Table of contents

1. Introduction to Genetics51m
2. Mendel's Laws of Inheritance3h 37m
3. Extensions to Mendelian Inheritance2h 41m
4. Genetic Mapping and Linkage2h 28m
5. Genetics of Bacteria and Viruses1h 21m
6. Chromosomal Variation1h 48m
7. DNA and Chromosome Structure56m
8. DNA Replication1h 10m
9. Mitosis and Meiosis1h 34m
10. Transcription1h 0m
11. Translation58m
12. Gene Regulation in Prokaryotes1h 19m
13. Gene Regulation in Eukaryotes44m
14. Genetic Control of Development44m
15. Genomes and Genomics1h 50m
16. Transposable Elements47m
17. Mutation, Repair, and Recombination1h 6m
18. Molecular Genetic Tools19m
- Genetic Cloning
  9m
- Methods for Analyzing DNA
  9m
19. Cancer Genetics29m
- Overview of Cancer
  21m
- Cancer Mutations
  7m
20. Quantitative Genetics1h 26m
21. Population Genetics50m
- Hardy Weinberg
  19m
- Allelic Frequency Changes
  31m
22. Evolutionary Genetics29m

15. Genomes and Genomics

Functional Genomics

Genetics

15. Genomes and Genomics

Functional Genomics

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2:14 minutes

Problem 18d

Textbook Question

A 3.5-kb segment of DNA containing the complete sequence of a mouse gene is available. The DNA segment contains the promoter sequence and extends beyond the polyadenylation site of the gene. The DNA is studied by band shift assay, and the following gel bands are observed.

Match these conditions to a specific lane of the gel.
3.5-kb fragment plus RNA polymerase II

Verified step by step guidance

Step 1: Understand the experimental setup. A band shift assay is used to study protein-DNA interactions. When RNA polymerase II binds to the DNA fragment, it alters the mobility of the DNA in the gel, causing a shift in the band position.

Step 2: Analyze the gel image provided. The gel contains five lanes, each showing bands corresponding to different experimental conditions. The lanes are numbered 1 through 5.

Step 3: Match the condition '3.5-kb fragment plus RNA polymerase II' to the appropriate lane. Look for a lane where the band is shifted compared to the control lane (which contains only the 3.5-kb DNA fragment without RNA polymerase II). This shift indicates the binding of RNA polymerase II to the DNA.

Step 4: Identify the control lane. Typically, the control lane will show the unaltered position of the 3.5-kb DNA fragment. Compare the band positions in the other lanes to this control to determine which lane shows the interaction with RNA polymerase II.

Step 5: Confirm the lane where the band is shifted upward or has altered mobility, as this indicates the presence of RNA polymerase II bound to the DNA fragment. This lane corresponds to the condition described in the problem.

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Key Concepts

Here are the essential concepts you must grasp in order to answer the question correctly.

Promoter Sequence

The promoter sequence is a region of DNA located upstream of a gene that initiates transcription. It serves as the binding site for RNA polymerase and transcription factors, facilitating the assembly of the transcription machinery. Understanding the promoter's role is crucial for analyzing gene expression and the effects of regulatory elements.

RNA Polymerase II

RNA polymerase II is an enzyme responsible for synthesizing messenger RNA (mRNA) from a DNA template during transcription. It plays a vital role in gene expression by transcribing protein-coding genes. The interaction between RNA polymerase II and the promoter is essential for initiating transcription, making it a key focus in studies of gene regulation.

Gel Electrophoresis

Gel electrophoresis is a laboratory technique used to separate DNA, RNA, or proteins based on their size and charge. In this method, samples are loaded into a gel matrix and subjected to an electric field, causing molecules to migrate. The resulting bands can be analyzed to determine the presence and size of specific fragments, which is critical for interpreting results in molecular biology experiments.

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Textbook Question

A 3.5-kb segment of DNA containing the complete sequence of a mouse gene is available. The DNA segment contains the promoter sequence and extends beyond the polyadenylation site of the gene. The DNA is studied by band shift assay, and the following gel bands are observed.

Match these conditions to a specific lane of the gel.

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Match these conditions to a specific lane of the gel.

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Match these conditions to a specific lane of the gel.

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Match these conditions to a specific lane of the gel.

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A 1.0-kb DNA fragment from the end of the mouse gene described in the previous problem is examined by DNA footprint protection analysis. Two samples are end-labeled with ³²P and one of the two is mixed with TFIIB, TFIID, and RNA polymerase II. The DNA exposed to these proteins is run in the right-hand lane of the gel shown below and the control DNA is run in the left-hand. Both DNA samples are treated with DNase I before running the samples on the electrophoresis gel.

Explain the role of DNase I.

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Textbook Question

A 1.0-kb DNA fragment from the end of the mouse gene described in the previous problem is examined by DNA footprint protection analysis. Two samples are end-labeled with ³²P, and one of the two is mixed with TFIIB, TFIID, and RNA polymerase II. The DNA exposed to these proteins is run in the right-hand lane of the gel shown below and the control DNA is run in the left-hand. Both DNA samples are treated with DNase I before running the samples on the electrophoresis gel.

Draw a diagram of this DNA fragment bound by the transcriptional proteins, showing the approximate position of proteins along the fragment.

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