Microbio Ch 12

Which of those below is NOT an important consideration when designing a fusion protein construct? A. Avoid hybridization of the fusion gene in the artificial construct. B. Reading frame is the same for both the fusion gene and reporter gene. C. Transcriptional start and stop signals are shared. D. Translational start and stop signals are shared.

A. Avoid hybridization of the fusion gene in the artificial construct. **For fusion protein constructs, ensuring that the reading frame, transcriptional start and stop signals, and translational start and stop signals are appropriately arranged and shared between the fusion gene and reporter gene are critical considerations. These ensure proper expression and translation of the fusion protein in the host organism.

Which of the following terms is used to describe a synthetic DNA fragment? A. DNA cassette B. DNA hybrid C. recombinant DNA D. artificial chromosome

A. DNA cassette **DNA cassette = synthetic DNA fragment that contains specific genetic elements (promoters, coding sequences, & terminators) designed for insertion into a larger DNA molecule (plasmid or genome). Used in genetic engineering & molecular biology experiments to introduce specific genetic elements into organisms.

The enzyme that covalently links both strands of a vector and inserted DNA in molecular cloning is _____. A. DNA ligase B. DNA phosphatase C. DNA hydrolase D. DNA transferase

A. DNA ligase

Which objective would be best to use a Southern blot rather than a Northern blot? A. Determine if a gene is present in a genome. B. Discover gene function. C. Identify regulatory gene-protein interactions. D. Quantify expression profiles of a gene.

A. Determine if a gene is present in a genome. **Southern blotting -- used to detect the presence & size of specific DNA sequences (genomic DNA). Useful for identifying presence or absence of a gene within a genome or for detecting genetic variations. Northern blotting -- used to analyze the presence, size, & abundance of specific RNA molecules (mRNA). Employed to study gene expression level

What is the first step in constructing a metagenomic library from RNA? A. The RNA must be converted to cDNA. B. The RNA must be amplified through PCR, producing many RNA copies. C. The RNA must be screened to identify the genes of interest. D. The RNA must be inserted into plasmid vectors.

A. The RNA must be converted to cDNA. **1st step involves converting the RNA molecules into cDNA using reverse transcriptase. Necessary b/c traditional cloning methods usually work with DNA rather than RNA. Once the RNA is converted to cDNA, it can be further processed for library construction, such as fragmentation, cloning into vectors, and transformation into a suitable host organism.

Which statement is TRUE? A. YACs are more likely than BACs to undergo recombination & rearrangement. B. BACs are more likely than YACs to undergo recombination & rearrangement. C. YACs and BACs undergo recombination and rearrangement at about the same rate. D. 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.

A. YACs are more likely than BACs to undergo recombination & rearrangement. **Yeast Artificial Chromosomes (YACs) are more likely to undergo recombination and rearrangement than Bacterial Artificial Chromosomes (BACs) -- b/c YACs are maintained in yeast cells, which possess a more complex & less stable genome compared to bacteria. YACs may suffer from genomic instability, leading to higher rates of recombination and rearrangement.

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 B. all of the nucleotide sequence of the gene of interest to conclusively identify the gene C. an antibody to specifically bind to the gene of interest D. at least three separate complementary regions of the gene of interest

A. a key complementary part of the target gene sequence of interest **Nucleic acid probes are designed to hybridize specifically to complementary sequences in the target gene of interest. Therefore, the probe must contain a sequence that is complementary to a specific part of the target gene sequence, allowing it to bind selectively to that gene. This complementary part of the probe enables specific detection and identification of the gene of interest.

Inserting a kanamycin resistance cassette into a catabolic operon to confirm the gene is essential in degradation of a particular compound would involve all of the following EXCEPT ____. A. a reporter gene B. ligation C. recombination D. transformation

A. a reporter gene **Inserting a kanamycin resistance cassette into a catabolic operon to confirm the gene's essentiality in the degradation of a particular compound would typically involve ligation, recombination, and transformation steps. However, a reporter gene is not directly involved in this process. Instead, the kanamycin resistance gene itself serves as a selectable marker to identify bacteria that have successfully incorporated the cassette into their genome.

