McCandless phenomenon

Adapted from McCandless's journal:

Death's a fierce meadowlark: but to die having made. Something more equal to centuries.Than muscle and bone, is mostly to shed weakness.The mountains are dead stone, the people. Admire or hate their stature, their insolent quietness,The mountains are not softened or troubled And a few dead men's thoughts have the same temper.

Bits of self-review:

Human's fragility clearly seen when emotions take over. Yet that's the main link between hearts. Balance's difficult to sustain, but possible still. Flexibility and maturity, plus joy; ur stance will be at different angles. McCandless, he was such a great guy, i must say. People said he lacked of senses, agreed; but why talk about weaknesses? Take the good parts and try to avoid the same mistakes. Can't wait to read about Khulafa' Ar-Rasyidin.

“There was an old person of Dean,

Who dined on one pea and a bean;

For he said, ‘More than that,

Would make me too fat,’

That curious old person of Dean.”

(One Hundred Nonsense Pictures and Rhymes. Edward Lear.)

In case readers are wondering what this rhyme is about, 'tis connected to the discovery of insulin functions, mainly to lower the blood glucose. i just find it catchy, hence the upload. [glucagon increases blood glucose]

via .jpg

History of my 2nd year

Been working straight 72 hours with only 4ish hours of sleep and yes, quoted from sheraz "you still alive man!" yet some of the short questions were unanswerable, especially for cell biology and pharmacology and just put anything that crossed my mind for essay parts, hopefully that will help inshaAllah! Im satisfied with the effort, just leave it to Allah and working for my last bits.

Random Thought(s)

Make use of your surrounding to get the most out of it. When you are at the lower side, there is always people around you; friends or completely strangers, to pull you to the brighter side. And when you're on your strong stands, why don't you try to get hold of others when they need them? One of the many reasons to keep you smile...

Keep giving although the value pays no mind, and it is very shocking of how much you will get back from it. Altruism it is, the survival of the ''nicest''.

One thing about human beings in this decade, (almost) all are suffered from heart disease. What is the meaning? It's the anger and jealousy that drive people crazy; they argue its only a way to participate in competition of life. I throw away my anger and jealousy, i feel much better :) but they always come back, we're human after all so allow for mistakes.

Random Thought

In a chess game, even a pawn can be promoted to become a queen, after all the obstacles; and a queen's fate is still in the player's hand. Wallahu 'alam.

Swimming in dream

I dreamt i swimmed calmly all night long last night, how cool is that? very relaxing although i still have 9 papers to go lol. My brain must be missing swimming pool very badly, its like about a year i havent go for swimming. A cool way how brain works to relax himself...

Molecular biology

Polymerase chain reactions

this is experimental technique used to make very large amounts of target DNA sequence in vitro. it allows DNA to become aplified several billion fold, effectively purifying the DNA away from the rest of the genome. DNA polymerase uses a single stranded DNA template to 'prime' DNA synthesis. simultaneously priming of both DNA strands at the edges of desired target sequenced by adding and annealing 2 specific primers. DNA is then synthesised using a DNA polymerase. 2 primers are different which are designed to be complementary with target DNA at different locations. it is necessary to have primers of at least 20 bases to ensure specificity.

3 steps of PCR
1. denaturation: denature double stranded DNA to single strands at 95 degree celcius.
2.Annealing: anneal primers to the single stranded DNA at 55 degree celcius
3. extension: DNA is extended by DNA polymerase in 5' to 3' direction at 60 degree celcius.

each step takes about 1 minute, thus one complete cycle takes about 3 minutes.

PCR reactions now have been automated using Taq polymerase. this means enzyme is only added at the beginning and not after every each denaturation step which is very laborious. cycles will continue provided that in the reaction there are sufficient primers and nucleotides.

application of PCR
1. cloning: to isolate genes whose genes are wholly or partially known. after cycles, isolate PCR products from a gel by cutting out the amplified fragments and ligate into vector. no need to screen the library.
2. detect rare events; for example the presence of rare virally infected cells or low abundance pathogens in sample
3. for molecular evolution studies
4. useful in forensic science to detect crime, CSI!
5. diagnose genetic disorder such as Duchenne Muscular dystrophy (musle degenerates)-multiplex pcr products



DNA repair
intro: cell possess systems which can recognise mismatches and structural distortions in DNA

2 main causes of cell damage: physical and chemical agents e.g. UV; errors in DNA replication

2 general classes of DNA damage: single base changes; structural distortions

5 repair systems:
1. direct repair: photoactivation, deoxyribopyrimidine

2.mismatch repair: uracil mismatched, uracil DNA glycosidase (UDG), DNA Pol 1 and DNA ligase, Mut S, Mut L, Mut H, Mut U

3. excision repair: very short, shor or long patch. enzyme UvrABC, UvrD, Dna Pol 1, DNA ligase

4. Tolerance repair: translesion systhesis polymerase (TSP), in e.coli polymerase IV and V, dinB, UmuC, UmuD, medical interest: xeroderma pigmentosum

5. retrieval repair: best repair, use other repair systems, SOS response, lexA, lexA box, SulA, cell division

Molecular biology

splicing event

splicing process:
introns interrupt the protein coding region of mRNA. intron sequences occur in DNA and transcribed into pre-mRNA. introns must be removed accurately. splicing rection is catalysed by SNURPS and takes plase in a complex called spliceosome. spliceosome complex consists of pre-mRNA and several different SNURPS. mature mRNA only exits nucleus after splicing process is complete. splice sites are specified by sequence at the ends of the introns at the end of introns at the 5' and 3' splice junctions. GU-AG rule is constant in all splicing process involving spliceosome.

