mol bio 2 lecture 2 false

NTPs are not depleted during the Nuclear Run On (NRO) procedure.

The text mentions that NTPs are depleted in the step where RNAPs that were engaged in transcription are halted, indicating that this statement is false.

You need to remember the sequences of the epitope tags listed in the text.

The text explicitly states that you do not have to remember these sequences, indicating that memorization is not required.

Gel shift assay (EMSA) is used for detecting nucleic acids.

The text does not mention gel shift assay (EMSA) as a method for detecting nucleic acids; rather, it is typically used for studying protein-nucleic acid interactions.

Nick translation is not a method for generating uniformly labeled nucleic acids.

The text explicitly mentions nick translation as one of the common methods for generating uniformly labeled nucleic acids, making this statement false.

All antibodies are specific to a single protein and cannot recognize epitope tags.

The text implies that antibodies can recognize specific epitope tags, which are short peptides, indicating that this statement is false.

Nitrocellulose filters bind double-stranded DNA.

The text specifies that nitrocellulose binds single-stranded nucleic acids and proteins, but not double-stranded DNA, making this statement false.

The substrates for end labeling include only DNA.

The text mentions that both DNA and RNA are substrates for end labeling, so the statement that it includes only DNA is false.

Protein A/G binds the variable region of IgG antibodies.

The text specifies that Protein A/G binds the Fc (constant) region of IgG antibodies, not the variable region, making this statement false.

The approach involved treating cardiomyocytes with a single concentration of homocysteine.

The text specifies that cardiomyocytes were treated with different concentrations of homocysteine, not just a single concentration, indicating a varied experimental approach.

Nuclear run on assays are a type of in vitro transcription assay.

Nuclear run on assays are distinct from in vitro transcription assays; they are performed in the nucleus to measure active transcription of genes, while in vitro assays are conducted outside of the cell.

Epitope tagging is unrelated to studying protein interactions.

Epitope tagging is a method used to study protein interactions by attaching a specific tag to a protein, allowing for its identification and analysis in various assays.

Gel shift assay (EMSA) is used to study gene expression directly.

Gel shift assay (EMSA) is primarily used to study protein-DNA interactions rather than directly measuring gene expression.

The Mayo Clinic is involved in detecting specific RNAs in intact cells or tissues.

The text specifies that the Mayo Clinic is involved in detecting specific RNAs in RNA samples, not in intact cells or tissues, making this statement false.

The stability of RNA hybridization is not influenced by temperature.

The stability of RNA hybridization is significantly influenced by temperature. Higher temperatures can disrupt the hydrogen bonds formed between complementary RNA strands, leading to denaturation. Therefore, temperature plays a crucial role in the hybridization process.

RNA hybridization is only relevant in the context of genetic research.

While RNA hybridization is indeed important in genetic research, it is also relevant in various other fields, including diagnostics, therapeutics, and molecular biology. Its applications extend beyond just genetic research, making it a versatile technique.

In a Northern blot, RNA bands are visible on the membrane after the process is complete.

The text indicates that the RNA bands are 'invisible' on the membrane initially, which means they are not visible until further steps like autoradiography are performed. Therefore, this statement is false.

The results of the experiments were not averaged or indicated with standard deviations.

The text clearly states that the results were averaged and standard deviations were indicated as error bars, which is important for understanding the variability of the data.

In vitro transcription assays are not used for labeling nucleic acids.

The text states that in vitro transcription assays are a method for labeling nucleic acids, which means they are indeed used for this purpose.

Epitope tagging is unrelated to studying protein interactions.

The text includes epitope tagging as a method related to studying protein interactions, indicating its relevance in this area.

The filter binding assay is a technique used for detecting proteins.

The text does not classify the filter binding assay as a method for detecting proteins; instead, it is listed among techniques for studying protein interactions.

Gel shift assay (EMSA) is a method used for studying gene expression.

The text does not mention gel shift assay (EMSA) as a method for studying gene expression; it is typically used for studying protein-DNA interactions.

Microarray is a method that can measure gene activity by examining the rate of transcription.

The text indicates that methods like microarray examine steady state RNA levels, which do not necessarily reflect the rate of transcription, thus making this statement incorrect.

The steady state RNA level reflects the rate of transcription.

The text explicitly states that the steady state RNA level does not necessarily reflect the rate of transcription, making this statement false.

Gene A has a high accumulation of RNA.

The text states that Gene A has lower accumulation compared to Gene B, indicating that Gene A does not have a high accumulation of RNA, thus this statement is false.

Nuclear run on (NRO) assays reveal the transcriptional activity of genes by looking at total steady state RNA.

