MICB Lecture 4

• Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the strain that causes the disease covid 19.
• What are viruses

  obligate, intracellular parasites
• Features of viruses

  protein + nucleic acid, small (nm)
• What virus and how many genes

  Parvovirus - 3 genes

  
• What virus and how many genes

  Mimivirus - 900 genes

  
• virion

  complete virus particle
• capsid

  protein coat around genome
• nucleocapsid

  nucleic acid + capsid and either DNA or RNA
• protomer

  protein subunit of capsid
• Simplest virions consist of only a nucleocapsid
• envelope virus: virions covered by a lipid membrane, those lacking a membrane are called naked viruses
• viruses lack ribosomes for protein synthesis, a mechanism for generating ATP and a cytoplasm
• naked virus: construct capsid from many copies of one protein and a few minor proteins
• enveloped virus: require both nucleocapsid proteins and additional proteins to anchor the membrane
• spikes: on enveloped virus, made from the virus, involved in attachment to host cell surface
• Morphological type

  Helical: hollow tubes with protein walls, ex: tobacco mosaic virus

  
• Influenza virus

  RNA is segmented and capsids are helical
• Morphological type

  Icosahedral: efficient way to enclose space

  • 20 triangular faces w/ ring shaped units of 5 or 6 protomers

  
• What symmetry and associated features

  Binal

  • icosahedral head (genetic info injected there, genome inside) and helical sheath
  • bacteriophages infect bacterial (and archaeal) cells
  • often results in cell lysis
  • CRISPR/Cas: bacterial defense mechanism to prevent phage attack

  A) T-4 bacteriophage

  
• What symmetry

  Complex:

  poxviruses

  • virions among the largest of the animal viruses
  • ovoid, brick shape

  
• Viral envelopes

  the capsid of some viruses is enclosed in an envelope (comes from host cell membrane)

  A) Envelope

  B) tegument

  C) capsid

  
• Name virus and proteins within it

  Hemagglutinin spike: binds host sialic acid

  Neuraminidase spike: cleaves host lipids/proteins to release virus

  envelope: lipid bilayer

  RNA replicase: use RNA template to make RNA

  Influenze subtype H5N2: H=hemagglutinin and N=neuraminidase

  A) influenza virus

  B) hemagglutinin spike

  C) Envelope

  D) rna replicase

  E) segmented RNA genome

  F) H5N2- subtype

  G) neuraminidase spike

  
• Genome

  all genetic material in an organism
• Viral genomes can be

  DNA or RNA

  ss or ds

  linear or circular

  genome encodes the viral proteins
• How to classify viruses

  over 2000 viruses have been described and placed with these key defining properties

  1. nucleic acid type
  2. capsid symmetry
  3. presence/absence of envelope
• Five features of Coronavirus

  Nucleic acid: RNA

  Symmetry/capsid: helical

  naked or enveloped: enveloped

  Genome architecture: +ss

  Baltimore class: IV
• How to cultivate bacteriophages

  bacteria and archaea cells
• how to cultivate animal viruses

  suitable animals, embryonated eggs

  animal viruses are grown in cell culture on monolayers of animal cells
• plaques

  results from lysis by virus, localized area of cellular destruction
• how to cultivate tissue (cell) cultures

  cell monolayers

  • plaques
  • plaque assays (virion numbers expressed as plaque forming units)
• Viral multiplication/infectious cycle

  attach to cell host - proteins initiate

  2. entry and uncoating

  3. synthesis of viral proteins and nucleic acids

  4. assembly of capsids

  5. release of virions
• Animal virus attachment

  viral surface proteins mediate attachment to host receptors - carbohydrates, proteins and lipids

  ex: influenza hemagglutinin, HIV gp (glycoprotein)120, SARS-CoV-2 ACE2 receptor
• ACE2 receptor

  cleaves hormone angiotensin, regulates blood pressure
• Animal virus entry

  virus genome or entire nucleocapsid enter cytoplasm, once inside some shed their capsid proteins (uncoating)
• Two types of entry

  Fusion: involves viral envelope glycoproteins or phospholipids that interact with proteins in the plasma membrane of host cell

  Endocytosis: enter ells by one of the endocytic pathways (including clathrin-dependent endocytosis and macropinocytosis), resulting endocytic vesicle contains virion and fuses with endosome

  A) Fusion

  B) endocytosis

  
• once viral infection of a host cell has occurred

  viral genome is replicated

  viral mRNA made (via transcription) used to make viral proteins (for translation)
• Central Dogma of information flow

  Replication: utilize DNA polymerase

  Transcription: DNA template to make RNA

  Translation: RNA template to make sequence of amino acids, then folded into protein

  DNA -> RNA -> protein

  A) replication

  B) transcription

  C) translation

  
• RNA viruses typically replicate in

  cytoplasm, use viral RNA replicase to make RNA
• Four types of RNA viruses

  dsRNA

  +ssRNA

  -ssRNA

  retroviruses
• +ssRNA

  genomes act directly as mRNA

  upon entry and uncoating, host ribosomes translate viral +RNA into protein

  ex: polio, zika