2 months

From 2 wks in Oulu to 2 months here and how things had changed.
It is snowing relatively heavy now because visibility has dropped a bit and the google forecast informed minus zero temperature for the entire week.
The daytime is shorter as well, from the sun setting at 9pm when I first came to now at around 4-5pm. The only good thing the early nightfall was that I can do more work since I concentrates better "at night". My room is also done up now with posters and lamps from ikea. Oh yea! I went to Helsinki and Stockholm last week when it was my autumn break. Ooooo....IKEA stuff from Sweden, totally authentic. I got H&M stuff there too which I realised was Sweden-export :). I would have gotten absolut vodka too except that I don't drink that stuff. mm not much anyway. :P I will prefer my sweet cider.

Thus far, I already had 2 examinations and a paper submission. The last exam was on Friday actually so I was really chiong-ing to read the assigned two books before the exams since I could not manage it during the break. But I think I will pass the exams. hopefully, if not I will have to take it another time which I sincerely hope not to. :P
Life as a student is really different but I think that is also because of a more mature outlook of life. Last night I invited frens over for dinner and to lounge in my sofa. That was just so nice and comfortable instead of the partying (which I had not been to one yet actually). On one hand I wished we could talk longer but on the other, work awaited as I seriously need to do some catching up after my trip - yes, i am definitely procrastinating with a blog entry now :P

I heard OP is around the corner - so good luck to all!! I will probably not do so well for OP here because they claimed that my singaporean accent is very strong. Accent? I was confused until I heard two Singaporeans in Stockholm ahhah. So ok, sometimes I tried to accommodate with clear pronunciation instead of letting my words tumble over my singaporean way. last night I was going to show my frens my travel trips videos when I stumbled upon the clip I made for 3L. The memories of a great time and I could not help it but watch it again before I head for bed. Then Deng also started to post 'My Dear Class' - I must say his camera is really pro hahha. 3G is really camwhorish but I really enjoyed the photos and others have such funny stuff like GL's hysterial rabbit talk and G's updates on hilarious stuff in class and his comic strips (I am not stalking!! serious!!)
As I wrote all these, I started to wonder, who read this blog now as it slowly sinks into oblivion like the titanic. But I will hold on to it a little longer as the name chansensei gets immortalize even in this little city oso I am holding on to this link.

Hugs to all, from the little oulu city. :)

2 weeks in Oulu

It has been 2 official weeks and somewhat it still feel a bit surreal but also like it has been so for quite a while. Lessons have started this week and while they are still mainly introductory except for Survival Finnish, I am excited by them all and remains keen to share my thoughts and experiences. Yah, experiences are truly something that can come with age though one classmate of mine refuses to believe that I am older than her, maybe because of my camwhoring antics. But others sense my subtle behavioral manners that spoke otherwise I think because I am composed most of the time and I will get things organised or facilitate interactions between people. Somehow, I still find myself very much in the teacher mode, taking care of my fellow classmates like staying behind to make sure everyone is accounted for when we move as a bunch, taking their pictures at random moments and sometimes dispense advice to them.
@ wk 2, I am happy to have known some of my classmates better and I now hang out regularly with an international bunch of Japanese, Russians, Turks, Iranians, Taiwanese, Brazilian and Indians. Perhaps there will be more to come.
But what school goes into full steam for all of us, let's hope that we still get to meet up occasionally.
School-wise, I really think it is a bigger world out here. With so many international students and with the quality of teachers here, I really feel like part of a global population and I realised that I can, too, contribute to a wider, global community. Here, our dreams get a little bigger. Still, for those who are doing your degrees overseas, while it could be the same for you too but don't forget to keep the heart and motivation true and clear. Egos and dreams do not have to correlate. But still, I do miss classroom teaching.
Perhaps some highlights:
- went to a Finnish sauna!
- Got a bicycle after a week at a steal!! :): In Oulu, cycling is a basic mode of transport and is supported by a good extensive cycling tracks! And here, the vehicles do give way to pedestrians and cyclists at junctions! This will of cos save me 6Euro for a roundtrip to downtown and time to walk to visit my friends.
- I can walk to school in 10 mins!! (isn't that all familiar :P) and I am happy to have the city library branch opposite my block! =) - and yes, they have some English books! :P
- bought a study table and chair from the recycle center yesterday. In Finland/Oulu, with things being so expensive, it is common to buy things from 2ndhand stores (definitely true for the poor students!) and recycle center. Next thing I need to get is a bigger bed, after which I can stop renting the same things and save costs. Shopping has thus become quite a pasttime for me now, in such stores and also in supermarkets.
- it is really like building an identity and creating space for yourself, getting everything from scratch. I am glad that previous occupants have left plenty of stuff for me to utilise like frying pan, pots and plates etc. At least I don't have to buy them. But just like last week, I cleaned out the kitchen and bathrooms, and bought stuff to make them more...homely? My flatmate does not care that much about the common area but I think it is important. And I managed to make him smile twice ahah. He looks a bit too serious but I supposed he found it amusing that I am buying things for the kitchen and I made him potato salad specially too when I made some for a bbq the other day. That is one point to me! :P
- Last wk was Oulu Day over the weekend. It is a day when museums are opened for free and there are performances in various venues of the city. There are banners and the market place gets more crowded. (see pics!). I went on Sat but skipped the Sunday to do work. :P
- This Friday, there was a simple reception in the city hall where the mayor of the city came to give a speech and there was food and drinks (champagne included :P) to welcome the international students. So cool! But what was nice was for a bunch of us to head down to coffee house later on for a nice chit-chat session :).
- Yesterday, my turkish fren brought us to play mini-golf!

