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    Table 3 1: Properties and Conventions Associated With The Common Amino Acids Found in Proteins

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    Amino acids can be classified into five main classes based on the properties of their R groups and their polarity or tendency to interact with water. The classes include: 1) Nonpolar, aliphatic R groups including glycine, alanine, valine, leucine, and isoleucine which have nonpolar and hydrophobic R groups that tend to cluster together within proteins. 2) Aromatic R groups including phenylalanine, tyrosine, and tryptophan which have polarizable, ring structures. 3) Polar, uncharged R groups including serine, threonine, cysteine, asparagine, and glutamine. 4) Posit

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    Table 3 1: Properties and Conventions Associated With The Common Amino Acids Found in Proteins

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    Amino acids can be classified into five main classes based on the properties of their R groups and their polarity or tendency to interact with water. The classes include: 1) Nonpolar, aliphatic R groups including glycine, alanine, valine, leucine, and isoleucine which have nonpolar and hydrophobic R groups that tend to cluster together within proteins. 2) Aromatic R groups including phenylalanine, tyrosine, and tryptophan which have polarizable, ring structures. 3) Polar, uncharged R groups including serine, threonine, cysteine, asparagine, and glutamine. 4) Posit

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    Amino acids can be classified into five main classes based on the properties of their R groups and their polarity or tendency to interact with water. The classes include: 1) Nonpolar, aliphatic R groups including glycine, alanine, valine, leucine, and isoleucine which have nonpolar and hydrophobic R groups that tend to cluster together within proteins. 2) Aromatic R groups including phenylalanine, tyrosine, and tryptophan which have polarizable, ring structures. 3) Polar, uncharged R groups including serine, threonine, cysteine, asparagine, and glutamine. 4) Posit

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    39 views2 pages

    Table 3 1: Properties and Conventions Associated With The Common Amino Acids Found in Proteins

    Uploaded by

    John Coop Cooper
    Amino acids can be classified into five main classes based on the properties of their R groups and their polarity or tendency to interact with water. The classes include: 1) Nonpolar, aliphatic R groups including glycine, alanine, valine, leucine, and isoleucine which have nonpolar and hydrophobic R groups that tend to cluster together within proteins. 2) Aromatic R groups including phenylalanine, tyrosine, and tryptophan which have polarizable, ring structures. 3) Polar, uncharged R groups including serine, threonine, cysteine, asparagine, and glutamine. 4) Posit

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    cC

    78

    Chapter 3 Amino Acids, Peptides, and Proteins

    TABLE 3 1 Properties and Conventions Associated with the Common Amino Acids Found in
    -

    Proteins

    pk, values
    Amino
    acid

    Abbreviation/ pK1
    Mr
    symbol

    R groups Glycine Alanine Proline Valine


    Leucine Isoleucine
    Gly
    7
    Methionine
    G Ala
    5
    89
    Aromatic R groups A Pro
    P Val
    11
    Phenylalanine
    V Leu
    5
    Tyrosine
    L He
    11
    Tryptophan
    I Met
    7
    M
    Polar, uncharged
    R groups
    Serine
    Phe F
    165
    Threonine Cysteine
    Tyr Y
    181
    Aspa ragine
    Tip
    204
    Glutamine
    W
    Positively charged R
    groups
    Ser
    10
    Lysine
    S
    5
    Histidine
    Thr
    Arginine
    T
    11
    Negatively charged Cys
    9
    C
    R groups

    pK2

    PKR
    ( COON) (--N11,1) (R group)
    -

    Hydropathy Occurrence in
    index*
    proteins (%)I
    Nonpolar, aliphatic

    2.3
    4
    2.3
    4
    1.9
    9
    2.3
    2

    9.6
    0
    9.6
    9
    10.9
    6
    9.6
    2

    1.83
    2.20
    2.38

    9.13
    9.11
    9.39

    ,10.07

    5.97
    6.01
    6.48
    5.97
    5.98
    6.02
    5.74

    -OA
    1.8
    1.6
    4.2
    3.8
    4.5
    1.9

    5.48
    5.66
    5.89

    2.8
    -1.3
    -0.9

    7.
    2
    7.8
    5.2
    6.6
    9.1
    5.3
    3.
    9
    3.

    2.2
    1
    2.1
    1
    1.9

    9.1
    5
    9.6
    2
    10.2
    8

    5.6
    8
    5.8
    7
    5.0
    7

    0.
    8
    -0.
    7
    2.
    5

    6.
    8
    59
    1_
    9
    4.

    Lys K
    14
    2.1
    8.9
    10.5
    9.7
    6
    His H
    8
    5
    3
    4
    .A scale combining hydrophobicity and
    hydrophilicity of R groups; it can be used to measure the tendency of an amino acid to
    Arg
    6.00
    7.59
    seek an aqueous environment (- values) or a hydrophobic environment (4 values). See Chapter 11, Fmrn Kyte, J. & Doolittle.,
    15
    1.8
    R
    9.1
    R.F. (1982) A simple method for displaying the hydropathic character of a protein. I, Mot Biol. 157, 105-132.

    -3.9

    5.
    9

    8.1
    8

    Aspartate
    Glutamate

    3.2
    -4.5

    'Average occurrence in more than 1,150 proteins. From Doolittle, R f. (1989) Redundancies in protein sequences, In Prediction of

    Protein Stoic Lure and the Principles of Protein Conformation (Tasman, 0.0 ed ), pp 599-623, Plenum Press, New York,

    Asp
    D

    133
    147

    1.88
    2.19

    9.60
    9.67

    3.6
    5
    4.2

    2.7
    7
    3.2
    2

    -3.5
    3.5

    5.
    3
    6.
    3

    Amino Acids Can Be Classified by R Group


    Knowledge of the chemical properties of the counon
    amino acids is central to an understandilig of biochemistry. The topic can be simplified by groupitig the amino
    acids into five main classw; based on the properties of
    their R groups (Table 1 ), in part it I heir polarity,
    or tendency to interact s,vith water ai biological p1 l (nom.
    pH 7.0). The polarity of the R groups varied idely, from
    nonpolar and hydrophobic Oval erinsolul )It') to highly
    polar and hydrophilic (water-soluble).
    The structures of the 20 common amino acids are
    shown in Figure 3-5, and some of their properties are

    listed in Table 3-1. Within each class there are


    gradations of polarity, size, and shape Of the R

    groups.
    Nonpolar, Aliphatic R Groups The R. groups in this class of

    aniino acids are nonpolar and hydrophobic. The


    side chains of Marline, valine, 'endue, and
    isoleucine I( nd to cluster together wilhin proteins,
    stabilwag
    pro
    _
    100
    h\
    riicmr:
    or
    h y d r o p h o b i c m i e r a m o u s wycine has the
    simplest structure. Although it is formally nonpolar,

    its very small side chain makcs mu) real col itribution
    to hydrophobic interactions, Mettionitne, ow' of
    the

    INVO snl fur-containing amino acids, has a non

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