Sunday, April 28

Project(s) ?

Hello everybody!
This is going to be a very short post. Just a few updates.

Earlier today I went to Westminster bridge to shoot video for teacher's day. It is a project entrusted to us (yes, I'm not the only one. My schoolmate Izzanee and I) by Abg Abu. Overall, it was a job well done though we have to do about 5 takes to do it right. So wait for it. I'll definitely post it here once it has been edited and published in front of all teachers. For now, let it be a secret.

After that, we went for a stroll and the day ends for me with lunch at Noodle Bar and Zuhur prayer at Soho Islamic Centre. I am glad that we did this project together. Alhamdulillah.

Once I have safely arrived home, I tidy up my work station and thinking space, and continue working on my application to Cancer Research UK. It is still in progress but I aimed to finish it tonight. So it's going to be all nighter today. :)

Having successfully committed myself on two projects despite being busy with preparing for the exams, I begin pondering on my next project. Of course it has to wait until I finished my exams.

The following are my upcoming projects. A little bit ambitious but I hope I will be able to do all of them.

1. Volunteering with Cancer Research UK and focusing on developing my knowledge and soft skills. I will be more specific on what sort of knowledge and skills I want to develop when time comes.

2. Upgrade my knowledge on argument, logics, organic chemistry and neuroscience.

3. Know and understand my family member better so that I can help them. I am thinking of doing serious psychological research to help them and focusing on what I can do for every single one of them.

4. Do more cooking and baking but this time I want to understand the science behind it so that I am aware of the nutritional value (healthy) and probably creating my own. I got this idea when I came across rows of books on science of baking and cooking.

5. Be fluent in Japanese specifically able to write stuff in Japanese like what I do now. My goal is to go through all the components (vocabulary, grammar and expressions) in Japanese for Busy People 1, 2 and 3. Also, thinking of joining Japanese society next year so that I can practice my Japanese.

6. Explore London.

7. Enhance my Quran memorisation

After mapping all of these in my mind maps, it seems like summer is not enough. However, this is just a rough idea. When time comes, I will prioritise and organise these projects. Adjustments might have to be made. Most importantly, I have written what I want to do this summer. So it is now time to get to works.
All the best!

Friday, April 26

Protein biosynthesis: Translation

Hello everybody!
Currently I am working on my knowledge of nucleic acids. I have to say it is one of the challenging topics in my degree due to the fact that there are so many uncertainties in the topics. However, we should appreciate what have been discovered and perhaps one day I will be able to conduct my own research to reveal the knowledge behind this class of biomolecules, nucleic acids.

Before I begin specifically to protein biosynthesis, I think it is best for me to give an overview of nucleic acid studies. This is taken from my lectures on nucleic acids and it may not cover all aspects of nucleic acids studies. Here is the list of all 5 topics that I am currently working on together with its subtopics.

  1. Nucleic acids as special biomolecule
    1. Nucleotides: Structure and function
    2. DNA: Secondary and tertiary structure
    3. Gene and genome organization
    4. Biosynthesis of nucleotides
  2. How genes work
    1. Transcription
    2. The genetic code
    3. Translation aka protein biosynthesis
  3. Regulating gene action
    1. Principals
    2. Gene regulation in bacteria
    3. Gene regulation in eukaryotes
  4. Changing the message
    1. DNA replication
    2. Mutation
    3. DNA repair
    4. DNA recombination and rearrangement
    5. Cell cycle and inheritance of traits
  5. The new genetics
    1. Recombinant DNA and biopharmaceuticals
    2. Nucleic acid hybridisation and diagnostics
    3. DNA sequencing and bioinformatics
    4. Ethical consideration
Now that we know what sort of things that I need to know, it is easier to put things into context. So today I am going to write on translation.

There are generally 4 stages of protein biosynthesis.
  1. Activation
  2. Initiation
  3. Elongation
  4. Termination 
There are two requirements for translation and they are:
  1. Carboxy end of the amino acid need to be activated so that peptide bond can be formed easier
  2. There must be a way to link between the information in the mRNA and amino acid such that the protein sequence follows those intended
The solution to this is by attaching  amino acids to tRNA and this process requires Mg-dependent amino acyl tRNA synthetase (as catalyst) and ATP.

Formation of an initiation complex.

In bacteria, start codon codes for formylmethionine. In human, its methionine.

1. Formylmethionine is attached to its appropriate tRNA
by amino acyl tRNA synthetase
to form amino acyl tRNA

2. mRNA attached to the 30s subunits (of ribosome)
This process require the participation of initiation factor F3.

3. anticodon triplet of tRNA is juxtaposed to the initiation codon of mRNA (5'AUG3')
This process require the participation of initiation factor F1, F2 and GTP.

4. 50s ribosomal subunit become bound to the mRNA-30s-tRNA-amino acid complex
bound GTP is hydrolysed
initiation factors are released

5. Ribosome is now ready to translate the reading frame with the initiation codon.

OK! Before we go further, since I am confused let us clarify a few things.
Ribosomes are made up of two subunits. In human it is the 80s subunits (30s subunit and 50s subunit) while in bacteria it is the 70s subunits (30s subunit and 40s subunit).

So what happens is mRNA binds to 30s subunits (initiation factor F3 is required),
aminoacyl tRNA (which carries methionine) binds to initiation codon of mRNA (5'AUG3') in which initiation factors F1, F2 and GTP are required forming mRNA-30s-tRNA-amino acid complex,
50s subunit binds to the complex
bound GTP is hydrolysed
initiation factors are released
and ribosome is now ready for translation.
Hence,translation is initiated.

For pharmacological purpose, this step can be inhibited by aminoglycosides (amino-modified sugars). Aminoglycosides are antibiotics like gentamycin, streptomycin etc.

Now that ribosome is ready for translation and reading frame has been determined, the process of elongation begins.

Translation is achieved by sequential repetition of three reactions between amino acids.

Step 3A: Binding the second aminoacyl tRNA
To clarify further aminoacyl-tRNA is the complex formed after mRNA has been attached to corresponding tRNA.
Two aminoacyl-tRNAs are orientated such that their anticodons are opposite their complementary code triplets on mRNA, and
the amino acids adjacent to each other are on the surface of 50s portion of the ribosome.

This step can be inhibited by tetracyclines, diphteria and ricin toxins.

Step 3B: Formation of the peptide bond
The two adjacent amino acids are linked by peptide bonds
RNA acts as ribozyme which in part catalyzes peptidyl transfer

Carboxyl group of formylmethionine is linked to the amino group of the second amino acid such that the dipeptide is attached to the second tRNA occupying the A site of the ribosome.

This step can be inhibited by chloramphenicol. If I may say, this drug is one of my most commonly used drug as I often develop chalazion and this is one of the treatment.

Step 3C: Translocation
The tRNA for formylmethionine is released from the P site,
tRNA in A site moves to P site, and
30s subunit moves one codon along the mRNA.

