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14 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 ...
David's user avatar
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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 ...
David's user avatar
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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 ...
acvill's user avatar
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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 ...
David's user avatar
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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 ...
gilleain's user avatar
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8 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 ...
David's user avatar
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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 ...
Chris's user avatar
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7 votes
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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. ...
adjan's user avatar
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7 votes
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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 ...
Alan Boyd's user avatar
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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 ...
Roland's user avatar
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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 ...
David's user avatar
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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 ...
user 33690's user avatar
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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....
Ashafix's user avatar
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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 ...
user338907's user avatar
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6 votes
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Koshi and Goldstein substitution matrix

It seems that there IS a deletional bias across genomes Kuo & Ochman 2009: Based on over 5,000 indel events in noncoding regions, we found that deletional events outnumbered insertions in all ...
markur's user avatar
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5 votes
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What is the significance of cysteine in a protein sequence?

What can I infer if I get a high percentage of C from a protein sequence? A highly stable structure that is likely found in the extra-cellular space. Cysteine can form a disulphide bond with ...
James's user avatar
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If human proteins are synthesized from only 20 different amino acids, then how can there be such variety of proteins in human cells?

There are only 26 letters in the English language, and more than 80% of words are under 10 letters. Yet there are over a million English words. Nonsense words don't count. Now imagine the ...
anongoodnurse's user avatar
5 votes

How do I know which molecular structure is glycine's "base state"?

Short Answer: You need to define base state. Background: The point to keep in mind here is that the base state (as you call it) is not constant. As @jeppenielsen points out in the comments, amino ...
another 'Homo sapien''s user avatar
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Effect of mutation on phenotype

Yes. It is actually the case of most mutations that affect the phenotype! Only 1.5% of the human genome codes for proteins. About 5-10% of the human genome are regulatory sequences which do not ...
Remi.b's user avatar
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What is the function of cystine, cysteine, and cysteine protease?

I'm not sure as to what level of detail I should answer this question, but I will try to give you as much information as I can that I think will be relevant to.. whatever it is you are doing. ...
Bob's user avatar
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5 votes
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Why are dietary recommendations for methionine consumption combined with cysteine?

In humans, cysteine can be synthesized from methionine and tyrosine from phenylalanine (note that the reverse pathways do not occur). Because their synthesis requires essential amino acids and the ...
canadianer's user avatar
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Metabolic significance of aspartate transaminase in mammalian liver

Summary The primary metabolic function of aspartate transaminase, like other transaminases is to transfer nitrogen, in the form of amino groups, between 2-oxo acids. These reactions are readily ...
David's user avatar
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4 votes

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

I'm just converting @alwaysconfused's comment into answer (with a bit of more details). Yes, glycine does have a dipole moment (15.7 D), but when it comes to biochemistry, then the dipole moment on ...
another 'Homo sapien''s user avatar
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Essential amino acids

Bacteria and plants are able to synthesize all amino acids, as they are capable of nitrogen fixation. If animals eat plants, they get the essential amino acids needed for their proteins. Humans get ...
SeRe's user avatar
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What are "+" and "Ar" in consensus binding sequence of amino acids?

Ar means aromatic and + means positively charged residues. However, this is not a standard code (as of now). From the same ...
WYSIWYG's user avatar
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What difference do trans and cis configurations of amide groups bring to the polypeptide chain?

Apparently the trans configuration is more stable, so more amino acids with a trans configuration can be found within a polypeptide chain. Does this pose any significant characteristic to a ...
WYSIWYG's user avatar
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4 votes

Molecules responsible for reading amino acid language

Clarifying the premise As mentioned in my comment, the term “amino acid language” doesn’t really make sense as far as I’m concerned. Worse: nothing, to my knowledge, is ever reading an amino acid ...
Konrad Rudolph's user avatar
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Reading an amino acid physicochemical properties diagram

Polarity and hydrophobicity are not discrete phenomena and, therefore, categorizing amino acids as such has some measure of arbitrariness, especially at edge cases. It all depends on one’s definition. ...
canadianer's user avatar
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What would be the fate of protein made from D-amino acids after ingestion by humans?

One aspect of the basic biochemistry needed to approach this question is the fact that the enzymes that catalyse cellular reactions show various levels of specificity towards their substrates (...
David's user avatar
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4 votes

Is tyrosine hydrophobic or hydrophilic?

Tyrosine (Tyr or Y, 4-hydroxyphenilalanin) is usually reffered as polar amino acid because its hydroxyl groupe (polar is rather hydrophilic), but there is a catch with the benzen ring and stacking pi-...
Lukien Chumi's user avatar

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