p.16
Water as a Biological Solvent
Why is water considered an ideal biological solvent?
Due to its ability to dissolve a wide range of solutes, including polar and ionic compounds.
p.7
Water as a Biological Solvent
What makes water an ideal biological solvent?
Its ability to dissolve a wide range of substances due to its polarity.
p.47
pH and Its Effects on Living Cells
What is pKa used to express?
The relative strengths of both acids and bases.
p.11
Hydrogen Bonding in Water Molecules
How do water molecules form hydrogen bonds?
By interacting with unshared electron pairs on other oxygen or nitrogen atoms.
p.28
Water as a Nucleophile
What are some common electrophiles?
Carbonyl carbons in amides, esters, aldehydes, and ketones; phosphorus atoms of phosphoesters.
p.31
Dissociation and Ionization of Water
What is the process by which water ionizes?
Intermolecular proton transfer that forms a hydronium ion (H3O+) and a hydroxide ion (OH-).
p.27
Water as a Nucleophile
Do nucleophiles and electrophiles necessarily possess a formal negative or positive charge?
No, they do not necessarily possess a formal negative or positive charge.
p.44
pH and Its Effects on Living Cells
Why is knowledge of the dissociation of weak acids and bases necessary?
To understand the influence of intracellular pH on structure and biologic activity.
p.32
Dissociation and Ionization of Water
Why can an individual hydrogen or oxygen not be stated to be present as an ion or as part of a water molecule?
Because at one instant it is an ion, and an instant later it is part of a water molecule.
p.44
Buffers and Their Role in Living Cells
How are charge-based separations like electrophoresis best understood?
In terms of the dissociation behavior of functional groups.
p.2
Biomedical Importance of Water
What are some biomedical importance of water?
It serves as a solvent, participates in metabolic reactions, helps regulate body temperature, and provides cushioning for organs and tissues.
p.53
pH and Its Effects on Living Cells
What does the Henderson-Hasselbalch equation calculate?
It calculates the pH of a solution containing a weak acid and its conjugate base.
p.22
Noncovalent Interactions in Water
What type of interactions influence the structure of biomolecules?
Noncovalent Interactions.
p.46
pH and Its Effects on Living Cells
What is the relationship between the strength of an acid and its pKa value?
The stronger the acid, the lower its pKa value.
p.34
Dissociation and Ionization of Water
What does the dissociation of water represent?
The molar concentrations and the dissociation constant.
p.47
pH and Its Effects on Living Cells
How are the relative strengths of bases expressed?
In terms of the pKa of their conjugate acids.
p.50
Buffers and Their Role in Living Cells
What does the Henderson-Hasselbalch equation express?
The relationship between the pH of a buffer solution and the pKa.
What is the shape of a water molecule?
An irregular, slightly skewed tetrahedron with oxygen at its center.
p.18
Interaction of Water with Biomolecules
What interactions are maximized between polar groups on biomolecules and water?
Charge-dipole, dipole-dipole, and hydrogen bonding interactions.
p.53
Buffers and Their Role in Living Cells
What are the components of the Henderson-Hasselbalch equation?
The concentration of the weak acid, the concentration of its conjugate base, and the acid dissociation constant (pKa).
p.11
Hydrogen Bonding in Water Molecules
What is the key feature of a hydrogen nucleus in a water molecule?
It is partially shielded.
p.54
Buffers and Their Role in Living Cells
What is the definition of buffering in the context of weak acids or bases?
The ability to resist a change in pH following addition of strong acid or base.
p.26
Interaction of Water with Biomolecules
How does the double helix DNA structure interact with water?
It presents charged phosphate groups and polar hydroxyl groups from the ribose sugars to water while burying the relatively hydrophobic nucleotide bases inside.
p.18
Interaction of Water with Biomolecules
What does it mean for a biomolecule to be amphipathic?
It means it possesses regions rich in charged or polar functional groups as well as regions with hydrophobic character.
p.18
Interaction of Water with Biomolecules
How do biomolecules fold to position polar and charged groups on their surfaces?
To maximize energetically favorable interactions with water and minimize energetically unfavorable contacts with hydrophobic groups.
p.52
pH and Its Effects on Living Cells
What does pKa represent?
The negative logarithm of the acid dissociation constant (Ka).
p.25
Hydrogen Bonding in Water Molecules
How are the two strands of the DNA double helix held together?
Exclusively by noncovalent interactions, including hydrogen bonds and Van der Waals interactions.
p.22
Noncovalent Interactions in Water
What are the types of Van der Waals forces?
