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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What keeps pyridoxamine phosphate inside the aminotransferase enzyme active site?

In the function of an aminotransferase enzyme after the first substrate (amino acid) has been deaminated there seem to be nothing binding the resulting pyridoxamine phosfate to the rest of the enzyme (...
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How does labelled N from tyrosine appear in phenylalanine if the latter is an essential amino acid?

A certain question (not my course or instructor or even university) goes: Exposed to regular metabolic activity in a rat liver, a 13C label in tyrosine will not appear as a 13C label in phenylalanine....
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Koshi and Goldstein substitution matrix

In their article (Context-dependent optimal substitution matrices for exposed residues (Koshi-Goldstein, 1995)), more precisely in the substitution matrix displayed in Figure 2, one one hand, the ...
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What nutrients are necessary for Bacillus subtilis germination?

What are the necessary conditions to germinate Bacillus subtilis spores? Under laboratory conditions, spores of B. subtilis are often heat-activated for 30 min at 70°C to increase their germination ...
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Amino Acid mutation profile for human coronavirus: Why is the mutation from T to I so frequent?

Still watching the emerging lineages of SARS-CoV2 I noticed that the amino acid mutation from threonine to isoleucine seems to be particularly frequent. Counting mutations in a lineage with a lot of ...
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is pepsin able to break down proteins into amino acids in human stomach? [closed]

I'm trying to find out if pepsin can break down proteins into amino acids after they are converted to peptides. Is pepsin able to separate amino acid monomers from the peptides? can you please show me ...
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What do the colors mean in representations of amino acids?

I've seen sequences of amino acids depicted using colors, which I imagine correspond to whether the side chain is charged, etc. I can't figure this out, though, and I'm not a biologist or biochemist. ...
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Arrangement of Amino Acids in the Protein alphabet

I am a software engineer with little knowledge of molecular biology. However I am trying to understand some bioinformatics computer code where the protein alphabet appears to be represented as the ...
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What is the point of calculating extinction coefficients of a protein without Cys residues?

ProtParam computes various physico-chemical properties that can be deduced from a protein sequence. One of these parameters are "Extinction coefficients". They provide two values. One value ...
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The effect of low pH on HIV virus

I've read a couple of articles that state that HIV is an enveloped Retrovirus that is so sensitive to the acidity of the environment and it cannot survive or will be inactivated at pH below 7. What ...
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Would the amino acid profile of lab-grown human meat perfectly match the dietary nutritional amino acid requirements for humans?

Whey protein is the food which has the most ideal (yet not perfect) amino acid profile for humans, whereas gelatin for example has a very poor and incomplete amino acid profile for humans. Would human ...
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Do we find protein not of cellular origin in nature?

I read once that we have two sources for proteins: Protein that is made in cells Protein that is made in labs However, based on Miller–Urey experiment, it's argued that amino acids can be made from ...
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How does the order of the pairs of cross-links in DNA determine the arrangement of the amino acids?

Quoting Richard Feynman from Chapter 3 of his book Six Easy Pieces, when he talks about DNA: Attached to each sugar along the line, and linking the two chains together, are certain parts of cross-...
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Average masses of atoms / amino acids

I recognized that there is some controversy about the average mass of amino acid masses in different online sources. Expasy and Wikipedia report the same masses, but UWPR and Mascot report different ...
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What are the stretch of amino acids?

I found the words "stretch of amino acids" in a newspaper article. "This lipopeptide matches the stretch of amino acids in the spike protein of SARS-CoV-2 exactly." What is the &...
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Ion Chromatography System For Extracting Aminoacids from Microalgae

I am interested in extracting aminoacids from microalgae after having ruptured its membrane and carried out proteolysis. After some research, I came to the conclusion that ion exchange chromatography ...
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Proinsulin is an 84 residue polypeptide with six cysteines. How many different disulfide combinations are possible?

Generally cysteine residues form disulfide linkages - so how many combinations are possible out of (say) six residues. Also can cysteine form bonds with all the residues?
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Why are some protein sequences known but their 3D structure isn't?

Why are there some proteins that have a known amino acid sequence, but their 3D structure is not known? Wouldn't finding the former in a lab lead to the discovery of the latter? Please correct me if I ...
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Does my reasoning about the first emergence of proteins make any sense?

In order to make proteins, a cell uses ribosomes, which itself is a structure made out of proteins. The first ribosome couldn't have been created with the help of ribosomes though, as the ribosomes ...
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Which amino acids can be phosphorylated?

Definitely serine, tyrosine, and threonine. What about aspartate and glutamate? I thought the O- on the carboxylic acid side group could be phosphorylated but am getting mixed responses to this. Any ...
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how can we identify the novel protein amino acid sequence and function? [closed]

if there is a novel protein, how would you know the amino acid sequence and how would you determine the number of subunits and the function of that protein? Specifically what molecular techniques we ...
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What is the definition of a polybasic cleavage site?

I keep coming across the term "polybasic cleavage site" which is implicated in increasing the virulence of many viruses, but I'm struggling to find a definition. Is it just a sequence of amino acids ...
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Genes and proteins with a significantly inbalanced composition

According to Wikipedia, the median size of a protein-coding gene is 26,288 bp which makes it possible (from statistical considerations) that the nucleotides C, G, A, T appear in roughly equal amounts ...
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Can the human body store protein?

