7. DNA and Chromosome Structure

Eukaryotic Chromosome Structure

7. DNA and Chromosome Structure

Eukaryotic Chromosome Structure

2:25 minutes

Problem 18

Textbook Question

A survey of organisms living deep in the ocean reveals two new species whose DNA is isolated for analysis. DNA samples from both species are treated to remove nonhistone proteins. Each DNA sample is then treated with DNase I that cuts DNA not protected by histone proteins but is unable to cut DNA bound by histone proteins. Following DNase I treatment, DNA samples are subjected to gel electrophoresis, and the gels are stained to visualize all DNA bands in the gel. The staining patterns of DNA bands from each species are shown in the figure. The number of base pairs in small DNA fragments is shown at the left of the gel. Interpret the gel results in terms of chromatin organization and the spacing of nucleosomes in the chromatin of each species.

Verified step by step guidance

Step 1: Understand the role of DNase I in the experiment. DNase I is an enzyme that cuts DNA at regions not protected by histone proteins. Histone proteins are part of nucleosomes, which protect DNA from enzymatic cleavage. Therefore, DNase I treatment reveals the organization of chromatin and the spacing of nucleosomes.

Step 2: Analyze the gel electrophoresis results. Gel electrophoresis separates DNA fragments based on size, with smaller fragments migrating further down the gel. The stained bands represent DNA fragments of different sizes, which correspond to the regions of DNA that were not protected by histones and were cleaved by DNase I.

Step 3: Compare the banding patterns of the two species. Differences in the banding patterns indicate variations in chromatin organization and nucleosome spacing. For example, closely spaced bands suggest shorter nucleosome spacing, while widely spaced bands suggest longer nucleosome spacing.

Step 4: Interpret the chromatin organization for each species. If one species shows a pattern of evenly spaced bands, it suggests regular nucleosome spacing. If the other species shows irregular or fewer bands, it may indicate less organized chromatin or differences in nucleosome density.

Step 5: Relate the findings to the biological significance. Differences in chromatin organization and nucleosome spacing can affect gene expression, DNA accessibility, and overall genome regulation. Consider how these differences might reflect adaptations to the deep ocean environment for each species.

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Key Concepts

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

Chromatin Structure

Chromatin is a complex of DNA and proteins found in the nucleus of eukaryotic cells, primarily composed of histones. It exists in two forms: euchromatin, which is loosely packed and transcriptionally active, and heterochromatin, which is tightly packed and transcriptionally inactive. The organization of chromatin affects gene expression and DNA accessibility, making it crucial for understanding how DNA is protected or exposed during experiments like DNase I treatment.

Nucleosome Spacing

Nucleosomes are the fundamental units of chromatin, consisting of a segment of DNA wrapped around a core of histone proteins. The spacing between nucleosomes can vary, influencing the accessibility of DNA for transcription and other processes. In the context of DNase I treatment, the spacing determines which DNA fragments are protected from cleavage, leading to distinct patterns in gel electrophoresis that reflect the chromatin organization of each species.

Gel Electrophoresis

Gel electrophoresis is a laboratory technique used to separate DNA fragments based on their size. When an electric current is applied, negatively charged DNA moves through a gel matrix, with smaller fragments migrating faster than larger ones. The resulting banding pattern allows researchers to visualize and compare the sizes of DNA fragments, providing insights into chromatin structure and the effects of treatments like DNase I on different species' DNA.

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Textbook Question

The accompanying chromosome diagram represents a eukaryotic chromosome prepared with Giemsa stain. Indicate the heterochromatic and euchromatic regions of the chromosome, and label the chromosome's centromeric and telomeric regions.

Why are expressed genes not found in the telomeric region of chromosomes?

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Textbook Question

Do you expect the centromeric region to contain heterochromatin? Why or why not?

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Textbook Question

What term best describes the shape of this chromosome?

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Textbook Question

Histone protein H4 isolated from pea plants and cow thymus glands contains 102 amino acids in both cases. A total of 100 of the amino acids are identical between the two species. Give an evolutionary explanation for this strong amino acid sequence identity based on what you know about the functions of histones and nucleosomes.

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Textbook Question

In a study of Drosophila, two normally active genes, w⁺ (wild-type allele of the white-eye gene) and hsp26 (a heat-shock gene), were introduced (using a plasmid vector) into euchromatic and heterochromatic chromosomal regions, and the relative activity of each gene was assessed [Sun et al. (2002)]. An approximation of the resulting data is shown in the following table. Which characteristic or characteristics of heterochromatin are supported by the experimental data?Gene Activity (relative percentage) _Euchromatin Heterochromatinhsp26 100% 31%w⁺ 100% 8%

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Textbook Question

While much remains to be learned about the role of nucleosomes and chromatin structure and function, recent research indicates that in vivo chemical modification of histones is associated with changes in gene activity. One study determined that acetylation of H3 and H4 is associated with 21.1 percent and 13.8 percent increases in yeast gene activity, respectively, and that histones associated with yeast heterochromatin are hypomethylated relative to the genome average [Bernstein et al. (2000)]. Speculate on the significance of these findings in terms of nucleosome–DNA interactions and gene activity.

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Textbook Question

An article entitled 'Nucleosome Positioning at the Replication Fork' states: 'both the 'old' randomly segregated nucleosomes as well as the 'new' assembled histone octamers rapidly position themselves (within seconds) on the newly replicated DNA strands' [Lucchini et al. (2002)]. Given this statement, how would one compare the distribution of nucleosomes and DNA in newly replicated chromatin? How could one experimentally test the distribution of nucleosomes on newly replicated chromosomes?

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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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