A. Which of the following is a feature shared by all known viruses?
(a) They possess a double-stranded DNA genome.
(b) They contain functional ribosomes for protein synthesis.
(c) They replicate only within a host cell. (d) They are larger than 200 nanometers in diameter.
A. (c) They replicate only within a host cell
The defining characteristic of all viruses is their absolute dependence on a host cell for proliferation, making them obligate intracellular parasites.
* Rationale: Viruses must replicate only within a host cell [Q1-C, Q1-E]. This is because they lack the necessary components to carry out metabolic processes independently. They rely entirely on the host cell for three fundamental requirements [Q2-A]:
1. Building-blocks (such as amino acids and nucleosides).
2. Protein-synthesizing machinery (ribosomes).
3. Energy (in the form of ATP).
* Replication Process: A new virion (infectious particle) is never formed directly from a pre-existing virion. Instead, new virions are formed by the synthesis of individual components inside the host cell, followed by their subsequent assembly [Q1-E].
Explanation of Incorrect Options
The other options describe features that are specific to certain viruses but are not universal to the entire viral kingdom.
(a) They possess a double-stranded DNA genome
* Incorrect. The viral world is genetically diverse. Viruses are classified based on the nature of their genome (Baltimore Classification) [Q1-B].
* Viral genomes can be dsDNA (double-stranded DNA), ssDNA (single-stranded DNA), dsRNA (double-stranded RNA), or ssRNA (single-stranded RNA) [Q7-B]. Therefore, dsDNA is not a feature shared by all viruses.
(b) They contain functional ribosomes for protein synthesis.
* Incorrect. Viruses are fundamentally characterized by their lack of protein-synthesizing machinery. They must utilize the host cell’s ribosomes to translate their viral messenger RNA (mRNA) into proteins [Q2-A].
* The primary function of the virion is to serve as a gene delivery system to protect the genome and facilitate entry into the host cell [Q1-D]. It does not carry out independent protein synthesis.
(d) They are larger than 200 nanometers in diameter.
* Incorrect. Virus size varies dramatically. While some viruses (like Poxviruses) can be quite large, many others are significantly smaller, meaning a diameter greater than 200 nm is not a universal characteristic.
B. The Baltimore Classification system groups viruses primarily based on: (a) Their host species and tissue tropism. (b) Their type of genome and method of replication. (c) Their size and capsid symmetry (helical or icosahedral). (d) Whether they cause lethal or trivial diseases.
(b) Their type of genome and method of replication.
C. Which virus classification type is unique in utilizing (+)sense RNA with a DNA intermediate in its life cycle?
(a) Class III (dsRNA viruses)
(b) Class IV ((+)ssRNA viruses)
(c) Class VI ((+)ssRNA viruses with DNA intermediate)
(d) Class VII (dsDNA-RT viruses)
(c) Class VI ((+)ssRNA viruses with DNA intermediate)
- Class VI viruses (e.g., Retroviruses, such as HIV-1) = by the structure of their genome and their unique replication strategy:
1. Genome Type: These viruses possess a (+)ssRNA genome [Q7-B].
2. Replication Strategy: They utilize the enzyme reverse transcriptase to copy their (+)ssRNA genome into a DNA intermediate (often called a provirus) [Q7-B]. This DNA intermediate is typically then integrated into the host cell’s genome.
3. Conclusion: The process of using a (+)ssRNA genome with a necessary DNA intermediate during the life cycle perfectly matches the definition of Class VI.
D. The primary function of a virion is best described as: (a) Producing ATP and synthesizing essential building blocks. (b) Serving as a gene delivery system to protect the genome and aid entry into a host cell. (c) Carrying out protein synthesis outside the host cell. (d) Synthesizing polysaccharide enzymes and tRNAs.
b) Serving as a gene delivery system to protect the genome and aid entry into a host cell.
E. Which statement accurately describes the virus replication process compared to cell multiplication?
(a) A new virion is always formed directly from a pre-existing virion.
(b) A new virion is formed by assembly of components synthesized inside a host cell.
(c) Viruses synthesize new components independently outside a host cell.
(d) Virus replication involves formation directly from a pre-existing cell.
b) A new virion is formed by assembly of components synthesized inside a host cell. (A new virion is never formed directly from a pre-existing virion, but by synthesis of components followed by assembly.)
A. List three specific requirements (building blocks, machinery, or energy) for which viruses are dependent on their host cells.
A. Three requirements for which viruses are dependent on host cells are: building-blocks (such as amino acids and nucleosides), protein-synthesizing machinery (ribosomes), and energy (in the form of ATP).
