Study Guide Lec 13

Question 1

How does supercoiling arise? What is the difference between positive and negative supercoiling?

Answer 1

Supercoiling arises from topoisomerases catalyzing the overwinding (positive supercoiling) or underwinding (negative supercoiling) of the DNA double helix. Supercoiling may occur:
(1) when the DNA molecule does not have free ends, as in circular DNA molecules, or
(2) when the ends of the DNA molecule are bound to proteins that prevent them from rotating
about each other, as in linear eukaryotic chromosomes.

Question 2

What functions does supercoiling serve for the cell?

Answer 2

Supercoiling compacts the DNA.

Question 3

Describe the composition and structure of the nucleosome.

Answer 3

The nucleosome core particle contains two molecules each of histones H2A, H2B, H3, and H4, which form a protein core with 145–147 bp of DNA wound around the core. Chromatosomes contain the nucleosome core with a molecule of histone H1.

Question 4

What function does negative supercoiling serve for the cell?

Answer 4

Negative supercoiling helps to unwind the DNA duplex for replication and transcription.

Question 5

What are epigenetic changes?

Answer 5

hanges in gene expression that are passed on to cells or future generations, but do not involve alteration of the nucleotide sequence.

Question 6

How are epigenetic changes brought about?

Answer 6

Epigenetic changes are brought about by altering DNA structure, such as methylation of the DNA, or altering chromatin structure by modifying histones.

Question 7

The points at which spindle fibers attach to the chromosome are called what?

Answer 7

centromeres

Question 8

What are centromeres necessary for?

Answer 8

proper segregation of the chromosomes in mitosis and meiosis

Question 9

Most eukaryotic centromeres are characterized by _____ consisting of highly repetitive DNA.

Answer 9

heterochromatin

Question 10

Centromeres are thought to exist at specific locations on the chromosome because of ______ changes to chromatin structure at those locations.

Answer 10

epigenetic

Question 11

nucleosomes at centromeres often possess the variant histone CenH3. This special chromatin structure promotes what?

Answer 11

the formation of the kinetochore, to which spindle fibers attach

Question 12

____ are the ends of linear chromosomes in eukaryotes

Answer 12

telomeres

Question 13

What is the function of telomeres?

Answer 13

They cap and stabilize the ends of the chromosomes to prevent degradation by exonucleases or joining of the ends. Telomeres also enable replication of the ends of the chromosome by an enzyme called telomerase.

Question 14

Telomeric DNA

sequences consist of repeats of a simple sequence, usually in the form of what?

Answer 14

5′C (A/T)

Question 15

What is the difference between euchromatin and heterochromatin?

Answer 15

Euchromatin undergoes regular cycles of condensation during mitosis and decondensation during interphase, whereas heterochromatin remains highly condensed throughout the cell cycle, except transiently during replication.

Question 16

Nearly all transcription takes place in ____ regions, with little or no transcription of within ____ regions

Answer 16

euchromatic; heterochromatin

Question 17

The ___ value is the amount of DNA per cell of an organism.

Answer 17

C

Question 18

In regards to the different classes of DNA sequence variation that exist in eukaryotes, this class is present in only one or a few copies per haploid genome, represents most of the protein coding sequences, plus a great deal of sequences with unknown function.

Answer 18

unique-sequence DNA

Question 19

In regards to the different classes of DNA sequence variation that exist in eukaryotes, this class is a few hundred to a few thousand base pairs long, are present in up to several thousand copies per haploid genome. Some moderately repetitive DNA sequences consist of functional genes that code for rRNAs and tRNAs, but most are made up of transposable elements and remnants of transposable elements.

Answer 19

Moderately repetitive sequences

Question 20

Describe Highly repetitive DNA or satellite DNA

Answer 20

consists of clusters of tandem repeats of short (often less than 10 base pairs) sequences present in hundreds of thousands to millions of copies per haploid genome

Question 21

The introduction to this chapter discussed a study of telomere length in Romanian children. The study demonstrated that children raised in orphanages had shorter telomeres than children raised in foster homes. What effect, if any, do you think having shorter telomeres in childhood might have on adult life?

Answer 21

Somatic cells do not normally express telomerase, so their telomeres shorten with every cell division. People whose telomeres are already shorter in childhood may have reduced replicative lifespans for their somatic cells, leading to earlier aging for the immune system and cells and organs that the body needs to replenish continually, such as skin cells, intestinal cells, and blood cells. They may experience symptoms of aging earlier, and have shorter life expectancies.

Question 22

Based on the DNA sensitivity to DNase I illustrated in Figure 11.7, which type of chicken hemoglobin (embryonic or adult) is likely produced in highest quantity at the following tissues and developmental stages?
a. Erythroblasts during the first 24 hours

Answer 22

None—neither the embryonic nor adult hemoglobin genes show DNase I

Question 23

Based on the DNA sensitivity to DNase I illustrated in Figure 11.7, which type of chicken hemoglobin (embryonic or adult) is likely produced in highest quantity at the following tissues and developmental stages?
b. Erythroblasts at day 5

Answer 23

Embryonic—the embryonic hemoglobin gene, but not the adult genes, shows DNase I sensitivity, indicating an open chromatin conformation that is conducive for transcription.

Question 24

Based on the DNA sensitivity to DNase I illustrated in Figure 11.7, which type of chicken hemoglobin (embryonic or adult) is likely produced in highest quantity at the following tissues and developmental stages?
c. Erythroblasts at day 14

Answer 24

Adult—now the adult hemoglobin genes show DNase I sensitivity, but the embryonic gene is DNase I insensitive.

Question 25

Based on the DNA sensitivity to DNase I illustrated in Figure 11.7, which type of chicken hemoglobin (embryonic or adult) is likely produced in highest quantity at the following tissues and developmental stages?
d. Brain cells throughout development

Answer 25

None—neither embryonic nor adult hemoglobin genes show DNase I
sensitivity in brain cells at any time of development

Question 26

Would you expect to see more or less methylation in regions of DNA that are sensitive to digestion by DNase I? Why?

Answer 26

Less methylation. Regions of DNase I sensitivity are less condensed than DNA that is not sensitive to DNase I, the sensitive DNA is less tightly associated with nucleosomes, and it is in a more open state. Open states can represent areas of euchromatin which are undergoing DNA repair and/or transcription. Such a state is associated with less methylation.

Question 27

Suppose a chemist develops a new drug that neutralizes the positive charges on the tails of histone proteins. What would be the most likely effect of this new drug on chromatin structure? Would this drug have any effect on gene expression? Explain your answers.

Answer 27

Such a drug would disrupt the ionic interactions between the histone tails and the phosphate backbone of DNA and thereby cause a loosening of the DNA from the nucleosome. The drug may mimic the effects of histone acetylation, which neutralizes the positively charged lysine residues. Changes in chromatin structure would result from the altered nucleosome-DNA packing and possible changes in interaction with other chromatin modifying enzymes and proteins. Changes in transcription would result because DNA may be more accessible to transcription factors.