MrMention

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This is some notes that I have made, initially for myself, on amino Acids. It is definitely not to be taken as definitive. Also if anyone who have taken the exam already who can think of anything that is clearly missing (without violating AAMC's rule), please feel free to add to this. Additionally please excuse my butchering of the English language, I am sure there is/are a few Their where There should be... among many other errors. However, if there are factual errors please point them out immediately--thank you.

AAMC Require Us to Know:

Description:

. Absolute Configuration at the Alpha position
. Amino Acids as dipolar ions
. Classifications
*Acidic or Basic
*Hydrophobic or Hydrophilic

Reactions:


. Sulfur Linkage for Cysteine and Cystine
. Peptide Linkage: Polypeptides and Proteins
. Hydrolysis


Hydrophobic
-------------------------------Hydrophilic----------------------------------

Nonpolar [9]: Polar [6]: Acidic [2]: Basic [3]:

1. Alanine [Ala, A] Serine [Ser, S] Aspartic Acid [Asp, D] Histidine [His, H]

2. Phenylalanine [Phe, F] Cysteine [Cys, C] Glutamic Acid [Glu, E] Arginine [Arg, R]

3. Leucine [Leu, L] Threonine [Thr, T] Lysine [Lys, K]

4. Isoleucine [Ile, I] Tyrosine [Tyr, Y]

5. Valine [Val, V] Glutamine [Gln, Q]

6. Proline [Pro, P] Asparagine [AsN, N]

7. Glycine [Gly, G]

8. Methionine [Met, M]

9. Tryptophan [Trp, W]

I decided to scan the table to see if it comes out better, since it is losing its line spacing. Let's see if this works. So click on the link below for the table.

https://blu185.mail.live.com/mail/ViewOfficePreview.aspx?messageid=mgOlhR14FZ5RGPhAAjfeRzjA2&folderid=flinbox&attindex=0&cp=-1&attdepth=0&n=55595290




Alpha Amino Acids are so called because the amine is attached to the carbon in the alpha position to the carbonyl.

The amino acids differ from each other in their side chains (R groups.) These side chains (R groups), is attached to the alpha-carbon.

Recalling the Basic Structure (R Group) of all 20 Amino Acids:

Memory Aid for the "odd letter" Nonpolar:

For Phenylalanine note that Ph and the letter F both have the same phonetic sound. Therefore, the three letter code Phe will help you remember the one letter code, F, for Phenylalanine.

For Tryptophan picture yourself in your "minds eye" eating some turkey and falling asleep on your TRiP to Washington to meet the president after scoring 528 on your MCAT (wow, that is a stretch.) That should help you remember that Tryptophan three letter is TRP, and its one letter is W.

The remaining seven are straight forward. Also once you group the nonpolar in a certain order all nine are easy to recall. Alanine, then Phenylalanine, Leucine then Isoleucine...

Memory Aid for polar Amino Acids:

Putting and memorizing the six polar Amino Acids in the order as seen in the table above, one will notice that both the three and one letter code of the first three: Serine, Cysteine and Threonine, are straight forward to remember. This will leave us with the remaining three Tyrosine, Asparagine and Glutamine to commit to memory.

Now keeping them in the order from the above table, we start with Tyrosine. For Tyrosine I usually just picture it in my "minds eye" as tYrosine or I am wearing a large gigantic Y around my neck mark Tyrosine instead of a tie. Then move on to Glutamine and Asparagine. Notice that both Glutamine and Asparagine's three letter code ends with the letter N. As for Glutamine (here comes the stretch), wow, what a "Cute Amine," or "Q Amine." Hence, the one letter code for Glutamine is Q. I told you it was a stretch. Meanwhile, Asparagine is at the very eNd of the above Polar Amino Acids table. That is Asparagine not only has an N at the ended of its three letter code, but also an N, as its one letter code.

Memory Aid For The Acidic Amino Acids:

To recall the one letter codes for the two Acidic Amino Acids: either remember that Glutamic Acid is made with GLUE [this statement has not been evaluated by the Food and Drugs Administration.] This will give you E for Glutamic Acid's one letter code. Meanwhile, D comes just before E for Aspartic Acid's one letter code.

Or

Maybe you are running a drug lab making "Acid" and it gets raided by the DEa. So D for Aspartic Acid and E for Glutamic Acid.


