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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49 views

Where did the first proteins, without the aid of ribosomes, came from?

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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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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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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effect of amino acid limitation in CHO cells

I would like to know the effect of individual amino acid and their role in CHO cell growth and their effects on their metabolic pathway if any. And also if there is an amino acid which has an effect ...
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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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132 views

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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21 views

Is there exist a table to describe the probability of pairs of AA appeared in different protein secondary structures?

Is there a table or matrix to show the statistic probability of 2 or 3 AAs existed in different protein secondary structure? For example the number of abc( a/b/c are all AA ) in alpha-helix is 100 and ...
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2answers
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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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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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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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1answer
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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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92 views

Tryptophan structure

Currently trying to memorize the different amino acid structures for my own learning purposes. I think I am confusing myself, and would like clarification to see if it matters where the NH and double ...
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1answer
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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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is consuming collagen actually good for skin/joint health? [duplicate]

A coworker of mine insists on drinking a very expensive collagen supplement for their skin health. It seems like a gimmick- Doesn't the digestive process breakdown proteins to their constituent amino ...
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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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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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4answers
118 views

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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1answer
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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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2answers
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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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2answers
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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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1answer
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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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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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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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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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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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1answer
213 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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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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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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1answer
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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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0answers
2k views

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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2answers
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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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0answers
106 views

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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1answer
3k views

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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1answer
98 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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2answers
2k 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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1answer
132 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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2answers
429 views

Understanding the Amino Acids

I'm having little trouble studying general relativity or quantum field theory, but remembering all the amino acids and being able to think about them is something that's completely, utterly and ...
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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 ...
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1answer
152 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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1answer
160 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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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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2answers
15k views

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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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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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 ...