p.1
Ionization behavior of water, weak acids, and weak bases
What topics are reviewed in terms of equilibrium constants, pH, and titration curves?
The ionization of water, weak acids, and weak bases.
p.4
Role of hydrogen bonds in giving water its unusual properties
What unusual properties of water are a consequence of attractions between adjacent water molecules?
Higher melting point, boiling point, and heat of vaporization compared to most other common solvents.
p.12
Role of hydrogen bonds in giving water its unusual properties
What is the optimal geometric arrangement for hydrogen bonds?
When the acceptor atom is in line with the covalent bond between the donor atom and hydrogen.
p.2
Buffering against pH changes in biological systems
What makes a buffer that resists changes in pH in response to added acid?
An aqueous solution of a weak acid and its salt.
p.23
Intermolecular interactions in aqueous systems
What is the length of a carbon-carbon single bond?
About 0.154 nm (0.077 nm + 0.077 nm).
p.21
Solubility of polar and nonpolar biomolecules in water
What is the effect of clustering fatty acid molecules in micelles on the hydrophobic surface area exposed to water?
It exposes the smallest possible hydrophobic surface area to the water, requiring fewer water molecules in the shell of ordered water.
p.21
Hydrogen bonding in water
How does hydrogen bonding between water and polar solutes affect water molecules?
It causes an ordering of water molecules, but the energetic effect is less significant than with nonpolar solutes.
p.18
Intermolecular interactions in aqueous systems
Why are nonpolar compounds like benzene and hexane hydrophobic?
They are unable to undergo energetically favorable interactions with water molecules and interfere with hydrogen bonding among water molecules.
p.1
Role of hydrogen bonds in giving water its unusual properties
What are the attractive forces between water molecules and the slight tendency of water to ionize crucial for?
The structure and function of biomolecules.
p.4
Intermolecular interactions in aqueous systems
What types of interactions collectively have a significant influence on the three-dimensional structures of proteins, nucleic acids, polysaccharides, and membrane lipids?
Hydrogen bonds, ionic interactions, hydrophobic interactions, and van der Waals interactions.
p.14
Intermolecular interactions in aqueous systems
How does water interact with solute-solute hydrogen bonds in biomolecules?
Water replaces solute-solute hydrogen bonds with solute-water hydrogen bonds, screening the electrostatic interactions between solute molecules.
p.15
Importance of water as a solvent in living systems
What happens to the NaCl crystal lattice when it is dissolved in water?
It is disrupted as water molecules cluster about the Cl- and Na+ ions.
p.6
Role of hydrogen bonds in giving water its unusual properties
What is the nature of hydrogen bonds in terms of covalency and electrostatics?
Hydrogen bonds are about 10% covalent due to overlaps in the bonding orbitals and about 90% electrostatic.
p.16
Intermolecular interactions in aqueous systems
What determines the interaction of two polar moieties in biomolecules?
The highly localized dielectric constant, such as in a hydrophobic pocket of a protein
p.10
Intermolecular interactions in aqueous systems
What must be the value of the free-energy change (ΔG) for a process to occur spontaneously?
ΔG must have a negative value.
p.22
Intermolecular interactions in aqueous systems
What happens to electron clouds as two nuclei draw closer in van der Waals interactions?
Their electron clouds begin to repel each other, and at the point where net attraction is maximal, the nuclei are said to be at van der Waals contact distance.
p.18
Solubility of polar and nonpolar biomolecules in water
What happens when water is mixed with benzene or hexane?
Two phases form; neither liquid is soluble in the other.
p.5
Electron sharing and electric dipoles in water molecules
How does each hydrogen atom in a water molecule interact with the oxygen atom?
Each hydrogen atom shares an electron pair with the central oxygen atom.
p.12
Role of hydrogen bonds in giving water its unusual properties
What does the optimal arrangement of hydrogen bonds achieve?
