We’re rewarding the question askers & reputations are being recalculated! Read more.
24

Tryptophan For instance, is there a reason 'W' specifically was chosen for tryptophan (other than the fact that 'T' was taken)? Once you have assigned the other 19 amino acids, there are only 7 letters of the alphabet left: B, J, O, U, W, X, and Z. (Certainly not a nice Scrabble hand to have!) If one wants to use a letter found within the name of the ...


22

In the original German paper [1] Adolf Strecker used Aldehyd-Ammoniak or aldehyde-ammonia as a precursor, that's where the name derives from: Vor einigen Jahren habe ich gezeigt, daſs Aldehyd-Ammoniak und Blausäure beim Erwärmen mit verdünnter Chlorwasserstoffsäure sich zu einer schwachen Basis, Alanin genannt, vereinigen [...]: $$\ce{\underset{\text{...


16

For this, you can use the Henderson-Hasselbalch equation. Using the degree of dissociation, $\alpha$, this can be written as $$\mathrm{pH} = \mathrm{p}K_\mathrm{a} + \log\frac{\alpha}{1- \alpha}$$ Rewriting to solve for $\alpha$: $$\alpha = \frac{1}{10^{\mathrm{p}K_\mathrm{a} - \mathrm{pH}} + 1}$$ As stated above, $\alpha$ is the degree of dissociation, ...


15

Since the $\mathrm{pI}$ is the $\mathrm{pH}$ at which the amino acid has no overall net charge, you need to average the $\mathrm pK_\mathrm a$ values relevant to the protonation/deprotonation of the form with no net charge. Here are the acid-base equilibria for tyrosine: The form with no net charge is in red (+1 and -1 cancel out to give no net charge). It ...


13

Some single letter codes that aren’t the amino acid’s starting letter actually make sense when viewed from certain angles. Here’s the list starting with the bloomin’ obvious: G — Glycine A — Alanine V — Valine L — Leucine I — Isoleucine P — Proline S — Serine T — Threonine C — Cysteine H — Histidine M — Methionine Some amino acids have a letter that ...


11

Any molecule can absorb UV light. What the question is probably going for is why those three molecules absorb at longer wavelengths than other amino acids. This has to do with the conjugated pi bonds from aromaticity. Looking at a list of amino acids, we can see that most of them don't have conjugated pi ystems. amino acids (source) Conjugated pi bonds ...


10

When learning about amino acids, the primary things that were pointed out were that they had an amino group and a carboxyl group... Why amino acid? Not carboxyl acid, or some mix of the two, or something else? You stated why it is called an amino acid, the name comes from the amine (amino) and the carboxylic acid (carboxyl group). Amines are weak ...


10

The three-letter designation came before the single letter code. The three-letter codes themselves went several refinements and revision finally accepted by IUPAC and International Union of Biochemistry under the leadership of HBF Dixon. Later single letter codes were proposed. (apparently, because they were tiresome to write). This proposal came from Czech ...


10

See IUPAC-IUB Commission on Biochemical Nomenclature A One-Letter Notation for Amino Acid Sequences The Journal of Biological Chemistry Vol. 243, No. 13, pp. 3557-3559, 10 July 1968. : The possibility of using one-letter symbols was mentioned by Gamow and Ycas (2) in 1958. The idea was systematized by Šorm et al. (3) in 1961. It was used by this group ...


9

Your textbook is imprecise. We consider whether a sidechain is acidic or basic based on the action of the sidechain when it is neutral. Because arginine's sidechain is basic, it preferentially picks up a proton, and hence becomes positively charged. (In the same vein, carboxylic acid sidechains are acidic because they preferentially lose a proton, and exist ...


9

Selenocysteine can be either of the following: $\ce{C3H8NO2Se+, C3H7NO2Se, C3H6NO2Se-}$ or $\ce{C3H5NO2Se^2-}$. This is because the neutral form of selenocysteine is both a base and a diprotic acid: the amino group can be protonated and both the carboxylic group and the selenol can be deprotonated.[1] The above graph taken from the chemicalize.com property ...


7

I don't have the textbook you've gotten this from, but unless there's a statement to the contrary, I suspect these are intended as examples of hydrogen bonding, rather than an exhaustive list of the only hydrogen bonding pattern which can exist. If you start to look at real structures, you will see both "directions" of hydrogen bonding (hydroxyl donor/...


7

The two forms of amino acids that your question asks about are called zwitterions (technically IUPAC says they should be called dipolar ions but the term zwitteron is pervasive). Since amino acids contain both acidic (the carboxylic acid) and basic (the amine) moieties the molecule is able to undergo what almost appears to be an intramolecular acid-base ...


6

User364914 may be confused by the "odd" formulas in Strecker's 1854 paper. At that time there was no universal agreement on the masses of atoms. Was carbon 6 or 12? Was oxygen 8 or 16? Strecker used 6 for carbon and 8 for oxygen. The aldehyde is acetaldehyde, $\ce{NH3}$ is OK, blausaure is hydrogen cyanide and $\ce{OH}$ is water. The corrected structures ...