While everything seems like fun and play but there was adjustment made and is still being made.
- I need to plan for my meals, from preparation to eating. Sure you can survive by getting take-out all the time but I also saw coming here as an opportunity to do my own cooking since I can use the kitchen. you should see my share of the cupboard. There are many stuff in there! Perhaps I should stop going to the supermarkets otherwise I will keep thinking of new dishes that I can do (and so I bought the stuff) but don't have that much time to cook really haha. But this really also means adjusting how I use time. There will not be food waiting for me anymore.
- cold weather. I was feeling cold when I first got here. The skin got dry and I felt tired. But now I have gotten used to the weather. In fact, I wore less these days, even less than my classmates and most Finns.
- The sun sets at 9pm. It is so weird that my dinner time gets screwed up.
- Like I said before, feeling a spot for myself in this apartment.
- Being by myself like this. I think I am too used to having pple around me.
I suppose all this will only get better with time. Let's see how things go.

this post came late

This post came late because there was the packing to do, the endless meet-up sessions with friends and to really try to be at home.
Then really, there were the ceaseless waves of affections from students that caught me off-guard and I was touched by them all - before I leave, on the day i leave and for Teachers' Day. They are all reminders of years meaningfully and well-spent in a vocation that I will surely missed. When a friend/colleague of mine bought me dinner and I started to relate how I saw on my own development as a teacher over past few years and how I enjoyed the lessons and lectures when I unexpectedly teared and had to pause for a break. How will this new change turn out? I have no idea as I tried to get used to the whole idea of studying again, adapt to a new environment and rewire my brain. One of my colleague said, because it is me, he was sure I can manage - well, I hope so. This morning I felt rather sad then I realised that I missed my own laughter = my usual dose of endorphin!! There is surely not many things I can laugh at or with here now. What are my students whom I can bully?! :P. The only thing I could do was smile and asked strangers what are all the stuff in finnish that I am buying. I must say that the people do look kind of serious here but they will drop that seriousness and smile with helpfulness. That is fun!!! :). I also make sure I smile first. No point having a sulky face yar? :) I still want to hahaha tho kekeke.

Mmm...I am deviating a little but I am really not too sure what to put down on this post because there was so many things.
First, I thank all of my students who taught me alot, who made me laugh (btw 3G - I watched the video many times hahahaha), who believed in me and who allowed me to linger in their memories longer.
There are also things I noted like how C will come up to me after every lesson to say thank you. It was an effort made to do so personally and I know. So I thank C. A couple of students said that they wanted to do well in biology to show their appreciation. But I value not your grades as much as you as a person with a heart of gold and resilience to take on new challenges. I saw and sensed that in many of you so I am already thankful. Don't belittle yourself for you have many strengths but you need to recognise them.

So on this TD, I also thank you for being part of my life.
now.. I can start blogging about Finland!! ;P

point to note

in the last piece of work:
1) thanks to KT, it should be icosahedral head. it is ICO.

2)

3)know that virus can take its envelope from any fellow of the endomembrane system. It doesn't have to be plasma memb all the time!!
But when describing in general, for the syllabus, we will stick to plasma memb as the one best studied.

Eg. Herpes Virus - the nucleocapsid is assembled in the nucleus. The capsid buds off from the inner nuclear memb trasiently before fusing with the outer memb so that you get the nucleocapsid into the cytoplasm where it bud into golgi vesicles containing the viral proteins --> you get an enveloped virus (with membrane) enclosed by the membrane of the golgi vesicles. The virus is released by exocytosis/fusion with cell membrane.
It is pretty cool! If u are confused, you got to draw it out!

4) Hijack - what does it possibly entail? (this is not a comprehensive list)
a) destroy the host's genome --> no competition
b) modify host's RNA polymerase for its own use
c) produces its own viral polymerase and disable host polymerase
d) produce viral-related sigma factor and destroy host cell sigma factor (for phages) - linked to b) ; you are going to learn about sigma factor soon!


