The tryptophan operon of E.coli.

Unlike lack operon tryptophan operon is an anabolic operon, which means that the structural genes are only transcribed when the amino acid tryptophan is absent from the source i.e. When the amino acid is available the structural genes are not synthesized. The enzymes are not required and hence the operon is shut off. The operon model was elucidated by Charles Yonofsky and his colleagues. The operon model consists of the following genes.
1) Structural genes - The structural genes are coded from A to the letter E and encoded for the enzymes required for tryptophan biosynthesis and the gene spans 6800basepairs.
TrpA - tryptophan synthase α
TrpB - tryptophan synthase β
TrpC - PRA Isomerase and InGP synthase
TrpD - Anthranilate synthase 2
TrpE - Anthranilate synthase 1.

2)The promoter and the operator region of 150 bp upstream to the structural gene TrpE.

3) Leader region of 162basepairs, situated between the operator and TrpE. And within the leader region the attenuator site is present. The leader region and its role is briefly explained below under regulation of operon by attenuation.

4) The Regulatory gene - TrpR upstream to the promoter. The promoter is 150bp in length

The Regulation of the Tryptophan operon.
1) Regulation by "Repression" - The Tryptophan operon is under the negative control just like the lac operon, but it is repressible whereas lac operon is inducible operon. By repressible i mean that the effector molecule can repress the operon. The operon is regulated by Repression by the transcription of the TrpR region i.e the Repressor gene which encodes for the "Aporepressor protein." However the Aporepressor protein is not an active Repressor itself, hence it binds with tryptophan to produce an active Repressor. This active Repressor binds to the operator thereby preventing the transcription of the structural genes by blocking the path for Rna polymerase. This phenomenon is known as "Repression" and it reduces Tryptophan biosynthesis by 70 fold hence reducing the cellular try levels.
In the absence of tryptophan the operon is turned on because no active repressor can be formed hence the operator is free for Rna polymerase to bind and carry on transcription of the structural genes.

Regulation of Tryptophan operon by "Attenuation" - To understand the attenuation mechanism we must first understand the details of the Leader region which consists of 4 regions - 1,2,3,4. And among these 1,2 2,3 and 3,4 are complementary. The region 1 consist the tryptophan coding sequence i.e. UGG UGG from 54-59 and region 4 consist of the stop coding sequence i.e. UGA from 69-71. The base pairing at 1 and 2 region causes pause signal, The base pairing at 3 and 4 region causes termination signal and the base pairing at 2 and 3 region causes the anti termination signal.
Mechanism - The model here is based on the fact that Transcription and Translation in prokaryotes is carried out as coupled process due to the lack of a membrane bound nucleus. Hence here the Ribosome position plays an important role in regulation which is ultimately decided by the Leader region. It can be explained as follows.
A) In the absence of Tryptophan - In the absence of Tryptophan the trpt.Rna.trp levels drops hence the Ribosome translating the mRna stalls at the Trp codons (54-49). Therefore the leader peptide is not completed. The Ribosome blocks the region 1, hence the region 2 and 3 base pairing occurs. Which is an anti termination signal therefore the Polymerase continues translating past the attenuator region and the structural genes. Therefore the Trp operon is turned on in the absence of Tryptophan.
B) In the presence of Tryptophan - In the presence of Tryptophan, sufficient trptRnatrp's are present, hence the Ribosome translate the mrna and finally stalls at the stop region on the Leader peptide. The stop codon is region 2 and (69-71) region. The covering of region 2 by Ribosome facilitates region 3 and 4 base pairing which encodes for the termination signal. Hence the Rna polymerase stalls there and the structural genes are not transcribed. The Trp operon is shut of In the presence of Tryptophan.

3) Regulation of Tryptophan operon by Feed back inhibition - If the amino acid Tryptophan accumulates at a faster rate than utilized then the feed back inhibition is triggered. The end product of the biosynthetic pathway recognize the 1st enzyme of the pathway and inacivates it by altering its confirmation hence the pathway is shut off. Once the conc falls the product is dissociated and the enabling pathway resumes.

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A question to answer!

You're at the supermarket, you go to the meat section (or the crying aisle, as I think of it) but there are no burgers, sausages, drumsticks etc....there's only a holding pen, and in this pen is a cow, a calf, a pig, a chicken, a lamb and a turkey.Picture them all there looking at you...confused and terrified, backing away. They don't know why they're there or what's going on. One by one you have to catch them and hold them down, they're trying to get away, they're screaming, but if you want meat you have to kill them. Could you do that? Cut their throats, watch them bleed out and slice them up?

On to the milk section (another crying aisle). No milk on the shelf, but there's a cow with a calf suckling. If you want milk, the calf has got to go. Could you pull the calf off of the mother, drag the calf away...never to see the mother again?...then milk the cow while she's crying and bellowing
and grieving for her calf?