This step can be inhibited by macrolides. An example of macrolides is erythromycin.

I should clarify that ribosome has two sites in which amino acyl-tRNA can attach to which are A site and P site.

The next amino acyl tRNA then enters unoccupied A site of the ribosome and these three reactions repeat.

Elongation continues until the ribosome encounters termination sequence.

Termination is catalyzed by release factors that cleave ester bond that joins peptide chain to the tRNA corresponding to the C-terminal amino acid.

Ribosome is recycled for next round of protein synthesis

The end.
Done with protein biosynthesis.

Dr Paul Long's lecture notes.
Occasional reference to journals in tthe US Library of Medicine National Institute of Health.

I have tried my best to paraphrase his lecture notes but at times I am confused and I don't want to lose the original meaning, so this might not always be the case but it's not a problem because you readers know who the works originally belong to. I am just using it for the exams that are coming up in a couple of weeks.

Anyway, writing helps me understand and digest complicated stuff. That is why I wrote a lot of academic stuff in my blog. Sometimes when I am doing further reading I realised that I made mistake in my blog. I have the intention to review it but it is just not possible so if you think my note is helpful don't just take my word for it. Use my note as trigger points not your primary source of information. Deal?

When I was proofreading my post, I realised I did one great mistake that is not using proper accepted citation. I am writing it so that my future me and I are aware that what I did is not academically accepted and therefore should be done properly.

So I thought as one of my career development, I would write a post on how to properly cite references based on King's citation guidelines. The truth is since I seldom do citation, I kind of forget how to do so and this post is evidence of it.

Thursday, April 25

Slept for 9 hours? 「9時間寝ました?」

Hi there!
This time around I would like to describe about my past few days which were so fantastic that it ends up with me sleeping for 9 hours. Hehe.

From last Friday the 16th of September, till yesterday, Sunday the 18th of September, I joined the Muslim Youth Camp (MYC) held by the Musolla Community (MUSCOM) with collaboration from the alumni. The event was indeed a very successful event. The theme for this event is 'Aku, kau dan ...'. It sounds very catchy isn't it?

Well, This is whatI wrote a couple of years ago. I thought I just post it. Then it made me think. Do I have to post it? Well, my decision is simple. Yes. Do you know why? This blog depicts part of me and part of me is writing random stuff. This is where I express my emotions. What I want to achieve is to inspire people to write their emotions. Pretty much like how I was inspired by Dr John Watson's blog from Sherlock (TV series). I don't expect people to read what I wrote. It is for future me to read what current me is thinking and feeling so thatit can bring back past memories, past achievements and ultimately past failure that I can learn from all over again.

After all, I'm doing it for myself. If there is anyone else inspired by it, then it's brilliant but that is not my primary focus. That is also why I decided to just write when I feels like it. I don't put rules. Like Nike said, just do it. So do it.

I just have few things to watch out for. I don't spread fitnah. At least I have no intention of doing so. I don't lie in my blog. I will make myself clear as much as I can if I think what I wrote might be offensive to some. That is just part and parcels of writing in public. You've got to watch out for what message you are sending no matter how small it is. Consequently, I am not 100% myself in this blog. If I can quantify it, I would say 49.376376376376376376%. Pretty close to half of me but not exactly hence the recurring decimal.

That's all for now. Bye! Have a good and productive day!
Dr SyafQ.92 - 4A* - (^-^) 私の文書を読んでくれてありがと。

UK interview trip: not so long time ago.

This is a post I wrote a long time ago on my interview trip to UK. Since I have lots of things to write but due to my circumstances I need to step back, reevaluate myself and make changes I think I should complete my old post. So here it is.

Hello there!
So today, I am writing in London trying to write an account of my journey yesterday.

I woke up at 5 am in the morning, got prepared and off to PD to pick up Pak Cik. Soon after, my father drove me to KLIA. At 9.00 am we reached KLIA and this is my first time despite several visits to KLIA going to KLIA in the morning because I will usually go to KLIA at night, thanks to my sister who always buy a night flight whenever she is travelling home. After checking in with a checked baggage of 23.5 kg which I was grateful as Qatar Airways do not charge anything for that extra 0.5 kg, we quickly headed to the boarding area. Passing through the immigration was not difficult but it was not easy as I am not used to it, Insya Allah after this everything will go on smoothly. Nothing funny at the moment but the fact that I was with Pak Cik is very fascinating. He taught me several ways of how to speed up the process of immigration checking. That is very handy as you can see when you reach the part where I wrote about my arrival to Heathrow Airport later.

Bla bla bla, I went inside Airbus A330-200 and straight away headed to seat 40K. The flight was awesome, the view was nice but I find long haul flight rather boring. The movies that they had in the personal tv was already seen. So nothing much to do other than sleeping, looking at the map all over again and looking some part of the world through a plane's window. Nevertheless, I managed to watch few shows. Such fun! (Miranda!)

After 7 hours of flight, I reached Doha. It was awesome to see how a desert can be transformed into such a modern city. Upon arrival, I wandered around the duty free shop, performed my prayer and connected to the internet just to update my journey. Five hours were just enough to indulge the beauty of Doha from the windows of Doha International Airport which currently is undergoing rapid renovation. At 4.30 pm, I checked in for my next connecting flight and Doha was about to embrace the coming of the night. The flight was scheduled to depart at 5.20 pm. However, since the flight is not full, by 5.00 pm boarding process had completed and the flight embarked the journey earlier than planned. I would say the second flight is more worse than the first flight. Firstly, I was entering my sleeping mode so I spent considerable amount of time trying to get a good sleep but I couldn't as the engine was too loud. I never thought air travel could be this much daunting. Note from me to past me. Wait till you get on 14 hour flights from KL to London, you'll be much more daunting.

I was supposed to write my first experience in a long haul flight and first experience to UK alone but today (25/4/2013) I don't see the point of doing that. Partly, because I have lost the details of my emotions at that time and partly because I have no interest in reminding myself of dark past. At least not for now. So I think I'll just end this post with a couple of tips on a long haul flight.

1. Bring own entertainment. No matter how much interesting the movie list in my personal tv, I can't focus on it. It ends up like trapped in a room with nothing to do other than pretending to be sleeping or enjoying the outdoor view.

2. Bring own pillow, face mask and ear plug. It might seems trivial but it does increase my level of comfort by 100-fold if I can quantify it.

3. Supply yourself with motivation. Tons of them.

4. Do a lot of walking. So choose aisle seat if you don't want to bother disturbing the person next to you. Talking about aisle seat, I always got aisle seat but for some reason I am always the one that has to move to other seats which are not aisle seat. It's quite annoying. Hope to have better luck next time.

5. Drink a lot of water or fruit juices. Consequently, it gives you excuses to escape from awkward conversation.

6. If you can, avoid sitting near emergency exits. It's a hassle though there is no emergency. Again this helps prevent awkward conversation like when the person next to you ask whether you understood what the stewardess is saying.

