How Do You Know if an Amino Acid Is Hydrophobic or Hydrophilic

Amino acids are the edifice blocks of living things. Long chains of amino acids make up proteins, which in turn make up many structural and functional cell components.

I like to think of the prison cell as a cocky contained city where the nucleus is the capital, the mitochondria is the power found and and then on. Only then y'all take your workers, transportation organization and the very construction of the prison cell city, which are all made of proteins- which in turn are made of amino acids.

The complication of a protein structure is determined past its sequence of amino acids and the chemic nature of their variable group side chains. The MCAT requires understanding the nature of polar and nonpolar side chains and the twisting and conformations acquired by hydrophobic and hydrophilic interactions

And yes, you should be memorizing each amino acid for the MCAT. This includes the side chain, full name, 3-letter name and unmarried letter of the alphabet abbreviation. But don't simply stick the words and structures onto flashcards hoping to force it into your retention. You need to actively tackle each amino acrid individually.

For a quick reference list download my costless Amino Acid Cheat Sheet Report Guide

1. Write out the full proper name
2. Draw the amino acid structure and variable group
3. Write out the 3-letter of the alphabet and unmarried letter abbreviations
4. Verbalize something unique about this specific side chain- out loud! The more than funny and crazy the connexion, the easier you volition recollect it.
5. Echo the naming/drawing process once RIGHT AWAY
6. Repeat weekly until you feel SOLID with this information

The Basic Structure of an Amino Acid

The amino acid gets its name from its ii primary functional groups. The amino acid has a key chiral carbon called the alpha carbon (blackness). Attached to the central carbon you lot have a hydrogen cantlet (gray), an amino or NH2 group (green), and a carboxylic acid COOH group (regal). Finally we have the R group (red), which is a variable side chain.

At that place are 20 different amino acids distinguished by their unique side chains. They range from a unproblematic hydrogen atom (glycine) to a complex 2-band resonating aromatic organization (tryptophan).

While the fully-neutral version above is how most students written report amino acids, and the form we'll use in this commodity, keep in mind that this is technically incorrect.

Amino Acid in Zwitterion Course

Since the carboxyl grouping is acidic and the amino group basic, the two will exist as a zwitterion in their conjugated charged forms in physiological pH. More than on zwitterion and amino acid charges in my next commodity (link to follow).

One final concept before we break downwardly the individual amino acids, and that is the 3-dimensional protein structure. In a biological arrangement structure determines function, so agreement amino acid characteristics is primal to understanding structure and ultimately protein function.

Chief Structure of a three-D Poly peptide
The start and more of import determination cistron of protein structure is the sequence of amino acids. If the polypeptide concatenation is attached in a unlike lodge, you lot get a very different overall structure.

Secondary Construction of a iii-D Protein
The secondary construction comes from backbone hydrogen bonding interactions. The peptide bond turns every former carboxyl and amino group into an amide functional group. The secondary structure of alpha helix and beta pleated sheets come from hydrogen bonding between the partially negative oxygen on the carbonyl and the partially positive hydrogen on the nitrogen.

Tertiary Structure of a 3-D Protein
The tertiary structure is where the existent 3-dimensional folding is introduced, and this is the outset fourth dimension y'all'll notice side-chain interactions. THIS is where knowledge and understanding of amino acrid side chains are critical.

Let me repeat myself, tertiary structure is the first fourth dimension you'll see variable R-group side chain interactions on the polypeptide concatenation. Many students misfile this with secondary structure, which is merely backbone interactions.

Fourth Construction of a 3-D Multi-Polypeptide Protein
4th structure refers to the variable group interactions between unlike polypeptides to form a single larger protein.

Fourth structures are not constitute in every poly peptide. If the poly peptide contains only a unmarried amino acrid strand, so the highest level of folding is its tertiary structure. Nevertheless, if the poly peptide is made upwards of multiple polypeptide subunits, then the fourth structure is what holds the dissimilar polypeptides together.