Ok!! That's all I have !!

Sorry folks but was away in Hongkong with my parents until Wed. Great trip but no need to do my travel blog since I fell sick on Day 1. But it was a great trip! :)

Cheers

Clearing Up

Was told that I should update this blog more often.
I did not realise that pple do drop in because this blog has gone relatively quiet for about 2 years before the unexpected surge in traffic this year due to the pressing need for more time to discuss several topics.
Also, even since I started my lecture series, there was barely enough time to sleep, eat and mark so blogging has to take a back seat.=)
yesterday felt like the end of a marathon when I collapsed on Thurs night after NDP celebration and dinner with my class. I finally see more of the camwhoring side of them with the 1-8 poses :).
Even the next day on Friday when I slept in a little later, I felt a little wasted in the afternoon and a short nap just to get back into the rhythm again. It was too much for me lah - staying up until 3-4am for the entire wk and not including those usual late nights that accompanied lectures last wk.

But I was glad that lectures went well and most of the students seemed to be able to get the big idea. And with it, I felt my own development and growth as a lecturer over the past few years. The ability to draw connections and try to convey materials in its beautiful simplicity without assaulting the senses with too much details. well...at least two students from another class told me that they were able to understand and did not sleep in my lectures. It was actually always exciting to lecture just that the preparation could be really exhausting. Haha, I think I am just slow in that because I like to imagine and rehearse my lectures in my head as I prepared the powerpoint slides. But like my bro said, this flow of ideas and thoughts can be very important - just the way I would expect my student to be thinking as they process the information or write it down. The logic and beauty of life.
I think I am going to miss lectures for a while.

This wk was spent on clearing my backlog of marking and reorganising the virus material(and preparing bacterial answers and mcqs). I would get home in the evening, slept for an hour or slightly more just so that I could be awake later in the night and wee hours of the morning to clear the marking and to work out some notes/amendments I promised to provide. So much to work on so that I can leave in peace, knowing that I have wrapped up this challenging topic nicely so that students will have an easier time studying it and therefore appreciating it. Virus can be quite cool! Sighz...so much more I want to and can teach them. But then I know they will be in good hands :)

Got to stop here. too tired. hahah will write on the farewells another time. I still have a list of stuff to clear :) Eeks!

counting down

even though I had totally no concept of time and date, I suddenly realised that my time with the classes and the staffrm will come to an end very soon.
With so many things still on the plate, the end is blocked by the piles in front of me.There is so much I want to teach, so much things I want to do in school, to be there for people, to bring some laughs to an intense environment that I felt a little guilty at leaving them all behind, the dreams and the hopes I held in the education system.

When I was (much) younger, I wanted to go away, leaving everything behind to explore a new world. I saw the excitement on my friends' faces when they left while I saddened by their departure, I thought to myself then that I do not want to be the one left behind. But now that the role has reversed, I realised there is a nagging hurt even for the one who leave. Maybe it is an age thing because when you are younger you have less baggage in life or maybe because I was simply contented where I was.
Still, while the heart was feeling a little overwhelmed, the lagging mind realised that the move is logical and for the better, and a rare opportunity not to be missed.
So the mind will drag the heart along like the plasma membrane dragging and separating the replicated bacterial chromosomes. But I guess eventually things will be set right. there is no right or wrong but just a change.

The Sensei has to forge ahead and do what he always advised the students. Be brave!

But I realised I did slow down in these few weeks so much so that I can feel the songs I listen to. No longer are they background music to accompany me while clearing work but suddenly, they touched me again like they once did in past. Sharing one that goes way back:



——————————————

Stayed up almost the entire night (except for 2 hours of sleep) to sort out the powerpoint. It was amazing that I managed to stay awake all the way for lessons and lectures until 6pm before I gave up, packed my work and went home. I think I am getting too old for such endurance test. Crashed at home for 2 hours and now am up and running again. One more to go.

aftet Hodge Lodge

Was told that I have to know this WAKA WAKA!

raNdoM

21st

Definitely not mine :) but attended another bday birthday last night and realised that this was the 3rd one this year with the same bunch of ex-students.
Over the course the years, these fellows have changed and I too wondered if I did.
When I started to shift back the stuff in school back home early this wk, I was also reading the cards and notes written by these kids to realise my own progression over the same period of time.
I paused and asked myself if there exists a need to leave because there are still so much I can learn, so much to give and so much more to do as a teacher and as a person. Then I remembered that this trip was started with an ideal bigger than myself for I knew deep down that this journey will bring more to others in time to come.
Be brave and find that adventurous side again!

