Lecture 2

Question 1

List 5 reasons why viruses need to build a particle to protect their genomes?

Answer 1

• 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)

Question 2

What is a genetic economy?

Answer 2

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

Question 3

In terms of stability, what do viruses have to be able to accomplish while still being meta-stable?

Answer 3

• 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

Question 4

what is a virion?

Answer 4

a mature infectious virus particle

Question 5

what is a capsid?

Answer 5

the protein shell that encloses and protects the viral nucleic acid

Question 6

what is a capsomere?

Answer 6

the morphological unit of the icosahedral capsid

Question 7

what is a nucleocapsid?

Answer 7

the structure composed of the capsid containing the nuceic acid or core

Question 8

what is the core of a virus?

Answer 8

the internal part of the virus particle that consists of the nucleic acid and closely associated proteins

Question 9

what is the envelope of a virus?

Answer 9

the viral membrane consisting of a lipid bilayer containing spike proteins

Question 10

what are spike proteins?

Answer 10

viral glycoproteins that project from the envelope

Question 11

Can the capsid be considered a “stable brick”?

Answer 11

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?

Question 12

What are the two general mechanisms viruses have evolved for packaging their genomes?

Answer 12

• helical capsids
• capsids with icosahedral symmetry

Question 13

What type of viruses typically have helical capsids?

Answer 13

plant viruses and bacteriophages

Question 14

What are naked animal viruses?

Answer 14

• they are non-enveloped
• these type of viruses have never been found

Question 15

Are helical capsids rigid or flexible?

Answer 15

can be either rigid or flexible, depends on the capsid

Question 16

What is the general structure of a helical capsid?

Answer 16

• it is a planar net of identical subunits
• this then gets rolled to become the helical capsid
• forms long tube like/rod structure

Question 17

What are nucleocapsids?

Answer 17

• 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

Question 18

Are helical capsids open or closed structures?

Answer 18

open structures, the end of the rod is not sealed

Question 19

what is a protomer?/

Answer 19

another word for nucleic acid protein

Question 20

What are the two types of helical capsids?

Answer 20

• flexible
• rigid (structure of nucleic acid is firm/tight which creates the shape of the virus)

Question 21

What are icosahedrons and what are their building blocks?

Answer 21

• icosahedrons are twenty sided geometrical structures that form a sphere
• the basic building block is the triangle

Question 22

Are viral capsids perfect icosahedrons?

Answer 22

• no, not “perfect” icosahedrons
• but their structure are built using similar geometric principles (triangles as building blocks)

Question 23

What are the three geometric principles for icosahedral symmetry?

Answer 23

• threefold axis
• fivefold axis
• twofold axis

Question 24

What is the threefold axis?

Answer 24

• one of the geometric principles for icosahedral symmetry
• the center of one of the triangular faces

Question 25

What is the fivefold axis?

Answer 25

* one of the geometric principles for icosahedral symmetry * verticies of the capsids * 12 verticies on the icosahedral symmetry

Question 26

What is the twofold axis?

Answer 26

* one of the geometric principles for the icosahedral symmetry * occurs at the spot between two triangles (length wise)

Question 27

Describe the properties of the icosahedral capsid.

Answer 27

*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

Question 28

What is unique about retroviruses and capsid structure?

Answer 28

pentamers, such as HIV, have an unusual capsid structure.

Question 29

How do most eveloped viruses aquire their envelope?

Answer 29

* by budding through a membrane of the host cell into some extra-cytoplasmic compartment

Question 30

Why do enveloped viruses not always have to kill the cell in the course of replication?

Answer 30

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

Question 31

How do non enveloped viruses typically escape cells?

Answer 31

they have to lyse the infected cell to escape

Question 32

What type of virus is harder to get rid of? Enveloped or non-enveloped?

Answer 32

enveloped viruses

Question 33

What does the presence of an envelope provide viruses with the ability to do?

Answer 33

the presence of an envelope also provides viruses with an opportunity to insert virally encoded glycoproteins (spikes) into the envelope

Question 34

What are the roles of glycoproteins/spikes for an enveloped virus lifecycle?

Answer 34

* entry and host determination * assembly and egress * evasion from the vertebrate immune system

Question 35

What can the viral genome consist of?

Answer 35

the viral genome can consist of either RNA or DNA but never both

Question 36

what is mRNA defined as?

Answer 36

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)

Question 37

what is a strand of DNA that contains the same polarity of an mRNA strand defined as?

Answer 37

a positive strand (+)

Question 38

What is the RNA and DNA complement of the positive strand defined as?

Answer 38

the minus strand (-)

Question 39

How are positive strands synthesized?

Answer 39

positive strands are synthesized using minus strands as a template and vice versa

Question 40

What are the characeristics of a virus if they are comprised of DNA?

Answer 40

* 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

Question 41

What are the characteristics of a virus if it is comprised of RNA?

Answer 41

* 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)

Question 42

Where do most dna viruses replicate?

Answer 42

in the cell nucleus

Question 43

where do most rna viruses replicate?

Answer 43

in the cytoplasm

Question 44

Are there exceptions to where the rna and dna virus can replicate?

Answer 44

yes, there are important exceptions

Question 45

What are the two classification schemes for virus classification?

Answer 45

1. the classical system 2. the baltimore classification system

Question 46

What is the classical system?

Answer 46

viruses grouped according to their shared physical properties rather than their host

Question 47

What are the four characteristics used in the classical classification system?

Answer 47

* 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

Question 48

what is the baltimore classification scheme?

Answer 48

*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