Chapter 2

Describe the kind of interactions that occur between molecules.

Molecular interactions include hydrogen bonding, van der Waals forces, ionic interactions, and hydrophobic interactions, which influence the physical and chemical properties of substances.

Discuss why water is a good medium for life.

Water is a good medium for life because it has a high specific heat, is a universal solvent, supports chemical reactions, and provides a stable environment for biological processes.

Identify why nonpolar moieties aggregate in water.

Nonpolar moieties aggregate in water due to hydrophobic interactions, where nonpolar substances minimize their exposure to water by clustering together, thus reducing the disruption of hydrogen bonding among water molecules.

Describe how dissolved molecules alter properties of water.

Dissolved molecules can change the properties of water by affecting its boiling and freezing points, altering its pH, and influencing its electrical conductivity and viscosity.

Explain how weak acids and bases behave in water.

Weak acids partially dissociate in water, establishing an equilibrium between the acid and its ions, while weak bases partially accept protons, influencing the pH without fully dissociating.

Identify how buffers work and why we need them.

Buffers work by absorbing excess hydrogen ions (H+) or hydroxide ions (OH-) to maintain a stable pH in a solution, which is crucial for maintaining homeostasis in biological systems.

Summarize how water participates in biochemical reactions.

Water participates in biochemical reactions as a reactant or product, facilitates hydrolysis and condensation reactions, and helps dissolve reactants, making them more accessible for reactions.

What are the roles of water in the body?

Water serves as a solvent, regulates temperature, participates in biochemical reactions, and provides structural support to cells.

What is pH?

pH is a measure of the acidity or basicity of a solution, defined as the negative logarithm of the hydrogen ion concentration.

What is pKa?

pKa is the negative logarithm of the acid dissociation constant (Ka) and indicates the strength of an acid; a lower pKa value means a stronger acid.

What is the dissociation constant (Kd)?

Kd is a measure of the affinity between a ligand and a protein, defined as the concentration of ligand at which half of the protein is bound.

What is the Henderson-Hasselbalch equation?

The Henderson-Hasselbalch equation relates pH, pKa, and the ratio of the concentrations of the deprotonated and protonated forms of a weak acid.

What is entropy in biochemical reactions?

Entropy is a measure of disorder or randomness in a system; in biochemical reactions, it reflects the number of possible arrangements of molecules.

What is enthalpy in biochemical reactions?

Enthalpy is the total heat content of a system; in biochemical reactions, it reflects the energy changes during bond formation and breaking.

What is Gibbs free energy (ΔG)?

Gibbs free energy (ΔG) is a thermodynamic quantity that indicates the spontaneity of a reaction; a negative ΔG indicates a spontaneous process.

What is standard free energy (ΔG0)?

Standard free energy (ΔG0) is the change in Gibbs free energy at standard conditions (1 M concentration, 1 atm pressure, and 25°C).

What is the equilibrium constant (Keq)?

The equilibrium constant (Keq) is a ratio of the concentrations of products to reactants at equilibrium, indicating the extent of a reaction.

What is the isoelectric point (pI)?

The isoelectric point (pI) is the pH at which a molecule, such as a protein, carries no net electrical charge.

How does pH affect the charge on a small peptide?

The charge on a small peptide varies with pH due to the ionization of its amino acid side chains; at certain pH levels, the peptide may be positively, negatively, or neutrally charged.

What are Van der Waals forces?

Van der Waals forces are weak attractions between molecules due to transient dipoles; they play a crucial role in the stability of protein structures.

What are hydrogen bonds?

Hydrogen bonds are strong dipole-dipole attractions between a hydrogen atom covalently bonded to an electronegative atom and another electronegative atom.

What are hydrophobic interactions?

Hydrophobic interactions occur when nonpolar molecules aggregate in aqueous environments to minimize their exposure to water, contributing to protein folding.

What is the difference between non-covalent interactions and covalent bonds?

Non-covalent interactions (like hydrogen bonds and Van der Waals forces) are weaker and reversible, while covalent bonds involve the sharing of electrons and are generally stronger and more stable.