The Model Student

J said A must be a model student with her positive attitude in learning and incessant questioning. I thought for quite a long time and started asking myself, what is a model student?
There is no definition of one because it is relative. There are some teachers who insisted on perfect silence while others preferred a bombardment of questions during lessons. There are others who loved the natural high achievers but there are also others who preferred those flapping in water but brimming with potential.
to me, I think we be who we are but know to be kind, respectful, sincere and generous with our friends, peers and teachers/seniors. And it is more than what you do in class but also outside class that speaks of you.

If J goes by that definition, I am definitely not a model student in sec sch or jc (but I am a friend of singa! ahha) but i would be one in uni yet still i know one of my lecturers does not like me for asking too much questions =P

changes/ new questions

- Pls note the 1 correction in the Summary ; contributed by YF
- the following are good questions posed by students over the hols:


Could I just find out, is the human genome considered a segmented genome? Segmented genome = genes arranged on more than 1 strand of nucleic acid?

I guess so if you used that definition alto i am not aware of the term being used for human genome. It is more likely to be a term used to differentiate the type of viral genome. Because virus, being so small and needed very few genes, it can also easily have all its genes on one strand of nucleic acid.
Diff fields in biology used terms differently.

What are the sources of the viral envelope? The notes mention nuclear, vacuolar and plasma membranes. Could it come from the other membraneous organelles like golgi or ER? Some websites mention that it could come from the golgi membrane too. Or are these three mentioned because there is greater tendency for viruses to find themselves surrounded by these membranes inside a cell but less likely (still possible?) to be surrounded by e.g. ER or a chloroplast?

Yes, in fact i am more towards having the viral envelope coming from nuclear membrane, ER or Golgi, plasma (and will ignore vacuolar).
And no chloroplast.
Where the envelope comes from deps on the types of virus but typically examples will refer to plasma membrane but let's not forget about the rest!!
I need to draw this out for you all to see how is this possible so we will leave it here first.

Does naked virus mean that it doesn't have an envelope or that it ONLY has a nucleocapsid and nothing else? So is a bacteriophage a naked virus? Since it doesn't have an envelope but it has other structures besides a nucleocapsid. Or is the tail fibre, base plate etc considered part of the capsid?

Naked virus is without envelope.
because you wouldnt have only naked DNA/RNA floating around so yes, the nucleic acid will be encloseed by capsid proteins.
tail fibres, base plates are not part of capsid but these are not impt in the classification. in other words, you can classify virus as naked or enveloped; with or without a membranous envelope.
So your phages are naked viruses despite having the tails and base plates.


For viruses, why do some bacteria undergo lytic cycle while some go lysogenic? wouldn't it make more sense to just lyse repeatedly and kill off as many cells as possible?

A temperature phage undergoes a lytic or lysogenic cycle depending on the environment its host is in. If the bacteria is in a environment with a lot of nutrients such that it is conducive for growth, the phage will see this as a great opportunity to undergo lytic cycle because it means that out there, there will be many bacteria to infect (since the bacteria are likely to be growing exponentially!) Joy to the phages which can infect many many more!. COnversely, if the bacteria is in a medium with little nutrients and are not actively dividing, the phage will do into the lysogenic cycle and wait for a better moment.
Another possible scenario is UV light. If there is irradiaton of bacteria by UV light, the phage will undergo lytic cycle. Reason being that to the phage, if the DNA of the bacteria is damaged, it may limit/impede cell division of the bacteria so it rather escape and find another host while it still can!!
PS: I don;t mean to make the virus sounds so lively cos we know that they are intermediate betw being a living and non-living things yah? They are pretty economical tho =)

The notes wrote that the SER catalyses the synthesis of carbohydrates, but er when i checked campbell reece it was stated that it metabolises carbohydrates and synthesises lipids): so which is it?

The notes also highlighted that the SER is also known to be involved in the synthesis of lipids. (impt!!)
As for carbohydrates, SER is known to metabolise it, rather than synthesise it.
Golgi Apparatus is where the bulk of carbo is synthesised tho.
But what other specific roles of SER do you know?

The classic example to study SER is liver cells where it is in abundance and have highly specific roles (which are what we study)

when they say that the RER is a membrane factory for the cell as it "adds membrane proteins and phospholipids to its own membrane".. what does it really mean? does it mean that the proteins produced by its ribosomes are directly incorporated into its membrane without going through modification by the golgi apparatus..? and i also read in campbell that the RER synthesises its own phospholipids [not in notes].. so are those the phospholipids that are incorporated into the membrane? >< (then what are the phospholipids produced by the SER for? D: ) does it matter anyway ><


It is inaccurate to talk about RER as membrane factory. we usually just refer to ER as the membrane factory. There is no need to make a distinction.
The basic idea is that phospholipids are synthesised at the ER where they are first incorporated. Through budding off and fusing, phospholipids may be added to any membrane-bound organelle involved in the endomembrane system (chloroplast and mitochondria are not included). For example if the plasma membrane needs to expand like after mitosis and the cell gets bigger in size to achieve optimal surface area: vol ratio, the additional PL are made at the ER and transported via Golgi A before fusing with exisiting plasma membrane.
Also, if the ER needs modified proteins, it can obtain them from vesicles budding off from the GA. the trafficking is two-way not just one-way. so that is not a problem.


