CHAPTER 2 - WATER & PH

water

_ is the predominant chemical component of living organisms.

tetrahedron

Water molecule is an irregular, slightly skewed _ with oxygen at its center

polar

Water is _ because oxygen is more electronegative than hydrogen

105

The _ angle between the two hydrogen atoms differs slightly from the ideal tetrahedral angle, 109.5°.

hydrogen bond

slight positive H + slight negative O, N, F

covalent bond

bond in water:

positive

hydrogen partial _ charge: The strongly electronegative oxygen atom in a water molecule attracts electrons away from the hydrogen nuclei

negative

hydrogen partial _ charge: two unshared electron pairs of oxygen

dipole

asymmetric charge distribution

high dielectric constant

Water’s strong dipole is responsible for its _

dipole, dielectric constant

Its strong _ and high _ enable water to dissolve large quantities of charged compounds such as salts.

hydrogen bond

A partially unshielded hydrogen nucleus covalently bound to an electron-withdrawing oxygen or nitrogen atom can interact with an unshared electron pair on another oxygen or nitrogen atom to form a _.

3.5

On average, each molecule in liquid water associates through hydrogen bonds with _ others

hydrogen bond

These bonds are both relatively weak and transient, with a half-life of a few picoseconds. (because they break and reform constantly)

18

The exceptional capacity of this relatively small, _ g/mol, molecule to form hydrogen bonds profoundly influences the physical properties of water and accounts for its high viscosity, surface tension, and boiling point.

high viscosity

water resists flowing more

high surface tension

water forms droplets and insects can walk on its surface

high boiling point

water must absorb a lot of heat before it boils because many hydrogen bonds must be broken

water

_ can serve simultaneously both as a hydrogen donor and as a hydrogen acceptor.

hydrogen donor

hydrogen attached to oxygen or nitrogen that it can "share" in a hydrogen bond

hydrogen acceptor

lone pair of electrons that can attract a hydrogen

covalent bond

The _ is the strongest force that holds molecules together

noncovalent

_ forces, while of lesser magnitude, predominate in stabilizing the folding of the polypeptides and other macromolecules into the complex three-dimensional conformations essential to their functional competence as well as the association of biomolecules into multicomponent complexes

polar

hydrophilic, charged

nonpolar

hydrophobic, uncharged

amphipathic

Most biomolecules are _; that is, they possess regions rich in charged or polar functional groups as well as regions with hydrophobic character.

hydrophobic

Proteins tend to fold with the R-groups of amino acids with _ side chains in the interior

amino acids

__ with charged or polar amino acid side chains (eg, arginine, glutamate, serine) generally are present on the surface in contact with water.

folding

This pattern minimizes energetically unfavorable contacts between water and hydrophobic groups. (water would have to rearrange around them, energetically unfavorable, requires more energy and less stable)

folding

It also maximizes the opportunities for the formation of energetically favorable charge-dipole, dipole-dipole, and hydrogen bonding interactions between polar groups on the biomolecule and water.

hydrophobic interaction

_ refers to the tendency of nonpolar compounds to self-associate (group together) in an aqueous environment.

water molecules

Self-association minimizes the disruption of energetically favorable interactions between and is therefore driven by the surrounding _. (not by a "hydrophobic bond", but because water pushes them together)

structure

While the hydrogen atoms of nonpolar groups such as the methylene groups of hydrocarbons do not form hydrogen bonds, they do affect the _ of the water with which they are in contact.

number of orientations

Water molecules adjacent to a hydrophobic group are restricted in the _ (degrees of freedom) that permit them to participate in the maximum number of energetically favorable hydrogen bonds. (low entropy - forced into an order of arrangement)

entropy

disorder or randomness

enthalpy

energy stored in interactions like hydrogen bonds

entropy

Maximal formation of multiple hydrogen bonds, which maximizes enthalpy, can be maintained only by increasing the order of the adjacent water molecules, with an accompanying decrease in _.

second law of thermodynamics

systems naturally move toward a state with lower free energy

enthalpy, entropy

It follows from the second law of thermodynamics that the optimal free energy of a hydrocarbon-water mixture is a function of both maximal _ (from hydrogen bonding) and highest _ (maximum degrees of freedom)

droplets

non-polar molecules tend to form _ that minimize exposed surface area and reduce the number of water molecules whose motional freedom becomes restricted (water moves freely & less hydrogen bonds are disrupted) (explains why proteins fold and the structure of the cell membrane)

salt bridges

Electrostatic interactions between oppositely charged groups within or between biomolecules are termed _

salt bridges

_ are comparable in strength to hydrogen bonds but act over larger distances. 

