Busy

I realised there is only 8 wks left in this semester. Nightmare for the teachers.
I know that I probably shouldnt be typing in this blog right now but Slagoon said recently that I should get a life so - nope, typing here is not the alternative life! - so I decided to relate my escapist life for a while. Or not.

I started my volunteer work again last saturday when we had a youth-volunteer session out at macRitche for an overnight camp. Working with new volunteers and staff is always a great challenge because sometimes adults are the hardest to manage but I think this group will get along fine although i realised that I m considered one of the oldies. So, despite my weariness that afternoon without my siesta, I got myself out of my inert state and got a little bossy to get things moving which everyone somehow assumed to be the teacher-trait. Err..where did that come from?
I got three youths under me, ranging from 14-16. They are cool kids without all the piercing I saw in another although I sensed quiet angst in two which I think I need to contain and diffuse. It was a tough day but I think we got along well after checking one another out. It will be a long journey to take together for the year.

-----------------------------

Last Sunday we had ORA softball carnival. A day of play and reunion.
I unhappeningly brought some marking down although in the end I only managed a script - and that was definitely not the highlight of the event :).
I finally met up with T after so many years. Writing this post reminded me to send him a bday greeting which I always did because he is the yearly joke, born on 1st April. =P So we got together, catching up over light throws with those familiar throwing styles. He was always the bubbly one, full of exuberance while I am supposedly level-headed, setting things properly. So here I am presenting to you, the captain and vice-capt of '97, with the extra kilos:



------------------------

Some students asked me about my decision to teach since they got the moe invites for the moe scholarship talk. It is a long story but if you are really interested, next time then :)

No time liao. i need to churn out some work.

Question of the week_30 Mar

It was as if I am replying to fan mail but then that was just my imagination in brillant burst of colours.

Student from another class:


I remember in your genome lecture, you told us to change the label for the strand containing the 5'-TATAAT-3' sequence from coding to non-coding. But, isn't template=antisense=noncoding? So the 5'-TATAAT-3' sequence should correctly be on the coding strand, as in the given diagram. I know rj teachers say template=sense=coding, but it doesn't corroborate with textbooks and websites i refer to. The coding, aka sense strand, should be the strand that is identical in base sequence to the primary mRNA transcript, albeit T is replaced by U. I.e. coding=sense=non-template.

Reply

Your query is totally justifiable. In fact, I would have concurred with you on this one because that was exactly how I know the strand as: template-antisense-noncoding.
But there are actually two school of thoughts on this issue: template strand =antisense/sense

And I admit my inertia in the transmission of the altered information during lecture, but if I may refer you to your TYS, there are at least two questions N02 and J95 Q15/16 where the template strand is taken to be the sense strand and thus our stand in this issue. =)

Thus I would like to advise you to make reference to TEMPLATE STRAND
when refering to DNA transcription etc for clarity and to be on the safe side :)

Cheers

Last Entry B4 Common Test

What your teacher do in his free time sometimes:
think of possible misconceptions or highly contestable areas of discussions with himself. dun you ever read something or realise something out of the blue that just doesn't fit right in your schema of knowledge but yet cannot pinpoint the source until you start a discussion with yourself? or with someone for that matter. or felt that impulse for a thorough check as you flipped thru pages n pages of books or webpages?

Anyway, here is something which I try to reconcile after spending quite a large part of my day talking to my alter-ego.

Question:
How is the resting membrane potential (RMP) restored after hyperpolarization?


Well, after an extensive search, this issue is actually not very well-documentated but reference has often been made to a role of Na+/K+ pump in restoring the RMP. Most would not even discuss it (with particular reference to ion movements) and simply refer to a restoration of RMP with the efflux of K+ ions.

Sub-Question: If Na+/K+ pump is involved, wouldn't the membrane potential be even more hyperpolarized? - note the pump will exchange 3 Na+ (out) for 2 K+ (in), thus there is a net outward ionic current.
So here is my thought which I believed is correct and reasonably so after consulting several books, reading in-betw lines and based on prior knowledge of the field.

After hyperpolarization has occured, the two voltage-gated channels (Na+/K+) are closed so we are only going to take a look at the leak channels of Na+ and K+.

Because now the membrane is now more -ve inside, there is a greater attraction for the Na+ as the ion - greater Na+ influx. Concurrently there is a greater attraction for the K+ in the cells as well so there is less K+ efflux. The interplay between the two ions movements will eventually bring the membrane potential to RMP.

How does Na+/K+ pump come to play?

Because the pump will naturally cause nett -ve charge in the cell, it helps to facilitate the ions movements.

THUS, it would be more accurate to say that the Na+/K+ pump HELPS to restore the RMP.

(The above is OFS)


You may ask: Do we need to know about leak channels?


Yup yup yup. But only in the context of how RMP is established.
And you should know that Na+/K+ pump is critical in maintaining the Na+ and K+ ionic gradient across the membrane but not with the formation of AP.



A penny for your thoughts?

