Thanks to KL for pointing this out:
This is to inform you of the following amendment for the Jun P.
Qn 21: A
Qn 22 : A
Bio Bulletin 2
1) We know that in the tale of endosymbiosis, chloroplasts and mitochondria have prokaryotic origins and one of the main features is the presence of the double membrane. Hence does this make the nucleus a prokaryote in the distant past?
This question is unresolved at the moment. Reference:
http://www.sciam.com/article.cfm?articleID=000E9461-AB74-1C75-9B81809EC588EF21
(Extract)
The nucleus also has some superficial similarities to these organelles: a two-layered membrane surrounds them all; they each have their own genome; and they are capable of reproducing. "It's easy to get [these features] when you're essentially swallowing a symbiont," says Hyman Hartman, a research scientist at the Massachusetts Institute of Technology who studies the origin of life. "It doesn't take a rocket scientist to [suggest] the nucleus had an endosymbiotic origin."
Subsequent molecular data only fanned these speculative flames by revealing that the eukaryotic genome is a mixed breed. Genetic sequences indicate that eukaryotic genes for building and manipulating DNA, RNA and proteins seem to come from archaea, whereas genes for metabolism and other cellular functions likely hail from bacteria. "The heart of the problem is that the logic of the eukaryote is very different from the logic of the prokaryotic cell, yet there has been a huge input from the prokaryote to the eukaryote," Hartman says.
..............
Martin, however, points out a number of sticking points for any endosymbiotic model. First, although the membrane surrounding the nucleus appears similar to those of mitochondria and chloroplasts, all of which have two layers, the nuclear membrane is unique. It is a single layer folded on itself, its pores are much different from those in bacteria, and it disintegrates when the cell divides. Second, even though the enzymes that build DNA and RNA do their work in the nucleus, that doesn't mean their genes necessarily started out there. "The argument that the nucleus is an endosymbiont (given by a number of authors) is just not borne out by our knowledge of the structure and function of the nucleus," concludes Anthony Poole of Massey University in New Zealand.
------------------------------------
2. Meristem. Are they only found at the root tip?
Nope.
A meristem is a tissue in all plants consisting of undifferentiated cells (meristematic cells) and found in zones of the plant where growth can take place.
The following exist:
1 Shoot apical meristems
2 Root apical meristems
3 Stem apical meristem
4 Intercalary meristem
2.5 Floral meristem
Reference: http://en.wikipedia.org/wiki/Meristem
------------------------------------
Role of auxins + cytokinins. We know about how their relative ratio affect root and shoot growth. What about their individual self?
It is rather hard to classify because their effects are broad-based. You can see them as ligands but when they bind to receptors on different cells, diff responses will result because of...... (you should know)
But below may be the parts you are interested in:
"cytokinins are compounds that stimulate cell division or cytokinesis, although they may also do other things. Proper regulation of cell division also requires auxin, which is needed to cause DNA synthesis before a cell can divide."
Reference: http://www.bio.indiana.edu/~hangarterlab/courses/b373/lecturenotes/hormones/hormone1.html
-------------------------------------
Branchpoint sequence (splicing)
To talk about this for splicing is really getting into the specifics which I do not expect students to know at this level but since this was mentioned, here is a good reference: www.devbio.com/ article.php?ch=5&id=50
To cut a long story short, there is a consensus sequence UAUAAC (branchpt) found within the intron that will cause the formation of a lariat (phosphodiester bond) as an intermediate and this subsequently still lead to the joining of the exons. This is a model proposed.
----------------------------------
Attenuation
This contributes to the termination of transcription in Prokaryotes.
Attenuation is means of controlling transcription of a particular mRNA through the formation of translation-dependent alternative RNA structures (-ve feedback)
Below shows attenuation in trp operon. In a nutshell, the mRNA can form various loops and when trp is high, a different RNA loop structure is formed to prevent complete transcription of all the genes in the operon.
--------------------------------------
And yes. TATA box like the pribnow box are found on the non-template strand but such detail is not critical. Most of the references just req you to state that TATA box is found in promoter and promoter is upstream of the initation site. Do you know the significance of TATA box besides as a recognition site by RNA polymerase? Check your prelims answer.
so what about for the rest of control elements? It is less clear. It seemed to be possible to exist on either strands. then again the same advice apply. Doesn't matter.