To verify a gene was cloned into a vector successfully, sequencing the vector as well as _____ are commonly performed. A. agarose gel electrophoresis B. fluorescence in situ hybridization C. protein purification D. northern blots

A. agarose gel electrophoresis **DNA or RNA fragments can be separated from each other by gel electrophoresis (technique that employs an agarose gel to separate nucleic acid fragments based on differences in size & charge)

At which time period(s) during PCR thermocycling is/are hottest in temperature? A. during DNA denaturation B. during primer annealing C. during primer extension/elongation D. Both the first and last cycles are hotter in temperature than all other cycles.

A. during DNA denaturation **During DNA denaturation step of PCR thermocycling, temp is the highest, as it needs to be sufficiently high to separate the dsDNA into ssDNA. This step usually occurs at temperatures around 90-95°C.

What molecular mechanism/feature does site-directed mutagenesis exploit to introduce a mutation at a specific site? A. flanking complementary bound nucleotides permit non-complementary base pairing B. methylated nucleotides disrupt DNA polymerase's proofreading C. nucleotide substitution when one is depleted D. transposase-induced base pair changes

A. flanking complementary bound nucleotides permit non-complementary base pairing **Site-directed mutagenesis relies on the use of short synthetic oligonucleotides that are complementary to the target DNA sequence except for a few nucleotides at the desired mutation site. When these oligonucleotides are introduced into the DNA, they hybridize to the target sequence through complementary base pairing. During DNA replication or repair, the mismatched bases are often incorporated, leading to the introduction of the desired mutation at the specific site.

It is possible to rapidly screen for mutations in regulatory genes using _____. A. gene fusions B. defective proteases C. microinjection D. Southern blotting

A. gene fusions

One of the more formidable obstacles to mammalian gene cloning is the presence of _____. A. introns B. exons C. repressors D. integrators

A. introns **Obstacles to expression of genes from mammalian or other eukaryotic sources in bacteria include: (1) genes must be placed under control of bacterial promoter, (2) any introns, (3) codon usage, & (4) many eukaryotic proteins require host modification after translation to yield active form

If a foreign gene is cloned into an expression host, it is important that the host itself _____. A. not produce the protein being studied B. produce the protein in larger amounts than the vector C. repress the genetic expression being studied D. produce signal proteins to tag the host protein

A. not produce the protein being studied

Which of the following is NOT a limitation to using auxotrophs to prevent the spread of genetically modified genes to wild populations? A. Auxotrophs may mutate in ways that allow them to synthesize the limiting nutrient. B. Auxotrophs self-destruct using self-toxins when this method is applied. C. Auxotrophs often cross-feed from the metabolites of other organisms in the environment. D. Back mutation to the wild type may occur.

B. Auxotrophs self-destruct using self-toxins when this method is applied. **Auxotrophs = strains of organisms that have lost the ability to synthesize certain essential compounds & require them to be supplemented in their growth medium Sometimes used in genetic engineering to prevent the spread of GM genes to wild populations. However, the statement that auxotrophs self-destruct using self-toxins is not accurate -- Auxotrophs may have limitations such as those described in options A, C, and D, but self-destruction via self-toxins is not a characteristic method of preventing the spread of genetically modified genes using auxotrophs.

Which of those listed below is LEAST similar in what is being studied & concluded? A. fluorescence in situ hybridization B. GFP fusion protein C. Northern blot D. RT-PCR

B. GFP fusion protein

Which of the following is NOT a common step in molecular cloning using plasmids? A. Fragment DNA into small segments. B. Hybridize DNA sequences with slightly mismatched oligonucleotides. C. Ligate DNA into vectors. D. Insert the vectors into a host.

