Flying Off

I am back. For a while. Perhaps the next few mintues typing on this page.
Thanks to slagoon for attempt to keep the the blog vibrant in activity. =)

Right now I am in an almost blank-out state after working furiously on next year's notes for the past 5 days. It was like those days in Uni when I would work endlessly for days on one paper assignment after another. Then at the end, when all have been submitted, the body would crash out physiologically with an immense sense of relief. I ALMOST missed that feeling. ;P
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That day, I had a discussion with some teachers on overseas CIP:

I am sure that doing overseas CIP has its benefits because I have seen my own group of teens grew from it and it also allowed me to see a different side of them after working with them for months locally. As a facilitator, we can appreciate the changes we observed in our own team but what does it mean for the participants?

From a teen's point of view, why do you join overseas CIP? Could we have spent the same amount of time and resources to do local community work?
For those who had been on a project before, does that mean that you are more involved in local community work?

Really, whether it is CIP overseas or local and it doesn't even have to be a Project, to get us to doing some good around in this world. It comes with a sense of compassion and the simple awareness of other's needs.
When my brother went backpacking in Australia for a month, he bought burgers for the homeless lying around on the streets to fill their stomachs. And I thought that was just so amazing of my brother. And it also struck the point that we can do good anywhere even when we are on holidays, when we are usually oblivious to the rest of the world except the touristy attactions.

I think I am not too coherent already. I need sleep.
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Last point - I am flying off this SUnday!! After 4 years, I am really going back to Yunnan to visit one of my kids (the whereabout of the rest is unknown), wandering on my own in search of his obscure location. . I guess it is about time to make this journey.
What will I do there? I 'aint too sure. He used to write about chatting all-night long along the yangtze river. But I think we are too far away from the river in this new school he is studying. Perhaps we will just chat and talk about life and how his is going to turn out. Perhaps I can help him ifor his educatiotn so that life can be better for him and his family? And knowing him, he will do good for his village and people around him. Perhaps I will start a chain reaction of pay it forward. it will all be 4 days later.


From 4 years back...

Hiatus

This blog will undergo a breakdown for a while, in line with its publisher's mental state.
Staying up too late to craft out answers for the revision work took its toll on his physiological balance.
Thus a hibernation session has been scheduled, as according to Dr Wolala's prescription.

Until next time!

BBQ with Q

Another class outing, another disaster.
As many can attest on Tues night, my brain neuronal system is not very wired to my limbs as I took on the DDR for the first time in my life.
Juggling with my legs and getting tangled in the mesh of beats are my specialty. I can't bear to see any related clips.

But I enjoyed it. Trying things (within my knowing limits and getting embarrassed) is also my specialty because there is something to look forward to in a challenge, personal or otherwise as we continually push our limits to determine our comfort zone and capability. And I admit, I used to want to try it when younger but never did. haha.
Perhaps more practice will hardwire some relevant motor neurons in place so that I can get more combo points next time!

The stress of standing on that little mat had me totally fizzled out when I got home.

Blind as a Bat

"Ok! Time's up! No more writing!"
In times like these, there are always a few who scribble their last words in that trailing 3-5 seconds. And in times like these, teachers will often turn a blind eye for a while.
BUT to continue beyond a certain time point, it totally messed up my integrity. To do it blatantly? It totally messed up my tolerance.
We are not talking about one adhering to the given command or any remote flexibility one should have in dealing with students in times of difficulties but of fairness to the rest of the population.
Caught one a few days ago in direct frontal view when collecting scripts. Please don't give me that black face and be indignant when what you are doing is so wrong. It totally crossed the line. As my mind deliberates between several options, I eventually gave a warning. Full-stop.

I am not trying to ruin a life here but your reactions speak volumes about you.
Anyway that two lines? Usually pointless for an essay. Although I may be wrong.

TimeOut

It is the holidays thus I did not expect readers to pop in. But then, it is THEIR holidays :P and mine haven't really started.
Work still persists in its tenacity with invilgilation, preparing lectures/notes/powerpoint for next year (one set down and another to go) and even getting the post-promo revision going. I must admit I am still trying to craft the answers which have been sitting in a pile beside my comp for a while. Apologies for not being able to give immediate feedback. I still have pple not handling in yet but I will have a wonderful surprise for them next year so I am not going to let such irresponsible behaviour affects me until I get the answers out especially since I have so many scripts to scrutinize.
*cough* for dramatic effect - I awaits my holiday patiently as I get all these work out of my tray. =)

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I have been doing some interesting reading. So here are something to think about:

1) An insurance salesman knock on the door of a home in a housing development. When a lady answers he asks," How many children do you have?" She replies, "Three." When he asks, "What are their ages?" she decides tht he is too cheeky (like anonymous) and refuses to tell him. After he apologizes for his apparent rudeness he asks for a hint about the children's ages. She says, "If you multiply their three ages you get 36." (their ages are exact numbers). He thinks for a while and asks for another hint, When she says, " The sum of their ages is the number on the house next door," he immediately jumps over the fence to determine this number. This done, he returns to the lady and ask for one last hint," All right," she says, " the eldest plays the piano!" He then knows their ages. Do U?


2) When Professor Leopold Ruzicka determined the molecular structure of muscone and civetone, he saved the life of many African civet cats n Asian musk deer that are mistreated and killed respectively in order to obtain their prized perfumed scents. Apparently, women find the smell of diluted musk pleasant and their sensitivity to it varies with their menstrual cycles, peaking at the time of ovulation. Note: Male sweat contains some compounds with a musky fragance.
Nonetheless, musk's value lies in its ability to act as a fixative in perfumes to maintain its fragrance. (Civet cat secrete similar compounds)
Interesting.

