General Biology: Fundamental Concepts and Molecular Foundations

Water: Structure, Properties, and Biological Roles

Hydrogen Bonding in Water

Water molecules exhibit unique properties due to their ability to form hydrogen bonds, which are essential for many biological processes.

• Hydrogen Bonds per Water Molecule: Each water molecule can form up to four hydrogen bonds—two through its hydrogen atoms and two through its lone pairs on oxygen.

• Ice Lattice: In the crystalline lattice of ice, each water molecule forms four hydrogen bonds, creating an open, hexagonal structure that accounts for ice's lower density compared to liquid water.

• Example: The high boiling point and surface tension of water are due to extensive hydrogen bonding.

Cohesion and Adhesion

Cohesion refers to the attraction between molecules of the same substance, while adhesion is the attraction between different substances.

• Cohesion: Responsible for water's surface tension and phenomena such as capillary action in plants.

• Example: Capillary action in plants demonstrates cohesion, as water molecules stick together while moving up plant vessels.

Hydration Shells

When ionic or polar substances dissolve in water, water molecules surround the solute particles, forming a hydration shell.

• Formation: Water forms hydration shells around ions in solutions like salt water, stabilizing the ions and allowing them to remain dissolved.

• Nonpolar Substances: Substances like vegetable oil, fat, and beeswax do not form hydration shells because they are hydrophobic.

Physiological Functions of Water

Water is vital for numerous physiological processes in living organisms.

• Thermoregulation: Water helps regulate body temperature through sweating and heat absorption.

• Acid-Base Balance: Water acts as a solvent for acids and bases, helping maintain pH balance.

• Transport: Water transports nutrients and waste products in blood and other fluids.

• Example: All of the above are essential functions of water in the body.

Chemical Bonds and Molecular Structure

Types and Strengths of Chemical Bonds

Chemical bonds hold atoms together in molecules and vary in strength and biological significance.

• Covalent Bonds: Formed by the sharing of electron pairs between atoms; strongest type of bond in biological molecules.

• Ionic Bonds: Formed by the transfer of electrons from one atom to another, resulting in oppositely charged ions that attract each other.

• Hydrogen Bonds: Weak attractions between a hydrogen atom covalently bonded to an electronegative atom (like oxygen or nitrogen) and another electronegative atom.

• Van der Waals Interactions: Weak, transient attractions between molecules due to temporary dipoles.

Bond Strength Sequence (Strongest to Weakest):

Bond Type	Relative Strength
Covalent	Strongest
Ionic	Strong
Hydrogen	Weak
Van der Waals	Weakest

Isotopes

Isotopes are atoms of the same element with different numbers of neutrons.

• N-15 Isotope: Nitrogen-15 has 7 protons, 8 neutrons, and 7 electrons.

• Notation: 7p+, 8n0, 7e-

Anions

Anions are negatively charged ions formed when atoms gain electrons.

• Formation: Typically formed by non-metals.

• Charge: Have more electrons than protons.

• Attraction: Attracted to the anode (not cathode) in electrolysis.

Acids, Bases, and pH

pH and Proton Concentration

The pH scale measures the concentration of hydrogen ions (protons) in a solution.

• Low pH: Indicates a high concentration of protons (acidic solution).

• High pH: Indicates a low concentration of protons (basic solution).

• Equation: $pH = -\log_{10}[H^+]$

Biological Molecules

Monomers of Nucleic Acids

Nucleic acids (DNA and RNA) are polymers made up of nucleotide monomers.

• Nucleotide: Consists of a phosphate group, a five-carbon sugar, and a nitrogenous base.

Functional Groups in Amino Acids

Amino acids have a central carbon attached to an amino group, a carboxyl group, a hydrogen atom, and a variable side chain (R group).

• Threonine: Contains amino, carboxyl, hydroxyl, and methyl groups, but not a phosphate group.

Metabolism of Biomolecules

Cells metabolize carbohydrates, proteins, and fats for energy, but not all biomolecules are used for this purpose.

• Vitamins: Not metabolized to generate energy; they function as coenzymes or cofactors.

Fatty Acids: Saturated vs. Unsaturated

Fatty acids are classified based on the presence of double bonds in their hydrocarbon chains.

• Saturated Fatty Acids: Have only single carbon-carbon bonds.

• Unsaturated Fatty Acids: Have one or more double carbon-carbon bonds.

Protein Structure

Proteins have four levels of structure, each contributing to their function.

• Primary Structure: Sequence of amino acids.

• Secondary Structure: Local folding (e.g., alpha helix, beta sheet).

• Tertiary Structure: Overall 3D folding of a single polypeptide chain.

• Quaternary Structure: Association of multiple polypeptide subunits, held together by various interactions (not exclusively ionic bonds).

Polysaccharides

Polysaccharides are long chains of monosaccharide units and serve as energy storage or structural molecules.

• Examples: Starch, cellulose, and glycogen are all polysaccharides.

Proteins in Muscle Contraction

Muscle contraction relies on the interaction of thick and thin myofilaments composed of specific proteins.

• Thick Myofilaments: Principal protein is myosin.

• Thin Myofilaments: Principal protein is actin.

Cell Structure and Function

Cell Boundaries

Cells are surrounded by membranes that define their boundaries and separate internal from external environments.

• Plasma Membrane: Surrounds the cytoplasm in all cells.

• Cell Wall: Found outside the plasma membrane in plant cells, providing structural support.

Plant vs. Animal Cells

Plant and animal cells share many organelles, but some are unique to plant cells.

• Chloroplasts: Organelles found only in plant cells, responsible for photosynthesis.

• Other Organelles: Peroxisomes, cell membrane, and Golgi apparatus are found in both plant and animal cells.