NRO assays specifically look at nascent RNA, which is newly made or synthesized RNA, rather than total steady state RNA. This distinction is crucial for understanding gene activity.

In conditions with many engaged RNAPs, there are low levels of nascent transcription.

The text indicates that in conditions with many engaged RNAPs, there are higher levels of nascent transcription, not low levels.

Transcripts produced during NRO are unlabeled.

The text states that transcripts produced during NRO are labeled, which makes this statement false.

NTPs refer to the five nucleotides needed for transcription.

The text clarifies that NTPs refer to four specific nucleotides (ATP, CTP, GTP, and UTP), making this statement false.

Identifying and quantifying labeled NRO transcripts reveals which genes are inactive.

The text specifies that identifying and quantifying labeled NRO transcripts tells you which genes are active and how active they are, not inactive, making this statement false.

RNAs produced before the experiment will be analyzed in the NRO experiment.

The text clearly mentions that 'RNAs produced before the experiment will not be analyzed,' which means only RNAs synthesized during the experiment are considered.

The polymerase engaged in transcription pauses because there are NTPs available.

The text indicates that 'The polymerase that was engaged in transcription now pauses because there are no NTPs available,' meaning the lack of NTPs causes the pause, not their availability.

In vitro transcription assays are not used for labeling nucleic acids.

The text lists in vitro transcription assays as a technique related to labeling nucleic acids, which means they are indeed used for this purpose.

Epitope tagging is unrelated to studying protein interactions.

The text includes epitope tagging as a method related to studying protein interactions, indicating its relevance in this area.

The gel shift assay (EMSA) is used for detecting nucleic acids.

The gel shift assay (EMSA) is primarily used for studying protein-nucleic acid interactions, not directly for detecting nucleic acids themselves, which makes this statement false.

In vitro transcriptional analysis allows us to examine transcription events that took place in vivo.

The text clarifies that in vitro transcriptional analysis allows examination of transcription events in a cell-free system, which is distinct from in vivo conditions where events occur within the living cell.

The complexity of the cell and nucleus is beneficial for studying transcription events.

The text suggests that studying transcription in a cell-free system is advantageous because it removes the complexity of the cell and nucleus, implying that this complexity is not beneficial for such studies.

In vitro transcription analysis is performed in vivo.

The text specifies that in vitro transcription analysis is conducted in a test tube, indicating that it is not performed in vivo, making the statement false.

A labeled NTP mix is used to measure the length of the RNA transcript in in vitro transcription analysis.

The text indicates that a labeled NTP mix is used for detection, not specifically for measuring the length of the RNA transcript, which is a separate aspect of the analysis, making the statement false.

In vitro transcription reactions were performed with decreasing amounts of the transcription factor.

The text mentions that the in vitro transcription reactions were performed with increasing amounts of the transcription factor, not decreasing amounts.

The term 'novel' refers to something that has been reported or studied before.

According to the text, 'novel' refers to something that has not been reported or studied before, indicating its newness.

In vitro transcription reactions were performed with decreasing amounts of the transcription factor.

The text indicates that the transcription reactions were performed with increasing amounts of the transcription factor, not decreasing amounts, making this statement false.

The transcription reactions were incubated for several hours.

The text specifies that the transcription reactions were incubated for several minutes, not hours, which makes this statement false.

In vitro transcription analysis is performed in vivo.

The text specifies that in vitro transcription analysis is conducted in a test tube, indicating that it is not performed in vivo, making the statement false.

A labeled NTP mix is used to measure the length of the RNA transcript in in vitro transcription analysis.

The text indicates that a labeled NTP mix is used for detection, not specifically for measuring the length of the RNA transcript, which is a separate aspect of the analysis, making the statement false.

The transcriptional template used in Run Off Transcription is a restriction fragment of RNA.

The text specifies that the transcriptional template is a restriction fragment of DNA, not RNA, making this statement false.

RNAP binds to the transcriptional start site (TSS) during transcription.

According to the text, RNAP binds to the promoter and transcribes from the transcriptional start site (TSS), but it does not bind to the TSS itself, making this statement false.

The TSS is always located at the end of the promoter sequence.

The text states that 'The TSS is often within the promoter sequence,' indicating that it is not always at the end, thus making this statement false.

The RNA fragment produced in the example is 327 bp in length.

The text specifies that the RNA fragment will be 327 nt in length, not bp. Therefore, this statement is false.

The distance from the TSS to the distal end of the restriction fragment is 327 nt.

The text indicates that the distance is 327 bp, not nt. Thus, this statement is false.

Transcription with the G less cassette requires GTP.

The text explicitly mentions 'No GTP' in the context of the G less cassette, indicating that GTP is not required for transcription with this method.