7. Avoid seat near or close to seats with children bassinet unless you can stand baby's crying throughout the flight.

8. Avoid seat near the toilet because you din't just get to hear the annoying flushing sound, you also sometimes get to smell what's in it. Sometimes people queue up near the toilet. When they do, be prepared not to have your own privacy.

9. Avoids sitting in the middle because there's higher chances you get to seat beside talkative person. The logic behind it is this. Talkative person has higher tendency to sit where there are lots of people. Middle seats equivalent to larger number of people hence larger chances to meet such person.

Most of this is my own experience. I don't usually act like this. In fact, I don't actually mind talking to people. It's just that in a flight my physiology become very distinct and sensitive. You do not want to seat beside me in a flight. I get moody. My leg becomes restless. I go to the toilet very frequently. I can't sit still. I'm just not me. Allah knows why.

So, that's it for now. Hope it helps.
Dr SyafQ.92 - 4A* - (^-^) 私の文書を読んでくれてありがと。

What to do when you are overwhelmed with something?

Hi there!
If you still unaware, I am in a panic attack. I can't focus on my studies which I really need to do now efficiently. So I decided to write it out.

First step, stop! Stop what you are doing and keep calm. Now the question is how to keep calm. Lucky for us, we have several ways among those are reciting the quran which I am going to do right after. It is becoming important to remain calm and composed in this time so that our efforts will not go to waste. When I am in a panic attack, I hyperventilate. I shivers a lot. My hand goes numb. My mind goes numb. I feel restless and all those negative things appear. Not to mention the sudden sleepiness and urge to eat.

Therefore, remember Allah. Zikrullah. There must be sin that I have committed. So take a step back and ask for repentance because he is the Most Forgiving but you have to follow the steps that the prophet has taught us. Stop, regret, seek forgiveness and repair the situation. Bottom line is to reflect. I'm not going to do that here because it's personal.


Now that I am calm. We have to get back to business.
Focus on your objectives. Break it down and take little steps to go towards it.

So, what are you still waiting for. Let's do it.

Oh right. This morning I went to the clinic for spasm. My GP wants to prescribe me with diazepam. She did give alternative which is using diclofenac diethyl ammonium gel. Well, diazepam is a controlled drug (CD). Being a CD, I decided I want to try the alternative first even though it's not the best treatment for spasm. Now I regret it. It hurts like hell. I think I just need to calm down and relax. So yeah. Let's do it.

If by next Monday my spasm hasn't subsided, I'm going to ask for diazepam. I should have chosen that but I have to take responsibility of my own decision. Deal with it Syafiq. It's your choice. :\

Wednesday, April 24

Excuse no more.

Hello everybody!

It's been quite a while. No excuses. I am just quite busy with my study and sorting out my finances as last night, I got my allowance for the next three months. Alhamdulillah. To be honest, I am  freaking out because exam is just around the corner. So I thought I write something to make myself feel better.

So, why am I freaking out?
Lots of things in my mind. I need to let it out.

Syafiq, you know what, most people survive their degree. Stop worrying so much and focus on things that you can do. Focus on your must, want and wish lists. Everything will be fine insha Allah. Just don't forget to keep yourself calm and composed, and pray to Allah that he blesses you with quality revision time.

Earlier today, I went to Lloyds TSB Bayswater to withdraw my house rent. On my way, I met Kak El. Do you know who is she? Well, as much as I hope it to be Kak Ell that we all know, she is actually the JPA officer in charge at JPA London office. Since my house is just 5 minutes walk to her office, I always go to her office to tend to matter pertaining to JPA. Don't get me wrong. She's married and pregnant. Also, she is expecting her baby this June. If Kak El happen to be reading this, just know that my prayers are always with you and may Allah protects you from all danger. We talked a little bit about my life. She asked me about my summer plan and I confidently said to her that I am volunteering at Cancer Research UK though the real thing is I am still working on completing the application form because there are quite a number of questions to answer. Insha Allah, I will make it. The questions are a little bit like short answer questions in 200 words. She was happy for me and asked me to write a short report about it. I knew this is my chance to show JPA my passion towards research so that when it comes to 2016 and when I am applying to Oxford for my DPhil study, I have not just support from JPA, I will be able to put her as my references to show how serious I am to pursue neuroscience. Hope everything goes well in 3 years time. Amin. Hence, I will definitely do it. Syafiq, don't forget ye!

Having said that, I think it is best to include JPA in my academic life decision making process as much as I get my parents involved. The reason being so that they will understand why I make such decisions. In fact, by involving them in my decision making, I am not on my own. Instead of just my mind and thought alone, having them involved would increase the amount of thought put into my decision making. Consequently, I am well informed of my decision and and hence able to live with it. So, my academic coaches now are my parents, Prof David Thurston and JPA.

I love doing what I do. I am grateful for what I have. I could never have received this much without mercy and bless of Allah. I went through trouble times. Trouble that no normal people could ever imagined. Trouble that I always keep to myself. See. It all paid off now. That is why Allah will never test us out of our own capability. Without all the sufferings, I could never be in this position. I have to say I have certain conflict with people that is important to my life. Well, that is life. No matter how hard it is, you just have to go through it. Now that I am aware of what those conflicts are even though it may be I am the only one who realised that it is a conflict, I am keen to resolve them. Not all at once of course. Hence, the very first conflict that I am going to resolve now is usrah.

I am going to do it now. Here. Just a word of caution. The next part of the writing is not intended in any way to offence anyone. It is just an expression of my thought and it may be wrong. Don't be put off by that.

Before I begin, I would like to set the context. If you ask me in person, I would never be able to say what I am going to write the reason being I am a little bit insecure. When I am insecure, I have my own defence mechanism and one of them is that I will go towards the direction that you want me to go. So if you want to really know what I am thinking, you shouldn't control what I am going to say. By that I mean you don't ask me questions. You give your expectation and I will fulfil that. Also, as part of my defence mechanism if you are being judgemental or I think you may be judgemental, though you didn't control what I am saying, I am not going to open up. I only allow myself to be vulnerable and insecure in front of the Creator and my parents if I can control what is happening afterwards. I'm not a liar but I do withhold my thinking until I feel comfortable.

So, what is all the fuss about usrah?

To be honest, nothing big. Nothing. I am fine with it because this method has been devised by intelligent peoples who try to solve the world problems. The fact that they are trying on itself is excellent enough.

