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Questions tagged [amino-acids]

Amino-acids are organic acids with an amino group in the alpha position (alpha-acids). They are the structural units of proteins and involved in many biochemical pathways.

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Why 20 amino acids instead of 64?

This question got me thinking about amino acids and the ambiguity in the genetic code. With 4 nucleotides in RNA and 3 per codon, there are 64 codons. However, these 64 codons only code for 20 amino ...
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Why are amino acids in biology homochiral?

Why are nearly all amino acids in organisms left-handed (exception is glycine which has no isomer) when abiotic samples typical have an even mix of left- and right-handed molecules?
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What is the prehistory of amino acids in cells?

As a followup to Why 20 amino acids instead of 64? and What is the smallest number of amino acids required for life?, I am trying to understand the prehistory of amino acids in cells. All living ...
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What is the smallest number of amino acids required for life?

Is there any hypothesis on the minimum number of amino acids required for life?
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What is the explanation for the smaller number of tRNA than codons?

Translation, or decoding, of the four-nucleotide language of DNA and mRNA into the 20–amino acid language of proteins requires tRNAs and enzymes called aminoacyl-tRNA synthetases. To participate ...
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What happens to dextrorotatory amino acids in humans?

As indicated by this question, most of the amino acids in the human body have the L-chirality. As enzymes also have handedness, what happens to the D-amino acids that end up within the human body? Are ...
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Is there any evolutionary advantage of selection of L-amino acid over D-amino acid?

After listening to a scientific talk, I had this question that why in the natural selection process, are the L-amino acids selected over the D- form. However, we still we produce D-amino acids; ...
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Why are 3 nucleotides used as codons for amino-acid mapping in DNA?

DNA is made of 4 unique nucleotides. When coding for a protein, a sequence of 3 nucleotides is used to code for each amino acid. Why are codons 3 nucleotides in length? A related question can be ...
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Where can you find the quantities of each amino acid of a particular protein or food?

Taking a potato as an example. If I wanted to know how much µg or % of each of it's amino acids there are in 1 gram of pure potato protein, where can I find this information? Is there a freely ...
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How can a three-base codon evolve from a two-base codon?

Inspired by this question among others. It's widely suggested that the current 3-base codon system of encoding protein sequences in DNA evolved from an earlier 2-base codon system. This makes sense ...
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Is consuming proteins different vs. consuming amino-acids and how?

Yesterday I had a discussion with a friend. He said that consuming proteins and amino-acids is different. He said that those who grow muscles would agree on that. I wanted to argue against that ...
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How to compute properties of peptides ?

I have been tasked with writing a program for computing properties of a give set of peptides. These peptides are given as 1-letter amino acid sequences and I need to compute the following : Length of ...
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Classifying Polypeptides (and/or Proteins)

Since polypeptides are a linear chain of twenty amino acids, each having a single letter abbreviation (e.g. Alanine = A). So can a polypeptide be represented as just the sequence (say: ADN for an ...
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How are amino acids neutral at physiological pH?

Amino acids with non‐ionizable side chains are zwitterions when they are at physiological pH, pH 7.4. This is what my book says. But I do not understand why. The Pka for a carboxyl group is around 3 ...
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Why is leucine amino acid used the most in proteins and tryptophan the least?

The amino acid leucine, is used in proteins more than others. Leucine with 9.1 percent (its average in more than 1.150 different proteins) is used most and tryptophan with 1.4 percent is used less ...
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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?

How many different kinds of polypeptides, each composed of 12 amino acids, could be synthesized using the 20 common amino acids? The book's answer is $20^{12}$. However, I disagree. This result ...
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Histidine aromaticity

I understand that the imidazole ring in histidine is aromatic. I also realize that it retains it's aromaticity when protonated. I am wondering why it is not mentioned at all in basic text books such ...
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Why is glycine considered a nonpolar amino acid but a polar molecule?

Glycine has a dipole moment, so why is it considered a nonpolar amino acid when discussing its occurrence in proteins? Also, is the backbone of a protein nonpolar?
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What is the last heavy atom of an amino acid?

I'm a electrical engineer and I'm learning about bioinformatics. I was reading this paper that uses the last heavy atom to search for active sites of a protein but what would be a heavy atom? Is it ...
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Whole genome amino acid composition tool?

I'm interested in a statistical tool to get bacterial codon usage at genomic level. Ideally, the tool should be flexible to analyse hundreds of bacterial genomes. I've looked in MeSH terms database ...
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Are there any effects of elevated Cysteine levels on cognitive function?

I'm looking at this diagram of homocysteine metabolism and see two distinct pathways that the amino acid may get metabolized to: with vitamin B12 it gets converted back into methionine, while with B6 ...
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Specificity of Protein Kinases in Signaling Pathways..?

In most of the signaling pathways the activated receptor when activates Protein Kinase through the action of secondary messenger, then these protein kinases almost always phosphorylate on the specific ...
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Is tyrosine hydrophobic or hydrophilic?

I’ve seen tyrosine classified as a hydrophobic amino acid due to its aromatic ring in some textbooks and as hydrophilic due to its hydroxyl group in other textbooks. How does tyrosine actually ...
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Can proteins move outside cells?

I am trying to learn about basic cell biology, and have what is probably an extremely simple question. So this is how I understand it so far: Proteins are made from amino acids. This process is ...
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Why do asparagine and glutamine have two different abbreviations? [closed]

I'm looking at amino acid abbreviations and on every site I visit, asparagine and glutamine have two different abbreviations. Is there a reason for this? Do they represent different forms of the amino ...
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What are 'acid stable' amino acids?

