Discussion Assignment #7

Problem Solving

Superficially, the replication of DNA is pretty simple. Just unzip, plug in the spare parts by complementary base pairing, and stitch up the new backbone.

However, there are a lot of irritating little details and problems with this process, and the actual operation of DNA replication has complexities which are important ways to solve those problems.

So that's the subject of this exercise--exploring the solutions of problems and complications in DNA replication. The solutions to these problems involve, among other things, a list of vital enzymes. Be sure to include the names of the enzymes required to solve the problems below.

So what are those complexities? Here's a short list:

DNA is a very stable molecule, but its stability depends upon its double stranded nature. Single stranded DNA is very vulnerable to a number of kinds of damage to which double stranded DNA is largely immune. Most mutation, for instance, occurs during the brief periods when DNA is single stranded. So to take a huge DNA molecule and separate its two strands for its entire length--thus rendering it all single stranded at once, and for however long it takes to complete all the operations of replication--is a very bad idea. So how can long DNA molecules be replicated without making them be single stranded for long periods of time?

DNA is very long. Very long. The solution to #1 means that the molecule must be replicated progressively, not all at once. How can a very long DNA molecule get itself replicated in a relatively short period of time?

The primary DNA replication enzyme, DNA Polymerase, is highly specific in a number of ways. One of those specificities is that it can only add new nucleotides to an already existing growing strand of nucleotides. This is a problem because it means that DNA polymerase is not capable of actually starting the process itself. How does replication get started? You will need to identify an enzyme involved in this solution.

DNA polymerase is also highly specific in that it can only build new polynucleotide strands in the 5' to 3' direction--new strands must always run from 5' to 3'. But the two strands of DNA are antiparallel to each other--one runs 3' to 5', the other from 5' to 3'. Both sides have to be replicated. How is this puzzle solved in DNA replication? What's the name of the scientist credited with this discovery?

DNA is double stranded, and the two strands twist around each other. The solution to #2 above would require that these two strands be pulled apart, thus tightening the twist between Origin points. This would lead to accidental breakage of the polynucleotide strands as the twists got compressed into smaller and smaller lengths. How is this problem avoided in DNA replication? What is the nams of the enzyme needed to solve this problem (it has several; any of them will do)?

Finally, the solutions to #2, #4 and #5 all leave us with an embarrassing problem: single stranded breaks in the polynucleotides of our new DNA molecules. How are these breaks repaired? Again, you'll need to identify the enzyme involved.

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