in our notes, it was stated that a transport vesicle moves to the plasma membrane in the process of exocytosis. do we need to make the distinction between the type of vesicle it is here, and if so, shouldn't it be a secretory vesicle?

transport vesicle is very generic term. it can be a vesicle going to the plasma member or to other organelle like lysosomes or back to ER.
but as i mentioned in class, if you know the contents are going out of the cell via exocytosis, pls use secretory vesicles. that clearly defines its role and is awesome.

Polymerisation of HbS

Before I forget. The polymerisation of HbS.

DNA review summary; corrected

All of them are up as promised.
Am sorry that it took quite a while. All the worksheets have been placed in your class pigeonholes on Mon.
for any question, you can email me.




AS was kindly pointed out, pls note the following mistake:
Chain termination for translation:
it will stop when the stop codon is in the 'A; site not 'E' site
The release factors will end the 'A'site

DNA and genomics MCQs_with comments

M&M comments

I hope our laughter during the day was reassuring

C said that this site was getting too depressing...is it? =P
All the laughters had been spent in school that's why. HAHAHAH.

So I decided to write something happy here to balance it out.
Today is PTM day and we had such a good time talking behind the students' backs!! Heh! =)
But the greatest takeaway was knowing that the class has come along nicely and that we are now one big family if not working towards. And to know that even in my absence, they will be there for one another

MCQ answers only

I hope to be able to run through some of these questions in class.
But look through first k?!!!

thanks!

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?

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)

________________________

Amendments and Otherwise

nO.1

Water Potential Notes
As pointed by D, on page 3, (c) pressure potential for plants only -
bullet number 3 - when a plant cell is in a solution with a higher (less negative) water potential, there is a net movement of water into the cell.

nO.2
Does nucleotide has one or three phosphate(s)?
It can be one, two or three, which also means that the term is non-specific.

To be specific, the raw material for DNA replication or transcription are deoxyribonucleoside triphosphates and ribonucleoside triphosphates.
Otherwise, we used the term free XXnucleotides very loosely.

You should know that nucleotide = nucleoside (pentose sugar + nitrogenous base) + phosphate grps

nO.3
Why are the dividing cells in tutorial so dark? Shouldn't there be only a dark spot known as nucleolus for cells in interphase?

Actually the diagram given wasn't so good. For cells in interphase, yes, you should be able to see the nucleolus quite well!:)

Cells in prophase are quite easily identified. I usually look for those in late prophase when you should be able to see individual chromosomes very well.
At interphase, you will not be able to see individual chromosomes.
One should note that mitosis is a continuous process so there are always intermediates stages.

PS: The chromosomes are usually stained so that one can see the them easily for the mitotic process.

http://www.vcbio.science.ru.nl/en/image-gallery/show/PL0096/labels/
http://www.microscopy-uk.org.uk/mag/artnov04macro/jronionroot.html
http://course1.winona.edu/sberg/IMAGES/anaphas.JPG
(for practice?)

Enzyme MCQs

LT test 2
D asked about using rate in length change to determine the rate of digestion. he pointed out that the change in length would decrease as the circle gets bigger.
I agreed. The method provided is a rather crude one (qn asked to estimate)
A better option is to use Area. In fact, we do have scripts that used area and we accepted it as well. =)

The Cat Is Out of the Bag

It finally jumped out, delivered in a mix-bag of sadness and relief.
Relief because it has been a weight on my mind for a while, unable to share and always trying to find the right moment. I wanted to let my R know during class camp but they were having such a good time that the moment never came. Then I realised perhaps there will never be a right moment.
Sadness because when it was out, it felt so real. I wasn't ready for it and wished I had more time instead of the short intermission to talk to R. But on hindsight, it was for the better before words get choked.
I am going to miss them more now after the class camp. Did they realise that they are a great bunch as one?

So the heart was a little squashed today.

Broke the news to all my classes. It is true. Saying farewell was not easy but at this age, I also know that it is not wise to leave your goodbye at the very end.
The only consolation is in knowing that even if I stay this year, I wouldn't be able to stay until the end of next year to witness their graduation.

Half-way through the day, I realised that being a teacher also means that even when you felt a little battered and wanted to sit down somewhere to contemplate, you still have to continue to ensure the smooth running of events for the students

---
I started the year tentatively,wary about getting too involved with the classes in case I do go off (after sending in my application in Jan) but it was difficult to keep that distance and not wanting to know them better. When the acceptance came as a surprise three wks ago, I wished that I could have done even more and better.
----
Coming to the end of the week.
Like any other time, we have to make the best out of what ever we have.

