Viruses- Structure Flashcards
Baltimore scheme of viral classification
As there are thousands of viruses with lots of variation, viruses can be difficult to classify. The Baltimore scheme classifies viruses into one of seven categories based on their genetic material
Baltimore categories (7)
- Double stranded DNA
- Single stranded DNA
- Double stranded RNA
- Single stranded (+) strand RNA
- Single stranded (-) strand RNA
- Single stranded (+) RNA with DNA intermediate
- Gapped double stranded DNA
Basic viral structure
Viruses are basically a proteinaceous box that contains genetic material (DNA or RNA). The genetic material must be delivered to the target cell so that it can continue its existence by multiplying.
All viruses must
Produce mRNA. This includes + strand RNA, - strand RNA, and double stranded RNA viruses. DNA viruses must produce mRNA also, but single stranded DNA must be converted to double stranded DNA first. Transcription can’t happen on single stranded DNA.
Gapped double stranded DNA genomes
Contain double stranded DNA, but one of the strands is gapped (there is a gap in the strand). The virus will then use the machinery in the host cell to fill this gap. Once the gap is filled, the genome is essentially double stranded DNA that will be used to produce mRNA
Viral genome
The nucleic acid (DNA or RNA) inside of the viral “box”. It contains all of the information necessary to produce the proteins and factors that can mediate viral replication and orchestrate cellular machinery for its own use- essentially copying and packaging its genetic material.
Viral replication
Producing more than one virus particle using the one virus that has infected the cell. Viral replication involves more than just replicating viral nucleic acid
Stages of the viral replication cycle (7)
- Attachment
- Entry into the cell
- Uncoating of the viral particle- genetic material is uncoated inside of the cell
- Genome replication
- Expression of the genome- structural proteins are produced
- Assembly- the structural proteins allow the genome to be packaged into the virus particle
- Release of the assembled virus particle from the host cell
Attachment
The virus recognizes and attaches to the target cell. This is a highly regulated process where the surface proteins on the virus interact with the surface proteins or molecules on the host cell.
Viral genome replication
The virus will produce many copies of its genetic material. Some viruses do this in the cytoplasm, while others do this in the nucleus. For DNA viruses, genome replication in the nucleus makes more sense
Virion
An infectious, fully functional virus particle. Components of a virion include the nucleic acid, necessary enzymes and proteins, and surface proteins.
HIV structure
An enveloped virus containing surface proteins gp120 and gp41. Its genome contains two + strand RNA. HIV contains a reverse transcriptase, designating it as a retrovirus.
Tobacco mosaic virus (TMV) structure
Infects plants, specifically tobacco plants. Its genome is one RNA strand, which is complexed with a virally encoded protein called code protein. Multiple of these protein subunits coat the genetic material to create a functional virion. Doesn’t have a “box”, just a helical RNA strand coated with proteins.
Pox virus structure
Irregular, dumbbell shaped virus. It is an enveloped virus with a host-membrane derived envelope and a capsid (which gives it its irregular structure)
Adenovirus structure
The virus that causes the common cold. Not enveloped. Has a capsid (“box”) and an irregular structure. The capsid is the outer layer, which is composed of protein units called hexons and pentons. Protein 9 functions as a glue which holds the pentons and hexons together and helps to form a stable capsid structure. Contains surface fibers that protrude out of the penton subunits in the virion, helping with it to recognize and attach to the target cell.
Packaging of the viral genome
May be packaged in a capsid or just be wrapped in proteins as in TMV. Some viruses have extra packaging in the form of an envelope outside of the capsid, while others do not.
Functions of the viral capsid
The capsid is also known as the core of the virus. It protects the viral genome and delivers it to the correct site in the host cell by making it bind to specific host cell receptors and fuse with the plasma membrane. The capsid also helps the virus to uncoat and reveal its genome once it gets to the correct site inside the host cell. Some structural proteins can still remain complexed to the viral genome, and guide the genome through subcellular compartments to get to the site of replication
SARS-CoV-2 structure
An enveloped virus that does not have a capsid. Has a 29 kilobase + strand RNA molecule as its genome. The genome is complexed with virally encoded nucleoproteins. The genome is then packaged into an envelope that is derived from a host cell
Where can a viral envelope be derived from?
