acceptable statements..

Do read my previous post first before reading this one..

..

So, whats an acceptable way to phrase our observations in the ATP example?

you can say:
1) HYDROLYSIS of ATP releases energy (automatically hydration is assumed to be involved as part of the process)
2)Formation of ADP(aq) and phosphate(aq) from ATP releases energy
See? the above 2 statements are simple but harbours no misconceptions;

However misintepretation of statement (1) often leads pple to make statement (3):

(3) Breaking of the phosphoester link/ P-O bond releases energy.
This statement is wrong.; since breaking the bond requires energy. subsequent hydration of the phosphate and ADP is what releases energy.

So now you learn, while 2 statements may seem/sound the same, they essentially mean very different things, because a statement may contain implications, assumptions(as in statement 1) and context. These subtle things are what what people misread or miss out, because of their incomplete understanding.

Remember, in making statements, beware of implications, assumptions and most importantly, context.

Oversimplification breeds misconceptions

For all students who've done biology and chemistry at O lvls and Alvls, have you ever wondered about this: in biology you are taught that ATP is a high energy molecule, when its phosphoester link is hydrolysed ie ATP -> ADP + Pi (inorganic phosphate) energy is released.

Yet in chemistry you are taught that bond breaking (as happens during hydrolysis), REQUIRES energy? So which is correct? why the apparent contradiction?


This really stems from the oversimplification of the hydrolysis process taught in bio.
1) the so called inorganic phosphate is simply the phosphate PO4^3- ion or the hydrogen phosphate HPO4^2- ion. (they in equilibrium under cellular pH conditions)

2) ATP and ADP do not exist as neutral molecules either, their phosphate groups are deprotonated and so ATP and ADP are anionic.

Rewrite the eqn ATP^4-(aq) -> ADP^2-(aq) + HPO4^2-(aq)

The key difference is something as minor as the (aq)!
The P-O bond in the phosphoester link is actually quite weak so it requires little energy to hydrolyse (but energy is still required). However after the reaction, you've got TWO ions instead of just one. The phosphate ion is a small ion that forms ion dipole interactions readily with water; ie formation of HYDRATED HPO4^2- ion releases large amounts of energy.
Having two ions instead of one means more energy is release from hydration. and for those who take thermodynamics at higher levels they should also know that the entropy of the system increases.

So overall the reaction releases free energy.

Ther are many other misconceptions actually propogated in sec sch science eg ..octet rule as a driver of reactions in chem.. and in bio some people use the word oxalate for example to refer to oxalic acid, when in fact oxalate is the anion of the acid (after its deprotonated)...

I think simplification is good when it allows you to deal with issues without getting bogged down by too many details. But it should be done accurately and also set in a right context.
Oversimplification of anything, not just science but also in many current affairs issues, philosophy, religion, on the other hand, propogates misconceptions, clouds sound judgement, and mislead people.

Look at the masses of ignorant, misdirected people in this world....myself included

Last words on SPAA

Some last words on SPA

1. Make sure you study the suggested solutions to extra practice SPA. Note how each of the section is presented. Compare against you own and see the difference.

2. For theory and reliability please take special note.

3. Also note that you MUST still study for the functional groups not discussed in the extra practice.

4. So sorry I didn't manage to mark the extra practice. As it was submitted to me only on wednesday afternoon, and i had meetings for the whole wedneday afternoon still late evening; usually i would completely mark all your work. Regardless, please take ownership of your learning and work; make sure you self-mark using the answer key and correct as necessary. Good luck!

Last words on SPAA

Some last words on SPA

1. Make sure you study the suggested solutions to extra practice SPA. Note how each of the section is presented. Compare against you own and see the difference.

2. For theory and reliability please take special note.

3. Also note that you MUST still study for the functional groups not discussed in the extra practice.

4. So sorry I didn't manage to mark the extra practice. As it was submitted to me only on wednesday afternoon, and i had meetings for the whole wedneday afternoon still late evening; usually i would completely mark all your work. Regardless, please take ownership of your learning and work; make sure you self-mark using the answer key and correct as necessary. Good luck!

