Friday, November 2, 2012

Viva voce #3

During the last practical exams I shared my experience.(Read here) I shared certain questions with answers which the examiner asked me during the practicals. Even this time, I'm going to share a few questions and answers with you. Here we go,

This time I had 2 lab exam (Practicals), number one - Bio informatics and two - Molecular biology.
Let us start with the Bio informatics lab.

Bio informatics: 

In this Bio info practicals, we were provided with two exercises - one must be done using various bio info tools such as Clustal W, T-coffee, BLAST P, BLAST-N, PHYLIP etc.,
The other exercise is PERL programming! :( :'( 
The first exercise using tools is very simple, but, I find the programming, let it be any programming, it's very difficult :'( Even in the model practicals, I couldn't debug the program :(
So, I worked really hard to learn the PERL! I was working with my lap for a whole day. And atlast, I got good confidence that I could write my own program! :)
On the exam day, I got output for my program with out any errors :) 

And the viva voce, that was very simple :) I scored 9/10 :)

Okay, let us see some of the questions that examiner asked me. 

1) Question: What are the tools you are using here for Multiple sequence alignment?
Answer: I used CLUSTAL W & T-COFFEE for aligning the given 8 protein sequences. 

2)   Question: What is a phylogram?
Answer: It is a phylogenetic tree which can be drawn using both CLUSTAL W & T-COFFEE and the distance in the tree shows the evolutionary relationship between the sequences.

3) Question: What do you mean by distance?
Answer: Distance in the phylogenetic trees are calculated based on the differences between the sequences. i.e., distance shows how much the sequences are different.

4) Question: I'm giving you a protein sequence which contains mutation, and I'm telling you the function of that protein sequence, how will you identify the region of mutation?
Answer: It's very simple, we have to get the protein sequence with the mentioned function from any of the protein data bases and the we have to compare the mutated sequence with that original sequence, now, we can get the mutated region!

The questions were very simple and answered them right :) 

Now, let us discuss the molecular biology viva voce questions:

Experiment I got was "Linearise the given pDNA at E.CoR1 site"

1) Question: Procedure for Restriction digestion of pDNA?
Answer: pDNA has Multiple Cloning Site, which has several restriction sites. These restriction sites have specific sequences which are not repeated elsewhere in the pDNA. So, we have to choose a restrictions site and a corresponding restriction enzyme with corresponding buffer. We have to take 1 micro gram of DNA in an eppendorf along with 1 micro liter of buffer. To this 7 micro liter of nano pure water must be added.The enzyme must be added atlast (1 micro liter - 10 units). This sample must be incubated or digested at 37 degree celsius for an hour. Then, this sample can be used and Agarose gel electrophoresis must be performed.

2) Question: What is the site you are using here for restriction?
Answer: E.coR1

3) Question: Whether there will be only one E.coR1 site?
Answer: Yes, because, the main objective of our experiment is to linearise, and as I explained earlier there will be only one restriction E.coR1 site, If there are more than one E.coR1 site, then it would lead to fragmentation of DNA.

4) Question: Whether the linearised and the non linearised plasmid will move the same in the agarose gel?
Answer: No, the non linearised, i.e, circular DNA will move faster through the pores due to the circular shape, while, the linearised one moves slower.

That's it Viva over, answered all the questions :) :)

Hoping for "s" grade (90 to 100%) as maximum and "A" grade(80 to 90 %) as minimum.

Got any more questions regarding this? Comment then. I'll try answering you :)
Wish you a good day!

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