mol bio 2 lecture 2 trues

Transcription assays are used to study gene expression.

Transcription assays are specifically designed to analyze the process of transcription, which is a key aspect of gene expression.

GAPDH was used as a loading control in the experiments.

The text states that GAPDH was used as a loading control during the RT PCR process, which is a standard practice to ensure accurate quantification of target gene expression.

RNAPs pause when NTPs are lacking during the NRO procedure.

The text explicitly states that RNAPs pause when NTPs are lacking, making this statement true.

Chromatin immunoprecipitation (ChIP) is a technique mentioned for studying gene expression.

The text includes chromatin immunoprecipitation (ChIP) as a method relevant to studying gene expression, confirming its importance in this context.

Modified nucleotides are incorporated throughout the nucleic acid in uniform labeling methods.

The text states that a modified nucleotide is incorporated throughout the nucleic acid, which is a key aspect of uniform labeling methods.

Random priming is a method for generating uniformly labeled nucleic acids.

The text lists random priming as one of the common methods for generating uniformly labeled nucleic acids.

The His epitope tag consists of six histidine residues in its peptide sequence.

The text mentions that the His epitope tag has the peptide sequence H H H H H H, which consists of six histidine residues, confirming this information.

The FLAG epitope tag has the peptide sequence D Y K D D D D K.

The text explicitly states that the FLAG epitope tag corresponds to the peptide sequence D Y K D D D D K, confirming its accuracy.

The HA epitope tag has the peptide sequence Y P Y D V P D Y A.

According to the text, the HA epitope tag is defined by the peptide sequence Y P Y D V P D Y A, which is clearly stated.

The Myc epitope tag has the peptide sequence E Q K L I S E E D L.

The text provides the peptide sequence E Q K L I S E E D L for the Myc epitope tag, confirming its validity.

Chromatin immunoprecipitation (ChIP) is a technique used in gene expression studies.

The text lists chromatin immunoprecipitation (ChIP) as a method relevant to studying gene expression, confirming its importance in this area.

The filter binding assay is used to detect protein-DNA interactions in vitro.

The text states that the filter binding assay was one of the first assays for detecting protein-DNA interactions in vitro, confirming that this statement is true.

ChIP can identify DNA sequences on the genome that are bound by a protein of interest.

The text mentions that ChIP tells you which DNA sequences on the genome are bound by a protein of interest, making this statement true.

To perform ChIP, fragmented chromatin is isolated from cells.

The text states that fragmented chromatin is isolated from cells as part of the ChIP process, confirming the statement's accuracy.

Autoradiography is used to detect the probe protein complex in a Gel Mobility Shift Assay.

The text states that the shift in mobility of the probe is detectable by autoradiography, confirming that this statement is true.

Indirect labels are small labels that are tightly and specifically bound by other molecules.

The text describes indirect labels as small labels that are tightly and specifically bound by other molecules.

The product of end labeling is end labeled DNA or RNA.

The text clearly states that the product of the end labeling process is end labeled DNA or RNA, confirming that this statement is true.

A second molecule is needed for the detection of indirect labels.

The text clearly states that a second molecule is required for the detection of indirect labels.

Labeling nucleic acids is an important technique in studying gene expression.

Labeling nucleic acids is crucial for various assays that detect and analyze gene expression, making it a key technique in molecular biology.

Western blot is a method used for detecting proteins.

Western blotting is a widely used technique for detecting specific proteins in a sample, confirming its role in protein detection.

Immunoprecipitation (IP) is a technique used to study protein interactions.

Immunoprecipitation (IP) is specifically designed to isolate and study protein interactions, making it a fundamental technique in protein research.

Chromatin immunoprecipitation (ChIP) is a method for studying protein interactions with DNA.

Chromatin immunoprecipitation (ChIP) is a technique that allows researchers to study the interactions between proteins and DNA, thus providing insights into gene regulation and expression.

RNA samples consist of a mixture of all the RNAs in the cell.

The text states that an RNA sample consists of a mixture of all the RNAs in the cell, confirming the statement is true.

Tissue images used in the study were obtained from Servier Medical Art.

The text mentions that tissue images were obtained from Servier Medical Art, confirming the statement is true.

Hybridization is a method used to detect RNA transcripts.

The title of the review indicates that the focus is on detecting RNA transcripts by hybridization, confirming the statement is true.

Isolating RNA is a step in the process of detecting specific RNAs.

The text lists 'Isolate RNA' as part of the process, indicating that isolating RNA is indeed a step in detecting specific RNAs, making this statement true.

RNA hybridization is a process that involves the binding of RNA molecules to complementary sequences.

RNA hybridization refers to the process where RNA strands bind to each other based on complementary base pairing, similar to DNA hybridization. This is a fundamental concept in molecular biology, particularly in techniques such as Northern blotting and in the study of gene expression.

