How do we know that viral and bacterial chromosomes most often consist of circular DNA molecules devoid of protein?

What is the experimental basis for concluding that puffs in polytene chromosomes and loops in lampbrush chromosomes are areas of intense transcription of RNA?

In the discussion, 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?

In the discussion, 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 do we know that satellite DNA consists of repetitive sequences and has been derived from regions of the centromere?

Write a short essay that contrasts the major differences between the organization of DNA in viruses and bacteria versus eukaryotes.

Contrast the size of the single chromosome in bacteriophage and T2 with that of E. coli. How does this relate to the relative size and complexity of phages and bacteria?

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

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

During what genetic process are lampbrush chromosomes present in vertebrates?

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

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

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

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

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

Contrast the various categories of repetitive DNA.

Define satellite DNA. Describe where it is found in the genome of eukaryotes and its role as part of chromosomes.

Contrast the structure of SINE and LINE DNA sequences. Why are LINEs referred to as retrotransposons?

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.

Assume that a viral DNA molecule is a 50-µm-long circular strand with a uniform 20-Å diameter. If this molecule is contained in a viral head that is a 0.08-µm-diameter sphere, will the DNA molecule fit into the viral head, assuming complete flexibility of the molecule? Justify your answer mathematically.

How many base pairs are in a molecule of phage T2 DNA 52-µm long?

The human genome contains approximately 10⁶ copies of an Alu sequence, one of the best-studied classes of short interspersed elements (SINEs), per haploid genome. Individual Alu units share a 282-nucleotide consensus sequence followed by a 3'-adenine-rich tail region [Schmid (1998)]. Given that there are approximately 3 x 10⁹ base pairs per human haploid genome, about how many base pairs are spaced between each Alu sequence?

The following is a diagram of the general structure of the bacteriophage chromosome. Speculate on the mechanism by which it forms a closed ring upon infection of the host cell.