Memory Aid for the Basic Amino Acids:

First remember the phrase King HAL.


The pronunciation of the word Arginine will help you remember that Arrrginine's one letter code is R.

To remember that the one letter code for lysine is K, I just say the basic Amino Acids are King HAL--Histidine, Arginine and Lysine. Where the K in King represent the one letter code for Lysine.

Meanwhile, Histidine is very straight forward.

Before we continue on, please make a note of the following three Amino Acids:

Glycine:

Glycine's R group is just another Hydrogen (H.) This also makes glycine the only achiral amino acid (of the 20.)

In the Glycine molecule, the side chain is just another hydrogen atom. That is, Glycine’s alpha carbon does not have four different things bonded to it. It has two hydrogen atoms. Hence, Glycine is not optically active. Another way of putting it is Glycine is achiral, it does not rotate plane-polarized light.


Proline:

All Amino Acids of biological significance are alpha amino acids with the Exception of Proline. Notice also that Proline has a cyclical structure as its side chain. Proline is not considered an alpha amino acid because its amino group is attached not only to the alpha carbon, but also to the delta carbon to form a ring structure.

Owing to this cyclical structure, Proline tends to fit into the corners of protein Molecules.

The bottom line is "turns" are caused by Proline. This is owing to the fact that Proline I cyclic, and therefore it cannot rotate freely about its sigma bonds. Therefore, the protein chain has to "turn."

Again: Proline is not an alpha structure and is usually found on the corners of protein molecules.


Cysteine and Cystine:

The Sulfur containing moiety of two Cysteine molecules can interact in a way that a Sulfur – Sulfur bond forms, this is called disulfide linkage. This resulting dimer species is called Cystine.

Side Note on Methionine:

The codon for Methionine is AUG. This is the starting amino acid in a protein chain. That is the start codon for the synthesis of protein.

If you need a memory aid, try: Are yoU Going to the Mets game?

Or

Are yoU Going to get started?

The start codon codes for Methionine in eukaryotes and a modified Met (fMet) in prokaryotes.

Once more: Methionine is the first Amino Acid translation and is represented by AUG.


Now remember, there are three stop codon and one start codon. The three stop codons are as follow: UAA UAG UGA.

Again if one needs memory aids, try:

UAA: yoU Are Away

UAG: yoU Are Gone

UGA: yoU Go Away.



What charge does a given protein or amino acid have at certain pH?

Amino Acid in Acidic Environment:

In a very acidic environment, an amino acid tends to have a net positive charge. If you take an amino acid and put it in a very acidic environment [lots of H+ ions around] the amino group will pick up a proton, and it will be positively charged. The carboxyl group will remain protonated; unable to give up its proton under acidic conditions.


Amino Acids in Basic Environment:

If one take an Amino Acid and place it in a very basic environment [very little H+ around], the carboxyl group will certainly give up proton and it will be negatively charged. However, the amino group will remain neutral. Therefore, in a very basic environment an amino acid tends to have a negative charge at the carboxyl group, but no negative charge at the amino group.

Note Carefully:

When the surrounding pH is low (acidic environment), the amino acid tends to be protonated (because the amino group takes up a proton.)

Meanwhile, when the surrounding pH is high (basic environment), the amino acid tends to be depronated (because the carboxyl group gives up a proton.)

On the other hand, if the pH is not too high and not too low (Goldilocks situation), the amino acid has both a positive and negative charge—it’s a dipolar ion (Zwitterion.)

What is the isoelectric point for a given protein or amino acid?

Isoelectric Point:

The pH at which an amino acid carries no net charge, that is, the carboxyl group is negatively charged and the amino group is positively charged, is referred as the isoelectric point. Another way of saying that is the isoelectric point is the pH at which the amino acid is dipolar ion (Zwitterion.)



When amino acids get together to form proteins, hydrophilic amino acids tend to be located on the outside of proteins and hydrophobic amino acids tend to be located on the inside. That is because the hydrophilic amino acids can interact nicely with water and aqueous media like plasma, cytosol, intersititial fluid, and other watery liquids. The hydrophobic ones cannot. Recall that like dissolve like.

Calculating Isoelectric point:

For amino acids that carries neutral or acidic side chains, the isoelectric point is simply the average of pKa1 and pKa2.