On to the eggs...can you walk by the bedraggled, sick, miserable hens that are crammed into cages so small they can't even stretch their wings?... can you help yourself to their eggs without any concern for the misery they have to endure? And can you macerate small chicks just because they cannot lay eggs?

Imagine if what ends up at the supermarket also has to start at the supermarket...would you still go there?...would you take your children?...would you take part if you were face to face with your food?

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Light bulb jokes

Today i thought to create some sexist and funny light bulb jokes and here they're. I've tried to be neutral by posting both types of sexist jokes, so nothing against men or women in person. Your ideas are welcome to improve these.


Q: How many egotists does it take to change a light bulb ?
A: One, He holds onto the light bulb, and waits for the world to revolve around him.

Q: How many women does it take to change a light bulb ?
A: None. "It's a man's job."
A: Three: one to take out the old one, one to sweep up the broken glass and another to phone her boyfriend to put the new one in.

Q: How many sexists does it take to change a light bulb ?
A: None. Let the bitch cook in the dark.

Q: How many men does it take to change a light bulb?
A: None, they're too lazy and prefer to sit in the dark.

Q: How many men does it take to change a light bulb?
A: None, they prefer to move out of the house.

Q: How many men does it take to change a light bulb?
A: None, the tv provides enough light to change the channel.

Q: How many men does it take to change a light bulb?
A: None, they're smart enough to switch on the lamp.

Q: How many men and women does it take to change a light bulb?
A: One women to put it in his mans todo list and one man to change it five months later.

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Essence and existence part 2.

It has been a fundamental and traditional metaphysical view that essence precedes existence which means we have a higher order and predetermined purpose and we're here to fulfil that purpose. The concept of essence is also seen in Plato's work, in which he claims that truth is eternal, unchangeable and absolute and knowing that truth is the central goal of human philosophy. According to Plato we've an eternal existing nature and it's our duty to discover it through philosophical contemplation, and through reasoning. The human beings have a common eternal existing "essentialist" nature defined by reason.

Also Aristotle states that we humans are rational animals. The reason is the true self of every person and in the highest sense reason is a mans self. Aristotle has accounted in his (Metaphysic 1) "Essence corresponds to the ousia's definition; essence is a real and physical aspect of the ousia."
Most of the philosophers like Descartes, Leibniz, Kant and Hegel were of essential tradition.

After saying this consider an example of a seed - it has the whole tree existing in it, which means that it encloses the essence. The growth of the tree is already present and it's the essence only that's unfolding. That is the seed unfolds the essence and becomes existential. Hence it can be said that essence is the cause of existence. At the present age even scientific proof can be obtained by Kirlian photography which is developed in soviet Russia and photographs the aura and essence of the material object as shown in the image. Hence before the actual existence, the energy and essence can be confirmed to be present near the object.

In regard to Jean Paul Sarte claims, i believe that he has made statements on observation of a mature and adult human society, where he fails to account for innate conditions, infant tantrums, etc which claims for possessed special human nature. Also consider the example of a schizophrenic where the condition is in his/her nature and they can't help it. In regard to God his existence is not afflicted with laying norms of humans nature.
And in regard to existence of ashtray it took a conscious decision to make one on need. If the conscious decision came into being purely by coincidence why can't the whole existence turn up by coincidence? And if there is no conscious decision over our existence then we're not needed!

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Essence and existence.

What is existence - Existence is a fact of being present - "that it is"
What is essence - Essence is the description of existence - "what it is."

There has been a perennial debate over centuries over mans existence and whether it comes with a predetermined essence or not. Inorder to present both the existential and metaphysical points I'll cover it in 2 parts. Part 1 covering the existential and the latter metaphysical.
Part 1
The basic proposition of existentialism "Existence precedes essence" over traditional philosophical and metaphysical view that essence is fundamental/immutable/eternal than it's existence. To existentialists, the human being— through his consciousness creates his own values and determines a meaning for his life because, in the beginning, the human being does not possess any inherent identity or value. By posing the acts that constitute him, he makes his existence more significant
It is well claimed by Jean Paul Sarte in "Existentialism is humanism" that existence precedes essence, which gets a support from his closest Simone de beauvoir who states that "one is not born women, but becomes one."

Sarte and many existentialist's rules out and disbeliefs that any cosmic order determines human nature. However the concept can be questioned over the example of any object let's take an ashtray. It was created to specify certain purpose and it has a predetermined nature and properties for which it was created. Which can be simply stated as it's essence precedes it's existence. But Sarte claimed for such purpose that it's concept applies to humanity but not universally. The same cannot be stated for human beings since to accept an essence is to confine ourselves over a common meaning and a purpose. Over essence we become a mere object who are only to fulfil a higher ordained purpose which isn't conveyed to us.

