Some songs just keep popping into your head..mmm..just mine. =P
Titillating Question of Mid_eek
In line with the SATS mugging, I shall use more adjectives hahaa
Point Mutations (FYI):
1. Missense mutation: substitution of a nucleotide → change in amino acid e.g. sickle cell anemia
2. Nonsense mutation: substition of a nucleotide → form a stop codon → cause premature termination of polypeptide elongation.
3. Silent mutation: due to a degenerate code, substitution of a nucleotide that does not cause change in the resultant amino acid
4. Frameshift mutation: due to insertion/deletion of a nucleotide.
--------------------
Effect of pH in electrophoresis
For non-chemistry students:
Why pH is important in electrophoresis because amino acids have their own isoelectric point. At a particular pH, an amino acid may be neutral (zwitterion) while others will be positive or negative. Thus application of charge will separate them.
http://chimge.unil.ch/En/ph/1ph81.htm (see the example)
--------------------
Why twins have different fingerprints
Since I always forget half of what I read, better you read it :P
http://forensic-evidence.com/site/ID/ID_Twins.html
--------------------
Since we use PolyT oligomer as a primer for mRNA (template) to eventually form ds cDNA, would that also imply that the resultant ds cDNA has polyA and polyT sequences within it?
Interesting perspective and the answer is YES.
Point Mutations (FYI):
1. Missense mutation: substitution of a nucleotide → change in amino acid e.g. sickle cell anemia
2. Nonsense mutation: substition of a nucleotide → form a stop codon → cause premature termination of polypeptide elongation.
3. Silent mutation: due to a degenerate code, substitution of a nucleotide that does not cause change in the resultant amino acid
4. Frameshift mutation: due to insertion/deletion of a nucleotide.
--------------------
Effect of pH in electrophoresis
For non-chemistry students:
Why pH is important in electrophoresis because amino acids have their own isoelectric point. At a particular pH, an amino acid may be neutral (zwitterion) while others will be positive or negative. Thus application of charge will separate them.
http://chimge.unil.ch/En/ph/1ph81.htm (see the example)
--------------------
Why twins have different fingerprints
Since I always forget half of what I read, better you read it :P
http://forensic-evidence.com/site/ID/ID_Twins.html
--------------------
Since we use PolyT oligomer as a primer for mRNA (template) to eventually form ds cDNA, would that also imply that the resultant ds cDNA has polyA and polyT sequences within it?
Interesting perspective and the answer is YES.
Trying 2 Take A Good Wkend Break
----------------------
Half-way through Friday, I was reminded of my next wedding dinner that very night.
I went with F and was surprised to see Q. C and J were missing from our team due to work.
The groom of the night was T and all three of us have not seen T for ages ever since JC because T somehow got out of our loop. But we all gathered that night and to be able to invite Q n F is no mean feat because as F self-declared, he is a diva. So why did we go after such a long absence of communication with T? Because all of us agree that our time together in secondary school was an important milestone in our lives, with endless happening outings, birthday celebrations and stayovers. And judging from the guests and our seating position, T must have thought so too. That night, however, was not 4 for 10* :P
PS: *only to be ruined by F whom I went to drink coffee with at J8 after the dinner and he who bought 2 slices of cake.
---------------------
Half-way through Friday, I was reminded of my next wedding dinner that very night.
I went with F and was surprised to see Q. C and J were missing from our team due to work.
The groom of the night was T and all three of us have not seen T for ages ever since JC because T somehow got out of our loop. But we all gathered that night and to be able to invite Q n F is no mean feat because as F self-declared, he is a diva. So why did we go after such a long absence of communication with T? Because all of us agree that our time together in secondary school was an important milestone in our lives, with endless happening outings, birthday celebrations and stayovers. And judging from the guests and our seating position, T must have thought so too. That night, however, was not 4 for 10* :P
PS: *only to be ruined by F whom I went to drink coffee with at J8 after the dinner and he who bought 2 slices of cake.
---------------------
Question of the week_20April
How does a restriction enzyme recognise 2 sites on a double-stranded DNA?
