27

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 amino ...


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{...


18

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 ...


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, ...


16

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 ...


14

I use ChemDraw Professional 19.1.1.32. If you follow File>Open Templates>Advanced BioDraw, you will find the black helix that I have reoriented from horizontal to vertical. The red helix was enlarged and colored red. I hope this is of help.


13

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 ...


12

This illustration may be a combination of two images, or simply a program I don't know about. However, there are many (3D) protein visualisation programs that can show alpha-helices such as PyMol, VMD or Yasara. Here you can ray-trace the image (i.e. transparent background) and then combine the illustration with something else, e.g. an illustration from ...


11

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 ...


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 bases, so ...


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 ...


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 ...


8

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 ...


8

Isoelectric point of an amino acid is the $\mathrm{pH}$ at which the molecule carries no net charge[1]. It can be calculated by the average of the relevant $\mathrm pK_\mathrm a$ values as you have mentioned. Your confusion seems to stem from choosing the relevant $\mathrm pK_\mathrm a$ values. For this we should refer to the titration curve of the amino ...


8

This answer is for ChemDoodle, but I think you can import SVG files into ChemDraw as well. Just take an SVG image of an alpha helix and copy and paste it into ChemDoodle. Or go to File -> Insert Image and select the SVG file from your computer. It doesn't have to be SVG, but they have advantages with scaling. Made this using this File from Wikipedia, but ...


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 ...


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

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 ...


7

Glutamine in aqueous solutions degrades slowly when stored in room temperature. Therefore, we can expect that rate of degradation is faster at higher temperatures. It is evident that the hydrolysis product of glutamine is 5-pyrrolidone-2-carboxylic acid (not glutaric acid as shown for enzymatic degradation) and ammonia (Ref.1): The Ref.1 states that: The ...


7

In order for molecules to precipitate out of solution, they need to aggregate together. Amino acids that have zero net charge can aggregate together much more easily than those that are charged. Molecules that have net charge need counterions to aggregate with them to offset the charges or the electrostatic repulsion will be too great. The concept of ...


6

if you cap then you “block” all of the peptides that you are synthesizing.(?) No, you don’t, the order of steps is important. First you try to couple your new amino acid to the solid phase. You will end up with uncoupled ends with free amino groups and coupled ends with a protected amino group. Then you cap, e.g. with phenoxyacetic acid anhydride. This will ...


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

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 ...


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 (...


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.


5

Interestingly, Ammonium salts come above acids in the seniority table for functional groups (Reference: Wikipedia). Also, the ion in question has an alkyl group attached to it, which makes the suffix aminium rather than the commonly used ammonium. (Reference: Gold Book, Wikipedia) This means that the correct name of the compound is 6-carboxyhexan-1-aminium. ...


5

This paper here which describes the isolation of Glutamine from beets, contains a note that Glutamine is rapidly hydrolysed in water at high temperatures. The paper includes procedures in water at 60C. edit: This paper here describes the degradation kinetics of L-Glutamine in aqueous solution to 5-pyrrolidine-2-carboxylic acid.


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