B. Hybridize DNA sequences with slightly mismatched oligonucleotides. **Major steps in gene cloning using restriction enzymes 1. Cut DNA w/ restriction enzyme 2. Add vector cut w/ same restriction enzyme 3. Add DNA ligase to form recombinant molecules 4. Introduce recombinant vector into a host

What is the difference between PCR and RT-PCR? A. Only PCR makes many copies of DNA rapidly. B. RT-PCR uses an RNA template whereas PCR uses a DNA template. C. Only PCR produces cDNA. D. PCR uses a single stranded template whereas RT-PCR uses a doublestranded template.

B. RT-PCR uses an RNA template whereas PCR uses a DNA template. **RT-PCR produces cDNA as well -- RNA is reverse transcribed into cDNA, using reverse transcriptase RT-PCR uses single strand which is very unstable

Cosmids are a type of _____. A. bacterial artificial chromosomes (BACs) B. cloning vector C. heat stable polymerase D. RNA/DNA hybrid

B. cloning vector -- plasmids w/ a lambda phage cos site, often exist exist as multiple copies in bacterial cells

If a protein that could be toxic to the expression host needs to be expressed in large quantities, then it is best to select an expression vector that ____. A. is not able to be replicated B. is inducible C. is attached to a normal cell promoter D. allows continual expression of the protein

B. is inducible **Selecting an expression vector that is inducible allows control over when the toxic protein is expressed -- expression can be induced only when needed, minimizing the potential toxic effects on the host organism during its growth and viability.

Polyvalent vaccines using vaccinia virus are highly favored by doctors & physicians but are especially challenging for those who develop them, because _____. A. coat proteins form a relatively rigid structure and do not allow much space for additional proteins to be expressed B. multiple foreign proteins simultaneously synthesized often disrupts each other's activity C. vaccinia and most other viruses engineered for vaccines contain only one restriction site for cloning in their genome D. virus genetic manipulation uses transfection, which is an inherently inefficient process

B. multiple foreign proteins simultaneously synthesized often disrupts each other's activity

To estimate the total concentration of a beneficial bacterial species in yogurt, _____ would provide the quickest results. A. fluorescence in situ hybridization B. qPCR C. RT-PCR D. a Southern blot

B. qPCR **Quantitative PCR (qPCR) is highly sensitive & efficient for quantifying the amount of a specific DNA target in a sample. It can provide rapid results & is commonly used for quantifying bacterial species in various samples, including yogurt.

The principle underlying how salmon were genetically engineered to grow faster is the ____. A. removal of a gene responsible for feeling full after eating B. replacement of inducible to constitutive hormone production C. resistance to bacterial infections which waste metabolic energy in the salmon to fight off D. addition of genes to enhance blood circulation and tissue development

B. replacement of inducible to constitutive hormone production **Gene for GH in native salmon is activated by light --> salmon grow rapidly only during summer months. In GM salmon, promoter for GH gene was replaced w/ promoter from another fish that grows at a more or less constant rate all year round --> salmon make GH continuously & grow faster

Cells that have "insertional inactivation" of the lacZ gene are ____. A. blue B. white C. yellow D. fluorescent Greek

B. white

Some proteins expressed at high levels form inclusions that are relatively insoluble. What is the most effective way to facilitate purification of these proteins? A. Use a reporter gene to locate the inclusion. B. Decrease the number of insertions in the vector. C. Produce the protein as a fusion protein. D. Switch to an expression host with a larger intracellular volume.

C. Produce the protein as a fusion protein **Producing the protein of interest as a fusion protein with a solubility-enhancing partner can help improve solubility & facilitate purification. Fusion partners can aid in protein folding and prevent the formation of insoluble aggregates or inclusion bodies, making purification easier.

Which of the following is NOT an example of synthetic biology? A. assembling gene sequences together into genome and creating a living organism from it B. creating a new metabolic pathway that produces a previously unidentified compound C. developing a novel polyvalent vaccine D. making Escherichia coli photographic

C. developing a novel polyvalent vaccine

Expression vectors are designed to ensure that _____ can be efficiently _____. A. mRNA / transcribed B. DNA / transcribed C. mRNA / translated D. DNA / translated

C. mRNA / translated

What makes eukaryotic transcripts easier to isolate than bacterial transcripts? A. Eukaryotic transcripts are not methylated but their genes are often methylated. B. Larger transcript size in eukaryotes enables easy size-selection methods. C. mRNA is polyadenylated in eukaryotes. D. Transcripts are the most abundant RNAs in eukaryotes.

