lecture+3.105

lecture+3.105 - Biological Sciences 105 Lecture 3, January...

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Biological Sciences 105 Lecture 3, January 11, 2011 Copyright Steven M. Theg, 2011. All federal and state copyrights reserved for all original material presented in this course through any medium, including lecture or print. 1 LAST TIME WE ENDED WITH THE IMPORTANCE OF WEAK FORCES Why talk about non-covalent interactions? They add up to very large and important forces in macromolecules. That is, the sum of many non-covalent interactions is considerable. Examples: Molecular shapes of macromolecules, i.e., proteins, DNA Non-covalent interactions also cause substrates to bind to enzymes. E + S E•S E + P The fact that the ES complex is held together by weak interactions is good in that it allows the complex to be broken quickly, increasing the rate of the enzyme- catalyzed reaction. Weak interactions facilitate change. WATER CHEMISTRY Why study it? Two properties that have profound influences on biochemistry. The first is the hydrophobic effect of excluding non-polar material - the entropic forces. The second is the fact that it ionizes to a low extent. This gives rise to pH and its associated effects, which are manifold. Water ionizes to a small extent, but it has profound influence on biochemistry. H 2 O + H 2 O ' H 3 O + + OH - H 3 O + is called a hydronium ion. It is always further hydrated. We could call it H 9 O 4 + , as below:
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Biological Sciences 105 Lecture 3, January 11, 2011 Copyright Steven M. Theg, 2011. All federal and state copyrights reserved for all original material presented in this course through any medium, including lecture or print. 2 For simplicity, we write the ionization reaction as: H 2 O ' H + + OH - It has been determined that pure water at room temperature has [H + ] = 10e-7 M. By examination of ionization reaction, [OH - ] = 10e-7 M. Define "p" function: - log 10 (something). For pure water at RT, p[H + ] = pH = 7.0. This is defined as neutral pH. Note that pH and other "p" functions are logarithmic. A change in pH of one unit = a ten-fold change in [H + ]. Even though the [H + ] is very small, 10e-7, it is critical for biochemistry. Changes in pH mediate many things in the cell, including protein structure, ATP synthesis, ligand/receptor interactions, etc. Biochemists need a clear understanding of pH. So, we are going to spend some time working with acid/base problems. Look at dissociation of water more closely (with k f /k r ): (We’re going to derive the ion product of water, which leads to the relation pOH = 14 - pH.) k f H 2 O ' H + + OH - k r The k's are the rate constants.
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Biological Sciences 105 Lecture 3, January 11, 2011 Copyright Steven M. Theg, 2011. All federal and state copyrights reserved for all original material presented in this course through any medium, including lecture or print. 3
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This note was uploaded on 01/18/2011 for the course BIS 105 taught by Professor Kennethhilt during the Spring '09 term at UC Davis.

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lecture+3.105 - Biological Sciences 105 Lecture 3, January...

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