My problems is however the content and how it is being conveyed.
Tadabbur al-quran. I understand it is not as beneficial if we just recite the Quran every single day without knowing its meaning. However, if we are to directly take the meaning just by reading the translation, that is where I don't think it is the right thing to do. Muslim scholars since the sahabah era had been doing so many things to ensure that they get proper and valid understanding of the quran. It is easy for sahabah to do so because the prophet Muhammad was with them. Hence, the prophet would have clear up any miscommunication and misconception. In fact, the sahabah knew the context in which the ayah is revealed. They knew arabic language. Hence, if we, with no proper and valid knowledge of asbabun nuzul, arabic languages, and all other tools accompanying them, derive the meaning directly from the translation, what is the level of confidence that you can place on that derivation such that it matches what allah wants us to do. How are we any different from the Christians and the Jews that use their holy scripture to justify what they are doing.

If meanings are taken out of context, we may not fully understand its meaning. Hence, do tadabbur al-Quran by learning it from accredited mursyid muslim scholars. One example is Ust Zahazan bin Mohamed. I have been following his tafsir quran session on IKIM ever since I was 14 and I am pretty much influenced by his thought. Also, my brief study of islamic shariah and Quran and Sunnah had shaped my thinking pattern. It's hard for me to get out of it now.

Listening is not enough. Reflect. You should reflect on yourself. Hence, my motto in life has always been everyday is a brand new day. Everyday is a brand new opportunity to improve ourselves. It is the little things that we do consistently everyday that matters. The worst that I want to be everyday is worst than yesterday. I just want to better everyday even if it is just one little tiny things in life.

True. Everything in the Quran is intended for us though it says about the Jews or the Christians or some other people that Allah mentions in the Quran. However, in order for us to be confidence that we are doing it the right way, it has to go through a proper channel. At least, if we make mistakes after doing all we can, we don't carry all the responsibility. The key is we have tried to ensure that we did all we can.

Hence, do I say we abandon usrah? No. I just said if you want to tadabbur al-Quran, you better find someone trusted to do so. Hence, usrah is not my first preference when it comes to tadabbur al-quran. I choose attending talks given by accredited muslim scholars. Why accredited? If we mistakenly believe them or they did something that is beyond our knowledge that only Allah knows, we don't bear the full responsibility because we have done something to ensure that we are doing it right.

The reason why I make myself go through 1 year of usrah is that I want to understand what is happening. I don't have the resources to change things from within and ultimately my life goal is a bit different hence changing from within is not an option for me. What is my life goal? Well, it is written all over this blog and my reason for doing this is to inspire myself. Of course if you find it inspiring Alhamdulillah.
After attending ISK and SH, it all becomes clear to me. The reason why I wait three days to write this stuff is because I am scared. I am scared because if I am wrong, then I am going to spread fitnah. and you know what, the sin of fitnah is way greater than the sin of murder. So I do hope if you find my thought to be thoughtful, please just check and validify it with someone who you trust. I have done it myself. I have got my parents behind my back. I tell them every single thing. Don't just take my words for it.

One of the points that I find disturbing.

Dakwah is compulsory (wajib).
If dakwah is wajib, what does constitutes dakwah because dakwah on its own is a vague term and require thorough knowledge? Answer: anything that will get us to the aim of dakwah.
I asked them what are the aims of dakwah? Answer: to make sure that every single person on earth knows about islam, to make sure that ustaziyatul alam is achieved.
My point is though it may be right, the argument is flawed. They give various evidences from the Quran but they don't give how the mursyid muslim scholars interpret it. Therefore, even if what they say is true, the fact that the argument is not connected with the prophet is a flaw in itself.

Though it sounds harsh, I totally believed that dakwah is a must for every single muslim. I have experienced being in tabligh community, being in a student islamic enthusiasts group, the hafiz of qurans and many other groups that is doing dakwah. However, only the musryid islamic scholars are able to make the connect the fact to the prophet. Why is that? Bcause they have knowledge. They learn from a teacher. Trusted teacher. I can't remember exactly their argument but the point is make sure what you believe is valid. Valid with evidences and thorough knowledge and studies. So check with trusted teacher. Don't take my words for it. I am a normal human being with limited knowledge. In fact, this whole writing might be so flaw that I am going to Naar for it. Nauzubillah. I am taking the risk because I am making a point here. and the point is make sure what you believe is valid. Again valid with evidences and thorough knowledge.

There are other points that I find disturbing but I guess I am not going to share it for I am afraid that I am flaw in itself. However, I do make the point. (Make sure what you believe is valid. Again valid with evidences and thorough knowledge.)

So, knowing that dakwah is compulsory, what will I do?
I have choices. And I have decided not to follow the path that are in front of me. I kept the reason to myself. Nevertheless, I am going to do dakwah. Dakwah in what way? Well that has to wait because I have spend considerable amount of time in front of computer and I don't want to use any more time. For the time being, take what I am writing critically.

As much as I am being critical, I would love if you are critical to me. Yes. It is painful and it will cost friendships but it has to be done. Truth is always bitter. Hopefully, to friends that have chosen this path, I respect all of you and never once I look down on you guys. I wish you all your success and may Allah grants us jannah. Having said that, I am actually frustrated because I might lose the ukhuwwah that we had. It's just fact of life.

Move on!
Everyone is moving on. The sooner you do it, the better you are at adapting to changes.

Finally, I would like to emphasise again so that there is no confusion. What I am saying is that I am choosing not to go down with the path that I am presented with. I am choosing to create my own path. Take home message for you reader is that don't just believe what you are told. Check for its validity, argument as well as the level of knowledge behind it. It is not wrong to point out how things go wrong. It becomes wrong when you force people to believe that you are right. Hope this will clear up any confusion. If you think that you want to challenge my view or get any clarifications, I suggest you write it in comment below (you could be anonymous) and I try to answer that. Just so you know, yes. I am going to be offended but that does not mean that you have to shut your mouth. Just face it. Pretty much like playing with fireworks. Once you have decided to play with fireworks, whatever happens after like burning your skin, accidentally killing someone's cat etc., you just have to bear with the consequences. That is how life works. If you can't accept it, tough! Hence, I am saying just say. I am not a judgemental kind of person but I do have emotions. It may take time for me to face it but I do face it. So don't afraid. I am sure many of you want to say something now that my blog has become more public than before.

Final note, our ultimate purpose in life is to become the servant of Allah and khalifah on earth. There are many ways to do it. Just look through the history of sahabah. All of them have different stories. There are plenty of doors to jannah and it is not the door that matter but being in jannah itself. Absolute requirement for jannah is the mercy of Allah. May Allah grants us His mercy.

(To be continued)

After all, Allah knows best. All praise be to Allah. May Allah protects us from the sin of riyak, takabbur, ujub and all other unseen diseases of the heart. Nauzubillah!

So, cheer up!

Monday, April 22

How to revise when exam is just around the corner?

Hey everybody!
It has been a while. Yesterday, a friend of mine asked me to motivate her for the exams. If you are reading this, you will know who you are. Using little knowledge of psychology that I have learned at King's, I think the problem behind her (and me as well that is why I come up with this solution) is exam anxiety. In fact, I was so freaked out a couple of weeks ago that I have decided not to talk to anyone and just be on my own in the library. It wasn't a wrong action but it was not ideal either. So I thought that I share with you the solutions that I have come up with so that if you are in similar situation, you can benefit. Of course, I have no evidence of success if you use my methods but logically I think this would help.

