Questions tagged [amino-acids]
This tag is for questions about amino acids, both natural and non-natural ones. It should only be applied to questions about the monomers. For peptides and proteins, use the proteins tag instead.
144 questions
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Does histidine or other amino acids give sodium bicarbonate test?
Histidine, like other amino acids, has a carboxyl group which indicates that it will give sodium bicarbonate test, i.e. involving brisk effervescence of CO2 gas. However, I actually couldn't find much ...
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Is the acetylated form of L-carnitine stable at room temperature?
I just noticed that the Acetyl-Carnitine supplement that I used to ingest, tastes and smells differently.
Based on my research L-Carnitine seems to be stable over long periods of time, but does the ...
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pH in a buffer of Glycin and HCl
I am struggling with a task. I have the amino acid Glycin with pKa1=2,3 and pKa2=9,6.
I have 1.0 liter 0.20 mol/L solution of glycin. I add 0.1 liter 1 mol/L HCl solution. What is the pH in this ...
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Is HCl in salt form reactive with metallized aluminium plastic film? [closed]
I’m in the process of packaging an amino acid that contains HCl in salt form. The mixture is 60% base and 40% HCl salt.
Will this react to metallized aluminium plastic?
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Isoelectric Point
How do we derive the formula of isoelectric point?
pI=(pKa1 + pKa2)/2
I read that isoelectric point is defined as the pH at which degree of protonation in amino group is same as degree of ...
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Why is the lysine side chain more basic?
As per PubChem: $pK_1 = 2.18$; $pK_2 = 8.95$; $pK_3 = 10.53$ at 38 °C, indicating that the side chain amino group is deprotonated at a higher pH, indicating it is more basic. I tried to justify this ...
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Is the amine nitrogen of methylglycinediacetic acid (MGDA) protonated?
MGDA is a tertiary amine with 3 acetic acid groups. I would like to know whether the amine Nitrogen of MGDA is protonated or not for a given pH value. I could not find any literature data which ...
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Esterification of Serine
I came across this question above, and I'm unsure about the reaction with H+(aq). The answer is that the amine group is protonated as usual, but I am not sure why H+(aq) doesn't catalyse ...
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Glycation of peptides (Maillard reaction) by reductive amination
I would like to link glucose to the primary amines in a peptide containing lysine. Can I just mix glucose and the peptide and add some cyanoborohydride to perform a reductive amination? As long as my ...
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Protein/polypeptide nomenclature, residue number superscripted or not?
When referring to a specific residue number of a given amino acid, should the residue number be superscripted or simply affixed?
For example, When referring to a Tryptophan residue at the 147th ...
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Will ethyl 2-amino-1H-imidazole-5-carboxylate undergo ester aminlysos with the primary amines of bPEI efficiently in methanol?
I was about to set up the following reaction, but before I do, I wanted to see if anyone has some suggestions or thinks this will not work:
24mmol Nboc protected ethyl 2-amino-1H-imidazole-5-...
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Why are proteins made up of alpha amino acids and not beta amino acids?
Why are proteins made up of alpha amino acids and not beta amino acids? Or gamma amino acids? My idea on this would be that a world with beta or gamma amino acids would be too complicated? Is that ...
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How to determine the charge of amino acid at certain pH? [duplicate]
Problem
What would charge would you expect on alanine when placed in a solution with a pH of 1.00?
Answer
Question
Let's say I am given a certain pH of 2.00 rather than 1.00 for the "acidic ...
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Experimental evidence for zwitterions
If I have a diprotic acid that is +1 positively charged in its fully protonated state, I can figure out the apparent equilibrium constants by titration with base. The net charge will be neutral after ...
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Why don't serine and threonine have a 3rd pKa
Serine and threonine both have an extra OH functional group and hence they should be able to dissociate when the pH gets high enough. However multiple amino acid pH charts do not show the 3rd pKa of ...
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what is the meaning by 'species' of glycine? [closed]
The question ask for the species of the (i) glycine hydrochloride (ii) glycine titrated with NaOH. When they mentioned 'species', what did they mean by it?
