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45

Brian Hayes wrote a very interesting article from a mathematical point of view: http://www.americanscientist.org/issues/pub/the-invention-of-the-genetic-code especially the "Reality intrudes" section. Basically people had created fancy mathematical reasons why it has to be exactly 20. Nature, being nature, does not follow the reasoning, but has its own ...


25

The first position of the anti-codon, the "Wobble" position, forms hydrogen bonds less well than do the second two. This means that the last position of the codon has less coding potential than the first two. The reason is that the anticodon is at the bottom of the anticodon loop of the tRNA, and so there backbone of the tRNA is bending back to pair with ...


21

I know that you are referring to the commonly ribosome-translated L-proteins, but I can't help but add that there are some peptides, called nonribosomal peptides, which are not dependent on the mRNA and can incorporate D-amino acids. They have very important pharmaceutical properties. I recommend this (1) review article if you are interested in the subject. ...


16

The ribosome holds the peptide-bound tRNA and aminoacyl-tRNA in the right orientation to catalyze the peptidyltransferase reaction. http://www.pnas.org/content/103/36/13327/F1.expansion.html If the incoming aminoacyl-tRNA was the other enantiomer, the amino acid moiety would not fit properly into the ribosome active site. In other words, the shape of the ...


14

There are two other ideas to throw in here. 1) just to add to KAM's thoughtful answer. There was also a thought that the last base also gives a lot of flexibility for GC content which responds to some 2) lets not forget that redundancy in the genetic code helps give some resistance to mutations which might be disruptive. the amino acids less disruptive ...


14

Th reason for this is that for the third base of the tRNA non-Watson-Crick pairing is allowed. This phenomenon is called "Wobble base pairing". See the figure (from here) for illustration (from here): If you have a look at the codon table for amino acids, than the variation in the code for one amino acid mostly happens on the third position (from here): ...


10

Yes. All proteins actually begin to get synthesized on cytoplasmic ribosomes but if they are going to be used for extracellular purposes, they are tagged and whole ribosome is taken to ER where protein synthesis is completed. The proteins are exocytosed with help of Golgi body, the post office tagging and packaging organelle (the Golgi body packages these ...


10

You can divide the 22 (including selenocysteine and pyrrolysine) proteinogenic amino acids into broad groups of similar amino acids. There are the hydrophobic amino acids like trypthophane, valine and leucine, the charged amino acids like glutamate and arginine and the polar amino acids like serine and threonine. There are some amino acids with unique ...


10

As far as I know, it is unknown why we only see left-handed and not right–handed amino acids. A recent article speculates that the weak force could be responsible for a tiny asymmetry in energy levels between the stereo-isomers. However, if the effect is tiny, its hard to see why it should have biological implications. In 2004, Tamura and Schimmel showed ...


10

For the most part they are not used. there are amino acid racemases, which interconvert L- and D- forms of some specific amino acids, which may be used in some particular biosynthetic or metabolic pathways. In particular I'm thinking of firefly luciferase which uses D-Cysteine as a re-dox reagent to regenerate the luciferin substrate that the light - ...


9

The amino acids asparagine and glutamine have hydrolysable amide groups on their R groups, as shown here: Note the leftmost amide group on both amino acids. When exposed to acid, these groups would hydrolyse, releasing ammonia. This was of interest when people used to determine amino acid compositions by acid hydrolysing purified proteins (example ...


8

Edward N. Trifonov is a professor at the Institute of evolution at University of Haifa, Israel. One of the main research topics in his group is the reconstruction of the origins of life. In one of his papers, The triplet Code From First Principles, he proposes the the chronological appearance of the 20 amino acids. There are a lot of hypothesis and testable ...


8

The normal results of an attempt to assemble proteins with mixed chiral amino acids is a protein that fails to fold. The general assumption due to this result is a choice has to be made very early on to use all right-handed or all left-handed amino acids. There doesn't seem to be any particular reason to choose one way over the other except for prevalence.


8

The central dogma of molecular biology: DNA makes RNA makes Protein DNA is a reference for proteins*, which are the functional molecules in cells. These are comprised of 20 unique amino acids, and each is coded for by a stretch of DNA known as a codon. Codons are always 3 base-pairs (nucleotides) in length. DNA is made of 4 unique nucleotides; (A)denine, ...


8

There's a fantastic database available from the United States Department of Agriculture that includes almost 9,000 common foods, including their nutritional information. This database is searchable and available from the USDA Agricultural Research Service. Here is a link for the online searchable database. Within the database you are able to search for a ...