RNA hybridization can occur between RNA and DNA molecules.

RNA hybridization can indeed occur between RNA and DNA molecules, as the RNA can bind to complementary DNA sequences. This is often utilized in various laboratory techniques, such as in situ hybridization, where RNA probes are used to detect specific DNA sequences.

A Northern blot involves the transfer of separated RNAs onto a membrane.

The text states that Northern blotting involves agarose gel electrophoresis with separated RNAs being transferred (blotted) onto a membrane, confirming that this statement is true.

Autoradiography is a step that follows the Northern blot process to visualize RNA bands.

The text mentions 'Membrane / Autoradiography' as a part of the Northern blot process, indicating that autoradiography is indeed a step used to visualize the RNA bands after they have been transferred to the membrane, making this statement true.

Homocysteine levels are elevated in heart failure.

The text states that in heart failure, homocysteine levels are elevated, indicating a direct relationship between heart failure and increased homocysteine levels.

The investigators aimed to understand how DICER expression is affected by homocysteine.

The text mentions that the investigators wanted to know how homocysteine affects the expression of the gene DICER, confirming their research focus.

Densitometry is used to quantify signal intensities in molecular biology.

The text defines densitometry as the process of quantifying signal intensities from analyses, including RT PCR signals, which is a common practice in molecular biology.

RT PCR was performed using an oligo dT primer for first strand synthesis.

The text mentions that RT PCR was performed with an oligo dT primer for first strand synthesis, which is a typical method used in such experiments.

Nuclear run on assays are a technique used for studying gene expression.

Nuclear run on assays are specifically mentioned as a technique for studying gene expression in the provided text, indicating their relevance in this context.

Western blot is a method used for detecting proteins.

The text explicitly mentions Western blot as a common method for detecting proteins, confirming its role in protein detection.

Immunoprecipitation (IP) and Co-IP are techniques used to study protein interactions.

The text lists immunoprecipitation (IP) and Co-IP as methods for studying protein interactions, confirming their use in this context.

Chromatin immunoprecipitation (ChIP) is a technique used to study protein interactions.

The text includes chromatin immunoprecipitation (ChIP) as a method related to studying protein interactions, confirming its application in this area.

FISH is a method used for detecting RNA levels.

FISH (Fluorescence In Situ Hybridization) is mentioned as one of the methods for detecting RNA levels, indicating its role in measuring gene activity.

The Northern blot method examines steady state RNA levels.

The text states that Northern blot is one of the methods used to detect RNA levels, which are generally steady state levels, confirming its focus on this aspect.

RT PCR is a method that can be used to measure gene activity.

RT PCR (Reverse Transcription Polymerase Chain Reaction) is listed among the methods for detecting RNA levels, confirming its use in measuring gene activity.

RNA seq is a method that provides a measure of gene activity.

RNA seq (RNA sequencing) is included in the list of methods for detecting RNA levels, indicating its role in measuring gene activity.

Gene C has a lower accumulation compared to Gene D.

The comparison section indicates that Gene C has lower accumulation than Gene D, confirming this statement as true.

The level of nascent RNA generated in the NRO analysis depends on the number of actively engaged RNA polymerase (RNAP) molecules.

The text states that the level of nascent RNA generated in the NRO analysis is dependent on the number of actively engaged RNA polymerase (RNAP) molecules on the gene of interest at the time of the experiment.

By looking only at nascent RNA, you can get a better picture of gene activity than by looking at total steady state RNA levels.

The text explicitly mentions that analyzing nascent RNA provides a better understanding of gene activity compared to analyzing total steady state RNA levels.

Nascent RNA refers to RNA that is newly made or synthesized.

The text defines nascent RNA as newly made or synthesized, confirming the accuracy of this statement.

Nuclei are isolated from cells during the Nuclear Run On (NRO) procedure.

The text states that the basic steps of the NRO procedure begin with the isolation of nuclei from cells, confirming that this statement is true.

Labeled NTPs are used to allow halted RNAPs to continue transcription for a few minutes during NRO.

The text indicates that nuclei are incubated with labeled NTPs to allow halted RNAPs to continue transcription, confirming this statement is true.

Sarkosyl prevents unengaged RNAPs from binding to DNA during the NRO procedure.

The text explains that sarkosyl blocks unengaged RNAP from binding to DNA, confirming that this statement is true.

Nuclear Run On (NRO) RNA is isolated to identify and quantify labeled transcripts.

The text states that NRO RNA is isolated and that the labeled transcripts produced can be identified and quantified, indicating that this statement is true.

Different labels and techniques are used to identify and quantify labeled nascent RNAs.

The text mentions that different labels and techniques are employed for the identification and quantification of labeled nascent RNAs, confirming the truth of this statement.