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Functional group for glycine that had being titrated (i) HCl (ii)NaOH
i am kinda confused with this question. They asked for the functional group of (i) glycine hydrochloride (ii) glycine that titrated with NaOH. I did take a look many times especially for glycine ...
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Can amino acids exist in the completely non charged state? [duplicate]
Typically amino acids can exist in three states, as far as I’m aware, which depend on the pH:
However, most of the time I see amino acids in a completely uncharged state when shown in textbooks or on ...
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How to draw L and D configuration for isoleucine and threonine?
I'm finding difficulties in drawing the D and L configurations of these two aminoacids, because, differently from the others, they have two chiral carbons (specifically α and β).
In particoular, in ...
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What are the relevant pK values on HEPES?
HEPES is 2-[4-(2-Hydroxyethyl)piperazin-1-yl]ethane-1-sulfonic acid. I have read (MA Al-Ghobashy, Bull of Faculty of Pharmacy, Cairo University 2014; 52: 71-78) that the sulfonic acid group is ...
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Do disulfide bonds determine the 3-dimensional structure of a protein or do they just stabilise the 3D structure?
I noticed that most disulfide bonds occur when two cysteine side chains exist in close proximity to each other. Do those cysteine side chains "look out" for each other during folding, that ...
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Histidine-Boc deprotectection
A question on Fmoc-solid phase peptide synthesis (SPPS). Is Boc-protected Histidine too labile? Merck's website shows Boc is labile to treatment with Piperidine. Anyone with such experience?
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IUPAC name for dicarboxylic acid with aldehyde and amine groups
The IUPAC name of the structure is:
(A) 3-amino-2-formyl butane-1, 4-dioic. Acid
(B) 3-amino-2, 3-dicarboxy propanal
(C) 2-amino-3-formyl butane-1, 4-dioic acid.
(D) 1-amino-2-formyl succinic acid
...
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Zwitterionic Form in Amino Acid
In my laboratory workbook, it has been mentioned that the zwitterionic form of the amino acid is the dominant form of the amino acid at pI and no movement of the molecules takes place under an ...
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Synthesizing octopine from arginine and 2-bromopropionic acid
I am a biologist, and organic chemistry lessons are a distant memory now. I am interested in synthesizing a small amount of octopine. Octopine is a natural molecule resulting from an enzyme-catalyzed ...
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Amino Acid Derivative Naming Conventions
Is there a trivial name for compounds based on glutamic acid, or other amino acids, where it is not the α-amino acid group that is functionalised? (I.e. that shown on the right)
Glutamylsulfonic acid, ...
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Resonance structure with allylic lone pair
Draw the appropriate resonance structure for 5-aminolevulinic acid:
As there is an allylic lone pair, my first arrow goes from the lone pair to form a π-bond, and the second goes from the π-bond to ...
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Definition of amino acid side chain
Is the α-carbon considered a part of amino acid side chain?
Is the nitrogen atom on the backbone is considered a part of the side chain of the proline?
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What will be the structure of cysteine at pH=4? [closed]
As per my understanding since pKa of RSH and the amino group is >4 hence they would be in cationic form while the acid should be in anionic form. So charge on cysteine would be +1. But while ...
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At physiological pH, why isn't the amide of glutamine protonated? [closed]
If the amide in the R group of glutamine has a pKa of 15, then pKa is certainly greater than physiological pH. We'd expect it to be pronated, then, but basically all diagrams of glutamine at ...
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Why do two programs assign different SMILES to one amino acid sequence?
I have an amino acids string "MKGK" and I would like to convert it into SMILES format.
I tried two approaches.
First with PepSMI which gives me:
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Hypothetical Alternative for Nitrogen [closed]
Recently I was surfing the internet and I found thisWikipedia article.
It states that
The element silicon has been much discussed as a hypothetical alternative to carbon. Silicon is in the same group ...
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pKa of the alpha proton of an alpha amino ester [closed]
Is there a theoretical pKa value for the proton on the alpha carbon of a methylated amino acid, or just a general alpha amino methyl ester?
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How can all amino acids point outwards from an alpha helix, if peptides are mostly trans?