From the host cell membrane or other subcellular membranes such as the endoplasmic reticulum or Golgi apparatus (like Covid)
Subunit
A single folded polypeptide chain
Icosahedral
A virus that has 20 faces. These faces may be composed of protein subunits that repeat multiple times. A non-enveloped, spherical virus will always have icosahedral symmetry. An enveloped virus will probably have icosahedral symmetry if it looks spherical and has a capsid
Structural unit
Also called a promoter or asymmetric unit. Capsids or nucleocapsids are built of protomers that are asymmetric. They might contain one or more subunits which come together to form the structural subunit
Capsid
The protein shell that surrounds the genome
Envelope
A viral membrane that is derived from the host cell lipid bilayer
Nucleocapsid
The core of the virus. It is the nucleic acid-protein assembly within a virion. A capsid is called a nucleocapsid if the virus has an envelope
Size of human viruses
Parvoviruses are one of the smallest viruses, and are 20 nanometers in size (the same size as an individual ribosome). Ebola virus is one of the largest, up to 1 micron in diameter.
Metastable
Viruses are considered metastable because they alternate between a stable state (protected genome) and unstable state (delivering the genome). The capsid and/or viral envelope protect the virus in the external environment and when its traveling inside the body. However, the genome must be uncoated after interactions with the host cell. Virions are spring loaded to unload and deliver the genome under the right conditions
Free energy changes during viral replication
- The virus is stable- energy has been put into assembling the virus
- An energy barrier (the energy used to assemble the virus) must be surmounted for the virus to enter an unstable state
- When the virus enters the unstable state, energy is released
How is the energy barrier for the virus to enter the unstable state surmounted?
Through interaction with the host cell receptors. When a virus is phagocytosed, the pH in the endosome changes, causing the capsid to become less stable and the genome to be released
Which factors define metastability?
- A stable structure is achieved by the symmetrical arrangement of asymmetrical subunits, compromised of many identical proteins. Subunit interactions are controlled and specific
- Unstable structure- achieved due to non-covalent (reversable) bonding that can break apart in response to a variety of stimuli and interactions
3 types of virus particles
- Icosahedral symmetry
- Helical symmetry
- Complex- viruses that do not fit into icosahedral or helical symmetry
Helical symmetry
TMV is an example- forms a tube-like structure and does not have an envelope. Plant viruses were able to survive without having an envelope. They enter plant cells through damage in the plant, without having to go through interactions with host cell surface proteins. Animal viruses with helical symmetry are always eneveloped
Capsids with helical symmetry
Tend to be composed of subunits that come together as a trimer. The trimers form one turn of the helical structure. The subunits also interact with each other and the nucleic acid (RNA in the case of TMV). This allows the proteins to coat the RNA molecule and form a large stable structure
Sendai virus (paramyxovirus)
Has a similar structure to TMV, but also has an envelope. The envelope can burst and release the nucleic acid coated with proteins into the cell. Animal viruses with helical symmetry are always enveloped, so they may not resemble helical viruses
Icosahedral viruses
Viruses with icosahedral symmetry appear spherical or round. All round capsids have precise numbers of proteins in multiples of 60s (60, 120, 180). a larger virus would have a larger triangulation number to make a viral capsid. Sizes vary, but capsid proteins are 20-60 kDA on average
Triangulation (T) number
The number of subunits or facets per triangular face. A larger triangulation number means that the virus is larger. Determines the size of viruses with icosahedral symmetry- in these viruses, each subunit has different bonding contacts with its neighboring subunit
Virus like particle (VLP)
Viral proteins are very specific in their interactions, so subunits can self-assemble into virus like particles. VLPs contain capsid proteins, not a genome. Can be used for vaccines or drug delivery
How are viruses enveloped?
Not all viruses are enveloped. The envelope is mostly derived from the lipid bilayer of the host cell, but can come from the nuclear membrane, ER, or Golgi membrane. Where the envelope comes from is specific to the virus. In HIV, the gp120 and gp40 proteins act as transmembrane proteins. Other proteins bring the genetic material along with the surface proteins, and the virus blebs off from the membrane, forming the envelope
Viral envelope glycoproteins
HIV, influenza, and SARS-CoV-2 all produce glycoproteins which produce from the viral surface. The glycoproteins can be arranged vertically, where they protrude from the viral membrane, or horizontally, where they are parallel to the viral membrane. Vertical glycoproteins have a globular head, hinge, and stem components.
Viral envelope glycoproteins structure
They have 3 domains- extracellular, transmembrane, and intracellular. Intracellular domains interact with the viral genome, since they have to bring it in for viral assembly. The extracellular domain is a globular domain that can be glycosylated. It can interact specifically with the target cell
Functions of viral envelope glycoproteins
They facilitate attachment, fusion, and serve as an antigenic site for targeting the virus in vaccines or treatments