Neutral A - Neutral B, eˉ - eˉ, δ+ - δ+.
p.56
pH and Its Effects on Living Cells
What factor hinders proton release from nearby acidic groups, raising their pKa?
The presence of local negative charge.
p.48
Buffers and Their Role in Living Cells
What is the relationship between Ka, [H+], and the concentrations of undissociated acid and its conjugate base?
When [R-COO-] = [R-COOH] or when [R-NH2] = [R-NH3+], then:
p.27
Water as a Nucleophile
What are nucleophiles and electrophiles?
Nucleophiles are electron-rich molecules that attack electron-poor atoms (electrophiles).
p.44
Biomedical Importance of Water
Where are functional groups that are weak acids found?
In proteins, nucleic acids, coenzymes, and intermediary metabolites.
p.36
Dissociation and Ionization of Water
Is the molar concentration of water significantly affected by dissociation?
No, it is considered to be essentially constant.
p.45
Buffers and Their Role in Living Cells
How do we express the relative strengths of weak acids and bases?
In terms of their dissociation constants.
p.15
Water as a Biological Solvent
Why is water considered an ideal biological solvent?
Due to its ability to dissolve a wide range of substances.
p.23
Noncovalent Interactions in Water
What are the two categories of Van der Waals forces based on distance?
Weak Van der Waals force (> 4 Angstrom) and Strong Van der Waals force (2 - 4 Angstrom).
p.10
Water as a Biological Solvent
What makes water an ideal biological solvent?
Its high dielectric constant.
p.54
Buffers and Their Role in Living Cells
What are the examples of biological buffers involved in maintaining a constant pH?
Phosphate, bicarbonate, and proteins.
p.21
Noncovalent Interactions in Water
How do Van der Waals forces compare to hydrogen bonds in terms of strength?
Significantly weaker than hydrogen bonds.
p.27
Water as a Nucleophile
Why is water considered an excellent nucleophile?
Because its two lone pairs of sp3 electrons bear a partial negative charge.
p.24
Interaction of Water with Biomolecules
How does water interaction influence the structure of biomolecules?
Water can form hydrogen bonds with biomolecules, affecting their conformation and stability.
p.8
Water as a Biological Solvent
Why is water considered an ideal biological solvent?
Due to its ability to dissolve a wide range of substances.
p.46
Buffers and Their Role in Living Cells
What are representative weak acids and their conjugate bases used for?
They are used to determine pKa values.
p.26
Interaction of Water with Biomolecules
What does the extended DNA backbone maximize?
The distance between negatively charged phosphates, minimizing unfavorable electrostatic interactions.
p.25
Noncovalent Interactions in Water
What stabilizes the structure of biomolecules?
Multiple forces, including noncovalent interactions.
p.49
pH and Its Effects on Living Cells
How is pKa defined?
pKa is defined as -log(Ka).
p.3
Biomedical Importance of Water
In what concentration is water present in most cells?
Between 70 and 85 percent.
p.30
Interaction of Water with Biomolecules
What is the role of proteases in the cell?
They catalyze the hydrolysis of proteins into their component amino acids.
p.17
Noncovalent Interactions in Water
What is the nature of noncovalent forces?
They can be either attractive or repulsive.
p.2
Noncovalent Interactions in Water
How do noncovalent interactions affect the chemical and biological properties of water?
They contribute to water's high surface tension, cohesion, and adhesion.
p.23
Noncovalent Interactions in Water
What type of interactions influence the structure of biomolecules?
Noncovalent Interactions.
p.7
Hydrogen Bonding in Water Molecules
What is a dipole?
A molecule with electrical charge distributed asymmetrically about its structure.
p.28
Water as a Nucleophile
What are some other nucleophiles of biologic importance?
Oxygen atoms of phosphates, alcohols, and carboxylic acids; sulfur of thiols; nitrogen atom of amines and of the imidazole ring of histidine.
p.44
pH and Its Effects on Living Cells
What are some examples of functional groups that are weak acids?
Carboxyl groups, protonated amino groups, and phosphate esters.
p.9
Water as a Biological Solvent
What does the high dielectric constant of water enable it to do?
Dissolve large quantities of charged compounds such as salts.
p.30
Water as a Nucleophile
What is a nucleophile?
A species that donates an electron pair to form a chemical bond.
p.49
pH and Its Effects on Living Cells
How is pH defined?
pH is defined as -log[H+].
p.35
Dissociation and Ionization of Water
What is the dissociation constant K for pure water?
