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 too—can 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

We’ll 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-COO-

At neutral pH: +H3N-CH2-COO

-

B. pKa values

The precise pK values for each dissociation vary with the structure of the amino acid’s R-

group. 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 doesn’t 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 two…if 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.