Labeled RNAs can be purified from the mixture of extracted RNAs using a special label.

The text indicates that a special label is used to allow for the purification of labeled RNAs from other RNAs, thus this statement is true.

RT PCR can only analyze a few genes at a time, while RNA seq can analyze thousands of genes simultaneously.

The text states that a few genes can be examined by RT PCR and that thousands of genes can be analyzed simultaneously by RNA seq, making this statement true.

The combination of NRO and RNA seq is referred to as GRO seq.

The text explicitly states that the combination of NRO and RNA seq is called 'GRO seq' for global run on sequencing, confirming the truth of this statement.

GRO seq is a technique that will be discussed in more detail later.

The text mentions that more details about the GRO seq technique will be provided later, indicating that this statement is true.

Only nascent RNAs will be labeled in the Nuclear Run On (NRO) experiment.

The text states that 'Only nascent RNAs will be labeled,' indicating that the labeling process specifically targets RNAs that are newly synthesized during the experiment.

RT PCR or RNA seq can be used to reveal that only nascent RNA from the Y gene was produced.

The text states that 'RT PCR or RNA seq would reveal that only nascent RNA from the Y gene was produced,' confirming the use of these techniques to analyze RNA production.

The paused polymerase can resume transcription once NTPs are added.

According to the text, 'The paused polymerase can now resume transcription because NTPs were added,' indicating that the addition of NTPs is necessary for the continuation of transcription.

Only Gene Y was transcriptionally active in the NRO experiment, as confirmed by the analysis of cDNA.

The text confirms that 'only Gene Y was transcriptionally active (and the GAPDH control),' indicating that the analysis of cDNA showed activity for Gene Y specifically.

Nuclear run on assays are a technique used for studying gene expression.

Nuclear run on assays are specifically mentioned as a technique for studying gene expression in the provided text, indicating their relevance in this context.

Western blot is a method used for detecting proteins.

The text explicitly states that Western blot is a common method for detecting proteins, confirming its role in protein detection.

Immunoprecipitation (IP) and Co-IP are techniques used to study protein interactions.

The text mentions immunoprecipitation (IP) and Co-IP as methods for studying protein interactions, confirming their application in this field.

In vitro transcription experiments can be used for studying genes and transcription itself in a cell-free system.

The text states that in vitro transcription experiments allow for the study of genes and transcription in a cell-free system, which is advantageous as it removes the complexity of the cell and nucleus.

Nuclear run-ons and methods for detecting RNAs provide information about gene expression in the cell.

The text mentions that nuclear run-ons and methods for detecting and quantifying RNAs give a picture of gene expression in the cell, indicating their role in examining transcription events.

In vitro transcription analysis allows molecular biologists to study genes/promoters and transcription factors.

The text states that in vitro transcription analysis is used to study genes/promoters and transcription factors, confirming the statement is true.

The components needed for in vitro transcription include Template DNA, NTPs, RNA Polymerase, and associated Transcription Factors if needed.

The text lists Template DNA, NTPs, RNA Polymerase, and optionally associated Transcription Factors as necessary components for in vitro transcription, confirming the statement is true.

In PAGE, smaller nucleic acids travel farther than larger ones.

The text explicitly states that in PAGE, smaller nucleic acids travel farther than larger ones, confirming the statement is true.

Common types of in vitro transcription templates include Run Off Transcription and G Less Cassette Transcription.

The text mentions Run Off Transcription and G Less Cassette Transcription as common types of in vitro transcription templates, confirming the statement is true.

The transcription factor studied by the molecular biologist is referred to as 'NTF'.

The text explicitly states that the molecular biologist is studying a novel human transcription factor called 'NTF'.

Buffer in molecular biology refers to an aqueous solution of a weak acid and its conjugate base used to maintain pH.

The text defines 'buffer' as an aqueous solution of a weak acid and its conjugate base used to maintain pH, which is a correct definition in the context of molecular biology.

All components of the reaction are dissolved in the 'buffer'.

The text states that all components of the reaction are dissolved in the 'buffer', which includes the necessary chemicals for the procedure.

NTF is an activator of RNAP II transcription.

The text states that the conclusion drawn from the analysis is that NTF is an activator of RNAP II transcription, which directly supports the truth of this statement.

The molecular biologist studied a novel human transcription factor called NTF.

The text explicitly mentions that a molecular biologist is studying a novel human transcription factor named NTF, confirming the accuracy of this statement.

The products of the transcription reactions were analyzed by PAGE electrophoresis and autoradiography.

The text confirms that the products of the transcription reactions were analyzed using PAGE electrophoresis and autoradiography, validating this statement as true.

In vitro transcription analysis allows molecular biologists to study genes/promoters and transcription factors.

The text states that in vitro transcription analysis is used to study genes/promoters and transcription factors, confirming the statement is true.