This question is unresolved at the moment. Reference:
http://www.sciam.com/article.cfm?articleID=000E9461-AB74-1C75-9B81809EC588EF21
(Extract)
The nucleus also has some superficial similarities to these organelles: a two-layered membrane surrounds them all; they each have their own genome; and they are capable of reproducing. "It's easy to get [these features] when you're essentially swallowing a symbiont," says Hyman Hartman, a research scientist at the Massachusetts Institute of Technology who studies the origin of life. "It doesn't take a rocket scientist to [suggest] the nucleus had an endosymbiotic origin."
Subsequent molecular data only fanned these speculative flames by revealing that the eukaryotic genome is a mixed breed. Genetic sequences indicate that eukaryotic genes for building and manipulating DNA, RNA and proteins seem to come from archaea, whereas genes for metabolism and other cellular functions likely hail from bacteria. "The heart of the problem is that the logic of the eukaryote is very different from the logic of the prokaryotic cell, yet there has been a huge input from the prokaryote to the eukaryote," Hartman says.
..............
Martin, however, points out a number of sticking points for any endosymbiotic model. First, although the membrane surrounding the nucleus appears similar to those of mitochondria and chloroplasts, all of which have two layers, the nuclear membrane is unique. It is a single layer folded on itself, its pores are much different from those in bacteria, and it disintegrates when the cell divides. Second, even though the enzymes that build DNA and RNA do their work in the nucleus, that doesn't mean their genes necessarily started out there. "The argument that the nucleus is an endosymbiont (given by a number of authors) is just not borne out by our knowledge of the structure and function of the nucleus," concludes Anthony Poole of Massey University in New Zealand.
------------------------------------
2. Meristem. Are they only found at the root tip?
Nope.
A meristem is a tissue in all plants consisting of undifferentiated cells (meristematic cells) and found in zones of the plant where growth can take place.
The following exist:
1 Shoot apical meristems
2 Root apical meristems
3 Stem apical meristem
4 Intercalary meristem
2.5 Floral meristem
Reference: http://en.wikipedia.org/wiki/Meristem
------------------------------------
Role of auxins + cytokinins. We know about how their relative ratio affect root and shoot growth. What about their individual self?
It is rather hard to classify because their effects are broad-based. You can see them as ligands but when they bind to receptors on different cells, diff responses will result because of...... (you should know)
But below may be the parts you are interested in:
"cytokinins are compounds that stimulate cell division or cytokinesis, although they may also do other things. Proper regulation of cell division also requires auxin, which is needed to cause DNA synthesis before a cell can divide."
Reference: http://www.bio.indiana.edu/~hangarterlab/courses/b373/lecturenotes/hormones/hormone1.html
-------------------------------------
Branchpoint sequence (splicing)
To talk about this for splicing is really getting into the specifics which I do not expect students to know at this level but since this was mentioned, here is a good reference: www.devbio.com/ article.php?ch=5&id=50
To cut a long story short, there is a consensus sequence UAUAAC (branchpt) found within the intron that will cause the formation of a lariat (phosphodiester bond) as an intermediate and this subsequently still lead to the joining of the exons. This is a model proposed.
----------------------------------
Attenuation
This contributes to the termination of transcription in Prokaryotes.
Attenuation is means of controlling transcription of a particular mRNA through the formation of translation-dependent alternative RNA structures (-ve feedback)
Below shows attenuation in trp operon. In a nutshell, the mRNA can form various loops and when trp is high, a different RNA loop structure is formed to prevent complete transcription of all the genes in the operon.
--------------------------------------
And yes. TATA box like the pribnow box are found on the non-template strand but such detail is not critical. Most of the references just req you to state that TATA box is found in promoter and promoter is upstream of the initation site. Do you know the significance of TATA box besides as a recognition site by RNA polymerase? Check your prelims answer.
so what about for the rest of control elements? It is less clear. It seemed to be possible to exist on either strands. then again the same advice apply. Doesn't matter.
Pls note that there will no longer be any structured time slot for revision ie. the tues and thurs slots as below
Pls arrange consultation with your tutors. Or sometimes if you pop into sr 7, you might find a bio tutor around even if you cannot catch your own tutor.
Pls find VJ P1 answers at RC. I have just uploaded it.
You will also find a post-promo exercise on Sanger. I would recommend that you do it. again on RC
Pls arrange consultation with your tutors. Or sometimes if you pop into sr 7, you might find a bio tutor around even if you cannot catch your own tutor.
Pls find VJ P1 answers at RC. I have just uploaded it.
You will also find a post-promo exercise on Sanger. I would recommend that you do it. again on RC
Bio Bulletin 2
Point 1: In specimen paper 1.
MCQ answer for Qn 3 is C as kindly pointed out by slagoon. There is a mistake in the answer given. That question is a past TYS question.
