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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.

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22 views

Polymorphism in Alanine Amino-acid [on hold]

I want to know what is meant by polymorphism of alanine amino-acid ?. Are alpha-alanine and beta-alanine considered as polymorphs...? Any suggestions are highly appreciated. Thank you.
2
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0answers
26 views

How to determine charge of compounds in solution with many amphoteric functional groups?

I am curating a metabolic model that has compounds such as NADH/NADPH/Etc. that have multiple ionize-able hydrogens. Normally with amino acids there are only a few hydrogen with varying pKas that ...
3
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0answers
37 views

Calculating amino acid mol/mol ratios

I am trying to understand how the authors calculated the TRP/LNAA (mol/mol) ratios in Table 1 in this paper. For example, when I calculate the TRP/LNAA (mol/mol) ratio for HPROT, I get 0.14 instead ...
3
votes
1answer
427 views

What's the difference between isoionic point and isoelectric point?

What's the difference between isoionic point and isoelectric point? My teacher uses them interchangeably, but Wikipedia states that isoionic point is when charges are balanced, while isoelectric point ...
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1answer
771 views

Difference between L&D and S&R in naming [duplicate]

What is the difference between L&D and S&R? Can we say S-alanine instead of L-alanine?
3
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2answers
31 views

Why does the isoelectric range decrease as an Alanine chain grows longer?

The pK1 and 2 values for alanine are 2.3 and 9.7. In the dipeptide Ala-Ala, they are 3.1 and 8.3 and in tri-peptide Ala-Ala-Ala, they are 3.3 and 8.0. Why does this trend in pKa values exist? Why does ...
7
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1answer
188 views

What does “sine” mean?

I see the suffix "sine" (seen/sin) a lot, adenosine, cytosine, lysine, tyrosine, etc. Most of where I hear it is in amino acid R groups, but it's usually only the prefix that is recognized as ...
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1answer
361 views

glycine hydrochloride salt how I can get it

I do not understand what Glycine•HCl salt is (concretely). Is it a mix between glycine and HCl salt (I don't know if HCl salt is existing...) or something else ? I understand that glycine is an ...
3
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1answer
52 views

Dissociation constants of leucine

Leucine is a type of amino acid. Let me write its chemical formula as $\ce{NH2-C5H10-COOH}$. On the wikipedia page, https://en.wikipedia.org/wiki/Leucine, there are two dissociation constants, one for ...
4
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2answers
508 views

Why is cysteine more acidic than serine?

How is that possible that the -I effect of $\ce{-SH}$ is greater than $\ce{-OH}$ group? In case of cysteine $\mathrm{p}K_\mathrm{a}$ value of $\ce{-COOH}$ is $1.96$, whereas in case of serine it is $...
0
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0answers
42 views

How do hydrolysis of proteins in acid and bases differ?

The question of how alkaline hydrolysis of proteins has been asked and answered. It's also known that both acids and bases can hydrolyze proteins study 1, study 2. But is there a difference? Isn't ...
6
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1answer
163 views

Is selenocysteine C3H6NO2Se or C3H7NO2Se?

I'm a beginner in chemistry, and recently I am interested in selenocysteine. While most websites (Wikipedia, ChemSpider) say it is $\ce{C3H7NO2Se}$, PubChem says it is $\ce{C3H6NO2Se}$. Which one is ...
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1answer
137 views

Basic amino acids

Amino acids having more number of amino groups than carboxyl groups are basic amino acids. Histidine has a 'NH' attached to 2 carbons and it is called basic amino acid. However, tryptophan (having >NH)...
0
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0answers
34 views

Formulation solubility?

Creatine is a popular sports/fitness supplement, generally sold as a powder to be mixed with water (usually like 5-10g creatine per serving). However, it is not very "soluble" in water -- barely 13.3g/...
0
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1answer
214 views

Zwitterion form of aminoacids

What I am wondering, are aspartic acid and glutamic acid at physiological pH present in zwitterion form. In my textbook it says that all aminoacids are at pH 7,4 or 7 in zwitterion form. I wonder how ...
4
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1answer
164 views

Why do α-amino acids have a C-H bond at the α-carbon?

