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33

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 ...


20

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 ...


17

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 ...


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

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 ...


9

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 ...


9

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 ...


9

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 - ...


7

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 ...


7

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.


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 ...


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. ...


5

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 ...


5

It is not suggesting a 2-base->3-base code in the way you are thinking, but of a non-coding, two-coding triplet pattern occurring first. This means you would have 16 different coding sequences with 4 possible spacing bases in between. Later, the spacing bases could become used as part of the code. Does that make more sense? Instead of AA,CG becoming ...


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 ...


5

When the amino acid comes to the ribosome it is in the form of an aminoacyl tRNA in which the carboxyl group of the amino acid is esterified with the 3' OH group of the ribose moiety at the 3' end of the tRNA. There is already a growing peptide bound in the P site of the ribosome with a free -COOH group which will react with the -NH2 group of the incoming ...


5

The more bases there are per codon the more information you can code for. There are only 22 different amino acids, in consequence we need minimum 3 bases per codon. 1 base-codon --> 4^1 = 4 possible codes which are: A / T / C / G 2 base-codon --> 4^2 = 16 possible codes which are: AA / AT / AC / AG / TT / TA / TC / TG / CC / CA / CG / CT / GG / GC / GT ...


5

I'm sure there are lots of ways of handling this, but there are only 20 of them (more or less). I really wanted to figure out how the amino acids resulted in the resulting protein structure. So I started to break them down into categories. The categories cannot draw boundaries exactly since one amino acid might belong to several categories in a unique ...


5

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 ...


5

This is mostly because of the nature of the amino acids. You need to have a Hydroxy-group in the sidechain of the amino acid which is the point where the phosphogroup is attached. Since this process needs to be reversible, this can only happen here. See the image below (from here) about the chemical structure: In eukaryotes not only these three are ...


4

The Biology Project from the University of Arizona provides the best explanation of Dr. Margaret Oakley Dayhoff's logic for the non-obvious single letter AA abbreviations: Glutamine ~ Q-tamine therefore, Q


4

ExPASy to the rescue! Although I didn't comb through all the tools, this nifty website provides quite the myriad of bioinformatics resources which most certainly contains the tool to calculate what you want. Bear in mind though, most tools will tell you the isoelectric point of your protein. However, bearing in mind the relationship between pI and pH (i.e. ...


4

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, ...


4

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, ...


4

Disulfide bonds form between different amino acids of a protein chain and the help to stabilize and maintain a distinct three dimensional form. In principle this looks like this (pipcture from the Wikipedia page on Disulfide bonds): Disulphide bonds (or bridges) can also hold different subunits of larger protein complexes together, one example for this ...


3

You ingest daily dietary protein which your body hydrolyzes to get all the building blocks for other proteins (amino acids). Also, from diet you can get essential amino acids that cannot be synthesized de novo by the organism which is more economical than amino acid synthesis. Other amino acids can be constructed by metabolic processes.


3

I have written a script that will get you started. It downloads all protein coding transcripts of the species of interest from Ensembl and prints the codon use for each codon on each transcript. You will need to install the Bio::EnsEMBL::Registry Perl module, see here for instructions. The script also uses the Math::Round module, everything else should be ...


3

Disulphide bonds occur in proteins, not amino acids, although they involve a covalent bond between two amino acids (both cysteine). The received wisdom is that disulphides are used as extra stabilisation of the structure of proteins which are secreted, or which have an extracellular domain. It's important to get hold of the idea that they do not occur in ...



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