p.19
Noncovalent Interactions
Why is reversible ionization crucial to the role of water in cellular function?
Because it allows for the expression of the extent of ionization of water in quantitative terms.
p.3
Noncovalent Interactions
What is the effect of the formation of noncovalent associations on the free energy of the system?
It contributes to a net decrease in the free energy of the system.
p.20
Noncovalent Interactions
How can the equilibrium constant for a given reaction at a given temperature be calculated?
If the equilibrium concentrations of all its reactants and products are known.
How many water molecules are hydrogen-bonded in the proton channel of cytochrome f?
Five water molecules are hydrogen-bonded to each other and to functional groups of the protein.
What happens when weak bases are dissolved in water?
They consume H⁺ by becoming protonated.
p.10
Biological Macromolecules
What happens to a cell in a hypertonic solution?
Water moves out and the cell shrinks.
What is the effect of NaCl on osmotic pressure compared to glucose?
NaCl, which dissociates in solution, has an effect on osmotic pressure that is twice that of an equal number of moles of a nondissociating solute such as glucose.
p.12
Noncovalent Interactions
What is the purpose of finding a concentration of sucrose in the extracting solution when isolating lysosomes?
To give an osmotic strength equal to that produced by the KCl and NaCl in the lysosomes, preventing swelling and lysis.
p.11
Noncovalent Interactions
What contributes to the osmolarity of blood plasma in multicellular animals?
The high concentration of albumin and other proteins.
p.1
Noncovalent Interactions
What is the relationship between thermal energy and weak interactions in aqueous solvent at 25°C?
The available thermal energy can be of the same order of magnitude as the strength of these weak interactions.
p.1
Noncovalent Interactions
How does the strength of noncovalent interactions compare to covalent bonds?
Noncovalent interactions are much weaker than covalent bonds.
How are interactions driven by the hydrophobic effect affected by a highly polar solvent?
They are substantially strengthened by a highly polar solvent.
p.8
Noncovalent Interactions
What occurs at equilibrium during osmosis?
The force of gravity operating on the solution in the tube exactly balances the tendency of water to move into the tube.
p.19
Noncovalent Interactions
What should the concentration terms be in nonideal solutions?
The activities, or effective concentrations, of each species.
What factors influence the strength of ionic interactions and hydrogen bonds?
The polarity of the solvent and the alignment of the hydrogen-bonded atoms.
What are the two types of hydrogen bonds mentioned?
Between neutral groups and between peptide bonds.
What did Linus Pauling suggest about the significance of hydrogen bonds for physiology?
He suggested that the significance of the hydrogen bond for physiology is greater than that of any other single structural feature.
p.1
Van der Waals Interactions
How much energy is sufficient to disrupt a mole of typical van der Waals interactions?
As little as 4 kJ of energy is sufficient.
p.13
Biological Macromolecules
What is the value of i for sucrose in the osmotic strength equation?
i_sucrose = 1, because sucrose does not ionize
p.21
Biological Macromolecules
How is the concentration of water in pure water calculated?
By dividing the grams of H2O in 1 L (1000 g/L) by its gram molecular weight (18.015 g/mol)
p.1
Noncovalent Interactions
How much energy is needed to break a mole of C—H bonds?
About 410 kJ of energy is needed.
p.23
Enzyme Substrate Binding
What is the concentration of OH⁻ in a solution with an H⁺ concentration of 1.3 × 10⁻⁴ M?
Not provided in the text.
p.8
Noncovalent Interactions
What is the relationship between osmotic pressure and the height of the solution column?
Osmotic pressure is proportional to the height (h) of the column.
p.20
Noncovalent Interactions
What does the equilibrium constant define for a given chemical reaction at a specified temperature?
The composition of the final equilibrium mixture, regardless of the starting amounts of reactants and products.
Which residues are involved in hydrogen bonding with water molecules in cytochrome f?
The peptide backbone atoms of valine, proline, arginine, and alanine residues, and the side chains of three asparagine and two glutamine residues.
How is the total hydrogen ion concentration from all sources expressed?
As the pH of the solution.
p.5
Macromolecular Structure
How do bound water molecules affect the x-ray diffraction pattern of hemoglobin?
They affect the x-ray diffraction pattern as though they were fixed parts of the protein.
p.12
Noncovalent Interactions
What happens to turgor pressure when a plant cell absorbs water?
The turgor pressure increases, stiffening the cell, the tissue, and the plant body.
p.9
Noncovalent Interactions
What happens to a cell in an isotonic solution?
The cell neither gains nor loses water.
p.14
Macromolecular Structure
Why do cells store carbohydrates as glycogen instead of low molecular weight sugars?