Two things came to mind. 1) You can find musk spray at Bodyshop. 2) Does people with body odour have more musky compounds? =)

MacRitchie: The Day When The Haze Did Not Go Beyond 100

3S
Anyone else with pictures? I realised that I did not take as many as I have hoped since it was the first trail and I was too busy keeping an eye out for the species.


3L
The posers which do justice to the cameraman ahah




3Q
So many running away from the camera...

A tribute to the one who insisted on making the Difference.

Announcement for CIP

I am passing on a message for a worthy cause:

hey everyone! (: 

i'm currently working at pathlight (school for autistic kids) and the autism resource centre (ARC). during the Pathlight school holidays, ARC will be organising many many enrichment programs for the kids (both autistic and normal), and the most popular program now is the sports camp! so we will need about 15 volunteers to help out at the sports camps!

basically the sports camp will involve bringing the kids to pasir ris park, east coast park etc. doing activities like rockclimbing, fishing, kiteflying, kayaking etc. yep. and volunteers will be attached to various groups, and you will get to interact quite a lot with the children!

miscellaneous information - 
- there are 2 sports camps, one for juniors (27-29 Nov) , and one for seniors (20-22 Nov).
- 3 day camp, 1st & 2nd day = 8.30 am to 5 pm 3rd day = 8.30 am to 9 pm
- food will be provided!
- 15 volunteers needed!
- can volunteer for only one camp.
- BRING YOUR FRIENDS ALONG!

anyway, in case you all are worried about the autistic kids, not to worry! they are all very cute!! and most of them are quite well-behaved. it is a challenge to learn how to interact with them (but still hugely satisfying when u succeed), and i think you all would have lots of fun if you join us for the sports camp (: yay! (and of course, i think we have much to learn from them actually. you will find out! haha.)

yep so do email me if you're interested, (me.zilin@gmail.com) [don't spam!] or sms/call me (that is if you have my number) (: yay! thanks for reading!

- Zi Lin (07SO3S)

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If you are free on those days, why not lend a help? It will be fun!!

The Post Promo Hot Deals

I have done a quick analysis of the Post-Promo Revision Exercise.
Those questions in red are meant for submission (an essay n a structured) for some. Questions in blue are interesing/challenging questions and I have added some comments for each topic.
Pls note that I only need the summary for the topic on 'photosynthesis' - there is no need to do any structured or essay for that. Nonetheless, I have highlighted questions you might want to take note so that you can give a better feel of the topics on 'photosynthesis' & 'respiration'.

A recap:
For summary: try out the learning outcomes; use them as heading
e.g.
Outline the functions of the membrane systems and organelles listed in (a)

mitochondria - .....
RER - .....


If you need extra time - pls inform me.
If you are going overseas for exchange/ CIP - pls inform me so that we can work something out.

At some point in time next year in 1st semester, I will go over the MCQs for 2000-2005. So since you are already revising, you might want to work on the McQs first.

Some of you might prefer to write out your summary instead of typing them out. Should that case arise - pls ensure your summary is legible and scan them before sending to me. Best if you can convert the images into a pdf file.


PS: I know that it is the hols and this blog will not be visited often. Pls kindly pass the msg to your classmates via class email to keep them updated especially since some have not emailed me back to acknowledge their recipient of the revision work even though I know they have it, thus i cannot inform them individually.

All In A Shot

Story of the Chocolates

When instructions to do a booklet were delivered, no one in my classes retorted with a 'why?' until much later (Jon) which I choose to ignore =P. Yet, voices were heard from other classes, demanding the purpose of this seemingly irrational or bland piece of work that does not appear to serve any merit. Why Why Why? They persisted.
This new syllabus is all about molecular biology, lamented the teachers. Your teachers are well-versed in molecular biology but at the same time, we had journeyed the old paths that observed life at the macro-level which is just as interesting - animal behaviour, plant physiology, human physiology, microbiology etc.

Biology is all about life. It does not stop at the molecular genetics as the physiologist, botanist, zoologist etc will tell you. What good is molecular biology when you cannot appreciate the system at large which surrounds us in plain view? And reading your booklets, I am sure you all had discovered new interesting facts about the plants which you can relate to another (*and so did I!)

Isaac said 'do in the love of bio' and I really hope you all did enjoy the trip and that the booklet was borne out of the love for life and not of grievances.

Choc for everyone for being so sporting about the MR walk and those booklets.
And....for the great time these past few months.... in case of any changes next year. Arigato.
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Parent-Teacher meeting was over. In my excitement to talk behind your back, I may have said too many wrong things. How wonderful.
Maybe I sounded too positive..shucks...it will haunt me in time to come.

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Gotta stop here. There is a departmental retreat tomorrow which I have to prepare.
Another set of instructionS as promisd:




The above have already been given to some of you so I will be waiting for the following:

1) a typed summary of each topic
2) a structured and an essay for each topic
3)(addition) do the TYS MCQs on topics covered thus far from 2000-2005. - i will take time to go through later. There could be mistakes in the TYS, some of which have already been noted by your classmates but I will leave it for discusion.

Dateline for each topic is to be noted.

How to do a summary: Use the learning outcomes given in that first page of your notes as the guide for your summary. You should cover all the learning outcomes!

I apologized first but I will identify the specific structured question and essay to be submitted by Thurs. I would like to have some time to do an analysis of the questions before I make the choices. Do the summary first.

We need to consolidate this year's work because the new syllabus is consistent for teh 2 years so you need knowledge from this year to carry you forth and also you will then not be swarmed by the need to cope with new topics while struggling with the old ones.

For those whom I have not asked to do the revision work, you may work on the identified questions given as well and submit to me (summary is optional). Trying working on the MCQs too.

