R is commonly one of 20 different side chains. At pH 7 both the amino and carboxyl groups are ionized.
Proteins consist exclusively of L-amino acids.
Amino acids are commonly joined together by an amide linkage, Peptide bond: The four atoms in each gray box form a rigid called a peptide bond. planar unit. There is no rotation around the C–N bond.
aminoor carboxylor Proteins are long polymers N-terminus HO CH2 HH C-terminus of amino acids linked by + peptide bonds, and they are always written with the CH2H O CH N-terminus toward the left.
The sequence of this tripeptide C is histidine-cysteine-valine. HN CH
These two single bonds allow rotation, so that long chains of amino acids are very fexible.
The common amino acids (Lys, or K) (Arg, or R) (His, or H) are grouped according to whether their side chains are
CH2 This group is CH2 very basic
CH2 because its NH
These nitrogens have a and one-letter abbreviations. NH3 is stabilized by C relatively weak affnity for an resonance. +H2N NH2 H+ and are only partly positive
Thus: alanine = Ala = A at neutral pH.
alanine valine aspartic acid glutamic acid (Ala, or A) (Val, or V) (Asp, or D) (Glu, or E)
C O O– (Leu, or L) asparagine glutamine proline phenylalanine (Asn, or N) (Gln, or Q) (Pro, or P) (Phe, or F) methionine tryptophan (Met, or M) (Trp, or W)
Although the amide N is not charged at neutral pH, it is polar.
(Ser, or S) (Thr, or T) (Tyr, or Y) (Gly, or G) (Cys, or C)
The –OH group is polar.
in proteins.
polar side chain on the hydrophobic core region outside of the molecule contains nonpolar can form hydrogen side chains bonds to water the distribution of its polar and nonpolar amino acids. The nonpolar (hydrophobic) side chains in a protein—belonging to such amino acids as phenylalanine, leucine, valine, and tryptophan—tend to cluster in the interior of the molecule (just as hydrophobic oil droplets coalesce in water to form one large droplet). This enables them to avoid contact with the water that surrounds them inside a cell. In contrast, polar groups—such as those belonging to arginine, glutamine, and histidine—tend to arrange themselves near the outside of the molecule, where they can form hydrogen bonds with water and with other polar molecules (Figure 3–5). Polar amino acids buried within the protein are usually hydrogen-bonded to other polar amino acids or to the polypeptide backbone.
Proteins Fold into a Conformation of Lowest Energy
As a result of all of these interactions, most proteins have a particular three-dimensional structure, which is determined by the order of the amino acids in its chain. The final folded structure, or conformation, of any polypeptide chain is generally the one that minimizes its free energy. Biologists have studied protein folding in a test tube using highly purified proteins. Treatment with certain solvents, which disrupt the noncovalent interactions holding the folded chain together, unfolds, or denatures, a protein. This treatment converts the protein into a flexible polypeptide chain that has lost its natural shape. When the denaturing solvent is removed, the protein often refolds spontaneously, or renatures, into its original conformation. This indicates that the amino acid sequence contains all of the information needed for specifying the three-dimensional shape of a protein, a critical point for understanding cell biology.