Point 2: why transgenic salmon is breed with wild-type? Isn't there a concern with genetic pollution which might wipe out the wild-type. (good qn by O.J)
Yes, genetic pollution a concern but such mating is also controlled. The reason why they do so is because despite the greater size and the consequential sexual attractiveness for greater mating chance, the offsprings of transgenic fish do not survive well; the mortality rate is higher. Thus to have the best of both worlds, the mating betw the 2 grps was performed.
---------------------
Non-bio related.
I have already received some data for references. Pls do not submit too late for me because there are several reasons:
1) I would like you to concentrate on your A's and not be distracted by all the applications
2) if you submit late to me after your A's, I might not be around to write it since I will also be out of town from 16 Nov onwards. Well there is still chance when I return on 2 Nov but I must get the forms on 2nd/3rd so that I can bring them along to Cambodia when I fly off to do volunteer work on the 3rd, and type it out and send on 18th when I return. Keep the dates in mind yah. Otherwise, we will have to negotiate ahahahh
3) to overcome 2, some of you have already submit the info but not the application - i am fine with that.
---------------------
For any changes in CCA records (esp for Thomas):
Pls head down to PE dept who is in charge of printing the new forms.
For T, the amendment has been made by Ms Lee *chem.
MCQ answer for Qn 3 is C as kindly pointed out by slagoon. There is a mistake in the answer given. That question is a past TYS question.
Point 2: why transgenic salmon is breed with wild-type? Isn't there a concern with genetic pollution which might wipe out the wild-type. (good qn by O.J)
Yes, genetic pollution a concern but such mating is also controlled. The reason why they do so is because despite the greater size and the consequential sexual attractiveness for greater mating chance, the offsprings of transgenic fish do not survive well; the mortality rate is higher. Thus to have the best of both worlds, the mating betw the 2 grps was performed.
---------------------
Non-bio related.
I have already received some data for references. Pls do not submit too late for me because there are several reasons:
1) I would like you to concentrate on your A's and not be distracted by all the applications
2) if you submit late to me after your A's, I might not be around to write it since I will also be out of town from 16 Nov onwards. Well there is still chance when I return on 2 Nov but I must get the forms on 2nd/3rd so that I can bring them along to Cambodia when I fly off to do volunteer work on the 3rd, and type it out and send on 18th when I return. Keep the dates in mind yah. Otherwise, we will have to negotiate ahahahh
3) to overcome 2, some of you have already submit the info but not the application - i am fine with that.
---------------------
For any changes in CCA records (esp for Thomas):
Pls head down to PE dept who is in charge of printing the new forms.
For T, the amendment has been made by Ms Lee *chem.
FYI
Besides the Post Prelim lectures Every Wed
17 Oct 12:05-13:55 LT1 Specimen Paper 2
24 Oct 7:55- 9:45 LT 1 June Paper
While you can still meet up with your tutors on an individual basis but there will also be tutors on Tues and Thurs in SR2 (this is an amendement: I think we are switching to SR7-10, just outside staff room after the 'hole') from 9am - 3pm (til 25th Oct)
Every Tues: 9-12pm (Mr Ngan and Ms Hor)
12-3pm (Mr Loo and Mr Ariff Chan)
Every Thurs: 9-12pm (Ms Tan and Ms Chua)
12-3pm (Mr ChanHK and Mr Nah)
17 Oct 12:05-13:55 LT1 Specimen Paper 2
24 Oct 7:55- 9:45 LT 1 June Paper
While you can still meet up with your tutors on an individual basis but there will also be tutors on Tues and Thurs in SR2 (this is an amendement: I think we are switching to SR7-10, just outside staff room after the 'hole') from 9am - 3pm (til 25th Oct)
Every Tues: 9-12pm (Mr Ngan and Ms Hor)
12-3pm (Mr Loo and Mr Ariff Chan)
Every Thurs: 9-12pm (Ms Tan and Ms Chua)
12-3pm (Mr ChanHK and Mr Nah)
Reply to Bio Bulletin 1
For the question posted.
I enjoyed reading the suggested answer posted in comments. Sounds like a physio student talking with so many factors considered (which is good) but allow me to sum it up =)
Before we talked about transcriptional control, let's look at the natural state of the chromatin.
1) DNA methylation.
For quite a handful of eukaryotes (not all), there is observed DNA methylation near certain genes and it is believed to be associated with the expression of tissue-specific genes with methylation inhibiting the TF and RNA polymerase from initiating transcription. Thus if you imagine a clone of stem cells, when some start to differentiate, the DNA of these differentiated cells might be methylated at certain parts so that certain genese are prevented from expressing. And this methylation is inheritable. Makes sense?