1.8 × 10^-9 * 55.56 = 1.0 × 10^-7.
p.37
Dissociation and Ionization of Water
What is the ion product Kw numerically equal to?
The product of the molar concentrations of H+ and OH- ions.
p.51
pH and Its Effects on Living Cells
What is the first step in solving the Henderson-Hasselbalch equation?
Take the log of both sides.
p.59
pH and Its Effects on Living Cells
What affects the pKa values of dissociating groups in the interiors of proteins?
Their local environment, including the presence or absence of water.
p.48
pH and Its Effects on Living Cells
What is the pKa for a weak acid?
The pH at which the concentration of the acid equals that of the base.
p.56
pH and Its Effects on Living Cells
How does the effect of adjacent charge change with distance?
It decreases with distance.
p.29
Water as a Nucleophile
What is the result of nucleophilic attack by water?
Cleavage of amide, glycoside, or ester bonds.
p.26
Interaction of Water with Biomolecules
What type of forces stabilize biomolecules?
Multiple forces, including interactions with water.
p.18
Interaction of Water with Biomolecules
What is the purpose of protein folding and phospholipid bilayer in relation to water?
To maximize energetically favorable interactions with water and minimize energetically unfavorable contacts with hydrophobic groups.
p.49
pH and Its Effects on Living Cells
What happens when the logarithms of both sides of the equation relating Ka and [H+] are taken and both sides are multiplied by -1?
The equation is rewritten as -logKa = pH.
p.3
Water as a Biological Solvent
How does the ability of water to solvate molecules influence biomolecule structure?
It influences the structure of the biomolecule.
p.20
Noncovalent Interactions in Water
What is a salt bridge in the context of biomolecules?
It is a term used to describe electrostatic interactions between oppositely charged groups within or between biomolecules.
p.37
Dissociation and Ionization of Water
For what type of solutions does Kw equal 10^-14 (mol/L)2?
For all aqueous solutions, even solutions of acids or bases.
p.2
pH and Its Effects on Living Cells
What is pH and how does it affect living cells?
pH is a measure of the acidity or alkalinity of a solution. It affects living cells by influencing enzyme activity and protein structure.
Why does ethanol affect the pKa of a charged species in water?
Because ethanol decreases the ability of water to solvate a charged species.
p.57
pH and Its Effects on Living Cells
What does the strength of an acid depend on?
The molecular structure of the acid.
p.12
Water as a Biological Solvent
Why is water considered an ideal biological solvent?
Due to its ability to dissolve a wide range of substances.
p.6
Water as a Biological Solvent
Why is water considered an ideal biological solvent?
Due to its ability to form dipoles and its role as a solvent for many biological molecules.
What constitutes a region of local negative charge in a water molecule?
The two unshared electron pairs of oxygen.
p.43
pH and Its Effects on Living Cells
What are the pH values of 2.0 × 10^-2 mol/L KOH and 2.0 × 10^-6 mol/L KOH?
a) For 2.0 × 10^-2 mol/L KOH, the pH value is 12.7. b) For 2.0 × 10^-6 mol/L KOH, the pH value is 8.7.
p.55
Buffers and Their Role in Living Cells
What are some examples of buffers used in laboratory experiments?
MES, inorganic orthophosphate, HEPES, Tris.
p.47
Buffers and Their Role in Living Cells
What is the relationship between a weak acid and its conjugate?
For any weak acid, its conjugate is a strong base.
p.10
Interaction of Water with Biomolecules
What are the ions represented by Na+ and Clˉ in water?
Sodium (Na+) and Chloride (Clˉ) ions.
p.54
Buffers and Their Role in Living Cells
What is the role of buffering in biologic maintenance of a constant pH?
To resist a change in pH by accepting or releasing protons.
p.11
Hydrogen Bonding in Water Molecules
What does hydrogen bonding favor in water molecules?
The self-association of water molecules into ordered arrays.
p.52
pH and Its Effects on Living Cells
What does pH stand for?
The negative logarithm of the hydrogen ion concentration.
p.21
Noncovalent Interactions in Water
What gives rise to Van der Waals forces?
Attractions between transient dipoles generated by the rapid movement of electrons of all neutral atoms.
p.40
pH and Its Effects on Living Cells
How is pH calculated from hydrogen ion concentration?
pH = -log(3.2 × 10^-4) = -0.5 + 4.0 = 3.5
p.32
Dissociation and Ionization of Water
What is the concept of water dissociation?