Cheers

Nelgect

Someone complained that I have not been updating my blog. But this wasn't even intended to be a personal blog although I had slipped up once in a while with little details here and there.=P with issues that perhaps are worth pondering about.

Today I received a list of parents whom I will be attending to this coming Saturday. 12 names on my list with a min of 15 minutes each. Mmmm...how much ill news and horrible things could I spew on my students in those short time spans? I would have to think them through with descriptions best-fit. Muahahahaha. Then I lamented. Where are some others whom I might want to consult for their child's best interests?

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I received a letter from China today. From a kid whom I have been sponsoring in his education for the past 4 years because in China, the old regulation required all children to be educated up to secondary school and many rural folks faced tough times with the fees that they have to cough up for that compulsory education. So I started sponsoring 4 kids after a YEP trip to China because fate decreed so when our paths met at the most unwilling point in time which I shall not elaborate here. Supporting 4 kids is no mean feat on the pocket and since I don't get pocket money when I was in Uni and all expenses were paid through my various sources of income, there came a time when I started counting my pennies and swore off fastfood etc so that I could send them the money.
Time flies and one successfully promoted to high school while the whereabouts of the oher three are less clear. The last I heard, two have gone off to study at other high school while one started working in another province at a tender age of 14. Most of the time, I would be conversing with this one kid who consistently send me letter (and vice versa) and we would be talking about things in general although with the age gap, I served as a mentor for him.
It is sad when the latest letter indicated his decision to drop out of school soon due to financial problem (I have been unable to sponsor him due to communication breakdown with this particular china agency that was set up to handle the monetary issues with regards to education sponsorship). I felt sad because I know he has always been working hard in his study all this while, trying to be less of a burden to his family finacial situation with the aim to improve life back home but, yet as I reminded him constantly, not to forget about being considerate and compassionate to the people around him. A mature fellow. I also said little but he should have grown since we last met.
Anyway it is perhaps time to take a flight and see how life have changed for him and me and how things can be worked out.

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Tolerance

As the PSI level maintains its toxic high for the past few days, the teachers wonder if the MR tour will die a natural death after all the efforts.

Another thing that had kept its all-time high was my tolerance level. While teachers got frustrated and cranky over their classes, I seemed to be in a world of my own - a world without the white slips or any dictatorship. Yet. Am I too laissez faire with my classes or are they as good as they seem to be? Reminding someone for rude behaviour the other day came through only as an afterthought and I don't think the delayed effect was best for our students. Perhaps years of working with youths of a different league have implanted an even more accepting and tolerant streak in me but here we are talking about a group of students who are supposed to be leaders and should have good character. At this age of theirs, how much 'training' do they need? How much does it take to greet someone as a sign of respect and out of pure courtesy or do we need to rigorously enforce that? Do they understand the concept of atrocious behaviour which is the equivalent of a heart-breaking experience for the teachers when they lied so badly or even conspired with unwilling parties on undesirable deeds? Today, someone got frustrated and cried when all we want is to be able to have some faith and trust in our students. Trust, which once broken, may never mend. Talk about the mushroom of cynical teachers.

I believe my students are good people. Perhaps sometimes, they need a proper signage to direct them but they are as wonderful as they are. We all need some faith and I refuse to succumb to that cynism that festers in the reality of working life because I am afterall, supposed to be the pinnacle of optimism for some. Well, at least until proven otherwise.

Return of Scripts

Today there was a showdown upon the return of the scripts.
Scutinizing their papers, students furiously punched their marks into their calculators to derive their final results. Some were pale on the lips before they sank into relief, others were tearing their hairs at the one or half mark.
It was also a time when you noticed those crestfallen faces or even resignation, a time when you could hear that audible sigh.

There are probably many whom I would like to get a pat to for good work (or as some claimed: the most improved award) but at the same time, there are others whom I would like to console or offer a listening ear to. I may laugh along but deep down, I am concerned especially when expectations are not met with those potential or at least students reaping what they deserve. Pardon me if I could not do any of these in time or too engrossed with swarms of students that hogged me.

Taking a step at a time, do not give up because every new exam is a fresh piece of hope. We all need some belief and confidence in ourselves otherwise we will not be able to overcome that mental barrier and because I believe you can do it.

bio worksheet for macritchie

For the upcoming practical sessions, we will be heading down to MacRitchie Reservoir!!
Hipee!!

In brief, group yourselves into 4-5, produce a brochure based on the species given in the worksheet below. Each group will present 2-3 species during the tour, so each class may want to split the work up to each group on who to present what. Details of marking citeria are given in the worksheet.

www.rjc.edu.sg/newrjc/deptsite
Alternative site if the above fails:
www.geocities.com/lekowala/mac.htm

Schedule:
3S will be going to MR this Fri and hand up brochure Next Mon
3L will go to MR next Mon and hand up the brochure on the same day.
3Q will go to MR next Wed and hand up brochure on the same day.


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Hear ye!

