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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Consequence of Plants as Incomplete Protein Source

Some years ago, in a 1000~ level biology course we learned that the DNA essentially encodes formulas for creating proteins from amino acids. While the human body can synthesize many many amino acids, ...
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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. ...
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Is cysteine deficiency possible?

Is there such a thing as cysteine deficiency in humans or other mammals? What effects would such a deficiency have? As I understand it, most cysteine for humans comes from dietary sources, though it ...
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Is there a cellular mechanism that detects Ribosomal damage?

What kinds of options, if any, do cells (Eukary and Prokary) have for detecting, and repairing damage in Ribosomes (of all types)? I am curious as to what happens when a cell sustains damage of some ...
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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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Edman method to identify peptides with Phenylisothiocyanate (PTH)

We all know that in this method the PTH reacts with the first amino acid (aa) from the N-terminal to the peptide and separates from it giving PTH-aa so that we can know the amino acids sequence in the ...
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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 ...
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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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Protein Design - Target Structure Specification

I'm curious about how protein structures are defined in general, but in particular, I'm wondering how a target structure can be specified without knowing the amino acid sequence. For example, in ...
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Is there a biological environment that we can we assume glutamate exists as glutamic acid?

In the body we almost always assume that glutamate exists as glutamate rather than glutamic acid. It is so commonly glutamate yet glutamic acid and glutamate share the abbreviations of Glu and E. From ...
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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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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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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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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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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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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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Which three functional groups are found in the general structure of amino acids? [closed]

Yes, I know, not two, but THREE. EDIT: Yes, sorry but I did quite a bit of research, searching my notes and textbook for the answer, but all I could find was TWO functional groups as a opposed to the ...
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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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Hormones and body mass

I was wondering how some animals (bulls, elephants etc.) become so large by only eating grass or plant based material and why some humans can build large amounts of muscle and mass without a proper ...
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bacterial cell wall degradation in humans

can human degrade the D-amino acid present in bacterial cell wall, I'm confused about it i have read somewhere that human can do so.If yes than why we need antibiotic to kill bacteria???If it is not ...
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What does the term 'modified residue position' in phosphorylation mean?

Does it mean the position of the amino acid in the protein sequence, or something else? For example, I came across the phrase "S 368 phosphoryation" where S is the modified residue and 368 is the ...
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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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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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Converting Ensembl Compara gene tree DNA alignment to corresponding amino acid alignment

I have Ensembl compara gene tree alignments (Compara.gene_trees.57.fasta.gz downloaded from ftp://ftp.ensembl.org/pub/release-57/emf/ensembl-compara/homologies/) in nucleotide format. According to ...
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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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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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Histidine - why essential for children?

Why is histidine an essential amino acid for children but not for adults ? What changes in the body occur which lead to the formation of histidine in adults but not in children ? What causes these ...
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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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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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Which is the correct statement on proteins?

I need help with one of the questions on my biochemistry assignment Choose the correct statement on proteins: a) proteins are folded by alpha-helix b) proteins can preserve their function even if ...
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What is the recommended PPM when foliar feeding L-amino acids

It is said that L-amino acids such as histidine, methionine, aspartic acid, glutamic acid, asparagine and glutamine can revert plant stomata closure, increase quality of fruits and assist maturity. It ...
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Why are Taurine and Arginine essential components of the feline diet?

Taurine and arginine play a key role in the feline diet but I am unaware as to where exactly they fit in.
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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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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 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 ...
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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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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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Why aren't D-amino acids used in proteins? [duplicate]

Possible Duplicate: Why are amino acids in biology homochiral? Why are only L-amino acids used in protein construction, and not D-amino acids?
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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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What is the role of Homocysteine in cognitive function?

I'm looking at this link : Homocysteine and cognitive impairments and am looking for more information on specific cognitive impairments associated with elevated levels Homocysteine. That article is ...
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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 ...
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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.
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How are proteins formed?

Somewhere, I have read that we need to consume proteins to make amino acids to make new proteins. What does it suggest? How do we make proteins from proteins?
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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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Are there examples of PTMs that add different chemical groups (and mass) to different amino acids?

I'm talking about this type of post-translational modifications. What I'm interested in is not whether some modifications can only occur on specific amino acids (that's clear), but if the nomenclature ...
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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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Why 22 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 22 ...
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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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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?