This is really a question I posed to myself. Dun you find it disturbing that an enzyme can cut at two identical sites at the same time? M... or Maybe Not :P
Just to clarify: A RE is usually made up of two identical subunits which will recognise the identical sequences (albeit in opp direction) on the 2 DNA strands to cut them.
------------------
If RE break the phosphodiester bonds, how are the H-bonds broken to, say, linearize the plasmid?
While we need an enzyme to cut the phosphop-bonds, at the temp we work with, the weak H_bonds are broken easily.
If so, wouldn't the two strands of DNA separate totally?
Here is an apt example: If you have one chopstick, you can break it easily. If you have 10?
-------------------
This is really a question I posed to myself. Dun you find it disturbing that an enzyme can cut at two identical sites at the same time? M... or Maybe Not :P
Just to clarify: A RE is usually made up of two identical subunits which will recognise the identical sequences (albeit in opp direction) on the 2 DNA strands to cut them.
------------------
If RE break the phosphodiester bonds, how are the H-bonds broken to, say, linearize the plasmid?
While we need an enzyme to cut the phosphop-bonds, at the temp we work with, the weak H_bonds are broken easily.
If so, wouldn't the two strands of DNA separate totally?
Here is an apt example: If you have one chopstick, you can break it easily. If you have 10?
-------------------
Wedding of Uncle
There were many promises to talk about this and that but as I stared at this screen, I got lost with my train of thoughts. The past few weeks have been busy and on Thurs, I was so tired that I nearly knocked into the wall so the weekend was a time for a good rest.
I went for my NS squad mate's wedding on Sat. We called him Uncle because he really looked beyond his years hahaha (at least 10 yrs) with ah peh's belly, stubs and hairdo but Uncle looked positively rejuvenated on his big day =).
That day when I met up with my long-lost softball pitcher, we talked about friends and weddings and how he has been turning down wedding invitations these days when too many come in. Although I haven't seen Uncle for years, ,his is one that I wouldn't miss. Uncle is a kind and generous soul and he took care of us during training days and I loved taking a ride on his bike hee because I enjoyed it when the bike makes a turn and your CG is off and you feel like falling for a while. (why am I talking about this?)
Back to the wedding. Actually, as a standard, one's red packet to a newly-wed can be pegged to the hotel or resturant he/she is holding the banquet. But I usually don't give a dam*. I will give based on his/her importance of me, in terms of friendship. Yet, when I arrived at the resturant, I did wonder if I have prepared more than the market rate. But the hesitation lasted only a while and I still give the original amount I planned for.
During the dinner, I met 3 of my squad-mates whom I have not seen for quite a while and we four gobbled down 10-person worth of dinner since no one wants to sit with us, and still lamented about how everyone is getting fat.
Then I overheard the waitress talking to her friend in Hokkien about Uncle being very generous with his selection of dishes, taking care of his guests with good food and how lucky the bride is. That conversation brought a smile to my face because it reminded me the goodness and sincerity of Uncle's heart and a reflection of his character which I couldn't agree more. And I realized that the ang pow I given was well-justified because it was really my appreciation of his friendship.
I am not sure when I will see Uncle again but am I glad that he had finally found someone to share his life with (given the fact that his BGR was a barrack topic last time)
---- Just a random thought. A student asked me about the wedding and in which 5 stars hotel it was held. Although this wedding was not held in any great hotel but in a resturant but I thought there was a lot of sincerity in it and I left the resturant, fatter and happy.
I went for my NS squad mate's wedding on Sat. We called him Uncle because he really looked beyond his years hahaha (at least 10 yrs) with ah peh's belly, stubs and hairdo but Uncle looked positively rejuvenated on his big day =).
That day when I met up with my long-lost softball pitcher, we talked about friends and weddings and how he has been turning down wedding invitations these days when too many come in. Although I haven't seen Uncle for years, ,his is one that I wouldn't miss. Uncle is a kind and generous soul and he took care of us during training days and I loved taking a ride on his bike hee because I enjoyed it when the bike makes a turn and your CG is off and you feel like falling for a while. (why am I talking about this?)
