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Table of contents

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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

7. DNA and Chromosome Structure

Eukaryotic Chromosome Structure

7. DNA and Chromosome Structure

Eukaryotic Chromosome Structure

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Supercoiling

Kylia Goodner

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Okay. So now let's talk about an interesting structure called supercoiling. Supercoiling is a tight, tight condensation or structure of chromosomes. It's like over tight, almost. So, if you have a rope, imagine you have 2 ropes. Right? And they are a double helix, so you just wrap one rope around the other, and you keep twisting it. Right? Keep twisting it. Eventually, it bunches up in the middle. You can do this with a rubber band or a hair scrunchie. You just keep twisting it. Right? Eventually, it twists up on itself because it has so much tension in those twists that it causes that structure to become something that it's not supposed to be, and that's called supercoiling.

Now, positive supercoiling causes DNA that is over rotated, and negative supercoiling is DNA that is under rotated. And essentially, both are bad. Right? There's a class of enzymes in the cell called topoisomerases, and these are enzymes that fix these altered rotations in DNA. So, type 1 relaxes the nu

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Related Practice

Textbook Question

Give descriptions for the following terms: chromosome territory

Textbook Question

Give descriptions for the following terms: nucleosome

Textbook Question

Give descriptions for the following terms: heterochromatin

Textbook Question

Give descriptions for the following terms: euchromatin

Textbook Question

Give descriptions for the following terms: G bands

Textbook Question

Give descriptions for the following terms: scaffold proteins

Textbook Question

Give descriptions for the following terms: nucleosome core particle

Textbook Question

In this chapter, we focused on how DNA is organized at the chromosomal level. Along the way, we found many opportunities to consider the methods and reasoning by which much of this information was acquired. From the explanations given in the chapter, what answers would you propose to the following fundamental questions: How did we learn that eukaryotic chromatin exists in the form of repeating nucleosomes, each consisting of about 200 base pairs and an octamer of histones?

Textbook Question

The human genome contains 2.9×10⁹ base pairs. Approximately how many nucleosomes are required to organize the 10-nm–fiber structure of the human genome? Show the calculation you use to determine the answer.

Textbook Question

In eukaryotic DNA,

how does the role of H1 differ from the role of H3 in chromatin formation?

Textbook Question

In eukaryotic DNA,

along a 6000-bp segment of DNA, approximately how many molecules of each kind of histone protein do you expect to find? Explain your answer.

Textbook Question

In eukaryotic DNA,

where are you most likely to find histone protein H1?

Textbook Question

In eukaryotic DNA,

where are you most likely to find histone protein H4?

Textbook Question

Describe the importance of light and dark G bands that appear along chromosomes.

Textbook Question

Describe the structure of giant polytene chromosomes and how they arise.

Textbook Question

What genetic process is occurring in a puff of a polytene chromosome? How do we know this experimentally?

Textbook Question

During what genetic process are lampbrush chromosomes present in vertebrates?

Textbook Question

Why might we predict that the organization of eukaryotic genetic material will be more complex than that of viruses or bacteria?

Textbook Question

Describe the sequence of research findings that led to the development of the model of chromatin structure.

Textbook Question

Describe the molecular composition and arrangement of the components in the nucleosome.

Textbook Question

Describe the transitions that occur as nucleosomes are coiled and folded, ultimately forming a chromatid.

Textbook Question

Provide a comprehensive definition of heterochromatin and list as many examples as you can.

Textbook Question

Mammals contain a diploid genome consisting of at least 10⁹ bp. If this amount of DNA is present as chromatin fibers, where each group of 200 bp of DNA is combined with 9 histones into a nucleosome and each group of 6 nucleosomes is combined into a solenoid, achieving a final packing ratio of 50, determine (a) the total number of nucleosomes in all fibers, (b) the total number of histone molecules combined with DNA in the diploid genome, and (c) the combined length of all fibers.

Textbook Question

Examples of histone modifications are acetylation (by histone acetyltransferase, or HAT), which is often linked to gene activation, and deacetylation (by histone deacetylases, or HDACs), which often leads to gene silencing typical of heterochromatin. Such heterochromatinization is initiated from a nucleation site and spreads bidirectionally until encountering boundaries that delimit the silenced areas. Recall from earlier in the text (see Chapter 4) the brief discussion of position effect, where repositioning of the w⁺ allele in Drosophila by translocation or inversion near heterochromatin produces intermittent w⁺ activity. In the heterozygous state (w⁺/w) a variegated eye is produced, with white and red patches. How might one explain position-effect variegation in terms of histone acetylation and/or deacetylation?

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.

Are you more likely to find the DNA sequence encoding the digestive enzyme amylase in a heterochromatic, euchromatic, centromeric, or telomeric region? Explain your reasoning. <>

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? <>

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.

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

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.

What term best describes the shape of this chromosome? <>

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.

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.[A diagram appears here]

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 Heterochromatin hsp26 100% 31% w⁺ 100% 8%

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.

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?

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.

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.

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. Examine the gel results and speculate why longer DNase I treatment produces different results.

Textbook Question

Spermatogenesis in mammals results in sperm that have a nucleus that is 40 times smaller than an average somatic cell. Thus, the sperm haploid genome must be packaged very tightly, yet in a way that is reversible after fertilization. This sperm-specific DNA compaction is due to a nucleosome-to-nucleoprotamine transition, where the histone-based nucleosomes are removed and replaced with arginine-rich protamine proteins that facilitate a tighter packaging of DNA. In 2013 Montellier et al. showed that replacement of the H2B protein in the nucleosomes with a testis-specific variant of H2B called TSH2B is a critical step prior to the nucleosome-to-nucleoprotamine transition. Mice lacking TSH2B retain H2B and their sperm arrest late in spermatogenesis with reduced DNA compaction. Based on these findings, would you expect that TSH2B-containing nucleosomes are more or less stable than H2B-containing nucleosomes? Explain your reasoning.

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?

Textbook Question

Human chromosome 5 and the corresponding chromosomes from chimpanzee, gorilla, and orangutan are shown here. Describe any structural differences you see in the other primate chromosomes in relation to the human chromosome.

Textbook Question

Because of its rapid turnaround time, fluorescent in situ hybridization (FISH) is commonly used in hospitals and laboratories as an aneuploid screen of cells retrieved from amniocentesis and chorionic villus sampling (CVS). Chromosomes 13, 18, 21, X, and Y (see Chapter 8) are typically screened for aneuploidy in this way. Explain how FISH might be accomplished using amniotic or CVS samples and why the above chromosomes have been chosen for screening.

Multiple Choice

Which of the following terms is used to describe 'open chromatin' which is loosely packaged DNA?

Multiple Choice

Histone proteins are responsible for what?

Multiple Choice

Which of the following is the correct order of chromosomal packaging levels?

Multiple Choice

What is the name of the enzyme that removes supercoils in DNA?

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