CHAPTER 2: WATER THE SOLVENT

CHAPTER 2: WATER THE SOLVENT FOR BIOCHEMICAL REACTIONS

Learning outcomes

1.       What is polarity?

2.       Why do some chemicals dissolve in water while others do not?

3.       Why do oil and water mixed together separate into layers?

4.       Why does water have such interesting and unique properties?

5.       What are acids and bases?

6.       What is pH?

7.       Why do we want to know the pH?

--- Water and Polarity

-          Water is the principal component of most cell

-          The geometry of water molecule and its properties as a solvent play a major role in determining the properties of living systems

-          Consists of two hydrogen atoms and one oxygen atom bonded together.

-          The oxygen atom attracts electrons more strongly than hydrogen, creating an uneven distribution of charge within the molecule

Electronegativity

-          The tendency of an atom to attract electrons to itself in a chemical bond

-          Left to right (across a period) = increasing

-          Top to bottom (down a group) = decreasing

Electronegativity of selected elements

--- Polarity

Polar Bonds

-          The difference in electronegativity between oxygen and hydrogen gives rise to a partial positive and negative charge

-          Unequal sharing of electrons

-          Example: h20

Non Polar Bonds

-          Electronegativity difference is small

-          Equal sharing of electrons

-          Example: 02

Dipole Moment

-          A measure of how polar a molecule is

-          It shows how the charges are distributed in a molecule

-          Shows the “direction” of the charge separation

!!! molecules can be classified as nonpolar or polar based on the distribution of charges. a molecule is considered nonpolar if its charge distribution is symmetrical, even if individual bonds are polar.

Dipoles

-          Bonds with positive and negative ends

-          The shape of a water molecule and its unequal charge distribution creates dipoles

-          Forms when a molecule attracts more electrons strongly, leading to a higher electron density

-          Due to an uneven distribution of electrons in bonds

--- Solvent Properties of Water

Why do some chemicals dissolve in water while others do not?

-          Some chemicals dissolve in water while others do not due to the polar nature of water and the type of intermolecular forces involved in the bonder

-          Water is a polar molecule making it a solvent that can interact with its polar nature

-          Ionic compounds with full and partial charges are more likely to dissolve in water due to electrostatic attractions with water molecule.

!!!! like dissolves like, unlike dissolves unlike

--- Ionic Bonds

-          Results from the attraction between positive and negative ions

-          Strong bonds alongside covalent bonds

-          Intramolecular forces

-          Interactions between a nonmetal and a mental

Intermolecular Forces

-          Interactions between molecules that hold them together in a substance

-          Generally weaker

-          Includes: hydrogen bonding, van der waals forces, and dipole-dipole

Intramolecular forces

-          Forces within a molecule that hold its atoms together

-          Stronger

-          Includes: covalent bonds and ionic bonds

--- Salt Bridges

-           Electrostatic interaction that depends on the attraction of unlike charges

-          When these charged groups come close in proximity within a protein structure, the resulting electrostatic bond is referred to as a salt bridge

-          Is like a magnet that forms when oppositely charged particles in biomolecules attract one another

-          Example: in proteins, certain amino acids have positive or negative charges on their side chains. when these charged parts come near each other, they attract and form a salt bridge bond

--- Intramolecular Forces

1.       Ion-Dipole Interactions

-          Occurs when ions (charged particles) interact with polar molecules in a solution

-          Mostly ionic salts

-          Polar

-          Disassociates into two ions: cations and anions

-          Electrostatic dealing with charges

2.       Van der Waals Forces

-          Weak interactions between molecules

-          Named after the scientist: Johannes Diderik van der Waals

-          Involves non-covalent bonds that do not result from fully charged ions but from partial positive and negative charges

-          These forces are temporary and fluctuate as molecules move and interact

3.       Dipole-Dipole Interactions

-          Occur between molecules that have dipoles, with a partial positive end attracting the partial negative end of another molecule

-          Occur between polar molecules, where there is an uneven distribution of charge, creating positive and negative ends within the molecule

-          When the ends attract one another, it results in an electrostatic attraction between the dipoles

Electrostatic attraction

-          Refers to attraction between static electric charges, where oppositely charged particles are drawn to each other due to the electrostatic forces between them

4.       Dipole- Induced Dipole Interactions

-          A molecule with a permanent dipole can induce a temporary dipole in a neighboring molecule that lacks a permanent dipole

-          When the permanent dipole molecule, approaches the nonpolar molecule, the electrostatic force between their dipole causes a distortion in the electron cloud of the nonpolar molecule

Electron Cloud – refers to a region or space around an atomic nucleus where electrons are most likely to be found; electrons move rapidly and do not follow a fixed path but exists in a cloud-like distribution around the nucleus

-          The distortion leads to the nonpolar molecule temporarily acquiring a partial positive and partial negative charge, creating a transient dipole.

Transient Dipole – temporary separation of charge within a molecule that normally lacks a permanent dipole moment; occurs due to asymmetric electron distribution caused by the proximity of another molecule with a permanent dipole.

-          The temporary dipole in the nonpolar molecule and the permanent dipole in the other molecule attract each other.

Electron density

-          Probability of finding an electron within a specific region around an atom or within a molecule

-          Represents the distribution of electrons in an atom

-          Forms when electrons move randomly

!!! heavy molecular weight means there would be no induced dipole interactions; it only occurs on lighter molecular weight

--- Strengths of Bonds

Hydrophobic

-          Does not dissolve in water

-          Nonpolar nature

-          Lacks a significant partial or full charge, making them poorly soluble in water

-          Examples: lipids and oils

Hydrophobic interactions

-          Occur between molecules that are nonpolar

-          Leading to the clustering of hydrophobic molecules to minimize contact with water

Amphipathic

-          Compounds that contain both hydrophilic (water-loving) and hydrophobic (water-repelling) regions within the same molecule

-          Attracts/interacts with both polar and nonpolar substances

--- Hydrogen Bonds

-          Type of non-covalent interaction that occurs between a hydrogen atom covalently bonded to a highly electronegative atom

-          Results in a strong electronegative atom

-          The electronegative atom has a lone pair of electrons that attracts a hydrogen atom (due to the difference in electronegativity between two atoms)

Comparison of properties of water

--- Acids, Bases, and pH

Acid Strength

-          Ability of an acid to donate a proton (hydrogen ion) when dissolved in water

-          Strong acids completely dissociate into ions in solution, while weak acids partially dissociate

-          The strength of an acid is determined by the stability of the resulting conjugate base after the proton is donated

Acid Dissociation Constant (Ka):

-          A numerical value that characterizes the strength of an acid in a particular solvent

-          Represents the equilibrium constant for the dissociation of an acid (HA) into a hydrogen ion (H+) and its conjugate base (A-)

-          The higher the value of Ka, the stronger the acid (greater tendency to dissociate and donate protons)

Why do we want to know the pH?

-          pH is a measure of the acidity or basicity of a solution, indicating the concentration of hydrogen ions present

-          control of pH is essential for maintaining optimum conditions for biochemical reactions and processes.

Henderson-Hasselbalch Equation

-          a mathematical relationship between the pKa of an acid and the pH of a solution containing the acid and its conjugate base.