Virus Structure and Replication Flashcards
describe the structure of different viruses and how viruses replicate based on their genome
1
Q
Ivanovski
A
Credited with discovering viruses. Studied tobacco mosaic disease
2
Q
Beijerinck
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Co-discovery of viruses
3
Q
Stanley
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Father of field of molecular molecular microbial pathogenesis, which is how microbes and components interact with hosts to cause disease.
4
Q
Virion
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complete extracellular viral particle
5
Q
Virus size range
A
20nm-300nm
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Q
Host range
A
viruses are specific about what organisms and tissues they infect
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Q
Bacteriophage
A
bacterial virus, also called a phage and represented by a Greek Phi; Ex: T4 phage
8
Q
Plant virus example
A
Tobacco Mosaic Virus
9
Q
Animal virus example
A
SARS
10
Q
Zoonotic example
A
Influenza and rabies
11
Q
Naked Virus
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viruses with only a nucleocapsids, either don’t have envelopes or have lost their envelope.
12
Q
strands of DNA roles (pos and neg)
A
DNA is double stranded with one plus strand and one minus strand. The plus strand is the coding, sense, and non-template strand. The minus strand is the non-coding, anti-sense, or template strand. The minus strand is what gets transcribed into mRNA.
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Q
Central Dogma
A
DNA, replicated–>transcribed–>mRNA–>translated–>protein
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Q
RNA review strand
A
positive RNA strand is mRNA and is translated into protein, minus strand of RNA cannot be translated.
15
Q
Different types of virus genomes
A
DsDNA
ss(+)DNA
dsRNA
ss(+)RNA
ss(+)RNA retrovirus
ss(-) RNA
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Q
dsDNA replication location
A
nucleus (excluding poxviruses –> cytoplasm)
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Q
dsDNA replication and mRNA synthesis
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-uses host or viral DNA polymerase to replicate,
-semiconservative
(-) DNA strand is transcribed into mRNA via host RNA polymerase
18
Q
ssDNA replication location
A
Nucleus
19
Q
ssDNA (+) replication and mRNA synthesis
A
-host DNA polymerase synthesizes a complimentary (-) DNA strand, forming a dsDNA intermediate
-Semiconservative
-the negative strand from the intermediate is used to make mRNA
20
Q
dsRNA replication location
A
cytoplasm
21
Q
dsRNA replication and mRNA synthesis
A
-The (-) RNA strand is copied by viral RdRP to make (+)ssRNA, which is used to make more RNA genomes
-The (-) RNA strand is used to make by RdRP to make +mRNA
22
Q
ssRNA (-) replication location
A
Cytoplasm (except influenza which replicated in the nucleus)
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Q
ssRNA (-) replication and mRNA synthesis
A
(-) RNA strand is copied by viral RdRP to make a complementary (+) strand which is then used to make new (-) RNA genomes
-The (-) RNA strand is used to make by RdRP to make +mRNA
24
Q
ssRNA (+) non-retrovirus replication and mRNA synthesis
A
The (+) RNA strand is copied by viral RdRP to make a complementary (-) RNA strand which is used to make more RNA genomes
The (+) RNA genome is ALREADY mRNA so there is no extra transcription step needed
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ssRNA (+) replication location
Cytoplasm
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ssRNA (+) retrovirus location
Nucleus
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ssRNA (+) retrovirus replication and mRNA synthesis
-The (+) RNA strand is reverse transcribed into (-) DNA by the viral enzyme reverse transcriptase which is then copied into dsDNA and integrated into the host genome
-Host RNA polymerase transcribes (+) RNA from the (-) DNA strand in the integrated viral genome
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Retrovirus
a type of virus with RNA and the reverse transcriptase enzyme to allow to convert to DNA
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Provirus
animal virus genome integrated within the host DNA; refers to the viral genome or a pro-viral state for the cell
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Temperate Virus
virus whose DNA integrates with host DNA or lay dormant and replicates with the host cell; undergoes the lysogenic cycle; temperate pages are bacteriophages that do this
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Protein capsid
made of capsomeres. Protect the viral nucleic acid. Virus specific proteins and enzymes are also located in capsid.
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Nucleocapsid
viral nucleic acid and capsid together
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Capsomeres
protein subunits that make up capsids
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Common viral shapes
Helical, Icosahedral, Complex and Pleomorphic
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Helical
spiral or rod-like structure with RNA or DNA wound inside. Held together non-covalently with hydrogen bonds and hydrophobic Vander Waal interactions. Only made of one protein but there are almost 2130 identical capsomeres of this protein.
