Amino Acids 101

What is an amino acid?

• Amino acids, or alpha- amino acids, are the “building blocks of
peptides and proteins”
• They are composed of amine and carboxylic acid groups,
separated by the alpha-carbon but the side chains on the alpha
carbon vary with the acid
• Amino acids are the subunits of proteins: amino acids make peptide
chains, peptide chains make polypeptides, polypeptides make
proteins!

How can we tell them apart?

The amino acids differ in the properties of their side
chains



Hydrophobic, non acidic (the H+ ion won’t associate

with water)

Leucine (Leu) Alanine (Ala) Tryptophan (Trp) Proline (Pro)

** Secondary amine (HNR2)

Methionine (Met) Phenylalanine (Phe) Valine (Val) Isoleucine (Ile) Glycine (Gly)
 Hydrophobic acidic (side chain is more acidic than water)
The pKa of water is 15.7

Tyrosine (Tyr) Cysteine (Cys)

(HO is acidic) (HS is acidic)

Hydrophilic nonacidic side chains

Serine (Ser) Asparagine (Asp) Glutamine (Gln) Threonine (Thr)

Hydrophilic acidic side chains

Glutamic acid (Glu) Aspartic acid (Asp)

Hydrophilic basic side chains (lone pairs on Nitrogen accept a
proton)

Histidine (His) Arginine (Arg) Lysine (Lys)

What do these all have in common?

Side chain

Amine
Carboxylic acid

So how do they make peptides?

By peptide bonding
• Covalent bond between amino acids
• Carboxyl group reacts with amino group,
releases H 2 O
What is the difference between a standard and nonstandard
amino acid?
• DNA codes for 20 different amino acids in humans. A
standard amino acid is one of these
• A nonstandard amino acid isn’t coded by DNA- they are
chemically modified from other standard amino acids

How do I put amino acids together?

When making a peptide chain, think like this:
1. Start with the amine (H2N) on the left
a. (this is assuming you are drawing the peptide
from N-terminus to C- terminus)
2. Then say, “alpha carbon, carbonyl… Nitrogen, alpha
carbon, carbonyl… nitrogen, alpha carbon, carbonyl”
a. You’ll notice that the carbonyls alternate
going “up” and “down”
3. Do this until you have drawn enough generic amino
acids for your chain
4. Then put your OH at the end for the rest of the
carboxylic acid group
5. Draw in wedges and dashes on the alpha carbons
a. Start with wedge, next will be a dash
6. Draw in hydrogens on the Nitrogens
7. Draw in side chains on the alpha carbons depending
on the name of the amino acid

Check out this example.

“Draw Ser-Leu-Ala-Thr-Asp”
• Amine on the left, then alpha carbon, carbonyl…
nitrogen, alpha carbon, carbonyl… keep repeating
pattern
• Count number of alpha carbons, should be equal to
the number of amino acids in your peptide chain
• Put OH on the end (part of carboxylic acid group)
• draw in dashes and wedges on alpha carbons,
starting with a wedge

• draw in hydrogens on the nitrogens- they should

also alternate up and down

• draw in side chains according to the amino acids

present in the peptide chain
There you have it! Ser-Leu-Ala-Thr-Asp!

Also, consider the electrostatic interactions. The Oxygens and

Hydrogens could interact with another peptide chain and have
hydrogen bonding...

Other important things to know about amino acids:

• Cysteine is an important amino acid because it
can form disulfide bridges. It is not
hydrophilic.
• Disulfide bridges link two cysteine residues
in a peptide

Why is this even important?!?

Amino acids make up 75% of your body! They make bodily
functions happen, allow chemical reactions to happen, and keep
you healthy. Ten of the twenty amino acids in DNA are already
present in the body, and ten “essential” amino acids must be
ingested regularly through food.
Works Cited:

Hardinger, Steven. Chemistry 14C: Lecture Supplement. 5th ed. Plymouth, MI:
Hayden-McNeil Pub., 2012. Print.

Hardinger, Steven. Chemistry 14C: Thinkbook. 9th ed. Plymouth, MI: Hayden-McNeil
Pub., 2012. Print.

Peptide Bond Image from

http://www.phschool.com/science/biology_place/biocoach/images/translation/peptbo
nd.gif

"Amino acid - Wikipedia, the free encyclopedia." Wikipedia, the free encyclopedia.
N.p., n.d. Web. 10 June 2012. <http://en.wikipedia.org/wiki/Amino_acid>.

"Dr. Hardinger's Organic Chemistry Page - UCLA." UCLA Chemistry and Biochemistry.
N.p., n.d. Web. 10 June 2012. <http://www.chem.ucla.edu/harding/index.html>.

All images of amino acids from Dr. Hardinger’s Chem 14C website

"What are Amino Acids?." wiseGEEK: clear answers for common questions. N.p., n.d.
Web. 10 June 2012. <http://www.wisegeek.com/what-are-amino-acids.htm>.