chapter 10

chromosomal sequences facilitate four important processes:

(1) the synthesis of RNA and cellular proteins, (2) the replication of chromosomes, (3) the proper segregation of chromosomes, and (4) the compaction of chromosomes so they can fit within living cells

Nucleosomes Become Closely Associated to Form a

30-nm Fiber

Centromeres

are regions that play a role in the proper segregation of chromosomes during mitosis and meiosis a segment of a eukaryotic chromosome that provides an attachment site for the kinetochore.

DNA gyrase promotes negative supercoiling. relaxes positive supercoils. cuts DNA strands as part of its function. does all of the above.

does all of the above.

Each octamer contains

eight histone subunits: two copies each of four different histone proteins The octamer of histones contains two molecules each of four different histone proteins: H2A, H2B, H3, and H4. These are called the core histone proteins.

heterochromatin

highly compacted regions of chromosomes, where DNA is usually transcriptionally inactive.

The role of cohesin is to make chromosomes more compact. allow for the replication of chromosomes. hold sister chromatids together. promote the separation of sister chromatids.

hold sister chromatids together.

A chromosome territory is a region along a chromosome where many genes are clustered. along a chromosome where the nucleosomes are close together. in a cell nucleus where a single chromosome is located. in a cell nucleus where multiple chromosomes are located.

in a cell nucleus where a single chromosome is located.

euchromatin

less compacted regions of chromosomes, where DNA may be transcriptionally active. usually capable of gene transcription--not as tightly wound so can "unzip" as heterochromatin cannot

radial loop domains

loops, often 25,000 to 200,000 bp in size, into which DNA is organized in the nuclear matrix and which are anchored to it at matrix-attachment regions.

internal nuclear matrix

a network of irregular protein filaments with many other proteins bound to them that is connected to the nuclear lamina and fills the interior of the nucleus.

introns

a noncoding intervening sequence found between exons. Introns are spliced out of the pre-mRNA prior to translation. noncoding intervening sequences

chromosome territory

a region in the cell nucleus occupied by a chromosome. The chromosome territories are nonoverlapping.

exons

a segment of RNA that is contained within the RNA after splicing has removed the introns. In mRNA, the coding sequence of a polypeptide is contained within the exons are regions of an RNA molecule that remain after splicing has removed the introns

matrix-attachment regions (MARs)

a site in the chromosomal DNA that is anchored to the nuclear matrix or scaffold.

origin of replication

a site on a chromosome that functions as an initiation site for the assembly of several proteins that begin the process of DNA replication.

Would you expect to find active genes in regions of heterochromatin or euchromatin?

active genes are found in the more loosely packed regions of euchromatin

A bacterial chromosome typically contains a few thousand genes. one origin of replication. some repetitive sequences. all of the above.

all of the above

the nuclear matrix has 2 parts

nuclear lamina & internal nuclear matrix

+ review questions on sakai study guide

okay

definition of a gene, know drawings, and charts from before western blots etc

okay

Negative supercoiling may enhance activities like transcription and DNA replication because it allows the binding of proteins to the major groove. promotes DNA strand separation. makes the DNA more compact. causes all of the above.

promotes DNA strand separation.

constitutive heterochromatin

regions of chromosomes that are always heterochromatic and are permanently transcriptionally inactive.

repetitive sequences

short DNA sequences that occur many times within a species' genome.

telomeres

specialized repeated sequences found at the ends of linear eukaryotic chromosomes.

Telomeres serve several important functions in the replication and stability of the chromosome such as

telomeres prevent chromosomal rearrangements such as translocations. they prevent chromosome shortening in two ways. First, the telomeres protect chromosomes from digestion via enzymes called exonucleases that recognize the ends of DNA. Second, an unusual form of DNA replication occurs at the telomere to ensure that eukaryotic chromosomes do not become shortened with each round of DNA replication

DNA supercoiling

the formation of additional coils in DNA due to twisting forces.

Chromosomes

the structures within living cells that contain the genetic material. Genes are physically located within the structure of chromosomes. Biochemically, a chromosome contains a very long segment of DNA, which is the genetic material, and proteins, which are bound to the DNA and provide it with an organized structure.

The chromosomes of eukaryotes typically contain a few hundred to several thousand different genes. multiple origins of replication. a centromere. telomeres at their ends. all of the above.

all of the above.

genome

all of the chromosomes and DNA sequences that an organism or species can possess.

nuclear lamina

A netlike array of protein filaments lining the inner surface of the nuclear envelope; it helps maintain the shape of the nucleus. quizlet^ my book: a collection of filaments that line the inner nuclear membrane.