What makes water a highly polar molecule?

The very different electronegativities of hydrogen (H) and oxygen (O).

What type of bonds can water form with itself and solutes?

Hydrogen bonds.

How do hydrogen bonds compare to covalent bonds?

Hydrogen bonds are fleeting, primarily electrostatic, and weaker than covalent bonds.

What type of solutes does water dissolve well?

Polar (hydrophilic) solutes and charged solutes.

Why do nonpolar compounds dissolve poorly in water?

They cannot hydrogen-bond with water and force an energetically unfavorable ordering of water molecules.

What structure do nonpolar compounds like lipids form in water?

Aggregates (micelles) where hydrophobic moieties are sequestered in the interior.

What influences the folding of macromolecules such as proteins?

Weak, noncovalent interactions, particularly hydrogen bonding and hydrophobic clustering.

What is osmotic pressure?

The tendency for water to move across a semipermeable membrane to equalize osmolarity.

What ions does pure water ionize into?

Hydronium ions (H3O+) and hydroxide ions (OH-).

What is the equilibrium constant for the ionization of water?

Keq=[H+][OH-]/[H2O].

What is the ion product of water (Kw) at 25°C?

Kw = [H+][OH-] = 10^-14 M^2.

How is pH defined in relation to hydrogen ion concentration?

pH = -log[H+].

What happens to pH as the acidity of a solution increases?

The pH decreases.

What is the acid dissociation constant (Ka)?

Keq = [H+][A-]/[HA].

What does pKa represent?

The relative strength of a weak acid or base on a logarithmic scale.

How does the strength of an acid relate to its pKa?

The stronger the acid, the lower its pKa.

What is a buffer?

A mixture of a weak acid (or base) and its salt that resists changes in pH.

What equation describes the pH of a buffer solution?

Henderson-Hasselbalch equation: pH = pKa + log([A-]/[HA]).

What buffer systems maintain physiological pH in cells and tissues?

Phosphate and bicarbonate (HCO3-) buffer systems.

What is the optimal pH for enzyme activity?

Usually close to pH 7.

What medical conditions can arise from pH imbalances in blood?

Acidosis (low pH) and alkalosis (high pH).

What roles does water play in biochemical processes?

Water acts as a solvent and a reactant in hydrolysis, condensation, and oxidation-reduction reactions.

What percentage of organisms is water?

Organisms contain 70-90 percent of water.

Why is water considered an excellent solvent?

Water is an excellent solvent for charged and polar substances due to its ability to form hydrogen bonds.

What are some examples of polar substances that dissolve in water?

Examples include amino acids, glycine, aspartate, lactate, glycerol, small alcohols, and carbohydrates like glucose.

What is the significance of water's high heat capacity?

Water's high heat capacity allows it to absorb and retain heat, which helps stabilize temperatures in biological systems.

What is the structure of a water molecule?

A water molecule has a tetrahedral structure with 4 electron pairs around an oxygen atom in sp3 hybridization.

Why is water a poor solvent for nonpolar substances?

Water is a poor solvent for nonpolar substances because they cannot form hydrogen bonds.

What is the role of water in chemical reactions?

Chemical reactions often occur in aqueous solutions, where water acts as a reactant or solvent.

What is the difference between condensation and hydrolysis?

Condensation is the process of joining molecules with the release of water, while hydrolysis involves breaking down molecules by adding water.

What are noncovalent interactions?

Noncovalent interactions include weak bonds such as hydrogen bonds, ionic interactions, dipole interactions, and van der Waals forces.

What is hydrogen bonding?

Hydrogen bonding occurs when a hydrogen atom covalently bonded to an electronegative atom interacts with another electronegative atom.

What is the significance of pH in biological systems?

pH measures the acidity or basicity of a solution, which affects enzyme activity and biochemical reactions.

What is a buffer?

A buffer is a solution that resists changes in pH upon the addition of small amounts of acid or base.

What is the Henderson-Hasselbalch equation?

