Lecture 2 Flashcards
List 5 reasons why viruses need to build a particle to protect their genomes?
- to protect against proteolytic and nucleolytic enzymes (enzymes that want to degrade the virus)
- extremes of pH (ex. only some viruses can withstand the acidity of the stomach)
- extremes of temperature
- various forms of natural radiation (UV)
- shearing by mechanical forces (large DNA viruses)
What is a genetic economy?
the information necessary to specify the structural proteins must not exhaust the coding capacity of the genome. Essentially, the virus wants to get away with having as few genes as possible, so it can use less energy
In terms of stability, what do viruses have to be able to accomplish while still being meta-stable?
- the particle must be stable enough to protect the nucleic acid with in the extracellular environment
- but it must also be “not stable enough (hence meta)” because virus particles also mediate the attachment of the virus to an approproate host cell and deliver the genome to the interior of that cell, where the particle is at least partially disassembled
what is a virion?
a mature infectious virus particle
what is a capsid?
the protein shell that encloses and protects the viral nucleic acid
what is a capsomere?
the morphological unit of the icosahedral capsid
what is a nucleocapsid?
the structure composed of the capsid containing the nuceic acid or core
what is the core of a virus?
the internal part of the virus particle that consists of the nucleic acid and closely associated proteins
what is the envelope of a virus?
the viral membrane consisting of a lipid bilayer containing spike proteins
what are spike proteins?
viral glycoproteins that project from the envelope
Can the capsid be considered a “stable brick”?
no, it is not a stable brick. Rather, it is a molecular machine, a selective genome delivery device. There must be a mechanism for the selective incorporation of the viral genome into the capsid?
What are the two general mechanisms viruses have evolved for packaging their genomes?
- helical capsids
- capsids with icosahedral symmetry
What type of viruses typically have helical capsids?
plant viruses and bacteriophages
What are naked animal viruses?
- they are non-enveloped
- these type of viruses have never been found
Are helical capsids rigid or flexible?
can be either rigid or flexible, depends on the capsid
What is the general structure of a helical capsid?
- it is a planar net of identical subunits
- this then gets rolled to become the helical capsid
- forms long tube like/rod structure
What are nucleocapsids?
- the association of viral capsid proteins with viral nucleic acid
- many different RNA viruses build nucleocapsids using helical symmetry
- the dimensions of these nucleocapsids can vary between different types of viruses
Are helical capsids open or closed structures?
open structures, the end of the rod is not sealed
what is a protomer?/
another word for nucleic acid protein
What are the two types of helical capsids?
- flexible
- rigid (structure of nucleic acid is firm/tight which creates the shape of the virus)
What are icosahedrons and what are their building blocks?
- icosahedrons are twenty sided geometrical structures that form a sphere
- the basic building block is the triangle
Are viral capsids perfect icosahedrons?
- no, not “perfect” icosahedrons
- but their structure are built using similar geometric principles (triangles as building blocks)
What are the three geometric principles for icosahedral symmetry?
- threefold axis
- fivefold axis
- twofold axis
What is the threefold axis?
- one of the geometric principles for icosahedral symmetry
- the center of one of the triangular faces
What is the fivefold axis?
- one of the geometric principles for icosahedral symmetry
- verticies of the capsids
- 12 verticies on the icosahedral symmetry
What is the twofold axis?
- one of the geometric principles for the icosahedral symmetry
- occurs at the spot between two triangles (length wise)
Describe the properties of the icosahedral capsid.
*he mentioned this is a possible good short answer question
- 5 fold axis of symmetry at the axis
- 3 fold axis of symmetry is at the center of one of the triangular faces
What is unique about retroviruses and capsid structure?
pentamers, such as HIV, have an unusual capsid structure.
How do most eveloped viruses aquire their envelope?
- by budding through a membrane of the host cell into some extra-cytoplasmic compartment
Why do enveloped viruses not always have to kill the cell in the course of replication?
since enveloped viruses can acquire their envelope through budding, rather than lysing the cell, they do not have to kill the cell in the course of replication. Rather, non-enveloped cells generally HAVE to lyse the cell in order to escape the cell
How do non enveloped viruses typically escape cells?
they have to lyse the infected cell to escape
What type of virus is harder to get rid of? Enveloped or non-enveloped?
enveloped viruses
What does the presence of an envelope provide viruses with the ability to do?
the presence of an envelope also provides viruses with an opportunity to insert virally encoded glycoproteins (spikes) into the envelope
What are the roles of glycoproteins/spikes for an enveloped virus lifecycle?
- entry and host determination
- assembly and egress
- evasion from the vertebrate immune system
What can the viral genome consist of?
the viral genome can consist of either RNA or DNA but never both
what is mRNA defined as?
mRNA is defined as the positive strand (+) because it contains immediatelt translateable information (does not necessarily mean it will get translated, but it is of the right polarity to be done)
what is a strand of DNA that contains the same polarity of an mRNA strand defined as?
a positive strand (+)
What is the RNA and DNA complement of the positive strand defined as?
the minus strand (-)
How are positive strands synthesized?
positive strands are synthesized using minus strands as a template and vice versa
What are the characeristics of a virus if they are comprised of DNA?
- linear or circular
- single stranded or double stranded
- single stranded viruses can be either (+) or (-) polarity
- or it can be partially double stranded and circular
What are the characteristics of a virus if it is comprised of RNA?
- linear only
- single stranded or double stranded
- single stranded viruses can be either plus or minus polarity or both (ambisense- single stranded RNA virus and portions are positive or negative)
- monopartite (single piece of RNA) or multipart/segmented (multiple genome segments)
Where do most dna viruses replicate?
in the cell nucleus
where do most rna viruses replicate?
in the cytoplasm
Are there exceptions to where the rna and dna virus can replicate?
yes, there are important exceptions
What are the two classification schemes for virus classification?
- the classical system
- the baltimore classification system
What is the classical system?
viruses grouped according to their shared physical properties rather than their host
What are the four characteristics used in the classical classification system?
- nature of the genetic material in the virion (DNA or RNA, plus or minus, single or double stranded, multi or single parted)
- symmetry of the capsid (helical or icosahedral)
- naked or enveloped
- dimensions of the virion and capsid
what is the baltimore classification scheme?
*it is a molecular biologists view of virus classification
- based on the central dogma: DNA makes RNA makes protein
- All viruses must produce mRNA that can be translated by cellular ribosomes
- in this classification scheme, the unique pathways from various viral genomes to mRNA define specific virus classes on the basis of the nature and polarity of their genomes