6

Yes, the arginine side chain is an excellent hydrogen bond donor. Charged N-H groups are even better hydrogen bond donors than the corresponding neutral N-H groups. Here is an article that gives examples of arginine side chains in hydrogen bonds. It showcases bidendate hydrogen bonds (i.e. two hydrogen bonds from the arginine side chain) with carboxylates ...


5

You might think that the term "amino acid" comes from the more systematic names of these molecules, where the amine is a substituent. Common name systematic name glycine 2-aminoethanoic acid alanine 2-aminopropanoic acid valine 2-amino-3-methylbutanoic acid cysteine 2-amino-3-mercaptopropanoic acid serine ...


5

No it is not, as there is no carboxylic acid functionality present. An amino acid is defined in this Wikipedia article as follows: Amino acids are organic compounds containing amine ($\ce{-NH2}$) and carboxyl ($\ce{-COOH}$) functional groups, along with a side chain (R group) specific to each amino acid.


5

In the most general sense, the term α-amino acid does encompass doubly substituted structures like those you mention. After all, the name doesn't specify any particular substitution, or lack thereof, at the α-carbon. The name only really means that there is an amino group α to a carboxylic acid, i.e. one carbon away. Similar nomenclature is used to describe ...


5

The nomenclature here is based on counting the number of backbone peptide bonds rather than the number of aminoacids. This does not apply the usual naming convention. If you look at the wikipedia page on "peptide (amide) bond", it states A peptide bond is an amide type of covalent chemical bond linking two consecutive alpha-amino acids from C1 (carbon ...


5

As their name imply, each amino acid has at least one amine and one acid functional group, but in most amino acids, the basicity of the amine is offset by the carboxylic acid group at physiological $\mathrm{pH}$, and hence considered neutral. Amines are basic because the nitrogen has an unshared electron pair that can accept an $\ce{H+}$ more readily than ...


5

The number of isomers are ${9}$ as shown below. AlaAla has ${4}$ isomers. AlaGly has ${2}$ isomers. GlyAla has ${2}$ isomers. GlyGly has ${1}$ isomer.


4

It may be hard to see from a 2D-drawing, but there are simply no more available lone pairs on arginine than the ones protonated in form $\ce{A}$. The guanidine group ($\ce{H2N-C(=NH)-NHR}$) is isolobal to a urea group, and indeed guanidine behaves much like urea except for the common differences between $\ce{C=O}$ and $\ce{C=NH}$. The lone pairs of $\ce{-...


4

You only took two examples into consideration. What about serine and glutamine or threonine and asparagine? Also, serine can hydrogen bond to another serine or a threonine … What I was trying to point out in this first paragraph is that these examples are really only single examples. Maybe they are trying to show how the same group (hydroxy group and amide ...


4

The reason amino acids exist largely in their zwitterionic form at biological $\mathrm{pH}$ (usually around 7) is due to the $\mathrm{p}K_\mathrm{a}$ of the constituent groups. It's not that the oxygen 'wants' to lose a proton, but more that at that $\mathrm{pH}$ the equilibrium lies towards the deprotonated state (things are rarely 100% protonated/...


4

Good question. First let's recognize that thiols (-SH) are more acidic functional groups than the corresponding alcohols (-OH) (some rationale here). So if we were talking about pKr we would see around 8 for cysteine's thiol side chain and around 15 for serine's alcohol side chain. Now, to address your question about the carboxyl acidity, pK1, of these ...


4

According to Textbook of metabolism and metabolic disorders (1964): The ribosides derived from purines have the suffix -osine; those from pyrimidines, the suffix -idine. The corresponding deoxyribosides, with the exception of thymidine, do not have any such simple designation. Occasionally, instead of, for example, guanine-deoxyriboside, the term deoxy-...


4

The above reaction is a modification of Gabriel phtahlimide synthesis from here: This procedure, known as the Gabriel synthesis, can be used to advantage in aminating bromomalonic esters.Since the phthalimide substituted malonic ester has an acidic hydrogen (colored orange), activated by the two ester groups, this intermediate may be converted to an ...


3

By Henderson relation we have $$\mathrm{pH=pI=p}K_\mathrm{a}+\log\left(\frac{[\ce{A-}]}{[\ce{AH}]}\right)$$ So if $\mathrm{pH - p}K_\mathrm{a} < 0$ then $[\ce{A-}] < [\ce{AH}]$ And if $\mathrm{pH - p}K_\mathrm{a} > 0$ then $[\ce{A-}] > [\ce{AH}]$ If you want then to know the exact proportion you need to know the concentration of your amino-...


3

In the backbone of a polypeptide, you would find amide bonds formed from the amino (NH2) and carboxyl (COOH) groups of two amino acids. Water is lost in this condensation process: The peptide backbone is considered to simply be the repeating Cα–C–N units. In the peptide shown below (a hexapeptide), the backbone is bolded. The side chains of each amino acid ...


3

I like MarvinSketch. You can run it in your browser or on your computer. Under Insert > Template, you can find all the amino acids. Once you've inserted one, select Calculations > Protonation > Isoelectric point and click OK. You'll get a window that looks like this showing the net charge versus pH (I picked a pretty boring one, but other amino acids produce ...


Only top voted, non community-wiki answers of a minimum length are eligible