2) decondensation/condensation of chromatin.
So some genes are a no-go. but what about those that can work/
we know that DNA is wound up with histones forming nucleosomes and then 30nm fibre. But you would also know that gene transcription can only take place if the chromatin decondense (greater than 30nm) to allow for the access of TF and RNA polymerase. In this aspect, there are many proposed mechanisms. The reader talked about histone methylation....I need to check that. The histones can be modified in many ways and while methlyation is one of them, I am not 1oo% clear on their effect but I can tell you that the most regarded one is acetylation of the histone's cysteine residues, making it negative. So let you to go and imagine why this -ve charge is important in decondensation k?
Cool yah? =P =)
I enjoyed reading the suggested answer posted in comments. Sounds like a physio student talking with so many factors considered (which is good) but allow me to sum it up =)
Before we talked about transcriptional control, let's look at the natural state of the chromatin.
1) DNA methylation.
For quite a handful of eukaryotes (not all), there is observed DNA methylation near certain genes and it is believed to be associated with the expression of tissue-specific genes with methylation inhibiting the TF and RNA polymerase from initiating transcription. Thus if you imagine a clone of stem cells, when some start to differentiate, the DNA of these differentiated cells might be methylated at certain parts so that certain genese are prevented from expressing. And this methylation is inheritable. Makes sense?
2) decondensation/condensation of chromatin.
So some genes are a no-go. but what about those that can work/
we know that DNA is wound up with histones forming nucleosomes and then 30nm fibre. But you would also know that gene transcription can only take place if the chromatin decondense (greater than 30nm) to allow for the access of TF and RNA polymerase. In this aspect, there are many proposed mechanisms. The reader talked about histone methylation....I need to check that. The histones can be modified in many ways and while methlyation is one of them, I am not 1oo% clear on their effect but I can tell you that the most regarded one is acetylation of the histone's cysteine residues, making it negative. So let you to go and imagine why this -ve charge is important in decondensation k?
Cool yah? =P =)
Bio Bulletin 1
Do U know.........
1) TATA box is on the non-coding strand?
Usually we make mention about promoter being upstream of the gene in question, then we talk about TATA box sequences. You can take promoter as a region upstream but when we try to dissect the issue of "where is the TATA sequence? On which strand can it be found?"...the answer is as above. (check out the picture in your notes).
Non-coding strand - non-template strand = the strand that is complementary to the one used to transcribe for mRNA.
If you are a visual person, do not confuse this with DNA replication. In DNA replication, you can have two DNA polymerases on each strand. But in transcription, RNA polymerase is a huge molecules that take both strands into account and recognise the TATA box before unwinding and separating the strand for transcription. These pictures may help
2) adenine is related but is not equivalent of adenosine?
Adenine is the purine as we know.
ribose+adenine = adenosine
deoxyribose + adenine = deoxyadenosine
adenosine triphosphate = adenosine with 3 phosphate grps.
3) * Extra * Extra
Transcription factors can be further categorized into two types: general & specific.
General TF will bind to promoter.
Specific TF will bind to other control elements.
It is general because promoters are quite typical so the same grp of TF is applicable for all. Finer control comes with the specific TF.
Question for today for you to ponder: How do you ensure that genes are not transcribed until required?
1) TATA box is on the non-coding strand?
Usually we make mention about promoter being upstream of the gene in question, then we talk about TATA box sequences. You can take promoter as a region upstream but when we try to dissect the issue of "where is the TATA sequence? On which strand can it be found?"...the answer is as above. (check out the picture in your notes).
Non-coding strand - non-template strand = the strand that is complementary to the one used to transcribe for mRNA.
If you are a visual person, do not confuse this with DNA replication. In DNA replication, you can have two DNA polymerases on each strand. But in transcription, RNA polymerase is a huge molecules that take both strands into account and recognise the TATA box before unwinding and separating the strand for transcription. These pictures may help
2) adenine is related but is not equivalent of adenosine?
Adenine is the purine as we know.
ribose+adenine = adenosine
deoxyribose + adenine = deoxyadenosine
adenosine triphosphate = adenosine with 3 phosphate grps.
3) * Extra * Extra
Transcription factors can be further categorized into two types: general & specific.
General TF will bind to promoter.
Specific TF will bind to other control elements.
It is general because promoters are quite typical so the same grp of TF is applicable for all. Finer control comes with the specific TF.
Question for today for you to ponder: How do you ensure that genes are not transcribed until required?
