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?
Showing posts with label replication. Show all posts
Showing posts with label replication. Show all posts
Out of Syllabus (OFS) Questions
nO.1
R/S between tRNA, mRNA and rRNA in translation.
we had discussed extensively on the roles of tRNA and mRNA in translation but often skip rRNA. We only know rRNA as a component of ribosomes but what are they doing in ribosomes?
Let's appreciate the fact that different rRNAs are found in the 2 ribosomal subunits.
So what are their roles?
1) Peptidyl transferase is an enzyme found in the large ribosomal subunit that catalyse the formation of a peptide bond between the polypeptide chain (peptidyl-tRNA) in P site and the adjacent aa (aminoacyl-tRNA) in the A site of the ribosome. Now the elongated chain is now attached to the tRNA at the A site.
This peptidyl transferase is rRNA in action = it is a ribozyme, an RNA enzyme.
2) They are known to interact with
a) mRNA (rRNA in small subunit - translation step 1: small subunit binds to the mRNA..=)),
b) anti-codon regions and 3'CCA ends of the tRNAs at the P and A sites (rRNA in both subunits - no prize for guessing which for which).
3) also the subunit are able to interact because of interaction between the rRNAs in the 2 subunits!
COol yeah?!
Actually rRNA is not as well-studied so I will stop here.
_____________________________
nO.2
Proofreading mechanism of DNA polymerase in details
DNA polymerase has intrinsic 3'-> 5' proofreading exonuclease activity
(exo=outside; nuclease=enzyme that cleave nucleotides; exonuclease = enzyme that remove/cleave nucleotides from the terminal)
From Wiki:
When an incorrect base pair is recognized, DNA polymerase reverses its direction by one base pair of DNA. The 3'-5' exonuclease activity of the enzyme allows the incorrect base pair to be excised (this activity is known as proofreading).
How does the DNA polymerase know when there has been a mistake?
anticodon and codon pairing is very impt btw the tRNA (AC) and mRNA (C).
Incorrect base pairing --> conformation is altered/distortion in shape of the regular double helix which is recognised as a mismatch of base pair to initiate the exonuclease activity.
NOTE: not all DNA polymerase have proofreading capability (there are many types of DNA polymerase but the one we are interested in for replication has such capability)
________________________
R/S between tRNA, mRNA and rRNA in translation.
we had discussed extensively on the roles of tRNA and mRNA in translation but often skip rRNA. We only know rRNA as a component of ribosomes but what are they doing in ribosomes?
Let's appreciate the fact that different rRNAs are found in the 2 ribosomal subunits.
So what are their roles?
1) Peptidyl transferase is an enzyme found in the large ribosomal subunit that catalyse the formation of a peptide bond between the polypeptide chain (peptidyl-tRNA) in P site and the adjacent aa (aminoacyl-tRNA) in the A site of the ribosome. Now the elongated chain is now attached to the tRNA at the A site.
This peptidyl transferase is rRNA in action = it is a ribozyme, an RNA enzyme.
2) They are known to interact with
a) mRNA (rRNA in small subunit - translation step 1: small subunit binds to the mRNA..=)),
b) anti-codon regions and 3'CCA ends of the tRNAs at the P and A sites (rRNA in both subunits - no prize for guessing which for which).
3) also the subunit are able to interact because of interaction between the rRNAs in the 2 subunits!
COol yeah?!
Actually rRNA is not as well-studied so I will stop here.
_____________________________
nO.2
Proofreading mechanism of DNA polymerase in details
DNA polymerase has intrinsic 3'-> 5' proofreading exonuclease activity
(exo=outside; nuclease=enzyme that cleave nucleotides; exonuclease = enzyme that remove/cleave nucleotides from the terminal)
From Wiki:
When an incorrect base pair is recognized, DNA polymerase reverses its direction by one base pair of DNA. The 3'-5' exonuclease activity of the enzyme allows the incorrect base pair to be excised (this activity is known as proofreading).
How does the DNA polymerase know when there has been a mistake?
anticodon and codon pairing is very impt btw the tRNA (AC) and mRNA (C).
Incorrect base pairing --> conformation is altered/distortion in shape of the regular double helix which is recognised as a mismatch of base pair to initiate the exonuclease activity.
NOTE: not all DNA polymerase have proofreading capability (there are many types of DNA polymerase but the one we are interested in for replication has such capability)
________________________
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