Announcement:

RJC in-house Sci Research Proj - if you have signed up for the project, and those interested, a short briefing (< 1hr) will take place at B34 at 2pm on Wed 18/10.

movie choice

If you are into movie, especially macabre ones, try this cute site:

http://us.mms.com/us/dark/index.jsp

We awaits

A tiring week thus far and I am so glad to have handed in the deliverables this evening after the consecutive late nights and a sleepless one yesterday as I ploughed through many minute details to produce the new bio website. Voila! Hopefully it was be ready by tomorrow when the IT department upload it. Does anyone even know of its existence? Zombie-zone today as I got ready for open house as well since I was the i/c for bio unit - and that was the other mad rush, to get the poster designs out for printing by Tues morning. Whoa! Although the bio-related ones are done ahead of time, I had to rush out those for science department and abandon my street art idea when time become an issue.
Geez. I cannot be doing this too often. At my age, such late nights have serious detrimental repercussion to my body system and you just cannot rebound as readily the next day.

http://www.rjc.edu.sg/subjects/biology/bioweb2006.swf (new biosite)

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How did my class fare for Promo? No one has gotten a U so that is one piece of good news but if you are asking for personal slips, I will leave the surprise to next Mon.
Overall, the same story goes, there will be students whom I think can do much better, some I realised that they really need help in, and others who ally any concern I might have if any. Still we cannot relax too much because there is so little time left.
I havent seen the overall analysis of classes yet but one of my classes got the lowest average for MCQs and I nearly have a cardiac arrest then as I contemplate their possible fates. But they made it up in other areas later on. ;) Have faith.

Oh. Everyone will be promoted. =)

N You know what, Have a good weekend.

Agonizing Moments

This is quick break.
Because I am marking my classes.

There are times when your heart sings and there are times when your heart cries.
This emotional rollercoaster is too much for the weak-hearted.
I need more exercise to strength my heart.

Weekend is here and that pretty good news because I will be done with H2 marking by today and my good friend is getting married tomorrow so we are going to chill out tonight. So you can start imagining your classmate 10 years down the road. Throw in a baby too if you must 'cos I just met another on the road the other day with that bundle of surprise. And a balding head. =)

One More Day

After Pia-ing for hours today, I finally caught up a bit with my marking. Great! After that would be several other things on my platter.

Tutorial are ready for collection but we are not going through next wk so that is good news since everyone else is tearing his/her hair with PW.

Woes to the Teacher

The marking starts and multiple red pens are put on the stand-by.
It is an exhausting process and it is a depressing job.

Stuck in that little cubicle while other depts rejoiced in their near-completion and relaxation.
Your heart skipped a beat and the sky turned gloomier without the aid of the haze when you worried about students who dun seem to be getting the grades when you know that they have worked very hard - that caused me to drop my fishball during lunch yesterday when I was distracted. My poor fishball.
When you are the slowest in marking. Shucks!
When you can't get the tagboard out.

peace and calm, I need to meditate.

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Then I remembered something from Escaflowne.
Worrying only makes things worse. I need to have faith in them that they will/have overcome all odds so that they can move forward later on and afterall, I am only seeing a small bit of the big picture.

Mug Mug Mug

Mug Mug Mug
I am sure you are in the heat of things now.

I did not manage to catch/see a few of you for the past one and a half week esp some of the 3S's but I understand that you may be trying to clear that huge pile of bio readings and not ready to see me...so I can only wish you the best.

Good Luck to all yah!

Why repressible operon- anabolic and inducible - catabolic

A question ask by Phil but my edumail is down so I couldnt get to reply via that channel. A good question nonetheless.

A repressible operon is such so that the end-product of an anabolic pathway can regulate the pathway as negative feedback - no wastage of resources; no need to produce more product.

A inducible pathway is also to prevent wastage of resources because it will only be 'on' if the conditions are right e.g. in the case of the lac operon, if there is a ready source of glucose, why waste energy to hydrolyse lactose?

Format of Paper

Knock knock.
Pls check your 'Revision Promotional Examination 2006'for the format yah?
Although it could be lying somewhere in that stack of chemistry notes.

Provirus? Is it actively transcribed?

Nope.

A provirus is not active while integrated into a host genome in this way. Instead, it is passively replicated along with the host genome and passed on to the original cell's offspring; all descendants of the infected cell will also bear proviruses in their genomes. Eventually, in response to changes in the host's environmental conditions or health, the provirus will be activated and will serves as a template for massive transcription of its viral genome.

http://en.wikipedia.org/wiki/Provirus

What happens to T4 Empty Capsid after Injection ?

What happens to the empty capsid after the phage genome has been injected into the bacteria?

It usually remains on the cell surface until environment favors its dissociation
(activation energy necessary for dissociation of capsids is very high)

Neo-Darwinism versus Darwinism

What is Neo-Darwinism about?

When Darwin proposed his theory, he did not account for 'why are there variations in a population?'. His theory was based on observations that he made and with the underlying clause that there is always variation in a population.

In Neo-Darwinism, with the knowledge of molecular biology, Darwin's theory was expanded to account for 'why are there variation in a population' for a complete picture which we have already done so in tutorials:
1) heritable differences: meiosis (crossing over + independent assortment) + random fusion of gametes
2) mutations (gene and chromosomal)

Amendment to Sensei-tional test

Pls note below.

Today I realised that many still have not caught on to this site yet.
I understand 'cos I barely check online forum while in school too in the past, well-intended things might be.

Do let your classmates know if anything rises and that some answers can be found on this site via your class email.

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As kindly pointed out by Jordan,
In Bio Essence: DNA genomics Exercise:

The answer to 2(c), For Transcription: it should be RNA polymerase instead.
DNA polymerase is used in replication not transcription.

I will make all the above corrections and update the already uploaded files by 7pm.
Thanks!

Consultation Slots

Ok I am worried about some of you but I also know that some of you have reserved these few days to bury yourself in the tons of information. FYI:

Fri:
12 pm - Azura
2 pm - Shu Zhang
4 pm - Amanda

Sat:
2pm - Zhang Rui
3:30pm - Weiquan n Poh

If you would like to see me, drop me a note or check with the above students if you can join in at the prescribed slots.
I can stick around for a whlie so dun paiseh about timing - just check with me

Conceptual Answers to Ur Questions

This post was with reference to some questions posed by some students:

How does inbreeding result in a loss of genetic variation?
> i know that there is a collection of recessive alleles
> but isn't there crossing over to create variation?

