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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 ...
26
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. ...
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 ...
17
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):
...
16
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 ...
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 ...
13
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 - ...
12
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.
$$\begin{array}{|...
12
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 ...
11
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 ...
11
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 ...
11
The answer to this question emerges from an examination of the structure of tyrosine — or, more strictly, the tyrosyl residue, which is how it exists in proteins, the concern of the question:
It has both hydrophobic and hydrophilic features and can exhibit both
behaviours depending on the circumstances.
The ring is aromatic and hydrophobic, but 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
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 ...
9
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.
9
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, (...
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 paper ...
9
You can certainly refer to short peptides by their sequence. I don't know of any exact boundaries, but I've seen tripeptides referred to by either their three letter codes (Ala-Asp-Asn) or even the chemical name (alanylaspartylasparagine) although obviously that gets ridiculous pretty quickly.
As the largest known protein, titin also has the longest IUPAC ...
8
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, ...
8
The first part of your question illustrates a common confusion of beginners between the physiochemical properties of free amino acids in solution, and the properties of that part of an amino acid that remains after it has participated in a condensation reaction to form part of a polypeptide. They are different. (It was for that reason that I modified the ...
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 example)...
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 ...
7
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 ...
7
Aminoacyl-tRNA sythetases are highly specific to their corresponding amino acid. First, the activation site, where the amino acid binds, constitutes a complex network of intermolecular interactions. For example, threonine, catalyzed by threonyl-tRNA synthetase, is very similar to valine and serine. Valine has a methyl group instead of the hydroxy group of ...
7
In my experience neither is preferred.
When simply presenting a protein sequence, e.g. in the context of a database of proteins encoded by a genome, then the one-letter code tends to be used.
When showing an alignment of a DNA sequence with the encoded protein sequence both can be used, although personally I prefer the one-letter code for this too ...
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.
...
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