The Henderson-Hasselbalch equation relates pH, pKa, and the concentrations of an acid and its conjugate base.

What is the dissociation constant (Ka)?

Ka is the equilibrium constant for the dissociation of an acid in water, indicating its strength.

What is the relationship between pH and pOH?

The relationship is defined by the equation pH + pOH = 14.

What is the significance of the dissociation of water?

The dissociation of water is a rapid and temperature-dependent process that establishes the equilibrium of H+ and OH- ions.

What is the role of hydrophobic interactions in proteins?

Hydrophobic interactions help stabilize protein structure by burying hydrophobic amino acids within the protein core.

What is the function of acetate/acetic acid buffer system?

The acetate/acetic acid buffer system helps maintain a constant pH in the presence of added acids or bases.

What is the significance of entropy in dissolving sugar in iced tea?

Dissolving sugar into iced tea is energetically favorable due to an increase in entropy as the sugar dissolves.

What is the equilibrium constant (Keq)?

Keq is the ratio of the concentration of products to the concentration of reactants at equilibrium.

What is the meaning of pKa?

pKa is the negative logarithm of the acid dissociation constant (Ka) and indicates the strength of an acid.

What happens to the pH when a strong acid is added to a solution?

The pH decreases significantly due to the large Ka of strong acids.

What is the effect of temperature on the dissociation of water?

The dissociation of water is temperature-dependent, affecting the concentration of H+ and OH- ions.

What is the role of ionic bonds in organic molecules?

Ionic bonds in organic molecules often involve ionic groups with one or more net charges.

What is the significance of van der Waals interactions?

Van der Waals interactions are weak attractions between all atoms, contributing to molecular stability.

Which of the following statements concerning H2O is INCORRECT?

Hexagonal ice forms more hydrogen bonds per H2O molecule than liquid water.

What is the relationship between liquid water and hexagonal ice regarding entropy?

Liquid water has higher entropy than hexagonal ice.

Why is water considered a good solvent?

Water is a good solvent for polar molecules.

What is the dipole moment of water molecules?

Water molecules exhibit a dipole moment where the oxygen atom has a partial negative charge and the hydrogen atoms have partial positive charges.

How do nonpolar molecules interact with water compared to polar molecules?

Nonpolar molecules disrupt the water lattice more than do polar molecules.

Which of the following pairs is matched correctly?

Ionic bonds - neutralized by nearby oppositely charged groups.

What are Van der Waals forces?

Van der Waals forces are weak attractions between molecules that are not mediated by permanent whole charge differences.

What does steric repulsion refer to?

Steric repulsion dominates at short distances between molecules.

What are dipole interactions?

Dipole interactions are electrostatic interactions between molecules that have permanent dipoles.

What are hydrophobic interactions?

Hydrophobic interactions contribute to the structure of proteins, typically occurring on the protein surface.

Which statement about protons in water is FALSE?

Protons are immediately hydrated to form hydronium (oxonium) ions.

How can pH be calculated?

pH can be calculated if the ion product of water (Kw) is known.

What is true about the dissociation of water?

The dissociation of water is temperature-dependent.

What is true about weak electrolytes?

Weak electrolytes dissociate only partially in water.

What is the relationship between pH and pOH?

The pH and pOH must always add to 14 at 25°C.

What is the function of a buffer system such as acetate/acetic acid?

To maintain a constant pH in the event the concentration of an acid or alkali increases.

What is the purpose of a buffer system?

To keep the solution within one pH unit of the pKa.

What happens when table sugar dissolves in iced tea?

Dissolving table sugar into iced tea is energetically favorable due to an increase in entropy as the sugar dissolves.

What does a negative value for ΔS indicate?

A negative value for ΔS indicates that the solute is becoming more ordered, which is not the case when sugar dissolves.

What happens to free energy when sugar dissolves?

There is a decrease in free energy due to broken weak interactions between sugar molecules.

What is the effect of solvation layers on sugar crystals?

The dissolution of sugar crystals results in an increase in free energy because there is no longer a solvation layer around the sugar crystal.