To contain a large mass of glycogen with minimal effect on the osmolarity of the cytosol.
Why are N2, O2, and CO2 poorly soluble in water?
Because they are nonpolar.
p.2
Noncovalent Interactions
What types of noncovalent interactions are continually forming and breaking?
Ionic, hydrophobic, and van der Waals interactions.
p.13
Biological Macromolecules
What does T represent in the osmotic strength equation?
The absolute temperature (Kelvin)
Why is proton hopping faster than true diffusion?
Proton hopping is faster than true diffusion because it involves rapid short 'hops' of protons between hydrogen-bonded water molecules, rather than the slower process of ions moving through the solution.
p.19
Noncovalent Interactions
Are equilibrium constants dimensionless?
Yes, equilibrium constants are dimensionless.
p.6
Macromolecular Function
How is electron flow coupled in cytochrome f?
Electron flow is coupled to the movement of protons across the membrane, likely involving 'proton hopping' through the chain of bound water molecules.
p.10
Biological Macromolecules
What is the effect of extracellular osmolarity on water movement across a plasma membrane?
Water moves across the plasma membrane in the direction that tends to equalize osmolarity outside and inside the cell.
p.7
Noncovalent Interactions
Why are colligative properties called 'colligative'?
Because the effect of solutes on these properties is tied to the concentration of water in solutions, not the chemical properties of the solute.
p.9
Noncovalent Interactions
What is the osmolarity of a solution?
The product of the van’t Hoff factor (i) and the solute’s molar concentration (c).
p.14
Biological Macromolecules
Why are solute concentrations accurate to only one significant figure?
Because of the precision limitations in measurements.
p.4
Noncovalent Interactions
What provides many opportunities for weak interactions in enzymes and receptors?
Their extensive surfaces relative to their substrates or ligands.
What are the two types of ionic interactions?
Attraction and repulsion.
How is pOH defined?
pOH is defined by the expression pOH = -log[OH⁻], analogous to the expression for pH.
What explains the high ionic mobility of H⁺ ions compared to other monovalent cations?
The high ionic mobility of H⁺ ions is explained by proton hopping, which is much faster than the true diffusion experienced by other monovalent cations such as Na⁺ and K⁺.
p.19
Noncovalent Interactions
What is the position of equilibrium of any chemical reaction given by?
Its equilibrium constant, K_eq.
p.21
Biological Macromolecules
What does Kw represent in the context of water's ion product?
Kw represents the ion product of water at 25°C
p.3
Noncovalent Interactions
How does stability, as measured by the equilibrium constant, vary with binding energy?
It varies exponentially with binding energy.
p.5
Noncovalent Interactions
How can bound water molecules be detected in aqueous solutions?
By nuclear magnetic resonance.
How can the ionization of water be measured?
By its electrical conductivity.
p.7
Noncovalent Interactions
What causes water molecules to move from one region to another?
Water molecules tend to move from a region of higher water concentration to one of lower water concentration, in accordance with the tendency in nature for a system to become disordered.
What role does proton hopping likely play in biological systems?
It likely plays a role in biological proton-transfer reactions.
p.4
Noncovalent Interactions
Why do macromolecules exhibit much greater molecular stability than expected?
Due to the cumulative effect of many weak interactions such as hydrogen bonding, ionic interactions, van der Waals forces, and hydrophobic clustering.
What makes water a highly polar molecule?
The very different electronegativities of hydrogen and oxygen.
Why do nonpolar (hydrophobic) compounds dissolve poorly in water?
They cannot hydrogen-bond with the solvent, forcing an energetically unfavorable ordering of water molecules at their hydrophobic surfaces.
p.15
Noncovalent Interactions
What produces osmotic pressure across a semipermeable membrane?
The movement of water to equalize the osmolarity in two compartments separated by the membrane.
What is the hydrophobic effect?
A type of noncovalent interaction where nonpolar molecules aggregate to avoid contact with water.
p.13
Biological Macromolecules
What do c1, c2, and c3 represent in the osmotic strength equation?
The molar concentrations of each solute
p.8
Noncovalent Interactions
Which equation approximates osmotic pressure?
The van't Hoff equation: Π = icRT.
What happens to a water molecule when it acquires a proton during proton hopping?
When a water molecule acquires a proton during proton hopping, it becomes a hydronium ion.
p.19
Noncovalent Interactions
How is the equilibrium constant (K_eq) for a generalized reaction A + B ⇌ C + D defined?
K_eq = ([C]_eq [D]_eq) / ([A]_eq [B]_eq)
p.3
Noncovalent Interactions
How do the cumulative effects of noncovalent interactions compare to covalent bonds?