Before I begin, I think it is important to recognise the forces behind this ideas. Just skip this paragraph if this is not relevant to you. First, it is my parents who constantly think for me to help me solve my problems. Secondly, my seniors and friends who I had observed and asked and probably stalked in facebook. Thirdyl, Tony Buzan's books ranging from 'Buzan's Study skills: mind maps, memory techniques, speed reading and more!' , as well as 'The mind map book: unlock your creativity, Boost your memory, change your life'. These are where my ideas come from. After knowing something, I then use my mind to translate all the information into things that I can definitely do. So here they are.

First of all, you need to convince yourself that you've done enough. You've cover everything in the syllabus and you will be able to answer every single question given in the exam. Of course, you have to anticipate that there will be unexpected question that is difficult. Knowing all that, now we need to devise strategies on how we can retrieve information from our brain and apply it to answer unexpected questions or even the expected and obvious one.

Secondly, knowing what you need to do, acknowledge yourself that you are capable of doing that. Repeat capable. Self-esteem and self-confidence are important.

Thirdly, let us start doing. So where to start? You have to be calm. Absolute calm. Remember that the key thing in the exam is to answer the question. So whatever you do make sure that you read and understand the question thoroughly. If you have trouble doing that, know that it is because of the anxiety and you need to calm down. I suggest you recite selawat or al-fatihah or any other prayer to calm your mind. Then, break the question down. Start with the obvious one.

Fourthly, know that the previous steps are just rhetorical in the sense that there's no much that you can do to prepare for the exams. Believe me. Now I am going to tell you how to increase your confidence. Make 3 lists which I call it as must, want and wish list. How do you do that? Go through your syllabus, or your lecture notes, your books, your notes, your recording etc and extract from it and put into your must list things that you have to be able to do. Absolutely must. Then, put in the want list and finally wish list.

To give you an example. Suppose we are studying on a topic called pharmacy law. I know that as a pharmacy I need to absolutely know what are the requirements for labelling medicinal product, the requirements for validating prescription, the counselling point, requirement for register. In other words, the letter of the law. Hence, these items will be in my must list. Then, I also need to know what should I did if these requirements are met, adjustments that I should do, phone calls that I should make and any other secondary information that I need to know but not absolute. These items will go into my want list. Finally, I also need to know how these requirements are be made, I need to know the spirit of the law, who the law is protecting, what are the punishment if the law are not met and any other stuff that you cover in the lecture but not in greater detail. These items will go into my wish list.

Now that you know what exactly in each list, cover your must list first. By cover I mean you need to be able to memorise or do exactly what you are required to do in the list.

Fifthly, doing the list is going to be time consuming. So what I suggest you to do is that go through your course material. As you go, identify whether the information that you are reading is must, want and wish. If it is must, then you have to cover it now. But if it is want or wish, make a note like writing on another piece of paper or using flag or anything as long as you know where to go to when you are covering your want and wish list. The point here is to ensure that you cover every single important thing first before covering the less important stuff.

Sixthly, a few approaches that you can use when doing your must, want and wish list. Use your instinct. Use your lecturer's note. Think about what they say important. Also, items in the must list are like the building block of the topics. Absolute things that you need to know in order to completely answer the question. You know, sometimes from little information we can use it in the exams to make the points using the best evidence that we have. The key thing is if you forget anything or you think you have no idea how to answer the question, you have at least a little bit of clue from which you can think further and logically to answer the question.

I think this is it. I am in exam mode as well and I freaked out as well. But we are lucky because we are muslims. What we do is just sunnatullah. Remember, we have syariatullah. However, in order for us to be in the best shape for the exams, we have to do the best sunnatullah as well as the best syariatullah. Hope this help.

That's it from me for now. Just an update. I am currently completing my application for volunteering at Cancer Research UK. Do pray that I get the volunteering opportunity. See you then! Bye.

Friday, April 19

Drug metabolism.

Hi everyone!
We meet again.

I can't keep my promise now. The one about usrah thing because we have to wait till after sunday. Anyway, I have one topic to discuss with all of you.

You should have expect it. It is about drug metabolism.
Before I begin, I want to give you a little bit of background. One of the areas that pharmacist are concerned with are pharmacokinetics. It deals with mathematical description, prediction, and understanding of time course of drug actions in a human body. When we talk about pharmacokinetics, we pharmacists are usually concern about ADME. ADME stands for absorption, distribution, metabolism and excretion. Hence, the topic today is a branch of drug metabolism. This topic overlaps with pharmacodynamics (Pharmacodynamic concerns with physiological and biochemical actions of drugs on human body. Pharmacokinetics and pharmacodynamics are strongly related to each other and it is difficult to separate both of them hence we are going to discuss both). If it is still not obvious to you, we tend to simplify it as follow. Pharmacokinetics (PK) concerns about what the body does to the drug and pharmacodynamics (PD) concerns about what the drug does tot he body. Crystal clear so far?
Moving on. Today, we are going to discuss drug metabolism.

So what is drug metabolism or in other words I could say biotransformation of drug?
In order to understand drug metabolism, let us start with a few basic facts.

Where does drug metabolism occur?
Roughly speaking, most tissue carry out drug metabolism but at different extent. Major site of drug metabolism includes liver (specifically hepatocytes and parenchymal cells), gastrointestinal tracts (specifically enterocytes), lungs, kidneys, plasma and skin. (They are arranged in descending order or importance)

Drug metabolism consists of two phases. Phase I and phase II.
Phase I concerns with making the compound more soluble and prepare the compound for phase II reactions. Phase II is the detoxification pathway in which a compound is modified so that it can be eliminated by the body through certain pathway.

Just an analogy to simplify phase II (as Dr Richard Parsons put it in his lectures), phase II reactions are like putting a handle on the door. With the handle, we don't have to concern about the shape of the door as long as the handle is the one that is recognised by the body, the door can be eliminated. In this case, the compound.

This has tremendous advantage. The body can ultimately handle any kind of compound that is in the blood. Subhanallah. How perfect Allah's creation is.

Drug metabolism reaction is catalysed by enzyme.
There are two major enzymes families that are involved. They are cytochrome P450 (cyp450) and flavin monooxygenase (FMO).
I do want to go through catalytic cycle of both enzymes but it seems impossible to write such thing in this blog. In fact, it's time consuming. So I decided to scan my notes. Have a look at it. You may have to do some extra readings because my note is very basic. I suggest reading this one book entitled Introduction to Drug Metabolism written by G. Gordon Gibson and Paul Skett. It's a very good book.