Take 5 pictures for sharing

follow this link to see the photos which I have taken for take5. you can dl them for remembrane too :)

To be done after common test.

www.flickr.com/gp/7316076@N05/G232NK


Hang In There

Questions of the week_09 Mar

Alright, this is an extremely lengthy post which I took care to craft in hope to bring a more wholesome view to this amazing topic yet trying not to put down information in overly-saturated form.
TOFS - totally out of syllabus.
The rest I think are cool information that will bring a better appreication of information in notes =) cheers!

Drop a note if you need to.

1. Why is a myelinated neuron faster in the transmission of signals?
Myelin sheath provides an insulating layer which impedes the loss of ions across the membrane thus as an action potential travels down the axon, there is little loss of current/energy and thus improves speed of conduction. (awati for diagram)

2. Since Na+ ion is larger than K+ ion (in the hydrated form), can the K+ ions enter the Na+ channel? (TOFS)
No. The conductance of a channel for an ion is not soiely based on size but also the R-groups that line the walls of the channel. Interaction of the ions with the R-groups also contributes to the ion selectivity nature of the channel (in energy terms – we’ll stop here).


3.How is it possible for a given neurotransmitter to produce opposite effects in different tissues? (in notes - For T Flea – if I have not mistaken the question)


The post-synaptic potential (excitatory or inhibitory) really depends on the nature of post-synaptic receptor and the ion channels associated with it.

For example, acetylcholine (ACh) released at the neuromuscular junction (NMJ) btw motor neuron and skeletal muscles will bind to its receptor on the Na+ channels at the post-synaptic membrane, opening the Na+ channels* to depolarize the cell (excitatory)

On the other hand, ACh can also be released at the neuromuscular junction between vagus nerve and cardiac muscles will eventually lead to the opening of Cl- channel which will hyperpolarise the cells (efflux of Cl- - inhibitory)

--------------------------------------------
*
NOTE:
when the ACh-gated ion channel is opened at the neuromuscular junction, the channel is big enough to allow the passing of both Na+ and K+ .
Nonetheless, there is a NET influx of Na+ due to the greater electrochemical gradient thus depolarization (EPSP) is observed, thus it is also correct to make the following reference:
- ACh binds to its receptor on the Na+ channel at its post-synaptic membrane.

4.Since the amplitude of the action potential that arrives at the synaptic terminal is always the same, does that mean that the resulting potential change at the post-synaptic membrane is always the same?

Nope.
While the amplitude of an action potential that arrives at the synaptic bulb is always the same, the frequency of the action potentials arriving at the region might be different.
During summation, there are two issues to be noted:
Is the resulting voltage above threshold? If so, what is the strength of the stimulus?
If the resulting voltage/stimulus is above threshold, all the Na+ channels will be opened* for the depolarization phase.
Then comparing a strong and a weak stimulus, the former will generate action potentials at a higher frequency.

Taking the lead from there, having a series of action potential at higher frequency will also mean that synaptic terminal will be depolarized more often and thus increase the rate of neurotransmitter released for a greater response at the post-synaptic membrane.

5. If the synaptic vesicles keep fusing with the pre-synaptic membrane for neurotransmitter release, won’t the synaptic knob just become bigger and bigger?

Sounds reasonable but it does not happen because there is constant recycling of synaptic vesicles from the pre-synaptic membrane via endocytosis =)

6.Why is a sensory neuron bipolar/ cell body in the middle somewhere? (TOFS)


A bipolar sensory neuron allows the formation of an extensive network of dentrites to receive information from the external environment.
(Oops! After thinking about the question after class, the facilitation of nutrient transport hypothesis does not stand up very well based on what we understand about the distribution of various types of neurons.)

7.Inactivation gate of Na+ channel? (TOFS)

The Na+ channel involved in action potential operates on a two-gate system: activation gate and inactivation gate.
At resting membrane potential, the activation gate is closed while inactivation gate is opened.
When threshold potential is reached, the activation gate will open to allow influx of Na+
After some time, a delayed response in inactivation gate will have it closes its gate. Thus forbidding the continual influx of Na+
During hyperpolarization, the activation gate is once again closed while the inactivation gate will open  back to norm.



---------------------------------
Some additional notes for you:

- signal transmitted at the NMJ btw motor neuron and skeletal muscles is always excitatory but the EPSP generated has to overcome the threshold potential so that action potential will be initiated by neighbouring voltage-gated Na+ channels for transmission along the muscle fiber.