Individually weak, but cumulatively significant.
What does the pH scale designate?
The H+ and OH- concentrations.
p.6
Macromolecular Function
What is the significance of the iron ion in the heme of cytochrome f?
The iron ion in the heme facilitates electron flow during photosynthesis.
p.5
Macromolecular Function
Why are tightly bound water molecules essential for many proteins?
They are essential to the function of many proteins.
p.5
Macromolecular Function
What is proton hopping?
A process where protons move through a membrane, facilitated by bound water molecules.
p.4
Noncovalent Interactions
What types of weak interactions contribute to the stability of macromolecules?
Hydrogen bonding, ionic interactions, van der Waals forces, and hydrophobic clustering.
What drives the formation of aggregates like micelles and bilayer vesicles in nonpolar and amphipathic compounds?
The hydrophobic effect, which sequesters hydrophobic moieties in the interior and allows polar moieties to interact with water.
p.1
Noncovalent Interactions
How much energy is required to break a mole of C—C single bonds?
About 350 kJ of energy is required.
p.8
Noncovalent Interactions
What happens to water in the initial state of osmosis?
Water flows from the beaker into the tube to equalize its concentration across the membrane.
What is proton hopping?
Proton hopping is the process where protons make short 'hops' between a series of hydrogen-bonded water molecules, resulting in a rapid net movement of a proton over a long distance.
p.19
Noncovalent Interactions
How can the equilibrium constant be approximated in most cases?
By measuring the concentrations at equilibrium.
p.22
Noncovalent Interactions
How can the concentrations of H+ and OH- be calculated at neutral pH?
From the ion product of water: Kw = [H+][OH-] = [H+]^2 = [OH-]^2
p.10
Biological Macromolecules
What happens to a cell if the inward movement of water is not counterbalanced?
The plasma membrane would distend and eventually cause the cell to burst (osmotic lysis).
p.5
Macromolecular Structure
What is shown in Figure 2-9 regarding hemoglobin?
The crystal structure of hemoglobin with and without bound water molecules.
p.12
Noncovalent Interactions
Why does lettuce wilt?
Lettuce wilts because the loss of water reduces turgor pressure.
p.12
Noncovalent Interactions
Why must biochemists perform fractionations in isotonic solutions when isolating organelles?
To prevent excessive entry of water into the organelles and the swelling and bursting that would follow.
p.14
Biological Macromolecules
How is the required sucrose concentration calculated?
(0.26 mol/L) * (342 g/mol) = 88.92 g/L
p.4
Noncovalent Interactions
What results from the binding of a hormone or neurotransmitter to its cellular receptor protein?
The result of multiple weak interactions.
p.2
Noncovalent Interactions
What are the four types of noncovalent interactions among biomolecules in aqueous solvent?
Hydrogen bonds, ionic interactions, van der Waals interactions, and hydrophobic effect.
p.13
Biological Macromolecules
How is the osmotic strength of a sucrose solution calculated?
Π_sucrose = RT(i_sucrose * c_sucrose)
p.8
Noncovalent Interactions
How is osmotic pressure (Π) measured in the final state?
As the force that must be applied to return the solution in the tube to the level of the water in the beaker.
p.3
Van der Waals Interactions
What are van der Waals interactions?
Interactions between any two atoms in close proximity.
p.22
Noncovalent Interactions
What happens to [OH-] when [H+] is greater than 1 × 10^-7 M?
[OH-] must be less than 1 × 10^-7 M
p.6
Macromolecular Function
What is the role of water in the proton channel of cytochrome f?
Water is bound in the proton channel of cytochrome f, which is part of the energy-trapping machinery of photosynthesis in chloroplasts.
How can the ionization of water be described?
By an equilibrium constant.
p.10
Biological Macromolecules
What happens to a cell in an isotonic solution?
There is no net water movement.
p.7
Noncovalent Interactions
What happens when two different aqueous solutions are separated by a semipermeable membrane?
Water molecules diffuse from the region of higher water concentration to the region of lower water concentration, producing osmotic pressure.
p.12
Noncovalent Interactions
What do buffers used in cellular fractionations commonly contain to protect organelles from osmotic lysis?
Buffers commonly contain sufficient concentrations of sucrose or some other inert solute.
p.4
Macromolecular Structure
What determines the most stable (native) structure of macromolecules?
The maximization of weak interactions.
What types of compounds form hydrogen bonds with water and are water soluble?
Alcohols, aldehydes, ketones, and compounds containing N—H bonds.
p.3
Noncovalent Interactions
What must happen to dissociate two biomolecules associated noncovalently through multiple weak interactions?
