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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1:37 minutes

Problem 18c

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 alone

Verified step by step guidance

Step 1: Understand the context of the problem. A band shift assay is used to study DNA-protein interactions. In this case, the 3.5-kb DNA fragment contains the complete sequence of a mouse gene, including the promoter and polyadenylation site. The gel bands observed represent different conditions of the DNA fragment being studied.

Step 2: Focus on the condition described: '3.5-kb fragment alone.' This means the DNA fragment is not interacting with any proteins or other molecules. It is simply the isolated DNA segment being analyzed.

Step 3: Recall that in a band shift assay, the DNA fragment alone will migrate through the gel based on its size and charge. Since no proteins or other molecules are bound to the DNA, its migration will be unaltered, and it will appear as a single band corresponding to its size.

Step 4: Match this condition to the specific lane of the gel. The lane representing the '3.5-kb fragment alone' will show a single band at the position corresponding to the size of the DNA fragment (3.5 kb). This is typically the control lane in the assay.

Step 5: To confirm, compare the migration pattern of the DNA fragment alone to other lanes where DNA-protein interactions may be present. The '3.5-kb fragment alone' lane should have the simplest pattern, with no shifts or additional bands.

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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 contains specific binding sites for RNA polymerase and transcription factors, which are essential for the regulation of gene expression. Understanding the promoter's role is crucial for interpreting how the gene is activated or silenced in response to various signals.

Polyadenylation Site

The polyadenylation site is a sequence in the mRNA that signals the addition of a poly(A) tail, which is important for mRNA stability, export from the nucleus, and translation efficiency. In the context of the DNA segment, knowing where the polyadenylation site is located helps in understanding the full length of the mRNA produced from the gene and its functional implications.

Band Shift Assay

A band shift assay, also known as an electrophoretic mobility shift assay (EMSA), is a technique used to study protein-DNA interactions. In this assay, DNA fragments bound to proteins migrate more slowly through a gel than unbound DNA, resulting in distinct bands. This method is essential for analyzing how transcription factors interact with the promoter region of the gene in question.

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Related Practice

Textbook Question

A 2-kb fragment of E. coli DNA contains the complete sequence of a gene for which transcription is terminated by the rho protein. The fragment contains the complete promoter sequence as well as the terminator region of the gene. The cloned fragment is examined by band shift assay. Each lane of a single electrophoresis gel contains the 2-kb cloned fragment under the following conditions:

Lane 1: 2-kb fragment alone

Lane 2: 2-kb fragment plus the core enzyme

Lane 3: 2-kb fragment plus the RNA polymerase holoenzyme

Lane 4: 2-kb fragment plus rho protein

Explain the relative positions of bands in lanes 1 and 4.

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Textbook Question

Metagenomics studies generate very large amounts of sequence data. Provide examples of genetic insight that can be learned from metagenomics.

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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.

3.5-kb fragment plus TFIIB and TFIID

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Textbook Question

Match these conditions to a specific lane of the gel.

3.5-kb fragment plus TFIIB, TFIID, TFIIF, and RNA polymerase II

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Textbook Question

Match these conditions to a specific lane of the gel.

3.5-kb fragment plus RNA polymerase II

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Textbook Question

Match these conditions to a specific lane of the gel.

3.5-kb fragment plus TFIIB

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Textbook Question

What are DNA microarrays? How are they used?

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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.

Explain the role of DNase I.

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