Now that yous understand the significance of side-concatenation characteristics, let's dive into amino acids. Keep in mind that since the parent amino and carboxyl groups are 'busy' with primary/secondary construction, they are NOT analyzed when studying side-concatenation properties and characteristics.
This means you lot ignore any potential polarity on both the carboxyl and amino groups and Just expect at the side chains.

Non-Polar Hydrophobic Amino Acids

Hydrophobic, equally the proper name implies is hydro – water, phobic – fearing. Hydrophobic amino acids have little or no polarity in their side bondage. The lack of polarity ways they have no manner to interact with highly polar h2o molecules, making them water fearing.

There are only five atoms that will appear in your amino acrid variable groups: H, C, North, O, and S.
Only consider polarity when you lot have N, O, S as the 'bulk' factor. I'll point these out equally they occur. However, if all yous run into are Cs and Hs you should automatically recognize a water-fearing amino acrid.

Glycine
Gly
Chiliad

Glycine is a unique amino acid in that it doesn't really have an R group. When you think 'variable R group,' you should think of carbon fastened to other atoms. But glycine only has a hydrogen at its side chain position. Since glycine has 2 hydrogen atoms, i each on the parent and side chain, information technology'due south the only symmetrical and thus achiral amino acid. Since hydrogen is not-polar, glycine is a hydrophobic amino acid. The Hydrogen side-concatenation makes glycine the smallest amino acrid.

Alanine
Ala
A

Alanine is a uncomplicated amino acid which has just a methyl or CH3 group as its side chain. Since you lot come across goose egg only carbon and hydrogen, Alanine is a non-polar hydrophobic amino acrid. It's important to recognize that this is a very small amino acid and capable of existence 'wedged' into tight loops or chains.

Valine
Val
V

Valine is another unproblematic amino acid with simply an isopropyl variable group. Just like alanine, we see zippo but carbon and hydrogen, making valine a non-polar hydrophobic amino acid.

Leucine
Leu
L

You can recognize leucine every bit having the same variable group as valine but with an extra CH2 grouping. Or yous can only recognize its isobutyl side concatenation.
See this video if you're not familiar with branched side chains like isopropyl or sec-butyl. Since leucine has just Cs and Hs, it's a water fearing non-polar amino acrid.

Isoleucine
Ile
I

Isoleucine, as the name implies, is an isomer of leucine. The departure is the placement of the CH3 for a sec-butyl rather than a isobutyl side chain. Just like its isomer, isoleucine is nonpolar and hydrophobic.

Methionine
Met
One thousand

Methionine is the first potentially tricky amino acid. It's side chain contains mostly Cs and Hs but with an embedded sulfur atom. While you lot may remember it's hydrophilic, pay careful attention to the location of the sulfur atom. Embedded in the concatenation and fastened to just carbon atoms, sulfur is partially 'hidden' from the exterior surround.

While y'all don't have to know electronegativity values for the MCAT information technology helps to understand that S = two.58 and C = 2.55. Since the departure in electronegativity is less than 0.5, there is NO polarity on this sidechain.
You must likewise recognize methionine every bit the showtime codon AUG in RNA translation to proteins.

Phenylalanine
Phe
F

To assist yous remember that Phenylalanine is F remember that 'ph' is pronounced as an 'F'. Don't mix this up with P for proline.
Pay attention to the structure of phenylalanine. It has a single carbon group with an attached benzene ring. Phenyl is the name for a benzene substituent, and this molecule has a benzene (phenyl) attached to the structure of alanine. Since phenylalanine has nothing just Cs and Hs in its aromatic side chain, information technology is nonpolar and hydrophobic.

Tryptophan
Trp
W

This is a catchy one. Notice the Northward-H in this side chain. Due north-H should be polar and capable of hydrogen bonding. All the same, there are ii reasons this amino acid is still non-polar and hydrophobic.

1. The N-H grouping is a tiny portion of the very large side chain.
2. Expect carefully at nitrogen, and more importantly, at its lone pairs. Nitrogen's electrons are integral to the conjugated aromaticity for the tryptophan side chain. In other words, retrieve of its electrons as 'likewise distracted' by resonance to pay much attention to the external h2o environment.