I've just started studying biochemistry and I read that a general $\alpha$-amino acid looks like (ignore the ionisation for now): My question is: why isn't the general $\alpha$-amino acid formula ...
0
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1answer
1k views

pH of an amino acid solution

I'm trying to help a friend of mine with this chemistry question: What is the pH of a $1.0M$ solution of glycine? They're given that the pKa of COOH is $2.4$ and the pKa of the amine group is 9.6. ...
14
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2answers
515 views

Etymology of alanine

Oxford dictionary online gives etymology of alanine as: Coined in German as Alanin, from aldehyde + -an (for ease of pronunciation) + -ine. But I see no resemblance to the aldehyde structure in ...
3
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0answers
480 views

Xanthoproteic test for phenylalanine

I read on the net that phenylalanine gives a negative result with xanthoproteic test and the reason that was given was that the benzene ring is deactivated and hence the extent of nitration is very ...
2
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0answers
273 views

Titration homework question

My friend sent me this for his homework, and I haven't done a titration calculation in years. A student titrated $\pu{10.00 mL}$ aliquots of her unknown amino acid solution with standard $\pu{0....
2
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2answers
2k views

Why does tryptophan absorb UV light?

Why is that tyrosine, phenyalanine, and tryptophan absorb UV light while other amino acids don't even absorb visible light? Does it have something to do with aromatocity?
4
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2answers
2k views

Formation of zwitterion from amino acids

Why it is easier for the carbonyl group to lose a proton to become negatively charged and the amino group to accept a proton to become positively charged ? I know it has to do with the very polar ...
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2answers
60 views

Is the molecule in the attached image technically an amino acid?

Is the molecule pictured below an amino acid? Not necessarily one of the common (natural) amino acids.
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1answer
599 views

Oxidation State of Amino Group

What is the oxidation state of nitrogen the following amino acid: I figured it must be -III: Hydrogen is always +I Both electrons of the N-C bond are near the nitrogen (higher electronegativity). ...
0
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0answers
105 views

Hydrolysis of silk protein

I want to know how you would break down silk proteins into amino acids/peptides, and the end product be almost purely the silk or at least nontoxic for consumption/topical use (dehydrated into a ...
0
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1answer
210 views

(Single) Amino acid rotational degrees of freedom [closed]

When defining the rotational degrees of freedom for a single molecule, should we just include the psi and phi angles (red lines in the picture) or the rotation around every single bond (yellow lines ...
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2answers
404 views

Acid/Base behaviour of Amino Acids

My book states that nitrogen-containing rings are generally referred to as bases, and that under acidic conditions they can each bind an $\ce{H+}$. However, does this increase or decrease the ...
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1answer
224 views

How Can an Amino Acid Be Non-Polar?

Looking at the structure of an amino acid (as a zwitterion), it seems that the part of the molecule with the amino group and the carboxylic acid group are quite polar (the amino group has a positive ...
1
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1answer
226 views

How to change the chirality of amino acids?

Is it possible to change the chirality of the amino acids? I understand such a process is called "stereoinversion". Take a levorotatory amino acid and turn it into it's dextrorotatory counterpart (...
3
votes
1answer
102 views

Why aren't the R-side-chains of acidic and basic amino acids the site of polypeptide synthesis?

If polypeptides are synthesized by acid-base reactions between the carboxyl group of one amino acid and the amine group of another amino acid, what stops the formation of a peptide bond between the ...
2
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0answers
67 views

What is the Iso electric point of the given amino acid? [closed]

I am not sure about three but for two acidic parts we take the mean of the two.. But what about three?
1
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0answers
19 views

How to create a Non Water loving Vegatable Oil Foam?

I am trying to create a vegetable oil foam (or large quantity of air bubbles) and as I am not a Chemist by far. First I was thinking of using Amphiphilic surfactant, but I don't want this foam to be ...
22
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4answers
2k views

Where did amino acids get their one-letter codes?

Some of the amino acids have a one-letter code that's just the first letter of the name of the amino acid. This makes sense and obviously since there is more than one amino acid that begins with the ...
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1answer
519 views

Is glycine achiral? [duplicate]

In this video (10:20>) the woman says that the Glycine is not chiral because it has 2 different group only rather than four. Then I can understand from her things that amino acid can be chiral just ...
3
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3answers
124 views

How do amino acids look like at the isoelectric point?

