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):
...
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 ...
12
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 ...
12
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
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, (...
10
One peptide that comes to mind is the metabolically important reducing tripeptide glutathione — γ-L-Glutamyl-L-cysteinylglycine:
This is synthesized from cysteine, glutamate and glycine by reactions catalysed by glutamate cysteine ligase and glutathione synthase:
Synthesis of glutathione (GSH) — two subunits of glutamate cysteine ligase (GCL) are shown
...
9
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, ...
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 ...
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
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 and ...
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
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 ...
6
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 ...
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
It sounds like your question is "what are the rules to protein folding?"
That's not the only way to read your question.
Protein Folding is a unique problem - a 1D sequence maps to a 3D object. Since proteins mediate nearly all biochemical transformations and therefore mediate life's processes, protein folding one of the great unsolved problems in ...
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
TL/DR: these are borderline, complicated cases. There is no broad consensus on whether cysteine and tyrosine should be considered hydrophobic or polar. Proline is clearly nonpolar though.
The reason for the confusion is that are there several ways to define and measure polarity and hydrophobicity for amino acids. First, the polarity and hydrophobicity of ...
6
The PubChem format description is not that easy to find:
https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/asn_spec/pcsubstance.asn.html
And the ASN file linked here:
https://pubchemdocs.ncbi.nlm.nih.gov/data-specification
I am correct in saying that the numbers in the 'element' array are corresponding to Atomic Numbers?
Yes, 1 is hydrogen, 6 is carbon, ...
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 way,...
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 ...
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