SPAz Again!

Hi pple! ready to go SPAz?

Somethings i wanna highlight so you dun go spaz during SPA. (haha i'm so punny)


1.When creating ur mtd make sure that for the test u choose you are careful to predict the correct outcomes.

2. Make sure the procedure you write is IN STEP with your method! some students propose a mtd like say use 2,4 DNPH first then use Na2CO3, but in their procedure its some other order!!

3. THEORY and RELIABILITY: again pls, be specific for the question. like for eg when describing the theory abt silver halide test for R-X, since we are using chloroethane, you should adapt the theory for that compound. So you'd write that OH- hydrolyzes chloroethane, to liberate Cl- ion. Dont bother to write general things like RX and X- ion.

What I mean is, answer the question!!!

4. LIMITATIONS. many students are not good at this. they tend to copy wholesale from notes.
i)Please answer in proper qn context. Like for eg 24DNPH test for aldehyde, the notes limitations says that it can give +ve for ketones too... now, whats the point of writing that if there arent any ketones ard anyway?? in this context, 24 DNPH gives an unambiguous +ve

ii) note that hydrolysis requires strong heat, while acid base neutralisation does not ( for amides vs ammonium salts for eg)



5. SPELL the name of the reagents. 2,4 dinitrophenylhydrazine

6. CONDITIONS!! be specific. like especially (aq), state symbols, and warming.

7. when giving procedure, be specific about the + and - observations!!
so again dont give general statements like.. observe for gas that turn red limus blue.

You should write:
add 2 cm3 dil NaOH(aq) to 1 cm3 of sample and heat strongly for 5 mins in boiling water bath.
Test for gas evolved using moist red litmus paper.
N-methyl propanamide will evolve gas turning moist red litmus blue, while compunds x y and z will not.

Notice If you have to test for gas, you shd describe how you are going to do it, as in "test for gas using..."

You should also specifiy the observations (both +ve or - ve) for the compounds being tested on.

8. Remember to DISSOLVE SOLIDS.

9. Remember to specify, "to fresh samples of cpds..." when describing procedure

10. for safety concerns, write both the measures taken and WHY these measure are taken. eg, do expt in fume cupboard to prevent toxic fumes from escaping to environment.

ok break for now

This is for the frenchies!

Haha you gotta watch this!

http://www.youtube.com/watch?v=1NhSQARojp0



Haha la marche de l'empereur!!!
Its damn funny.

bounce!

You gotta try this! its so fun. you can pick'em up and throw them around. haha

Erm its done by this guy.

How religious words slip, slide, perish

I read this article on the straitstimes, 1 Oct 2006, sunday, by Janadas Devan. Its so good I am reproducing it here in full, for educational purposes.

