Why alanine is hydrophobic

These residues can be found close to the interface between a protein and solvent. These residues are normally located inside the protein core, isolated from solvent. They participate in van der Waals interactions, which are essential for the stabilization of protein structures. In addition, Cys residues are involved in three-dimensional structure stabilization through formation of disulfide S-S bridges, which may connect different parts of a protein structure, or even different subunits in a complex.

We should note here that also in the case of Cys some disagreement exist on its assignment to the hydrophobic group. For example, according to some schemes, it is hydrophobic, while others consider it to be polar since it is often found close to, or at the surface of proteins.

It is often found at the surface of proteins, within loop- or coil without defined secondary structure regions, providing high flexibility to the polypeptide chain. This flexibility is required to facilitate sharp polypeptide turns in loop regions.

The reason for this is that its side chain makes a covalent bond with the main chain, which constrains the phi-angle of the polypeptide in this location see the section of the Ramachandran plot. The importance of Gly and Pro in protein folding has been discussed in Krieger et al. Distribution of amino acids in proteins The preferred location of different amino acids in protein molecules can be quantitatively characterized by calculating the extent by which an amino acid is buried in the structure or exposed to solvent.

The image below provides an idea about the distribution of the different amino acids within protein molecules. While hydrophobic amino acids are mostly buried, a smaller fraction of polar groups are also found to be buried, while charged residues apparently are exposed to a much higher degree.

The vertical axis shows the fraction of highly buried residues, while the horizontal axis shows the amino acid names in one-letter code. Image from the tutorial by J. Wampler ,. The hydrogen is covalently attached to one of the atoms called the hydrogen bond donor and interacts with the other the hydrogen bond acceptor. In proteins essentially all groups capable of forming H-bonds both main chain and side chain are usually H-bonded to each other or to water molecules.

Due to their electronic structure, water molecules may accept 2 hydrogen bonds, and donate 2, thus being simultaneously engaged in a total of 4 hydrogen bonds. Water molecules may also be involved in the stabilization of protein structures by making hydrogen bonds with the main chain and side chain groups in proteins and even linking different protein groups to each other. Cysteine is a very important amino acid when it comes to tertiary and quaternary structure.

This covalent bond is much stronger and more permanent when compared to the standard tertiary and quaternary interactions. Take a close look at tyrosine.

What do you see? On the one hand, we have a very polar and hydrogen-bond capable OH group, but on the other hand, the OH is tiny when compared to the size of the benzyl group CH2-phenyl. Hydrophilic as the name implies comes from hydro-water and philic — loving. Polarity comes from a 0. The electronegativity difference is enough to create a slight separation of charge or polarity. And since like attracts like, these partially charged groups will be attracted to oppositely charged or partially charged groups such as water.

These groups will twist the polypeptide chain in order to interact with each other and with water. Hydrophobic groups will twist away from these side chains.

Think of serine as alanine with an OH group attached. Unlike tyrosine, the OH is the majority in this molecule and its polarity is enough to influence the entire group. 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. I do put my heart and soul into this and offer a mix of free material and paid services including tutoring and a full fledged MCAT program.

I was super overwhelmed especially with my MCAT date coming up in just under 6 weeks. Thank you so much for your support and step-by-step guides! Glad to help Jenny.

How do you feel about your upcoming exam? Leah this is amazing! Thank you for all you detailed hard work. It makes learn all the aspects much easier! Your email address will not be published. Save my name, email, and website in this browser for the next time I comment. The true key to successful mastery of alkene reactions lies in practice practice practice. However, … [Read More Click for additional cheat sheets.

Click for additional MCAT tutorials. Click for additional orgo tutorial videos. The MCAT requires understanding the nature of polar and nonpolar side chains and the twisting and conformations caused by hydrophobic and hydrophilic interactions And yes, you should be memorizing each amino acid for the MCAT. For a quick reference list download my free Amino Acid Cheat Sheet Study Guide Write out the full name Draw the amino acid structure and variable group Write out the 3-letter and single letter abbreviations Verbalize something unique about this specific side chain- out loud!

The more funny and crazy the connection, the easier you will remember it.