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Fundamental Chemistry Concepts for Biology and Organic Chemistry

Study Guide - Smart Notes

Tailored notes based on your materials, expanded with key definitions, examples, and context.

Atoms and Atomic Structure

Definition and Components of Atoms

An atom is the smallest unit of an element that retains the properties of that element. Atoms are the fundamental building blocks of matter and are composed of subatomic particles.

  • Nucleus: The central core of the atom, containing protons and neutrons.

  • Proton: A positively charged particle located inside the nucleus.

  • Neutron: A particle found in the nucleus with no electrical charge.

  • Electron: A negatively charged particle that orbits the nucleus in energy levels.

Energy Levels and Electron Arrangement

Electrons occupy specific regions called energy levels around the nucleus. Each energy level can hold a limited number of electrons:

  • The first energy level can hold 2 electrons.

  • The second energy level can hold 8 electrons.

  • The third energy level can hold 18 electrons.

For an atom to be stable, its energy levels must be filled according to the number of electrons present.

Example: An atom with 8 electrons will have 2 electrons in the first energy level and 6 in the second energy level.

Additional info: The stability of an atom is often determined by the completion of its outermost energy level (octet rule).

Elements and the Periodic Table

Definition and Properties of Elements

An element is a pure substance that cannot be broken down into simpler substances by chemical means. There are about 90 naturally occurring elements, all listed on the Periodic Table.

  • Only 25 elements are essential for living organisms.

  • 96% of the mass of a human is composed of carbon (C), hydrogen (H), nitrogen (N), and oxygen (O).

Atomic Number and Atomic Mass

  • Atomic Number: The number of protons in the nucleus of an atom; also equals the number of electrons in a neutral atom.

  • Atomic Mass: The sum of protons and neutrons in the nucleus.

Example: Carbon has an atomic number of 6 (6 protons) and an atomic mass of 12 (6 protons + 6 neutrons).

Ions and Isotopes

Ions

Ions are atoms or molecules that have gained or lost electrons, resulting in a net charge.

  • Number of protons does not change in ions.

  • Example: Na+ has lost one electron compared to neutral sodium.

Isotopes

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

  • Example: Carbon-12 (6 protons, 6 neutrons), Carbon-13 (6 protons, 7 neutrons), Carbon-14 (6 protons, 8 neutrons).

Compounds, Molecules, and Chemical Bonds

Compounds and Molecules

  • Compound: A substance made of two or more different elements bonded together (e.g., NaCl, H2O).

  • Molecule: A group of atoms held together by covalent bonds (e.g., O2).

Covalent Bonds

Covalent bonds form when two atoms share electrons.

  • Polar Covalent Bond: Electrons are shared unequally, resulting in partial charges (e.g., H2O).

  • Nonpolar Covalent Bond: Electrons are shared equally (e.g., H2, ethane).

Ionic Bonds

Ionic bonds form when atoms transfer electrons, resulting in oppositely charged ions that attract each other.

  • Example: Na+ + Cl- → NaCl

Hydrogen Bonds

Hydrogen bonds are weak attractions between a hydrogen atom in one molecule and a highly electronegative atom (such as oxygen or nitrogen) in another molecule. These bonds are crucial for the structure and properties of water and biological macromolecules.

  • Hold water molecules together.

  • Help stabilize large molecules like proteins and DNA.

Properties of Water

Polarity and Hydrogen Bonding

Water is a polar molecule due to the uneven distribution of electrons between oxygen and hydrogen atoms. Oxygen has a stronger pull on electrons, making the oxygen side slightly negative and the hydrogen side slightly positive.

Cohesion and Adhesion

  • Cohesion: Attraction between molecules of the same substance (e.g., water molecules stick together).

  • Adhesion: Attraction between molecules of different substances (e.g., water and glass, causing meniscus and capillary action).

High Specific Heat Capacity

Water can absorb large amounts of heat due to its hydrogen bonds, helping regulate temperature in organisms and environments.

Evaporative Cooling

As water evaporates, it removes heat from surfaces, providing a cooling effect (e.g., sweating).

Versatile Solvent

Water's polarity makes it an excellent solvent, capable of dissolving many substances essential for life.

Solutions, Acids, and Bases

Solutions

  • Solution: A homogeneous mixture of two or more substances.

  • Solute: The substance dissolved (e.g., iced tea mix).

  • Solvent: The substance doing the dissolving (e.g., water).

  • Water is often called the "universal solvent" due to its ability to dissolve many substances.

pH Scale

The pH scale measures the concentration of hydrogen ions (H+) versus hydroxide ions (OH-) in a solution. The scale ranges from 0 (most acidic) to 14 (most basic).

  • pH 7: Neutral (pure water)

  • pH < 7: Acidic (more H+ ions)

  • pH > 7: Basic (more OH- ions)

Examples:

  • Pure water: pH 7

  • Soda: pH 3

  • Hair remover (Nair): pH 13

Additional info: The formula for pH is .

Chemical Equations

Reactants, Products, and Coefficients

Chemical equations represent the transformation of reactants into products during a chemical reaction.

  • Reactants: Substances that undergo change.

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

  • Coefficients: Numbers placed before compounds to indicate the number of molecules involved.

  • Subscripts: Numbers within chemical formulas indicating the number of atoms of each element in a molecule.

Example Equation:

  • Reactants: Glucose () and oxygen ()

  • Products: Carbon dioxide (), water (), and energy

Additional info: This equation represents cellular respiration, a key process in biology and biochemistry.

Summary Table: Atomic Particles

Particle

Charge

Location

Proton

+1

Nucleus

Neutron

0

Nucleus

Electron

-1

Energy levels/orbitals

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