It puts the positive charge of the hydrogen ion directly between the two partial negative charges.
p.16
Solubility of polar and nonpolar biomolecules in water
What is largely responsible for the ease of dissolving salts such as NaCl in water?
The increase in entropy (randomness) of the system
p.10
Intermolecular interactions in aqueous systems
What is the equation for the free-energy change (ΔG)?
ΔG = ΔH − TΔS, where ΔH represents the enthalpy change and ΔS represents the change in randomness.
p.20
Impact of water's properties on biological molecules
What is a special case of the hydrophobic effect in biological systems?
The formation of lipid bilayers in biological membranes.
p.18
Effect of hydrogen bonding on the structure of biomolecules
What is the effect of adding hydrophobic solutes to water?
It may result in a small gain of enthalpy due to the breaking of hydrogen bonds between water molecules.
p.8
Impact of water's properties on biological molecules
What happens to heat when ice melts or water evaporates?
Heat is taken up by the system.
p.9
Hydrogen bonding in water
Why is ice less dense than liquid water?
The crystal lattice structure of ice makes it less dense than liquid water.
p.14
Importance of water as a solvent in living systems
How does water dissolve salts like NaCl?
By hydrating and stabilizing the Na+ and Cl- ions, weakening the electrostatic interactions between them.
p.3
Buffering against pH changes in biological systems
What pH range is considered life-threatening for humans if blood pH falls outside of it?
Conditions that produce blood pH outside the range of 7.3 to 7.5 are life-threatening in humans.
p.1
Impact of water's properties on biological molecules
How has the course of evolution been shaped?
By the properties of the aqueous medium in which life began.
p.14
Intermolecular interactions in aqueous systems
What is the effect of water on the electrostatic interactions between ions in salts?
Water weakens the electrostatic interactions between ions, counteracting their tendency to associate in a crystalline lattice.
p.2
Intermolecular interactions in aqueous systems
What role do noncovalent interactions play in biomolecular recognition?
Noncovalent interactions, influenced by water's properties as a solvent, are responsible for the strength and specificity of recognition among biomolecules.
p.11
Solubility of polar and nonpolar biomolecules in water
Why do uncharged but polar biomolecules such as sugars dissolve readily in water?
Because of the stabilizing effect of hydrogen bonds between the hydroxyl groups or carbonyl oxygen of the sugar and the polar water molecules.
p.23
Intermolecular interactions in aqueous systems
How are atoms depicted in space-filling molecular models?
In sizes proportional to their van der Waals radii.
p.16
Intermolecular interactions in aqueous systems
Over what distance do ionic attractions or repulsions operate in water?
10 to 40 nm, depending on the electrolyte concentration
p.19
Solubility of polar and nonpolar biomolecules in water
What is the relationship between the surface area of a hydrophobic solute and the entropy decrease?
The number of ordered water molecules, and thus the magnitude of the entropy decrease, is proportional to the surface area of the hydrophobic solute.
p.22
Intermolecular interactions in aqueous systems
What are van der Waals interactions?
Weak interatomic attractions that occur when two uncharged atoms are brought very close together, influencing each other's electron clouds.
p.18
Electron sharing and electric dipoles in water molecules
What do the arrows in the diagram of hydrogen sulfide represent?
The arrows represent electric dipoles; there is a partial negative charge (−) at the head of the arrow and a partial positive charge (+) at the tail.
p.8
Role of hydrogen bonds in giving water its unusual properties
Why is much thermal energy required to destabilize the crystal lattice of ice?
To break a sufficient proportion of hydrogen bonds.
p.7
Role of hydrogen bonds in giving water its unusual properties
What happens when one hydrogen bond breaks in liquid water?
Another hydrogen bond forms, with the same partner or a new one, within 0.1 picoseconds.
p.5
Electron sharing and electric dipoles in water molecules
What dictates the geometry of a water molecule?