All the interactions must be disrupted at the same time.
Given [H+] = 1.3 x 10^-4 M, how do you solve for [OH-]?
[OH-] = Kw / [H+] = (1 x 10^-14 M^2) / (1.3 x 10^-4 M) = 7.7 x 10^-11 M
What is the range of H+ and OH- concentrations in any aqueous solution?
Between 1.0 M H+ and 1.0 M OH-.
What must be taken into account to explain many of the solvent properties of water?
The small degree of ionization of water to hydrogen ions (H⁺) and hydroxide ions (OH⁻).
What is the tendency of water molecules in terms of ionization?
Water molecules have a slight tendency to undergo reversible ionization to yield a hydrogen ion (H⁺) and a hydroxide ion (OH⁻).
p.10
Biological Macromolecules
What is osmotic lysis?
The bursting of a cell due to the inward movement of water causing the plasma membrane to distend.
p.11
Noncovalent Interactions
What mechanism do bacteria and plants use to resist osmotic pressure?
They have a nonexpandable cell wall of sufficient rigidity and strength.
p.11
Noncovalent Interactions
Why do macromolecules have less effect on the osmolarity of a solution compared to their monomeric components?
Because osmolarity depends on the number of dissolved particles, not their mass.
p.23
Enzyme Substrate Binding
Why does NaOH dissociate completely in water?
Because NaOH is a strong base.
p.21
Biological Macromolecules
How is the ion product of water (Kw) calculated?
Kw = (55.5 M)(1.8 × 10^-16 M) = 1.0 × 10^-14 M^2
p.3
Noncovalent Interactions
Why is the simultaneous disruption of multiple weak interactions between biomolecules very unlikely?
Because the interactions fluctuate randomly.
What should you ensure in all calculations?
Be sure to round your answer to the correct number of significant figures.
How does the pH scale differ from an arithmetic scale?
The pH scale is logarithmic.
p.5
Macromolecular Function
What role do bound water molecules play in photosynthesis?
They provide a path for protons to move through the membrane by a process known as proton hopping.
p.7
Noncovalent Interactions
How does solute concentration affect colligative properties?
The effect of solute concentration on colligative properties depends only on the number of solute particles (molecules or ions) in a given amount of water.
How does the high ionic mobility of H+ affect acid-base reactions in aqueous solutions?
It makes acid-base reactions exceptionally fast.
p.11
Noncovalent Interactions
How do freshwater protists living in a hypotonic medium prevent osmotic lysis?
They have a contractile vacuole that pumps water out of the cell.
p.11
Noncovalent Interactions
Why is storing fuel as polysaccharides advantageous for cells?
It avoids an enormous increase in osmotic pressure in the storage cell.
p.13
Biological Macromolecules
How is the osmotic strength of the lysosomal contents calculated?
Π_lysosome = RT[(i_KCl * c_KCl) + (i_NaCl * c_NaCl)] = RT[2(0.1 mol/L) + 2(0.03 mol/L)] = RT(0.26 mol/L)
p.8
Noncovalent Interactions
What is osmotic pressure (Π) measured as?
The force necessary to resist water movement.
p.20
Noncovalent Interactions
What is the degree of ionization of water at equilibrium at 25°C?
Only about two of every 10^9 molecules in pure water are ionized at any instant.
p.6
Macromolecular Function
What is the function of the bound heme in cytochrome f?
The bound heme, with its iron ion, facilitates electron flow during photosynthesis.
p.16
Equilibrium Constants
What must be taken into account to predict the state of ionization of solutes in water?
The relevant equilibrium constants for each ionization reaction.
p.7
Noncovalent Interactions
What are colligative properties?
Colligative properties are physical properties of the solvent that are altered by solutes, including vapor pressure, boiling point, melting point, and osmotic pressure.
What is 'proton hopping'?
A series of proton hops between hydrogen-bonded water molecules causing the net movement of a proton over a long distance in a short time.
p.9
Noncovalent Interactions
What happens to a cell in a hypertonic solution?
The cell shrinks as water moves out.
p.11
Noncovalent Interactions
How do cells actively maintain osmotic balance with their surroundings?
Cells actively pump out Na+ and other ions into the interstitial fluid.
Why are NH3 and H2S very water soluble?
Because they are ionizable.
p.15
Noncovalent Interactions
How do weak, noncovalent interactions influence the folding of macromolecules?
In large numbers, they decisively influence the folding of macromolecules such as proteins and nucleic acids.
p.13
Biological Macromolecules
What do i1, i2, and i3 represent in the osmotic strength equation?
