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    Chapter4 Amino Acid

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    There are 20 standard amino acids that are the building blocks of proteins. Amino acids have an amino group and a carboxylic acid group bonded to the same carbon, giving them amphoteric properties. At physiological pH, they exist as zwitterions. Amino acids can bond together via peptide bonds to form polypeptides and proteins. The side chains of amino acids determine their properties and influence protein structure and function. Chirality of amino acids is important as life preferentially produces specific stereoisomers.

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    Chapter4 Amino Acid

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    kidpu
    665 views25 pages
    There are 20 standard amino acids that are the building blocks of proteins. Amino acids have an amino group and a carboxylic acid group bonded to the same carbon, giving them amphoteric properties. At physiological pH, they exist as zwitterions. Amino acids can bond together via peptide bonds to form polypeptides and proteins. The side chains of amino acids determine their properties and influence protein structure and function. Chirality of amino acids is important as life preferentially produces specific stereoisomers.

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    There are 20 standard amino acids that are the building blocks of proteins. Amino acids have an amino group and a carboxylic acid group bonded to the same carbon, giving them amphoteric properties. At physiological pH, they exist as zwitterions. Amino acids can bond together via peptide bonds to form polypeptides and proteins. The side chains of amino acids determine their properties and influence protein structure and function. Chirality of amino acids is important as life preferentially produces specific stereoisomers.

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    Download as pdf or txt
    665 views25 pages

    Chapter4 Amino Acid

    Uploaded by

    kidpu
    There are 20 standard amino acids that are the building blocks of proteins. Amino acids have an amino group and a carboxylic acid group bonded to the same carbon, giving them amphoteric properties. At physiological pH, they exist as zwitterions. Amino acids can bond together via peptide bonds to form polypeptides and proteins. The side chains of amino acids determine their properties and influence protein structure and function. Chirality of amino acids is important as life preferentially produces specific stereoisomers.

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    Chapter 4 Amino Acids

    General Properties

    • There are 20 standard amino acids. With exception of proline, all have
    primary amino group and a carboxylic acid bonded to same carbon.
    • Carboxyl group and amino group all have pKa values around 2.2 and 9.4
    respectively
    • Note that at physiological pH of 7, amino acids are charged as shown to
    left. They can act as either acid or base.
    • Also referred to as zwitterions
    • This imparts special properties e.g. some have melting points of 300 C,
    just like salts. Also very soluble in water and not organics.
    Peptide Bonds
    • Peptide bond formed from
    elimination of water from 2
    amino acids resulting in CO-
    NH linkage.
    • Can have di-, tri-, oligo- and
    poly-peptides.
    • Proteins composed of linear
    polymer of amino acids.
    • Large number of proteins
    can exist. A small protein of
    100 amino acids can have
    20100 or 1.27x10130 possible
    unique polypeptide chains.
    Classification of amino acids
    • Side chains of amino acids are responsible
    for many of the unique properties of
    proteins
    • 3 major classes of sides chains
    – hydrophobic
    – charged
    – polar
    – can also count 4 classes if Gly considered in own class
    • The 20 different amino acids are
    commonly abbreviated with 1 or 3-letter
    codes
    Hydrophobic Amino Acids 1
    Hydrophobic Amino Acids 2
    Charged Amino Acids
    Polar Amino Acids 1
    Polar Amino Acids 2
    Hydrophobic Amino Acids 1
    Disulfide-linked Cys residues
    • Two adjacent cysteine
    residues can be
    oxidized to form a
    disulfide bond
    • disulfide bonds are
    usually found in
    extracellular and not
    intracellular proteins
    – inside of cell is a
    reducing
    environment
    • disulfide bonds can
    stabilize protein
    structure by providing
    crosslink
    Significance of Side Chains
    • Select number can participate in
    “chemistry” of enzyme active sites. Those
    with charged or polar groups provide
    interesting catalytic groups.
    • Function of nonpolar amino acids? A
    protein folding issue. Can think of protein
    as hydrophobic core made of different
    Lego pieces. These pieces have to fit
    together in compact fashion.
    Acid-Base Properties of Amino Acids
    • Titration curve for glycine
    – Note that one starts with
    all groups in acid form.
    – Note how many
    equivalents are added
    – Note that at 0.5 and 1.5
    equivalents, pH is equal to
    pK of group being
    titrated.
    – Note pH which gives zero
    charge is the isoelectric
    point. Calculated as (pK1+
    pK2)/2
    – Note where the buffering
    capacity is best
    More Titration Curves
    Environment and pKas
    • pKa are influenced by environment.
    • To predict influence of environment, examine the charge of
    the acid and the conjugate base. E.g. His side chain has a
    cationic acid and neutral base whereas Asp has neutral acid
    and anionic base.
    • Do groups near the acid stabilize the acid or the base. E.g.
    if negative charge near a His residue, it would stabilize the
    positive charge of the acid, thereby making it a weaker acid
    and increasing the pK. Local environment can be:
    – Positively charged
    – Negatively charged
    – Hydrophobic
    • Based on above, explain why pK of a-carboxyl and a-amino
    group is lower than expected.
    Misc. about proteins and nomenclature
    • Proteins have complex titration curves.
    Many ionizable side chains whose pKs can
    be shifted by local environment
    • Isoelectric point of proteins can be
    calculated based on amino acid sequence
    or experimentally determined with
    isoelectric focusing.
    • Assignment: determine the pI of a
    hexapeptide: Gly-Glu-Asp-His-Lys-Ala
    Optical Activity

