CH 11 Mastering Genetics

The second order of chromatin packing occurs when nucleosomes coil together to form a fiber that is 300 nm in diameter.

FALSE The second order of chromatin packing occurs when nucleosomes coil together to form a solenoid fiber that is 30 nm in diameter.

Compare the characteristics of heterochromatin and euchromatin.

Heterochromatin: deeply stained; more condensed; replicated late in S phase; few genes present; associated with telomeres and centromeres. Euchromatin: weakly stained; less condensed; replicated early in S phase; more genes present; Correct Chromatin exists in different states of compaction and relaxation that regulate access to DNA by regulatory proteins. Heterochromatic regions of chromosomes are relatively inaccessible to transcriptional proteins either transiently (in the case of facultative heterochromatin) or nearly always (in the case of constitutive heterochromatin). In contrast, in euchromatic chromosome regions, transcriptional proteins and enzymes are more easily able to gain access to DNA.

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.

Most of the amino acid residues of H4 interact either with DNA or other histone proteins; therefore, most of the H4 amino acid sequence is under functional constraint.

What is the primary mechanism of chromosome compaction in E. coli?

Proteins organize the chromosome into loops that are supercoiled to form the nucleoid.

Nucleosome positioning along the DNA can influence where transcriptional regulatory proteins are able to bind DNA. If a nucleosome is bound to an enhancer sequence, it may outcompete a regulatory protein from binding the same sequence. Conversely, if an enhancer sequence is in the linker DNA where the nucleosome is absent, the regulatory protein does not have to compete with the nucleosome. The position of the nucleosome can alter the accessibility of a sequence of DNA to DNA binding proteins. Suppose that this region of DNA contained several enhancer sequences that bind highly conserved regulatory proteins to stimulate transcription of a gene in this region, and that binding is more efficient when the enhancer sequence is not associated with a nucleosome. Use this information to complete these sentences.

Since sea urchins have longer linker DNA segments than Drosophila melanogaster, when this region of DNA is moved to the sea urchin it is likely that these enhancer sequences will fall within linker DNA. With more enhancer sequences available in sea urchins to bind regulatory proteins that stimulate transcription, the same region of DNA will likely generate more RNA transcripts. Correct In sea urchins, fewer nucleosomes occupy the same region of DNA (362 vs. 512 in Drosophila melanogaster); therefore, there is less competition between nucleosomes and regulatory proteins for the same enhancer sequences. So, when the region of DNA is moved to the sea urchin genome, there would be more binding of regulatory proteins that stimulate transcription, and more RNA transcripts would be expected to be produced.

The beads-on-a-string form of chromatin is known as which of the following?

The 10-nm fiber

What makes up the protein component of a nucleosome?

Two tetramers of histone proteins The protein component of a nucleosome is composed of two tetramers of histone proteins. One tetramer is composed of two units each of histones H2A and H2B, and the other is composed of two units each of histones H3 and H4.

Chromatin structure is dynamic. In regions of highly condensed chromatin, such as the centromere, the boundary between heterochromatin and euchromatin is variable. Genes that are near this boundary region can be influenced by either type of chromatin in what is referred to as position effects. Recall the early Drosophila melanogaster experiments by Hermann Muller where the repositioning of the w + allele (normal activity of the w + allele produces red eye pigment) by translocation or inversion near this boundary of chromatin produced intermittent w + activity. In the heterozygous state (w +/w), a variegated eye is produced, with white and red patches.

When heterochromatin spreading does not reach the new location of the w + allele, the gene will be transcribed, producing red eye patches. Even though eye color phenotypic variegation exists within the eye, all cells have the same genotype. When heterochromatin spreading encompasses the new location of w + allele, the gene is not transcribed, producing white eye patches. All cells within the eye have the same genotype, so differences are attributed to epigenetic changes. White patches in the eye are the result of silencing the w + allele by spreading of heterochromatin. On the other hand, when the heterochromatin does not spread into the w + allele, gene expression is normal, resulting in red patches in the eye. This results in a variegated eye phenotype.

What is a chromosome territory?

a small region of the interphase nucleus that is occupied by a single chromosome or portion thereof

Which type of chromosome structure is characterized by the centromere position very near the end of the chromosome with the short arm composed of highly repetitive (satellite) DNA?

acrocentric

Which of the following are examples of heterochromatin?

centromeric DNA telomeric DNA Barr body repetitive DNA Repetitive DNA is often associated with heterochromatin. At the centromere, these heterochromatic repetitive sequences facilitate binding of spindle fibers during segregation of homologous chromosomes and sister chromatids. Telomeric repetitive sequences are involved in the maintenance of the chromosome's structural integrity. In other cases, entire chromosomes can be heterochromatic as occurs during X-inactivation in mammalian females where the inactive chromosome forms a highly condensed Barr body. The heterochromatin is the tightly packed form of DNA. These are classified into two types as constitutive and facultative heterochromatin. These types of heterochromatin play role in expression of genes. The characteristic feature of heterochromatin is existence of genetically inactive sequences, which are called satellite sequences. This, it usually contains repetitive sequences of DNA. The different examples of heterochromatin are centromere, telomere, repetitive DNA, and Barr body. The Barr body is present on, second inactivated X-chromosome of females.

