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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2k views

Are peanut proteins similar to chicken meat proteins?

I'm studying amino acids content in vegetable food. I was looking at peanut protein and noticed its similarity with chicken meat, as you can see in the table below (quantities are measured in grams). ...
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Plant vs animal protein digestibility?

The protein scoring methodologies ( https://en.wikipedia.org/wiki/Protein_Digestibility_Corrected_Amino_Acid_Score) rate plant proteins of a lower quality than animal proteins. Now I can understand ...
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Are amino acids of viruses L or D enantiomers?

I read a note saying that the amino acids of viruses are D enantiomers but I can't understand how that's possible since their human host can't even recognize that type.
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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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108 views

The insulin protein of apes & chimpanzees [closed]

How many amino acids do the insulin protein of apes and chimanpzees compose of?!
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601 views

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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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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1answer
41 views

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
923 views

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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855 views

Pros and cons of amino acid structure vs DNA sequences for evolutionary comparison [closed]

This is an analysis question for a lab on the amino acid differences in beta globin amongst different primates, and using such differences to construct a cladogram and infer evolutionary relationships ...
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3answers
152 views

Do different chiral centers on ligands cause different confirmational changes and effects in their target proteins?

Say pathogenic bacteriaA makes toxinA, which had D-amino acids instead of L-amino aids, does this difference in chirality cause a different conformational change in the receptor or enzyme, thus ...
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How do I know which molecular structure is glycine's “base state”?

I was looking up the chemical structure of glycine, and I found the following two images: and . My question is, what is the "base state", or the "natural state" of glycine? Under what scenarios ...
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Given an amino acid sequence, how to determine the structure (helix, beta sheet etc)? [duplicate]

Assume there's a short sequence of an amino acids. MAKMGSKKKAGHGGKEKLENMGE I am using molecular structuring softwares to look at secondary structure. But it's ...
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121 views

Isoelectric point of aspartate [closed]

On the 3rd diagram (from left), the one with net charge = -1 , Why did it lose the H to OH- from the CH2CO2H from the neutral form ? I was told that while moving to the right , the OH- will take H+...
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1answer
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How does aminoacyl-tRNA synthetase recognize different tRNAs?

There are about 20 aminoacyl-tRNA synthetases, one for each amino acid. Each aminoacyl-tRNA synthetase has a binding site that recognizes a specific amino acid, and other binding areas that recognize ...
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How many genes are needed for a living organism? [duplicate]

I am interested in this question as I'm doing research into early life on earth which is believed to have been single-celled. Therefore, by extension, it seems only logical that the first life would ...
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1answer
457 views

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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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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1answer
273 views

What difference do trans and cis configurations of amide groups bring to the polypeptide chain?

Hi I was just wondering whether there would be any difference to the structure of the polypeptide chain, or any changes to a proteins characteristics, if it has more amide groups with a cis or trans ...
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226 views

Molecules responsible for reading amino acid language

The molecules responsible for reading the language of amino acids and nucleotides is: RNA polymerase enzyme mRNA tRNA DNA I don't actually understand what "reading amino acid ...
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1answer
8k views

What is difference between High quality and low quality proteins [closed]

I have seen in news that some bodybuilder died of taking steroids; when I went through details I learned that "low quality proteins" contributed to their death. I have studied about linkages in ...
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1answer
591 views

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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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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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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The difference between the two ways of glycine represntation [closed]

I'm confused because I see now two different way to represent the glycine amino acid. while I understand the first way of the representation the second one I don't understand at all. I believe that ...
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2answers
245 views

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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What is the significance of cysteine in a protein sequence?