Cell Structure and membrane MCQs

ROG - for test tmr, pls put down the mark you got from the last lecture test on the RH corner of your paper? I lost the data when I changed laptop. will remind again.

too Much

I got frustrated in class today. In retrospect, a big part of the frustration came from within me, in realising that we spent so much time marking and having meetings - one after another - that I had difficulty finding time to craft up better answers, to revisit and think through the questions again and to make learning worthwhile for the students each time I stepped into the classroom. With changes in the scheme of work and the attempts (or over-attempts) to do more things, I felt myself lagging behind. I don't mind staying up until 4 am to complete my markings but I asked myself, surely we can do better?

There was less time to deliberate and discuss in class and it was rushing tutorials from one to another (esp in time for test) that I panicked, worrying that the students did not know what I was talking about and that a lesson went to waste. I don't mind having the buzz in my class but I worried that students did not get what I was trying to say.
Then again, maybe I worried too much.
How much can I worry about them, I realised. I can only try my best to deliver and hope that they had picked up as much from me as possible - the skills and the content. How can I possibly dictate their learning?
(I must have said this before. If I did, it is a reminder to myself that I need to be objective about this)

I sometimes change the answers not because the answers were not accurate or good but I wanted something more comprehensive and wholesome that really brings out the essence of the topic, to show that one truly understands the topic and is able to relate to it.I wanted to tell a story. Often, we list a series of points to help us mark the scripts but a list of facts say nothing about one's level of understanding and I wanted to raise the bar for them. Hopefully.

I had aired my concerns to my bosses and hopefully we will have quality time with the students.

Another day. Time to start marking again.

A whole new week

Friday marks the end of my lectures for term2. For H2 that is. Hipee!! :)
It had been a week of lectures, references and marking. At least 3 days in a row, I stayed up til 3am to finish up the work.
Tues was the worst because I got so upset with my lousy lecture that I stayed up to redo my powerpoint with brand new animations. At least I am proud of my newly created animation :P.
Wed, I went home to nap from 8-11pm then started marking tutorials until 4am before another round of nap to take on the world.
Thurs, I stayed up to improve my slides and create new slides for the next half of lecture.
Friday, ended with a happy note. I was quite pleased with lecture except for the fact that LT1,once again,jinxed me again with no sound and a broken down projector (replaced with a portable one). I recalled that fateful day when I had to use transparencies in LT1 some years ago.
Whoosh! At least one big item is off the checklist and now for the rest. 6th more weeks and I crossed my fingers with all the looming deadlines.
_________

Two separate lecture grps and in each case, I caught someone taking pictures of my slides. Was it rude or was my slide that good? Should we condone such actions? What do we expect from them?

Fear of not doing well

It is always 'been a while since I last blogged'. I think I have been playing fb games too often to distract myself from all the piling work which unfortunately will never decrease. Of course, there were times when I want to blog but was just too tired like 2 wks ago when I was running short on sleep again and I realised that as I grew older, the lack of sleep makes me more snappy. I remembered it wasn't this bad last time because my friend once asked me if I will be grouchy when I suffered from the lack of food or sleep and I replied none of the above - she wanted to make sure I don't snap at her when we went backpacking haha. But I guess now one of them has won the contest. [2 weeks ago I was on a super tight schedule to prepare lecture notes, a mini-lecture, marking tutorials & practicals and trying to get out of the holiday inertia which actually wasn't much of one since I doing marking 5 out of 7 days. I don't know why this year the marking felt so endless. geez.] Anyway I did snap a little when someone fooled around in lab that week. I think my brain wasn't functioning that well then so for the first time, I took off and left the lab. Standing outside the lab, I was trying to decide if I should blow my top or if the sense of irritation was due to the lack of sleep and so I shouldn't really scold the kid. Ok, in the end I didn't when I walked back in.

So why this entry anyway? Because I wrote a mail to my CT class recently and I think I would like to share the message with all my ex-students. Something for you to ponder over:

As many of us prepare for interview, be it for next wk's medicine, for some scholarship or a post down the line in the future, it is very easy to get carried away with the fear of not doing well and so our faces crunch up during interview as we tried to think of the most intelligent or even witty answers.

RELAX

Truth is, no matter how good you think your answers may be or even how good you are, there is no reason to worry to hit the bull-eye, philosophically-speaking.

Each batch of interview or each year, the assessors may look for something different in a cohort. For medicine, there are years when they want sportsman to spice up the faculty or they want people heavily involved in community etc because they want diversity to jazz up this community that is getting homogenous. Then another year, they may feel that there are too many sportsman so they go back to choosing academically strong students and it goes on. Thus to a certain extent, some choices were pre-determined. And this scenario is applicable to all communities and faculties as the world progresses these days.
So why worry?