The shapes of the outer electron orbitals of the oxygen atom.
p.2
Ionization behavior of water, weak acids, and weak bases
How do the water molecule and its ionization products influence biological systems?
They profoundly influence the structure, self-assembly, and properties of all cellular components, including proteins, nucleic acids, and lipids.
p.2
Effect of hydrogen bonding on the structure of biomolecules
What combined effects powerfully influence the three-dimensional shape and stability of biological molecules and structures?
The combined effects of hydrogen bonds, ionic interactions, and the hydrophobic effect.
p.15
Intermolecular interactions in aqueous systems
Why are ionic interactions between dissolved ions stronger in less polar environments?
Because there is less screening of charges by the nonpolar solvent.
p.16
Solubility of polar and nonpolar biomolecules in water
Why are nonpolar gases like CO2, O2, and N2 poorly soluble in water?
Because their movement from the disordered gas phase into aqueous solution constrains their motion and the motion of water
p.10
Intermolecular interactions in aqueous systems
Why is the increase in entropy (ΔS) important for the melting and evaporation of water?
Because ΔH is positive for melting and evaporation, the increase in entropy (ΔS) makes ΔG negative and drives these changes.
p.20
Intermolecular interactions in aqueous systems
What structure do amphipathic compounds form in aqueous solutions to increase entropy?
They form structures such as micelles and lipid bilayers.
p.17
Solubility of polar and nonpolar biomolecules in water
How is carbon dioxide transported in aqueous solution?
Carbon dioxide forms carbonic acid (H2CO3) and is transported as the bicarbonate ion (HCO3-), either free or bound to hemoglobin.
p.1
Impact of water's properties on biological molecules
What are all aspects of cell structure and function adapted to?
The physical and chemical properties of water.
p.9
Hydrogen bonding in water
Why does ice float on liquid water?
Because ice is less dense than liquid water.
p.14
Solubility of polar and nonpolar biomolecules in water
Which types of biomolecules does water readily dissolve?
Water readily dissolves charged biomolecules, including compounds with ionized carboxylic acids, protonated amines, and phosphate esters or anhydrides.
p.3
Buffering against pH changes in biological systems
At what pH do enzymes that catalyze cellular processes function optimally?
Enzymes have evolved to function optimally at near-neutral (physiological) pH.
p.2
Ionization behavior of water, weak acids, and weak bases
How can the ionization behavior of water and weak acids and bases be represented?
By one or more equilibrium constants.
p.13
Role of hydrogen bonds in giving water its unusual properties
When is the attraction between partial electric charges in a hydrogen bond greatest?
When the three atoms involved in the bond lie in a straight line.
p.15
Intermolecular interactions in aqueous systems
What factors determine the strength (force) of ionic interactions in a solution?
The magnitude of the charges (Q), the distance between the charged groups (r), and the dielectric constant (ε) of the solvent.
p.19
Solubility of polar and nonpolar biomolecules in water
What are micelles?
Stable structures of amphipathic compounds in water, where nonpolar regions cluster together and polar regions interact with water.
p.10
Role of hydrogen bonds in giving water its unusual properties
Why do hydrogen atoms covalently bonded to carbon atoms not participate in hydrogen bonding?
Because carbon is only slightly more electronegative than hydrogen, making the C—H bond only very weakly polar.
p.9
Hydrogen bonding in water
What structure is created by the hydrogen bonds in ice?
A regular crystal lattice.
p.7
Role of hydrogen bonds in giving water its unusual properties
How many hydrogen bonds does each water molecule form in ice?
Four hydrogen bonds, forming a regular lattice structure.
p.14
Solubility of polar and nonpolar biomolecules in water
What functional groups in biomolecules are mentioned as being dissolved by water?
Ionized carboxylic acids (—COO⁻), protonated amines (—NH₃⁺), and phosphate esters or anhydrides.
p.3
Buffering against pH changes in biological systems
How do enzymes that function in intracellular compartments of low or high pH behave?