An A less cassette, C less, or T less cassette would not work for transcription analysis.

The text states that an A less cassette, C less, or T less cassette would have worked too, indicating that these alternatives are valid for transcription analysis.

The transcribed portion of the G less cassette contains G nucleotides on the coding strand.

The text specifies that the transcribed portion of the template is a DNA sequence that contains no G nucleotides on the coding strand, making this statement false.

Nuclear run on assays are a type of in vitro transcription assay.

Nuclear run on assays are distinct from in vitro transcription assays; they are performed in the nucleus to measure active transcription of genes, while in vitro assays are conducted outside of the cell.

Immunoprecipitation (IP) and Co-IP are methods used to detect nucleic acids.

Immunoprecipitation (IP) and Co-IP are techniques used to study protein-protein interactions, not for detecting nucleic acids.

Gel shift assay (EMSA) is used to study protein interactions.

Gel shift assay (EMSA) is primarily used to study the binding of proteins to nucleic acids, not direct protein-protein interactions.

Labels used in molecular biology can only be used for detection and not for purification of nucleic acids.

The text mentions that 'Some labels can also be used for purifying/isolating specific nucleic acids from mixtures,' indicating that labels serve both detection and purification functions.

The Creative Commons license mentioned in the text allows for the use of images without any restrictions.

The text refers to a Creative Commons license (https://creativecommons.org/licenses/by/3.0/) but does not state that it allows for unrestricted use. Creative Commons licenses typically have specific conditions that must be followed, such as attribution.

Radioactive atoms can only be used in vitro and not in living cells.

The text mentions that radioactive isotopes can be incorporated into nucleic acids in vitro or in living cells, which means they can be used in both contexts, making this statement false.

Cells can differentiate between a normal nucleotide and a radioactive one.

According to the text, cells cannot tell the difference between a normal nucleotide and a radioactive one, indicating that this statement is false.

Fluorophores can be used in living cells.

The text indicates that fluorophores generally cannot be used in living cells, making this statement false.

Indirect labels can be detected on their own.

The text states that indirect labels cannot be detected on their own and require a second molecule for detection.

Indirect labels can be used for purifying labeled nucleic acids without any additional molecules.

The text specifies that a second molecule is needed for purification of the nucleic acid that contains the indirect label, indicating that they cannot be used for purification on their own.

Streptavidin binds weakly to biotin.

The text mentions that streptavidin binds extremely tightly to biotin, indicating that this statement is false.

Biotin cannot be attached to nucleic acids in vitro.

The text indicates that biotin can be attached to nucleic acids in vitro, making this statement false.

BrU has a major advantage of being highly toxic to living cells.

The text mentions that BrU has relatively low toxicity, which contradicts the statement that it is highly toxic, making the statement false.

In vitro transcription assays are not related to gene expression studies.

The text states that in vitro transcription assays are a technique for studying gene expression, indicating their relevance to this field.

Epitope tagging is unrelated to studying protein interactions.

The text mentions epitope tagging as a method used in the context of studying protein interactions, indicating its relevance.

Gel shift assay (EMSA) is used for detecting nucleic acids.

The text indicates that the gel shift assay (EMSA) is used in the context of studying protein interactions, not specifically for detecting nucleic acids.

5′ radiolabeling with T4 Polynucleotide Kinase (T4 PNK) transfers a radioactive phosphate group from the α position of ATP to the 5′ hydroxyl group of DNA or RNA.

The text specifies that T4 PNK transfers a radioactive phosphate group from the γ position of ATP (γ P ATP), not the α position, making this statement false.

The text discusses all common methods for generating uniformly labeled nucleic acids in detail.

The text specifies that it will only discuss in vitro transcription, implying that not all methods are covered in detail.

Bacteriophage RNA polymerase requires additional protein factors to function effectively in vitro.

The text mentions that phage RNA polymerases do not require additional protein factors, indicating that the statement is false.

Phage RNA polymerases are difficult to synthesize in the lab.

The text states that phage RNA polymerases are easy to synthesize in the lab, which makes the statement false.

The T7 promoter sequence is located downstream of the polymerase’s promoter sequence in the transcription process.

The text indicates that the DNA sequence is cloned into a plasmid vector downstream of the polymerase’s promoter sequence, not the T7 promoter sequence, making this statement false.

RNA polymerase incorporates the beta phosphate into the new RNA molecule.

The text specifies that RNA polymerase incorporates the alpha (α) phosphate into the new RNA molecule, not the beta phosphate, making this statement false.

Incoming nucleoside triphosphates are not involved in RNA synthesis.

