14
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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 ...
- 2,368
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 ...
- 24.3k
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 ...
- 24.3k
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 ...
- 8,256
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 ...
- 24.3k
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 ...
- 9,432
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 ...
- 880
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 ...
- 24.3k
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 ...
- 51.5k
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. ...
- 2,106
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 ...
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7
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 ...
- 5,675
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 ...
- 24.3k
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 ...
- 1,955
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....
- 695
6
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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 ...
- 4,678
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 ...
- 1,769
5
votes
What signals a ribosome to stop production when the cell is out of available amino acids?
When cells run out of amino acids, more and more of their tRNAs remain uncharged. This elevated ratio of uncharged/charged tRNAs trigger complex signalling pathways that control amino acid ...
- 261
5
votes
Where can you find the quantities of each amino acid of a particular protein or food?
Go to WolframAlpha and enter 1g potato in the input field:
Then scroll down in the results to Protein and amino acids and click the more button in the top right hand corner to get the following list ...
- 519
5
votes
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Why do asparagine and glutamine have two different abbreviations?
The abbreviation Asx (B) is used if it is uncertain whether the amino acid at a given position in a peptide sequence is Asparagine or Aspartate. Similarly, Glx (Z) is used when there is uncertainty ...
- 5,675
5
votes
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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 ...
- 24.7k
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 ...
- 11.3k
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 ...
- 14.1k
5
votes
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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 ...
- 68k
5
votes
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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.
...
- 556
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 ...
- 17.6k
4
votes
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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 ...
- 425
4
votes
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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 ...
- 35.2k
4
votes
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Are alpha-ketoglutarate and glutamate involved in all transamination reactions?
The major transaminases such as the aspartate transaminase and alanine transaminase involve the glutamate α-ketoglutarate interconversion. Even the GABA aminotransferase employs glutamate/α-...
- 35.2k
4
votes
Why do asparagine and glutamine have two different abbreviations?
Asparagine (Asn) and glutamine (Gln) are derived forms of the amino acids aspartic acid (Asp) and glutamic acid (Glu).
Both amino acid pairs (Asn/Asp, Gln/Glu) consist of the same carbon backbone,
...
- 41
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