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Icosahedral
A symmetrical (5-3-2 folds symmetry) with 20 identical triangular faces
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icosahedral viruses that have dsDNA
Herpes simplex Virus (dsDNA)
Varicella-Zoster Virus (dsDNA)
HPV (dsDNA)
Adenoviruses (dsDNA)
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icosahedral viruses that have ss (+) RNA
Poliovirus (ss+RNA)
Rhinovirus (ss+RNA)
Hepatitis A (ss+RNA)
Dengue Virus (ss+RNA)
Zika Virus (ss+ RNA)
Rubella (ss+RNA)
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Viral transformation
a process, in this case caused by a virus, where a normal host animal cell becomes cancerous (transformation is also defined as a type of genetic transfer which is unrelated to this definition)
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Vaccination (immunization)
inoculation of a host with inactive, weakened, attenuated, or a similar species/strain, or pathogen-products to stimulate protective immunity
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Antigen
anything that causes an immune response
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Adaptive Immune Cells
cells that have memory
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How vaccines work (general)
train the immune system by exposing it to a harmless form of a pathogen, immune memory
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Primary response (vaccine)
body's first response to the vaccine or pathogen. Antibody levels increase slowly, peak at about 10 days, then decrease
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Secondary response (vaccine)
body's response to subsequent exposure to the same pathogen/vaccine. Fast, strong, and effective immune response, and adaptive immune cells produce high levels of antibodies. About 10-1000x greater immune response. Slower decline of adaptive immune cells and antibodies but it never decreases to baseline.
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Gardasil
Gardasil is a vaccine that protects against Human Papillomavirus (HPV), which can cause cervical cancer, genital warts, and other HPV-related cancers.
How does this work?
-Contains HPV virus-like particles
-Triggers the immune system to create antibodies against HPV.
-If exposed to HPV later, the immune system quickly neutralizes it before infection occurs.
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How does Gardasil work?
Dose 1
Introduces HPV virus-like particles to the immune system.
immune cells produce some antibodies but level are low
Adaptive immune cells begin forming for future protection
Dose 2 --> Given 2 months after
Stronger antibody response than the first dose.
More memory cells develop, improving long-term immunity.
Helps reinforce immune recognition of HPV.
Dose 3: --> Given 6 months after
Triggers the strongest and most sustained antibody response, acts as a booster.
Ensures long-term immune memory, reducing the chance of infection.
Provides years of protection against HPV-related diseases
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Envelope
Not all viruses have this. They are found external to nucleocapsid and consist of a lipid bilayer stolen from the host cell
They contain viral glycoprotein spikes that help the virus attach to the host cell
interesting note: viruses with an envelope tend to be better at immune invasion but are more fragile than tough, resistant viruses that do not have an envelope and just their nucleocapsid.
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Enveloped Viruses
Herpes Simplex (1&2) (dsDNA)
Varicella Zoster (dsDNA)
Influenza (A,B,C) ss(-)RNA
SARS-CoV-2 ss(+)RNA
HIV ss(+)RNA retrovirus
Rabies ss(-)RNA
Dengue Virus ss(+)RNA
Zika Virus ss(+)RNA
Ebola ss(-)RNA
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Naked Viruses
Norovirus ss(+)RNA
Poliovirus (ss(+) RNA
HPV dsDNA
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Virus Life Cycle
1.) Attachment (Absorption)
2.) Penetration
3.) Biosynthesis
4.) Maturation
5.) Release
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Attachment
Virus binds to specific host cell receptors using capsid proteins (non-enveloped viruses) or envelope glycoproteins (enveloped viruses).
Ex: Influenza binds to sialic receptors on respiratory cells
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Penetration Enveloped
Enveloped viruses: Enter via membrane fusion (e.g., HIV) or endocytosis (e.g., Influenza).
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Penetration Non-Enveloped
Non-enveloped viruses: Enter via direct penetration (e.g., Poliovirus) or endocytosis.
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Penetration Phages
Bacteriophages: Inject DNA into host through a contractile tail (e.g., T4 phage).
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Biosynthesis
- genome replication and protein production
Ex: Example: SARS-CoV-2 (an RNA virus) uses RNA-dependent RNA polymerase to replicate.
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Biosynthesis DNA Viruses
DNA viruses → Replicate in the nucleus using host or viral DNA polymerase.
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Biosynthesis RNA viruses
RNA viruses → Replicate in the cytoplasm using viral RNA polymerase.
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Biosynthesis Retroviruses
Retroviruses → Convert RNA into DNA via reverse transcriptase (e.g., HIV).
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Maturation (Assembly)
Viral genome is packaged into capsids, and envelope proteins (if present) are incorporated.