---Article Begins ---

JOHN Duns Scotus, Byzantium, jihad - Pope Benedict XVI mentioned all three in his controversial address to the University of Regensburg on Sept 12. His Holiness didn't say so, but those proper nouns also gave us 'dunce' (an idiot, a dullard), 'byzantine' ('extremely complicated, inflexible, underhand', especially in politics, as the Oxford English Dictionary defines the adjective) and 'Holy War'.
How did that happen, and why? What do these transformations, or transmogrifications, tell us about religion - or rather, about some aspects of it?
Let's begin with Duns Scotus. Born in Scotland in the town of Duns, he became one of the 13th century's most eminent theologians. Doctor Subtilis (the Subtle Doctor) was the title popular opinion conferred on him, for his philosophy was thought to be especially intricate and subtle, just as Thomas Aquinas, the other great 13th century theologian, was known as Doctor Angelicus (the Angelic Doctor).
Pope Benedict criticised Duns Scotus for his voluntarism - the theory that God should be conceived as Will, not Logos or reason. In contrast to Thomas Aquinas, Pope Benedict noted, Duns Scotus believed that one 'can only know God's voluntas ordinata', or His ordained or established will.
God said, let the bird fall off the tree, and the bird duly fell off the tree; no use asking why, we can only know it was God's will. Such notions gave rise 'to the image of a capricious God, who is not bound to truth and goodness', Pope Benedict noted. Rejecting this view of God, His Holiness stressed: 'God acts with logos.'
Duns Scotus, though, didn't become a derogatory eponym - a name that becomes an everyday word - because of his voluntarism. Indeed, his influence lasted for centuries, and his followers, known as 'Scotists' or 'Dunsmen', dominated English universities up to the late 16th century.
The Dunsmen became known as the 'Duns', a byword for 'pedants', and later 'Dunce', a byword for 'dullards', because of the intemperate manner in which they had opposed the humanism of the Renaissance. No need to ask why the bird fell, they said. All one need know is that there is a first cause - God's will. An undue interest in second causes - the province of science - will only serve to diminish one's faith in the first.
It is altogether apt that our word 'dunce' commemorates the religious obscurantism that almost throttled modern science at its birth in the Renaissance. Sub specie eternitatis, or in the light of eternity, faith and reason may not be opposed, as Pope Benedict argued. But sub specie history, let's not forget, faith did indeed try to stifle reason for centuries. That the first 'dunces' were religious men registers that important truth.
Now, for our second word, 'byzantine', the adjective: It derives, of course, from Byzantium, the ancient Greek city on the Bosporus that Constantine the Great rebuilt as Constantinople in 330, and that is now known as Istanbul. It became the capital of the eastern empire when the Roman empire was split in two in 395. The Byzantine empire lasted for 1,123 years, till May 29, 1453, when Constantinople fell to the Ottoman Sultan Mehmet II.
John Julius Norwich, in his magisterial history of Byzantium, blames the 18th century historian Edward Gibbon for the bad press the Eastern empire has received. 'Like all classically educated Englishmen of his day,' Norwich writes, Gibbon 'saw Byzantium as the betrayal of all that was best in ancient Greece and Rome.'
Its art seemed sumptuous and intricate, lacking the balance and proportion of classical Western art; its Eastern Orthodox religious practices seemed familiar and yet bizarrely foreign; its politics were devious and complex. In a word, Byzantium seemed byzantine to the West, primarily because it was eastern.
Interestingly, Pope Benedict quoted one of the last Byzantine emperors, Manuel II Paleologus, on the subject of Islam. 'Show me just what Muhammad brought that was new,' Pope Benedict reported him asking a learned Persian in 1391.
'God is not pleased by blood,' Manuel II told the Persian, 'and not acting reasonably is contrary to God's nature.' Such a statement was self-evident to Manuel, Pope Benedict argued, because he was 'shaped by Greek philosophy'.
