Chapter 2: Water

Hydrolases

Enzymes that catalyze hydrolysis reactions resulting in a reaction that is almost always exergonic.

pH Optimum

Enzymes typically show maximal catalytic activity at a characteristic pH, called the pH optimum

Dissociation Constant (K_a)

Equilibrium constants for ionization reactions. Stronger acids have larger dissociation constants (K_a's), weaker acids have smaller dissociation constants (K_a's)

Understanding Osmolarity

The effect of solutes on osmolarity depends on the number of dissolved particles, not their mass. A gram of polysaccharide composed of 1,000 glucose units has the same effect on osmolarity as a milligram of glucose

Amphipathic Compounds in Aqueous Solutions

The nonpolar regions of the molecules cluster together to present the smallest hydrophobic area to the aqueous solvent, and the polar regions are arranged to maximize their interactions with the solvent

Ordering of Macromolecules

1. The unique structure of each macromolecule determines its function. 2. Noncovalent interactions play a critical role in the structure and thus the function of macromolecules. 3. The monomeric subunits in polymeric macromolecules occur in specific sequences, representing a form of information upon which the ordered living state depends.

Useful Buffer Range

A buffer has a range of pH's in which it is most useful. *This range is within one pH unit of its pKa. A buffer is most effective at a pH close to its pKa*. Therefore, the slope of each titration curve is much lower near its midpoint than near its wings.

van der Waals Radius

A measure of how close that atom will allow another to approach

Condensation Reaction

A reaction in which the elements of water are eliminated to form a bond. In living organisms, these endergonic reactions are coupled to exergonic hydrolysis reactions to allow them to occur

Neutral pH

A solution is said to be neutral when there are exactly equal concentrations of H^+ and OH^-, as in pure water

Acids and Bases

Acids may be defined as proton donors and bases as proton acceptors

Hydrogen Bonds

An electrostatic attraction between the oxygen atom of one water molecule and the hydrogen of another.

pKa

Analogous to Ph. The stronger the acid, the lower the pKa. The weaker the acid, the higher the pKa.

Buffers

Aqueous systems that tend to resist changes in pH when small amounts of acid (H^+) or base (OH^-) are added. Buffers consist of weak acid and conjugate base or vice versa

Water as Solvent

As an ionic compound dissolves, there is a large increase in entropy. This leads to ionic compounds easily dissolving in water

"Flickering Clusters" of Water Molecules

At any given time, most of the molecules in liquid water are engaged in hydrogen bonding, but the lifetime of each hydrogen bond is just 1 to 20 picoseconds before breaking and re-bonding with another partner or the same one all within 0.1 ps. "Flickering clusters" refers to the short-lived groups of water molecules interlinked by H bonds in liquid water

Using Nonpolar Gases in Biological Systems

Because many biologically important gases are not water soluble, some organisms have water soluble carrier proteins for these gases or convert the gases into an ion to transport it into biological systems.

Nonpolar Gases are Poorly Soluble in Water

Biologically important gases such as CO2, O2, and N2 are nonpolar making them poorly soluble in water. Also, the movement of gas molecules in an aqueous solution is constrained and also constrain the motion of water molecules as well leading to a decrease in entropy. These two reasons are why these gases poorly dissolve in water

Hydrophilic

Compounds that dissolve easily in water

Clathrates

Crystalline compounds or nonpolar solutes and water

pH

Defined by the expression of -log[H^+]. pH greater than 7 are alkaline or basic meaning the concentration of OH^- is greater than that of H^+. Conversely, solutions having a pH less than 7 are acidic

Henderson-Hasselbalch Equation

Describes the shape of the titration curve of any weak acid

Polar Molecules

Dissolve readily in water because they can replace water-water interactions with more energetically favorable water-solute interactions

Hydrophobic

Don't dissolve easily in water but instead dissolve easily in nonpolar solvents such as chloroform and benzene. Lipids and waxes are hydrophobic

Review of Free Energy Change

Free energy change must have negative value for a process to occur spontaneously: ΔG = ΔH - TΔS, where ΔG represents the driving force, ΔH the enthalpy change from making and breaking bonds(energy input or output), and ΔS the change in randomness.

Equilibrium Constant, K

Gives the position of equilibrium of any chemical reaction and is given by products over reactions.

