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    BDC 2

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    KH KH KH
    lecture notes

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    BDC 2

    Uploaded by

    KH KH KH
    11 views3 pages
    lecture notes

    Copyright

    © © All Rights Reserved

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    lecture notes

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    © All Rights Reserved
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    Download as docx, pdf, or txt
    11 views3 pages

    BDC 2

    Uploaded by

    KH KH KH
    lecture notes

    Copyright:

    © All Rights Reserved
    Download as DOCX, PDF, TXT or read online from Scribd
    Download as docx, pdf, or txt
    of 3

    In non-ideal systems, like a cell,

    , where constant = dielectric constant/relative permittivity.

    Hydrogen Bond:

    L-enantiomer of amino acids are predominant in the cells.


    Condensation Polymerization:

    Primary Structure: The sequence of amino acids


    Secondary Structure: Folding driven by peptide backbone interactions.
    >Due to resonance, the N is partially doubly bonded- meaning that the bonds cannot rotate. Then,
    we can represent a polypeptide backbone as a series of planes with C-regions in between.
    (in the picture above, GREEN means double bond character)

    These free rotations make beta-sheets primarily,


    or alpha-helices.

    Beta Sheets:
    Alpha Helices: Has 3.6 residues per turn, caused by carbonyl oxygen of residue i which will
    hydrogen bond to a residue 3.6 positions away.

    Super-secondary Structures:

    Tertiary Structure: Folding due to side-chain interactions with water.


    >Normally, finding a conformation would be decreasing entropy, and be unfavorable.
    However, water, able to tumble into different orientations and form multiple hydrogen
    bonds has a very large entropy, allowing the protein conformation to happen.
    >Hydrophobic residues, however, make water constrained, decreasing entropy. Because
    of this, hydrophobic residues are kept away from water.
    >Protein folding is cooperative (so is protein denaturing. Cooperativity can happen in
    direction. It doesnt have to be constructive.
    >In reality, there are hydrophobic residues on cell surface, but they serve by being involved
    in protein and ligand interactions.
    Electrostatic Forces: Weakened at cell surface b/c water has a high dielectric constant
    H-Bonds: Usually between peptide groups and water at surface, and at core, usually
    between peptide groups. H-Bonds are highly directional.
    Van der Waals: Very influential when therere lots of them.
    Quaternary: Interactions between more than one polypeptide chain

    Fibrous Proteins: Play structural roles, and elongated/filamentous in shape. (Ex: collagen, actin)
    Globular Proteins: Carry out most of the cell chemistry (synthesis, transport, metabolism).
    >Folded very compactly. Its tertiary structure is the major determinant of function
    Membrane Protein: Very high proportion of hydrophobic proteins. Theyre partially buried in the
    membrane and are called peripheral-membrane proteins
    >They can also be fully integrated in the lipid bilayer and span the membrane
    multiple times. These are called integral membrane proteins.

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