PI = (pKa1 + pKa2)/2


However, for amino acids with basic side chains (our friend HAL who we met a minute ago), the isoelectric point is found by averaging pKa2 and pka3.

PI basic: (pKa2 + pKa3)/2

Memory Aid for the Amino Acids with Ring Structure in their R Group:

Now recall that all amino acids have basically the same structural back bone, they only differ at their R group. With the exception of Glycine each amino acid has a carbon at its R group.

Now remember this: HTTPP makes good vaccines for all “ring” diseases except for Threonine Mellitus. That is Histidine, both Amino Acids that start with P (Phenylalanine and Proline), and two of the three that start with T (Tryptophan and Tyrosine) has a ring structure in their R group. So Histidine, Tyrosine, Tryptophan, Proline and Phenylalanine all have a ring structure in their R group—Threonine does not.


Now let’s get started with Glycine and build from there.

Glycine:

Glycine is the simplest of the amino acid. There are only three groups on the glycine since the R group is hydrogen (H.)

Glycine's R group is just another Hydrogen (H.) This also makes glycine the only achiral amino acid (of the 20.)

In the Glycine molecule, the side chain is just another hydrogen atom. That is, Glycine’s alpha carbon does not have four different things bonded to it. It has two hydrogen atoms. Hence, Glycine is not optically active. Another way of putting it is Glycine is achiral, it does not rotate plane-polarized light.

Alanine:

For Alanine, we simple replace one of the H on Glycine with a methyl (CH3) group. Every other Amino acid will have this carbon going forward.

From here on it is imperative that we recall this basic Alanine structure. Since, we shall be using this basic structure to remember many of the others.

Valine:

Valine’s one letter code is V, so just picture in your “mind’s eye” a giant letter V sitting on top of the Amino Acid back bone and you should recall that Valine has two CH3 group at the end of its R Group. Again, we are slowly building from the basic initial Amino Acid back bone.


Both Leucine and Isoleucine could be viewed has having a Butyl group, but let’s try a different approach.

Leucine:

If you already recalled Valine, just thing of Leucine as an amino acid with an additional Carbon at the start of the R Group.

Isoleucine:

Now Isoleucine is like a Sec-butyl group attached to the amino acid background (this includes the alpha carbon.)

Or better yet, picture a giant letter L isolated on top of the carbon back bone.

Phenylalanine:

Phenylalanine is just the Alanine back bone of our basic amino acid structure from before with a phenyl group (Benzene ring) attached to the Alpha carbon. The very name will ensure that we easily remember the structure of this one.

Tryptophan:

Since, we already recalled that we felt asleep on our TRiP to Washington. From the one letter code for Tryptophan we can remember that the Amino Acid Tryptophan has a double (W) ring structure. The ending ring may just be remembered as benzene. Which leave us with trying to recall the middle ring. Now realize that this ring looks like pentene. So the structure may be viewed (starting with our basic Alanine back bone) as a pentene with an Ammonium (not quite) peak and a benzene ring at the end/top. As you practice drawing it out a few times, your “true” memory will help you recall that the double bond carbon is closer to the amine peak.

Methionine:

Now this one is really stupid, but for Methionine picture yourself heading to McDonald’s and ordering a double Swiss cheese burger. Here the M in McDonald's would represent Methionine. So starting with the alanine back bone we sandwich a Sulfur molecule between two Carbons.

Proline:

Proline maybe viewed as connecting (constructing) a pentane ring on the basic Amino Acid back bone.


Polar R Groups:

On page 182 of Berkeley Review Organic Book #II they have the following mnemonic for the polar Amino acids: “See There, my CysTyr does not have a Glue Ass,” for Serine, Threonine, Cysteine, Tyrosine, Glutamine and Asparagine.


Serine:

Serine can be remembered as Alanine alcoholic cousin. That is, once we remember the basic structure for Alanine then we add an OH group to get Serine.

Tyrosine:

Tyrosine maybe viewed as Alanine with a Toluene group attached to the Alpha carbon of the basic amino acid back bone. Toluene group attached to your Alanine.

Threonine:


Cysteine:

Cysteine just has a thiol (SH) group on the alpha carbon. In other words, Cysteine is just a Alanine with a thiol (SH) group attached.

Asparagine:


Glutamine:

Acidic R Groups:

Aspartic Acid:

Aspartic Acid can be viewed as simple on additional carboxylic group on the Basic Alanine structure.