B. Define the term oncogenic virus and provide three examples of animal viruses thought to cause forms of cancer.
B. An oncogenic virus is a virus that is able to cause cancer. Three examples are: Epstein-Barr virus, certain human papillomaviruses, and the hepatitis B virus (and some retroviruses).
C. Explain the difference between direct terminal repeats (DTRs) and inverted terminal repeats (ITRs) found in some virus genomes
C. Both DTRs and ITRs are repeat sequences often found at the ends (termini) of linear virus genomes. DTRs (Direct Terminal Repeats) are repeat sequences in the same orientation, whereas ITRs (Inverted Terminal Repeats) are repeats where the sequence at one end is complementary to and in the opposite orientation to the sequence at the other end.
D. Describe the structure and function of the envelope in an enveloped virion, noting the type of host membrane from which most virion membranes are derived.
D. The envelope is a lipid–protein structure generally located at the virion surface, enclosing the nucleocapsid. It contains proteins (mostly integral and glycosylated) that aid entry into host cells, sometimes by fusing the virion membrane to a cell membrane. Most virion membranes are derived from host cell membranes that undergo modification before incorporation into virions.
E. Contrast Helical symmetry and Icosahedral symmetry in virus capsids, and provide one specific example of a virus utilizing each.
E. Helical symmetry: The nucleic acid is coiled in the form of a helix, and many copies of the same protein species are arranged around the coil. Example: Influenza viruses (ssRNA) or measles viruses. Icosahedral symmetry: The capsid is constructed from 20 equilateral triangles arranged around the face of a sphere, often built from discrete structures called capsomeres. Example: Papillomaviruses.
A. Describe the two main general mechanisms by which enveloped viruses gain entry into a host cell. Both processes culminate in what necessary step?
3. Uncoating and Entry Mechanisms:
A. The two main mechanisms for enveloped virus entry are: (1) Fusion of the virion envelope with the plasma membrane (e.g., HIV), or (2) Endocytosis followed by fusion of the virion envelope with the endosome membrane (e.g., Influenza virus). Both processes involve the fusion of the virion envelope with a cell membrane.
B. Explain the complicated entry and uncoating strategy employed by Adenovirus, including the final destination of its DNA genome.
3. Uncoating and Entry Mechanisms:
B. Adenovirus, a nonenveloped virus, induces receptor-mediated endocytosis. It then disrupts the endosomal membrane, releasing part of the capsid and its DNA genome into the cytosol (trimmed-down virus). The trimmed-down virus then docks onto a nuclear pore and releases its DNA directly into the nucleus.
C. How do some enveloped viruses, such as the Influenza virus, utilize the acidic environment of the endosome to facilitate uncoating? Specify the viral protein channel involved.
3. Uncoating and Entry Mechanisms:
C. After endocytosis, the endosome acidifies (pH 4.8–5.0). The acidic conditions cause a part of the hemagglutinin (HA) protein to fuse the viral envelope with the vacuole’s membrane. Concurrently, the M2 ion channel allows protons (H
+
) to move through the viral envelope and acidify the core of the virus, causing the core to disassemble and release the viral RNA and core proteins.
D. Briefly describe the role of microtubules and nuclear pores in the intracellular transport of virus components, specifically mentioning how larger viruses manage to pass through nuclear pores.
3. Uncoating and Entry Mechanisms:
D. Once inside the cell, viruses often use one of the host’s transport systems, such as microtubules, to reach a particular location (e.g., the nucleus). The nuclear pores act as gatekeepers. Small virions/nucleocapsids (e.g., parvovirus) can pass through the nuclear pore complex. Larger viruses must either shed some of their load to form slimmer structures or uncoat at a nuclear pore (complete or partial removal of the capsid) to release the genome.
A. Describe the mechanism by which many viruses, utilizing IRES (Internal Ribosome Entry Sites), shut down host cell translation while promoting their own. Which host initiation factor is cleaved?
Viral Gene Expression and Molecular Biology
A. IRES sequences are often used by viruses as a means of shutting down translation in the host cell so that the cell’s translational machinery operates only on viral mRNA. The virus accomplishes this by cleaving the initiation factor eIF-4G so that it cannot interact with eIF-4E. This interaction is usually necessary for the 5’ cap to 3’ poly-A tail loop formation needed to initiate cap-dependent host translation.
B. Explain two distinct mechanisms (excluding IRES) that viruses use to read a second ORF (Open Reading Frame) within a polycistronic mRNA molecule.
B. The two mechanisms (excluding IRES) are:
1. Leaky scanning: A 40S ribosomal subunit may overlook the ORF 1 start codon and initiate translation at the start of ORF 2.