Variation comes in all form. You are right to sasy that crossing over of non-sister chromatids of homologous chromosomes ensures variation but it is more significant at the individual level. Comparatively, there is a loss in the genetic variation because of the crossing over is done within a particular gene pool. No matter how you cross within a population, you are going to get only that few alleles (nelgecting mutation) for a gene. If you have cross/inter-breeding, you are open to more alleles and thus there is increased in genetic variation because the gene pool has expanded in quality.

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How genetic uniformity would hamper the abiliy of species to adapt to ecological changes? (4)

> i know that there is little variation for natural
> selection to work on, but will it be extremely harmful or curb
> their chances of survival?

Yes because we are talking about the ability to survive into the next generation. So a change in environment can render the destruction of every individual in the population if there is no variation to increase the chances of survival for the species in the form of selected few who can continue the propagation of the species.

Thus I think as a guide you could have:
- genetic uniformity - no variation in population e.g. asexual reproduction which is conducive in a constant/stable environment
- But ecological changes e.g. environment/climate/predation can result in the destruction of every individual of a population if no variation exists.
- Because variation in a population will ensure that ..........
- thus the surviving few can reproduce and .........

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To add to the post on Neutral Theory, do you know that when we talk about molecular homology we are examining the molecular homology of a particular amino acid sequeneces that give rise to a particular (conserved) protein e.g. mitochondria?

Consultation

Please be informed that I have invilgilation duties on Thurs (8-11) n Fri (8-12).
Will only be able to see you after duty.

Am already taken up on Thurs 11-12:30 WQ
Fri: to be confirmed. ZR and Az can drop me a mail?

Bio SenSei-tional Test 2006 (Answers)

Pls note that there is an amendment to answer on HIV versus lambda phage comparison:
HIV enter the cell by "direct fusion of membrane" not endocytosis.
FLu influenza virus enter by endocytosis.
I thot i have made the amendment but apparently not when I checked just now.


Took some time to tweak so here it is

Bio Essence: DNA Genomics

Finally as promised for Bio Essence: DNA genomics

Calcium chloride in Transformation

The exact reason/mechanism involved in the use of CaCl2 too increase cell permeability is not well-known. Its function was determined through empirical means / trial and error. =)

Making Sense of the Neutral Theory

Neutral Theory noted that at the molecular level, evolutionary changes that occured are selectively neutral and is driven by genetic drift rather than by natural selection. (you already know this)

Because of selective neutrality in mutations (no effect on fitness), polymorphism is found within a population and all of its individuals can reproduce to pass on their different alleles. With that, the only determinant for the propagation of a particular allele will be genetic drift - chances that a particular allele will be passed on, which increases in a smaller population.



The theory sets the basis for the Molecular Clock:
Kimura, King and Jukes made the assumption that most aa substitution

- occur at a constant rate and
- are selectively neutral
(=the substitution is not lethal and does not affect the fitness of the organism)

Since the fitness of organism is not affected despite the mutation, we can thus track the changes in aa sequences over a long period and we can also observe polymorphism within a population.

And since the substition occurs at a constant rate, by observing the aa sequences diferences of particular proteins or genes for two species, we can deduce their evolutionary history i.e their approximate period of divergence from a common ancestor.

If a particular gene is important in function, variation in the resultant aa sequences will not be observed frequently

How enveloped viruses enter cells

Made a booboo yesterday.

There are two ways by which enveloped virus enter cells.

For the flu influenza virus, it does so via endocytosis. Indeed, the nucleocapsid is enclosed in two layers of membranes but the membranes will then fuse to release the nucleocapsid into the cytoplasm where the capsid will be digested away (uncoated) and reveal the nuclei acid.

For HIV virus, there is direct fusion of viral membrane with the cell membrane such that the nucleocapsid enter the cell directly and will be digested ......blah.

Mutation of LacZ gene and Allolactose

Mutation of LacZ gene can result in a non-functional beta-galactosidase.
Beta-galactosidase can engage in two pathways. One to lyse lactose to glucose and galactose and the other to convert lactose to allolactose. Allolactose is indeed an isomer of lactose but its presence needs the working of beta-galactosidase aka does not occur naturally.
Thus with a mutated beta-galacosidase, no allolactose can be formed. repressor proteins cannot be removed from operator. No structural genes in lac operon will be transcribed.

FYI: Permease is a membrane bound protein that facilitate the movement of lactose into the bacteria. If the LacY gene is mutated and a non-functional permease is expressed, no lactose will enter the cell and thus no allolactose can be formed as well.

Distal trpR regulatory gene

Someone goes:
Why is the trpR regulatory gene distal while lac operon's LacI gene proximal to the promoter? What is the purpose? Isn't it better to have the regulatory gene close to the operator for quick access and a better response to environmental changes?

Yea. However in the case of the trp repressor, the protein has been found to be capable of binding to at least 5 other operators in other operons as well. Thus its distal nature in trp operon could have been a compromise.

Cheers

Epistasis versus Linked Genes

Epistasis

Epistasis is used to describe the situation where one gene can mask the phenotypic effects of a different gene.
Typically, the two genes are involves in an enzymatic pathway that affects ONE phenotype.


CASE: When Bateson and Punnett crosses two different varieties of white-flowered plants, all their F1 generation plants had purple flowers!!!

Colorless precursor ---EnzymeC--> Colourless intermediate ---EnzymeP---> Purple pigment

Imagine the crossing: CCPP x ccPP --> CcPp (both genes have a dominant allele; enzyme C and P are functional)

However for the F2 generation you get a ratio of 9 purple :7 white !