My textbook in biochemistry ("Biochemistry" - Berg,Tymoczom Gatto, Stryer) tells me that:
"Almost all peptide bonds in proteins are trans" (p. 40)
At the same time, it states the ...
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What does the following diagram represent?
Suppose, the following is a diagram of a protein's polypeptide chain:
What does this diagram represent?
What are the letters A, E, M, W, L, N, S, etc. represent? (I suppose these are amino acid ...
user93950
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Decarboxylation of primary amino acids
Since primary amino acids like glycine, alanine can't be decarboxylated under oxidative conditions, what would be the best catalyst for this reaction?
I was thinking about copying decarboxylases with $...
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What is the pI of lysine tripeptide?
What the the $\mathrm{pI}$ of a tripeptide of lysine?
$$
\begin{array}{l|ccc}
\hline
\text{Group} & \ce{Lys{-}α{-}NH3+} & \ce{Lys{-}ε{-}NH3+} & \ce{Lys{-}α{-}COOH} \\
\hline
\mathrm{p}K_\...
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Nitrogen with shortest bond length in histidine?
The question asks what nitrogen in the ring of histidine has the shortest bond length.
I was thinking that since it has resonance, the initial thought of the nitrogen with the $\pi$ bond is incorrect. ...
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Reason for protonation of amino group in amino acids at near neutral pH
What happens to the amino group when amino acid is added to a near neutral solution? How does it come about gaining an extra proton?
I understand what happen to the carboxyl group, since it is a ...
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Does spoiled milk have something else in it besides lactic acid that gives its characteristic taste and odor?
Even slightly spoiled milk has a taste that I don't like, while plain yogurt tastes either great, or at least nowhere near as bad. A dozen sources (all of them) say that the spoiled odor and taste of ...
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Carbon atoms types in amino-acids [closed]
I'm looking for a table or another kind of schema where I can find which type of carbon atoms (sp3, sp2 etc.) are present in each amino-acid.
In my biochemistry books these informations are not ...
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Is glycinate ligand a monoanion or a zwitterion?
Glycinate as far as I can guess from the structure is a monoanion with negative charge on oxygen atom (though that negative charge is resonating). But when I used this logic in my exam it costed me 4 ...
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Possible mechanism by which a methyl glycinate hydrochloride salt in toluene (insoluble) reacts with an acid chloride through the nitrogen atom?
I'm trying to work out a possible mechanism for the reaction of a methyl glycinate hydrochloride salt in toluene (it is insoluble) with an acid chloride, reacting through the N-terminus. As the amine ...
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How do point mutations affect complementary base-pairing and widths of the nucleotide pairs?
Point mutations are divided into two categories: transitions and transversions. Since point mutations only occur during DNA replication (an integral process of both mitosis and meiosis), the mutated ...
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Depicting a mechanism of peptide bond formation with protonated and deprotonated amino group
I've noticed that some textbooks and video lectures use an amino acid wherein the amino group has two hydrogens, and others use an amino acid with three hydrogens in the amino group (in the formation ...
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Do side chain carboxylic acids need to be protected in peptide synthesis?
Consider the synthesis of the dipeptide Glu–Ala (image). The amino acid Glu (glutamic acid) has two carboxyl groups, where one of them should reacts with the amine group from the other amino acid. ...
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Why is the side chain of lysine more basic?
According to the images below, the NH3+ on the side chain of lysine is less acidic than the NH3+ closer to the COO-. Why is this? Wouldn't the NH3+ have an intramolecular H-bond with a negatively ...
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Red Compound from Glycine and Glycerol?
I got an unexpected reaction which I'm trying to explain to myself:
I mixed 10 parts glycerol with 1 part glycine at ~90C and to my great surprise the mixture turned from transparent to a tint of red. ...
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how is the esterification of amino acid carried on in this reaction
i was asked to synthesis this compound from this amino acid, i first alkylated the alpha carbon using enolate alkylating method then i esterficated the amino acid but i'm doubtful that my steps are ...
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Which amino acids can be totally synthesized? [closed]
I can't find information regarding which amino acids (say the proteinogenic ones or in general) can be totally synthesized. Is there a reference?
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