Chapter 2 : Water Lets Jump into …. Water. Opening figure: fatty acid in a clathrate with waters of hydration (more dense than surrounding water) around the carboxyl.

Learning goals: What kind of interactions occur between different type of molecules in water. Why water is a good medium for life Why nonpolar moieties aggregate in water How dissolved molecules alter properties of water How weak acids and bases behave in water: to be able to solve weak acid problems with the Henderson-Hasslebalch equation. How buffers work and why we need them How water participates in biochemical reactions

Structure Review

ICE Review

Common H-bonds in Biochemistry Review

Some Biologically Important H-bonds The last two are important in protein and nucleic acid structure.

H-bond Strength and Alignment Review

Importance of Hydrogen Bonds Source of unique properties of water Structure and function of proteins Structure and function of DNA Structure and function of polysaccharides Binding of substrates to enzymes Binding of hormones to receptors Matching of mRNA and tRNA “I believe that as the methods of structural chemistry are further applied to physiological problems, it will be found that the significance of the hydrogen bond for physiology is greater than that of any other single structural feature.” –Linus Pauling, The Nature of the Chemical Bond, 1939

Water as a Solvent Water is a good solvent for charged and polar substances amino acids and peptides small alcohols carbohydrates Water is a poor solvent for nonpolar substances nonpolar gases aromatic moieties aliphatic chains

Polarity (or not) of some common biochemicals

Solvation and Hydration Spheres The cartoon only shows waters of hydration being one layer thick. But in reality it is more for a couple of layers.

Review

Flickering Clusters and Clathrate Cages What is important is that the flickering cluster life time is in nano-seconds, so it’s really “flickering”. The clathrate water around a non polar surface last longer, but with no more bond energy than flickering clusters.

The Hydrophobic Effect Refers to the association or folding of nonpolar molecules in the aqueous solution Is one of the main factors behind: protein folding protein-protein association formation of lipid micelles binding of steroid hormones to their receptors Does not arise because of some attractive direct force between two nonpolar molecules

Fatty acids in water begin to form micells which are fairly stable Fatty acids in water begin to form micells which are fairly stable. This can take time, but in the lab we can make this happen faster in a sonicator….adding sound energy to facilitate fatty acids movement until they find others and the hydrophobic interactions take over.

Substrates Must Displace Water to Bind Enzymes  Substrates usually bind into pockets rather than slight indents, so the waters interacting with the substrate must be pushed aside as the substrate enters the pocket (or clefts which we will do in Chapter 6 with Chymotrypsin).

Approximate Bond Strength, kJ/mole 12-30 20 <40 0.4 – 4.0 Distance,nm 0.3 0.25 - 0.2 The weak bonds are Exceptionally Important !

Water Bound to Hemoglobin Each red dot is a water molecule. Hb purified from water Hb with Water Removed

Proton Hop and Hydronium

Water Bound in a Protein Channel (Cytochrome f) Facilitates Proton Hopping – see later in Photosynthesis Cytochrome f is in cholorplasts. You are familiar with cytochromes a, b and c in the mitochondria. Proton hopping by Hydroniums.

Solutes decrease vapor pressure, review.

Osmotic Pressure Review

Cell Response to Osmotic Pressures

Plants Use Osmotic Pressure Venus fly-trap uses osmotic pressure to cause movement and trap the insect.

Plants Use Osmotic Pressure Review Protection Against Wind

Ionization of Water Keq = [H+][OH-] / [H2O] = 1.8 x 10-16 M Concentration of water - one liter = 1,000g Mole Wt Water = 18.015 [H2O] = 55.5 M Kw = [H+][OH-] = Keq x [H2O] = 1 x 10-14 M2 for pure water [H+] = [OH-] so, [H+] = 10-7 M pH is negative log [H+] , for pure water = 7.0 Review

Most life and biochemistry is near neutral and into the acid Most life and biochemistry is near neutral and into the acid. What is the pH inside a cell? Of the stomach?

pH = pKa + log ( [A-] / [HA] ) Weak Acids HA ↔ H+ + A- K e = [H+][A-] / [HA] = Ka Henderson-Hasselbalch Equation Rearranges Ka pH = pKa + log ( [A-] / [HA] ) when pKa = pH … [A-] = [HA] Weak acids try to hold on to the proton…dependent on pH. Know this well, we will be doing problems with the Henderson Hasselbalch equation which you had in General Chemistry. What about strong acids: what happens when HCl for example is added to water? All this is review !

pKa’s speak to the strength of the weak acids pKa’s speak to the strength of the weak acids. Check out the difference in carboxyl pka’s. Phosphate has three pKa’s keep these in mind, we will use it later in the course.

