Download Viral Replication and Genetic Engineering Principles: Exercises and Questions and more Exams Biology in PDF only on Docsity!
Viral Replication and Genetic
Engineering Principles
Viral Replication
Viral Replication Dependence
Viral replication is independent of the host cell's DNA but dependent on the host cell's enzymes and metabolism. Viral replication is not dependent on both the host cell's DNA and the host cell's enzymes and metabolism. Viral replication is dependent on the host cell's DNA, RNA, enzymes, and metabolism.
Expressing Eukaryotic Genes in Prokaryotic Hosts
A major issue encountered when trying to express a eukaryotic gene in a prokaryotic host is the inclusion of introns in eukaryotic genes. Other issues include different codon usage and different promoters for RNA polymerase between eukaryotes and bacteria. The different nucleic acid structure between eukaryotes and prokaryotes is not a major issue.
Early and Late Viral Proteins
Early and late viral proteins are classified according to their relative time of synthesis following host infection. They are not classified based on their evolutionary appearance in virus genomes, stability during infection, or transmission into virions.
Genetic Material Transfer
Gene transfer through a gene transfer agent allows genetic material to be transferred from a virus-like particle that lacks genes for its own replication. This process is distinct from conjugation of an F+ plasmid, transduction by a dsDNA phage Mu, and transformation of a linear piece of DNA.
Viral Replication Location
Viral replication occurs intracellularly. Viral replication does not occur extracellularly. Viral replication can occur both intracellularly and extracellularly, depending on the virus involved.
Viral Genome Types and Translation
Positive-sense single-stranded RNA (positive ssRNA) viruses can be directly used for translation. Double-stranded RNA (dsRNA) viruses and negative-sense single- stranded RNA (negative ssRNA) viruses cannot be directly used for translation. Retroviruses, which have a positive ssRNA genome, can also be directly used for translation.
Viral Size Measurement
Viral size is generally measured in nanometers. It is not typically measured in micrometers, picometers, or centimeters.
Cloning Vectors
Cosmids are a type of cloning vector, which are distinct from bacterial artificial chromosomes (BACs). Cosmids are not a type of heat-stable polymerase or RNA/DNA hybrid.
DNA Introduction Methods
Transformation, transduction, and conjugation are all methods that may introduce foreign DNA into a recipient.
CRISPR-Cas System
The CRISPR-Cas system relies on the DNA/translated activity of the Cas9 protein to edit genomes. It does not rely on the mRNA/transcribed or mRNA/translated activities of Cas9.
Viral Latent Infection
For a virus to cause a latent infection, it must possess double-stranded DNA (dsDNA). Viruses with single-stranded DNA (ssDNA), double-stranded RNA (dsRNA), or any other type of viral genome can also lead to latent infections.
Insertional Inactivation of lacZ
Cells that have 'insertional inactivation' of the lacZ gene are white. They are not blue, yellow, or fluorescent green.
Viral Genome Size
Viroids generally have the smallest viral genomes.
Recombination in E. coli
The colonies grown on a minimal medium after mixing two mutant strains of E. coli may be due to recombination. They are not necessarily due to back mutation (reversion).
Easiest Organisms to Grow in the Lab
Prokaryotes are typically the easiest organisms to grow in the laboratory, compared to plants, animals, and fungi.
Viral Particle Characteristics
Viral particles are metabolically inert. They are smaller than bacterial cells. They do not necessarily contain an envelope to prevent degradation outside a host. They do not necessarily exhibit cell lysis under particular conditions.
Selective Media for E. coli Mating Experiment
To score recombinant colonies from an Hfr × F- mating experiment in E. coli, you would use a minimal medium supplemented with streptomycin. A minimal medium alone or a minimal medium supplemented with threonine would not be appropriate.
Competence
Competence requires special proteins such as a cell wall autolysin. It is not true that competence is not required for transformation, commonly occurs with high efficiency in nature, or cannot occur naturally in bacteria.
F Plasmid Effects
When a cell contains an F plasmid that is not integrated into the chromosome, it is no longer able to produce a pilus. Mutation rates are not decreased, and the cell is not considered an Hfr cell.