The continuous recombination of hydronium and hydroxide ions to form water molecules.
p.19
Hydrogen Bonding in Water Molecules
What are hydrogen bonds?
Intermolecular bonds between hydrogen and oxygen or nitrogen of neighboring molecules, acting as a bridge between the participating molecules.
p.52
Buffers and Their Role in Living Cells
What is the Henderson-Hasselbalch equation used for?
Calculating the pH of a buffer solution.
p.19
Hydrogen Bonding in Water Molecules
How do hydrogen bonds compare to covalent and ionic bonds in terms of strength?
Considerably weaker than covalent and ionic bonds, but stronger than most noncovalent bonds.
p.4
pH and Its Effects on Living Cells
What is the pH scale used to measure?
The concentration of protons or acidity of aqueous solutions.
p.36
Dissociation and Ionization of Water
What is the relationship between Kw and K?
Kw is incorporated into the dissociation constant K to provide a useful new constant.
p.33
Dissociation and Ionization of Water
What is the probability of a hydrogen atom in pure water existing as a hydrogen ion?
Approximately 1.8 × 10^-9.
p.46
pH and Its Effects on Living Cells
How are weak acids expressed in terms of pKa?
Weak acids are expressed as pKa, where pKa is related to Ka as pH is to [H+].
p.50
Buffers and Their Role in Living Cells
What does the Henderson-Hasselbalch equation describe?
The behavior of weak acids and buffers.
What does hydrogen bonding account for in water?
Relatively high viscosity, relatively high surface tension, and relatively high boiling point.
How does water's dielectric constant affect the strength of interaction between oppositely charged particles?
It decreases the force of attraction between charged and polar species relative to water-free environments with lower dielectric constants.
p.49
pH and Its Effects on Living Cells
What is the relationship between the prevailing hydrogen ion concentration and the dissociation constant (Ka)?
When the associated (protonated) and dissociated (conjugate base) species are present at equal concentrations, the prevailing hydrogen ion concentration [H+] is numerically equal to the dissociation constant, Ka.
p.47
Buffers and Their Role in Living Cells
What is the numerical subscript assigned to each dissociation in polyprotic compounds?
A numerical subscript is assigned to each dissociation, numbered starting from unity in decreasing order of relative acidity.
p.39
pH and Its Effects on Living Cells
What does low pH value correspond to?
High concentrations of H+.
p.38
pH and Its Effects on Living Cells
How is pH calculated for a solution?
1. Calculate the hydrogen ion concentration [H + ] 2. Calculate the base 10 logarithm of [H + ] 3. pH is the negative of the value found in step 2.
p.38
pH and Its Effects on Living Cells
What is the definition of pH?
The negative log of the hydrogen ion concentration.
p.31
Biomedical Importance of Water
Why is the ability of water to ionize of central importance for life?
Because water can act both as an acid and as a base.
p.45
Buffers and Their Role in Living Cells
What is the expression for the dissociation constant (Ka) for weak acids?
Shown below are the expressions for the dissociation constant (Ka) for two representative weak acids, R-COOH and R-NH3+.
Why do hydrogen atoms have a partial positive charge in a water molecule?
Due to the strongly electronegative oxygen atom attracting electrons away from hydrogen.
p.30
Interaction of Water with Biomolecules
Why is careful control of the activities of enzymes required in the cell?
To ensure that they act only at appropriate times.
p.30
Water as a Biological Solvent
Why are amide and phosphoester bonds stable in the aqueous environment of the cell?
Due to the stability of these bonds, hydrolysis is not favored.
p.39
pH and Its Effects on Living Cells
What do bases do?
They are proton acceptors.
p.39
pH and Its Effects on Living Cells
What happens to strong acids in strongly acidic solutions?
They completely dissociate into anions and protons.
p.3
Water as a Nucleophile
What is the biomedical importance of water as a nucleophile?
It is a reactant or product in many metabolic reactions.
p.3
Biomedical Importance of Water
What are the essential factors for the regulation of water balance?
Thirst mechanism, antidiuretic hormone, and evaporative loss.
How are the hydrogen atoms and unshared electrons arranged in a water molecule?
The hydrogen atoms and unshared electrons occupy the corners of the tetrahedron.
p.21
Noncovalent Interactions in Water
How does the strength of Van der Waals forces change with distance?
They decrease as the sixth power of the distance separating atoms.
p.30
Interaction of Water with Biomolecules
What determines the rate at which a reaction will proceed toward its equilibrium point?