    • All amino acids except for gly rotate


    polarized light
    • Optically active molecules have
    asymmetry such that mirror images
    are not superimposable
    • Terms: asymmetic centers, chiral
    centers, enantiomers.
    • Enantiomers physically and
    chemically indistinguishable by most
    techniques
    Systems for describing enantiomers

    • Direction which a cpd rotates


    polarized light. Dextrorotator
    (rt) also (+) or levorotatory (lf)
    also (-). Determined by
    polarimeter.
    • Fischer convention is related to •The RS system depends on atomic
    glyceraldehyde and uses D or L. numbers. Lowers is placed behind
    • All amino acids from proteins chiral center. Number then from
    have L stereochemical highest to lowest. R is clockwise
    configuration. and S is counter clockwise.
    Diastereomers

    L-threonine is 2S-3R, name the other diasteromers


    Spectroscopy of amino acids

    Only the aromatic amino acids absorb light in the UV region


    Determination of extinction coefficient for a protein
    • Variety of methods available, this one is useful when the sequence
    is known
    • Edelhoch et al. [Biochemistry (1967) 6, 1948-1954]
    • From known sequence, determine Trp and Tyr content
    • With purified protein of interest, determine the absorbance at 280
    nm (or maximum near this wavelength) in buffered solution
    • Take sample of known absorbance, dissolve in 6 M guanidine
    hydrochloride in 0.02 M phosphate, pH 6.5. Record absorbance at
    288 and 280.
    • Use 2 simultaneous equations to determine the number of Trp and
    Tyr:
    – Abs. (288nm)= NTrp4815 + MTyr385
    – Abs. (280) = NTrp5690 + MTyr1280
    • Calculate concentration of Trp and Tyr. Divide by number of Trp
    and Tyr per enzyme to obtain concentration of enzyme in solution.
    Prochiral

    • Prochiral: replacement of one of the substituents


    turns achiral center into a chiral one. Enzymes, like
    you, can recognize and distinguish between pro R
    and pro S atoms.
    More prochiral
    H
    H • Planar molecules can also have
    C
    prochiral nature.
    C
    O CH3
    Acetaldehyde has a re face
    H3C O and si face. Reduction of one
    re face
    si face
    side versus the other yields a
    different stereoisomer (if
    using deuterium or tritium).
    • Enzymes (dehydrogenases)
    have different preferences
    H H for re or si face of substrates
    C
    OH HO
    C • For example, if the aldehyde
    H3C D CH3 is reduced with deuterium
    D
    based on the re or si side, the
    two different enantiomer
    products are formed.
    Chirality and life
    • Ordinary synthesis of chiral molecules
    produces racemic mixtures. Ordinary
    methods do not show stereochemical
    preference.
    • A fact of life: biosynthesis of substances
    having asymmetric centers almost produce
    pure stereoisomers.
    • Using this criteria, examination of amino
    acids in meterorites always show racemic
    mixture. Thus not based on life.
    • Not known why life has shown this
    preference.

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