They show their greatest activity and stability at those pH values.
p.6
Role of hydrogen bonds in giving water its unusual properties
How are hydrogen bonds represented in the book?
Hydrogen bonds are represented by three parallel blue lines.
p.13
Role of hydrogen bonds in giving water its unusual properties
What happens to the strength of a hydrogen bond when the bonded moieties are structurally constrained?
The hydrogen bond is weaker.
p.13
Solubility of polar and nonpolar biomolecules in water
Why are nonpolar solvents like chloroform and benzene poor solvents for polar biomolecules?
Because they are nonpolar and do not dissolve polar biomolecules easily.
p.22
Intermolecular interactions in aqueous systems
What is the effect of substrate binding to an enzyme on ordered water molecules?
Binding of substrate to enzyme releases some of the ordered water molecules.
p.20
Intermolecular interactions in aqueous systems
How do nonpolar regions of molecules achieve thermodynamic stability in aqueous solutions?
By clustering together, minimizing the number of ordered water molecules required to surround hydrophobic portions, and increasing the entropy of the system.
p.18
Buffering against pH changes in biological systems
How do polar or charged solutes like NaCl compensate for lost water-water hydrogen bonds?
By forming new solute-water interactions, resulting in a generally small net change in enthalpy (ΔH).
p.1
Importance of water as a solvent in living systems
Where did the first living organisms on Earth likely arise?
In an aqueous environment.
p.4
Solubility of polar and nonpolar biomolecules in water
Why do polar biomolecules dissolve readily in water?
Because they can replace water-water interactions with energetically favorable water-solute interactions.
p.5
Electron sharing and electric dipoles in water molecules
What is the bond angle in a water molecule?
104.5°, slightly less than the 109.5° of a perfect tetrahedron.
p.12
Role of hydrogen bonds in giving water its unusual properties
What is shown in Figure 2-4?
Some biologically important hydrogen bonds.
p.6
Electron sharing and electric dipoles in water molecules
What charges do the hydrogen and oxygen atoms in a water molecule have?
Hydrogen atoms have localized partial positive charges (δ+), and the oxygen atom has a partial negative charge (δ−).
p.6
Effect of hydrogen bonding on the structure of biomolecules
How does the bond dissociation energy of hydrogen bonds in liquid water compare to covalent bonds?
The bond dissociation energy of hydrogen bonds in liquid water is about 23 kJ/mol, compared to 470 kJ/mol for the covalent O—H bond in water or 350 kJ/mol for a covalent C—C bond.
p.13
Importance of water as a solvent in living systems
Why is water considered a polar solvent?
Because it readily dissolves most biomolecules, which are generally charged or polar compounds.
p.19
Solubility of polar and nonpolar biomolecules in water
What is the hydrophobic effect?
The phenomenon where nonpolar regions of molecules cluster together to minimize hydrophobic area exposed to water, while polar regions maximize their interaction with water.
p.21
Solubility of polar and nonpolar biomolecules in water
What are amphipathic biomolecules and give examples?
Amphipathic biomolecules have both polar and nonpolar surface regions. Examples include proteins, pigments, certain vitamins, sterols, and phospholipids of membranes.
p.20
Intermolecular interactions in aqueous systems
Why do long-chain fatty acids form highly ordered water molecules around their hydrophobic alkyl chains?
To minimize the number of ordered water molecules required to surround the hydrophobic portions, thereby increasing the entropy of the system.
p.17
Solubility of polar and nonpolar biomolecules in water
Which three gases are polar and dissolve readily in water?
Ammonia (NH3), nitric oxide (NO), and hydrogen sulfide (H2S).
p.4
Solubility of polar and nonpolar biomolecules in water
Why are nonpolar biomolecules poorly soluble in water?
Because they interfere with water-water interactions but are unable to form water-solute interactions.
p.5
Electron sharing and electric dipoles in water molecules
Why is the bond angle in a water molecule slightly less than that of a perfect tetrahedron?
