Chemical Bonding in Biology

Chemical Bonding in Biology

• Matter takes up space and has mass, it is composed of elements.
• Elements are substances that cannot be broken down, while compounds consist of two or more elements.
• Isotopes of an element differ in the number of neutrons.
• Example: Oxygen exists as isotopes with 8 protons but varying numbers of neutrons (8, 9, or 10).

Chemical Bondings

• Covalent bonds involve the sharing of valence electrons between atoms.
• Non-polar covalent bonds share electrons equally, making the molecule hydrophobic (e.g., O2, CH4).
• Polar covalent bonds share electrons unequally due to differences in electronegativity, resulting in partial positive and negative charges and making the molecule hydrophilic (e.g., H2O).

Factors Affecting Electronegativity

• Atomic number: Higher proton count increases the nucleus's pull on electrons.
• Atomic radius: Smaller atoms have higher electronegativity because bonding electrons are closer to the nucleus.

Ionic Bonds

• Form when an atom transfers one or more electrons to another.
• A cation is a positively charged ion, and an anion is a negatively charged ion.

Hydrogen Bonds

• Form between hydrogen and highly electronegative atoms like nitrogen (N), oxygen (O), and fluorine (F).
• The positive pole of one water molecule is attracted to the negative pole of another, forming a hydrogen bond.

Van Der Waals Bonds

• Weak bonds that occur only when atoms and molecules are very close together.

Water Properties

• Water is a polar molecule with hydrogen bonds.
• Cohesion: Water molecules stick to each other, responsible for surface tension.
• Surface tension: The workload required to break the surface of water.
• Adhesion: Water adheres to other substances due to its polarity.
• Capillary action: Water moves up defying gravity, example plants cohesion and adhesion assists in moving up xylem to get water.

Water's Thermal Properties

• High specific heat: Requires a significant amount of heat to raise 1 gram of water by 1°C.
• Resistance to temperature changes stabilizes temperatures.
• High heat of vaporization: Requires a large amount of heat to convert liquid water to gas.
• Evaporative cooling: Occurs because the “hottest” molecules are likely to leave as gas, cooling the remaining liquid.

Density

• Water expands upon freezing, making ice less dense and able to float.

Water as a Solvent

• Solution: Homogenous mixture of substances.
• Solvent: Dissolving agent of a solution.
• Solute: Substance that is dissolved.
• Aqueous solution: Water is the solvent.
• Water dissolves polar (hydrophilic) molecules, since water is polar, it has partial negative and partial positive forces.

Formation and Breakdown of Macromolecules

• Monomers are repeating units that form polymers.
• Polymers are chains of macromolecules.
• Dehydration reaction: Bonds two monomers with the loss of H2O.
• Hydrolysis: Breaks bonds by adding H2O.

Carbon and Organic Chemistry

• Carbon: Backbone of life, it can make complex molecules because it has four valence electrons.
• Organic chemistry: Study of carbon compounds.
• Hydrocarbons: Only hydrogen and carbon (nonpolar).

Isomers Types

• Isomers: Same numbers of atoms but different structures and properties
• Structural Isomers: Different covalent arrangements.
• Cis-trans Isomers: Difference in spatial arrangements due to inflexibility in double bonds.
• Enantiomers: Mirror images but differ in shape because of asymmetric carbon.

Proteins

• Are the most diverse macromolecules made of polymers of amino acids joined by peptide bonds.
• A protein’s shape determines its function.
• Antibodies protect from diseases
• Enzymes catalyze chemical reactions
• Messenger transmit signal
• Polypeptides: polymers of amino acids
• Shape determines function

Nucleic Acids

• Nucleotides: Nucleic acid building blocks composed of three parts
• Nitrogenous Base
• Five Carbon Sugar
• Phosphate
• Pairing is antiparallel

Lipids

• Lipids are nonpolar and hydrophobic.
• They include fats, phospholipids, and steroids.
• Fats: glycerol and fatty acids
• Triglyceride: 3 fatty acids bonds via ester linkage
• Unsaturated lipids: Packed less tightly and are liquid due to double bonds that create kinks.
• Saturated lipids: Pack tightly and are solid due to lack of double bonds.
• Steroids: lipids characterized by a carbon skeleton consisting of four-fused rings, ex Cholesterol

Eukaryotic and Prokaryotic Cells

• Cells are the basic functional unit of life.
• Prokaryotic cells: Less complex and smaller.
• Eukaryotic cells: Larger, more complex, and contain membrane-bound organelles
• Both Contain:
• Plasma membrane
• Genetic information (DNA)
• Ribosomes
• Compartmentalization: Organelles have their own specific functions.
• The Endomembrane System: Includes the nuclear membrane, ER, Golgi apparatus, plasma membrane, and lysosomes.
• The Cytoskeleton's Microtubules provide structural support and maintain cell shape.

Molecules and Membranes

• Cell membranes are composed of phospholipid molecules and are amphipathic.
• The Plasma Membrane is selectively permeable.
• Integral Proteins are embedded into lipid bilayer and include transmembrane proteins and others partially embedded.
• Peripheral Proteins are not embedded, they are loosely bound to the surface and can attach to integral proteins.
• Membrane Carbohydrates are important for cell recognition and some use glycoproteins as receptors.

Transport Across Membranes

• Vesicles fuse to the membrane to form a bilayer.
• Exocytosis: Refers to the fusion of vesicles with the cell membrane to release contents outside of the cell.
• Endocytosis: Refers to the capture or bringing of contents into the cell.
• Phagocytosis: A cell engulfing a particle to later digest it via engulfment.
• Pinocytosis: Extracellular fluid that is gulped into a tiny vesicle.
• Receptor Mediated: Binding of specific solutes to receptors triggers vesicle formation to be triggered.

Tonicity and Osmosis

• Isotonic Solution: Same solute concentration inside and outside the cell resulting in no next water movement.
• Hypertonic Solution: Higher solute concentration outside the cell than inside resulting in water loss from cell.
• Hypotonic Solution: Lower solute concentration outside the cell resulting in water gain in cell.

Cell Metabolism and Thermodynamics

• Metabolism: All chemical reactions in organism.
• Catabolic Pathways: Breakdown of complex molecules with the release of energy (e.g., cellular respiration).
• Anabolic Pathways: Consume energy to build complex molecules (e.g., photosynthesis).
• Kinetic Energy: Energy of motion.
• Potential Energy: Stored energy based on an object's position.

Free Energy

• Exergonic Reactions: Reactions that release energy.
• Endergonic Reactions: Reactions that absorb energy.