The amino acids differ in the properties of their side chains. Hydrophobic, non acidic (the H+ ion won t associate with water)

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1 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 (HNR 2 ) Methionine (Met) Phenylalanine (Phe) Valine (Val) Isoleucine (Ile) Glycine (Gly)

2 Hydrophobic acidic (side chain is more acidic than water) The pka of water is 15.7 Tyrosine (Tyr) (HO is acidic) Cysteine (Cys) (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)

3 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

4 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 (H 2 N) 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)

5 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

6 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.

7 Works Cited: Hardinger, Steven. Chemistry 14C: Lecture Supplement. 5th ed. Plymouth, MI: Hayden-McNeil Pub., Print. Hardinger, Steven. Chemistry 14C: Thinkbook. 9th ed. Plymouth, MI: Hayden-McNeil Pub., Print. Peptide Bond Image from nd.gif "Amino acid - Wikipedia, the free encyclopedia." Wikipedia, the free encyclopedia. N.p., n.d. Web. 10 June <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 <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 <http://www.wisegeek.com/what-are-amino-acids.htm>.

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