15.5 Proteins

229

Table 15.6 The natural amino acids in alphabetical order.phiφ denotes a benzene ring. Square brackets

denote a ring structure

Name

Superscript normal a^a

Superscript normal b^b

PolaritySuperscript normal c^c

FormulaSuperscript normal d^d

script upper A Superscript normal eA^e

Alanine

ala

A

A

–CHSubscript 33

8.2

Arginine

arg

R

+

–(CHSubscript 2 Baseline right parenthesis Subscript 3 Baseline2)3–NH–C(NHSubscript 2 Baseline right parenthesis Subscript 2 Superscript plus Baseline2)⁺

2

3.9

Asparagine

asn

N

P

–CHSubscript 22–CONHSubscript 22

4.4

Aspartic acid

asp

D

minus−

–CHSubscript 22–COOSuperscript minus⁻

4.8

Cysteine

cys

C

P

–CHSubscript 22–SH

3.4

Glutamine

gln

Q

P

–(CHSubscript 2 Baseline right parenthesis Subscript 2 Baseline2)2–CONHSubscript 22

3.6

Glutamic acid

glu

E

minus−

–(CHSubscript 2 Baseline right parenthesis Subscript 2 Baseline2)2–COOSuperscript minus⁻

4.8

Glycine

gly

G

A

–H

7.6

Histidine

his

H

+

–CHSubscript 22–[CSubscript 33NSubscript 22HSubscript 3 Baseline right bracket Superscript plus Baseline3]⁺

2.2

Isoleucine

ile

I

A

–CH(CHSubscript 33)–CHSubscript 22–CHSubscript 33

4.6

Leucine

leu

L

A

–CHSubscript 22–CH(CHSubscript 3 Baseline right parenthesis Subscript 2 Baseline3)2

7.3

Lysine

lys

K

+

–(CHSubscript 2 Baseline right parenthesis Subscript 4 Baseline2)4–NHSubscript 3 Superscript plus⁺

3

7.0

Methionine

met

M

A

–(CHSubscript 2 Baseline right parenthesis Subscript 2 Baseline2)2–S–CHSubscript 33

1.6

Phenylalanine

phe

F

A

–CHSubscript 22–phiφ

3.5

Proline

pro

P

A

–[CSubscript 33NHSubscript 7 Baseline right bracket Superscript normal f Baseline7]^f

5.5

Serine

ser

S

P

–CHSubscript 22–OH

7.8

Threonine

thr

T

P

–CH(OH)–CHSubscript 33

6.5

Tryptophan

trp

W

A

–CHSubscript 22–[CSubscript 88NHSubscript 66]

1.2

Tyrosine

tyr

Y

P

–CHSubscript 22–phiφ–OH

3.4

Valine

val

V

A

–CH(CHSubscript 3 Baseline right parenthesis Subscript 2 Baseline3)2

6.9

Superscript normal a^aThree-letter abbreviations

Superscript normal b^bOne-letter code

Superscript normal c^cA, apolar; P, polar;plus+, positively charged (at physiological pH);minus−, negatively charged

Superscript normal d^dOf the side chain (residue)

Superscript normal e^e% abundance, from M. O. Dayhoff, ed., Atlas of Protein Sequence and Structure, Vol. 5. Washington

DC: National Biomedical Research Foundation (1972)

Superscript normal f^fIncorporates the backbone—NHSubscript 22 in a ring structure

cytoplasm. Native globular proteins are compact stable structures with no or very

few polar residues in their interior (core). The transition from a random coil to an

ordered globule is called folding.

The governing feature of the polypeptide is the ability of the peptide unit –N–C–

C(=O)– to accept and donate H-bonds. Geometrical constraints allow theiith residue

in a chain to bond with theleft parenthesis i plus or minus 3 right parenthesis(i ± 3)th residues to form thealphaα-helix, which is the primary

structural element of proteins. Very simple polypeptides (e.g., polyalanine) form a

purealphaα-helix. Most globular proteins, made up of many different amino acids, contain

shortalphaα-helices joined by turns—short polypeptide segments of no special structure.