I tend to see terms amino acid, acid stable amino acid, and free amino acids used often in ...
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What are “primary amino acids and secondary amino acids”? Context: analysis of amino acid content using reversed-phase HPLC

In a Russian document I'm translating, an HPLC system is used to analyse the amino acid content of a substance. The detector wavelength is set at 262 nm for "secondary amino acids" and 338 nm ...
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Are There Rules for How Proteins Are Formed?

Proteins are formed by stringing together different amino acids. Different amino acids have different properties (such as being attracted to or repelled by water, positively or negatively charged, ...
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Amino acid compatibility

The (human) genetic code encodes 20 amino acids. They form a protein using peptide bonds. Each amino acid has a carboxyl group (COOH) and an amino group (NH2) that can potentially form a peptide bond. ...
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What are the functions of disulphide bonds?

What are the functions of disulphide bonds between amino acids in proteins or peptides?
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D/L configuration for amino acids

Why would this be "L-cysteine"? This is taken from the answer key for my biochem final. From what I understand if the -NH3(+) is on the left then the alpha-amino acid is in the L-configuration. Am ...
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Why are excess amino acids toxic?

While learning about deamination, I learnt that excess amino acids must be converted to urea and excreted, since the nitrogenous group can alter the pH and affect proteins. But shouldn't the pH stay ...
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Why don't amino acids get linked in the functional groups of acidic and basic amino acids?

There are 'acidic' and 'basic' amino acids like aspartate and histidine. When protein is synthesized with those amino acids, what ensures that the to-be-assembled amino acids will not bond to the ...
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Effect of mutation on phenotype

Is there a type of mutation that changes the phenotype of an organism, but not the protein sequence?
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List of amino acid frequency of different foods? [duplicate]

I'm trying to write a little application calculating the biological value of protein content of different meals using the amino acid frequency of different foods. The idea is that the user can ...
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Needleman Algorithm for Optimal Alignment of two Amino Acid Sequences

I want to compute the optimal alignment of two amino acid sequences as per the following definition from a patent: "The percentage of identity between two peptidic or nucleotidic sequences is a ...
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What would be the fate of protein made from D-amino acids after ingestion by humans?

There are some natural peptides made of D-amino acids, rather than the L-amino acids normally found in nature. It is now possible to chemically synthesize artificial proteins made of D-amino acids. ...
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Confusion on polarity and hydrophobicity of Proline, Tyrosine and Cysteine?

I will list here several sources that state differently on the polarity and hydrophobicity of Proline and Tyrosine: From the article Amino Acid on Wikipedia, it states that Proline is a special case, ...
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How does beta branching stop alpha helices from forming?

I am told that beta branching interferes with alpha helix formation. Problem is that I don't see how beta branching has anything to do with alpha-helix formation. Beta-branches are on the outside of ...
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Nomenclature of enzymes involved in synthesis of glutamine

I am considering nitrogen fixation and in my lecture notes, there is the statement The glutamine synthetase- glutamate synthase system requires use of an ATP molecule as well as reducing power. ...
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Are there any enzymes without aromatic amino acids?

I'd like to try a new spectroscopic technique to study enzymatic reactions (which reaction doesn't especially matter, something simple and with fast kinetics like catalase would do fine - I'm just ...
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Why does Glutamine have the symbol Q?

Spent a half hour googling this and the best I could find was this: Now for some rhymes: Arginine = R. R we having fun yet? Asparagine = N The kNights of Ne say "Ne". Glutamine is a cute amine ...
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What is the function of cystine, cysteine, and cysteine protease?

I am not a biologist, and I have a probably dumb biological question. For some purpose, I need to understand the function of the CTNS gene, and here is the definition of it: "This gene encodes a ...
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What is the preferred way to abbreviate amino acids?

Amino acids are often denoted using either a 3-letter abbreviation or a 1-letter notation, e.g. Glutamine is denoted via $\mathrm{Gln}$ or $\mathrm{Q}$. When one notation should be preferred over ...
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1answer
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How do aminoacyl-tRNA synthases distinguish between similar amino acids?

How do aminoacyl tRNA synthases recognize the right amino acid for their tRNA? What is the structural reason behind the selective recognition? I have difficulty in seeing how, for example, leucine and ...
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How to interpret this PubChem record of L-Alanine

Using the PUG service from NCBI, I am retrieving 3d structure data for a molecule. Raw data here. I am trying to understand this record, specifically for the purpose of rendering in a 3D coordinate ...
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What signals a ribosome to stop production when the cell is out of available amino acids?

In the production of a protein molecule, there have to be a ready supply of free-floating amino acids. When a given codon for adjoining, say, serine comes up, how are the serine molecules found out of ...
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1answer
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Thermodynamics of Forming Peptide Bonds

Which of the following shows the correct changes in thermodynamic properties for a chemical reaction in which amino acids are linked to form a protein? A) +ΔH, +ΔS, +ΔG B) +ΔH, -ΔS, -ΔG C) +...
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Why do three nucleotides code for one amino acid? Why not 5 nucleotides? [duplicate]

We all know why there are 3-base codons, and why there aren't any 2-base codons. But why is there not a 4-base a 5-base codon?
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How do you calculate or predict the charge of a protein at pH 7?

How do you calculate or predict the charge of a protein at pH 7 given a fasta sequence? Any papers or online servers to do this is well appreciated.