DNA & Genomics : Replication, Transcription, Translation

Disclaimer: most videos do not cover all the things highlighted in notes so just get a feel of the processes.


Replication
Video 1
http://www2.le.ac.uk/Members/jlb34/research/replication%207v3-3.swf/view
Video 2
http://highered.mcgraw-hill.com/olcweb/cgi/pluginpop.cgi?it=swf::535::535::/sites/dl/free/0072437316/120076/micro04.swf::DNA%20Replication%20Fork
(however, this V2 lacks SS binding proteins!)

Question posed:
Why can't DNA polymerase (the other one) catalyse the formation of the phosphodiester bonds between the adjacent nucleotides of Okazaki fragments if it is able to elongate the Okazaki fragment after removing the RNA primer ? Why do we resort to DNA ligase?

Good Question!
We need to consider the nature of the 2: DNA polymerase and DNA ligase, both of which are enzymes.What is the important thing about enzymes? They have a substrate specific active site.
when DNA polymerase elongate the Okazaki fragments, the phosphodiester bond is formed between the free 3'OH end and a free nucleotide (nucleoside triphosphate). The reaction/formation of the bond also involve the removal of pyrophosphate (PPi) - the 2-phosphate group.

On the other hand, the substrate for DNA ligase is different. They are the free 3'OH end and a single 5' phosphate group extending from the adjacent fragment. The ligase only needs to join them up!

Thus although both involves the formation of phosphodiester bond, the different substrates involved demands the use of different enzymes.

Transcription

Video1:



Consider or note the following questions.
1) How are 2 DNA strands separated? (compare to transcription)
2) what happens to the 2 DNA strands as the RNA polymerase move along (and read) the template strand in the 3'-> 5' direction
3) what kind of nucleotides are involved? (compare to transcription)
4) where does transcription start? (compare to transcription)

Translation
Video 1:
http://highered.mcgraw-hill.com/sites/0072507470/student_view0/chapter3/animation__how_translation_works.html
Video 2:
http://www.vcell.ndsu.edu/animations/translation/movie-flash.htm


Consider or note the following questions in understanding the process.
1) the mRNA is being read in what direction? (compare to R and T above)
2) In what sequence does the following binds to mRNA: small ribosomal subunit, large ribosomal subunit, initiator aminoacyl-tRNA carrying methonine.
3) Which site will methionine reside in initially?
4) By how much does the ribosome move each time?
5) What does the stop codon encode for? Or does it encode for anything?