For neuron-neuron transmission, however, there can be both IPSP and EPSP on the post-synaptic membrane

- action potential – do they all look the same?
This question is posted by me because I don’t know how many of you are going to become doctors so you should be aware that the shape of the action potential we are examining now is for a typical nerve cell but action potential found in the nerves of the hearts is of a different distinct form/shape which is also very interesting. =)

Stay Tuned for A Jittery Jitter 2

After an exhilarating session in class with Fleas and being bombarded with OFS questions, I shall attempted to sum it up over the weekend for the many if not, all confused mind. Of cos, there were also very interesting questions posed by SQ.
So catch the questions of the week

Additional References

I have cleared homeostasis tutorial with the Fleas so here are some references which might be of interest to you, given the bombardment:

a) To find out the consequences of hyperglycemia or simply the health concerns a diabetic patient face:

http://www.cdc.gov/diabetes/faq/concerns.htm

b) Diabetes and Exercise Concerns

http://www.medic8.com/healthguide/articles/exerciseanddiabetes.html

c)Still confuse about 2nd messengers?

http://www.answers.com/topic/second-messenger

Take 5

When I looked back at my JC (and even secondary sch) life, I realized that I do not have many photos to remember those days by. I remembered D brought an analogue camera to snap pictures of our class in action, I have quite a handful from the drama performance, standard fare for softball but that's about all.
Then voila, came the age of the digital cameras.

So here are the shots of my students as they wandered in a perpetual state of confusion and delirium throughout their JC life.



Poll

I overheard a conversation last week.
The theme of the conversation set me thinking for quite a while.
At this level, how much effort should a teacher expend on his/her students if they do not bother with the subject at all? After repeated efforts, is it justified for the teacher to just walk away? Some find it real hard to do it because they forsee the consequences, not for themselves, but for the students who are going to reap the consequences at the end of the day. Others calmly let it be, because the students have to learn to bear their own consequences for their efforts. Will that be too high a price to pay? The time and effort could be better spent on others who are willing to learn.

Instead of having the question running around in the head, let take a poll from the ground! :)


Question of the week_2 Mar

Additional Misconception
Other Molecules that enter the Mitochondria:
NADH and FADH2

NOTE:
In oxidative phosphorylation, the NADH and FADH2 needed have two sources: from glycolysis in the cytosol and Krebs cycle in the matrix.

NADH from glycolysis has its electrons and protons shuttle across the the double membrane via shuttle systems to the FAD and NAD+ in the matrix, to reduce them to FADH2 and NADH respectively. The NADH does not transverse across the double membrane.

Nonetheless, the main bulk of FADH2 and NADH are formed in the matrix when pyruvate from glycolysis enters the matrix to undergo Krebs cycle.

----------------------------------

Was it Unclear?

Intracellular signalling is a complicated affair. We can spend weeks on it discussing the various receptors for different ligands and the different intracellular molecules involved for each. So apologies if things do get fuzzy but I will try my best to clear the air.

J asked about the need for a relay molecule to induce a signaling cascade. (as shown in notes)
Is it true for both types of receptors?

Yes.
The term ‘relay molecules’ is really a very generic one. Any molecules in the cascade can be considered a relay molecule.
However there was an attempt to differentiate the kinases and other proteins that are readily activated by the receptors.
When receptors are activated, as an immediate follow up, they can either activate a kinase directly or a non-kinase intermediate like G-proteins and your second messengers e.g. cAMP or even a docking protein (not taught) thus to simplify matters for both types of receptors, the term ‘relay molecule’ is coined instead.

Thus it is perfectly fine to say the receptors will activate a relay molecule which will trigger off a phosphorylation cascade by kinases (in the generic sense) unless you know the exact mechanism like for example the well-known G-protein-adenylyl cylase-protein kinase A pathway or any even given pathway.


------------------------------------

Evolution Baggage

Why do we call Photorespiration an Evolution Baggage?

The question arises because oxygen can compete with carbon dioxide for Rubisco and in so doing, reduce the efficiency of hexose sugar formation via the Calvin cycle as an alternative pathway (photorespiration) is engaged to produce glycolate and glycerate phosphate from RuBP instead, with the release of CO2 and consumption of ATP.

So where does the evolution part come in?
According to the hypothesis, eons ago, the atmosphere is made up of more CO2 and less O2, so carbon dioxide does not face much competition from oxygen for Rubisco so there was no strong selection pressure for a Rubisco that would exclude O2 from its active site. But as the O2 proportion in our atmosphere increase with respect to CO2, the rubisco still retains its chance affinity for O2 and thus perform photorespiration which makes carbon fixation less efficient.

Question: In that case, why doesn’t Rubisco co-evolve to only bind to carbon dioxide?
We are not too sure at the moment and we do not know if Rubisco can be beneficiall to the plants in other ways.
But some plants have attempted to overcome the problem with alternative pathways. To know more, google C4 plants and CAM plants. =)

On the same train of thought….glycolysis is actually a good old way to generate ATP.

Why oxygen is scarce in the eons-old past, early prokaryotes generates ATP exclusively from glycolysis which does not require oxygen. In fact, glycolysis is the most widespread metabolic pathway, suggesting its important role in the early history of earth. It being in the cytosol also play tribute to its historical past before the symbosis of prokaryotes to generate membrane-bound organelles in eukaryotes.

Lecture Test I 2007

The test was not very well done. This would be my grading system based on overall results:

0-10: buck up; fuzzy concepts; need a fair amount of work
10-15: so-so; less fuzzy concepts; need some work
16-20: not bad, shows some clear understanding
20 and above: well-done

Below is something you should take note of, some misconception or inappropriate usage of terms. Print them and attached to test if need to.




ZZZ....