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Protein-biomolecules

Discussion of all aspects of biological molecules, biochemical processes and laboratory procedures in the field.

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Protein-biomolecules

Postby hobaoau » Fri Jan 26, 2007 3:10 am

I'm new member.
I got some questions that i have look up in some books but still can't get the clear interpretation:
1/ How does the shape of protein(a-helix, B-Sheet and random loops) affect on the functions of protein? In my opinion, i think the difference is just the shape but the sequence of amino acids is not changed.
2/ what is the significance of protein in the living organism?
3/ Why do some people believe that the carbonhydrate is not as important as lipid? Meanwhile some kinds of lipid such as cholesterol(steroid) cause heart attack and stroke.
4/ As everybody know that there are only 20 amino acids of over 100 amino acids in cell participate in produce proteins but how can we have a astronomical number of proteins. show me the calculation if you can.
5/How can the cells determine the kinds of protein they want to synthesise?
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Postby rui_benfeitas » Sat Feb 17, 2007 1:24 pm

Hello! Let me try and answer your questions.

1.How does the shape of protein(a-helix, B-Sheet and random loops)
affect on the functions of protein?


In my opinion, i think the difference is just the shape but the sequence of amino acids is not changed.
If you have a protein with a certain sequence of aminoacids, that sequence can organize itself in different ways, depending on the interactions they (aminoacids) can have with each other (Hydrogen bonds, hidrophobic interaction, ionic bonds...). These type of interactions make the protein have different shapes and therefore, different sites to interact with each other.
For instance, regulatory proteins have different sites to interact with other proteins (such as efectors) and DNA. So, as an enzime has an active site to link a specific substract, it can only link with it if the active site has the correct shape (once again, made not only by the sequence of aminoacids but also by the shape).
You can have different proteins with similar shapes doing different things (and the opposite is also true!):
- Prions are proteins with B motifs that change other proteins with
similar shapes (but different quimical structures) into prions themselves.

"2/ what is the significance of protein in the living organism?"

Proteins are, in my opinion, the most important biomolecules in every living organisms. As you may now, every information of each organism is contained in its genetical code (DNA or RNA). That code can be translated into mRNA and then into proteins and these proteins are the reflection of the starting information. The proteins are important to regulate mechanisms of signal transduction, can link huge amounts of information and are responsible for lots of very important pathways in every living being. Do a little search on google or wikipedia on "enzymes" for instance.


"3/ Why do some people believe that the carbonhydrate is not as important as lipid? Meanwhile some kinds of lipid such as cholesterol(steroid) cause heart attack and stroke."

I can only think about the big importance that glycogen and starch have. Sorry not to help you much on this one... This is a bit silly:
no living organism can survive without carbohydrates!!!


"4/ As everybody know that there are only 20 amino acids of over 100 amino acids in cell participate in produce proteins but how can we have a astronomical number of proteins. show me the calculation if you
can."

Now, as Im not really sure about this, Im going to wait for some replies... I think this way: Imagine you have only 20 letters to write a sentence. You can repeat the same letters in all words and in the same word (AAA AA AA AAAA A) or you can have different words with different letters (ABC DE FG HIJKL M). If you want just to write a word of only 5 letters with different combinations of the 20 letters you can have, you will get 20x20x20x20x20=3200000 different words (although they may not say anything ;) ). With aminoacids is the same thing. You will have that same 20 letters to form a huge word. That depends on the amount of amino acids the protein can get. If you want to form proteins with 50 aminoacids, you will have 20^50=1.12589x10^65 different proteins (now, turn this into proteins with several thousands of aminoacids). Of course this doesnt happen just like this. You need to have a functional sequence, with starting codons (in you mRNA) to enconde a methionine aminoacid (the first in
every protein) and a stop codon (that doesnt enconde any aminoacid but it tells to stop the traduction), and in the middle you need to have some other specific sequences, that are different in each protein.

"5/How can the cells determine the kinds of protein they want to synthesise?"


Now this is a hard question I had recently. The mechanism by wich a cell can synthesise different proteins is a very complex thing. It may be the most challenging thing to geneticists understand. As you can have lots of different exterior impulses that will get your cell to response in different ways; you can have different amounts ofsubstracts (for your enzimes) and you can have lots of different regulatory factors (proteins) (just to start...) its a really difficult thing to know how a cell will encode which protein. That is what many scientists use their careers for. One thing I can say: a chromosome has a linear amount of DNA (a sequence of genes) that can be silenced (turned into heterochromatin) or activated (turned into
euchromatin) in different ways, at different times. So, its the
different interactions that take place within a cell (and out of it)
that will determine what gene to be encoded into a protein.

Hope I answered your doubts. If you still have any, send me a private
message.
:)
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Postby sdekivit » Sat Feb 17, 2007 4:02 pm

next time don't make someones homework ;)
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Postby rui_benfeitas » Sun Feb 18, 2007 3:01 pm

He he he he he he 8)
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Postby oncolozist » Mon Feb 19, 2007 7:29 pm

Well, for starters for the ques dat remain unanswered all i know is dat
Twenty amino acids are encoded by the standard genetic code and are called proteinogenic or standard amino acids. Other amino acids contained in proteins are usually formed by post-translational modification, which is modification after translation in protein synthesis. These modifications are often essential for the function or regulation of a protein; for example, the carboxylation of glutamate allows for better binding of calcium cations, and the hydroxylation of proline is critical for maintaining connective tissues and responding to oxygen starvation. Such modifications can also determine the localization of the protein, e.g., the addition of long hydrophobic groups can cause a protein to bind to a phospholipid membrane.
Also Hundreds of types of non-protein amino acids have been found in nature and they have multiple functions in living organisms. Microorganisms and plants can produce uncommon amino acids. In microbes, examples include 2-aminoisobutyric acid and lanthionine, which is a sulfide-bridged alanine dimer.

Moreover In humans, non-protein amino acids also have biologically-important roles. Glycine, gamma-aminobutyric acid and glutamate are neurotransmitters and many amino acids are used to synthesize other molecules, for example:

Tryptophan is a precursor of the neurotransmitter serotonin
Glycine is a precursor of porphyrins such as heme
Arginine is a precursor of the hormone nitric oxide
Carnitine is used in lipid transport within a cell,
Ornithine and S-adenosylmethionine are precursors of polyamines,
Homocysteine is an intermediate in S-adenosylmethionine recycling
Also present are hydroxyproline, hydroxylysine, and sarcosine. The thyroid hormones are also alpha-amino acids.

Some amino acids have even been detected in meteorites tooooo :shock: , especially in a type known as carbonaceous chondrites. This observation has prompted the suggestion that life may have arrived on earth from an extraterrestrial source.

All i have to say is dat the nonstandard amino acids are usually formed through modifications to standard amino acids. For example, homocysteine is formed by the transsulfuration pathway from cysteine, while dopamine is synthesized from tyrosine, and hydroxyproline is made by a posttranslational modification of proline.

And about ur doubt about which proteins to synthesise wen.. hw is it know n by a cell... I hope u know dere is something called cell regulation and operon models about gene regualation and control!!! :idea:

I hope this post completes all ur ques and doubts!!
:)
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