C. mRNA is polyadenylated in eukaryotes.

The Ti plasmid is best suited for genetically manipulating ____. A. Agrobacterium spp B. fish C. plants D. viruses

C. plants

Using a host defective in proteases is likely to be necessary when ____. A. engineering a complete metabolic pathway requiring several different enzymes B. overproducing proteins C. producing a small protein D. engineering transgenic animals with immune systems

C. producing a small protein

Which process results in the production of a hybrid polypeptide? A. vector fusion B. operon fusion C. protein fusion D. translational fusion

C. protein fusion **Genes encoding 2 proteins are fused to share the same trancriptional & translational start & stop & yield 1 hybrid polypeptide

A(n) _____ gene is a gene that encodes a protein that is easy to detect and assay. A. encoder B. translational C. reporter D. recorder

C. reporter

Recognizing pathogens that contain multiple unique proteins which enable the human immune system to recognize just one and mount an effective response has opened the door on development of some vaccines only being ____. A. attenuated carrier viruses B. monovalent C. subunit vaccines D. purified protein administered

C. subunit vaccines

Which of the following sequences is a palindrome, characteristic of many recognition sequences for restriction endonucleases? A. TTGCCGA AACGGCT B. GGGGGGG CCCCCCCC C. GTAATG CATTAC D. GAATTC CTTAAG

D. GAATTC CTTAAG **sequence that reads the same forwards and backward

What is the most important advantage of Pfu polymerase over Taq polymerase? A. Unlike Taq polymerase, Pfu polymerase functions well at relatively high temperatures. B. It is from a bacterium, not an archaean, so it is more effective for replicating eukaryotic DNA. C. Pfu polymerase removes the need for primers during PCR. D. Unlike Taq polymerase, Pfu polymerase has proofreading activity.

D. Unlike Taq polymerase, Pfu polymerase has proofreading activity. **Pfu polymerase is even more thermostable than Taq & it has proofreading activity

After digesting a DNA sequence, a restriction endonuclease can generate ____. A. blunt ends B. overhangs C. sticky ends D. blunt ends, overhangs, or sticky ends

D. blunt ends, overhangs, or sticky ends **Restriction enzyme EcoRI makes staggered cuts, leaving short, ss overhangs called sticky ends. EcoRv cuts both strands of DNA directly opposite each other, resulting in blunt ends.

A poorly immunogenic vaccine often suggests the foreign proteins were not properly recognized by the immune system due to a lack of ____ necessary, which can also be engineered to occur with additional molecular manipulations. A. complex folding B. methylation C. glucosylation D. glycosylation

D. glycosylation

One challenge in cloning human somatotropin is that _____. A. it consists of multiple polypeptides, making synthesis complex B. its gene cannot be cloned as cDNA C. it can only be expressed by eukaryotic cells D. it is susceptible to digestion by bacterial proteases because it is a small protein hormone

D. it is susceptible to digestion by bacterial proteases because it is a small protein hormone **Human somatotropin gene was closed as cDNA from mRNA. cDNA was then expressed in bacterial expression vector. Main problem w/ producing short polypeptide hormones is their susceptibility to protease digestion

Cloning vectors can be distinguished from expression vectors by ____. A. carrying ori genes for replication of the cloned sequence B. having a multiple cloning site (MCS) C. having a high copy number per cell D. lacking a promoter site upstream of the insertion site

D. lacking a promoter site upstream of the insertion site

A polymerase chain reaction (PCR) copies an individual gene segment in vitro with a(n) ______ primer(s). A. individual RNA B. individual DNA C. pair of RNA D. pair of DNA

D. pair of DNA

The genes encoding green fluorescent protein (GFP) and β-galactosidase are typically used in cloning as _____. A. transcription regulators B. global control genes C. promoter sequences D. reporter genes

D. reporter genes

True or false -- PCR rapidly produces many copies of entire DNA molecules.

