Chapter 10 Questions

What are the general features of the organization of sites along a bacterial chromosome?

1. A bacterial chromosome is usually circular and is usually of one type. 2. It typically contains a few million base pairs of DNA. 3. Several thousand genes are found interspersed along the chromosome; short intergenic regions are found between genes. 4. One origin of replication is present. 5. Repetitive sequences are often present, but they are not as abundant as those found in eukaryotic species.

Outline the ways that a eukaryotic chromosome may be compacted.

1. The DNA is wrapped around histones to form nucleosomes. 2. The nucleosomes are brought closer together to form a 30-nm fiber. 3. The 30-nm fiber is anchored to protein filaments to form radial loop domains. 4. In a metaphase chromosome, the protein filaments form a more compact scaffold, which results in a chromosome that is much shorter.

What is the diameter of a nucleosome?

11 nm

Assume linker DNA averages 54 bp in length. How many molecules of H2A would you expect to find in a SNA sample that is 46,000 bp in length?

200 bp for each nucleosome and linker region (146 + 54) 46,000/200 = 230 nucleosomes 2 H2A molecules per nucleosome = 460 H2A molecules

With regard to the 30-nm fiber, the solenoid model suggests a ________ structure and the zigzag models suggests a more _________ pattern of nucleosomes.

helical; irregular

Mechanisms that make the bacterial chromosome more compact include the formation of ______ ____________, DNA _____________, and ______ __________.

loop domains; supercoiling; crossing over

tRNA genes are an example of a ____________ repetitive sequence.

moderately

DNA gyrase promotes __________ supercoiling, relaxes __________ supercoils, and cuts ____ _______ as part of it's function.

negative; positive; DNA strands

The compaction leading to a metaphase chromosome involves the formation of ___________ and a ______ fiber, as well as __________ and further compaction of the ______ ______.

nucleosomes; 30-nm; anchoring; radial loops

A bacterial chromosome is about 4 million bp in length and is organized into about 100 loops that are about 40,000 bp in length. If it were stretched out linearly, how long would one loop be? If a bacterial chromosomal loop is circular, what would be its diameter?

one loop - 40,000 base pairs, 1 base pair = .34 nm 40,000 x .34 = 13.6 micrometers Diameter = 4.3 micrometers

In Noll's experiment to test the beads-on-a-string model, exposure of nuclei to a low concentration of DNase I resulted in:

several bands of DNA in multiples of 200

Suppose a bacterial DNA molecule is given a left-handed twist. How does this affect the structure and function of the DNA?

A left handed twist is negative supercoiling, which makes the chromosomes more compact. It also promotes DNA functions that involve stand separation, including gene transcription and DNA replication.

What is a chromosome territory?

A region in a cell nucleus where a single chromosome is located.

In regards to the action of DNA gyrase, describe the step that requires the use of ATP.

ATP is needed so that the DNA held in the upper jaws can pass through the break in the DNA and move to the region of the lower jaws

What are the components of a single nucleosome?

About 146 bp of DNA and eight histone proteins

Would you expect to find active genes in heterochromatic or euchromatic regions?

Active genes are found in more loosely packed euchromatic regions.

Describe what happens to cohesion from the beginning of prophase to anaphase.

At the beginning of prophase, cohesion lines the region between sister chromatids. It is first removed from the arms of the sister chromatids, but remains in the centromeric region. At anaphase, the cohesion at the centromeres is degraded, which allows the sister chromatids to separate.

Which of the following terms should not be used to describe a Barr body? A. Chromatin B. Euchromatin C. Heterochromatin D. Chromosome E. Genome

B and E. A barr body is composed of a type of highly compacted chromatin called heterochromatin. Euchromatin is not so compacted. A Barr body is not composed of euchromatin. A Barr body is one chromosome, the X chromosome. The term genome refers to all the types of chromosomes that make up the genetic composition of an individual.

Compare the structure and cell localization of chromosomes during interphase and M phase.

During interphase, the chromosomes are found within the cell nucleus. They are less tightly packed and are transcriptionally active. Segments of chromosomes are anchored to the nuclear matrix. During M phase, the chromosomes become highly condensed, and the nuclear membrane is fragmented into vesicles. The chromosomal DNA remains anchored to a scaffold, formed from the nuclear matrix. The chromosomes eventually become attached to the spindle apparatus via microtubules that attach to the kinetochore, which is attached to the centromere.

Beginning with the G1 phase of the cell cycle, describe the level of compaction of the eukaryotic chromosome. How does the level of compaction change as the cell progresses through the cell cycle? Why is it necessary to further compact the chromatin during mitosis?