What is the importance of cysteine-cysteine in amino acid sequence? What can I infer if I get a high percentage of C from a protein sequence?
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1answer
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Identifying whether amino acids are hydrophobic or hydrophillic [closed]

How do you figure out whether an amino acid is hydrophobic or hydrophilic? (other than memorization) I know that it has something to do with the R groups of the amino acids, and that polar molecules ...
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101 views

How to convert PDB file of Amino Acids to rotamer tuples list of all AAs instances

Either by Python command, or via specific application (like Chimera) publicly available. Please provide example or link to one of. I have to detect AA location within MAP (density) 3D matrix. And to ...
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1answer
47 views

Difference in variance of Cys in protein sequences [closed]

Suppose I have got two sets of proteins (amino acid sequences). In one set, I find that the variance in the percentage concentration of the Cys is way more (65.34) than the variance of Cys in the ...
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235 views

Essential amino acids

Humans and the majority of animal species cannot synthesize essential amino acids (Info: Campbell biology 9th edition). However, meat, eggs, et cetera provide all required essential amino acids. And ...
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What are “+” and “Ar” in consensus binding sequence of amino acids?

So I was reading this paper and found a figure as below: I understand that [LEAM] means any of LEAM residues, pS is phosphoserine and X means any amino acid residue. What is [+] here ? Is both R and ...
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1answer
74 views

Catalytic Triad of Serine Proteases

Is serine considered an acid in the catalytic triad involved in the mechanism of action of serine proteases? It is donating a proton to His but I am not sure if this really qualifies as an acid?
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Amino Acid requirement + intake in relation to diet + meat type [closed]

I was arguing with a friend: I said: The Yulin festivals cannot be condemned by western culture, as we also kill animals in equally cruel ways. She said: It isn't just that the killing is cruel, ...
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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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1answer
39 views

Using exogenous genes to reduce the set of essential amino acids?

Various organisms have sets of essential amino acids that they cannot synthesize themselves, but rather that they must obtain from food. Humans have 9 of these amino acids. However, obviously certain ...
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1answer
126 views

Amino acids in human cancer cells expose dextrorotation?

I would like to know if the amino acids in the human cancer cells are dextrorotatory or levorotatory. I mean the majority of them. They expose levorotation just like the amino acids in the normal ...
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1answer
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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?

I know that human proteins are synthesized using only 20 different amino acids. However, how can there be thousands of different proteins in human cells, if we only use 20 amino acids to make them?
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1answer
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Are alpha-ketoglutarate and glutamate involved in all transamination reactions?

Is it true that for all biochemical transamination reactions, that alpha-ketoglutarate and glutamate serve as the amino group acceptor and donor, respectively? If this is true, then is it safe to ...
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Question about DNP derivatives of amino acids (specifically epsilon-DNP-lysine)

I have a pretty basic biochemistry question but am having trouble finding the answer to it: Normally, 1-Fluoro-2,4-dinitrobenzene (DNFB) reacts with just the amino terminus of amino acids. However, ...
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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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4answers
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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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1answer
948 views

Why would the citrulline content of the watermelon be so high?

Citrulline is a non-proteinogenic amino acid (that is, citrulline is an amino acid that is not coded for in mRNA), and it is an important metabolic intermediate in the Urea Cycle. The Urea Cycle is ...
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1answer
77 views

Is it possible to grow E. coli K12 with algal amino acids as the sole carbon source?

Instead of glucose or glycerol, is it possible for E coli to grow on an amino acid mixture as the sole carbon source and, if so, what should the concentration be?
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On which amino-acids residue is the SDS acting on?

I would like to know exactly what is the mechanisme of the SDS, and I would like to know on which amino-acids residue the SDS is acting on. Can you help me please ? Thank you in advance !
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Is Roundup toxic?

Roundup, as we all know, is a herbicide that kills weeds. It does this by preventing the production of amino acids in plants. One of these amino acids is tyrosine. Tyrosine is a nonessential amino ...
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1answer
2k views

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 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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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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Properties that can be derived from amino acid sequences [closed]

What are the properties that can be derived from an amino acid sequence apart from those mentioned in the website? In the mentioned website, the properties that can be calculated from amino acid ...