**I'll put my notes here later.**

Moving on.
What sort of reactions are in phase I metabolism?
They include:
1. oxidation
2. reduction
3. hydrolysis
4. hydration
5. dehalogenation

We can actually predict how the drug is metabolised in human body and hence predict the structure of metabolites. A couple of notes. Key point in phase I metabolism is making the drug more hydrophilic. It may not necessarily means that the metabolites are inactive. In fact, some drugs are actually inactive unless being metabolised by the liver first. The reason for that is to enable absorption of drug, the drug needs to be lipophilic as it has to cross lipid bilayer. When in blood, the drug is biotransformed to active hydrophilic drug. A good example of the drug is aspirin. What patient takes is actually acetysalicylic acid and it is pharmacologically inactive. In the liver, acetylsalicylic acid is biotransformed to salicylic acid which binds to COX receptor and hence block pain pathways. (It's a bit advance here and it's already PD.)

Once the drug has undergone phase I reactions though some drug may not have to, they will undergo phase II reactions. At this point, the drug is being deprived of its pharmacological action and excreted via different routes. The reactions in phase II metabolism includes:
1. glucuronidation
2. sulphation
3. glutathione conjugation
4. acetylation

These are the reactions that happen in most tissue to enable excretion of drugs from our body.

In addition to this, it is also important to discuss factors affecting drug metabolism. Fundamentally speaking, it is divided into two: internal and external factors.
Internal factors include genetic variation, age: geriatrics or neonates, disease like cirrhosis.
External factors include like induction, inhibition and interaction.

In this post, I have no intention of going deeper into drug metabolism. I just want to give you readers a brief overview of what drug metabolism entails. Toxicology deals basically with this in greater details and I am totally going to pick this subject during my fourth year because it's fun.

That is it for now. It's maghrib now. After prayer, I am going to continue with drug metabolism in greater details focusing on each specific reactions in phase I and II. My ultimate aim is to be able to predict what biotransformation will occur on a drug candidate and which enzyme will be responsible for it and hence predict the structure of metabolites.

OK. I'm done for now. See you later. All the best!

Missing old life: mixture of feelings.

Hi everybody!
Just a quick post from me as I have drug metabolism to revise after this.

Earlier today when I was checking myself how am I doing, I realised that I could have never achieved what I have today if I didn't go through what I did in the past.
I would to reminisce my old stories but I don't think I am able to do that in such a short time span. So, what I would do is to pick up some of the best memories.
Just so you know, while I am writing this post, I listen to song that have lots of memories in it and they are 'Diari seorang lelaki' by PrettyUgly, 'Pupus' by Dewa19, 'The Hobbit' from The Lord of the Ring, 'Manisnya senyumanmu' by Elite and my most favourite one 'More than words' by Extreme.

First of all, why these songs? These are the songs in my playlist when I was in form 2 (14 y/o). So, it kind of remind me my mood during that time. That was the time when I started realised my potential. I joined the debating club during these time. I had lots of fun with my debate buddies. I just want to list some of them so that they know how much I miss them. They are Ust Idris, Ijam, Haizeer, Afiq, Kak Ellya, Abg Danial, Kak Mas, Nashorn (not sure how to spell it), Anis, Aqmal, and others. There are few people that I forget their names. I'm sorry. Probably we are not close enough during that time. It is also the first time I represent my school for debate. I was a second speaker. Oh, how much I miss being in debate team. Anyway, this post is not just to remind myself of the past and regret about it. I aimed to remember all the excitement and channel it to motivate myself. I don't even have a picture of us together. So sad. If you guys happen to read this which I think very unlikely, I want to wish you guys all the best in your future endeavour.

Talking about future endeavour, I just want to share a few updates. Ijam is in University College Cork doing medicine (Be a good muslim doctor Ijam), Haizeer and Afiq are in Universiti Teknologi Petronas doing engineering (I can't remember which engineering. Sorry about that. All the best guys), Kak Ellya is in Cairo doing medicine (All the best Kak Ellya), Abg Danial is in Australia doing law (All the best Abg Danial), Kak Mas is in Yamaguchi doing chemical engineering (All the best Kak Mas. Hope to see you at King's or UK for your PhD. Amin!), Nashorn is in IIUM doing law (All the best Nashorn), Anis is currently at INTEC preparing to do law in UK (can't wait to see you at King's Anis. All the best), Aqmal is currently at Kolej MARA Seremban doing ??? (Sorry Aqmal, I don't know what you're doing but you have all my best wishes).

OK. Done with compliments.
Now, we have to get back to our topics. I really miss school life. Totally.

Secondly, now that exam is in less than a month, I hope that we can all succeed. However, in order to achieve what we want, our actions should match our goal. If you want to achieve first class, you have to act like a first class student. Having said that, I am freaking out whether I am on par with my goal. So I decided to share with you guys what I think is the act of a first class student. I collected the information from various motivational seminar that I have attended, websites, books and most importantly people's wisdom.

1. Begin with the end in mind.
This is a concept that I took from Stephen Covey. It's very simple. We have to know what we want in order to achieve it. Be very specific but not impossible to achieve.

2. Measurable actions
Now that we know what we want, we need to devise strategies on how to get it. The strategies however have to be devised in such a way that it leads us to our goal. This require thorough research, extensive readings, asking people who have succeed through it and most importantly the discipline to do it. To illustrate this, suppose I want to become a world class swimmer, First I need to know what is a world class swimmer. Just a random example. Let say a world class swimmer need to be able to swim 50 m in 30 seconds. Hence, we need to direct our practice to achieve that. Among measurable actions that we can do is to do exercise to strengthen our thigh muscle for at least one hour a day and so on. Make a complete list of everything that you have to do. After that, in order to ensure that what you do is right, have someone verify it. I would suggest someone who has wide experience in the area that you goal is in. Better still, someone who had already achieve what you want to achieve. There are many ways to verify your actions. You don't have to be direct. Make a conversation and manipulate it to get what you want.

3. Just do it.
As Nike put it, just do it. This is where our discipline, our metal strength come into play.

4. Tackle any problem.
If you do it correctly, you will definitely encounter problem. Hence, everyday take time to do self reflection to identify the problems and find solution to them. Believe me. This step is very crucial.

5. Keep reviewing yourself.
Although it sounds the same as previous step, actually the point that I am trying to make is broader. Broader in the sense that you don't just identify problem but you recognise achievements. Reward or punish yourself accordingly. I would suggest for rewards to be something that you like and for punishment to be something that makes you closer to your targets.

I guess that is it. For some of you, you may have time limit to achieve your goal. For others, time is not a factor. Whatever it is, keep checking your status and make improvements.

These are just a summary of what I think is necessary. In reality, I do apply all seven steps of Stephen Covey's seven habits of highly successful people. Not just that, I also employ Tony Buzan's mind mapping technique to direct my brainstorming.

The key thing about my approach is that I like and tend to use technique that have been researched thoroughly either by thinking, experiments or even experience. Remember, experience is the best teacher. Hence, talking to people who have gone through what we are going through is beneficial.

