17 votes
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What is the explanation for the smaller number of tRNA than codons?

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): ...
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13 votes
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What is the last heavy atom of an amino acid?

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 ...
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Where can you find the quantities of each amino acid of a particular protein or food?

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 ...
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12 votes

Why is glycine considered a nonpolar amino acid but a polar molecule?

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 ...
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12 votes
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Is tyrosine hydrophobic or hydrophilic?

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 ...
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11 votes
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Arrangement of Amino Acids in the Protein alphabet

As suggested by tyersome's comment, the amino acids are grouped by their physiochemical properties. Let's add some commas: DE,KRH,NQ,ST,PGAVIL,MC,FYW aspartic ...
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10 votes
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Peptides neither produced by the ribosome or the non-ribosomal peptide synthase complexes

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 ...
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9 votes
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What are 'acid stable' amino acids?

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 ...
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9 votes
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Classifying Polypeptides (and/or Proteins)

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 ...
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8 votes

Amino Acid mutation profile for human coronavirus: Why is the mutation from T to I so frequent?

The change from C to T (or U in the case of RNA) can happen via the oxidation and deamination of the Cytosine (see reference 1 for the explanation of the mechanism). The mechanisms looks like the ...
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7 votes

Is there any evolutionary advantage of selection of L-amino acid over D-amino acid?

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 ...
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7 votes
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How many different kinds of polypeptides, each composed of 12 amino acids, could be synthesized using the 20 common amino acids?

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, ...
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D/L configuration for amino acids

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 ...
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How do aminoacyl-tRNA synthases distinguish between similar amino acids?

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. ...
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What is the preferred way to abbreviate amino acids?

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 ...
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7 votes
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What do the colors mean in representations of amino acids?

There is no ‘standard’ colour scheme for amino acids in the sense of one recommended by a standards or professional organization for biochemists. There are several schemes used in practice — either by ...
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6 votes

How many different kinds of polypeptides, each composed of 12 amino acids, could be synthesized using the 20 common amino acids?

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\...
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6 votes

Are There Rules for How Proteins Are Formed?

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. ...
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6 votes
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What are the functions of disulphide bonds?

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 ...
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What are the functions of disulphide bonds?

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 ...
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6 votes
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Specificity of Protein Kinases in Signaling Pathways..?

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 ...
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6 votes
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Is there any evolutionary advantage of selection of L-amino acid over D-amino acid?

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 ...
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6 votes
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Is cysteine deficiency possible?

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 ...
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6 votes
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How does aminoacyl-tRNA synthetase recognize different tRNAs?

You give the answer in your question: binding areas that recognize a particular tRNA through unique identity sites at the acceptor stem and/or anticodon loop of the tRNA. The point is that ...
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6 votes

Why are excess amino acids toxic?

Firstly excess amino acids are deaminated to form keto acids and not urea. Urea is formed utilising the ammonium released as a consequence of deamination via Ornithine-Arginine cycle Secondly the ...
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6 votes
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Confusion on polarity and hydrophobicity of Proline, Tyrosine and Cysteine?

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 ...
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6 votes
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How to interpret this PubChem record of L-Alanine

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....
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6 votes

About the definition of ketogenic amino acid

The fundamental 'problem' with acetyl-CoA is that it cannot be converted to glucose via the tricarboxylic acid (TCA) cycle: a two-carbon compound (acetyl-CoA) enters the TCA cycle, but two carbons are ...
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5 votes

Specificity of Protein Kinases in Signaling Pathways..?

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 ...
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