Chapter 7

A. Explain the replication problem at the end of eukaryotic chromosomes. B. Explain why bacterial chromosomes don't have this problem. C. Explain how eukaryotic cells overcome the problem described in (A.). Include an explanation of this process. D. Explain which type of cells, specifically, have the activity described in (C.) and why it's important to those cells.

A. At the end of replication, there is overhang on one of the newly synthesized strands. This is because when the final primer is removed, there is no way to fill the gap via conventional replication. If the chromosome were to replicate with this gap, we would get a chromosome that is shortened, causing other types of issues. B. Bacterial chromosomes do not have this problem since they are circular and not linear. C. Eukaryotes overcome this problem with telomeres. Telomeres act as caps that protect the region of overhang on the new chromosome. Telomeres are added via an enzyme called telomerase. Telomerase binds to a special RNA molecule that contains a complementary sequence. It adds nucleotides to the overhang strand. When the overhang is long enough, matching strand can be made by the normal DNA replication machinery, such as an RNA primer and DNA polymerase, producing double-stranded DNA. D. This is an important process in humans, specifically somatic or body cells. It is important because telomeres shorten as we age. As chromosomes replicate, the DNA strands become shorter and shorter. Telomeres help prevent genes from being lost in this process. Telomeres play a big role in cancer cells. Many cancer cells have shortened telomeres but active telomerase.

Eukaryotic chromosomes have multiple origins of replication whereas bacterial chromosomes only have one. A. Compare and contrast eukaryotic vs bacterial chromosomes. B. Explain why it is necessary for eukaryotic cells (and not bacterial cells) to have multiple origins of replication.

Eukaryotic chromosomes are located in the nucleus while prokaryotic chromosomes are located in the nucleoid. Eukaryotes have several linear chromosomes, while prokaryotes have one circular chromosome. In eukaryotic organisms, DNA is wound around histone proteins, and then compacted by supercoiling and folding. In prokaryotic chromosomes, DNA is supercoiled and compacted by nucleoid-associated proteins. Eukaryotic chromosomes also tend to be much much larger than prokaryotic chromosomes due to their complex nature and need for more genetic material. Overall, there are many differences, but not many similarities. Eukaryotic cells have multiple origins of replication due to their size. In order to complete DNA replication in a timely manner, it is necessary to begin replication at several origins (does not occur simultaneously). It would take far too long if there were only one. Eukaryotes also have several chromosomes, versus prokaryotes which only have one.

How does DNA gyrase remove extra twists during replication?

Figure 7-21. In a of the figure, the supercoiled genetic material begins to unwind, allowing the parental strands to be separated from each other. DNA gyrase is a type of topoisomerase. These enzymes catalyze the cleavage of two supercoiled strands to prepare for DNA replication. Specifically, the DNA must be unwound in order to expose a region in which primase can bind and initiate replication. In b of the figure, regions of the coils are removed. This is done so that the DNA strands are able to rotate and re-join each other following the replication fork.

Compare and contrast (similarities and differences) in the origin of replication and the initiation of DNA replication between bacterial and eukaryotic cells.

In prokaryotes, such as bacteria, DNA replication is initiated at the origins of replication. Proteins bind to the oriC region where the two strands are separated and replisome components are recruited to the replication forks of both strands. In eukaryotes, DNA replication is also initiated at the origins of replication. Also like prokaryotic cells, proteins bind to a region to begin the separation of the DNA strands. Replisome components are then recruited to the replication forks. In eukaryotes, the Origin Replication Complex, a complex made up of proteins, is what binds to the origin of replication, where as in prokaryotes, DNA proteins bind. In both kinds of cells, replisome components are called to the replication forks. Replication of eukaryotic cells is dependent on the presence of two proteins, where as they are not needed in prokaryotes.

Werner Syndrome

Werner syndrome is the dramatic and rapid change of appearance and features associated with normal aging. Individuals with this disorder typically look much older than they are. They also develop health issues that are typically associated with older age, such as cataracts and osteoporosis (thinning of bones). It is cause by a mutation in a particular gene called the WRN gene, which produces the Werner protein. This protein is responsible for the maintenance and repair of DNA. The Werner protein also assists in the process of DNA replication. Cells with a mutation may divide more slowly or stop dividing earlier than normal, causing issues with growth. Also, the altered protein may allow DNA damage to accumulate, which could impair normal cell activities and cause the health problems associated with Werner syndrome. We know that, as our DNA replicates, the strands of DNA become shorter and shorter. In individuals with Werner syndrome, their telomeres are shortened at an accelerated rate.

DNA polymerase III

adds the bulk of the dNTPs to the newly synthesized strands and proofreads to avoid mismatches

Helicase

breaks hydrogen bonds between complementary strands of DNA and unwinds the DNA

Topoisomerase

cuts and reseals the polynucleotide backbone of DNA to relieve supercoiling and stress

Primase

makes the primer needed to initiate DNA replication

DNA polymerase I

replaces the RNA primer with dNTPs

Ligase

seals the nicks (between a phosphate and a sugar on the lagging strand) in the backbone of DNA, generating a continuous strand