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    N H H C C O: 7.012 Chemistry Review ANSWERS

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    Glendon
    1) The document summarizes information about the MIT Biology Department course 7.012 on introductory biology. 2) It provides examples of non-covalent interactions between groups on a protein substrate. Hydrophobic groups interact through van der Waals forces while hydrophilic groups can interact through hydrogen bonding or ionic interactions due to charges. 3) It analyzes how modifications to a substrate analog affect binding to the protein. The addition of a charged group repels binding through charge repulsion. A polar group favors the dissolved state through hydrogen bonding with water.

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    N H H C C O: 7.012 Chemistry Review ANSWERS

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    Glendon
    36 views2 pages
    1) The document summarizes information about the MIT Biology Department course 7.012 on introductory biology. 2) It provides examples of non-covalent interactions between groups on a protein substrate. Hydrophobic groups interact through van der Waals forces while hydrophilic groups can interact through hydrogen bonding or ionic interactions due to charges. 3) It analyzes how modifications to a substrate analog affect binding to the protein. The addition of a charged group repels binding through charge repulsion. A polar group favors the dissolved state through hydrogen bonding with water.

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    Chem A

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    1) The document summarizes information about the MIT Biology Department course 7.012 on introductory biology. 2) It provides examples of non-covalent interactions between groups on a protein substrate. Hydrophobic groups interact through van der Waals forces while hydrophilic groups can interact through hydrogen bonding or ionic interactions due to charges. 3) It analyzes how modifications to a substrate analog affect binding to the protein. The addition of a charged group repels binding through charge repulsion. A polar group favors the dissolved state through hydrogen bonding with water.

    Copyright:

    Attribution Non-Commercial (BY-NC)
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    36 views2 pages

    N H H C C O: 7.012 Chemistry Review ANSWERS

    Uploaded by

    Glendon
    1) The document summarizes information about the MIT Biology Department course 7.012 on introductory biology. 2) It provides examples of non-covalent interactions between groups on a protein substrate. Hydrophobic groups interact through van der Waals forces while hydrophilic groups can interact through hydrogen bonding or ionic interactions due to charges. 3) It analyzes how modifications to a substrate analog affect binding to the protein. The addition of a charged group repels binding through charge repulsion. A polar group favors the dissolved state through hydrogen bonding with water.

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    MIT Biology Department

    7.012: Introductory Biology - Fall 2004


    Instructors: Professor Eric Lander, Professor Robert A. Weinberg, Dr. Claudette Gardel

    7.012 Chemistry Review ANSWERS


    This is the simplest correct bonding
    arrangement of the atoms and charges.
    H O
    N C
    H
    Solution O O H C C4
    C H
    Substrate
    H C H
    C C H
    H H
    C C H C
    N C H
    H H C C 3
    H H H H C
    1 O H
    C C C S H H
    O
    H
    H C H
    Protein
    C2
    2) Non-covalent Interactions
    a)
    Group Interaction(s) of Group with Substrate Classification of Group
    ionic (hydrogen also possible) hydrophilic-charged
    (1)
    VDW (neither C nor S is electronegative hydrophobic
    (2) enough to cause a H-bond to form)
    VDW (all non-polar bonds) hydrophobic
    (3)
    H-bond (VDW also possible) hydrophilic-polar
    (4)

    1
    3)

    O O H3 C O
    (-) charge repels C C
    (-) charge of side group (1).
    Can still H-bond
    O with side group (4).
    C H3 N
    O Analog 2
    (binds)
    Analog 1 O O
    (does not bind) C

    Polar group interacts


    N unfavorably with
    H3 N H hydrophobic environment.*
    Analog 3
    (does not bind)

    * Note: a more complete way to look at these cases is:


     Binding of substrate (S) and protein (P) to form complex (S-P) is an equilibrium:

    S + P S-P complex
    (dissolved (dissolved (dissolved
    in water) in water) in water)
    • Compared to the normal substrate, the extra COO - group in analog 1 destabilizes

    (raises the free energy of) the S-P complex because of the charge repulsion,

    shifting the equilibrium to favor free S and P.

    • Compared to the normal substrate, the addition of the polar N-H group (which
    can H-bond with water) in analog 3 stabilizes (lowers the free energy of) free S in

    solution, shifting the equilibrium to favor free S and P.

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