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Ch. 10 - Eukaryotic Chromosome Abnormalities and Molecular Organization
Sanders - Genetic Analysis: An Integrated Approach 3rd Edition
Sanders3rd EditionGenetic Analysis: An Integrated ApproachISBN: 9780135564172Not the one you use?Change textbook
All textbooksSanders 3rd EditionCh. 10 - Eukaryotic Chromosome Abnormalities and Molecular OrganizationProblem 26a
Chapter 10, Problem 26a

DNase I cuts DNA that is not protected by bound proteins but is unable to cut DNA that is complexed with proteins. Human DNA is isolated, stripped of its nonhistone proteins, and mixed with DNase I. Samples are removed after 30 minutes, 1 hour, and 4 hours and run separately in gel electrophoresis. The resulting gel is stained to make all DNA fragments in it visible, and the results are shown in the figure. DNA fragment sizes in base pairs (bp) are estimated by the scale to the left of the gel. Examine the gel results and speculate why longer DNase I treatment produces different results.

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Step 1: Understand the role of DNase I in the experiment. DNase I is an enzyme that cleaves DNA at regions not protected by proteins, such as histones. This means that DNA bound to histones or other protective proteins will remain intact, while unprotected regions will be fragmented.
Step 2: Analyze the gel electrophoresis results. Gel electrophoresis separates DNA fragments based on size, with smaller fragments migrating further down the gel. The gel shows DNA fragment sizes at different time points (30 minutes, 1 hour, and 4 hours). Longer DNase I treatment results in smaller fragments appearing on the gel.
Step 3: Relate the results to the mechanism of DNase I activity. Over time, DNase I continues to cleave unprotected DNA regions, breaking them into progressively smaller fragments. This explains why longer treatment times result in smaller DNA fragments being visible on the gel.
Step 4: Consider the implications of histone protection. The presence of histones or other DNA-binding proteins protects certain regions of the DNA from DNase I cleavage. These protected regions remain intact, while unprotected regions are fragmented over time.
Step 5: Speculate on the biological significance. The results suggest that DNase I treatment can be used to study chromatin structure and identify regions of DNA that are bound to histones or other proteins. This technique is valuable for understanding gene regulation and chromatin organization in cells.

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Key Concepts

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

DNase I Function

DNase I is an enzyme that cleaves the phosphodiester bonds in DNA, effectively breaking it down into smaller fragments. Its activity is influenced by the presence of proteins bound to the DNA; it cannot cut DNA that is protected by these proteins. Understanding how DNase I interacts with DNA is crucial for interpreting the results of the gel electrophoresis.
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Gel Electrophoresis

Gel electrophoresis is a laboratory technique used to separate DNA fragments based on their size. When an electric current is applied, smaller fragments move faster through the gel matrix than larger ones, allowing for size estimation. Analyzing the resulting band patterns helps determine the extent of DNA degradation by DNase I over time.
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Time-Dependent Enzyme Activity

The duration of DNase I treatment affects the extent of DNA degradation. Longer exposure allows more time for the enzyme to act on unprotected DNA, resulting in smaller fragments. By comparing the gel results at different time points, one can infer how the enzyme's activity varies with time and the implications for DNA-protein interactions.
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Related Practice
Textbook Question

A boy with Down syndrome (trisomy 21) has 46 chromosomes. His parents and his two older sisters have a normal phenotype, but each has 45 chromosomes.

What term best describes this kind of chromosome abnormality?

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Textbook Question

A boy with Down syndrome (trisomy 21) has 46 chromosomes. His parents and his two older sisters have a normal phenotype, but each has 45 chromosomes.

What is the probability the next child of this couple will have a normal phenotype and have 46 chromosomes? Explain your answer.

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Textbook Question

Experimental evidence demonstrates that the nucleosomes present in a cell after the completion of S phase are composed of some 'old' histone dimers and some newly synthesized histone dimers. Describe the general design for an experiment that uses a protein label such as ³⁵S to show that nucleosomes are often a mixture of old and new histone dimers following DNA replication.

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Textbook Question

DNase I cuts DNA that is not protected by bound proteins but is unable to cut DNA that is complexed with proteins. Human DNA is isolated, stripped of its nonhistone proteins, and mixed with DNase I. Samples are removed after 30 minutes, 1 hour, and 4 hours and run separately in gel electrophoresis. The resulting gel is stained to make all DNA fragments in it visible, and the results are shown in the figure. DNA fragment sizes in base pairs (bp) are estimated by the scale to the left of the gel. Draw a conclusion about the organization of chromatin in the human genome from this gel.

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Textbook Question

Genomic DNA from the nematode worm Caenorhabditis elegans is organized by nucleosomes in the manner typical of eukaryotic genomes, with 145 bp encircling each nucleosome and approximately 55 bp in linker DNA. When C. elegans chromatin is carefully isolated, stripped of nonhistone proteins, and placed in an appropriate buffer, the chromatin decondenses to the 10-nm fiber structure. Suppose researchers mix a sample of 10-nm–fiber chromatin with a large amount of the enzyme DNase I that randomly cleaves DNA in regions not protected by bound protein. Next, they remove the nucleosomes, separate the DNA fragments by gel electrophoresis, and stain all the DNA fragments in the gel.

Approximately what range of DNA fragment sizes do you expect to see in the stained electrophoresis gel? How many bands will be visible on the gel?

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Textbook Question

Genomic DNA from the nematode worm Caenorhabditis elegans is organized by nucleosomes in the manner typical of eukaryotic genomes, with 145 bp encircling each nucleosome and approximately 55 bp in linker DNA. When C. elegans chromatin is carefully isolated, stripped of nonhistone proteins, and placed in an appropriate buffer, the chromatin decondenses to the 10-nm fiber structure. Suppose researchers mix a sample of 10-nm–fiber chromatin with a large amount of the enzyme DNase I that randomly cleaves DNA in regions not protected by bound protein. Next, they remove the nucleosomes, separate the DNA fragments by gel electrophoresis, and stain all the DNA fragments in the gel.

Explain the origin of DNA fragments seen in the gel.

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