An interview is a face-on assessment, to see in real life the person who did the writing and to determine (hopefully) if the material written has been blown out of proportion. But the key thing, esp for medicine, is still the smile and sincerity. In those minutes, you will be like seeing a patient, so be compassionate. It is the first impression of a patient as seen from the eyes of the interviewers. Anyway, please pity them :) cos they are sitting in the whole day or days dealing with young fellows like you , sometimes irritating sometimes CMI and most of all, some of them were made to go down to conduct the interviews when they prefer to stay in their offices...mmmm... maybe playing farmville? Or one of current fav of Zooworld!! :)
So don't worry! :) I guess during the intermission period when interviewees come in and out, they may just whip out their iphones and start playing these games and feed their animals hahah.

In a recent book I read by a renowed education fellow, he noted that it was wrong to assess one based on an interview whereby the candidates are supposed to come up with a super witty or good model answer spontaneously or within a given time-frame (some interviews are like that)- and that was the impression given to us by tv programms.
why is it wrong is because all of us come with differently personalities (Myers-Briggs yah?) . Some of us preferred style is to consider the scenario carefully while others tend to be more impulsive and dive in. Of cos there are others who are really superb. this kind of tests does no justice to people who like to contemplate and look at things from all perspectives who are equally important in an organisation.
Anyway, there is no need to be pressured to come up with a super-fast response for I have learnt too (or rather because I am not quick-minded haha) , to take my time to consider my responses and be sincere and truthfully about it.

So what I am saying is that an interview is no indication of your ability and the many wonderful qualities you have as a person.
There are many times when we simply could not figure out why some people pass an interview and others dun so the selection is really dependent on the candidates in the year, projected future based on current global progress and even wimps and fancies of the interviewers. So many variables which we cannot control. so why worry hahah.

To prepare yourself, I ask you to take some time to consider again why you want the interview, the scholarship, the post.
this is very impt: only when you look deeply into what you want and why you do certain things, can you convince others of your dreams and purposes.
only when you believe in yourself can you convince others to believe in you.

And if it helps, think of zooworld when you go for interviews

dun be disappointed ok?

The night before the results were out, my CT rep asked me not to give her the disappointed look when I passed her the results.
I was surprised at her comments because there was the exact thing I cannot do because I remembered the look on my form teacher's face when she handed me my O levels results. It wasn't that I did very badly, although I was naturally disappointed at not being able to replicate or emulate my results for the prelims, but somewhat I felt rejected and from that moment, for a young boy, things fell apart.

The recovery was slow but meaningful.

Many years down the road as I sat on the other side of the table, I asked who am I to judge each set of results? So it was with no expectation when I gave them out because at the end of the day, all of us need to deal with our own disappointments and that is more than enough for one to handle. I can offer them a shoulder or a word of wisdom but I will never be disappointed in them because I know they have given your best shot and there are things beyond any of our control. So as long as it takes them to the next level, I will be happy for them and will be proud of them because knowing all my kids, I know they have much to offer to this world, to the people around them and to blossom in their own capacity in time.

Adios, classes of 2009. Continue to move on with dreams because the best has yet to come. N Thank you for everything.

Tomorrow is just another day

Writing this blog because once my Swoosh-kid said he dropped during exam time because he couldn't get to sleep. So I wondered if tonight insomnia will hit some of my kids.

Some declared tmr as Judgement Day but I beg to differ. Tmr is, however, the day a new journey will start. No matter how the results go, remember that the judgment was by others and only represent a part of you. Whether good or bad, it is important not to let the judgment of others on a part of you fully determine who you are. A new journey awaits ahead for you to explore your potential in many other areas.
Life after JC can be more exciting and some of my kids simply blossoms after that. We all find our own defining moments.

Regards, all the best kiddos! javascript:void(0)

Everything New

This is the 2nd time I fell sick this term and for the same thing - sore throat and its accompanying ailments.
One more time and I shall conclude that the condition is reproducible with my niece and nephew as the causes.
But was on MC yesterday but went to school still to conduct the practical because I meant it to be a follow-up from the lesson the day before and I promised the kids I would close it with all the questions I left hanging.
I was glad that lesson was in the morning because by noon, my head felt like it was stuffed with cotton wool and I validated my mc and went home to sleep off the daze (after informing the h3 class that I cmi and would have to push the lesson to next wk).
A lot of sleep and water did the trick and I felt immensely better today altho the head is still in a drugged state.

Went for lesson just now and today we got a new teacher and she spoke so fast that I could not string my thoughts together. Blamed it on the mist-filled mind but I knew better that for a strong visual but weak audio learner, it will never be easy. I saw words dance erratically in the air and images collide as she went into high gear and verbosity reigned. Does anyone else experience the same thing? I will have to work harder to rewire my neurons so that I can be a more adequate audio learner. sighz..my classmates are so much better at it.