Manuel II, by this account, seems altogether rational and non-violent - a Byzantine Mahatma Gandhi almost - compared to the marauding Ottoman Turks who were pressing in on Constantinople.
Actually, he was nothing of that sort. 'He shared a love of literature and the traditional Byzantine passion for theology,' notes Norwich, but he was 'a man of action' - and devious and underhand, a byzantine man of action, one might add.
He fought with his father and brothers, his fellow emperors in the constellation of small states that made up the shrivelled Byzantine empire of his time. He travelled to Venice, Rome, Paris and London, trying to drum up support for another 'full-blown international Crusade' against the infidels. He made common cause with the infidels, taking part in their campaigns to expand their sultanate, even at the expense of the last remaining Byzantine strongholds in Asia Minor. Manuel II resembles nothing so much as a contemporary Lebanese Christian politician, navigating the byzantine politics of that war-ravaged, multi-religious country.
It is not in the least surprising that such a man, trapped in the politics of his time, would have said: 'Show me just what Muhammad brought that was new, and there you will find things only evil and inhuman, such as his command to spread by the sword the faith he preached.'
Manuel tried to do the same himself, inviting the Western Christians to join him in another Crusade against the infidels. 'Why beholdest thou the mote that is in thy brother's eye, but considerest not the beam that is in thine own eye,' asked the gentle Galilean in his Sermon on the Mount. Christ's words, needless to say, apply as much to Christians as they do to Muslims, Hindus and Buddhists. And of course, all - Christians as well Muslims, Hindus as well as Buddhists - are united in believing that while casting out the motes in the others' eyes is a matter of the utmost urgency, casting out the beams in their own is an irrelevance for they are but mere figments of the others' crazed delusions.
Finally, jihad and jihadist, which are often translated loosely as 'holy war' and 'warrior', respectively. As countless Islamic scholars have pointed out, these translations misrepresent grossly what the words mean.
Jihad derives from the Arabic root ghd, meaning 'to strive', 'to make an utmost effort' or 'to struggle'. The struggle in question covers everything from striving to attain perfect faith to promoting justice. To equate jihad with terrorism is sacrilegious.
'While Al-Qaeda may call themselves 'jihadists' to legitimise their atrocities, I do not see why you need to trumpet their misrepresentations,' a Muslim Singaporean wrote to me recently, objecting to my use of the word in an article. My correspondent was right.
James Fallows in a recent Atlantic Monthly article listed 'an alternative lexicon', assembled with the advice of Islamic scholars, that he hoped would deny terrorists the legitimacy of sanctified language. 'These include hirabah ('unholy war') instead of jihad; irabists ('terrorists') instead of jihadists; mufsidoon ('evildoers') instead of mujahideen; and so on.'
That is sensible advice, but it is doubtful if the meanings of religious words can be cleaned up so easily. Consider, for instance, how the following simple words have come down to us: 'giddy', 'enthusiasm' and 'fanatic'.
Giddy is from the Old English gydig, meaning 'possessed by God'. Enthusiasm comes from the Greek en, in + theos, God, meaning 'inspired by God' or 'God in us'. And fanatic comes from the Latin fanaticus, 'of or relating to a temple', deriving as it does from the noun fanum, temple.
How did giddy come to mean 'overexcited, mentally intoxicated, excitable, frivolous'; enthusiasm, mere 'strong interest or great eagerness'; and fanatic, 'frenzied, mad' - and now simply 'fan', as in 'football fan', which derives too from the same fanaticus?
Religious words slip, slide, perish, lose their meaning, get distorted, become corrupt, precisely because the religious, like the irreligious, slip and slide, distort their faith, give way to irrationality, become corrupt. Corruptio optimi pessima.
Corruption of the best is the worst.

