Why is tryptophan nonpolar

All amino acids have a carboxyl terminus called the C-terminus and an amino terminus called the N-terminus , but they differ in their residual groups. Amino acids are bonded together by a covalent linkage called a peptide bond [6]. The core amino acid structure is:.

Where R is the side chain unique to each different amino acid. Large amino acids form the rigid region of the polypeptide backbone while the small amino acids form the flexible regions of the polypeptide allowing the protein to fold into its three-dimensional shape. On the peptide backbone there is flexible rotation around the peptide bond and there is a rigid planar peptide which is caused by a partial double bond. This is what allows the polypeptides primary sequence to fold to an alpha helix which is one strand coiled.

A beta strand is two strands coiled to an antiparallel helix. The core of the polypeptide is made up of the hydrophobic amino acids like phenyalanine , tyrosine , and tryptophan [8].

These three amino acids are also aromatic and are the largest amino acids. The other hydrophobic amino acids, but are not aromatic, are: proline, valine, isoleucine, leucine and methionine. Amino acids are referred to as chiral due to the alpha carbon being connected to four different groups. They can exist as one of two mirror images referred to as the Levorotatory L isomer and the Dextrotatory D isomer with only the L form of the amino acid isomer present within proteins [9].

Amino acids in solution at neutral pH exist predominantly as dipolar ions, or zwitterions. In the dipolar form, the amino group is protonated, and the carboxyl group is deprotonated. The ionization state of an amino acid varies with pH [10].

A series of amino acids joined by peptide bonds form a polypeptide chain, and each amino acid unit in a peptide is called a residue. Two amino acids can undergo a Condensation reaction to form a dipeptide, accompanied by the loss of a water molecule [11].

The common amino acids are grouped according to their side chains [12]. For example, acidic, basic, uncharged polar, and non-polar. For acidic side chains, the amino acids are: Aspartic acid D and Glutamic acid E formed by the addition of a proton to the amino acids aspartate and glutamate. Proline is also known as an amino acid. It is not essential to the human diet since it can be synthesized in the body from glutamic acid [13].

Unlike other amino acids that exist in the transform in polypeptides , proline can exist in the cis-form in peptides. Proline is the only cyclic amino acid. This makes series polar and very hydrophilic. There are multiple ways to look at this group. You can think of it as serine with an extra methyl group, or as valine but with an OH replacing one of the methyl groups. Like serine, this variable group is polar and hydrophilic. However, with partial charges and H-bonding capability at both the carbonyl oxygen AND the NH2 groups, we get a polar hydrophilic amino acid.

Glutamine has the same structure as asparagine but with an extra gluttonous CH2 in its chain. Just like asparagine, it is polar and hydrophilic. Acidity and basicity in amino acids is yet another source of confusion among students. If it starts out as an acid, does it become a base?

How do I find the charge? And so on. When a carboxyl group is deprotonated, you get a conjugate base SALT. Same for the base. The acidic amino acids should look very familiar compared to asparagine and glutamine. Amides discussed above are polar, but if the NH2 is swapped for an OH group, you get an acidic carboxyl group.

Aspartic acid refers to the protonated acidic form of the amino acid. This is the standard nomenclature for carboxylic acids. Think of ethanoic acid. Its common name is acetic acid. When deprotonated you get acetate. Acids are very stable in water since they are partially charged in their protonated form and fully charged in their deprotonated form. This makes them highly hydrophilic. Like aspartic acid, glutamic acid is very stable in water and thus hydrophilic. Basic amino acids contain a nitrogen atom with a lone electron pair capable of attacking a hydrogen atom.

When a basic amino acid is subjected to a low acidic pH, it will grab one of the free protons in solution to form a conjugate acid salt. These are easily recognize by the positive nitrogen in the side chain.

Lysine is a simple basic amino acid. Despite a long and potentially hydrophobic chain, it has a basic NH2 at the end. Salts are charged and therefore definitely hydrophilic. Arginine is confusing and makes me say ARGh or R for short. The 2 single-bound nitrogen atoms can use their lone pairs to resonate with the carbon and double bound nitrogen atom. However, the double-bound nitrogen uses its pi bond to resonate, leaving its free lone pair shown in black to act as the basic nitrogen on this group.

Histidine is another tricky base for the same reason as arginine. WHICH nitrogen is the basic one? Look at the drawing here, particularly at the lone pairs on the 2 nitrogen atoms. The histidine ring is a heterocyclic aromatic compound. The upper nitrogen atom does not have a pi bond.

This means it must use its lone pairs to participate in resonance. The lower nitrogen atom already has a resonating pi bond. This leaves its lone electrons shown in black free to grab a proton, making this the basic atom. In conclusion Amino acids are a critical component to biological structures and to your understand of biology and biochemistry on the MCAT.

This is a beautiful explanation. Im so glad I found it! Appreciate the work you have put into this. Now when I look at an a. This is my first visit but certainly not the last! I was a bit scared of understanding the spagetti monster diagrams of biomolecules like proteins; but now they seem very friendly. Thanks a lot Leah for an amazing synopsis of proteins for someone who is trying to understand them via functional groups.

Hi Leah—this is really helpful, thank you! Would other polar amino acids that have NH or OH groups become deprotonated or protonated? So, if youre looking at the charge of a polypeptide chain, you look at both ends for COOH and NH3 to be protonated at different pHs and at the acidic and basic side chain of the five amino acids listed, but would you care about the other amino aids present, or will their protonation not change?

Thank you! This was extremely helpful! My biochem exam is tomorrow and this helped clarify many points. Thank you. Hi Leah, This is amazing! I just had one question: I understand why you classified Tyrosine as hydrophobic. But many textbooks including mine, it has Tyrosine as hydrophilic. Do you think you can help me? The key is understanding rather that just cold memorization. You are selfless, dedicated and committed. I wonder how much time and effort you put in these videos and virtual tutorials.

God richly bless you. Sign up to join this community. The best answers are voted up and rise to the top. Stack Overflow for Teams — Collaborate and share knowledge with a private group. Create a free Team What is Teams? Learn more. Why are Tyrosine and Tryptophan considered hydrophobic? Ask Question. Asked 1 year, 3 months ago. Active 11 months ago.

Viewed 7k times. Improve this question. Mathew Mahindaratne Nip Dip Nip Dip 1 1 silver badge 4 4 bronze badges. Add a comment. Active Oldest Votes. Following image shows 20 amino acids categorized to polar 10 and non-polar groups 10 : All 10 non-polar amino acids are hydrophobic and 10 polar amino acids are hydrophilic.