The text mentions incoming nucleoside triphosphates as part of the RNA synthesis process, indicating that they are indeed involved, making this statement false.

In vitro transcription assays are not related to gene expression studies.

The text lists in vitro transcription assays as a technique for studying gene expression, which directly contradicts the statement that they are not related.

Epitope tagging is unrelated to studying protein interactions.

The text includes epitope tagging as a method for studying protein interactions, which means it is indeed related to this area of study.

Gel shift assay (EMSA) is a method used for detecting proteins.

The text categorizes gel shift assay (EMSA) under studying protein interactions rather than directly detecting proteins, making the statement false.

Western blots are a direct method of examining gene expression.

The text describes Western blots as an indirect method of examining gene expression, making this statement false.

Blocking in the Western Blot process involves using a solution of water to coat the membrane.

The text specifies that blocking is done with a protein solution, often milk or bovine serum albumin (BSA), not water, making the statement false.

Detection in Western Blot is typically done using a method called fluorescence.

The text indicates that detection is usually done by chemiluminescence, not fluorescence, making the statement false.

The membrane used in the Western Blot is blocked with a specific protein solution.

The text mentions that 'Membrane is blocked with a non specific protein solution', which means the statement is false as it incorrectly states that a specific protein solution is used.

After the first antibody is applied, excess antibody is not washed off.

The text specifies that after incubating with the first antibody, excess antibody is then washed off, indicating that this step is necessary.

Chemiluminescence substrate is added before the second antibody is applied.

According to the text, the chemiluminescence substrate is added after the second antibody (HRP) is applied, not before.

The most common type of antibody is immunoglobulin A (IgA).

The text specifies that the most common type of antibody is immunoglobulin G (IgG), not immunoglobulin A (IgA), making this statement false.

Different species have identical amino acid sequences on their constant regions of IgG antibodies.

The text indicates that different species have different amino acid sequences on their constant regions, which makes this statement false.

The secondary antibody is generated in the same animal as the primary antibody.

The text specifies that the secondary antibody is generated in a different animal than the primary antibody, making this statement false.

The secondary antibody can be of any class of antibody regardless of the primary antibody's class.

The text indicates that the secondary antibody must also be specific for the class of primary antibody, meaning this statement is false.

The study found that high levels of argininosuccinate synthase protein (ArSu) are associated with a good prognosis in human gastric cancer.

The text indicates that increased expression of ArSu predicts poor prognosis in human gastric cancer, making the statement false.

The investigators were interested in determining whether low levels of ArSu could indicate advanced gastric cancer.

The text specifies that the investigators were interested in high levels of ArSu as an indicator of advanced gastric cancer, not low levels, making the statement false.

In vitro transcription assays are not used for labeling nucleic acids.

The text lists in vitro transcription assays as a technique related to labeling nucleic acids, which means they are indeed used for this purpose.

Epitope tagging is unrelated to studying protein interactions.

The text includes epitope tagging as a method related to studying protein interactions, indicating its relevance in this area.

The gel shift assay (EMSA) is used for detecting nucleic acids.

The gel shift assay (EMSA) is typically used for studying protein-nucleic acid interactions, not directly for detecting nucleic acids alone, which makes this statement false.

Generating a commercial antibody for a protein of interest is always quick and inexpensive.

The text mentions that generating a commercial antibody can be costly and time-consuming if one is not available for the protein of interest, indicating that this statement is false.

The epitope tag sequence is typically added to the 5’ end of the ORF for a C terminal tag.

The text states that the epitope tag sequence is added to the 5’ end of the ORF for an N terminal tag, not a C terminal tag. Therefore, this statement is false.

The epitope tag sequence is added upstream of the stop codon for an N terminal tag.

The text specifies that the epitope tag sequence is added to the 3’ end of the ORF (upstream of the stop codon) for a C terminal tag, not for an N terminal tag. Thus, this statement is false.

Labeling nucleic acids is not a common method in studying gene expression.

The text mentions 'Labeling nucleic acids' as a topic, indicating that it is indeed a common method used in studying gene expression, making the statement false.

Chromatin immunoprecipitation (ChIP) is unrelated to studying gene expression.

The text includes 'Chromatin immunoprecipitation (ChIP)' as a method related to studying gene expression, indicating that the statement is false.

Antibody epitope interactions in immunoprecipitation are weak and do not allow for purification of low abundance proteins.

The text mentions that antibody epitope interactions are quite strong (high affinity), which allows proteins to be purified even if they are in low abundance, indicating that this statement is false.

Protein immunoprecipitation is only effective for proteins that are abundant in the source material.

The text clearly states that immunoprecipitation can purify proteins even if they are in low abundance, which contradicts this statement and makes it false.