A

Acid Base Tirations: Note that acetate has two forms: Associated (HA)  pKa (half associated, half dissociated)  Dissociated (A-).

Weak acids have different pKas FIGURE 2–18 Comparison of the titration curves of three weak acids. Shown here are the titration curves for CH3COOH, H2PO-4, and NH+4 . The predominant ionic forms at designated points in the titration are given in boxes. The regions of buffering capacity are indicated at the right. Conjugate acid-base pairs are effective buffers between approximately 10% and 90% neutralization of the proton-donor species.

The imidazol group of the amino acid Histidine is a weak acid (one of the nitrogens, is it the imid or azole?).

Enzymes have pH optima Related to their Function

Review

Water as a Reactant Most polymerizations are dehydrations and depolymerization reactions (Ex: digestive enzymes) are hydrations.

Pretty Picture

Problem 18 in Chapter 2 1 liter of 0.1 M glycine. a. what pH’s is glycine a good buffer due to its amino group:

Problem 18 in Chapter 2 1 liter of 0.1 M glycine. a. What pH is glycine a good buffer due to its amino group: NH3+ Glycine = CH2-COO- pKa’s = 2.34 and 9.6 So it would be good +/- 1.0 from each pKa which would be from 1.3 to 3.3 and 8.6 to 10.6 for the amino group. The buffering region is around each pKa. Buffering capacity is dependent on pH: at pH 1.3 glycine is not a good buffer of further acid addition, but is of further hydroxide addition. What about at pH 2.3 and 9.6?

Problem 18 in Chapter 2 I liter of 0.1 M glycine. NH3+ Glycine = CH2-COO- pKa’s = 2.34 and 9.6 I liter of 0.1 M glycine. b. in a 0.1 M solution, pH 9.0 what fraction has the amino group as –NH3+ ? Example of a Clicker Question: R-NH3+ is HA A- H2O H+ OH-

Problem 18 in Chapter 2 I liter of 0.1 M glycine. NH3+ Glycine = CH2-COO- pKa’s = 2.34 and 9.6 I liter of 0.1 M glycine. b. in a 0.1 M solution, pH 9.0 what fraction has the amino group as –NH3+? pH = pKa + log A/HA 9.0 = 9.6 + log A/HA log A/HA = -0.6  A/HA = 0.25  0.25HA = A HA + A = 0.1M so HA + 0.25HA = 0.1 M :: 1.25HA = 0.1M so HA = 0.08 M…and that is 80% of 0.1M so  not asked: A = 0.02 M or 20%

Problem 18 in Chapter 2 I liter of 0.1 M glycine. NH3+ Glycine = CH2-COO- pKa’s = 2.34 and 9.6 I liter of 0.1 M glycine. c. How much 5M KOH is needed to change pH from 9 to 10 for 1 Liter of 0.1M glycine?

Problem 18 in Chapter 2 I liter of 0.1 M glycine. NH3+ Glycine = CH2-COO- pKa’s = 2.34 and 9.6 I liter of 0.1 M glycine. c. How much 5M KOH is needed to change pH from 9 to 10 for 1 Liter of 0.1M glycine? pH = pKa + log A/HA 10 = 9.6 + log A/HA so: log A/HA = 0.4 thus A/HA = 2.5  2.5HA = A HA + A = 0.1 M  HA + 2.5 HA = 0.1 M  3.5HA= 0.1M so HA at pH 10 = 0.029 moles/L from pH 9 HA is converted to A by adding OH-, that is HA is lowered from 0.08M to 0.029M or a change of 0.051 moles 0.051 moles/5 moles/L = 0.01 L  10 ml of 5M KOH

Problem 18 in Chapter 2 I liter of 0.1 M glycine. NH3+ Glycine = CH2-COO- pKa’s = 2.34 and 9.6 I liter of 0.1 M glycine. d. When 99% of glycine is in its –NH3+ form, what is the pH of solution due to it’s amino group? (functionally reworded from the text) pH = pKa + log A/HA so this is easy HA dominates, so it will be on the acid side of the pKa. A is only 1% or 0.01 so the log of A/HA ≈ -2 thus pH = 9.6 – 2 = or 7.6

Things to Know and Do Before Class General Chemical Properties of Water. pH definition and what it means+how to calculate it. Strong vs Weak Acids. Henderson-Hasselbalch Equation and how to do calculations with it. Weak bonds and their relative bond strength. Make sure you are able to do EOC Problems calculating pH (2-5, 8), pH affects solubility (14) and uptake of aspirin (15) and rest on buffers (11): They are part of Class Clicker Questions and Case Study (aspirin).