Light G bands that appear along chromosomes contain

euchromatic regions

Dark G bands that appear along chromosomes contain

heterochromatic regions

What process is responsible for position effect variegation?

inactivation of a gene due to its incorporation in a heterochromatic region of the chromosome

Histone Protein

is a small, basic polypeptide that is positively charged and bind tightly to negatively charged DNA

G band

is darkly stained region of compacted chromosome that have been stained with Giemsa

CEN sequence

is the DNA sequence located at centromere

Nucleosome core particle

is the complex containing two H2A/H2B dimers and two H3/H4 dimers, around which DNA is wrapped

Nucleosome

is the nucleosome core particle wrapped with core DNA.

Nucleoid

is the region of a bacterial cell that contains the bacterial chromosome.

Heterochromatin

refers to more condensed regions of chromosomes, which contain DNA that is relatively inaccessible to transcription factors and RNA polymerase.

Chromosome territory

refers to the region of the nucleus occupied by a particular chromosome

Euchromatin

refers to the relatively less condensed regions of chromosomes, which contain DNA that is readily accessible to transcription factors and RNA polymerase.

What are the two principal mechanisms of bacterial DNA compaction?

supercoiling, folding into loops

What is the primary function of histone H1?

to stabilize the 30-nm solenoid

Assume that the DNA associated with a nucleosome core particle plus the DNA in the linker adds up to 200 bp. Approximately how many base pairs are found in the linker region?

-54 Approximately 146 bp of DNA is wrapped around the nucleosome core particle. Therefore 200 bp - 146 bp = 54 bp of linker DNA. This is the amount of DNA present in the "string."

The human genome contains 3.42×109 base pairs. The length of linker DNA in mammals is 50 base pairs. Approximately how many nucleosomes are required to organize the 10-nm-fiber structure of the genome?

1.7×10^7 Each nucleosome is wound by about 146 bp of DNA. This nucleosome consists of a histone core consisitng of four different histone proteins such as H2A, H2B, H3 and H4. Hence total stretch of DNA between 2 nucleosomes would be total DNA wound on a nucleosome + linker DNA which would be 146 + 50 = 196bp. Each such 196 bp would have a single nucleosome, hence the total number of nucleosomes would be 3.42/196 x 10^9 bp = 1.7*10^7

Referring to the image, there appears to be a span of 13 "beads" present. Ignoring the DNA before the first bead and after the 13th bead, how much DNA is present in the photo?

2546 Since there are 13 nucleosome core particles connected by 12 linker regions: (13 x 146) + (12 x 54) = 2546 bp

The length of linker DNA segments varies somewhat among organisms. The length of the linker DNA in sea urchin is 110 base pairs. Suppose it were possible to move the entire region of DNA (92,672 base pairs long) from Drosophila melanogaster into the genome of a sea urchin. Approximately how many nucleosomes would be required to organize this region into the 10nm fiber structure?

362 nucleosomes Each nucleosome repeat is composed of the DNA (146 bp) wrapped around the core nucleosome particle plus the linker DNA (110 bp in this case). Therefore each repeat accounts for 256 (146 + 110) base pairs of DNA. Since the region is 92,672 bp long, then approximately 362 nucleosomes (92,672/256) would be required to organize the region into the 10nm fiber structure.

Which of the following best describes the overall composition (by mass) of eukaryotic chromatin?

50% DNA, 50% protein

A large gene-containing region of DNA in the fruit fly Drosophila melanogaster‎ is 92,672 base pairs long. The length of linker DNA in Drosophila‎ is 35 base pairs. Approximately how many nucleosomes are required to organize this region of DNA into the 10nm fiber structure?

512 nucleosomes Each nucleosome repeat is composed of the DNA (146 bp) wrapped around the core nucleosome particle plus the linker DNA (35 bp in this case). Therefore each repeat accounts for 181 (146 + 35) base pairs of DNA. Since the region is 92,672 bp long, then approximately 512 nucleosomes (92,672/181) would be required to organize the region into the 10nm fiber structure.

How many total polypeptide chains would be present in a single nucleosome core particle?

8 Two molecules each of four histones - H2A, H2B, H3, and H4 - join together to form an octameric (eight-member) nucleosome core particle.

Based on discussions of specific proteins and structures in bacteria, archaea, and eukaryotes in this and other chapters, briefly describe your view of the evolutionary relationship between the three domains of life.

Archaea share characteristics with bacteria and eukarya but are more like eukarya in terms of transcriptional machinery, translational machinery, and chromosomal packaging. This is consistent with Carl Woese's proposed evolutionary tree, in which archaea share a more recent common ancestor with eukarya than either group does with bacteria.

What function do histone proteins perform in archaeal chromosomes? b) How is this function accomplished? c) What function is performed by histones in eukaryotes that is apparently not performed by archaeal histones?

Archaeal histones are likely to be involved in compacting chromosomal DNA. b) Archaeal histones form nucleosomes. c) Archaeal histones do not appear to assemble DNA into transcriptionally inactive heterochromatin.

Which of the following statements best describes bacterial genome organization?

Bacterial genomes may consist of a single, circular chromosome or multiple chromosomes that may be linear or circular.

What is the first order of chromatin packing?

Coiling around nucleosomes The first order of chromatin packing occurs when DNA coils around nucleosomes, whereby DNA is reduced to about one‑third its original length

Which type of DNA produces a light band when treated with Giemsa stain?

Euchromatin Euchromatin contains actively transcribed genes. Since it is not highly condensed, it does not bind significant amounts of Giemsa stain and appears as a light band.