Amino Acids

Learning the structure and function of the 20 amino acids is not difficult. It requires critical thinking, discovering patterns, and 1-2 hours. We will analyze each amino acid to learn its side chain, functional group type, 3 letter code, and 1 letter code.

Backbone for all amino acids (X= side chain): H3N-XCH-COO

1.Glycine:

X= H (Nonpolar)

Gly,G

Simplest amino acid so gets “first choice” of 3 letter and 1 letter code (there are other amino acids that start with G but they do not get G as their 1 letter code!)

2. Alanine:

X= CH3 (Nonpolar)

“All”anine= Glycine except with “All” the hydrogens and extra carbon! (CH3 instead of H!)

Ala,A

Second simplest amino acid so gets “first choice” of 3 letter and 1 letter code (there are other amino acids that start with A but they do not get A as their 1 letter code!)

3. Valine:

X= CH-(CH3)2 (Nonpolar)

The V in Valine looks like a peace sign! Valine is a girl with short fingers making a peace sign(CH joint with two CH3 fingers coming off)

Val, V

V and Val are the first portions of the name so amino acid so gets these as the 3 letter and 1 letter code.

4. Leucine:

X= CH2-CH-(CH3)2 (Nonpolar)

Leucine is like Valine except 1 carbon longer! Leucine is a taller boy with long fingers making a peace sign.

Leu, L

5.Isoleucine

X=  HC(CH3)CH2CH3

Isoleucine has the same formula as leucine except instead of a peace sign it is a “middle finger” ie the longer chain is now in the middle (middle finger) and there is a short finger on the side. 

6.Methionine:

X= CH2-CH2-S-CH3 (Nonpolar because sulfur is capped with CH3)

“Meth” “smells bad” so does sulfur. Methionine has 3 carbons and a sulfur which is capped with a CH3 thus preventing it from reacting or making the amino acid basic.

Met, M

7. Phenylalanine

X = CH2-BenzeneRing (Nonpolar because benzene ring is nonpolar)

Alanine with a benzene ring on it. Don’t forget the extra carbon!

Phe, F

The 1 letter code can be memorizing by thinking “Feenylalanine”

8. Tryptophan

X= 2 Huge Blocks with a nitrogen-containing pentagon and benzene

Trp, W

“Whiptophan” so W is 1 letter code. T,R, and P will be taken by other amino acids.

 

9.  Serine

X= CH2OH (Polar because of OH)

Alcoholic version of alanine

Ser, S

10. Cysteine

X= CH2SH (Polar because of S)

Sulfur version of alanine

Cys, C (NOT S!)

11. Threonine

X=HO-HC-CH3 (Polar because of OH)          

Like alcoholic valine except one of the CH3 is completely replaced with an OH

Thr, T

Simplest of all the amino acids that start with letter T so gets first choice to have T as 1 letter code!

12. Tyrosine

X= CH2BenzeneOH

Like Phenylalanine with an OH on it (Phe + Ser = Tyr)

Tyr, Y

Y is the second letter in tyrosine so it is used as 1 letter code becase T is already taken by threonine.

13. Proline

X= (Nitrogen on backbone)-CH2CH2CH2-(Central Carbon on backbone) (Polar because the N involved from backbone)

Proline is a pro at breaking protein structures because it causes a kink

Pro,P

14. Asparagine

X=CH2CONH2 (Polar because of NH2 and C=O)

Like aspartate except COO replaced with NH2

Asn, N

Asparagine is an assassiN taking the place of aspartate. Rather than Asp, we write asN because the N correlates to the N to signify the Nitrogen in the molecule. Since A and S are already taken, N is our 1 letter code.

15. Glutamine

X=CH2CH2CONH2 (Polar because of NH2 and C=O)

Like glutamate except COO replaced with NH2

Gln, Q

Glutamine is so Qute-amine! Q from qutamine is the 1 letter code since G, L, and N were already taking. We write Gln rather than Glu because Glu is for glutamate and the N in Gln helps signify the extra nitrogen in the amino acid. 

16. Lysine

X= CH2CH2CH2CH2NH3 (basic because of nitrogen)

Lysss = sound of long slivering snake (long carbon tail)

Small NH3 cap

Lys, K

K= koaLa (L for lysine, L in KoaLa which started with K. L,Y, S 1 letter codes already taken.)

17. Arginine

X=CH2CH2CH2NHCNH2NH2 (basic because of nitrogen)

ARRRRginine is on a pirate’s ship with a complex docking bay surrounding the central carbon. The docking bay has 3 portals, like the 3 nitrogen coming off the tip of the chain.

Arg, R
R= aRRRRGinine

18. Histidine

X=CH2-RingW/2Nitrogens (basic because of nitrogen)

19. Aspartate/Aspartic Acid

X=CH2COO (acidic because of COO)

Asparagine w/out the NH2

Asp, D

asparDate D= 1 letter code

20. Glutamate/Glutamic Acid

X=CH2CH2COO (acidic because of COO)

Longer Aspartate

Glu, E

glutamatE E=1 letter code

 

Problem: Draw In The Side Chains and Label Each Amino Acid With The 3 and 1 Letter Code