Organic Chemistry

994 CHAPTER 23 Amino Acids, Peptides, and Proteins

23.16 Protein Denaturation

Destroying the highly organized tertiary structure of a protein is called denaturation.

Anything that breaks the bonds responsible for maintaining the three-dimensional shape

of the protein will cause the protein to denature (unfold). Because these bonds are weak,

proteins are easily denatured. The totally random conformation of a denatured protein is

called a random coil. The following are some of the ways that proteins can be denatured:

• Changing the pH denatures proteins because it changes the charges on many of
  the side chains. This disrupts electrostatic attractions and hydrogen bonds.


• Certain reagents such as urea and guanidine hydrochloride denature proteins by
  forming hydrogen bonds to the protein groups that are stronger than the hydro-
  gen bonds formed between the groups.


• Detergents such as sodium dodecyl sulfate denature proteins by associating with
  the nonpolar groups of the protein, thus interfering with the normal hydrophobic
  interactions.


• Organic solvents denature proteins by disrupting hydrophobic interactions.


• Proteins can also be denatured by heat or by agitation. Both increase molecular
  motion, which can disrupt the attractive forces. A well-known example is the
  change that occurs to the white of an egg when it is heated or whipped.

Summary

Peptidesand proteinsare polymers of amino acidslinked

together by peptide(amide) bonds. A dipeptidecontains

two amino acid residues, a tripeptidecontains three, an

oligopeptidecontains three to 10, and a polypeptidecon-

tains many amino acid residues. Proteins have 40 to 4000

amino acid residues. The amino acidsdiffer only in the

substituent attached to the Most amino acids

found in nature have the Lconfiguration.

The carboxyl groups of the amino acids have values

of and the protonated amino groups have values of

At physiological pH, an amino acid exists as a

zwitterion. A few amino acids have side chains with ioniz-

able hydrogens. The isoelectric point(pI) of an amino acid

is the pH at which the amino acid has no net charge. A mix-

ture of amino acids can be separated based on their pI’s by

electrophoresis or based on their polarities by paper

chromatographyor thin-layer chromatography. Prepar-

ative separation can be achieved using ion-exchange

chromatographyemploying a cation-exchange resin. An

amino acid analyzer is an instrument that automates

ion-exchange chromatography. A racemic mixture of amino

acids can be separated by a kinetic resolution.

The amide bonds that link amino acid residues are called

peptide bonds. A peptide bond has about 40% double-

bond character. Two cysteine residues can be oxidized to a

disulfide bridge. Disulfide bridges are the only covalent

bonds that can form between nonadjacent amino acids. By

convention, peptides and proteins are written with the free

amino group (the N-terminal amino acid) on the left and

the free carboxyl group (the C-terminal amino acid) on

the right.

'9.

' 2 pKa

pKa

a-carbon.

To synthesize a peptide bond, the amino group of the

first amino acid must be protected (by t-BOC) and its car-

boxyl group activated (with DCC). The second amino acid

is added to form a dipeptide. Amino acids can be added to

the growing C-terminal end by repeating these two steps:

activating the carboxyl group of the C-terminal amino acid

with DCC and adding a new amino acid. Automated solid-

phase peptide synthesisallows peptides to be made more

rapidly and in higher yields.

The primary structureof a protein is the sequence of its

amino acids and the location of all its disulfide bridges. The

N-terminal amino acid of a peptide or protein can be deter-

mined with Edman’s reagent. The C-terminal amino acid

can be identified with carboxypeptidase. Partial hydrolysis

hydrolyzes only some of the peptide bonds. An exopeptid-

asecatalyzes the hydrolysis of a peptide bond at the end of a

peptide chain. An endopeptidasecatalyzes the hydrolysis of

a peptide bond that is not at the end of a peptide chain.

The secondary structureof a protein describes how local

segments of the protein’s backbone folds. A protein folds

so as to maximize the number of stabilizing interactions:

covalent bonds, hydrogen bonds, electrostatic attractions

(attraction between opposite charges), and hydrophobic in-

teractions (interactions between nonpolar groups). An

a and a coil conformationare

types of secondary structure. The tertiary structureof a

protein is the three-dimensional arrangement of all the atoms

in the protein. Proteins with more than one peptide chain are

called oligomers. The individual chains are called subunits.

The quaternary structureof a protein describes the way the

subunitsare arranged with respect to each other in space.

A-helix, B-pleated sheet,

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