Biology Study Guide - Chapter 2: Basic Chemistry

Definition of Matter:
- Matter is defined as anything that has mass and occupies space.
States of Matter:
- Matter exists in three states: solid, liquid, and gas.
Composition of Matter:
- All matter (both living and non-living) is composed of elements.

Definition of Element:
- An element is a substance that cannot be broken down into substances with different properties; it is composed of one type of atom.
Key Elements in Organisms:
- Six elements make up 95% of the body weight of organisms, known by the acronym CHNOPS:
1. Carbon (C)
2. Hydrogen (H)
3. Nitrogen (N)
4. Oxygen (O)
5. Phosphorus (P)
6. Sulfur (S)
Element Composition:
- The composition of Earth's crust and its organisms includes various elements, with notable percentages shown in diagrams (not provided in detail here).

Definition of Atom:
- An atom is the smallest part of an element that displays the property of the element.
- An element and its atom share the same name.
Subatomic Particles:
- Atoms are composed of subatomic particles:
- Protons:
  - Positively charged (+1)
  - Mass: 1 atomic mass unit (amu)
- Neutrons:
  - No charge (0)
  - Mass: 1 amu
- Electrons:
  - Negatively charged (−1)
  - Very low mass (negligible in calculations)
Atom Structure:
- Atoms consist of a central nucleus containing protons and neutrons, with electrons orbiting in shells around the nucleus.

Atomic Symbol:
- Each element is represented by one or two letters for unique identification (e.g., H = hydrogen, Na = sodium, C = carbon).
Atomic Number:
- The atomic number is equal to the number of protons in each atom of an element.
Mass Number:
- The mass number of an atom is equal to the sum of the number of protons and neutrons in the atom's nucleus.
- The atomic mass is approximately equal to the mass number.

Structure:
- Atoms of an element are arranged horizontally by increasing atomic number in rows called periods, and vertically in groups.
- Atoms within the same group share similar binding characteristics.
- Atoms shown in the periodic table are electrically neutral, meaning the atomic number equals the number of electrons and protons.

Definition of Isotopes:
- Isotopes are atoms of the same element that differ in the number of neutrons (hence different atomic masses).
- Some isotopes are radioactive and spontaneously decay, emitting energy in forms of rays and subatomic particles, which can be either helpful or harmful.
Examples of Carbon Isotopes:
- Carbon-12 ( ${}^{12}_{6} ext{C}$ )
- Carbon-13 ( ${}^{13}_{6} ext{C}$ )
- Carbon-14 ( ${}^{14}_{6} ext{C}$ )

Electron Dynamics:
- Electrons are attracted to the positively charged nucleus, thus it requires energy to hold them in place. It also takes energy to push them away.
- The further away the shell, the more energy required to maintain stability.
Chemical Behavior:
- Electrons primarily determine the chemical behavior of atoms due to their potential energy related to their position.

Bohr Model:
- The Bohr model helps visualize the electron arrangement around the nucleus, describing energy levels (shells).
- For atoms with atomic numbers ≤ 20, the following rules apply:
1. The first energy shell can hold up to 2 electrons.
2. Each additional shell can hold up to 8 electrons.
3. Lower shells are filled first before electrons are added to higher shells.

Definition of Valence Shell:
- The outermost energy shell is referred to as the valence shell and is crucial in determining the chemical properties of an atom.
Octet Rule:
- The valence shell is most stable when it has eight electrons, with an exception for atoms with one shell, which are stable at two electrons.
Chemical Reactivity:
- The number of electrons in the valence shell dictates whether an atom will give up, accept, or share electrons to complete its octet.
- Atoms with filled valence shells are stable, while those that are not are reactive.

Molecule Definition:
- A molecule consists of two or more elements bonded together.
Compound Definition:
- A compound is specifically a molecule containing at least two different elements bonded together (e.g., CO2, H2O, C6H12O6).
Chemical Formula:
- Indicates the number of each kind of atom in a molecule.

Water as a Polar Molecule:
- The shape of a water molecule and its polarity allows for hydrogen bonding.
Hydrogen Bonds:
- Weak attractions between slightly positive hydrogen atoms and slightly negative atoms.
- Hydrogen bonds can occur between different molecules or within the same molecule.
- A single hydrogen bond can be easily broken, but many bonds are collectively strong, crucial in maintaining structures of proteins and DNA.

Hydrogen Bonding Effects:
- Water has unique chemical properties due to its hydrogen bonds, leading to a high heat capacity, allowing it to absorb significant heat with little change in temperature.
Heat of Vaporization:
- Water has a high heat of vaporization as hydrogen bonds must be broken to evaporate water, which is important for cooling mechanisms in organisms.
Solvent Properties:
- Water is an excellent solvent due to its polarity. Polar substances dissolve readily, while hydrophobic molecules do not.
Cohesion and Adhesion:
- Cohesion refers to water molecules clinging to one another due to hydrogen bonding; it leads to high surface tension.
- Adhesion is the ability of water to cling to other polar surfaces, facilitating capillary action in plants.
Density Properties:
- Ice is less dense than liquid water, which allows it to float, providing insulation on frozen bodies of water.

pH Scale:
- pH measures hydrogen ion concentration in a solution. Water ionizes into H+ and OH- ions.
- Acids increase H+ concentration when dissolved in water, while bases either take H+ ions or release OH- ions.
pH Values:
- The pH scale ranges from 0–14:
- Acidic: 0 to <7
- Neutral: 7
- Basic (>7 to 14)
- It is logarithmic, where each change in pH reflects a 10-fold change in H+ concentration.
Buffers:
- Buffers are chemicals that maintain pH within narrow limits, essential for organism health.
- For humans, normal blood pH is 7.4. Deviations can lead to life-threatening conditions like acidosis or alkalosis, prompting built-in regulatory mechanisms.