Horizontal Gene Transfer in Archaea
Horizontal gene transfer frequently occurs in nature and has been used to perform genetic studies in the laboratory for archaea. It is not infrequent in nature or limited to genomic sequencing studies.
Cellular Receptors
Cellular receptors may be composed of combinations of proteins, carbohydrates, and/or lipids. They are not limited to only proteins, carbohydrates, or lipids.
Restriction
Restriction is a general host mechanism to prevent the invasion of foreign nucleic acid. It is not a viral process whereby the host's DNA ceases normal functioning or the virus prevents other viruses from entering the cell.
Specialized Transduction
The minimal amount of genetic information required for specialized transduction would include the att region, cos site, and a helper phage.
Bacteriophage Receptors
Iron transport proteins can act as receptors for various bacteriophages. Flagella, sugar transporters, and cilia cannot act as receptors.
Screening for Regulatory Gene Mutations
Gene fusions can be used to rapidly screen for mutations in regulatory genes. Defective proteases, microinjection, and Southern blotting are not appropriate methods for this purpose.
Advantages of Lysogeny
Lysogeny confers resistance to infection by viruses of the same type, which provides a strong selective advantage for the host cell. It does not necessarily prevent cell lysis or confer resistance to infection by viruses of a different type or strain.
Plasmid Characteristics
A plasmid may replicate independently of the chromosome, be integrated into the chromosome, or be transferred cell-to-cell during conjugation.
CRISPR System
The CRISPR system recognizes foreign DNA sequences that have previously entered the cell and directs the Cas proteins to destroy them. It does not facilitate homologous recombination, repair DNA, or synthesize gene transfer agents.
Synthetic Biology Examples
Assembling gene sequences into a genome and creating a living organism, as well as creating a new metabolic pathway, are examples of synthetic biology. Making E. coli photographic is not an example of synthetic biology.
Retroviral Enzymes
Reverse transcriptase is an enzyme that would be found in the virion of a retrovirus, but not in a bacteriophage. Lysozyme, methylase, and restriction enzymes are not unique to retroviruses.
Hfr Strain Characteristics
Hfr strains of E. coli have an integrated F factor and transfer the complete F factor to recipient cells at a high frequency. They do not lack an F factor or have it as a plasmid.
T4 DNA Packaging
The packaging mechanism of T4 DNA involves cutting of DNA from DNA concatemers. It does not involve linear or circular genetic elements.
Lysogeny Conditions
Lysogeny is favored when the cI repressor protein predominates in bacteriophages. Cro protein predominance or cI protein repression does not favor lysogeny.
Protein Modifications
Glycosylation, not complex folding, methylation, or glucosylation, is a common post-translational modification.
F+ Strain Characteristics
F+ strains of E. coli have the F factor as a plasmid. They do not lack an F factor, have an integrated F factor, or transfer the F factor to recipient cells at a high frequency.
Lambda Phage Life Cycle Control
For lysogeny to occur in lambda phage, the cI repressor protein must predominate. Cro protein predominance or cI protein repression does not favor lysogeny.
Vaccine Development
Recognizing pathogens with multiple unique proteins has enabled the development of monovalent vaccines, not just attenuated carrier viruses or subunit vaccines.
Lambda Phage Characteristics
Lambda is a temperate phage that infects E. coli and has a linear double-stranded DNA genome. It is not replicated by the rolling circle mechanism, and it always circularizes upon entering the host cell.
Hfr Strain Integration
Hfr strains of E. coli integrate into the chromosome at the same locus most of the time, although there may be some variation. They do not integrate at a single specific site or at loci that cannot be accurately determined.
Natural Transformation
High-efficiency, natural transformation is common in both Bacteria and Archaea. It requires specialized DNA uptake, DNA binding, and integration proteins, and does not usually involve plasmids.
Genetic Engineering of Salmon
The principle underlying how salmon were genetically engineered to grow faster is the addition of genes to enhance blood circulation and tissue development. It is not the removal of a gene responsible for feeling full, replacement of inducible to constitutive hormone production, or resistance to bacterial infections.
Linear DNA Transformation
Integration of linear transforming DNA into the chromosome is catalyzed by the RecA gene. It is not true that integration is not required for expression or that it almost never occurs due to restriction endonuclease degradation.
