ATP generation, no ribosomes

Obligate Intracellular Parasite

Requires a living host for replication and survival (all viruses)

bacteriophage

A virus that infects bacteria

nucleocapsid

capsid (protein coat) and nucleic acid (viral genome) together

nucleic acid of viruses

DNA or RNA; linear or circular or segmented; double or single stranded

capsid

protein coat surrounding a virus, determines the shape of a virus

capsomeres

repeating or identical protein subunits that make up capsids

genome of viruses

primary characteristic used to classify viruses; aka how do they make RNA?

envelope and shape

Secondary characteristic for determining virus classification

baltimore classification

a classification scheme that groups viruses into seven classes according to how the mRNA is produced during the replicative cycle of the virus

naked virus

virus without an envelope; nucleocapsid only, more resistant to disinfectants ; fully assemble before release because host dies

enveloped virus

A virus enclosed within a phospholipid bilayer derived from its host cell

Matrix or tegument

protein layer attaching envelope to the nucleocapsid

host range

the spectrum of host cells a virus can infect; determined by attachment proteins on the outside of a virus

spike proteins

protruding structures of virus that are recognized by antibodies

tail fibers

Allow the bacteriophage to attach to the host cell

fiber proteins

on capsid of naked viruses

icosahedral capsid

Virus structure with 20 triangular faces.

helical/filamentous capsid

Rod-shaped, form a continuous helix around the nucleic acid (genome)

complex capsid

No symmetrical form, often found in bacteriophages; contains "core" structure that contains the genome

complex-tailed bacteriophages

-head: icosahedral, contains genetic material

-tail: injects genome into host cells

-tail fibers: attachment

1. Host cell recognition and attachment

2. Genome entry

3. Biosynthesis

4. Assembly/Maturation

5. Release (and transmission)

General Scheme of viral replication:

virion

single, infectious virus particle; can be productive or latent

productive (lytic phage) virion

making or capable of making large amounts of; giving good results

latent (lysogenic) virion

Viral genome integrates or replicates as a circular DNA (non-productive or no virions are produced); can still affect host even when not productive (Ex: chicken pox)

tail fibers bind to bacterial host cell "receptor" (LPS, pilli, porin)

Host cell recognition and attachment (phage lytic infection):

complex phage will inject genome alone into host using potential energy; sometimes uses lysozyme to make a hole in peptidoglycan

Genome entry (phage lytic infection):

some phage digest host bacterial genome; gene expression is regulated by regulators (early genes/proteins, late genes/proteins)

Biosynthesis (phage lytic infection):

early genes/proteins

modify or alter host's replication or transcription

late genes/proteins

build the phage tail, capsomeres, etc; ex: lysozyme to break out

generalized transduction (only if a mispackaging event happens); complex phage virion assembly is complicated and follows a specific, step-by-step process

Assembly/maturation (phage lytic infection):

Many phase will lyse and kill host; burst size = number of virions released (productive infection, so more virions

Release (phage lytic infection):

plaque

a clearing in a bacterial lawn resulting from lysis by phages; phage infection occured

temperate phage

A phage that is capable of reproducing by either the lytic or lysogenic cycle

prophage

the viral DNA that is embedded in the host cell's DNA; during lysogenic cycle

induction

When infection switches to lytic pathway

specialized transduction

a highly specific part of the host genome is regularly incorporated into the virus

environmental conditions, the nutritional state of the host, and molecular, density-dependent signaling. Favorable conditions typically favor lysogeny, while environmental stress (UV light, DNA damage) triggers the lytic cycle

What determines if a bacteria will enter the lytic cycle?

phage conversion

Prophage genes give the host bacterial cell new properties (new phenotypes), even in the lysogenic state; prophage are considered mobile genomic elements

mobile genomic elements

DNA segments capable of moving within a genome (intracellularly) or between cells (intercellularly) via transposition or horizontal gene transfer

filamentous phage

typically don't directly burst/kill the host but use host secretion or pili structure to exit; Some are always Productive, some can also go Latent

1. Bacterial restriction enzymes

2. CRISPR

bacterial defenses against phage

bacterial restriction enzymes

cut DNA molecules at specific DNA sequences called restriction sites; cut foreign DNA

methylation

helps distinguish self from non-self

CRISPR

bacteria integrate phage sequences in their own genome after surviving infection; creates a memory; crRNA and CAS proteins

- spikes (enveloped) or fiber proteins

- more than 1 host receptor may be utilized

- receptors are the host's

- determines host range and tissue tropism

How do viruses recognize the host cell?

tissue tropism

the range of tissue types that a virus can infect

- endocytosis (animal host cell) (only way for naked virus)

- Fusion (envelope fuses at host plasma membrane)

How do viruses enter the genome?

uncoating

once inside the host, the capsid is broken down to release the genome

proteases

enzymes that break down proteins; viral proteins are often translated as one large polypeptide then processed by these enzymes

viral genome (need viral mRNA) and virus proteins

biosynthesis involves making more...

Dna polymerase

DNA --> DNA; Host or viral enzymes

RNA polymerase

DNA ---> RNA; Host or viral enzymes

Replicase

RNA ---> RNA; viral enzyme only

Reverse transcriptase

RNA ---> DNA; viral enzyme only

HPV; uses DNA polymerase and RNA polymerase

DNA viruses biosynthesis

provirus

Viral DNA that inserts into a host genome; genome is replicated when the host's is replicated; typically DNA viruses (like HPV)

viral oncogenes

pieces of DNA from viruses that infect a normal cell and cause it to become malignant

Sars-CoV-2; use replicase; replicates viral genome and makes more viral mRNA; +RNA can also serve as mRNA and be directly translated first, no need to package replicase protein in the nucleocapsid

+RNA ---> -RNA ---> +RNA

+RNA viruses biosynthesis

Measles, influenza; Use replicase; host ribosome cannot directly translate the -RNA strand, so the virus must use replicase to make +RNA first; Replicase is packaged in the nucleocapsid

-RNA ---> +RNA ---> +RNA

-RNA & dsRNA viruses biosynthesis

HIV; use reverse transcriptase; host transcribes genome and viral mRNAs; DNA copy integrates into host genome, CAN'T be eliminated

RNA ---> DNA ---> RNA

reverse transcribing RNA viruses biosynthesis:

Hepatitis B; use reverse transcriptase; starts with a DNA genome that enters the host nucleus first, then RNA polymerase transcribes into mRNA, then Reverse transcriptase replicates mRNA into DNA

DNA ---> RNA ---> DNA

reverse transcribing DNA viruses biosynthesis:

antigenetic drift

slow, small changes in the virus; ex: mutations, mistakes in replicase and reverse transcriptase, new flu strain

antigenetic shift

a large, rapid change; recombination and reassortment; ex: flu pandemics

exocytosis and budding of the cell membrane (HIV)

How do enveloped viruses release?

often apoptosis, some might use vesicles

How do naked viruses release?

viroid

single-stranded RNA molecule that has no surrounding capsids or virions; no ORFs (can't make proteins); most infect plants, not well understood

prions

infectious protein particles; no genome; very stable, resistant to heat, and proteases; leads to aggregates in the brain