Amino Acids Reading: Pp.

71-81 OBJECTIVES -Identify the 20 amino acids found in proteins that are coded for by the genetic code; know and be able to draw/recognize their structures and the 3-letter and 1-letter abbreviations for each. -Classify the amino acid side chains as nonpolar, polar, positively or negatively charged. Understand how these will interact in aqueous solution -Understand the acid/base behavior of amino acids; be able to draw and/or decipher titration curves of amino acids. Given any pH you should be able to assign a charge to any of the 20 amino acids. Pay close attention to His, Tyr, Cys side chains. -Know the approximate pKa values of alpha- and R-group-carboxyl groups (2-4), alpha- and R-group-amino groups (9-11), and for tyrosine (10), cysteine (8), lysine (10), histidine (6), and arginine (12) -Understand disulfide bond formation -Define and be able to calculate pI -Know which amino acids are modified by post-translational modifications to become nonstandard aas OUTLINE I General structure and chemistry A. All 20 standard aas are alpha-amino acids. -alpha-carbon is bonded to an amino group, a carboxyl group, a hydrogen atom, and an R group, also known as the side chain. B. Stereochemistry - only L isomers are protein constituents. II Classification of amino acids based on their R-groups A. Nonpolar (Some texts put Glycine here) Alanine Proline Valine Leucine Isoleucine Methionine Phenylalanine Tryptophan

B. Polar, but uncharged (Some texts put Glycine here) Serine Threonine Tyrosine

Cysteine -disulfide bond Asparagine Glutamine

C. Positively charged Lysine Arginine Histidine

D. Negatively charged Glutamate Aspartate

III Nonstandard AAs

IV Acid/ base behavior, pI A. AAs are Zwitterions, amphoteric B. pKa values

C. pI

D. Titration curves

NOTES I General structure and chemistry Proteins are amino acid polymers.

A. All 20 standard amino acids (aas, or AAs will be used as abbreviations) are alpha-amino acids. -alpha-carbon is bonded to an amino group, a carboxyl group, a hydrogen atom, and an R group, also known as the side chain. (Proline is a little bit different; it is strictly considered an -imino acid, but we will talk about it as an amino acid) There are 20 naturally occurring amino acids that are commonly found in proteins. They all have common structural features as well as unique ones that give each AA its distinctive properties.

B. Stereochemistry The alpha carbon atom of (almost all) AAs is a chiral center. Therefore, two stereoisomers, designated D and L, exist for each AA, although only the L isomers are protein constituents. In the L-form, when shown in projection formulas, the amino group is positioned to the left of the alpha carbon.

II Classification of amino acids based on their R-groups Amino acid characteristics are the result of their R groups. Amino acids are classified according to the properties of their R groups. A. Nonpolar R groups These amino acids with NONpolar side chains are relatively hydrophobic, but also still have two charged groups (an amino group, a carboxyl group) at pH 7.0

Alanine: Ala, R = methyl group Valine: Val, R = isopropyl group Leucine: Leu, R = a four C hydrocarbon side chain Isoleucine: Ile, R = a 4C hydrocarbon side chain too Methionine-has nonpolar thioether group Proline: Pro, R = side chain that wraps around attaching to alpha amine N to form a cyclic structure. Thus Pro is a secondary amine or an imino acid. Pro is rigid, reduces structural flexibility of proteins, often found at the bends of folded proteins.

Phenylalanine, Tryptophan

These absorb 280 nm UV light (mostly Tryp), which means that most proteins do toocan be used as a technique to quantify proteins in solution.

B. Polar, but uncharged R groups Gly is the only AA that does not have a chiral carbon Serine Threonine R groups have OH groups Hydroxyl-H H-bonds to the O of water Cysteine R= CH2-SH, Most importantly, Cys side chains can be oxidized to form covalently linked dimeric amino acid called cystine; linked by disulfide bond. (Very nonpolar.) Asparagine Glutamine R= have amide groups, CH2-C(NH2)=O, H-bonds possible because of -NH2 Tyrosine can form hydrogen bonds through its -OH group. This group is also relatively reactive and can be covalently modified. This ability is often used by cells to alter protein function. Tyr also absorbs 280 nm UV light C. Positively charged R groups (at pH 7, but wait) Lysine R= -(CH2)4-NH3+ Has a second primary amine group Arginine Has a + charged guanidino group Histidine has an imidazole group NOT + charged at pH 7, but pKa of side chain is 6.0. (lower N is the one that can have extra H+) These amino acids are also hydrophilic. Important in electrostatic interactions between substances (EG. DNA binding).

D. Negatively charged R groups at pH 7 Glutamate R= -CH2-CH2-COO Aspartate R= -CH2-COO -

These AA's are charged so are hydrophilic Asp and Glu can be readily converted to their corresponding amides, glutamine (Gln) and asparagine (Asn), by swapping the hydroxyl group of the side chain carboxyl group for an amine group.

III Nonstandard AAs Several found in proteins All derived from standard ones, which are altered AFTER they are incorporated into a polypeptide (no codons for the nonstandard ones) Extra functional groups added Well see some of them in certain proteins (hydroxylysine, hydroxyproline, in collagen, a fibrous protein of connective tissue)

IV Acid base behavior A. AAs are Zwitterions, amphoteric In aqueous solution, AAs are dipolar ions or zwitterions. The amine group can be protonated and the carboxyl group can lose its H+. Thus amino acids can act as acids or bases (amphoteric). Other properties associated with this condition are high solublility in water and high melting temperature (ca. 300 C). Both the amino and carboxyl ends can ionize in solution.

Look at glycine as an example At low pH's: +H3N-CH2-COOH--- fully protonated At high pH's H2N-CH2-COOAt neutral pH: +H3N-CH2-COOB. pKa values The precise pK values for each dissociation vary with the structure of the amino acids Rgroup. These pK values are tabulated in your text. For the alpha-carboxyl groups, pK ranges from ~1.80 to 2.4. For alpha-amino groups, pK ranges from ~9.0 to 11. (Note that these above pK values apply only to the alpha carboxyl and alpha amino groups; side chain groups may also be ionizable.)

For Example, Glycine: pK for -COO- is 2.3, pK for -NH3+ is 9.6. These pKa values are actually lower than for similar groups in other, simpler molecules. Due to intermolecular interactions --repulsion, attraction--- within the molecule itself. But, the pKa of a particular functional group in an amino acid is its own, and doesnt change with the change of surrounding solution pH.

C. pI Look back at titration curve of glycine; At a pH of 5.97, exactly at the point of inflection between the two stages in the titration curve, glycine is present as its dipolar form, fully ionized but with NO NET CHARGE. It will not move in an electric field. This is definition of isoelectric pt or pI. Property of the WHOLE molecule, takes into account all the ionizable groups and all their charges. Can be calculated by adding two pKa values, and dividing by twoif only two pKa values. More later.

D. Titration curves Amino acids with ionizable R groups have even more complex titration curves. EG. Glutamate Lysine YOU SHOULD BE ABLE TO DRAW AND/OR INTERPRET TITRATION CURVES OF ANY AMINO ACID FOR THE QUIZ.