False PCR (Polymerase Chain Reaction) is a technique used to amplify a specific segment of DNA, not entire DNA molecules. It is designed to amplify a particular DNA sequence of interest, often for the purpose of making enough of it for further analysis or experimentation. The process involves repeated cycles of heating and cooling to make copies of that specific DNA segment. So, while PCR does rapidly produce many copies of DNA, it does not amplify entire DNA molecules.

True or false -- Genetically modified plants resistant to the herbicide glyphosphate contain a gene from Bacillus thuringiensis.

False. Genetically modified (GM) plants resistant to the herbicide glyphosate typically contain a gene derived from Agrobacterium sp. strain CP4, which encodes an enzyme called 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS). This enzyme is not affected by glyphosate, allowing the plant to survive while the surrounding weeds are killed. However, Bacillus thuringiensis (Bt) genes are often used in GM plants to confer resistance to specific insect pests by producing insecticidal proteins. These two traits, glyphosate resistance and Bt insect resistance, are often incorporated into the same plant cultivars to provide multiple layers of protection against weeds and insect pests.

True or false -- High expression levels of a eukaryotic gene in a bacterium such as Escherichia coli cannot be accomplished due to the presence of introns.

False. High expression levels of a eukaryotic gene in a bacterium such as Escherichia coli can be accomplished, even though bacterial cells lack the machinery to properly process introns. This can be achieved by cloning the gene into an expression vector that contains bacterial promoters and ribosome binding sites optimized for bacterial expression. Additionally, the removal of introns from the eukaryotic gene sequence through cDNA synthesis or other methods can further enhance expression in bacteria.

True or false -- One problem with both BACs and YACs is that genetic regions of these chromosomes cannot be subcloned.

False. One advantage of both BACs and YACs is that they are amenable to subcloning. BACs and YACs are vectors used to clone large DNA fragments, typically spanning hundreds of thousands to over a million base pairs. Once a DNA fragment is cloned into a BAC or YAC vector, it can be further manipulated and subcloned into smaller vectors for various applications, such as sequencing, functional analysis, or gene expression studies. Therefore, genetic regions within BACs and YACs can indeed be subcloned for further experimentation.

True or false -- The lacZ gene is commonly used as a reporter gene, because its substrate lactose is well known and easily measured.

False. The lacZ gene is commonly used as a reporter gene not because lactose is its substrate, but because it encodes beta-galactosidase, an enzyme that can cleave certain substrates like X-gal (5-bromo-4-chloro-3-indolyl-beta-D-galactopyranoside) or ONPG (ortho-Nitrophenyl-beta-galactoside), producing a detectable color change or signal. These substrates are not naturally occurring in cells; they are added to the media to detect the activity of the beta-galactosidase enzyme. This colorimetric or fluorogenic reaction allows for easy measurement of gene expression or promoter activity in various assays.

True or false -- DNA ligase mediates the insertion of foreign DNA into a vector, but it will only be able to do so if the inserts and vector have matching sticky or blunt ends.

True

True or false -- The key steps in cloning a foreign gene into a vector, regardless of the application, involve isolating the insert fragment, ligating the insert into a vector, and transforming it into a host.

True

True or false -- Green fluorescent protein (GFP) is used for detecting translational activity of a fused protein, whereas lacZ reporters are used to detect transcriptional activity of a fused gene.

True. Green Fluorescent Protein (GFP) is often used as a reporter gene to study the localization and movement of the protein it is fused to. When the fused protein is translated, the GFP part of the protein will fluoresce under certain conditions, allowing researchers to visually track the protein within the cell. This makes GFP a tool for detecting translational activity. On the other hand, lacZ is a gene that codes for the enzyme beta-galactosidase in E. coli. When fused to another gene of interest, the activity of beta-galactosidase can be used as an indicator of the transcriptional activity of the fused gene. When the fused gene is transcribed, the lacZ part of the transcript will be translated into beta-galactosidase, which can be detected using a colorimetric assay. This makes lacZ a tool for detecting transcriptional activity.