Because of crowding by the nonbonding orbitals of the oxygen atom.
p.12
Role of hydrogen bonds in giving water its unusual properties
What is the significance of the hydrogen bond arrangement in biological molecules?
It helps in holding molecules or groups in a specific geometric arrangement, which is crucial for their function.
p.15
Importance of water as a solvent in living systems
How does water dissolve many crystalline salts?
By hydrating their component ions.
p.11
Solubility of polar and nonpolar biomolecules in water
What is the role of hydrogen bonds in the solubility of biomolecules in water?
Hydrogen bonds stabilize interactions between polar biomolecules and water, enhancing solubility.
p.23
Intermolecular interactions in aqueous systems
Why are atomic radii at the point of bonding shorter than van der Waals radii?
Because the joined atoms are pulled together by the shared electron pair.
p.10
Intermolecular interactions in aqueous systems
What happens to the entropy of the aqueous system during melting or evaporation?
The entropy increases as the highly ordered arrays of water molecules in ice relax into less orderly hydrogen-bonded arrays in liquid water or into the wholly disordered gaseous state.
p.21
Solubility of polar and nonpolar biomolecules in water
What is the hydrophobic effect and its significance in biological membranes?
The hydrophobic effect favors the aggregation of nonpolar regions and is the most important determinant of structure in biological membranes.
p.18
Solubility of polar and nonpolar biomolecules in water
Why do polar molecules dissolve better than nonpolar molecules even at low temperatures?
Polar molecules dissolve far better even at low temperatures than nonpolar molecules at relatively high temperatures.
p.5
Electron sharing and electric dipoles in water molecules
What is the arrangement of the outer-shell electron pairs around the oxygen atom in a water molecule?
A nearly tetrahedral arrangement.
p.11
Effect of hydrogen bonding on the structure of biomolecules
Why does butanol have a relatively high boiling point?
Because it has a polar hydroxyl group and can form intermolecular hydrogen bonds.
p.6
Role of hydrogen bonds in giving water its unusual properties
What type of bond joins two H2O molecules?
A hydrogen bond joins two H2O molecules.
p.10
Intermolecular interactions in aqueous systems
Why do the melting of ice and the evaporation of water occur spontaneously at room temperature?
Because the tendency of water molecules to associate through hydrogen bonds is outweighed by the energetic push toward randomness.
p.22
Intermolecular interactions in aqueous systems
How are transient electric dipoles formed in van der Waals interactions?
Random variations in the positions of electrons around one nucleus may create a transient electric dipole, inducing a transient, opposite electric dipole in a nearby atom.
p.9
Hydrogen bonding in water
How many hydrogen bonds does each water molecule form on average in liquid water at room temperature and atmospheric pressure?
Each water molecule hydrogen-bonds with an average of 3.4 other water molecules.
p.4
Role of hydrogen bonds in giving water its unusual properties
What causes liquid water to have great internal cohesion?
Attractions between adjacent water molecules.
p.3
Buffering against pH changes in biological systems
Why are biological systems buffered?
To maintain a narrow pH range in which their macromolecules retain their functional structure, which depends on their ionization state.
p.23
Intermolecular interactions in aqueous systems
What is the van der Waals radius?
It is a measure of how close an atom will allow another to approach.
p.15
Electron sharing and electric dipoles in water molecules
What does the dielectric constant of a solvent reflect?
The number of dipoles in the solvent.
p.19
Intermolecular interactions in aqueous systems
How do water molecules behave around a nonpolar solute?
They form a highly ordered cagelike shell to maximize solvent-solvent hydrogen bonding.
p.21
Solubility of polar and nonpolar biomolecules in water
What stabilizes the micelle structure formed by fatty acid molecules?
The entropy gained by freeing immobilized water molecules stabilizes the micelle.
p.20
Intermolecular interactions in aqueous systems
What happens to the entropy of the system when nonpolar regions of molecules cluster together?
