Saturday, 5 December 2009

Biochemistry Exams - Sample Papers Exposed

Hi Students,

Welcome in the new section of the BioFreaks Biochemistry Blog. In this section we will work with the previous years exam papers. Simply as that:) Today we start with 2008/2009 3rd year undenominated science paper which you can find here:

2008/2009 3rd year Undenominated Science Semester I

If this is a wrong paper please let me know:)

Ok. Let's go!!

Question 1. Discuss the role of polymerases (DNA and RNA) in eukaryotic DNA replication.

Before we go into the answer to that question please have a quick look at this animation McGraw Hill - DNA replication fork, which actually is great overview of the DNA replication process.

To answer the question you need to remember that in DNA replication process are required:
- DNA polymerases (Polymerase III and I) - DNA synthesis
- RNA polymerase (called primase) - RNA primer synthesis on lagging strand
- helicases - DNA unwinding
- DNA ligase - strand ligation
- other proteins - which for example enhances fidelity and procesivity of the DNA replication process or those that monitor replication fork stability.

You all know well that each DNA strand has two different ends (5' end with phosphate group and 3' end with the hydroxyl group). DNA polymerases are able to elongate the new DNA strand only in 5' to 3' direction. Just remember that 3'OH end is the only one which can attack the 5'TriPhosphate on the newly incoroporated nucleotide to form a bond (never the other way around, see the figure below).

The other feature of the DNA polymerases you have to keep in mind is that they cannot start DNA replication without primer (DNA must be at least partially double stranded to be a substrate for DNA polymerases).

Because of those reasons one strand is processed continuesly and the other one in fragments (called Okazaki fragments). Once the primer is added by RNA polymarase leading strand (continues one) can be relplicated. For the lagging strand (discountinous one) it looks different but it is still easy:). It starts the same way, RNA polymerase add primer, DNA Polymerase III extend the primer, then it is replaced by DNA Polymerase I (remember that RNA polymerase add U opposite to A not T, so primer must be replaced) and then short DNA fragments are ligated (fused) by DNA ligase. And the story starts again till whole DNA molecule is replicated.

To sum up:
- we need both DNA and RNA polymerases to replicate DNA,
- leading strand - RNA Pol adds primer, DNA Pol III replicate the strand,
- lagging strand - again RNA Pol adds primers but this time DNA Pol III and I cooparate to replicate the strand which at the end is fused by DNA ligase.

It is a good idea to put a simple fugire together with your discussion as it always indicated you understand what is happening on the molecular level. Start with the figure like the one below and then discuss the question. Another adventage of having the picture is that you focus will easilly focus on what you have to write about.

Picture taken from McGraw Hill animations

That would be it for the Question 1. If you have any problems with the answer or there is something not clear do not hesitate to contact me by leaving the comment or at

Cya soon:) Question 2 is coming:)


1 comment:

  1. Hello there, I was looking for ligase topic and I came across your blog, very informative and entertaining, it shows that your an expert in your field.
    I will definitely be back for more. Keep it up!