True or false -- Due to well-developed molecular tools and careful screening designs, functional genes can be isolated directly by isolation from the environment rather than cultivating the diverse species in a microbial community.

True. Advances in molecular biology techniques, such as metagenomics and single-cell genomics, have enabled the direct isolation and characterization of functional genes from environmental samples without the need to cultivate the diverse microbial species present in a community. Metagenomics involves the direct extraction and sequencing of DNA from environmental samples, allowing researchers to access the genetic material of entire microbial communities. By applying bioinformatics tools and careful screening designs, functional genes with desired properties can be identified from metagenomic datasets. Similarly, single-cell genomics enables the genomic analysis of individual microbial cells, providing insights into the genetic potential and functional capabilities of uncultivated microorganisms. These approaches have revolutionized the study of microbial diversity and have led to the discovery of novel genes and metabolic pathways with biotechnological applications.

True or false -- An operon fusion has a transcriptional signal from one gene fused with the translational start and coding sequence from another.

True. An operon fusion involves combining the regulatory region (transcriptional signal) of one gene with the translational start and coding sequence of another gene. This fusion allows the transcriptional activity of the regulatory region to control the expression of the downstream gene. It's a common technique used in molecular biology to study gene expression and regulation.

True or false -- One method to circumvent issues with introns when expressing a eukaryotic gene in a bacterium is to simply clone the mature transcript.

True. Cloning only the mature transcript of a eukaryotic gene, which excludes introns, is indeed a method to circumvent issues with introns when expressing the gene in a bacterium. Bacteria lack the machinery to process introns found in eukaryotic pre-mRNA, so cloning only the mature transcript ensures that the gene can be properly transcribed and translated in a bacterial host. This approach simplifies gene expression and avoids potential complications associated with intron splicing and processing in bacteria.

True or false -- One fundamental technique of genetic engineering includes the ability to cut DNA into random fragments.

True. Cutting DNA into random fragments is a fundamental technique in genetic engineering. This process is typically done using restriction enzymes, which recognize specific DNA sequences and cleave the DNA at those sites, generating fragments of varying sizes. These random DNA fragments can then be used in a variety of molecular biology techniques, such as cloning, PCR, sequencing, and gene mapping.

True or false -- DNA polymerases from Escherichia coli cannot be used to artificially copy gene sequences with a thermocycler.

True. DNA polymerases from Escherichia coli can be used to artificially copy gene sequences with a thermocycler. While Taq polymerase, derived from Thermus aquaticus, is commonly used in PCR, DNA polymerases from E. coli and other organisms can also be employed in PCR reactions. For example, some variants of DNA polymerase I from E. coli, such as Klenow fragment, have been used in PCR.

True or false -- Developing vaccines for humans relies heavily on manipulating and engineering vectors.

True. Developing vaccines for humans often involves manipulating and engineering vectors to deliver antigens into the body. Vectors can be viral, bacterial, or non-viral in nature and are engineered to carry and deliver specific antigens to induce an immune response. These vectors can be modified to enhance antigen expression, increase immunogenicity, and ensure safety. Vector-based vaccines have been developed for a variety of infectious diseases and are a crucial tool in modern vaccine development efforts.

True or false -- A common reporter protein is green fluorescent protein (GFP).

True. Green fluorescent protein (GFP) is indeed a common reporter protein used in molecular biology and biotechnology. It emits green light when exposed to certain wavelengths of light, making it useful for visualizing and tracking the expression and localization of proteins in cells and tissues.

True or false -- Modification enzymes typically methylate specific bases within the recognition sequence to prevent digestion of the nucleotide sequence by restriction endonucleases.