Enzymes in the cell, which are protein catalysts.
p.25
Hydrogen Bonding in Water Molecules
What is the name of the specific hydrogen bonding between nucleotide bases in DNA?
Watson-Crick base pairing.
p.39
pH and Its Effects on Living Cells
What happens to weak acids in acidic solutions?
They dissociate only partially.
p.17
Interaction of Water with Biomolecules
What do noncovalent forces involve interactions with, besides the biomolecule itself?
Water, which forms the principal component of the surrounding environment.
What significantly contributes to the properties of water?
Hydrogen ions and hydroxide ions.
p.2
Buffers and Their Role in Living Cells
What is a buffer and what is its role in living cells?
A buffer is a solution that resists changes in pH. Its role in living cells is to maintain a stable pH environment, crucial for cellular functions.
p.32
Dissociation and Ionization of Water
How are individual ions or molecules considered in the context of water dissociation?
They are not considered; instead, the probability of a given hydrogen being present as an ion or as part of a water molecule is referred to.
p.20
Noncovalent Interactions in Water
What are electrostatic interactions?
Interactions that occur between oppositely charged atoms or groups.
p.19
Hydrogen Bonding in Water Molecules
What causes the hydrogen nucleus to become weakly attracted to the lone pair of electrons of an oxygen or nitrogen of a neighboring molecule?
Sufficiently polar covalent bonds between hydrogen and oxygen or nitrogen.
p.4
pH and Its Effects on Living Cells
Give an example of a condition causing alkalosis.
Vomiting of acidic gastric contents.
What are some properties of water that account for its physical and chemical behavior?
High polarity, hydrogen bonding, high specific heat, and high heat of vaporization.
p.37
Dissociation and Ionization of Water
How does Kw change with temperatures below 25°C and above 25°C?
It is somewhat less than 10^-14 at temperatures below 25°C and somewhat greater than 10^-14 at temperatures above 25°C.
p.20
Noncovalent Interactions in Water
How do electrostatic interactions influence the shape and function of biomolecules?
They help influence the shape and function of biomolecules.
p.14
Interaction of Water with Biomolecules
Which biomolecules can serve as both hydrogen acceptors and donors of unshielded hydrogen atoms for formation of hydrogen bonds?
Alcohols, carboxylic acids, and amines.
p.32
Dissociation and Ionization of Water
What does it mean to state that the probability that a hydrogen exists as an ion is 0.01?
It means that at any given moment in time, a hydrogen atom has 1 chance in 100 of being an ion and 99 chances out of 100 of being part of a water molecule.
p.4
pH and Its Effects on Living Cells
Give an example of a condition causing acidosis.
Diabetic ketosis and lactic acidosis.
p.39
pH and Its Effects on Living Cells
What happens to strong bases like KOH and NaOH?
They are completely dissociated even at high pH.
What effect does the dielectric constant have on pKa?
It may be observed by adding ethanol to water.
p.14
Interaction of Water with Biomolecules
Which functional groups can participate in hydrogen bonding with water?
Aldehydes, ketones, amides, alcohols, carboxylic acids, and amines.
p.30
Interaction of Water with Biomolecules
What do nucleases catalyze in the cell?
They catalyze the hydrolysis of the phosphoester bonds in DNA and RNA.
p.58
pH and Its Effects on Living Cells
How does the medium affect the pKa relative to its value in water?
It may either raise or lower the pKa.
p.37
Dissociation and Ionization of Water
What is Kw used to calculate?
The pH of acidic and basic solutions.
p.20
Noncovalent Interactions in Water
How does the strength of electrostatic interactions compare to hydrogen bonds?
They are comparable in strength to hydrogen bonds but act over larger distances.
p.33
Dissociation and Ionization of Water
For every hydrogen ion or hydroxide ion in pure water, how many water molecules are there?
0.56 billion or 0.56 × 10^9 water molecules.
p.20
Noncovalent Interactions in Water
Give an example of an electrostatic interaction in determining the three-dimensional structure of proteins.
The interaction of NH3+ and COO-.
p.2
Noncovalent Interactions in Water
How do noncovalent interactions contribute to the stability of macromolecules?
They help in maintaining the three-dimensional structure of macromolecules, such as proteins and nucleic acids.
p.20
Noncovalent Interactions in Water
What do electrostatic interactions facilitate in terms of binding to proteins and nucleic acids?
They facilitate the binding of charged molecules and ions to proteins and nucleic acids.