The MCAT requires you to recognize that this is a large and bulky amino acrid. Only since it's a multiple choice test you can simply memorize that tryptophan is the ONLY amino acid with TWO fused rings.
In fact, it's and then big it can TRIP (trp) over itself and cry out Waaaaaa (W)
(Note on mnemonics: The funnier, weirder, or dirtier the mnemonic, the more than likely you will remember it. Keep this in mind for med-school.)

Proline
Pro
P

Proline is a unique amino acid since it's THE Only ONE that incorporates the backbone into its side chain. The proline side chain is a iii-carbon concatenation that loops around and attaches dorsum to the parent amino grouping. This means that unlike the other amino acids, proline does Non accept a hydrogen atom on its nitrogen when part of a polypeptide concatenation.

However, y'all cannot forget that nitrogen is Not REALLY part of the variable group, which ways it cannot contribute any polarity. Since we simply have 3 CH2 groups to analyze we go a nonpolar hydrophobic side chain. This parent-loop creates a bulge and does non permit a proline-containing chain to be linear, which means yous'll often find it in loops and at the finish of an alpha helix.

Polar Hydrophobic Amino Acids

*This is a sticky section, and depending on where you research you may notice the following categorized equally polar or nonpolar, hydrophilic or hydrophobic. Pay attention to the presence of polar groups that are small compared to the overall sidechain, or very weakly polar and therefore hydrophobic.

Cysteine
Cys
C

Cysteine has a slightly polar S-H, but its polarity is and so mild that cysteine is unable to properly interact with water making it hydrophobic.

Cysteine is a very important amino acrid when information technology comes to tertiary and quaternary structure. Nearly side-chain interactions include polar/charged interactions or non-polar Van Der Waals and London dispersion. However, cysteine's side chain is capable of forming a disulfide span, which is a covalent bonds between 2 sulfur atoms through side chain oxidation and removal of 2 hydrogen atoms. This covalent bond is much stronger and more permanent when compared to the standard tertiary and quaternary interactions.
This is also the crusade for experimental fault in determining protein size/length for proteins with multiple subunits.

Tyrosine
Tyr
Y

Some students see this as OH leaking from a tire (tyr).

Accept a close look at tyrosine. What do you meet? It looks like the aromatic phenylalanine with an OH group at the para position (ortho/meta/para 2nd video).

On the one manus, we have a very polar and hydrogen-bail capable OH grouping, but on the other paw, the OH is tiny when compared to the size of the benzyl grouping (CH2-phenyl). This conundrum is a common source of confusion, but if you understand this, you'll recognize that tyrosine, while polar, is still a hydrophobic amino acrid.

Polar Hydrophilic Amino Acids

Hydrophilic as the proper noun implies comes from hydro-water and philic – loving.
Polarity comes from a 0.5-i.ix difference in electronegativity betwixt bound atoms. While you don't have to know these values for the MCAT, y'all should recognize that polar bonds will exist when N and O are leap to non-carbon atoms.
The electronegativity difference is plenty to create a slight separation of charge or polarity. And since similar 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 h2o.
Hydrophobic groups will twist away from these side chains.

Serine
Ser
S

Call up 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 grouping. This makes serial polar and very hydrophilic.

Threonine
Thr
T

In that location are multiple ways to look at this group. Yous can recollect of information technology equally serine with an extra methyl group, or as valine but with an OH replacing i of the methyl groups. I remember THREEonine as having 3 different groups: CH, CH3, and OH.
Similar serine, this variable grouping is polar and hydrophilic.

Asparagine
Asn
N

Try this: Slur your speech as yous say 'asparagine' really fast. Information technology sounds like you're saying AS…Northward, which is how I call up the 3-letter of the alphabet abbreviation for this amino acid. The NH2 at the cease of this molecule makes y'all call back 'base,' just wait at it'due south neighbor. NH2 nigh a carbonyl forms an amide, which doesn't like to deed as an acid or base under standard physiological conditions. 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
Gln
Q

I think of both 'glut' amino acids as gluttons having 'consumed' an extra CH2 group. Glutamine has the aforementioned structure every bit asparagine but with an extra gluttonous CH2 in its chain. Just like asparagine, information technology is polar and hydrophilic.