Polyvalent Vaccine Challenges
Polyvalent vaccines using vaccinia virus are challenging to develop because the coat proteins form a relatively rigid structure, which does not allow much space for additional proteins to be expressed.
C) Produce the protein as a fusion protein.
Temperate Bacteriophage Infection
- As a consequence of infection by a temperate bacteriophage such as lambda, the host cell:
D) May lyse or may continue to divide and replicate both itself and the prophage.
Virus Particle Structure
- When packaged in the virion, the complete complex of nucleic acid and protein is known as the virus:
C) Nucleocapsid.
Complementation in Bacteria
- The production of a functional gene product by transforming bacteria that lack a lacZ gene with a plasmid containing a lacZ gene is known as:
A) Complementation.
Enveloped Virus Hosts
- The hosts for most enveloped viruses are:
B) Animals.
Conjugation in E. coli
- In which of the following matings would chromosomal genes be transferred most frequently in Escherichia coli?
D) F+ x F+
Transposition Types
- Transposition is a(n):
D) General recombination event.
Retroviruses and Medical Importance
- Retroviruses are medically important viruses because:
D) They include some viruses that cause cancer and HIV.
Retroviral Genome Composition
- The genome of retroviruses contains genes to make all of the following except:
B) Repressor proteins.
Prophage Formation
- Prophage formation occurs after lambda infection if:
A) The cI gene is transcribed and cI protein accumulates.
Archaea Genetic Systems
- A factor that has delayed the development of laboratory-based genetic systems in Archaea is:
D) Many archaea grow in extreme or unusual conditions that make the use of agar and traditional mutant screening techniques problematic.
Auxotroph Limitations
- A limitation to using auxotrophs to prevent the spread of genetically modified genes to wild populations is that:
B) Auxotrophs often cross-feed from the metabolites of other organisms in the environment.
Transformation, Transduction, and Conjugation Features
- Features common to transformation, transduction, and conjugation are:
B) 1, 2 (unidirectional transfer of genes and incomplete gene transfer).
Ti Plasmid Applications
- The Ti plasmid is best suited for genetically manipulating:
C) Plants.
Bacterial Conjugation States
- The state in which a bacterial cell contains an F plasmid but no chromosomal genes are transferred during conjugation is the:
B) F+ state.
Synthetic DNA Terminology
- The term used to describe a synthetic DNA fragment is:
C) Live hosts.
Restriction Endonuclease Products
- After digesting a DNA sequence, a restriction endonuclease can generate:
B) Overhangs. C) Sticky ends.
HIV Genome Composition
- The HIV genome consists of:
B) Two identical ssRNA molecules.
Bacterial Gene Transfer
- In the bacterial world, a gene located on the chromosome would be the LEAST likely to be transferred.
Viral Infection Process
- When a virus enters a host cell in which it can replicate, the process is called:
B) Infection.
Viral Lysis Products
- The visible areas of cell lysis on a bacterial lawn caused by viral infection are called:
B) Plaques.
T4 Phage Transcription Control
- The specific order of T4 phage gene transcription is accomplished by:
C) Each group of T4 genes has a different promoter that indicates the order in which they should be transcribed based on the affinity of the promoter for the host RNA polymerase.
Fusion Protein Design Considerations
- An important consideration when designing a fusion protein construct is:
A) Avoid hybridization of the fusion gene in the artificial construct.
Human Somatotropin Cloning Challenge
- One challenge in cloning human somatotropin is that:
D) It is susceptible to digestion by bacterial proteases because it is a small protein hormone.
T4 Phage DNA Protection
- The T4 phage protects its DNA from host restriction endonucleases by:
A) Glucosylating cytosine bases in the T4 genome to prevent DNA cleavage.
Nucleic Acid Analysis Techniques
- The technique that is LEAST similar to the others in what is being studied and concluded is:
C) Northern blot.
Nucleic Acid Probe Design
- The principle behind nucleic acid probe design is that the probe itself must contain:
A) A key complementary part of the target gene sequence of interest.