salt bridges

_ often facilitate the binding of charged molecules and ions to proteins and nucleic acids.

van der waals forces

arise from attractions between transient dipoles generated by the rapid movement of electrons in all neutral atoms. (temporary dipoles from moving electrons)

van der waals forces

Significantly weaker than hydrogen bonds but potentially extremely numerous, _ decrease as the sixth power of the distance separating atoms. Thus, they act over very short distances, typically 2 to 4 Å.

dna double helix

The _ illustrates the contribution of multiple forces to the structure of biomolecules.

covalent bond

bond between 2 DNA strands

hydrogen bond

bond between nucleotide bases (hydrophobic)

van der waals forces

bond between stacked purine and pyrimidine bases

dna double helix

The _ presents the charged phosphate groups and polar hydroxyl groups from the ribose sugars of the DNA backbone to water while burying the relatively hydrophobic nucleotide bases inside.

nucleophiles

donate electrons to attack other molecules during chemical reactions (electron rich)

nucleophiles

nucleus loving, has extra electrons, lone pair from O

electrophiles

electron poor, accepts electrons

nucleophiles

oxygen atoms of phosphates, alcohols, and carboxylic acids; the sulfur of thiols; and the nitrogen atoms of amines and of the imidazole ring of histidine

electrophiles

carbonyl carbons in amides, esters, aldehydes, and ketones and the phosphorus atoms of phosphoesters.

hydrolysis

Nucleophilic attack by water typically results in the cleavage of the amide, glycoside, or ester bonds that hold biopolymers together. This process is termed _.

hydrolysis

breaking chemical bonds by adding water (thermodynamically favored reaction)

condensed

opposite of hydrolysis, cell removes water

water

when monomer units such as amino acids or monosaccha- rides are joined or condensed together to form biopolymers, such as proteins or starch, _ is a product.

enzymes

_ accelerate the rate of hydrolytic and other chemical reactions when needed

proteases

_ catalyze the hydrolysis of proteins into their component amino acids

nucleases

_ catalyze the hydrolysis of the phosphoester bonds in DNA and RNA

group transfer

transfer from donor to acceptor

group transfer

transfer of a chemical group G from a donor D to an acceptor A to form an acceptor group complex, A—G

group transfer

_ purpose: to build larger molecules, to release energy, to activate molecules, to break down molecules

enzymes

many of the group transfer reactions responsible for the biosynthesis of macromolecules are, in and of themselves, thermodynamically unfavored... solution --> _

hydronium ion, hydroxide ion

Since water can act both as an acid and as a base (amphoteric), its ionization may be represented as an intermolecular proton transfer that forms a _ and a _

acid

donates H

base

accepts H

probability

An individual hydrogen or oxygen cannot be stated to be present as an ion or as part of a water molecule. At one instant it is an ion; an instant later it is part of a water molecule. Individual ions or molecules are therefore not considered. We refer instead to the _ that at any instant in time, a given hydrogen will be present as an ion or as part of a water molecule.

1, 99

a hydrogen atom has _ chance in 100 of being an ion and _ chances out of 100 of being part of a water molecule.

dissociation constant

equilibrium tendency of the reaction

55.56

Pure water thus is _ molar

ion product

actual concentrations of H+ and OH- in water

pH

measure of how acidic or basic a solution is

pH

introduced by Sörensen. negative log of the hydrogen ion concentration

basic

7 above

acidic

7 below

high

Low pH values correspond to _ concentrations of H+

low

high pH values correspond to _ concentrations of H+

acid

proton donors

base

proton acceptors

strong acid

_ (eg, HCl, H2SO4) completely dissociate into anions and protons even in strongly acidic solutions (low pH).

weak acid

_ dissociate only partially in acidic solutions

strong base

_ (eg, KOH, NaOH), but not weak bases like Ca(OH)2, are completely dissociated even at high pH

acid

_ protonated species, conjugate base: unprotonated species

base

_ deprotonated form, conjugate acid: protonated form 

pKa

The stronger the acid, the lower is its _ value

pKa

_ is used to express the relative strengths of both weak acids and weak bases using a single, unified scale

conjugate acid

the relative strengths of bases are expressed in terms of the pKa of their _

equal

the pKa of an acid group is the pH at which the protonated and unprotonated species are present at _ concentrations.

Henderson-Hasselbalch Equation

The _ Describes the Behavior of Weak Acids & Buffers

buffering

Solutions of weak acids or bases and their conjugates exhibit _, the ability to resist a change in pH following addition of strong acid or base.

pKa

The _ of a functional group is also profoundly influenced by the surrounding medium. The medium may either raise or lower the pKa relative to its value in water, depending on whether the undissociated acid or its conjugate base is the charged species.