transesterification:
step 1. 2'OH group of adenosine nucleotide in the intron attacks the phosphodiester bond at 5' splice site. bonds breaks and new phosphodiester bond is formed.
step2. 3'OH group of free 5' exon attacks 3' splice site. net result of this is the exons are joined and introns are released as branched lariat structure.
since the number of phosphodiester bond is constant, no energy is used in this process.

self splicing introns pure: pure preparations of some RNA transcripts slowly splice the introns IN THE ABSENCE OF ANY PROTEINS.

group I introns: this occurs in nuclear rRNA genes in protozoan. the event involves the 2 transesterifications. role of 3'OH of G cofactor is similar to that of 2'OH of the branch point adenosine in spliceosomal mechanism. but G cofactor is not part of RNA chain i.e it is not carried together like the spliceosomal machinery components.

group II introns: this group of introns occur in mitochondria and chloropast in plants and fungi. introns fold into conserved secondary structure containing stem loops. the splicing mechanism also involves the 2 transesterifications similar in spliceosomal splicing. SNURPS in spliceosome functions similar to the stem loops in group II introns. thus it is hypothesised that spliceosome mechanism probably had evolved from self-splicing mechanism. secondary structures of group II self splicing introns and U SNURPS present in spliceosome. maturases bind to group II intron and increase the rate of splicing. maturases is said to stabilise the 3D structure of intron while SNURPS is said to stabilise the structures in spliceosomal splicing.




DNA topology

the great majority of DNA in living cells occurs as B form. there are certain flexibilities within B form. 1. the number of base pairs per turn of helix can be altered. 2. helix in the cell is not straight, but rather coil in 3D space. 3. there are certain sequence feature where bends occur. 4. transcription and replication require strand separation.

supercoiling: the DNA in the cell is coiled in 3D and this introduces torsional stress into the molecule. this is known as supercoiling, which can be either negative or positive: negative supercoiling is when the twist of the DNA is opposite to the right hand of the helix. positive supercoiling is when the twist of supercoiling is in the same direction as the turn of the helix.

the torsional stress can be accomodated in 2 ways: 1. formation of superhelices 2. altering the number of base pairs per turn of helix. these 2 possible responses can be incorporated into a single concept; the linking number, L or the total number of times that the strands cross each other in a plane. formula that can be use L=W+T where W is the writhing number, corresponds to the superhelicity and T is the the twisting number, the helical winding measurement.

topoisomerases: this is an enzyme that can alter the number of DNA molecules and there are 2 types of topoisomerase:

Type 1 topoisomerase: this type breaks one strand of the DNA, pass the other strand through and gap and seal the break. linking number, L changes by +/- 1.

Type 2 topoisomerase: this type breaks both strands of the DNA and pass ANOTHER PART OF HELIX through the gap and seal the break. the linking number change by +/-2. example of this type of topoisomerase is DNA gyrase in DNA replication.

Nothing to envy

Everyone is talking about the new iPhone which is coming out this month. Some people busy with their pre-order; some just updating their status, wishing to have more money in their bank account to participate in the so-called world lifestyle contest. I used to be very envious of every single thing that people haveand i still am, to be honest.
But, a reminder for myself and people out there, what it is for? Whats the purpose? Can it gives any benefits to our beloved Palestinian brothers who suffer the Gaza crisis? With one single product from Apple, they can make us forget. What if Apple is working with the Laknatullah Israelis? No, im not saying they are because i dont know anything about them, im just giving an assumption to think about. Dont change your mind yet because of a single sentence. Make your own research, and think again before you do something. Which one do you want to choose, the lifestyle here in this world or the lifeafter? This is perfectly a reminder for myself and if it does make the readers think, that's good. I want to invest for my lifeafter starting every single day, i dont want to miss the joy im giving to others, not only for myself. Im much happier when i know even one pence i give will help others.
Talking about giving, i want to quote from Friday khutba last week. Even if you give 1000 or even a million but if you do not do the obligation, for example myself as muslim to pray 5 times a day which is still a big problem for me, dont even bother about the other kindness you did. It makes me think, Allah is the Most Merciful and every single deed counts. I've tried my best to be as near as i can to achieve 'good muslim' title but to be frank, praying 5 times a day is still hard to achieve the 'istiqamah' status especially Subuh prayer. But again, i quote from somewhere i can't remember, even Rasulullah (PBUH) said "even the heaven for me is not a guarantee not until I got blessing from Allah the Almighty". and i believe although if im standing between the line that separate the Heaven and Hell, i pray to You to make it easy for me inshaAllah.
Remember, the older we grow, the more money we get, the closer we are to our death. Im not a good muslim yet i still wish to do the best to achieve this. Amin.

Fav Tutor

Again, my tutor does the miracle. He helps me to calm down a bit, syukur alhamdulillah. Key point: understand and keep calm.

Nervous

O Lord, please make it easy for us and do not make it difficult. Amin.

Different walks of life

Dear life,

I was stunned today by how much the surrounding can teach me about 'you'. Different people from different continents, different countries, different races, different ages that walk pass through me everyday have different kind of 'you' but we are all leading the equal sum. And how dare am i to say that 'you' are so unfair? I heard a story from a friend which i thought is having a normal 'you' based from his expression, but actually deep inside his heart, no one knows really. I bet i am learning to be an adult now, and i guess my brain structure is changing too (it was from my neurobiology lecture though, brain changes when learning as an adult). 'You' are that beautiful when i can see 'you' from different angles and i guess the word "lucky" does not really affect me now. Hope i can hold onto the beautiful side of 'you' until the Time comes, all the best for me and 'you': life deary :)

*Bunuh orang macam bunuh ayam. Wahai Israel, the time will come. It will.