Despite of this some atheists assume that we're possessed by special human nature which fulfils our role among fellow humans. Against which Sarte argues that no human nature is common to everyone, we define our nature which abides and commensales with the society. However this radical freedom, should be accompanied by radical responsibility.

The precedence of existence, which devoid the essence for our creation put a question mark over the presence of God and it's essence of creation of humanity, which is discussed in the next part.

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Philosophers on death.

Death has always been a mystery and an exciting topic for philosophers. Here are the excerpts of some of the philosophers and their take on death.

Plato
[Death], “Is this something that the separation of soul from the body? It died when the body is separate from the soul remains alone, apart, with himself, and when the soul, separated from the body, left alone, apart, with itself “…

Marcus Aurelius.
He who has seen present things has seen all, both everything which has taken place from all eternity and everything which will be for time without end; for all things are of one kin and of one form.

Socrates
Death may be the greatest of all
human blessings. To fear death, my friends, is only to think ourselves wise, without being wise: for it is to think that we know what we do not know. For anything that men can tell, death may be the greatest good that can happen to them: but they fear it as if they knew quite well that it was the greatest of evils. And what is this but that shameful ignorance of thinking that we know what we do not know?

Hegel
“Death, if we want to name and this unreality, is the most dangerous thing. This is not the life that recoils in horror at the death and preserves pure destruction, but life is death, and remains even in death, which is the life of the mind. ”

Arthur Schopenhaur
“Death is the moment of liberation from a narrow and uniform individuality, which, far from the inner substance of our being, is rather as a kind of aberration. ”After your death you will be what you
were before your birth.

Heidegger
“This means that one end by the
death does not mean, for human
reality, being-in-my-purpose be-
finished, it means the end for a being who is the being that exists. Death is a way of being human reality that assumes, as it is: When a human comes to life, it is already old enough to die. ”

Sartre
The darkness of death is like the
evening twilight; it makes all objects appear more lovely to the dying. [Death] “Not only the project that destroyed all projects and that destroyed itself. It is the triumph of the perspective of others on the point of view I am myself. ”

To conclude, here we've presented random views on the next topic I'll like to merge and give an overview of overall makeup on the topic. And I'll also like to discuss some moot points on death and after death.

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Fast fading faith.

In the jist of todays world the thing that is seemed to fade faster than anything is faith. Yes we all have lost our faith in everything our living, humanity, the world and the most important God. What can be the cause of such an important phenomenon that goes unseen in our daily lives is important for us to understand. The primary major cause is the inadvertent and ignorant lifestyle. We seemed to be very much interested in the world around us than what's happening within us.
The absurdity of life starts from the point of life when men becomes unknown of his internal life.

The lack of knowledge and apart from this most importantly the correct pious knowledge is aloof in our lives. We've forgotten the basic principles and basic school of philosophy in our lives and are just going abruptly where everyone's heading to. So the major thing here is to just give a halt to your life and concentrate on the footsteps where you're leading. We may foresee ourselves in this materialistic world but what about the world without the Maya. And yes it does exist as you were born without those vices that only come such a world.

The approach that everyone adopts to understand oneself is again inappropriate. What i believe is that no man or principle in the world can teach you to discover yourself the quest should began from within. The urge should come from your soul to understand one better. You should strife to maintain an inertia with the universe. The thing that aids in such a quest is the pious teachings of a Guru. Though it's an individual choice but the Guru should not be a mortal being but the basic affirm believes that can be applied to everyone and in every aspect. So the only strong contender can be a religious or any relevant script that you may perceive. The mystical teachings can be revealed by anyone any sentient being but what matters is how that teaching is conceived and perceived by you. The better understanding can only come when it's taught by your soul rather than any practical teaching enforced on it. A book especially the correct one can do a major difference in your lives. I have conceived the same ideas but from my religions holy book- Yes i am always astonished and obliged that i am having a scripture as my Guru and it has helped me to develop and follow the principles that I've learned from the same. And to correct you, you have the freedom of choice so you're not bounded to a single belief. Any scripture can lead your life and explain to you the correct meaning of your living though it's the only one you that are creating with it.

Anyone who says that they have only one life to live, i assume they've not read a book. And in the end let me leave you with this quote.
A book is the only place in which you
can examine a fragile thought without breaking it, or explore an explosive idea without fear it will go off in your face. It is one of the few havens remaining where a man's mind can get both provocation and privacy. - Edward P. Morgan.
And let me also assert you that the major principles can only be conceived by a book written by a pious soul in ecstasy...

So start the discovery and unleash the locked doors of your spirit and taste the gleam of the pious inner world...

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