7

This is one of my favorite charts demonstrating the complexity of amino acid properties: http://www.jalview.org/help/html/misc/aaproperties.html Histidine is probably the most complicated amino acid in this regard (just compare how many circles it falls into). But don't undersell Cysteine and Methionine; those sulfurs exhibit some surprising behavior, ...


7

You may also be interested in D-amino-acid oxidase (EC 1.4.3.3), a flavoprotein (FAD) highly specific for the D-form of amino acids, which was discovered by Hans Krebs in 1935 (see here), and which has a wide distribution (including in humans). The enzyme has been very thoroughly investigated, in particular by Massey & co-workers (see here for ...


7

Essentially, yes, "proteins that we consume form new proteins that are different". The processes are each of them topics for themselves. In short, consumed proteins are digested by peptidases (enzymes) in the stomach, breaking them down into their consituent amino acids. These are absorbed in the gut and transported in the blood to all cells. These take up ...


7

Biopython and the other bio-programming languages typically have examples of how to do this kind of thing. For example here is some python code for calculating some of these: http://biopython.org/w/index.php?title=ProtParam&redirect=no Many of the propensity scales are in this database: http://www.genome.jp/aaindex/ And there are also biojava ...


7

The current thinking amongst biophysicists is that if we all woke up tomorrow to find that someone had edited the book of life so as to exchange all of the L-'s and D-'s (and made similar mirroring changes to all of the molecules that any protein interacts with), everything would be exactly the same. Milton, et al. (Science, 1992) lent supporting empirical ...


7

Judging from what you have said, I assume that combinatorics is not a problem to you. I believe your problem is that you think Glu-(Met)x11 is equivalent to (Met)x11-Glu, just turned around. However, that is not a correct mindset. Amino acids are not symmetrical molecules, therefore reversed linear combination does not create a turned-around (be it chiral ...


6

That's quite a laundry list, and I doubt someone is going to sit down and give you hints for all of them. Note that some of the properties (like percent alpha helix) rely on prediction method (secondary structure prediction, in this case). "Net donated hydrogen bonds" sounds like it makes sense only for a given complex with a solved 3D structure. ...


6

Phosphorylation requires a nucleophile and hydroxyl oxygen acts like one. Serine, theronine and tyrosine get phosphorylated on the free OH group in their side chains. Nitrogen, in some cases also can act as a nucleophile. In case of histidine, the imidazole nitrogen is phosphorylated during bacterial chemotaxis signaling. As far as I know eukaryotes do not ...


6

As you say yourself, biological molecules are usually available in both chiralic possibilities, yet nature uses only one of the two possibilities. At some point in our molecular evolution (and at a very early one) L-amino acids were stochastically "chosen" over their D-equivalents (I think that the choices would have been equiprobable). There is no reason ...


6

Think of the amino acid choices as 12 seats. In the first seat, we have 20 choices. In the next seat, we have 20 choices, and this continues. Therefore, we have that $$ \underbrace{20\cdots 20}_{12\text{ times}} = 20^{12} $$ For your question about the the polypeptides, (Met)x11-Glu is not the same as Glu-(Met)x11, order matters. Up to this point, we ...


6

Cysteine deficiencies are possible, and one cause is the genetic disorder homocystinuria. Cysteine can be produced from methionine through a homocysteine intermediate, and defective genes for the enzymes involved can prevent proper cysteine production and cause a buildup of homocysteine. Patients have to eat a very carefully controlled diet with very low ...


6

We can look at the list of amino acids on wikipedia for a start. And we can look at this L-alanine: What makes your image confusing is that it's a Fischer Projection, and I hate those because you have to remember what way the stereochemistry goes. In Fischer Projections, vertical lines face away from you, while horizontal lines face towards you. So if we ...


6

As mentioned in the comments by Roland, this term is not common and is first used by the authors of the mentioned paper (also the package mentioned by Roland in comments - STING). From this link you can find the definition of the Last Heavy Atom which is possibly the most distal non-hydrogen (N, C, O, S) atom in the amino-acid side chain. ...


5

Initial letters of the names of the amino acids were chosen where there was no ambiguity. There are six such cases: cysteine, histidine. isoleucine, methionine, serine and valine. All the other amino acids share the initial letters A, G, L, P or T, so arbitrary assignments were made. These letters were assigned to the most frequently occurring ...



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