True. Modification enzymes, also known as DNA methyltransferases, methylate specific bases within the recognition sequence of restriction endonucleases. This methylation protects the DNA from being digested by the corresponding restriction endonucleases. This phenomenon is known as restriction-modification (R-M) systems, where the modification enzymes methylate specific bases in the DNA to mark it as "self," preventing the host organism's DNA from being degraded by its own restriction enzymes.

True or false -- One important advantage of eukaryotic cells as hosts for cloning vectors is that they already possess the complex RNA and posttranslational processing systems required for the production of eukaryotic proteins.

True. One significant advantage of using eukaryotic cells as hosts for cloning vectors is that they possess the complex RNA and posttranslational processing systems necessary for the production of eukaryotic proteins. These systems include mRNA splicing, mRNA transport, protein folding, posttranslational modifications (such as glycosylation, phosphorylation, and acetylation), and protein trafficking. Utilizing these systems in eukaryotic hosts ensures that the cloned gene is processed and expressed in a manner similar to endogenous genes, leading to proper protein function and activity. This is particularly important when expressing eukaryotic proteins that require specific modifications for proper function or when studying protein-protein interactions and signaling pathways.

True or false -- Regardless of the DNA polymerase used in PCR, such as Taq or Pfu, they all have an inherent inability to perfectly copy the template strand, which means the polymerases themselves occasionally make mutations in the sequences they copy.

True. Regardless of the DNA polymerase used in PCR, errors can occur during DNA replication, leading to mutations in the copied sequences. Both Taq polymerase and Pfu polymerase, as well as other DNA polymerases commonly used in PCR, are prone to introducing errors during DNA synthesis. These errors can result from the intrinsic error rate of the polymerase itself, as well as factors such as template sequence composition, reaction conditions, and the presence of inhibitors or contaminants. As a result, it's important to consider the fidelity of the DNA polymerase when designing PCR experiments, especially when high-fidelity amplification is required for downstream applications such as sequencing or cloning.

True or false -- An effective way to introduce DNA into plant cells is using the Ti plasmid, which comes from a plant pathogen.

True. The Ti (tumor-inducing) plasmid is derived from the soil bacterium Agrobacterium tumefaciens, which is a plant pathogen. Agrobacterium tumefaciens naturally transfers a segment of its Ti plasmid, known as T-DNA (transfer DNA), into the genome of infected plant cells, leading to the formation of crown gall tumors. Scientists have harnessed this natural mechanism to develop a powerful tool for introducing DNA into plant cells for genetic engineering purposes. By replacing the tumor-inducing genes on the Ti plasmid with genes of interest, researchers can use Agrobacterium-mediated transformation to deliver foreign DNA into plant cells, where it integrates into the plant genome and can be stably inherited by subsequent generations. This method is widely used in plant biotechnology for the production of genetically modified (GM) crops and the study of plant gene function.

True or false -- If vaccinia viruses would not both be immunogenic and relatively benign, they would likely not be a favored vehicle for vaccinations.

True. The immunogenicity and relative benignity of vaccinia viruses are key factors that contribute to their suitability as a favored vehicle for vaccinations. Vaccinia viruses are capable of eliciting robust immune responses, making them effective at inducing protective immunity against the target pathogen. Additionally, their relatively benign nature means that they typically do not cause severe disease in vaccinated individuals, minimizing the risk of adverse reactions. If vaccinia viruses lacked these properties, they would likely not be as favorable for use in vaccinations, and alternative vectors or vaccine platforms would need to be explored.

True or false -- Strong promoters used for genetic manipulation are usually regulated by specific molecules.

True. These promoters are designed to drive high levels of gene expression, and their activity can be controlled by regulatory elements that respond to specific inducers, repressors, or environmental cues. This allows for precise control over the expression of the gene of interest in the host organism.

True or false -- Although various codons often code for the same amino acid, it is important to choose the codon preferred by the expression host itself

True. While multiple codons may code for the same amino acid, the choice of codon can affect protein expression levels in a given host organism. Some codons may be translated more efficiently than others in specific organisms due to differences in tRNA abundance or codon usage bias. Therefore, selecting codons preferred by the expression host can optimize protein expression levels and improve overall efficiency.