Biology Chapter 16 - Application Questions

In a nucleosome, the DNA is wrapped around

histones

Describe the structure of a nucleosome, the basic unit of DNA packing in eukaryotic cells.

A nucleosome is made up of eight histone proteins, two each of four different types, around which DNA is wound. Linker DNA runs from one nucleosome to the next.

In analyzing the number of different bases in a DNA sample, which result would be consistent with the base-pairing rules?

A+G = C+T

What roles does complementary base pairing play in the replication of DNA?

Complementary base pairing ensures that the two daughter molecules are exact copies of the parental molecule. When the two strands of the parental molecule separate, each serves as a template on which nucleotides are arranged, by the basepairing rules, into new complementary strands.

A biochemist isolates, purifies, and combines in a test tube a variety of molecules needed for DNA replication. When she adds some DNA to the mixture, replication occurs, but each DNA molecule consists of a normal strand paired with numerous segments of DNA a few hundred nucleotides long. What has she probably left out of the mixture?

DNA ligase

Identify two major functions of DNA pol III in DNA replication.

DNA pol III covalently adds nucleotides to new DNA strands and proofreads each added nucleotide for correct base pairing.

What is the basis for the difference in how the leading and lagging strands of DNA molecules are synthesized?

DNA polymerase can join new nucleotides only to the 3' end of a pre-existing strand

What does it mean when we say that the two DNA strands in the double helix are antiparallel? What would an end of the double helix look like if the strands were parallel?

Each strand in the double helix has polarity; the end with a phosphate group on the 5′ carbon of the sugar is called the 5′ end, and the end with an ¬OH group on the 3′ carbon of the sugar is called the 3′ end. The two strands run in opposite directions, one running 5′ S 3′ and the other alongside it running 3′ S 5′. Thus, each end of the molecule has both a 5′ and a 3′ end. This arrangement is called "antiparallel." If the strands were parallel, they would both run 5′ S 3′ in the same direction, so an end of the molecule would have either two 5′ ends or two 3′ ends.

Griffith did not expect transformation to occur in his experiment. What results was he expecting? Explain.

He expected that the mouse injected with the mixture of heat-killed S cells and living R cells would survive, since neither type of cell alone would kill the mouse.

What two properties, one structural and one functional. distinguish heterochromatin from euchromatin?

Heterochromatin remains quite condensed during interphase and contains genes that are largely inaccessible to this machinery. Euchromatin is chromatin that becomes less compacted during interphase and is accessible to the cellular machinery responsible for gene activity.

What is the relationship between DNA replication and the S phase of the cell cycle?

In the cell cycle, DNA synthesis occurs during the S phase, between the G1 and G2 phases of interphase. DNA replication is therefore complete before the mitotic phase begins.

Describe the levels of chromatin packing you'd expect to see in an interphase nucleus.

Most of the chromatin in an interphase nucleus is fairly uncondensed. Much is present as the 30-nm fiber, with some in the form of the 10-nm fiber and some as looped domains of the 30-nm fiber. (These different levels of chromatin packing may reflect differences in gene expression occurring in these regions.) Also, a small percentage of the chromatin, such as that at the centromeres and telomeres, is highly condensed heterochromatin.

Compare DNA replication on the leading and lagging strands, including both similarities and differences.

On both the leading and lagging strands, DNA polymerase adds onto the 3′ end of an RNA primer synthesized by primase, synthesizing DNA in the 5′ S 3′ direction. Because the parental strands are antiparallel, however, only on the leading strand does synthesis proceed continuously into the replication fork. The lagging strand is synthesized bit by bit in the direction away from the fork as a series of shorter Okazaki fragments, which are later joined together by DNA ligase. Each fragment is initiated by synthesis of an RNA primer by primase as soon as a given stretch of single-stranded template strand is opened up. Although both strands are synthesized at the same rate, synthesis of the lagging strand is delayed because initiation of each fragment begins only when sufficient template strand is available.

If the DNA pol I in a given cell were nonfunctional, how would that affect the synthesis of a leading strand?

Synthesis of the leading strand is initiated by an RNA primer, which must be removed and replaced with DNA, a task that could not be performed if the cell's DNA pol I were nonfunctional. In the overview box in Figure 16.17, just to the left of the top origin of replication, a functional DNA pol I would replace the RNA primer of the leading strand (shown in red) with DNA nucleotides (blue). The nucleotides would be added onto the 3′ end of the final Okazaki fragment of the upper lagging strand (the right half of the replication bubble).

Interphase chromosomes appear to be attached to the nuclear lamina and perhaps also the nuclear matrix. Describe these two structures.

The nuclear lamina is a netlike array of protein filaments that provides mechanical support just inside the nuclear envelope and thus maintains the shape of the nucleus. Considerable evidence also supports the existence of a nuclear matrix, a framework of protein fibers extending throughout the nuclear interior.

Given a polynucleotide sequence such as GAATTC, can you tell which is the 5′ end? If not, what further information do you need to identify the ends?

You can't tell which end is the 5′ end. You need to know which end has a phosphate group on the 5′ carbon (the 5′ end) or which end has an ¬OH group on the 3′ carbon (the 3′ end).

The elongation of the leading strand during DNA synthesis

depends on the action of DNA polymerase

The spontaneous loss of amino groups from adenine in DNA results in hypoxanthine, an uncommon base, opposite thymine. What combination of proteins could repair such damage?

nuclease, DNA polymerase, DNA ligase

E. coli cells grown on 15N medium are transferred to 14N medium and allowed to grow for two more generations (two rounds of DNA replication). DNA extracted from these cells is centrifuged. What density distribution of DNA would you expect in this experiment?

one low-density and one intermediate-density band

In his work with pneumonia-causing bacteria and mice, Griffith found that

some substances from pathogenic cells was transferred to nonpathogenic cells, making them pathogenic