BCH Graduate Survey of Biochemistry

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1 BCH 5045 Graduate Survey of Biochemistry Instructor: Charles Guy Producer: Ron Thomas Director: Marsha Derosier Lecture 6 Slide sets available at:

2 David L. Nelson and Michael M. Cox LEHNINGER PRINCIPLES OF BIOCHEMISTRY Fifth Edition CHAPTER 2 The Foundations of Biochemistry 2008 W. H. Freeman and Company

3 Hydrogen ion concentration, covalent and non-covalent bonds, amino acids, peptides and proteins Now that you know something about water, check this out: The Miraculous Properties of Ionized Water (scam?). I got some for sale at a very attractive price if you want to buy some.

5 All the different types of bonds and interactions listed in Table 2-5 can be found in proteins (hemoglobin shown here), and not only are they present, they are essential.

of water are separated by a membrane that is impermeable to the solute, then water will move

7 Water is a polar solvent and when polar solutes are present in solution, they affect the colligative properties of the water, like that of vapor pressure, and when two compartments of water are separated by a membrane that is impermeable to the solute, then water will move across a membrane in the direction of the higher concentration of solute in what is called osmosis.

8 Since water is both a weak acid and a weak base, protons can be donated and accepted along a chain of water molecules with the net result of a long distance movement of a proton.

9 Water is a weak acid: and at equilibrium 1. H 2 O H + + OH - 2. K eq = [H + ][OH - ] [H 2 O] The dissociation constant of water is: K w = [H + ][OH - ] = 1 X at 25 C. Therefore, [H + ] = [OH ] = (10 14 ) 1/2 = 10 7 M for a neutral solution.

10 The ph of a solution can be described as: 3. ph = log(1/[h + ]) = -log[h + ] For any acid, its dissociation can be written: 4. HA H + + A - and the dissociation constant at equilibrium K a is written the same as equation 2: 5. K a = [H + ][A - ] [HA]

11 The ph of a weak acid is a function of [HA] and the dissociation constant, therefore if we solve for [H + ] in equation 5: 6. [H + ] = K a [HA] [A - ] and if we take the log of both sides of eq. 6 and change the sign, we obtain: 7. -log[h + ] = -logk a + log [A - ] [HA]

12 We can substitute ph for -log[h + ] and pk a for -logk a and we now have the Henderson-Hasselbach equation: 8. ph = pk a + log [A - ] [HA] This equation allows you to calculate the molar ratio of base to acid at a given ph if you know the pk. When the concentration of the base is equal to the undissociated acid, the ph of the solution is equal to the pk. Why?

13 Titration curves are shown for three different weak acids. Note the shape of the curves and the midpoint of the titrations where [HA] = [A ] which is defined as the pk a.

15 Of course there are compounds that are monoprotic, diprotic, triprotic and multiprotic, and each proton donor/acceptor functional group will have its own characteristic K a.

Proteins contain amino acids that have acidic and basic groups as part of their sidechains, and consequently, [H + ] concentration strongly influences state

16 Proteins contain amino acids that have acidic and basic groups as part of their sidechains, and consequently, [H + ] concentration strongly influences state of dissociation of the proton donor/acceptor functional which in turn influences the proteins structure and function. This is most easily seen with enzymes.

17 Acid/base properties of solutes dissolved in water like carbon dioxide in the air, and in our blood stream and oceans have profound biochemical, biophysical and biological consequences.

18 David L. Nelson and Michael M. Cox LEHNINGER PRINCIPLES OF BIOCHEMISTRY Fifth Edition CHAPTER 3 Amino Acids, Peptides and Proteins 2008 W. H. Freeman and Company

20 Etch this into your brain. This is a Fischer Diagram of Alanine and it is very important that when you think of diagrams of the general structure of amino acids, this is what you should see in your mind s eye where the methyl group can replaced by other R groups from hydrogen in Glycine to the aromatic ring of Tyrosine.

BCH Graduate Survey of Biochemistry

BCH Graduate Survey of Biochemistry BCH 5045 Graduate Survey of Biochemistry Instructor: Charles Guy Producer: Ron Thomas Director: Glen Graham Lecture 12 Slide sets available at: http://hort.ifas.ufl.edu/teach/guyweb/bch5045/index.html