The numbers of particles each solute yields in solution
p.3
Enzyme Substrate Binding
What types of interactions may be involved in the noncovalent binding of an enzyme to its substrate?
Several hydrogen bonds, one or more ionic interactions, the hydrophobic effect, and van der Waals interactions.
p.22
Noncovalent Interactions
How can [H+] be calculated if [OH-] is known?
From the ion product of water
How is the pH of a neutral solution at 25°C calculated?
pH = log(1 / 1.0 × 10^-7) = 7.0
What does a difference of 1 pH unit between two solutions indicate?
One solution has ten times the H+ concentration of the other.
What happens to hydrogen ions formed in water?
They are immediately hydrated to form hydronium ions (H3O+).
What ions migrate towards the cathode and anode in pure water?
H3O+ migrates toward the cathode and OH- migrates toward the anode.
p.9
Noncovalent Interactions
What is osmosis?
Water movement across a semipermeable membrane driven by differences in osmotic pressure.
p.11
Noncovalent Interactions
How do multicellular animals maintain osmotic balance?
Blood plasma and interstitial fluid are maintained at an osmolarity close to that of the cytosol.
p.4
Noncovalent Interactions
What reflects the complementarity between interacting biomolecules at the molecular level?
The complementarity and weak interactions between polar and charged groups and the proximity of hydrophobic patches on the surfaces of the molecules.
How does a hydronium ion participate in proton hopping?
A hydronium ion gives up a proton, which is then acquired by a water molecule some distance away, turning it into a hydronium ion.
What happens when weak acids are dissolved in water?
They contribute H⁺ by ionizing.
p.5
Macromolecular Function
What is the significance of the chain of five bound water molecules in cytochrome f?
They may provide a path for protons to move through the membrane.
p.12
Noncovalent Interactions
What are the major solutes in intact lysosomes mentioned in the text?
KCl (~0.1 M) and NaCl (~0.03 M).
p.14
Macromolecular Structure
How do liver and muscle cells store carbohydrates?
As the high molecular weight polymer glycogen.
p.11
Noncovalent Interactions
How do plants use osmotic pressure to achieve mechanical rigidity?
The high solute concentration in the plant cell vacuole draws water into the cell, but the nonexpandable cell wall prevents expansion.
p.3
Noncovalent Interactions
How can the stability of a noncovalent interaction be calculated?
From the binding energy, which is the reduction in the energy of the system when binding occurs.
Why is the value of 7 for the pH of a neutral solution not arbitrarily chosen?
It is derived from the absolute value of the ion product of water at 25°C.
p.5
Noncovalent Interactions
What is the difference between bound water molecules and bulk water in terms of their properties?
Bound water molecules have properties that are distinctly different from those of bulk water, such as not being osmotically active.
p.10
Biological Macromolecules
What happens to a cell in a hypotonic solution?
Water moves in, creating outward pressure, and the cell swells and may burst.
p.9
Noncovalent Interactions
What does the symbol 'i' represent in the context of osmolarity?
The van’t Hoff factor, a measure of the extent to which the solute dissociates into two or more ionic species.
What is the van’t Hoff factor (i) for dilute NaCl solutions?
2, because NaCl completely dissociates into Na+ and Cl-, doubling the number of solute particles.
p.4
Enzyme Substrate Binding
What is the main source of an enzyme's catalytic power?
The energy released when an enzyme binds noncovalently to its substrate.
p.20
Noncovalent Interactions
What is the relationship between the standard free-energy change (ΔG°) and the equilibrium constant (K_eq)?
The standard free-energy change (ΔG°) is directly related to ln K_eq.
What is the basis for the pH scale?
The ion product of water, Kw.
How does hydrogen bonding between water molecules affect the hydration of dissociating protons?
It makes the hydration virtually instantaneous.
Why is the movement of hydronium and hydroxide ions in the electric field extremely fast?
Due to high ionic mobility resulting from 'proton hopping'.
p.12
Noncovalent Interactions
What is the consequence of osmosis for laboratory protocols involving organelles?
Osmosis can cause excessive entry of water into organelles, leading to swelling and bursting.
p.9
Macromolecular Structure
What are plasma membranes more permeable to compared to most other small molecules, ions, and macromolecules?
Water, due to protein channels called aquaporins.
p.4
Macromolecular Structure
How is the three-dimensional shape of a polypeptide or polynucleotide chain determined?
By the principle of maximizing weak interactions.
How does water dissolve crystals of ionizable solutes?
By screening the electrical charges of ions and by increasing the entropy of the system.
p.15
Van der Waals Interactions
What defines the van der Waals radius of an atom?
The nearest approach of two atoms.