I am interested to know if a human body can store protein. Absolutely for the bodybuilders, does it really matter if they divide their protein consumption during the day or eat all of it in one meal ...
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Peptides neither produced by the ribosome or the non-ribosomal peptide synthase complexes

I read in Wikipedia: While there exist a wide range of peptides that are not synthesized by ribosomes, the term nonribosomal peptide typically refers to a very specific set of these as ...
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Tryptophan side-chain structure, how should it be orientated?

I would like some clarification on whether it matters where the NH and double bond are placed in these two structures of tryptophan (W) that I drew. I marked the right side as correct and the left ...
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How are proteins reused in the body? [duplicate]

Part of what we eat are proteins, and our body is in part build of proteins. Are the proteins of the body build based on proteins in food at all? Are proteins in food directly reused in the body, or ...
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A question about L-Citrulline

I know that L-Citrulline enters in the second step of urea cycle in the liver mitochondria and I wonder if a person takes an overdose of L-Citrulline wouldn't that cause mild hyperammonemia or at ...
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It there any experimental approach to determine the electronic structure of a given aminoacid inside a protein?

It there any experimental method to determine the electronic structure of a given amino acid inside a protein?
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Why does protein folding not depend on the order in which it is synthesized?

I read an article recently, written by researcher from Department of Biochemistry, University of Washington, which stated that: Similarly, success in de novo protein design bears on the question I ...
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How do mutations and protein synthesis link to cancer?

How do mutations and protein synthesis link to cancer? I know that a mutation in DNA can cause the triplet code on the mRNA to change so different amini acids are made and a different order means a ...
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Protein function and how it does not get affected with amino acid [closed]

How is it possible that a protein's function is not changed when an amino acid within it is replaced?
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Estimating diffusion constant of a protein based on number of amino acids

Is there a way to estimate the diffusion constant of a protein based on the number of amino acids it is comprised of. I know that the shape of the protein has an influence on the diffusion constant, ...
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The Collagen Triple Helix

In the amino acid sequence X-Hyp-Gly (where X can be any amino acid) of the triple helix can the Hyp residue be both hydroxyproline and hydroxylysine? In our textbook it says that the Hyp residue is ...
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Can 1.5 gigabytes encoded in the human genome really account for the complexity of a human being?

I read the human genome is 1.5 gigabytes in size. Thats actually not a lot; Photoshop probably takes more space. Mac OS takes 10+ gigabytes of space. Also, the genome is 1.5 gigabytes when counting ...
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Which are more beneficial: lyophilized or hydrolized collagen peptides?

Looking at two different manufacturing methods for collagen peptides: hydrolyzed vs lyophilized (freeze dried), I read that hydrolyzed results in a hydrophobic biolayer molecule collagen peptide. Re:...
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About the definition of ketogenic amino acid

I am studying biochemistry and have been looking at metabolic network diagrams showing the different intermediates of glycolysis and the citric acid cycle that amino acids can be converted to. I have ...
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How to do a nucleic acid or genome and amino acid search [closed]

I have been looking to find a database where i can search for genome and amino acid search. Are there any open source databases available for the same.
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Does every protein starts with Methionine amino acid [duplicate]

During process of protein synthesis we need AUG Codon to start translation .As we know this codon codes for Methionine amino acid so can we say that every protein starts with Methionine amino acid ?
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Why are dietary recommendations for methionine consumption combined with cysteine?

I want to understand the amino acids missing in certain vegetables. I looked up the US recommendations for amino acids (source: wikipedia). I don’t understand why they pair Methionine + Cysteine: 25 ...
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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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Amino acid substitutions near the receptor binding site HA protein in type A H3N2 influenza strains?

I have read the scientific paper, "Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution" by Björn F. Koel et al (http://science.sciencemag.org/...
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How does one predict how large of an effect on antigenic drift a substitution in the amino acid sequence of a surface protein of influenza has?

I know that some amino acid substitutions are more effective in causing antigenic drift than other substitutions based on their location in the 3d structure of the HA protein (proximity to the ...
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Organisms that use more than the 20+2 commonly occurring amino acids?

I know scientists have created synthetic bacteria, with a genetic code containing 6 letters instead of 4, with the aim of creating more complex proteins (using amino acids outside of the standard 20+2,...
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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 is gel used in electrophoresis?

In analysing amino acids content in a protein through gel electrophoresis, What's the purpose of the gel? Wouldn't putting the amino acid in the gel prohibit the amino acid from dissolving into the ...
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Net electrical load of a peptide

I have to determine the electrical charge of the next peptide chain: C - E - H - P I know that this page is not there to raise doubts about this style, but I have looked for resources on the ...
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What is the equation and mechanism of Hopkins-Cole Test reaction?

The Hopkins-Cole reaction or glyoxylic acid reaction, is a chemical test used for qualitative detecting of tryptophan in protein solutions. tryptophan + glyoxylic acid + sulfuric acid > violet ...
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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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mRNA and Protein relation [closed]

A and B are two different proteins: 1- can they have same mrna 2- is it possible that the gene types which encoding the synthase are same ? my answer is yes to both . because after protein synthased ...