Back to the wedding. Actually, as a standard, one's red packet to a newly-wed can be pegged to the hotel or resturant he/she is holding the banquet. But I usually don't give a dam*. I will give based on his/her importance of me, in terms of friendship. Yet, when I arrived at the resturant, I did wonder if I have prepared more than the market rate. But the hesitation lasted only a while and I still give the original amount I planned for.
During the dinner, I met 3 of my squad-mates whom I have not seen for quite a while and we four gobbled down 10-person worth of dinner since no one wants to sit with us, and still lamented about how everyone is getting fat.
Then I overheard the waitress talking to her friend in Hokkien about Uncle being very generous with his selection of dishes, taking care of his guests with good food and how lucky the bride is. That conversation brought a smile to my face because it reminded me the goodness and sincerity of Uncle's heart and a reflection of his character which I couldn't agree more. And I realized that the ang pow I given was well-justified because it was really my appreciation of his friendship.
I am not sure when I will see Uncle again but am I glad that he had finally found someone to share his life with (given the fact that his BGR was a barrack topic last time)
---- Just a random thought. A student asked me about the wedding and in which 5 stars hotel it was held. Although this wedding was not held in any great hotel but in a resturant but I thought there was a lot of sincerity in it and I left the resturant, fatter and happy.
Questions Long Overdue & Go Around In The Head
Bet you all miss bio updates ahahahaha
Phagemid: pBluescript (Additional)
- a plasmid with a phage origin of replication. It can be used to generate ssDNA when co-infected (of the host) with a helper phage which will recognise the phage origin of replication to initiate the replication. The phagemid is replicated along with phage DNA and packed into capsid. Packaging" of pBluescript II phagemids containing inserts is efficient since the pBluescript II vector is significantly smaller
*amended*Why use phagemid?
(I took the below information from the patent for phagemid. It is the idea of phage display if you look it under wikipedia)
The special feature of phagemids which can be used for a presentation of particular products, viz. ligands, is the presence of a gene on the phagemids which consists of a fusion between the gene for the product to be presented and a bacteriophage coat protein gene. An example for such a bacteriophage coat protein gene is gpIII, the gene for the coat protein III (pIII) of phages M13 or fd. This results, on superinfection with an M13-like phage in the production of phagemid particles in the supernatant where the ligand is physically coupled via the bacteriophage coat protein to the gene which encodes the ligand.
By randomly mutagenizing the ligand gene at a specific site, the invention in question provides a library of phagemids containing tens of millions of ligand variants. The concept of the present invention is that some of these variant ligands will have specific binding affinities for a particular target molecule. The subset of strongly binding phagemids can be selected by, for example, binding on a surface coated with the target molecule, the poorly binding majority of phagemids being washed away. The specific strongly-binding population is then eluted by, for example, weak acid. This enriched subpopulation of phagemids can then be amplified by reinfection and cultivation in Escherichia coli. Successive rounds of such binding and amplification lead to the enrichment of a few variant ligands which exhibit strong specific binding characteristics for the target molecule.
(Flea Mel, I hope this takes care of your question on co-infection although the part on smaller virus escaped me)
-------------------------------
Insulin Production from Animal Sources: do we maintain the animals or just culture their relevant cells?
Cell culture because it is more easily maintained as no lab will bother with keeping livestock - we leave that to the professional. But animal cells are larger (need more nurients) and yield is low so compared to bacteria, maintenance is still high.
-------------------------------
RNase A/B/C/D/E/F/G/H?
We can find Rnases A to H, all with relatively different roles or found in different tissues.
The letter H is not attributed to anyone in particular :)
" RNase H specifically degrades the RNA in RNA:DNA hybrids and will not degrade DNA or unhybridized RNA, it is commonly used to destroy the RNA template after first-strand complementary DNA (cDNA) synthesis by reverse transcription, as well as procedures such as nuclease protection assays."http://en.wikipedia.org/wiki/RNase_H
- If I may bring in a cross-unit thingy, you might have realised that RNase H can be present to remove the RNA primers during DNA replication too although DNA polymerase is capable of the removal of RNA primer as well - keep to the latter for now pls.
Yes, I did not kid you. The letter H is important.
----------------------
Terminal Transferase: Can it keep on adding nucleotides?