2. Ribosomal frameshifting: A ribosome shifts into a different reading frame (usually towards the end of ORF 1) upon encountering a specific sequence (frameshift signal) followed by a secondary structure (usually a pseudoknot). This causes the ribosome to skip the ORF 1 stop codon and continue reading ORF 2, producing an elongated version of the ORF 1 protein.
C. Explain the function of the Signal Sequence on viral proteins and how it directs the polypeptide-ribosome complex to the endoplasmic reticulum
C. The signal sequence is a series of hydrophobic amino acid residues, located either at the N-terminus or internally, that specifies the protein’s destination (to be incorporated into membranes). When the signal sequence is synthesized by a free ribosome, it directs the polypeptide–ribosome complex to the endoplasmic reticulum (ER), where protein synthesis continues.
D. Describe the complex transport functions of the Rev protein of HIV-1, detailing the roles of its nuclear localization signal and nuclear export signal.
D. The HIV-1 Rev protein has both a nuclear localization signal and a nuclear export signal. The nuclear localization signal ensures that Rev is transported into the nucleus, where it specifically binds to HIV-1 RNA. The nuclear export signal ensures that Rev and its RNA cargo are then transported from the nucleus to the cytoplasm via a nuclear pore.
A. In the context of virus genome replication, explain the concepts of semiconservative replication (DNA viruses) and conservative replication (dsRNA viruses).
A. Semiconservative replication (typical for dsDNA viruses) means that after a dsDNA molecule has been copied, each of the daughter molecules contains one strand of the original molecule. Conservative replication (seen in some dsRNA viruses) is the contrasting mode.
B. Describe the two modes of replication (θ and σ) utilized for replicating circular DNA molecules, noting the alternate name for the sigma mode.
The two modes are theta (θ) mode and sigma (σ) mode. The sigma mode is also known as the rolling circle mode of replication.
C. Define procapsid (or prohead) in icosahedral virus assembly, and explain the role of scaffolding proteins in the assembly of complex viruses like herpesviruses and tailed phages.
C. A procapsid (or prohead) is an empty protein shell constructed during the assembly of virions and nucleocapsids of many viruses with icosahedral symmetry. The procapsid is later filled with the virus genome to form the mature capsid. Scaffolding proteins are non-structural proteins temporarily present while the complex virion is under construction, maintaining structural integrity, but they are subsequently removed (often by a virus-encoded protease) from the procapsid and are not present in the mature virion.
D. Contrast the typical exit strategy of Bacteriophages with the general exit strategy of Animal Viruses (excluding lysis).
Bacteriophages are normally released from the infected cell when the cell bursts (lyses), a process initiated by virus-produced enzymes (lysins, such as lysozymes) that break bonds in the peptidoglycan of the host cell walls. Animal viruses do not lyse their host cells; instead, progeny virions are released from the cells over a period of time, often through budding from the cell surface membrane, or via vesicles that fuse with the plasma membrane, or using motor proteins attached to microtubules.
E. Describe the complex sequence of membrane acquisition and loss during the egress of Herpesvirus virions, starting from assembly in the nucleus.
E. Herpesvirus nucleocapsids assemble in the nucleus.
1. They bud through the inner nuclear membrane, acquiring a temporary envelope.
2. They then fuse with the outer nuclear membrane, losing this temporary coat to escape into the cytosol.
3. In the cytoplasm, they acquire tegument proteins (e.g., VP16).
4. They acquire the final virion envelope by budding into a vesicle derived from the Golgi complex.
5. The vesicle then fuses with the plasma membrane, releasing the virion (with a single membrane) from the cell.
A. Identify the three subfamilies of herpesviruses and provide a specific human disease associated with two of the viruses listed.
A. The three subfamilies of herpesviruses are: α-Herpesviridae, β-Herpesviridae, and γ-Herpesviridae. * HSV-1: facial, labial and ocular lesions. * VZV: chickenpox and shingles.
-
1. Basics of Cell Biology130
-
2. DNA83
-
3. RNAs and Protein82
-
4. Human Genome26
-
5.Cell Cycle and Cytoskeleton27
-
6. Transporting Process107
-
7. Mendelian Genetics41
-
8. Genetic Regulation24
-
9. Genes and traits89
-
10. Cell Signaling124
-
11. Viruses73
-
12. Bacteria19
-
13. Evolusion51
-
14. Selective Topic60
-
Practice 2. Lac operon21
-
Practice 3. Genetic Problems12
-
15. Cell Signaling102
-
16. neural Communication56
-
17. Technique51
-
18. Immunobiology136
-
19. Gene And Behaviour52
-
20. developmental genetics0
-
21. Biotechnology50
-
23. Molecular Medicine (Stem cell, Gene therapy, Vaccine)50