If you work out the punnett square for CcPp x CcPp, would you be able to determine which gametic combination will give rise to the white phenotype?


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For linked genes, we are usually refering to two different phenotypes that will be expressed still

Wobble Hypothesis

61 possible codons - 20 amino acids - all due to the degeneracy of code as given in the wobble hypothesis.

Under the Wobble Hypothesis, the third position in a codon can tolerate some mismatch. Thus a single type of tRNA can recognize more than one codon.
Example: a tRNA with anticodon sequence of 3'-AAG-5' can recognize a 5'-UUC-3' and a 5'-UUU-3' codon even though only the former is perfect match according to the AU/GC rule.

The ability of a single tRNA to recognise more than one codon makes it unnecessary for the cell to make 61 different tRNA molecules for 61 different codons.

It probably also provide some leeway for mutations? =)

Evolution Crossword

Here is the answer key to the crossword on evolution.
I think I only managed to show it to one class due to the disruption of schedule from SPA.

Cheers

Celebrating Life

Yesterday we mourned the demise of a friend, an acquaintance or a school mate.
Some students were affected while others carried on with their lives. Really, losses never strike us until they strike close.
With about a decade between the students and I, a handful of friends have already left me behind. Maybe it is age but there is perhaps, a better acceptance of such unfortunate incidents. Although the initial ain of loss will never be eradicated, it was at least buffered.

But I would never forget CF.
About a decade back, she disappeared from my/our lives, alledgedly murdered. It did not help that I actually saw her a week before her demise at a school performance. I had wanted to go up to her then and just say a word of 'hi'. But in the end, I decided not to when I saw her preoccupation with her clique and the crowd that separated us.
i didn't get to say hi and that thought lingered.

In my drawer lies the huge golden clip she gave to me when my folder was in a mess with paper astrewn. And with that, came the reminder that besides thinking of a loss, we should not forget about celebrating the living when emotions are tamed. Life moves on, just like the rising and setting of the sun. I am always glad for the family and friends around me and I am not afraid to express so to them because we are only alive in each instance. I have a peculiar dream a few years back and if it holds true perhaps, I would not be hanging around for too long. So, everyday I am happy because I see people I appreciate and care for everywhere - until I get upset by them - yet that only lasts so long. So try not to forget that 'hi' or smile as we celebrates life with people around us. As for CF, I willl always be glad that our paths have crossed and those memories that we shared.

Someone told me that I could have been more sensitive during lecture on Thurs.
But surely, someone who is upset may not choose to express it on his/her face and some of us have to remain strong for others.

Day 4

Day 2

It needs a bigger container i think.
The blue mark indicates its size yesterday

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Students laughed with me/at at the following things:
1) for no reason
2) for my weird pronunication
3) for my advanced* technolgical ability

I have a bit of hearing problem if no one noticed. I could not catch nuances of English words easily for as long as I remember, much handicapped in the auditory department. Thus my body compensate this deficiency with a stronger visual department, so sometimes when I speak, I see images or words...until I lost it and need to concentrate like tuning a fizzy television into clear screen.
But then it is alright. Do correct me when I need to revise my pronunication because sometimes my brain might process words in funny configurations. Thanks. Although I am sure someone did say pro-Kar-yotes to me before. =P

Tech stuff. We are all learning. Bleah.

Virus and Bacteria Tutorial

Before i forget which happens often whenever I go to classes for reasons unknown, here are the stuff which I would not be going through. They are meant for your own understanding and checking.

How Plasmid/Virus Integrate Into The Bacterial Genome + Recombination

Generalised Transduction

Snustad. Simmons. Jenkins: principles of genetics (575.1 SNU)
The above book covers bacteria and virus pretty well although it may be a bit extensive. For those who wants to know more, you can seek out this book in the library =)

To answer a question that was posed this morning Wed 12/9 (notes is not wrong but probably unclear).

Transduction:

1) Generalised - the phage can transfer any segment of the bacterium genome to another bacterium.
2) Specialised – only restricted segments of the bacterial genome is transferred (those close to the integration site)


Generalised Transduction

From the above diagram and notes:
a defective phage is one that contains bacterial DNA and no phage DNA.

At the end of the lytic cycle, viral DNA is being packed into the phage and so are some of the bacterial chromosome fragments. This packing error will give rise to some phages with viral DNA and others with only bacterial DNA. Size of the bacterial fragments will vary.
Since this defective phage does not contain viral DNA, (after adsorption and injection of the bacterial fragments into a new bacteria cell) no new bacteriophage is synthesized in the recipient bacterial cell.

Specialised Transduction

There is the lysogenic state and en face with an induction event, the excision of prophage is erroneous, removing a phage genome with some of its genetic material replaced by (particular) bacterial genetic material. The recombinant viral DNA that is produced this way is usually defective because some of its own genetic material is left behind.

This new circularized recombinant genome can still undergo replication because its origin of replication is intact and the DNA polymerase is non-discriminating  so you can get many of such DNA.

However, when the recombinant DNA is packaged within a capsid and the transducing particle injected it into a new bacterial cell, since part of the viral genome has been deleted, no progency virus can be formed in this bacterium because the necessary (viral) enzymes are not present*.
Recombination can take place as in diagram or there is integration of the DNA due to a common gene.


*this may be dependent on the site where the viral genome is cut, whether genes are removed. But usually they are and thus rendering the virus defective.





Specialised transduction


Examples of recombination close-up



Integration requires one-point




Recombination requires two-points





Diagram showing integration of F plasmid into bacterial chromosome.
Correct and Incorrect excision of F plasmid.

Updates I

I am sleep-deprived but so are quite a number of you, judging from your faces in classes.