Glutamic Acid:

Meanwhile, for Glutamic Acid, think of Alanine being Glued to acetic acid.

Or

Basically Aspartic Acid diabetic cousin who always eat too (two) many carbohydrates.

Basic Amino Acids R Group:

Lysine:

Lysine’s R Group may be remembered as a four Carbon sword with an Amine group (NH2) dragger at the end.

Arginine:

(I am sure everyone will come up with something better for Arginine (I am currently drawing a blank), but here goes...)

For Arginine I add an additional double bonded amine blade to the Lysine dagger to make it hit harder and I connect it all with an Nitro link.

or

A double amine winged Butyl fly. Meaning a four carbon chain on the main amino acid back bone, with two amine groups at the end carbon. However, we still need to recall that there is another nitrogen group between the last two carbons.


Histidine:

Recall that Histidine was one of the ring structure from the HTTPP vaccine we invented earlier. So we are basically attaching a ring structure to Alanine, which we already cemented into our collective memory. More specifically we are attaching a Pentene shaped ring. Now we need to also remember that it has two double bonds and two nitrogen where carbons should be.


Quick Fact:

All 20 standard amino acids may exist in either the D or the L configuration--except for the achiral Glycine. However, only the L-amino acids are found in proteins.

Nevertheless, some bacteria as D-amino acids such as D-alanine and D-glutamate in their cell walls. These D-amino acids prevent destruction of the bacterial cell wall by proteases.


***Note carefully: These are not perfect and are only aid to your true memory. After you draw them out a few time, using the above memory tricks as a guide, you should be able to "burn" them to your brain. This may just help you a little better than having to go over them 200 times.***

Here are a few links that may be more helpful:

Free on demand Biochemistry course

http://ocw.mit.edu/courses/biology/7-01sc-fundamentals-of-biology-fall-2011/biochemistry/biochemical-reactions-enzymes-and-atp/

http://ocw.mit.edu/courses/biology/7-01sc-fundamentals-of-biology-fall-2011/biochemistry/

https://www.coursera.org/course/introbiology?


Finding the net charge on an Amino Acid:



Memorizing the 20 Amino Acids




Quick Animation: Asparagine To Glutamine

http://www.biology.arizona.edu/biochemistry/problem_sets/aa/Anim/asp_gln.html


Here is a Blog post that some of you may find helpful

https://samsen.wordpress.com/2008/08/05/mnemonics-for-amino-acids/


Additional Resources:

It seems that Kaplan has done a great job with their Biochemistry book--I would be sure to know everything in that book and more. I believe a combination of Kaplan and Khan Academy with plenty of practice should help greatly with the biochemistry section of the test. [I have only spend about 10 minutes with the Kaplan book at the book store, so I cannot say 100% for sure, but do I like what I saw.]

Wishing everyone the best of success studying. Also please remember that this is only a supplemental starting point and should not be viewed as adequate for your MCAT Amino Acid content preparation.

I shall do some editing to fill in some stuff especially on Isoelectric point when I get to it.
 
Last edited:
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MrMention

MrMention

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I just realize that the table of amino acid comes out messed up once I post the thread. I am really not sure why it is that way, because if I go to edit it, it appears normal (properly space.)
 

BluMist

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I just realize that the table of amino acid comes out messed up once I post the thread. I am really not sure why it is that way, because if I go to edit it, it appears normal (properly space.)
use "Insert -> Code" to (somewhat) preserve spacing
Code:
1    2    3    4
1    2         4
1         3 
1              4
 
OP
MrMention

MrMention

5+ Year Member
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At a Bar near you.
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use "Insert -> Code" to (somewhat) preserve spacing
Code:
1    2    3    4
1    2         4
1         3
1              4
Hello BluMist:

Could you explain how to do that "Insert - > code" stuff please. Do I use the tab key on my computer? Thanks.
 

BluMist

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This is what I mean by Insert -> Code
You can figure out the spacing with tabs or spaces.
upload_2015-9-18_9-32-22.png
 

kingtal0n

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I always remember Arrrrrr ginine is for pirates

:D

Cystine kinda looks like it has a chapel
 
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MrMention

MrMention

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Werunthis:

Thanks, I really hope it helps a bit.

KingtalOn:

Cystine Chapel, cool...I like that.