Unit 2

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Hierarchy of Organization

  • The organization of matter progresses from simple to complex:

    • Atoms

    • Molecules

    • Macromolecules

    • Virus

    • Prokaryote (e.g., bacteria)

    • Eukaryote (e.g., Protist, Fungus, Plant, Animal)

Atoms, Bonds, and Molecules

  • Matter: The substance of which physical objects are made.

  • Atom: The smallest unit of an element that retains the properties of that element.

  • Protons: Positively charged particles located in the nucleus of an atom.

  • Neutrons: Neutral particles found in the nucleus of an atom.

  • Electrons: Negatively charged particles that orbit the nucleus of an atom.

  • Diagrams illustrate the structure of hydrogen and carbon atoms showing the particles in the nucleus and electrons in their orbits.

Different Types of Atoms

  • All atoms share a fundamental structure characterized by:

    • The presence of protons, neutrons, and electrons.

  • Element: A pure substance that cannot be broken down into simpler substances by chemical means.

Periodic Table

  • The Periodic Table of Elements displays all known chemical elements, organized by increasing atomic number.

Characteristics of Elements

  • Important characteristics include:

    • Atomic number: The number of protons in the nucleus of an atom, defining the element.

    • Mass number: The total number of protons and neutrons in an atom's nucleus.

    • Isotopes: Variants of a particular chemical element that have the same number of protons but different numbers of neutrons.

    • Atomic weight: The weighted average mass of an element's isotopes.

    • Electron Orbitals: Regions around the nucleus where electrons are likely to be found.

Bonds and Molecules

  • Molecule: A group of two or more atoms bonded together.

  • Compounds: Substances formed when two or more different elements bond together.

  • Chemical Bonds: Connections between atoms that allow the formation of molecules.

    • Types include:

    • Covalent Bonds: Bonds formed by sharing electrons between atoms:

      • Polar covalent bonds: Occur when electrons are shared unequally, leading to charged regions within the molecule.

      • Nonpolar covalent bonds: Occur when electrons are shared equally between atoms.

    • Ionic Bonds: Bonds formed when one atom transfers an electron to another atom, resulting in ions that attract each other (e.g., NaCl, sodium chloride).

    • Hydrogen Bonds: Weak attractions between a hydrogen atom of one molecule and a highly electronegative atom (e.g., oxygen or nitrogen) of another molecule.

Polarity

  • Polarity in molecules results from uneven electron sharing:

    • The water molecule (H2O) has a bent geometry leading to a partial negative charge near the oxygen atom and partial positive charges near the hydrogen atoms, due to oxygen being an electron hog, or more electronegative than hydrogen.

Oxidation-Reduction Reactions

  • Oxidation: The process in which an atom or molecule loses electrons.

  • Reduction: The process in which an atom or molecule gains electrons.

  • Redox Reactions: Reactions that involve the transfer of electrons between two species, crucial for energy exchange in cells.

Chemical Shorthand

  • In chemical reactions:

    • Reactants: Substances that undergo chemical changes.

    • Products: Substances formed as a result of the reaction.

    • Synthesis Reaction: A type of reaction where two or more substances combine to form a new compound (e.g., S + O2 ightarrow SO2).

    • Decomposition Reaction: A reaction where a compound breaks down into simpler products (e.g., 2 H2O2
      ightarrow 2 H2O + O2).

    • Exchange Reaction: A reaction involving the exchange of components between two compounds (e.g., HCl + NaOH
      ightarrow NaCl + H_2O).

Solutions

  • Solutes: The substances that dissolve (e.g., Na$^+$ & Cl$^-$).

  • Solvent: The substance in which the solute dissolves (e.g., H$_2$O).

  • Solution: A homogeneous mixture formed from solutes and solvents.

Aqueous Solutions

  • Hydrophilic Molecules: Substances that easily dissolve in water.

  • Hydrophobic Molecules: Substances that do not dissolve in water.

  • Amphipathic Molecules: Molecules that possess both hydrophilic and hydrophobic properties (e.g., phospholipids).

Acidity, Alkalinity, and the pH Scale

  • The ionization of water (H_2O) produces Hydrogen ions ([H^+]) and Hydroxyl ions ([OH^-]):

  • pH Scale: Ranges from 0 to 14, indicating the concentration of hydrogen ions:

    • 0-6: Acidic

    • 7: Neutral

    • 8-14: Basic

  • The formula for pH is: pH = - ext{log} [H^+].

pH and Ion Concentration

  • A table showing the relationship between molarity (mole/L) of H, H concentration, pH values from 0 to 14, and corresponding mole/L concentrations of OH ions.

The Versatility of Bonding in Carbon

  • The diverse bonding properties of carbon lead to numerous functional forms:

    • Carbon can form different shaped molecules through various bonding arrangements.

Functional Groups in Organic Molecules

  • Functional groups are parts of organic molecules participating in chemical reactions:

    • Amino group (-NH_2)

    • Carboxylic acid group (-COOH)

    • Hydroxyl group (-OH)

    • Methyl group (-CH_3)

    • Phosphate group (-PO_4^{3-})

    • Sulfhydryl group (-SH)

Macromolecules

  • Biochemicals: Organic compounds produced by living organisms.

  • Macromolecules: Large, complex molecules essential for life.

    • Monomer: The individual building blocks of macromolecules.

    • Polymer: A molecule composed of many monomers linked together.

    • Four biological macromolecules include:

    • Carbohydrates

    • Lipids

    • Proteins

    • Nucleic Acids