The compaction leading to a metaphase chromosome involves which of the following? The formation of nucleosomes The formation of the 30-nm fiber Anchoring and further compaction of the radial loops All of the above

All of the above

The plasmids we will use in this class typically have three important elements

An origin of replication. A selectable marker gene (e.g. resistance to ampicillin) A cloning site (a place to insert foreign DNAs)

C1. What is a bacterial nucleoid? With regard to cellular membranes, what is the difference between a bacterial nucleoid and a eukaryotic nucleus?

C1. The bacterial nucleoid is a region in a bacterial cell that contains a compacted circular chromosome. Unlike the eukaryotic nucleus, a nucleoid is not surrounded by a membrane.

C10. What is the function of a centromere? At what stage of the cell cycle would you expect the centromere to be the most important?

C10. Centromeres are structures found in eukaryotic chromosomes that provide an attachment site for kinetochore proteins, allowing the chromosomes to be sorted (i.e., segregated) during mitosis and meiosis. They are most important during M phase.

C12. Describe the structures of a nucleosome and a 30-nm fiber.

C12. A nucleosome is composed of double-stranded DNA wrapped 1.65 times around an octamer of histones. In the 30 nm fiber, histone H1 helps to compact the nucleosomes. The zigzag model is a three- dimensional model that describes how this compaction occurs. It looks like a somewhat random (zigzag) pattern of the nucleosomes within the 30 nm fiber. Another model is the solenoid model, which has a more regular, spiral arrangement of nucleosomes.

C13. 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?

C13. During interphase (i.e., G1, S, and G2), 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.

C15. Compare heterochromatin and euchromatin. What are the differences between them?

C15. Heterochromatin is more tightly packed than euchromatin. This is due to a greater compaction of the radial loop domains. Functionally, euchromatin can be transcribed into RNA, while heterochromatin is inactive. Heterochromatin is most abundant in the centromeric regions of the chromosomes and in the telomeric regions.

C20. What are the roles of the core histone proteins and of histone H1 in the compaction of eukaryotic DNA?

C20. The role of the core histones is to form the nucleosomes. In a nucleosome, the DNA is wrapped 1.65 times around the core histones. Histone H1 binds to the linker region. It may play a role in compacting the DNA into a 30 nm fiber.

C5. Coumarins and quinolones are two classes of drugs that inhibit bacterial growth by directly inhibiting DNA gyrase. Discuss two reasons why inhibiting DNA gyrase also inhibits bacterial growth.

C5. These drugs would diminish the amount of negative supercoiling in DNA. Negative supercoiling is needed to compact the chromosomal DNA, and it also aids in strand separation. Bacteria might not be able to survive and/or transmit their chromosomes to daughter cells if their DNA was not compacted properly. Also, because negative supercoiling aids in strand separation, these drugs would make it more difficult for the DNA strands to separate. Therefore, the bacteria would have a difficult time transcribing their genes and replicating their DNA, because both processes require strand separation. As discussed in Chapter 11, DNA replication is needed to make new copies of the genetic material to transmit from mother to daughter cells. If DNA replication was inhibited, the bacteria could not grow and divide into new daughter cells. As discussed in Chapter 12, gene transcription is necessary for bacterial cells to make proteins. If gene transcription was inhibited, the bacteria could not make many proteins that are necessary for survival.

C8. How are two topoisomers different from each other? How are they the same?

C8. Topoisomers differ with regard to the number of supercoils they contain. They are identical with regard to the number of base pairs in the double helix.

C9. On rare occasions, a chromosome can suffer a small deletion that removes the centromere. When this occurs, the chromosome usually is not found within subsequent daughter cells. Explain why a chromosome without a centromere is not transmitted very efficiently from mother to daughter cells. (Note: If a chromosome is located outside the nucleus after telophase, it is degraded.)

C9. 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 it may not be near a pole when the nuclear membrane re-forms during telophase. If a chromosome is left outside of the nucleus, it is degraded during interphase. That is why the chromosome without a centromere may not be found in daughter cells.

tandem repeats

Constitutive heterochromatin usually contains highly repetitive DNA sequences

E8. Consider how histone proteins bind to DNA and then explain why a high salt concentration can remove histones from DNA (as shown in Figure 10.18b). pg 250

E8. Histones are positively charged and DNA is negatively charged. Thus, they bind to each other by ionic interactions. Salt is composed of positively charged ions and negatively charged ions. For example, when dissolved in water, NaCl separates into individual ions, Na+ and Cl-. When chromatin is exposed to a salt such as NaCl, the positively charged Na+ ions can bind to the DNA and the negatively charged Cl- can bind to the histones. This would separate the histones from the DNA.

How do twisting forces affect DNA structure?