Anyway, I have/will be giving out revision worksheets which I prepared last night. Most of the questions are from 10-years series except for Evol and bateria/virus because they are new in the syllabus so I scoured for them, drawing from different sources.

Why we are doing TYS? Because ultimately you are going to take the A's next year and sometimes there is a discrepancy in how schools and cambridge set their questions .I learnt that you all don't have enough exposure to TYS and let's not wait til the last mintue yah? And although the syllabus has changed, some have remained and I predicting that the deviation for some should not be too great for the first year. Oh well, there is no harm doing them right?

Questions are selected based on past experiences with students aka these are the more problematic MCQs for selected topics. Other than these, most should be okay - you would have to try them out yourself next time/next year? Right now, all these should serve as practice.

Answers will be posted later so that those coming for remedial can discuss them. But I think I will set it for as a test for one of the classes....?mmmm... will need to think hard.

Will be posting some bacterial diagrams later that we can all appreciate their recombination beauty.

Oh for 3L, I have started hatching the eggs yesterday:

Questions to consider

I am taking a hiatus after the multiple postings. "huff 2 puff 2"

Consider these random questions first which came to mind and students seemed to have trouble grasping during the course of teaching or hearsay (will post them in comments)

1) What are the purposes/functions of mRNA? (students on remedial should know)
2) What is the neutral theory about?


mmm......until more random snippets of thoughts self-generate or diffuse through from the school community....zzz......

Hope holidays have been good

Polymorphism

I probably need a revision on this question posted but...


Polymorphism is a form of genetic variation that exists as discontinuous e.g. blood groups in humans. There are distinct forms for a particular feature.

This, of course, is in contrast with continuous variation.

Where does energy for tail sheath contraction come from?

Since virus does not generate energy on its own, we are confounded by how the tail sheath contract. (out of syllabus)



One school of thought:

Hydrolysis of ATP stored in tail sheath upon conformation change.
(mentioned in this paper http://jb.asm.org/cgi/content/full/183/1/358)


Another school of thought:

There is a conformation change that involves a change in energy states (high to low) when the tail sheath contracts, thus favorable.

http://72.14.235.104/search?q=cache:fvBMMNlafq8J:bilbo.bio.purdue.edu/~viruswww/Rossmann_home/publ/pdfs/425.pdf+contraction+of+tail+sheath+energy&hl=en&gl=sg&ct=clnk&cd=9

Interesting.

What is an Antigen?

Taken off the net (which I find appropriate):


A substance capable of inducing an immune response. Exposure to this substance results in production of a specific antibody or a sensitized lymphocyte that in turn interacts with the antigen. In some autoimmune diseases, the body's own tissues may act as antigens.

Usually reference is made to proteins from foreign bodies (virus, bacteria etc) but (keep it at the back of your mind that) proteins of one self can be considered presented as antigens too, particularly during the development of our immune system so that our immune cells are primed to recognise our cells later on.

HIV - Transmission + Where does the HIV antibodies come from?

To become infected with HIV, the virus must be:
1) in sufficient quantity
2) enter the bloodstream

Thus, it is not enough to come into contact with an HIV-infected fluid to become infected. Healthy, unbroken skin does not allow HIV to get into the body; it is an excellent barrier to HIV infection. HIV can thus enter the bloodstream directly through an open cut or sore, or through contact with the mucous membranes (and transported across membranes) in the anus and rectum, the genitals, the mouth, and the eyes.

HIV can be more easily passed from person to person, through blood, sexual fluids i.e. seminal and vaginal fluids and breast milk where HIV tend to be concentrated, in following ways:

1.unprotected sexual intercourse with another infected person

Is HIV only transmitted via blood?
No. In the event of sexual intercourse:

Male to female transmission: Semen carrying HIV can enter the body of the female partner through the mucosal lining of the vagina, cervix and uterus.

Female to male transmission: Vaginal secretions carrying HIV can enter the body of the male partner through the head of the penis, the exposed urethra, or other cuts, sores or lesions on the penis.


2.sharing of infected needles and syringes (e.g. injecting drug users)
3.mother-to-child transmission during pregnancy, childbirth or breastfeeding


During pregnancy, there can be transplacental transmission of HIV virus. Mechanism is poorly understood though it may be due to particular receptors. (http://www.cahr-acrv.ca/english/resources/abstracts_2004/abs/abs236.htm) (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=11745695&dopt=Abstract)

HIV is often passed on to the child during labour or delivery when there is direct contact with the mother's blood and bodily fluid. A caesarean section can apparently lower the risk. (note: Tutorial question examined the mutation of the virus after birth)


4.transfusion with contaminated blood or blood products




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The HIV Antibody Test detects whether proteins called antibodies,
which are produced in response to HIV, are found in the person's body.
Most people develop antibodies within 12 weeks of infection.
However, it is possible that the antibodies do not appear until six months
after the point of infection. This period of time when a person is infected
with HIV and has not developed antibodies to HIV is known as the
window period.
A positive result means that you are infected with HIV. You can infect others if you have sex with them.
A negative result means that you are either not infected or your infection was too recent to be detected. You need to repeat the test 3 months later.

But isn't the HIV latent? Where does the HIV antigens come from for the body's B cells to produce antibodies?

There is an inital phase when the HIV first enter the bloodstream and is active, causing a strong response from our immune system (thus all the antibodies) It is after that when it enter the latency period where by its number is low in the bloodstream but will persist in replication

(http://www.berkeley.edu/news/media/releases/2005/08/08_hiv.shtml) - quite a cool paper. Although the line of research is foreign to me but the concept is refreshing.