--------
Feb is almost over and I felt a sense of loss with my class(es). I barely knew them and I floundered with my decisions. Perhaps I was a little impatient with them because it was a great year last year, with everything so familiar and comfortable that I forgot the initial tentativeness and worry. Or maybe my expectations have grown which I should never have because every class will never be the same. still, I missed the happiness of every morning and my very own laughter. Perhaps it is the one-intake syndrome and it will pass and I will find my CG again, especially with so many changes occurring in school.

With the amended testimonial on my desk it is one more time and a final signature to seal the memories.

Before they come in...

Orientation will end next week and the whole cycle will start again. Just like that, a click of the finger and we are back at ground zero to do battle for another two years.
What will my new year's resolutions for my classes this year?... Will have to think about that.

You know age is catching up when you picked up a bat and do some swings, only to have an aching back for the next 3 days that almost incapacitated you, made you walk with a funny gait and applied yoko yoko for the first time ever. The only good thing that came out of it was a firmer trunk with less volume at the love handles. I probably imagined the latter but I really have to take care of this back of mine and start stretching before I become too brittle.

The last time I stopped at the softball trip to Chiang Mai. It was a nice trip - restful I dared say because I was finally able to sleep through the night since the start of the holidays. Perhaps there was just too much tension at the start, be it to meet the looming deadline of testimonials or to prepare my own Uni apps or to prepare the trip itself. So the trip was a good one and I enjoyed making the side trip for CIP recce, away from the kids and away from routine. The first day was spent surveying the potential new site, visiting the village where we constructed a water filtration system under CIP and to buy a computer and printer for my translator, Chala with the money collected.
It was at the village when I felt the impact of progress. Instead of straw houses, some houses are now made of concrete. There are now two churches and the village head had his own provision store too. Surveying the whole area from the top of the hill, I realised that our work had brought benefits. At the same time, as more and more help arrived and more and more villagers willing to buy concrete buildings from Habitat for the Humanity, the rustic charm of the 'village' which I once lived in will disappear.
2nd day was a 8-hour journey to Chala's orphanage to bring them the books and electronics. We traveled from 9am to 4pm, one-way because the driver decided to take a 'short-cut' that turned up to be a longer way because we had to go up and down a mountain. I could feel my stomach swimming with discomfort at the end of the ride down the mountain and was glad to stop for lunch to rest out the swirling motion.
The ride back was faster and I got back at 9pm. It was an entire day of traveling but it ended on a high note as I lied down on the bed and watched the fireworks went off outside my windows as the Thais celebrated the New Year with fanfare. It was a beautiful sight.
The next few days were a blur because we played games every day and it was a routine. But mango sticky rice saved the day! :)

-------

Speech in English had never been my forte because I had difficulty catching with the nuances of words and I believed that my hearing was awful --> so pardon my expression. After so many years, I realised why - because it was just so different from Chinese where a single word can hold a profound meaning on its own. But in English, you need to string words to express yourself. Why is it that I never see it that way? As a simple tool for communication.
For the same reason, I struggled when I took elementary French, trying to seek out non-existent depth in each word.
So I decided to work hard on my listening capacity and change the neuronal circuitry in my head. I started my Spanish lessons. I may not be good at this but I am definitely going to make an effort in it. I had already seen how readily my younger counterparts picked up the new language and their verbal verbosity in English. But I will get there.

__________

moral stand.
feathers were ruffled recently with the clashes of the titans in the world. I applauded at the showdown.
There are people who liked to bully their way through things, eliciting demands and not ready to compromise.
We all need the moral courage to now stand up and say 'no more!' - not with stubborn defiance but with compassion. Be courageous to earn less but be responsible for your fellow man in this world. Be courageous to have less so that you can give more.
We say we want to earn as much as possible. But what can we take away when we leave this world? We say we want to leave something for our descendant but don't they care? A father went to seek financial help to keep his 5-rm flat during the financial meltdown when he could be financially comfortable with a smaller flat. Why? Because he wanted to leave the flat to his kids. But how many kids live with their parents these days with some many ready to make their own nests?
There was a philanthropist cum businessman who told his children right from the start that he was not going to leave any inheritance to them. They had to earn their footing in this world. But what he did provide was good education, opportunities to learn and a good environment. All his children did well on their own merits and when he died, all his money went to the charities.

--------

And for the last entry today...
someone write a note to me recently and halfway through it, my eyes were already moist.
Sometimes it took us a long time to realise what we enjoy or what we are capable of. I am glad she found out the she did enjoy Biology at the end of her JC journey. What I was glad about was how she chose to pick herself up towards the end and persevered all the way instead of throwing in the towel.
Life is a journey and through it, we learnt more about ourselves and our abilities. No one can define it for us.