for 3R

Hi 3R

Solutions for the revision mini test.

Consultations ogay.

Dear all, if you want to see me for a consultation, please make prior appointment with me.

best is sms or write me a note.

Even those who have already made appointments with me verbally, please sms me!! Cos, I can't remember them :P bad memory

All the best to all of you out there!

Some useful online chem resources

Rod Beavon: one of the chief examiners in UK for edexcel exam. http://www.rod.beavon.clara.net/chemistry_contents.htm

Chemguide: Good for building foundation and explaining and visualizing concepts http://www.chemguide.co.uk/

More on tutorial 14b and proteins

Here's an FAQ on what you should do in terms of preparing for the proteins section for Chem H2 syllabus. What do you need to study??

I suggest you print this FAQ and append to your tutorial 14b. The FAQ also references tutorial 14b.

Q1. Is it important to know about how enzymes work (induced fit theory etc.)?

A1. No. However students must know that enzyme function depends on its structure, which means if the structure is lost through denaturation, function is lost too. The whole chunk about how enzymes work explains the structure function relationship.


Q2. So what is it that the students NEED to know?

A2. The tutorial is crafted according to SIOs of the syllabus. So its a good guide on what students need to know. Basically 4 major portions:

i) amides - hydrolysis, synthesis, and peptide sequencing. That’s tutorial qn 1,2,3

ii) Protein stucture - Mostly fact and recall. Definitions and esp FOCUS ON BONDING
involved. They also need to draw diagrams, which cannot be only memorized but must be practiced (to draw good diagrams) esp for secondary and tertiary. Tutorial Q4,5,6,10

Quaternary structure. Question 10: you notice there are only 6 marks awarded but 12 bullets in the answer key! Why?
Actually on the FIRST 6 bullets in the answer key are marking points. Those points give a DESCRIPTION of what the quaternary structure is.
The next 6 bullet points actually give the SIGNIFICANCE of the quaternary structure. SO students need to discern; the points from allosteric properties onward should be written if the question asks for SIGNIFICANCE of quaternary structure.
The specific use of haemoglobin as an example is an SIO. So students must know all these points.

iii) Denaturation - Students should know the process, how denaturation take place. They should also know the significance and explain: mainly loss of normal function such as structural strength(eg in rebonding) or catalytic property(rate of enzyme catalysed reactions) and solubility(coagulation). Tutorial questions 7,8,9

iv) Explaining observed phenomenon: examples are given in notes from pg44-45. They need to know them for experience. The examples are by no means exhaustive, and I do not know what's going to feature in the A lvls. The basic concept is that structural alteration(usually via denaturation)or structural differences alters observed function. So students should be exposed and familiar with as many examples as possible, and be able to explain when given any example. Tutorial Q7,8,9


Q3. What does allosteric properties mean?

A3. It means that the biochemical property of the protein is altered. If this word makes you feel uncomfortable feel free to expand. It should go something like "The significance of the quaternary structure is that the biochemical properties of the protein is changed; allosteric properties can arise in the quarternary complex."
A little bit more about allosteric properties: it has to do with altering enzyme active site property when something else binds to it at some other site other than its own active site.
So the haemoglobin example illustrates this... the haemoglobin sub-units are bound together by extensive side chain interaction, when an oxygen molecule bonds to one of the haem groups, its subunit's conformation alters. This forces a conformational change on the other subunits. The result is that their haem groups now have an increased tendency to bind oxygen.

For bio students you would have seen other egs of allosteric effects, eg from co-factors, co-enzymes, and allosteric inhibitors

Some exam techniques

This is with regard to time management and how extensive you need to answer your questions.

Elucidation Questions:

1) Most importantly you must give proper deduction of FG and reaction linked to observation:
eg A reacts wtih 2,4, dinitrophenylhydrazine to form hydrazone--> A has carbonyl group.
These are most important, since without proper deductions you may make mistakes in structures.

2) Give structures and label: these will be 1 mark per structure.

Normally for 10 marks, elucidating 4-6 structures plus all deductions will give full marks.

3) equations?: give these only if the question demands for them. IE the question states:" give equations for ALL reactions that take place"

If question implies that equations are optional: for eg, "deduce structures, and use eqns where appropriate", it means that the equations are used in place of deductions, so they share the same marks. IE if you are able to give full and complete deductions, equations become redundant and do not score more credit.

In these cases, I recommend especially when you are short of time not to write equations; simply do a good job with observations->deductions and structures and you will score.

But if you've got time, write the equations to secure 100% marks.

During tutorials I always demand a higher standard(120%) in order to train you up, and you need the practice to ground your foundation. But during exam, learn to discern good time management.

remember: 1 mark => 1.5 minutes. you may need to be faster than this for organic chem, because for stoichiometry, 1 mark may take a long time (calculations etc) to obtain.

That's it for now.

Something abt proteins

Hi all,

IMPORTANT CLARIFICATION: Some texts regards -S-S- disulphide link as part of primary protein sturcture. This is from definition that primary structure is made by covalent bonding. Also certain proteins exist as crosslinked polymers, hence the inclusion of -S-S- as primary structure.

BUT PLEASE TAKE NOTE: at A lvls, the primary structure is defined ONLY by the amino acid sequence joined up by peptide links. Please do not include S-S in its definition.