Figure 10.4 illustrates four possibilities. In Figure 10.4a, a double-stranded DNA molecule with five complete turns is anchored between two plates. In this hypothetical example, the ends of the DNA molecule cannot rotate freely. Both underwinding and overwinding of the DNA double helix can cause supercoiling of the helix. Because B DNA is a right-handed helix, underwinding is a left-handed twisting motion, and overwinding is a right-handed twist. Along the left side of Figure 10.4, one of the plates has been given a left-handed turn that tends to unwind the helix. As the helix absorbs this force, two things can happen. The underwinding motion can cause fewer turns (Figure 10.4b) or it can cause a negative supercoil to form

How does bacterial DNA become supercoiled?

In 1976, Martin Gellert and colleagues discovered the enzyme DNA gyrase,Page 232also known as topoisomerase II. This enzyme, which contains four subunits (two A and two B subunits), introduces negative supercoils (or relaxes positive supercoils) using energy from ATP

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

Negative supercoiling makes the bacterial chromosome more compact, so it fits within the cell. Alternatively, a left-handed twist promotes strand separation and thereby enhances DNA functions such as replication and transcription.

Chromosomes Are Further Compacted by Anchoring of the 30-nm Fiber into ___ ___ ___ along the ___ ___

Radial Loop Domains Along the Nuclear Matrix

intergenic region

The nontranscribed regions of DNA in a chromosome, located between adjacent gene

Describe the differences between unique and highly repetitive sequences in DNA.

Unique DNA, as mentioned, occurs once per haploid genome. Many genes in a genome are unique. By comparison, a highly repetitive sequence, as its name suggests, is a DNA sequence that is repeated many times, from tens of thousands to millions of times throughout a genome. It can be interspersed in the genome or found clustered in a tandem array, in which a short nucleotide sequence is repeated many times in a row.

condensin

a multiprotein complex that plays a role in the condensation of interphase chromosomes to become metaphase chromosomes.

30-nm fiber

a compact structure of associated nucleosome units that is 30 nm in diameter.

nucleoid

a darkly staining region that contains the genetic material of mitochondria, chloroplasts, or bacteria.

nucleosome

a double-stranded segment of DNA wrapped around an octamer of histone proteins

histone proteins

a group of proteins involved in forming the nucleosome structure of eukaryotic chromatin.

Thus far, we have examined two mechanisms that compact eukaryotic DNA: the wrapping of DNA within nucleosomes and the arrangement of nucleosomes to form a 30-nm fiber. Taken together, these two processes shorten the DNA nearly 50-fold. A third level of compaction involves interactions between the 30-nm fibers and a filamentous network of proteins in the nucleus called the nuclear matrix nuclear matrix (nuclear scaffold):

a group of proteins that anchor the loops found in eukaryotic chromosomes.

kinetochore

a group of proteins that attach to the centromere during meiosis and mitosis.

nucleus

a membrane-bound organelle in eukaryotic cells where the linear sets of chromosomes are found.

cohesin

a multiprotein complex that facilitates the alignment of sister chromatids.

With regard to the 30-nm fiber, a key difference between the solenoid and zigzag models is the solenoid model suggests a helical structure. the zigzag model suggests a more irregular pattern of nucleosomes. the zigzag model does not include nucleosomes. both a and b are correct.

both a and b are correct.

Mechanisms that make the bacterial chromosome more compact include the formation of micro- and macrodomains. DNA supercoiling. crossing over. both a and b.

both a and b.

Facultative heterochromatin

chromatin that can occasionally interconvert between heterochromatin and euchromatin

The chromosomal DNA in living bacteria is negatively supercoiled. Negative supercoiling has several important consequences, such as

the supercoiling of chromosomal DNA makes it much more compact. Therefore, supercoiling helps to greatly decrease the size of the bacterial chromosome. In addition, negative supercoiling also affects DNA function. To understand how it does so, remember that negative supercoiling is due to an underwinding force on the DNA. Therefore, negative supercoiling creates tension on the DNA strands that may be released by their separation (Figure 10.5). Although most of the chromosomal DNA is negatively supercoiled and compact, the force of negative supercoiling may promote DNA strand separation in small regions. This enhances genetic activities such as replication and transcription that require the DNA strands to be separated.

the function of cohesin is

to promote the binding (i.e., cohesion) between sister chromatids. After S phase and until the middle of prophase, sister chromatids remain attached to each other along their length. As shown in Figure 10.21, this attachment is promoted by cohesin, which is found along the entire length of each chromatid. In certain species, such as mammals, cohesins located along the chromosome arms are released during prophase, which allows the arms to separate. However, some cohesins remain attached, primarily to the centromeric regions, leaving the centromeric region as the main linkage before anaphase. At anaphase, the cohesins bound to the centromere are rapidly degraded by a protease aptly named separase, thereby allowing sister chromatid separation.

true or false Heterochromatin is most abundant in the centromeric regions of the chromosome and, to a lesser extent, in the telomeric regions

true