Acidic and Bones Amino Acrid Side Bondage

Acerbity and basicity in amino acids is even so another source of defoliation among students. If it starts out equally an acid, does it become a base of operations? How practice I find the charge? And then on.

Here's the fob: a carboxylic Acid in the side chain will give you an acidic amino acrid. When a carboxyl group is deprotonated, you get a conjugate base Salt. So if y'all come across the table salt version of a carboxylic acid side concatenation, while it is TECHNICALLY a 'conjugate base,' we'll simply refer to it every bit the salt version of the acidic amino acrid. Same for the base. Expect out for 'not-distracted' nitrogen atoms in the side concatenation.

Acidic Amino Acids

The acidic amino acids should look very familiar compared to asparagine and glutamine. And that's because everything about them is the aforementioned except for the terminal functional group. Amides (discussed to a higher place) are polar, but if the NH2 is swapped for an OH group, you get an acidic carboxyl grouping.

Aspartic Acrid / Aspartate
Asp
D

Aspartic acrid refers to the protonated acidic class of the amino acid. When deprotonated, you'll frequently see the conjugate base salt referred to as aspartate. This is the standard nomenclature for carboxylic acids.

Call up of ethanoic acid. Its common proper name is acetic acid. When deprotonated you go acetate. Acids are very stable in water since they are partially charged in their protonated class and fully charged in their deprotonated course. This makes them highly hydrophilic.

Glutamic Acrid / Glutamate
Glu
E

Once more we have a 'glutton' amino acid with an extra CH2 group. Glutamic Acrid refers to the protonated acidic form, and glutamate refers to the deprotonated cohabit base/common salt form.
Like aspartic acid, glutamic acrid is very stable in water and thus hydrophilic.

Basic Amino Acids

Bones amino acids incorporate a nitrogen atom with a lonely electron pair capable of attacking a hydrogen cantlet. When a bones amino acid is subjected to a low (acidic) pH, information technology will grab one of the free protons in solution to form a conjugate acid salt. These are hands recognize by the positive nitrogen in the side concatenation. Unlike the acidic amino acids, there are no 'usually used names' to memorize for these conjugate salts.

Lysine
Lys
K

Lysine is a simple basic amino acid. Despite a long and potentially hydrophobic chain, it has a basic NH2 at the end. In its basic deprotonated class, lysine is neutral and hydrophilic; however, if found in physiological pH, lysine volition pick up an H+ from solution to class an NH3+ salt. Salts are charged and therefore definitely hydrophilic

Arginine
Arg
R

Arginine is confusing and makes me say ARGh or R for brusque. Why? The basic portion of this variable group consists of an NH, C=Northward-H and NH2.
The two single-spring nitrogen atoms tin can use their solitary pairs to resonate with the carbon and double bound nitrogen atom. This makes their electrons UNAVAILABLE for acting every bit a base. Even so, the double-bound nitrogen uses its pi bond to resonate, leaving its free lone pair (shown in black) to act as the bones nitrogen on this group.
Argh!

Histidine
His
H

Histidine is another tricky base for the same reason as arginine. WHICH nitrogen is the basic one? Await at the drawing hither, particularly at the lone pairs on the two nitrogen atoms. The histidine ring is a heterocyclic aromatic compound. The upper nitrogen atom does not have a pi bail. This ways it must use its alone pairs to participate in resonance.
The lower nitrogen atom already has a resonating pi bond. This leaves its alone electrons (shown in blackness) complimentary to grab a proton, making this the basic atom.

In conclusion
Amino acids are a critical component to biological structures and to your sympathize of biology and biochemistry on the MCAT. And then, every bit you attempt to memorize everything about these 20 amino acids, it's of import that y'all also empathise why yous have polar and nonpolar amino acids, what makes the variable grouping hydrophobic or hydrophilic, and of course, the logic behind protonated/deprotonated acidic and basic amino acids.

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Source: https://leah4sci.com/understanding-amino-acid-side-chain-characteristics-for-the-mcat/

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