-S-S- link is weak and considered to be part of tertiary structure.

Please make sure you highlight this on your notes.

oh well.. i knew it!

You Are 72% Cynical

You're a full blown cynic... and probably even skeptical of these results. You have your optimistic moments, but most likely you keep them to yourself.

How Cynical Are You?

Promo Goals

I hope by now my students have set a good goal for their promo results... I know I have: top 5 in the cohort for 3R and 3H, and top 10 for 7B!

I know that many of you out there are stressed out and really busy, and I'm going to say here the same thing I wrote to my class' yahoogroups:

Life is like a marathon, and through it, sometimes we may feel discouraged or tired; the good thing is, how you end matters more than how you start. So PRESS ON! Lets end this year well!

Plan now and take necessary, proactive steps to attain your goal. Spot your weaknesses and plug them. Work on your basics if you are weak at them. Summarize your learning to key points. Summarize and define the strategies used to solve problems. Use these to make your practice more productive. Balance your equations.

Remember its not just practising a lot, its also practising the RIGHT WAY. So insist on doing your practice properly - proper understanding as opposed to copying, proper format as opposed to poor expression, properly writing out key points rather than have it all in one big mess(and missing out key and marking points). That's whats meant by studying smart. But still lotsa practice is needed for things like, helping with memory, and familiarity so that you can solve problems fast. If your old way of doing things didnt work for you, then you have to do it through new ways! No change = no improvement.

I've been too busy to blog recently yep so sorry for the lack of updates. I'm trying to press on till the end too :) - New notes coming soon.

SPAz

nuts about chem spaz? don't wanna be a spaz in the lab?

Watch the videos!

Seriously, go watch the videos, and visualize what you need to do for chem spaz. you need to get a level 8.

http://www.youtube.com/watch?v=bnQJ2q36d2E

http://www.youtube.com/watch?v=wIZ39gFsfqU

Make up SPA practice

For those who missed out on SPA practice, these are the make up schedules. Please inform me if you wanna go for any of these.

Also, for the real SPA, if you cannot come please have valid reason (its a national exam) like MC etc.If it is due to some school sanctioned event(away for competition etc) please let us know in advance as well.

Thanks.

Thursday...13 Jul...2 to 4pm...Chem Lab 1...Practice 2.........Chem Lab 4 Practice 1
Monday.....17 Jul...2 to 4pm...Chem Lab 4...Practice 1
Tuesday....18 Jul...2 to 4pm...Chem Lab 4...Practice 2
Thursday....20 Jul...2 to 4pm...Chem Lab 4...Practice 2
Wed..........26 Jul...2 to 4pm...Chem Lab 4....MOCK
Thursday....27 Jul...2 to 4pm...Chem Lab 4...MOCK

The doctor is IN!

Yo peeps,

i decided to set aside time to have consultations with pple

Its based on the free period/early days of the classes.
So if you are from a certain class and you got to see me, just approach me to make and appointment (otherwise i will assume i got no business for the day and close shop)

Make appointment in ADVANCE!~


The appointment will then usually be the timings we set aside here. Unless we make other special arrangements

So..
3R: Tuedays 11-12 or 1-2. I till take my lunch at the other slot tho
3H: Fridays 12-2
7B: Fridays 2-4

cya.

omg, i have sub average logical skills

Your IQ Is 120

Your Logical Intelligence is Below Average Your Verbal Intelligence is Genius Your Mathematical Intelligence is Exceptional Your General Knowledge is Exceptional

A Quick and Dirty IQ Test

What it all means is that i got no logical reasoning powers in my brain, although i look like i can really analyse stuff cos i can talk my way out of stuff. And Math is illogical dats why i'm exceptional. That includes general knowledge too. I mean stuff like the chemical formula of vanilla and chilli's capsaicin is similar is very illogical.

And finally i dunno why i'm a verbal genius, cos whenever i type or write, it comes out dsyelcix.