Biochemistry 1 Chapter 2 Water Study Guide PDF

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This is a study guide for chapter 2. This contains details about the concepts covered on the exam. This contains details about the concepts covered on the exam. This is composed of information from the book as a supplement as well as from the lectures as the main focus. The exam is based of the lect...

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Biochemistry 1 Chapter 2: Water Lecture 2 Water has unusual properties than most other solvents because they have strong intermolecular attraction for eachother. This is revealed by the structure of water. Water is a Polar Molecule

Structure of water molecule. The oxygen atom’s sp3 orbitals are arranged tetrahedrally. Two orbitals contain nonbonding electron pairs. A hydrogen bond in water. The strength of the interaction is maximal when the O-H covalent bond (460 kJ/mole) of one molecule points directly toward the lone-pair electron cloud of the other. H-bonding is a lot weaker than covalent bonding Structure of Liquid water forms three to seven-membered rings of hydrogen-bonded molecules, whereas ice forms six-membered rings. Liquid molecules are disorganized and are in continuous motion. Hydrogen bonds are DISTORTED. Structure of Ice. Each water molecule interacts tetrahedrally with four other water molecules. H-bonds are fixed and linear.

Water can form hydrogen bonds with other polar solutes.

In general a hydrogen bond can be represented as D-H××××A, where D_H is a weakly acidic hydrogen donor group such as O-H, N-H, and S-H, and A is a weakly basic acceptor such as O, N, or S. Hydrogen bonding by functional groups- Water forms hydrogen bonds with (a) hydroxyl groups, (b) keto groups, (c) carboxylate ions, and (d) ammonium ions. Water acts as a solvent for polar and ionic molecules The dipoles of surrounding water molecules are oriented according to the charge of the ion. Hydrophobic effectis defined as the tendency of water to MINIMIZE its contacts with hydrophobic molecule. This effect causes hydrophobic solutes to aggregate SPONTANEOUSLY. Transferring a nonpolar molecule to a nonpolar solvent is a spontaneous process. ΔH is positive and ΔS is positive, making –TΔS very large and negative. Entropy is the driving force that makes transfer to nonpolar solvents a spontaneous process where ΔG is negative. But why does entropy decrease for when nonpolar molecules enter water? Orientation of water molecules around a nonpolar solute. In order to maximize their number of hydrogen bonds, water molecules form a cage around the solute. The Free energy for dissolving nonpolar solute in water is unfavorable. Why do nonpolar molecules aggregate in water? The surface are of a nonpolar aggregate is LESS than the sum of the surface areas of the individual nonpolar molecules. Therefore the number of water molecules required to hydrate the

aggregated solute is LESS than the number of water molecules required to hydrate the individually dispersed nonpolar solute. Most biological molecules such as fatty acids are amphipathic. Hydrophobic Effect accounts for how amphipathic molecules for micelles, and cell membranes are formed. Model of a micelle. Figure shows of 20 molecules of octyl glucoside. Fatty acids pack in a more disorganized fashion that buries most of the hydrophobic groups and leaves the polar groups exposed. The hydrophobic tails are exposed on the micelle surface at any given instant. Macromolecular structures are determined by the collective influence of many individually weak interactions. Water moves by osmosis and solutes move by diffusion. Concentration of solutes affect water’s colligative properties (vapor pressure, boiling point, melting point, freezing point and osmotic pressure) of water •

Solutes depress (lower) the freezing point, making it more difficult for water molecules to crystallize as ice.

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Solutes make it more difficult for water molecules to escape from solution into gas phase.

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Solutes increase the boiling point for water.

Osmosis is also dependent on the concentration of the solute. Osmosis is the movement of SOLVENT from a region of high to region low concentration. (c) Osmotic pressure is the pressure that must be applied to the solution to prevent the inward flow of water and is proportional to the concentration of the solute. How do cells minimize osmotic influx of water and cell lysis?

Chemical Properties of water •

Water Ionizes to form Hydronium ions and hydroxide ions, but the reaction is expressed as H2O

H+ + OH-.

Proton jumping- Proton jumps occur more rapidly than direct molecular migration, accounting for the observed high ionic mobilities of hydronium ions in aqueous solutions. Water is acting as a base and acid. •

What is the Ionization constant (Kw) for water when experimentally the Keq determined by electrical conductivity for pure water is 1.8 x 10-16M at room temp.?

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Determination of [H+] and [OH-] from Kw.

Reciprocal relationship of pH and the concentrations of H+ and OH- of water. Solutions with relatively more H+ are acidic (pH7), and solutions in which [H+]=[OH-]=10-7 are neutral (pH=7). Note the logarithmic scale for ion concentration. Two solutions that differ in pH by 1 pH unit means that one solution has ten times the H+ concentration of the other. Acids and Bases Alter the pH. •

Proteins and nucleic acids have functional groups such as carboxyl groups and amino groups that act as weak acids and weak bases. The ionization of these groups influence the pH of the medium and in turn their structures and reactivities are influenced by the surrounding pH.

The strength of an acid is defined by its dissociation constant, Ka. It allows us to determine how well the acid is able to ionize and transfer a proton to water.

Shape of a titration curve is described by the Henderson-Hasselbach equation. Titration curves for acetic acid, phosphate, and ammonia. Titration curve reveals pKa of the acids. Although curves have similar shapes, they are vertically shifted along the pH axis, which means these acids have different pKas. Rank the pKas of these weak acids. The pH of a solution is determined by the relative concentrations of acids and bases using the Hendersson-Hasselbach equation Sample Calculation using the Henderson-Hasselbach equation •

Calculate the pH of a 1 L solution containing 0.1 M formic acid and 0.1 M sodium formate before and after the addition of 1 ml of 5 M NaOH. How much would the pH change if the NaOH were added to 1 L of pure water?

Titration of a polyprotic acid, that have multiple ionizable groups and therefore multiple pKas. The first and second equivalence points for titration of H3PO4 occur at the steepest parts of the curve. The pH at the midpoint of each stage provides the pK value of the corresponding ionization. Buffers-mixtures of weak acid and their conjugate base resist changes in pH. Examples of biological buffers are histidine, H2CO32-/HCO3Dialysis- technique used for separating large molecules from small molecules. A concentrated solution is separated from a large volume of solvent by a dialysis membrane. Only small molecules can diffuse through the pores in the membrane. At equilibrium, the concentrations of small molecules are nearly the same on either side of the membrane, whereas the macromolecules remain inside the dialysis bag....