Dam Methylation and Restriction in E. coli
- In E. coli, the adenine in the sequence GATC is methylated by the Dam enzyme, and a restriction endonuclease recognizes and cleaves dsDNA with the sequence GATC on either strand. The purpose of these two enzymes is that:
D) The enzymes protect E. coli from infection by preferentially degrading viral or other exogenous DNA that is not methylated.
YAC and BAC Recombination
- It is impossible to state with any certainty whether YACs or BACs are more likely to undergo recombination and rearrangement, because environmental factors play a major role in the probability of one or the other occurring.
Viral Disease Causation
- The majority of many important human viral diseases are caused by:
D) dsDNA viruses.
Site-Directed Mutagenesis Mechanism
- The molecular mechanism/feature that site-directed mutagenesis exploits to introduce a mutation at a specific site is:
Viral Diversity in Slow-Growing Prokaryotes
- In a natural population of diverse slow-growing prokaryotic cells, the type of viruses you would expect to be most common are:
D) Temperate bacteriophages.
Palindromic Sequences
- The sequence 5'-GAATTC-3' is a palindrome, characteristic of many recognition sequences for restriction endonucleases.
Viral Entry into Host Cells
- The major difference in viral entry between an animal cell and E. coli is that:
C) The virion fuses to the bacterial cell membrane of E. coli, while the genome is injected into an animal cell.
Viral Genome Composition
- The genome of most viruses consists of:
D) A pair of DNA.
Conjugative Transfer Proteins
- Proteins that are essential in conjugative transfer of DNA are:
Tra proteins.
Genetic Processes and Viral Infection
Genetic Processes
Pili
Pili are hair-like appendages found on the surface of some bacteria that facilitate the transfer of genetic material between cells.
SOS Repair
The SOS repair system is a bacterial DNA repair mechanism that is activated in response to DNA damage. It involves the upregulation of genes involved in DNA repair and the temporary inhibition of cell division.
Transduction
Transduction is the process by which bacterial DNA is transferred from one bacterium to another by a bacteriophage (virus that infects bacteria).
Transformation
Transformation is the process by which a bacterial cell takes up and incorporates foreign DNA from the environment, allowing the cell to express new genetic traits.
F-Strains of Escherichia coli
F-strains of Escherichia coli: - Do not have an F factor - Have the F factor as a plasmid - Have an integrated F factor - Transfer the F factor to other strains at a high frequency
Prophage Replication
A prophage (a virus genome integrated into a host's genome) can replicate: - Along with its host while the lytic genes are expressed - Along with its host while the lytic genes are not expressed - Independently of its host while the lytic genes are expressed - Independently of its host while the lytic genes are not expressed
Consequences of Deleting Late T4 Genes
Deleting the late T4 genes would have the following consequences: - The T genome would not be copied - T4 mRNA would not be produced - T4 capsid proteins would not be made - ATP would not be produced, and the T genome would not be packaged into the capsid
Genetic Techniques
Agarose gel electrophoresis: Separates DNA fragments based on size Fluorescence in situ hybridization (FISH): Visualizes the location of specific DNA sequences within cells Protein purification: Isolates and concentrates a specific protein from a complex mixture Northern blots: Analyzes the expression of specific RNA molecules
Genetic Processes and Vectors
Transformation/chromosome: Genetic material is incorporated into the host's chromosome Transduction/plasmids: Genetic material is transferred via a virus and maintained on a plasmid Recombination/chromosome: Genetic material is incorporated into the host's chromosome through recombination
Obstacles to Mammalian Gene Cloning
One of the more formidable obstacles to mammalian gene cloning is the presence of introns, which are non-coding sequences within eukaryotic genes.
Consequences of Viral Infection in Animal Cells
The possible consequences of viral infection in animal cells include rapid lysis, latent infections, lysogeny, and persistent infections that can lead to cancer.
Importance of Host Characteristics in Recombinant
Protein Expression
When cloning a foreign gene into an expression host, it is important that the host itself does not produce the protein being studied, as this could interfere with the analysis of the recombinant protein.
One-Step Growth Curve of Viruses
The growth of viruses in a culture is described as a one-step growth curve because there is only one step in the viral life cycle, which leads to only one replicative cycle in a culture.