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Release Enveloped
Enveloped viruses: via budding, acquiring their envelope from the host membrane (e.g., HIV, Influenza).
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Release Non-Enveloped
Non-enveloped viruses: Cause host cell lysis, releasing viruses (e.g., Poliovirus, T4 phage).
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Persistent Infection
infection that results in the continued presence of a pathogen within the infected cells or organism
(umbrella term encompassing both chronic virus and latent virus)
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Chronic Virus
a virus whose genome persists in a host cell with virions always being produced, sometimes with continual symptoms
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Latent Virus
a virus whose genome persists in a host cell, yet no detectable effect of infectious virus is present except during reactivation into a lytic infection. No active replication
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T4 Attachment
specific phage tail fibers bind to LPS (lipopolysaccharide- polymer of lipids and carbohydrates found in the outer membrane of Gram-negative bacteria like E.coli) receptors on the surface of E. coli.
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T4 Penetration
T4 phage injects its dsDNA into the bacterial cytoplasm via its contractile tail sheath. The tail sheath contracts, driving the phage genome into the host. The capsid remains outside host cell.
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Uncoating
Virus removes its capsid after entering host cell releasing genome into either the cytoplasm or nucleus
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T4 Biosynthesis
Viral DNA is replicated in the cytoplasm (because bacteria does not have a nucleus LOL). Note that this specific phage has dsDNA. Viral proteins, including lysozyme, are synthesized. Lysozyme is produced to break down the bacterial cell wall, enabling host lysis at release.
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Lysozyme
enzyme that destroys peptidoglycan by hydrolyzing the bond between the sugar backbone; produced by humans, some other eukaryotes, some prokaryotes, and some bacteriophages.
-produced by the virus during the biosynthesis phase. Uses lysozyme to break down bacterial cell wall. Sets up the cell for lysis and release
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T4 Maturation/Assembly
New specific phage virions are assembled in the cytoplasm: Capsid, tail, and tail fibers are formed, and the phage genome is packaged into the capsid.
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T4 Release
T4 phage produces lysozyme, which breaks down the bacterial cell wall, causing lysis and releasing hundreds of new phages.
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does HSV1 have envelope
yes
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HSV1 genome
dsDNA, linear about 152 kDa
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HSV1 nucleocapsid structure
icosahedral
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HSV1 attachment
Step 1: spiked glycoproteins (because it has an envelope) bind to the host heparin sulfate (which is a chained polysaccharide found in oral epithelial extracellular matrix, attaching to the cells of the mouth and lips
Step 2: viral coreceptor attaches, and allows for the fusion of the viral envelope with the host plasma membrane.
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HSV1 Penetration
nucleocapsid enters the cytoplasm and is transported to the nucleus where the nucleocapsid is uncoated and reveals the viral DNA and proteins.
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HSV1 biosynthesis (replication and transcription)
Replication takes place in the nucleus using viral DNA Polymerase. The linear DNA circularizes inside the host nucleus.
1.) Immediate-early (α genes): Regulatory proteins.
2.)Delayed-Early (β genes): viral specific proteins like DNA polymerase and other replication proteins.
3.) Late (γ genes): Encode structural proteins for capsid and envelope.
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HSV1 Maturation/Assembly
Newly synthesized viral DNA is packaged into nucleocapsids in the nucleus.
The virus buds into the Golgi, acquiring an envelope.
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HSV1 Release
Virion moves through the host endoplasmic reticulum and out of the host cell via exocytosis or lysis, spreading to nearby cells.
The virus may also enter a latent phase in neurons, where it persists in a dormant state and can later reactivate (e.g., during stress, immunosuppression).
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HSV1 incubation period
3-5 days. Lesions heal within 2-3 weeks
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Influenza genome
ssRNA (-), segmented (8 segments)
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Influenza nucleocapsid shape
helical but it can also be considered pleomorphic
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Influenza envelope?
YES
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Influenza Attachment
Hemagglutinin (HA) binds to sialic acid receptors on the host cell surface, initiating viral attachment.
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Influenza Penetration
The virus is taken up by endocytosis into the host cell. The virion moves inside the host cell and the envelope is removed. It moves to the host nucleus where it is uncoated to reveal viral RNA and RNA polymerase.
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Influenza Biosynthesis
Inside the nucleus, the (-) ssRNA genome is transcribed into mRNA by viral RNA polymerase. The mRNA is transported to the cytoplasm to synthesize viral proteins. The (-)ssRNA genome is also replicated into (+)ssRNA, which is then used to produce more (-) ssRNA genomes for new virions.