During interphase, the euchromatin is found primarily as a 30-nm fiber in a radial loop configuration. Most interphase chromosomes also have some heterochromatic regions where the radial loops are more highly compacted. During M phase, each chromosome becomes entirely heterochromatic, which is needed for the proper sorting of the chromosomes during nuclear division.

What are some differences between the types of sequences found in eukaryotic chromosomes versus bacterial chromosomes?

Eukaryotes have centromeres and telomeres, which bacterial chromosomes do not. Also, eukaryotes typically have much more repetitive sequences.

What is the function of the nuclear matrix?

Helps to organize and compact the chromosomes within the cell nucleus and also aids in their condensation during cell division.

Describe the characteristics of highly repetitive DNA.

It is a DNA sequence repeated many times, from tens of thousands to millions of times throughout the genome. It can be interspersed in the genome or found in clusters in a tandem array, in which a short nucleotide sequence is repeated many times in a row.

Why is strand separation beneficial?

It is needed for certain processes such as DNA replication and RNA transcription

Describe two key reasons why eukaryotic genomes vary greatly in their sizes.

More complex eukaryotes, such as mammals, have more genes than simpler eukaryotes, such as yeast. Also the amount of repetitive DNA can vary greatly among eukaryotic species.

What are two reasons for the wide variation in genome sizes among eukaryotic species?

One reason for variation in genome size is that the number of genes among different eukaryotes varies. A second reason is that the amount of repetitive sequences varies.

Negative supercoiling may enhance activities like transcription and DNA replication because it:

Promotes DNA strand separation.

What holds the loop domains in place?

Protein holds bacterial chromosome loops in place

What is an SMC protein? Describe two examples.

SMC stands for structural maintenance of chromosomes. SMC proteins use energy from ATP to catalyze changes in chromosome structure. Together with topoisomerase, SMC proteins have been shown to promote major changes in DNA structure. Two examples of SMC proteins are condensin/cohesin, which play different role in metaphase chromosome structure. Condensin promotes the proper compaction of metaphase chromosomes, while the function of cohesin is to promote the binding between sister chromatids.

Describe the distinguishing features of the solenoid model and zigzag model.

Solenoid depicts nucleosomes in a repeating spiral arrangement, whereas the zigzag model depicts a more irregular and dynamic arrangement of nucleosomes.

Explain why a chromosome without a centromere is not transmitted very efficiently from mother to daughter cell.

The centromere is the attachment site for the kinetochore, which attaches to the spindle. If a chromosome is not attached to the spindle, it is free to float around within the cell and may not be near a pole when the nuclear membrane reforms during telophase. If a chromosome is left outside the nucleus, it is degraded during interphase.

Describe what structural changes convert a region that is 300 nm in diameter to one that is 700 nm in diameter.

The radial loop domains become more tightly packed

What are the roles of the core histone proteins compared with the old of histone H1 in the compaction of eukaryotic DNA?

The role is to form nucleosomes. Histone H1 binds to the linker region and DNA wraps 1.65 times around the core histones. It may play a role in compacting the DNA into a 30-nm fiber

Coumarins and quinolone are two classes of drugs that inhibit bacterial growth by directly inhibiting DNA gyrase. Discuss two reasons why inhibiting DNA gyrate also inhibits bacterial growth.

These drugs diminish the amount of negative supercoiling in DNA, which is necessary to compact the chromosomal DNA and aids in strand separation. Bacteria might not be able to survive and/or transmit their chromosomes to daughter cells if their DNA were not compacted properly. Bacteria would also have difficulty replicating if their strands could not separate.

How is a bacterium that contains two nucleoids similar to a diploid eukaryotic cell, and how is it different?

They are similar because they both have two copies of each gene. The bacterium is different with regard to alleles. Where a eukaryotic cell can have tow different alleles for the same gene, a bacterium with two nucleoids has two identical chromosomes.

What biochemical properties would you expect from bacterial histone-like proteins?

They have the properties expected for proteins involved in DNA folding. They are all small proteins found in relative abundance within the bacterial cell. In some cases, the histone-like proteins are biochemically similar to eukaryotic histones. They tend to be basic (positively charged) and bind to DNA in a non-sequence-dependent fashion. However, other proteins appear to bind to bacterial DNA at specific sites in order to promote DNA bending.

A bacterial chromosome typically contains a few __________ genes, ____ origin of replication, and some ___________ sequences.

thousand; one; repetitive