Bond Dissociation Energy of H Bonds

Hydrogen bonds are relatively weak. Those in liquid water have a *bond dissociation energy* of about 23 kJ/mol.

Directionality of Hydrogen Bonding

Hydrogen bonds are strongest when the bonded molecules are oriented to maximize electrostatic interactions, which occurs when the hydrogen atoms and the two atoms that share it are in a straight line. This allows hydrogen bonds to hold two hydrogen-bonded molecules or groups in a specific geometric arrangement.

Buffer Systems in Cells

In cells and living systems, buffer systems are mainly based on *phosphate bicarbonate and the amino acid histidine*

Comparison of Titration Curves

In this image, the acid with the curve highest on the chart is the weakest acid and the one with the lowest curve is the strongest acid

Nonpolar Molecules

Interfere with water-water interactions but are unable to form water-soluble interactions. These molecules tend to cluster together in aqueous solutions

Optimum Buffering Capacity

Optimum buffering capacity occurs when the pH = pKa or when [HA] = [A^-].

Isotonic

Solutions of equal osmolarity. A cell neither gains nor loses water when surrounded by this solution

Micelles

Stable structures of amphipathic compounds in water

Structure of Water Molecule

The H-O-H bond angle is 104.5 degrees, slightly less than the 109.5 degree angle of a perfect tetrahedron because of crowding by the nonbonding orbitals of the oxygen atom

Dissociation of Biomolecules Bound by Noncovalent Bonds

The dissociation of two biomolecules associated noncovalently through multiple weak interactions requires all these interactions to be disrupted at the same time. Because the interactions fluctuate randomly, such simultaneous disruptions are very unlikely.

Common Hydrogen Bonds in Biological Systems

The hydrogen acceptor is usually oxygen or nitrogen; the hydrogen donor is another electronegative atom. Occurs with N-H, O-H, and F-H.

Covalent Character of H-Bond

The hydrogen bond is about 10% covalent due to overlaps in the bonding orbitals and about 90% electrostatic

Finding pKa from Titration Curve

The pKa can be determined experimentally; it is equal to the pH at the midpoint of the titration curve for the weak acid or base. Equal to pH when acid and base parts are equal.

Titration Curve

The plot of pH against the amount of acid/base added(usually base is added). Plot of pH vs. base added reveals pKa of weak acid

Van Der Waals Contact

The point where the van der Waals attraction from transient dipoles exactly balances the repulsive force caused by the electron cloud of each nuclei. Each atom has a characteristic *van der Waals radius*

Hydrolysis Reaction

The reverse of a condensation reaction in which a bond is cleaved accompanied by the addition of the elements of water. Responsible for depolymerization of proteins, carbohydrates, and nucleic acids.

Hydrophobic Interactions

The strength of hydrophobic interactions results from the system's achieving greatest thermodynamic stability by minimizing the number or ordered water molecules required to surround hydrophobic portions of the solute molecules. *Hydrophobic interactions among lipids and between lipids and proteins, are the most important determinants of structure in biological membranes*

Driving Force for Binding of a Polar Substrate to Complementary Polar Surface of an Enzyme

There is an entropy increases as the enzyme displac

Amphipathic

These compounds contain regions that are polar (charged) and regions that are nonpolar (uncharged)

Van't Hoff Equation (Osmotic Pressure)

This pressure, Π, is measured as the force necessary to resist water movement when two different aqueous solutions are separated by a semipermeable membrane (only water can pass through).

Hypertonic

This solution has a higher osmolarity than the cytosol. The cell will shrink as water flows out of the cell

Hypotonic

This solution has a lower osmolarity than the cytosol. The cell will swell as the water enters the cell from the outside.

Colligative Properties

Vapor pressure, boiling point, melting point, and osmotic pressure. The effect of solute concentration is dependent only on the number of solute particles in a given amount of water

Abundance of Water

Water is the most abundant substance in living systems, making up 70% or more of the weight of most organisms

Osmosis

Water movement across a semipermeable membrane driven by differences in osmotic pressure. An important factor in the life of most cells which have a cell membrane which acts very much like a semipermeable membrane

Van Der Waals Interactions

Weak attractions between any two molecules created by random variations in the positions of the electrons around one nucleus creates a transient electric dipole and induces one in the other nearby atom