TdT add to the 3-OH ends. The rate of addition of dNTPs and thus the length of the tail is a function of the ratio of 3´ DNA ends: dNTP concentration, and also which dNTP is used.
Industrial-wise, they have worked out the concentration for optimal results.
Phagemid: pBluescript (Additional)
- a plasmid with a phage origin of replication. It can be used to generate ssDNA when co-infected (of the host) with a helper phage which will recognise the phage origin of replication to initiate the replication. The phagemid is replicated along with phage DNA and packed into capsid. Packaging" of pBluescript II phagemids containing inserts is efficient since the pBluescript II vector is significantly smaller
*amended*Why use phagemid?
(I took the below information from the patent for phagemid. It is the idea of phage display if you look it under wikipedia)
The special feature of phagemids which can be used for a presentation of particular products, viz. ligands, is the presence of a gene on the phagemids which consists of a fusion between the gene for the product to be presented and a bacteriophage coat protein gene. An example for such a bacteriophage coat protein gene is gpIII, the gene for the coat protein III (pIII) of phages M13 or fd. This results, on superinfection with an M13-like phage in the production of phagemid particles in the supernatant where the ligand is physically coupled via the bacteriophage coat protein to the gene which encodes the ligand.
By randomly mutagenizing the ligand gene at a specific site, the invention in question provides a library of phagemids containing tens of millions of ligand variants. The concept of the present invention is that some of these variant ligands will have specific binding affinities for a particular target molecule. The subset of strongly binding phagemids can be selected by, for example, binding on a surface coated with the target molecule, the poorly binding majority of phagemids being washed away. The specific strongly-binding population is then eluted by, for example, weak acid. This enriched subpopulation of phagemids can then be amplified by reinfection and cultivation in Escherichia coli. Successive rounds of such binding and amplification lead to the enrichment of a few variant ligands which exhibit strong specific binding characteristics for the target molecule.
(Flea Mel, I hope this takes care of your question on co-infection although the part on smaller virus escaped me)
-------------------------------
Insulin Production from Animal Sources: do we maintain the animals or just culture their relevant cells?
Cell culture because it is more easily maintained as no lab will bother with keeping livestock - we leave that to the professional. But animal cells are larger (need more nurients) and yield is low so compared to bacteria, maintenance is still high.
-------------------------------
RNase A/B/C/D/E/F/G/H?
We can find Rnases A to H, all with relatively different roles or found in different tissues.
The letter H is not attributed to anyone in particular :)
" RNase H specifically degrades the RNA in RNA:DNA hybrids and will not degrade DNA or unhybridized RNA, it is commonly used to destroy the RNA template after first-strand complementary DNA (cDNA) synthesis by reverse transcription, as well as procedures such as nuclease protection assays."http://en.wikipedia.org/wiki/RNase_H
- If I may bring in a cross-unit thingy, you might have realised that RNase H can be present to remove the RNA primers during DNA replication too although DNA polymerase is capable of the removal of RNA primer as well - keep to the latter for now pls.
Yes, I did not kid you. The letter H is important.
----------------------
Terminal Transferase: Can it keep on adding nucleotides?
TdT add to the 3-OH ends. The rate of addition of dNTPs and thus the length of the tail is a function of the ratio of 3´ DNA ends: dNTP concentration, and also which dNTP is used.
Industrial-wise, they have worked out the concentration for optimal results.
Question of the week_6April
A quick one because I m feeling a tad feverish from a throat infection that had been rather persistant since Wed.
Question:
Can 2 F+ bacteria form a mating bridge with each other?
Answer:
Nope. There are some proteins which prevent such occurrence.
http://physicsforums.com/archive/index.php/t-129.html
-----------------------
I met up with another softballer last night. It has been a decade.
We had an interesting conversation on friends and weddings. I guess I will share another day when I get better. Nites!
Question:
Can 2 F+ bacteria form a mating bridge with each other?
Answer:
Nope. There are some proteins which prevent such occurrence.
http://physicsforums.com/archive/index.php/t-129.html
-----------------------
I met up with another softballer last night. It has been a decade.
We had an interesting conversation on friends and weddings. I guess I will share another day when I get better. Nites!
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