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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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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51 views

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: ...
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105 views

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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26 views

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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2answers
77 views

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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91 views

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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66 views

Why do ADULTS need protein in their diet, if they are not growing? [duplicate]

Why do ADULTS need protein in their diet, assuming they are not growing? What happens to the amino acids already present in the body? Why don't our bodies conserve them?
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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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75 views

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 ...
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114 views

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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64 views

Can two proteins have equal primary structure but different secondary structure?

I've been reading lately about primary (which I understand completely) and secondary (which I do not understand that well since I'm not very good at chemistry) structure of proteins. My question is: ...
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67 views

Is protein folding symmetric with respect to reversing the sequence order?

Suppose that I have two proteins, protein A and protein B, and suppose that the sequence of amino acids of protein B is exactly the reverse of the sequence of protein A. For example (these are made-...
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983 views

ATP Hydrolysis to AMP in the Urea Cycle. What is the Free Energy Change?

How is the hydrolysis of ATP into AMP and PPi in making arginosuccinate equivalent to the hydrolysis of 2 ATP?
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290 views

Reading an amino acid physicochemical properties diagram

I want to know if I am reading the venn diagram correctly and why there are discrepancies in the diagrams. I'm trying to determine which amino acids are considered hydrophobic and I am using this ...
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Microbiome Context for Amino Acid Essentials and Non-Essentials

Given what we are now learning about the diverse mix and variance of microbiomes (aka bacterias via human gut project), is it possible that synthesis of aminos can be done by specific bacteria and ...
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What is the active site (not metal binding site) of tyrosinase and other monooxygenase/oxidoreductases?

On https://www.uniprot.org/uniprot/P07524, tyrosinase is shown as a monophenol monooxygenase. However, the UniProt database only shows a metal (copper) binding site, when there is presumed to be an ...
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318 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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117 views

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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90 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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514 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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Where on an amino acid does it attach to the protein backbone? [closed]

I've been trying to find conclusive information regarding where within an amino acid (AA) it attaches to the protein backbone (PBB). I know that, coming off of the PBB, the AA side chain is connected ...
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1answer
36 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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746 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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634 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
136 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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2k views

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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93 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
2k views

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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400 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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217 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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205 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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5k 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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551 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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2answers
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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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2answers
324 views

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
215 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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1k views

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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8k views

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 ...