Chemical Properties
Covalent and Non-Covalent Bonds
Covalent Bonds
Strong and rigid, form the backbone of molecules.
Non-Covalent Bonds
Weaker interactions that allow for continuous forming/breaking, thereby enabling binding and release of molecules.
Types of Non-Covalent Bonds:
Hydrogen Bonds (dipole-dipole interactions)
Van der Waals Forces (London dispersion forces)
Properties of Water
Importance of Water
Biological Context:
Biological molecules adopt their shapes in response to the properties of water.
Water acts as the medium for biochemical reactions.
Water can participate directly in chemical reactions (substrate/product).
Central to energy processes: oxidizes and reforms during photosynthesis and energy expenditure.
Water Molecule Characteristics
Asymmetry and Dipole Moment
The water molecule has a significant dipole moment due to its asymmetric structure.
Solvent Properties:
Excellent solvent for polar (hydrophilic) compounds; can form hydrogen bonds.
Non-polar (hydrophobic) compounds do not dissolve in water.
Hydrogen Bonding in Biological Systems
Role of Hydrogen Bonds
Critical to the structure of biological molecules such as proteins and nucleic acids.
Hydrophobic Effect:
Non-polar groups try to minimize contact with water, influencing molecular orientation.
Solubility and Molecular Structure
Hydrophobic Effect Impact
Solubility in water affects the three-dimensional structure of biological compounds.
Driving force for membrane formation and protein/enzymes shapes.
R groups of amino acids can be either hydrophobic or hydrophilic; hydrophilic properties are diminished in peptide chains.
Amphiphilic Compounds
Definition
Compounds that have both polar and non-polar sections.
Orientation aims to maximize polar contacts with water and non-polar contacts among themselves.
Hydrogen Bond Dynamics
Functional Groups
Hydrogen bonds link functional groups in biological systems, such as in peptide linkages or DNA base pairing.
Conditions for Breaking Bonds:
Heat (melting)
High salt concentrations
Weakness and Strength of Hydrogen Bonds
Despite being weaker than covalent bonds, hydrogen bonds significantly influence the physical properties of substances.
Ionization and pH of Water
Water Ionization
A small proportion of water dissociates, forming hydronium ions (H3O+) and hydroxyl ions (OH-).
Proton hopping occurs, facilitating transfer between water molecules.
Equilibrium and Ionization of Water
Chemical Description
Relevant Equilibrium Equation:
H2O ⇌ H+ + OH-
Equilibrium Constant (Keq):
Keq = [H+][OH-]/[H2O]
For practical reasons, we approximate H+ as H3O+.
Molarity and Ionization Proportions
Pure Water Molarity
Molar mass of water = 18.015 g/mol
Molarity of pure water approximately 55.5 M due to negligible ionization.
pH, Ion Conductivity, and Biological Reactions
Ion Conductivity
Kw = 1.0 x 10^-14 indicates the balance of [H+] and [OH-].
Neutral pH defined as pH = 7.0 ([H+] = 1.0 x 10^-7).
Most biological processes occur between pH 6.5 and 8.0.
Acid-Base Chemistry
Bronsted-Lowry Reactions
Description:
Acid-base reactions can be modeled as:
HA + H2O ⇌ H3O+ + A-
HA represents any molecule that can donate a proton (acid).
pKa and pH Relationship
pKa Importance
pKa = - log(Ka), provides a measure of acid strength.
Buffered Solutions and Titration Info
Titration to Determine pKa
Measurements conducted at half-ionization points give pKa values.
Weak acids, notable for buffering pH, maintain stable environments amidst fluctuations.
Henderson-Hasselbalch Equation
Used to relate pH and concentrations of acids/bases:
pH = pKa + log([A-]/[HA])
Amino Acids and pKa Values
pKa Structure of Amino Acids
Titration curves reveal properties of amino acids, indicating their functional and structural aspects based on pKa values.
Isoelectric Point (pI) Calculation
Determined by averaging pKa values that define neutral species.