Biology 110 - Water and Life

3.1: Polar covalent bonds in water molecules result in hydrogen bonding
3.2: Four emergent properties of water contribute to Earth’s suitability for life
3.3: Acidic and basic conditions affect living organisms

3.1: Explain how hydrogen bonding results from polar covalent bonds.
3.2: Identify four properties of water that are important for life and describe how they result from hydrogen bonding.
3.3: Differentiate between an acid and a base; define pH and describe how it affects the processes of life.

The hydrogen bonds that hold water molecules together give water a collection of important unique properties.
These emergent properties of water make it essential for all life.

Covalent Bonds: In a covalent bond, atoms share electrons.
- Atoms with similar electronegativity form nonpolar covalent bonds (e.g., methane).
- Atoms with different electronegativity form polar covalent bonds (e.g., water).
- Electrons spend more time around the nucleus of the more electronegative atom.
- Resulting charges:
  - The more electronegative atom acquires a partial negative charge.
  - The less electronegative atom acquires a partial positive charge.
Hydrogen Bonds Formation:
- The polar charges in molecules create hydrogen bonds.
- The atom with the partial positive charge is always hydrogen.
- Hydrogen bonds pull water molecules closer to one another, influencing water's properties.
- Since electrons spend more time near oxygen, the oxygen atom retains a slight negative charge, whereas the hydrogen atoms exhibit slight positive charges.
Hydrogen bonds impart distinctive emergent properties to water.

Cohesion:
- The tendency of water molecules to stick together.
- Responsible for high surface tension due to hydrogen bonding among surface water molecules.
Adhesion:
- The tendency of water to form hydrogen bonds with substances other than water (e.g., paper towel).

Kinetic Energy:
- All moving objects possess kinetic energy, defined as energy of motion.
- Thermal energy is the kinetic energy associated with the random movement of atoms or molecules.
- Reflects total kinetic energy which depends on volume.
Temperature:
- Represents average kinetic energy of molecules in a body of matter, independent of volume.
Heat Measurement:
- Defined as the thermal energy transfer between two bodies.
- Calorie: Amount of heat required to raise 1g of water by 1°C.
- “Calories” on food labels refer to kilocalories.
- Specific heat: Amount of heat needed to change 1g of a substance's temperature by 1°C.
- Heat of vaporization: Amount of heat necessary for 1g of a liquid to change to a gaseous state.

Water expands upon freezing.
In liquid water, hydrogen bonds are continuously forming and breaking.
As it freezes, molecules slow down and hydrogen bonds become stable, locking molecules in place.
Less dense ice floats on water, and global warming greatly influences icy regions.

Solvent: Water acts as a dissolving agent, where other substances (solutes) dissolve.
A solution comprises one or more solutes homogenously dissolved in a solvent.
Hydrophilic substances: Polar or charged substances that readily dissolve in water.
Hydrophobic substances: Nonpolar substances that do not dissolve in water (do not form hydrogen bonds).

Molecular Mass: Sum of the masses of all atoms in a molecule; often measured in moles.
Mole (mol): Represents an exact number of objects, specifically $6.02 imes 10^{23}$ .
Example: To obtain 1 mol of sucrose (molecular weight 342 g/mol), weigh out 342 g.
Calculation of sucrose molecular mass:
- $ ext{C}{12} ext{H}{22} ext{O}_{11}$: $(12 imes 12) + (22 imes 1) + (11 imes 16) = 342 ext{ daltons}$

#5: Which property contributes to the high surface tension of water?
- A. Hydrogen bonding
- B. Polar covalent bonds
- C. Cohesion
- D. All of the above
Answer: D. All of the above
#6: Differentiate between hydrophilic and hydrophobic molecules.
- Hydrophilic: Polar molecules that readily dissolve in water.
- Hydrophobic: Nonpolar molecules that do not dissolve in water easily.

Measures acidity or basicity based on H+ concentration.
A neutral solution has equal amounts of H+ and OH- ions around pH = 7.
Acids: Chemicals that increase H+ concentration (e.g., vinegar, lemon juice).
Bases: Solutions where OH- ions exceed H+ ions.
pH Calculation:
$pH = - ext{log}[H^+]$

Acids have pH < 7 (high H+ concentration).
Alkaline (basic) solutions have pH > 7 (low H+ concentration).
Each pH unit represents a tenfold change in H+ concentration.
Many organisms aim for pH homeostasis around pH = 7.
Buffers: Solutions maintaining a constant pH by absorbing or releasing H+ ions.

4.1: Understand organic compounds and their origin on Earth.
4.2: Demonstrate how carbon’s atomic structure results in diverse molecular structures.
4.3: Identify chemical groups affecting biological molecule function.

Carbon can form four covalent bonds.
Carbon can bond with itself as well as with hydrogen, oxygen, and nitrogen.
Stanley Miller's Experiment (1953):
- Investigated the abiotic synthesis of organic compounds to explore life's origins.
- Concluded that complex organic molecules can form spontaneously under early Earth-like conditions.

Each carbon atom acts as a branching point for molecular structure, able to branch off in four directions.
Structural Formulas: Useful for visualizing molecular arrangements, though molecules are inherently three-dimensional, whose shapes are vital for function.
Valence of Atoms:
- The number of electrons needed to fill the valence shell indicates the atom's valence, or its capability for covalent bonding.
Carbon Skeletons:
- Carbon chains can vary in length, shape (straight, branched, or ring structures), and have double bonds.
- Hydrocarbons are carbon-based molecules comprising only carbon and hydrogen.

Isomers: Organic molecules with identical numbers of atoms but varying structures leading to different properties.
- Structural Isomers: Differ in covalent arrangements.
- Cis-trans Isomers (Geometric Isomers): Atoms are covalently bonded but differ spatially due to double bond inflexibility.
- Enantiomers: Mirror-image isomers characterized by an asymmetric carbon attached to four different atoms/groups.

Functional Groups: Chemically reactive groups directly involved in reactions.
Key Functional Groups:
- Hydroxyl group
- Carbonyl group
- Carboxyl group
- Amino group
- Sulfhydryl group
- Phosphate group
- Methyl group
Chemical reactivity and hydrophilicity are connected to these groups.