The components needed for in vitro transcription include Template DNA, NTPs, RNA Polymerase, and associated Transcription Factors if needed.

The text lists Template DNA, NTPs, RNA Polymerase, and optionally associated Transcription Factors as necessary components for in vitro transcription, confirming the statement is true.

In PAGE, smaller nucleic acids travel farther than larger ones.

The text explicitly states that in PAGE, smaller nucleic acids travel farther than larger ones, confirming the statement is true.

Common types of in vitro transcription templates include Run Off Transcription and G Less Cassette Transcription.

The text mentions Run Off Transcription and G Less Cassette Transcription as common types of in vitro transcription templates, confirming the statement is true.

Run Off Transcription is a type of in vitro transcriptional analysis.

The text states that 'Run Off Transcription is a type of in vitro transcriptional analysis,' confirming that this statement is true.

The transcriptional start site (TSS) is the first nucleotide that is read and copied into the RNA transcript.

The text clearly states that 'The transcriptional start site (TSS) is the first nucleotide/base that is read and copied into the RNA transcript by RNAP during transcription,' confirming this statement is true.

A restriction fragment is generated by digestion with restriction endonucleases.

The text defines a restriction fragment as 'a fragment of DNA generated by digestion with restriction endonucleases (restriction enzymes),' which makes this statement true.

Labeled NTPs are used in transcription analysis.

The text states that 'Labeled NTPs are used' in the context of transcription analysis, confirming that this statement is true.

An RNA of a specific length will be produced based on the distance from the TSS.

The text mentions that 'an RNA of a specific length will be produced,' which is directly related to the distance from the TSS, making this statement true.

In eukaryotic systems, some transcription factors are required for establishing the correct transcription start site (TSS).

The text explicitly states that in eukaryotic systems, certain transcription factors are necessary for establishing the correct transcription start site (TSS), confirming the statement is true.

In vitro transcription can be used to demonstrate that certain transcription factors are needed for transcription start site establishment.

The text mentions that in vitro transcription can be used to show that specific transcription factors are required, which supports the statement as true.

The G less cassette is used for examining transcription in vitro.

The text states that the G less cassette is another way of examining transcription in vitro, indicating its use in this context.

The G less cassette generates a transcript of defined length without cutting the template.

The text states that the G less cassette generates a transcript of defined length without having to cut the template with a restriction enzyme, confirming this statement as true.

The G less cassette was created decades ago and has been used by others since.

The text mentions that decades ago, someone generated the G less cassette and that others have used it since, making this statement accurate.

Transcription assays are used to study gene expression.

Transcription assays are specifically designed to analyze the process of transcription, which is a key aspect of gene expression.

Labeling nucleic acids is an important technique in studying gene expression.

Labeling nucleic acids allows researchers to track and analyze nucleic acids in various assays, which is crucial for studying gene expression.

Western blot is a method used for detecting proteins.

Western blotting is a widely used technique for detecting specific proteins in a sample, making it essential for protein analysis.

Epitope tagging is used to study protein interactions.

Epitope tagging involves adding a specific tag to a protein, which can then be used to study its interactions with other proteins.

The filter binding assay is a technique used to study protein interactions.

The filter binding assay is a method that can be used to analyze the binding interactions between proteins and nucleic acids.

Chromatin immunoprecipitation (ChIP) is a technique used to study gene expression.

Chromatin immunoprecipitation (ChIP) is used to analyze the interaction between proteins and DNA, which is a critical aspect of gene expression regulation.

Some types of labels allow nucleic acids to be detected in molecular biology techniques.

The text states that 'Some types of labels allows the nucleic acids to be detected, like probes in northern blots, FISH, and other types of hybridization experiments.' This confirms that certain labels are indeed used for detection purposes.

Labeled nascent RNAs can be purified from total RNA samples in a GRO seq experiment.

The text provides an example stating that 'labeled nascent RNAs in an NRO experiment can be purified from total RNA samples in order to sequence them (as in a GRO seq experiment),' confirming this statement as true.

The images used for labeling nucleic acids are obtained from Servier Medical Art.

The text explicitly states that the images are obtained from 'Servier Medical Art by Servier at https://smart.servier.com.' This confirms the source of the images used for labeling nucleic acids.

One or more phosphorus atoms (P) can be replaced with a radioactive form for direct detection.

The text states that one or more phosphorus atoms (P) can be replaced with the radioactive P form, indicating that this is a true statement.

Autoradiography is a method used to detect radioactive isotopes.

The text states that radioactive isotopes are detected by autoradiography, confirming that this statement is true.

Fluorescent compounds are attached to nucleotide bases in fluorophores.

The text specifies that a fluorescent compound is attached to a nucleotide base in fluorophores, confirming that this statement is true.