I think it's time already. Hopefully, this will help you readers. When I think about it, the second part of this post is totally unrelated to the topics. The only relation that I could think of right now between both of them is that the energy that I gathered from reminiscing old memories cleared up my mind, made me grateful of everything that I have achieved and consequently driving me forward towards my dream.

Next topic before I forgot, I want to speak my mind about 'usrah', dakwah, tarbiyyah and that kind of stuff because during lunch today, I was asked that question by a friend of mine and it makes me think about it. As a result, it became obvious and clearer to me.

I'm looking forward to Shahadatul Haq this Sunday. Hopefully, this will help me make a stand.
Just a couple of note in case you are offended or you make negative perception of me, I'm not against this kind of thing but I make choices and you have to respect me for that because I do respect your choices and I don't judge you on that. In the end, our ultimate goal is to enter jannah and there are many doors to it.

Ok. End of this post. Here we go, drug metabolism. See you later.

Wednesday, April 17

Carbohydrate Chemistry.

Hello everybody!
I am so tired of NMR spectroscopy so I decided to pause with NMR spectroscopy and do something else. This time I am going to discuss carbohydrate chemistry.
"I started writing this post a couple of days ago. Now that I'm on it. I decided to finish this post"

For organisation, I am going to start with monosaccharide, followed by disaccharide and I am going to end this with polysaccharide.
In this post, I am going to write a little bit about monosaccharides.
For the record, drawings of the structure will come later.


There are two main families of monosaccharides namely 2-ketose family and aldose family.
Min number of carbon is 3 and maximum is 9.

The fact that there is stereogenic centre in monosaccharide, each family of monosaccharide has its own stereochemical series. I don't want to go into this now. Maybe at some point later.

Most important monosaccharide in human health judging from its abundance in our diet is D-glucose, D-galactose and D-fructose.

For representation of structure, scientists in this area usually use Fischer projection and Haworth projection. Again, I don't want to go into details in this. It is there for you to appreciate it's existence.


Two types of disaccharide depending on its components: homogenous and heterogenous.
Heterogenous disaccharide includes sucrose and lactose.
Sucrose is made up of D-fructofuranose and alpha-D-glucopyranose making up alpha-D-glucopyranosyl-D-fructofuranoside.
Lactose is made up of beta-D-galactopyranose and alpha-D-glucopyranose making up beta-D-galactopyranosyl-alpha-D-glucopyranoside.

Homogenous disaccharide includes cellobiose, maltose and isomaltose. The reason why they are homogenous is because they are made up of the same monomer.
Cellobiose is made up of two beta-D-glucopyranose.
Maltose and isomaltose are made up of two alpha-D-glucopyranose. The different between both of them is how they are attached together. Maltose attach at 4-0 while isomaltose attach at 6-0.


Two major types of polysaccharide mainly homopolysaccharide and heteropolysaccharide.
Homopolysaccharide includes cellulose, starch and glycogen.
Cellulose is made up of repeating cellobiose. Its role is for supporting the structure of plant.
Starch has two components in it: amylose and amylopectin. Amylose is made up of repeating maltose while amylopectin is made up of repeating maltose and isomaltose. It functions as energy storage in plant.
Glycogen has the same structure as amylopectin in which it is made up of repeating maltose and isomaltose. However, amylopectin in glycogen has greater branching than amylopectin in starch. Its role is energy storage in animals mainly in liver and muscle cells.

Heteropolysaccharide includes glycoprotein, glycosaminoglycan and proteoglycan.
They are way more complicated than homopolysaccharide but they are extensively used in healthcare products. Glycosaminoglycan, if you like, is like cellulose but it's composition has been altered so that it may contain other atoms like nitrogen, oxygen etc. An example of this is hyaluronic acid. An example of proteoglycan would be heparin which is used as antihypertensive agents. Finally, glycoprotein which is way more complicated and it functions as cell recognition and cell signaling. The discussion of heteropolysaccharide is actually more extensive than this but given the scope of my syllabus, how little time that I have left and little interest in this area, this should be sufficient.

If you notice, this is just a survey of what scientist interested in carbohydrate is doing. It has many more dimensions to it like stereochemistry. In fact, it is Mr Emil Fischer, the first scientist that has been studying carbohydrate chemistry extensively, who responsible for the birth of organic chemistry. Thanks to him, stereochemistry has developed. Although judging from my struggle in stereochemistry these past few months I would say he is the reason for my miserables, his study nevertheless helps clarifying communication between scientist. For that as well, we thank him though I am inclined to believe that there may be muslim scholars that have already done what he did but due to what happened to scientific knowledge during the fall of abbasiyah empire it remains unknown, he did deserve the credits. After all, credit is not what we muslim scientist is after but the blessing of the Creator, Allah SWT.

So yeah. I better get going. Bye. See you later.

NMR Spectroscopy 1: The basics

Hello everybody!
This morning, I struggled with NMR spectroscopy. I thought I understand the theory. However, when I was asked to draw a 1H NMR Spectrum of a molecule, I couldn't do it. I wonder what is the problem. So, I thought I put it write here.

Here how it's going to go. Firstly, I am going to write in my own word the theory behind NMR Spectroscopy. Secondly, I am going to confront my problem that is drawing NMR Spectrum of a molecule. Ultimately, I want to make sure that I understand all relevant information and I am able to make use of it for whatever objectives I want to achieve depending on the question.

Before I begin, I would like to share with you the question that I have been asked.

Structure of phenobarbitone. Source: Wikipedia
 Q: Draw the 1H NMR Spectrum you would expect for the drug molecule. Annotate clearly on the spectrum the chemical shift, integration information and splitting patterns you would expect. (5 marks)

OK. Let's begin.

Properties of nuclei.
One of the properties of nuclei is that it has nuclear spin. However, not all nuclei have it. Nuclear spin is quantized and has the symbol I. The exact number of different energy levels that a nucleus has depends on the value of I of that particular isotope. (For my purpose, we do not want to go deeper into this.) Just concentrate on 2 different nuclei that is 13C and 1H. Both have only 2 different energy levels.

NMR uses a strong magnetic field.

In an NMR instrument, there is a large supercooled magnet that provides external magnetic field. When a sample is put into the instrument, all nuclei which possess nuclear spin will be in their lowest energy state. For the case of 13C and 1H, they both have two different energy levels; one is aligned with the external magnetic field (therefore, lower energy level) and the other one is against the external magnetic field (therefore, higher energy level).

The difference between the two energy levels can be measured.

Nuclei that possess nuclear spin and be in their lowest energy state in an external field is said to interact with the magnetic field. The difference between the two energy levels can be measured (how it is done will be explained later). The difference is given as :
ΔE = hf where ΔE is the difference in energy, h is the planck constant (h = 6.62606957 × 10-34 m2 kg / s ), and f is the frequency of the radio waves.
ΔE depends on:
  1. How strong the magnetic field is
  2. Magnetic properties of the nucleus itself
NMR uses radio waves to provide energy to flip nuclei from lower energy spin state to higher energy spin state.