Why are you here?
I know many of you are busy mugging and me too, am rounding things up for the year while pushing for new initiatives.
Although I had wanted to do some online survey or poll but I thought perhaps I can just ask for some response directly if you can, entertain me for a while =P. I want to consider if this blog should continue next year.
This blog was set up with the initial intentions of broadening the horizon of biology to some, answer questions posed in class but have no chance to discuss, pose answers to exercises that can be done by oneself...really bio-related stuff....until noted by SL, I digressed to more mundane stuff of my sappy life with random thoughts. Most of the time I shared because I think it is imporant or a learning point that we all can take to heart or some thing that I think would be good for us to pause and ponder, even for myself.
So why are you here? mmmm...I assume you are from my class? or not?
Does this blog mean anything to you? bio enrichment? entertainment from my boring existence? just dropping in to check for cartoons and clips?
Drop me a line if you want to and is free. The survey is open til end of year :P
Although I had wanted to do some online survey or poll but I thought perhaps I can just ask for some response directly if you can, entertain me for a while =P. I want to consider if this blog should continue next year.
This blog was set up with the initial intentions of broadening the horizon of biology to some, answer questions posed in class but have no chance to discuss, pose answers to exercises that can be done by oneself...really bio-related stuff....until noted by SL, I digressed to more mundane stuff of my sappy life with random thoughts. Most of the time I shared because I think it is imporant or a learning point that we all can take to heart or some thing that I think would be good for us to pause and ponder, even for myself.
So why are you here? mmmm...I assume you are from my class? or not?
Does this blog mean anything to you? bio enrichment? entertainment from my boring existence? just dropping in to check for cartoons and clips?
Drop me a line if you want to and is free. The survey is open til end of year :P
Updates
I know that some of you are biting your nails over other sch's prelim papers. Pls note that they will be sent for printing on monday after the tutors have a chance to look through them thus you can expect to get them on either tues or wed. =). Due to the change in syllabus, different schools may teach things differently or transmit diff information, so you have to remain cool. At least for the school i reviewed, all the things I have taught would be handy as background in answering some structured question.
--------------------------------------
Consultation slots are open for grabs but if possible let me know the day before so that I can plan my time well.
--------------------------------------
A clarification to make, two in fact.
1) At the presynaptic terminal of a nerve cell, there is a Na+/Ca2+ EXCHANGER not pump. There is a Ca2+ pump as well.
The difference? Ca2+ pump uses ATP. In fact it is also referred to as Ca2+ AtPase pump.
For the exchanger, no ATP is used. The protein makes use of the energy stored in the chemical gradient of Na+ (diffuse in) to exchange for a Ca2+ inward. Some may regard this as antiport (if you know the term).
http://www.ohsu.edu/ohsuedu/newspub/releases/022807calcium.cfm
2) ZH brought up a point on differences betw DNA and globular protein. He mentioned that the question was given before and the previous marking scheme accepted various component of synthesis.
If you ask me, I would accept it too. However for this prelims, the setter decided that he wanted to focus on protein structure, functions and characteristic and thus the difference in answer scheme. Pls go ahead and use the various component of synthesis if you cannot think of any other stuff during your exams. It can be accepted.
---------------
Another Friday night. I need to catch up on sleep especially after staying up for a few nights to write those little notes. Buzz out. ZZZzz
--------------------------------------
Consultation slots are open for grabs but if possible let me know the day before so that I can plan my time well.
--------------------------------------
A clarification to make, two in fact.
1) At the presynaptic terminal of a nerve cell, there is a Na+/Ca2+ EXCHANGER not pump. There is a Ca2+ pump as well.
The difference? Ca2+ pump uses ATP. In fact it is also referred to as Ca2+ AtPase pump.
For the exchanger, no ATP is used. The protein makes use of the energy stored in the chemical gradient of Na+ (diffuse in) to exchange for a Ca2+ inward. Some may regard this as antiport (if you know the term).
http://www.ohsu.edu/ohsuedu/newspub/releases/022807calcium.cfm
2) ZH brought up a point on differences betw DNA and globular protein. He mentioned that the question was given before and the previous marking scheme accepted various component of synthesis.
If you ask me, I would accept it too. However for this prelims, the setter decided that he wanted to focus on protein structure, functions and characteristic and thus the difference in answer scheme. Pls go ahead and use the various component of synthesis if you cannot think of any other stuff during your exams. It can be accepted.
---------------
Another Friday night. I need to catch up on sleep especially after staying up for a few nights to write those little notes. Buzz out. ZZZzz
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