The entropy of the system increases.
p.17
Solubility of polar and nonpolar biomolecules in water
Why are nonpolar gases poorly soluble in water?
The nonpolar nature of these gases and the decrease in entropy when they enter solution make them very poorly soluble in water.
p.9
Hydrogen bonding in water
How many hydrogen bonds does each water molecule form in ice?
Each water molecule forms four hydrogen bonds in ice.
p.5
Electron sharing and electric dipoles in water molecules
What causes the intermolecular attractions in water molecules?
The electron structure of the H₂O molecule.
p.12
Role of hydrogen bonds in giving water its unusual properties
When are hydrogen bonds strongest?
When the bonded molecules are oriented to maximize electrostatic interaction, with the hydrogen atom and the two atoms that share it in a straight line.
p.2
Importance of water as a solvent in living systems
How have the solvent properties of water shaped the evolution of living things?
Most small intermediates of metabolism, as well as nucleic acids and proteins, are soluble in water. Lipid bilayers, the likely forerunners of biological membranes, form spontaneously in water and are stabilized by their interaction with it.
p.11
Solubility of polar and nonpolar biomolecules in water
Which types of compounds tend to be soluble in water due to hydrogen bonding?
Alcohols, aldehydes, ketones, and compounds containing N—H bonds.
p.15
Importance of water as a solvent in living systems
Why is water effective in screening electrostatic interactions between dissolved ions?
Because it has a high dielectric constant.
p.19
Solubility of polar and nonpolar biomolecules in water
What happens to the entropy when hydrophobic compounds dissolve in water?
There is a measurable decrease in entropy.
p.22
Intermolecular interactions in aqueous systems
What happens to water molecules when an enzyme and substrate are separate?
Both enzyme and substrate force neighboring water molecules into an ordered shell.
p.21
Effect of hydrogen bonding on the structure of biomolecules
How does the hydrophobic effect contribute to the stability of protein structures?
The aggregation of nonpolar amino acids in protein interiors, driven by the hydrophobic effect, stabilizes the three-dimensional structures of proteins.
p.4
Role of hydrogen bonds in giving water its unusual properties
What provides the cohesive forces that make water a liquid at room temperature and a crystalline solid at cold temperatures?
Hydrogen bonds between water molecules.
p.12
Role of hydrogen bonds in giving water its unusual properties
Why are hydrogen bonds highly directional?
Because they are capable of holding two hydrogen-bonded molecules or groups in a specific geometric arrangement.
p.13
Effect of hydrogen bonding on the structure of biomolecules
What property of hydrogen bonds confers precise three-dimensional structures on protein and nucleic acid molecules?
The presence of many intramolecular hydrogen bonds.
p.6
Electron sharing and electric dipoles in water molecules
Why is oxygen more electronegative than hydrogen in a water molecule?
The oxygen nucleus attracts electrons more strongly than the hydrogen nucleus (a proton), making oxygen more electronegative.
p.19
Solubility of polar and nonpolar biomolecules in water
What is the free-energy change (ΔG) for dissolving a nonpolar solute in water?
ΔG is positive, indicating an unfavorable process.
p.22
Intermolecular interactions in aqueous systems
How does the release of ordered water molecules affect entropy during enzyme-substrate complex formation?
The release of ordered water molecules increases entropy, providing a thermodynamic push toward formation of the enzyme-substrate complex.
p.20
Intermolecular interactions in aqueous systems
What is the role of ordered water molecules in the stability of nonpolar regions in aqueous solutions?
Ordered water molecules surround hydrophobic portions of solute molecules, and clustering minimizes the number of these ordered water molecules.
p.17
Solubility of polar and nonpolar biomolecules in water
What role do water-soluble carrier proteins like hemoglobin and myoglobin play?
They facilitate the transport of oxygen.