Radio wave is in the frequency of 10^4 Hz to 10^8 Hz. The specificity of the spectrum is determined by the frequency of the radio waves i.e. each nuclei require certain frequency of radio waves to flip it from lower energy spin state to higher energy spin state.

The sample is irradiated with short pulse of radio waves of specific frequency. After irradiation, nuclei that is promoted to higher energy spin state will return to lower energy spin state. Energy is released as the nuclei fall back down and this energy can be measured.

Measurement obtained from NMR spectroscopy has to be Fourier transformed to obtained meaningful spectrum.

This is the confusing bit but since I am not an analytical chemist nor physical chemist, we can just accept the fact that the measurement of energy released has to be mathematically treated to produce typical NMR spectrum that we pharmacist can analysed.

The following diagram is an example of a typical NMR spectrum.
1H NMR spectrum of ethanol. Source: Wikipedia
At this moment, we are not going to interpret. I am just showing you the typical NMR spectrum. In reality, NMR spectrum is way more complicated than this and many research lab has been developing algorithm to improve the resolution (that is the ability to see each peak as distinct). We do not want to get deeper into this as this is for advanced study. I don't need it at the moment.

What kind of information does NMR Spectrum gives?
Fundamentally, NMR spectrum enables you to detect atomic nuclei and identify what environment it is in.

Several important information that you can gain from 1H NMR spectrum. (refer to the 1H NMR spectrum of ethanol for clarity)
  1. The number of peaks indicate the number of proton environment.
  2. The area under the peak or integration information tells you how many protons are there. Note: This information is in the form of ratio. In order to correctly identify how many protons are present, other techniques like Mass Spectroscopy should be used to precisely determine number of atoms in the molecule.
  3. The splitting pattern indicates the number of neighbouring nuclei that the nuclei interact with. Note that if the nuclei interact, they will have the same coupling constant. (usually written as J but it is not shown in this spectrum).
  4. Chemical shift tells you about the nature of the environment. This is the most difficult part of interpreting an NMR spectrum. However, we are going to go through this at some point in this post. Just wait for it.
Before we go through information in the NMR spectrum, I would like to first introduce you to chemical shift scale.

Chemical shift scale

The units for abscissa (or x-axis) is parts per million. Why is this the case? This is because the frequency of each nuclei environment depends on the strength of the external magnetic field. If the sample is run on a different NMR instrument or different strength of the magnetic field, the frequency at which that nuclei resonates will be different.
Before I continue, I would like to explain the meaning of the term resonates. In NMR spectroscopy, when nuclei is said to resonate it means that nuclei is absorbing energy from the radio waves so that it can be promoted to higher energy level spin state. As it falls down to lower energy level spin state, it releases energy which through several steps gives the NMR spectrum.
Hence, it will be difficult to say exactly where our signal is. Therefore, we defined our signal position by how far it is from a reference sample (tetramethylsilane is often used as reference), as a fraction of the operating frequency of the instrument.

Since the instrument usually has frequency of up to 900MHz and atomic nuclei resonates at frequency in Hz, it makes sense to use part per million. (Hz in MHz)

The ordinate represents relative amount of nuclei.

What gives each nuclei environment a distinct chemical shift?

Recall that we measure the energy released by nuclei as it falls down from higher energy level spin state to lower energy level spin state.
Each nuclei in a molecule resonate at different frequency. Why is this the case?
Logical deduction that we can make is is that the ΔE is difference for each nuclei. Recall that ΔE = hf.

Though the external magnetic field is constant for all nuclei, the magnetic field experienced by each nuclei is not exactly the same. .
Each nucleus is surrounded by electrons. In a magnetic field, electrons can generate tiny electrical current. Consequently, this electrical current will generate magnetic field.
Basic physics guys. Just to remind myself again. Suppose we have a wire and we coil it so that it forms a solenoid. When we pass current through it, magnetic field is generated.
This magnetic field which we will call local magnetic field will oppose the external magnetic field. Electron distribution around the nucleus vary for each environment. Two possible situations: shielding and deshielding.

When nucleus is protected by electrons around it, it is called shielding as the electrons shield the nucleus from external magnetic field. Consequently, the resonating frequency will shift upfield.
The vice versa is true. (More on this later.)

Take ethanol for example. I suggest you draw the structure in a piece of paper and follow my explanation. Oxygen atom is an electronegative atom which means in ethanol molecule electrons density will be higher towards the oxygen atom. As a result, proton attached to carbon next to oxygen atom will have less electron density hence deshielded. The nuclei will experience more external magnetic field i.e. greater energy difference. From ΔE = hf, we can infer that resonating frequency will also increase. Hence, the signal for CH2 is further downfield with regards to CH2 signal position without the oxygen atom.

I know things has become more difficult. Don't give up. You just need to get your head around it. I suggest you ensure that you understand everything up till this point. Read back from the beginning if necessary.

OK. Are you ready to continue?

Describing chemical shift.

If you find it difficult to follow the previous concept, I think one of the reason is that I haven't introduced the terminology to describe chemical shift.

First, I want to define chemical shift. Chemical shift is the resonating frequency with respect to standard as a fraction of frequency of instrument.

It's hard to explain the terminology without using a diagram. However, if you look into textbook of organic chemistry, you will find one.

When we are saying about the field i.e. magnetic field, we use downfield and upfield.
When we are saying about chemical shift, we use large or small.
When we are saying about frequency, we use high or low.
When we are saying about shielding, we use deshielded or shielded.

I think the best that I can do now is to give you example so that you understand.

So far, I would like to wrap up a few things before we continue.
Why each nuclei resonates at different frequency?

Each nuclei experience different magnetic field due to distribution of electrons around the nuclei leading to either shielding or deshielding.

What happens to resonating frequency when the nuclei is deshielded and vice versa?

Think about it this way. When a nucleus is deshielded, it experiences greater external magnetic field. Consequently, ΔE will increase. According to equation ΔE = hf, as ΔE increases, resonating frequency will also increase. Hence, the position of the signal will be further downfield.

OK. I think we are now ready to go to deeper.

Regions of the 1H NMR spectrum.

Many observations have been made and it is important to memorise the common proton environment.

Proton in:

CH3 = 1 ppm
CH2 = 2 ppm
CH = 3 ppm
Benzene = 7.2 ppm

Also, a diagram to help you remember the rough position of signal.

Our discussion on NMR spectroscopy has not finished. I am going to continue more on it tomorrow.

What is waiting tomorrow?
13C NMR spectrum
1H NMR spectrum
Chemical shift and factors affecting it
Coupling and coupling constant

Congratulations Syafiq for being productive!


Jonathan Clayden, N. G. (2012). Organic Chemistry. New York: Oxford University Press.