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(FYI)

HIV has been found in saliva and tears in very low quantities from some AIDS patients. It is important to understand that finding a small amount of HIV in a body fluid does not necessarily mean that HIV can be transmitted by that body fluid. Contact with saliva, tears, or sweat has never been shown to result in transmission of HIV.

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Does Oral Sex confer transmission of HIV?

Oral sex carries a lower risk, but again HIV transmission can occur here if a condom is not used - for example, if one partner has bleeding gums or an open cut, however small, in their mouth.

See study below.
The study was done on men-men relationship. However it should be noted that there is a much greater incidence of HIV transmission in a hetero-relationship. HIV is not a gay disease.

http://www.cdc.gov/hiv/resources/factsheets/oralsexqa.htm

Prophage: genome or entire cell?

Prophage: phage GENOME which is integrated into the bacterial chromosome. Upon the occurence of an induction event, the prophage is exercised from the bacterial chromosome.
Prophage is also considered as the latent form of a bacteriophage.

Where do the bacteria in our intestines (microflora) come from?

http://www.all-creatures.org/health/beneficial.html


Before birth the gastrointestinal tract of a normal fetus is sterile. During the birth process the newborn is inoculated, by passage through the birth canal, with organisms from the mother’s vagina and bowel.

Benefits to the infant begin immediately with this natural defense barrier of “friendly” bacteria standing against harmful microbes that will enter later on with touching, suckling, kissing, and caressing. The importance of this early invasion should not be underestimated. This initial invasion makes a permanent impression on our immune systems, thereby affecting a person’s well-being throughout his or her life.

Newborns delivered by cesarean section do not get a healthy dose of mother’s bacteria. Born through the abdomen, much of their initial bacteria come from the unhygienic environment of a hospital. However, this setback can be remedied by the initiation of proper infant feeding after birth – and helped by the addition of infant probiotics (see below).

Breast feeding encourages the growth of “friendly” bacteria known as Bifidobacterium. These vital organisms protect the baby from gastrointestinal infections that can result in illnesses severe enough to require hospitalization, and sometimes cause death. Mother’s milk contains sugars (galacto-oligosaccharides) which encourage the growth of these friendly bacteria. By the fourth day of life, Bifidobacterium represent 48% of the bacteria in breast-fed infants as opposed to 15% in bottle-fed infants.4 Eventually, over 95% of the bacteria become Bifidobacterium bacteria in an exclusively breast-fed baby. Introduction of small amounts of formula to a breast-fed baby will result in shifts from a breast-fed to a formula-fed pattern of the microflora. After weaning from breast milk – ideally after the age of 2 years – the child’s flora become similar to an adult’s.

Change the Diet – Change the Microflora

The partially digested remnants of our meals, after arrival in our large intestines, become the foods for our microflora. Each species of bacteria survives best on specific kinds of nutrients. In short, “friendly” bacteria prefer to dine on plant-food remnants, and pathogens thrive when the diet is low in plant foods and high in meat and other “junk-food.” Therefore, what we choose to eat determines the predominance of the bacteria species that will live in our gut. By changing from a diet based on animal- and highly processed-foods to whole plant-foods, you can suppress the growth of harmful bacteria and stimulate those that are beneficial. Major alterations in the microflora take place within one to two weeks of changing a person’s diet.

What does CAP binding protein do?

Finally. After two days of ceaseless typing and meandering through excessive information, your new set of notes for lecture is ready for collection. Bio rep please collect on Mon morning... I am brain dead....almost.

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Finally can get down to reply to the loads of fan mail that lies before me and sort out a series of questions in my head.

Disclaimer: All info published are based on current understanding.


Function of CAP binding protein in lac operon:

Lac operon has a weak promoter (low in efficiency). When bound to DNA, CAP bp-cAMP complex will increase the affinity of promoter region for RNA polymerase - this is done through an almost 90 degrees bending of DNA which allow CAP to directly interact with the polymerase at the promoter.

Consultation + Polycistronic versus?

moe email is back on service.

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I am back on a vengence.
Please note that as the moe account has been facing many trouble since its apparent facelit on 1 Sept thus if you are coming for consultation, kindly send/resend a mail to XXXX instead or just post a comment - it will reach me.

Those who I am meeting tomorrow - cya.

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Polycistronic mRNA - refers to mRNA which will give rise to many polypeptide chains i.e. many genes encoded within it

versus

Monocistronic mRNA - refers to mRNA which only give rise to ONE polypeptide chain i.e. one mRNA - one gene - one polypeptide; this is typical of eukaryotic cells.

Will be talking about it soon.

The rest of the questions will be tackled soon - need to rush something out by Fri

He-li-O

I decided to set up this site to share knowledge with everyone in my classes, in particular to deal with interesting questions and concepts that have been raised up by students, some of which may not be in the syllabus but are interesting learning points. (And I can get it down in print before I forget to get back to students=P) It also includes questions which flash through my boggled mind once in a while or to clarify issues present in class.

Biology is really about life . There was a period of time when I wanted to focus on cell and molecular work, only to take a step back and say, I want to know more about life in general as well otherwise my education in the field is not complete. Biology is huge and your teacher is not enlightened yet but will try his best to direct your path to the end of the tunnel where the light is.

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Please note:

Consultation during the September holidays will take place from Thurs - Sat (12-4pm)
Do let me know if you are coming down via email: chan_huang_kiat@moe.edu.sg otherwise I might not come down to school.
I might not be able to reply you readily because I will be away til Wed morning. My apologies but I will be down on Thurs definitely.
Do let me know if you need to see me beyond the above time slot.

Cheers for the mugging.

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There are some running questions in my head now. Will post them once I have the time. It is a busy holiday too. :P