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Influenza Maturation and Assembly
Newly synthesized viral proteins are transported to the plasma membrane. New ribonucleoproteins (RNPs) are packaged into viral nucleocapsids in the nucleus. Viral HA and NA proteins are embedded in the host cell's membrane, ready for virion assembly
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Influenza Release
The virions bud off from the plasma membrane and are free to infect new cells.
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Viral RNA Polymerase
No proofreading ability so it makes mistakes (mutations) causing slight variations between influenza viruses. Results of this include
1.) High mutation rate
2.) Antigenic drift
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High mutation rate influenza
due to the lack of proofreading ability in the viral RNA polymerase. mutations in genes encoding viral surface proteins (like Hemagglutinin (HA) and Neuraminidase (NA)) can help the virus evade the host's immune response.
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Antigenic Drift
refers to the slow, gradual accumulation of mutations in the genes that encode viral surface proteins, particularly Hemagglutinin (HA) and Neuraminidase (NA). This results in small changes in the viral antigens over time.
the changes occur during replication
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Influenza Antigenic Drift
The small changes in the HA and NA proteins can alter the virus's appearance to the immune system, making it harder for the host's immune memory (from prior infections or vaccinations) to recognize the virus.
This leads to seasonal flu outbreaks, where the virus gradually changes enough to partially evade immunity, but it doesn't cause large-scale changes to the virus.
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Antigenic Shift
Antigenic shift refers to a major, abrupt change in the influenza virus's antigenic composition. occurs when there is reassortment or genetic exchange between different viral strains.
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Influenza and Antigenic Shift
when two influenza viruses mix after penetrating the same cell during virion assembly. leading to the creation of a new influenza virus with a novel combination of HA and NA. The antigenic shift creates BIG pandemic potential
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Antigenic Drift
slow process where small mutations gradually change the virus over time, leading to seasonal flu outbreaks.
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Antigenic Shift
Antigenic shift is a major change in the virus caused by genetic reassortment, leading to pandemics.
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Human flu
2,6 linkage: This is found in human flu viruses. Human influenza viruses have HA proteins that prefer sialic acid with this 2,6 linkage.
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Sialic Acids
These are sugars found on the surface of cells as part of glycoproteins or glycolipids. They act as receptors for the flu virus. The flu virus's hemagglutinin (HA) protein binds to these sialic acids to enter the host cell.
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Avian Flu
2,3 linkage: This is typical for avian (bird) and equine (horse) flu viruses. The flu viruses that infect birds have HA proteins that have a high affinity for sialic acid with this 2,3 linkage.
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Swine Flu
Pigs as Mixing Pots: PANDEMICS
Pigs have both 2,3 and 2,6 linkages in their cells, making them a "mixing pot" for different flu strains. This allows the potential for reassortment between avian, swine, and human flu strains, creating new viruses that could affect humans and lead to pandemics.
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Polysomes
are clusters of ribosomes that are simultaneously translating the same mRNA molecule
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Poliovirus
Genome: ssRNA+
Enveloped: Naked
Capsid Structure: Icosahedral
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Poxvirus
Genome: dsDNA
Enveloped: Yes
Capsid Structure: Complex (brick-shaped)
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Epstein-Barr Virus
Genome: dsDNA
Enveloped: Yes
Capsid Structure: Icosahedral
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HPV
Genome: dsDNA
Enveloped: No (non-enveloped)
Capsid Structure: Icosahedral
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Herpes Simplex (1&2)
Genome: dsDNA (double-stranded DNA)
Enveloped: Yes
Capsid Structure: Icosahedral
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Varicella Zoster Virus
Genome: dsDNA
Enveloped: Yes
Capsid Structure: Icosahedral
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CMV
Genome: dsDNA
Enveloped: Yes
Capsid Structure: Icosahedral
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Influenza
Genome: ssRNA (single-stranded RNA, negative-sense, segmented genome)
Enveloped: Yes
Capsid Structure: Helical (inside the envelope)
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SARS-CoV-2
Genome: ssRNA (single-stranded RNA, positive-sense)
Enveloped: Yes
Capsid Structure: Helical
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HIV
Genome: ssRNA (single-stranded RNA, retrovirus)
Enveloped: Yes
Capsid Structure: Conical (icosahedral core inside)
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Prions
misfolded proteins that can cause disease. can induce other proteins to misfold in a similar manner. Ex: Mad Cow Disease, Creutzfeldt-Jakob Disease
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Viriods
small, circular RNA molecules that infect plants and cause diseases by disrupting the host’s cellular processes. They lack a protein coat and do not encode proteins.