At the isoelectric point amino-acids are neutral to the outside. It is however not known to my knowledge if the molecules are indeed in a zwitterionic form or just in its "normal" totally uncharged ...
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0answers
387 views

Which Pka to use to calculate Z-/HZ ratio of amino acids (henderson hasselbalch)?

I was wondering which $\mathrm{pK_a}$ to use when calculating the ratio of $\ce{HZ}$ to $\ce{Z-}$ of amino acids, the henderson hasselbalch formula used: $$\mathrm{pH} = \mathrm{p}K_\text{a} +\log\...
1
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2answers
608 views

Why do Asn-Ser and Gln-Thr have different H bonding patterns?

I noticed that Asn-Ser H-bonding is different from the H-bonding between Gln-Thr. However both have the same functional groups. I wasn't able to find any information about this. Maybe it's due to ...
3
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0answers
82 views

Can all nine essential amino acids be produced synthetically?

I would like to know if all nine of the essential amino acids can be produced synthetically with high purity without amines or other impurities through microbial activity during the production process....
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2answers
2k views

Why do amino acids hydrogen bond rather than ionic bond when they are forming secondary structures in proteins?

When peptide bonds are formed between amino acids, electron delocalisation causes the N to be more positive and the O to be more negative. As a result, why does 'hydrogen bonding' occur to form ...
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2answers
402 views

Where on the backbone does a peptide get protonated at low pH?

As a particular example, how does the backbone of a peptide look at $\mathrm{pH}~2$? Where does the backbone get protonated in such an acidic solution? I know that at low $\mathrm{pH}$ the free ...
0
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1answer
247 views

Correct way of drawing D-configuration with this stereochemistry?

Hello! I have completely memorized how to draw all 20 amino acids in the way seen in the picture (middle, between the "ball-and-stick" and fisher projection) By my understanding this is in the L ...
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1answer
157 views

Dissociation of 4-aminobenzoic acid in aqueous solution

I believe that 4-aminobenzoic acid's structural formula is $\ce{C7H7NO2}$ Hence, $$\ce{C7H7NO2 + H2O -> ?}$$ what are the dissociation products of the 4-aminobenzoic acid in aqueous solution ?
3
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2answers
2k views

salt bridge vs hydrogen bond

I saw this figure on Wikipedia: After seeing this image I got really confused about the difference between these two, or maybe the similarities. Ofcouse I understand that a hydrogen bond can be seen ...
9
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1answer
2k views

Why isn't the side chain of arginine totally protonated at low pH?

I was wondering why arginine cannot be protonated at $\mathrm{pH\ 0}$ on all the $\ce{N}$ atoms in the side chain, as they all have a free electron pair. As this image shows, it can only be protonated ...
2
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2answers
2k views

Can glutamic acid and arginine form H-bond at physiological pH?

I was wondering if, say, glutamic acid and arginine can form H-bonds at physiological pH? According to the figure arginine has a $\ce{NH3+}$ group and glutamic acid a $\ce{COO-}$ group at ...
4
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2answers
11k views

Ionization of amino acids

In my book it talks about amino acids. It says the general structure of an amino acid is as follows: However, on the next page it lists specific amino acids such as glycine shown here: My ...
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1answer
944 views

Amino acids: why is charge found by comparing pH and pKa and not pH to pKa + log [A-]/log[H+]

I am working on problems such as : The charges on the side groups at each pH are found by the following rule: At $\ce{pH < pK}$ a , ${H+}$ on, protonated At $\ce{pH > pK}$, ${H+}$ off, ...
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1answer
662 views

Why is arginine's positive side chain classified as basic and not acidic?

Arginine has a positive side chain. Doesn't this mean it wants to lose a proton H+? Isn't something that wants to lose or donate a proton an acid? Yet my book states, "arginine has a positively ...
11
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1answer
24k views

How do I calculate the isoelectric point of amino acids with more than two pKa's?

For most amino acids, the $\mathrm{pI}$ is simply the mean of the amino and carboxyl $\mathrm pK_\mathrm a$'s. However, for tyrosine and cysteine, which have more than one $\mathrm pK_\mathrm a$ value,...
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0answers
16 views

Looking for dataset of proteotypic and non-proteotypic peptide [duplicate]

I doing experimentation for peptide prediction using machine learning. I need some data for testing. My background is Computer Science. Any advice how to find proteotypic and non-proteotypic peptides....