Ch 2 Outline Atoms, Elements, and Chemical Bonds: Foundations for General Biology

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Ch 2

Atoms and Matter

Definition of Matter

Matter is anything that has mass and occupies space. All living and non-living things are composed of matter, which is made up of atoms.

Atoms: The smallest unit of matter that retains the properties of an element.

Structure of Atoms

Protons: Positively charged particles found in the nucleus of an atom.
Neutrons: Neutral particles (no charge) also located in the nucleus.
Electrons: Negatively charged particles that orbit the nucleus in energy shells.

Elements

An element is a substance that cannot be broken down into simpler substances by chemical means. Each element is defined by its number of protons (atomic number).

Atomic Number: The number of protons in the nucleus of an atom. Determines the identity of the element.
Atomic Mass: The sum of protons and neutrons in the nucleus.

CHONPS: The Six Most Important Elements in Living Organisms

The acronym CHONPS stands for the six most abundant elements in living organisms:

Carbon (C)
Hydrogen (H)
Oxygen (O)
Nitrogen (N)
Phosphorus (P)
Sulfur (S)

These elements are essential for the structure and function of biomolecules such as proteins, nucleic acids, carbohydrates, and lipids.

Trace Elements

Trace elements are elements required by organisms in very small quantities, but are vital for proper biological function (e.g., iron, zinc, copper).

Atomic Number and Atomic Mass: Practice

Each element has a unique atomic number and atomic mass. For example:

Element	Atomic Number	Atomic Mass	# of Protons	# of Neutrons	# of Electrons
Hydrogen (H)	1	1.008	1	0	1
Argon (Ar)	18	39.948	18	22	18
Oxygen (O)	8	15.999	8	8	8

Additional info: Neutron number is calculated as atomic mass (rounded to nearest whole number) minus atomic number.

Electron Distribution and the Bohr Model

Energy Shells

Electrons are arranged in energy levels or shells around the nucleus. The distribution of electrons determines the chemical properties and reactivity of the atom.

Bohr Model: A simplified model showing electrons in concentric shells around the nucleus.
First shell: Holds up to 2 electrons.
Second shell: Holds up to 8 electrons.

Periodic Table Organization

Rows (Periods): Indicate the number of electron shells.
Columns (Groups): Indicate the number of valence electrons.

Octet Rule

The octet rule states that atoms tend to gain, lose, or share electrons to achieve a full set of eight valence electrons, making them more stable.

Importance: Explains the chemical reactivity and bonding behavior of most elements.
Exceptions: Hydrogen and helium are stable with two electrons (duet rule).
Least reactive group: Noble gases (Group 18) are least reactive because they already have a full valence shell.

Chemical Bonds in Molecules and Compounds

Types of Chemical Bonds

Ionic Bond: Formed when electrons are transferred from one atom to another, resulting in oppositely charged ions that attract each other.
Covalent Bond: Formed when two atoms share one or more pairs of electrons.
- Nonpolar Covalent Bond: Electrons are shared equally between atoms (e.g., H2).
- Polar Covalent Bond: Electrons are shared unequally, creating partial charges (e.g., H2O).

Ions

Ions: Atoms or molecules that have gained or lost electrons, resulting in a net charge.

Hydrogen Bonds

Hydrogen Bond: A weak bond between a hydrogen atom covalently bonded to an electronegative atom (like oxygen or nitrogen) and another electronegative atom.
Example: Hydrogen bonds hold water molecules together and stabilize DNA structure.

Van der Waals Interactions

Van der Waals Interactions: Weak attractions between molecules or parts of molecules that result from transient local partial charges.

Electronegativity

Electronegativity: The tendency of an atom to attract electrons in a chemical bond. Higher electronegativity leads to stronger attraction for electrons.

Compounds and Molecules

Compound: A substance formed when two or more different elements are chemically bonded together (e.g., H2O).
Molecule: Two or more atoms held together by covalent bonds (can be the same or different elements).

Shape and Hybridization of Molecules

Electron Orbital Hybridization

When electron orbitals hybridize, atoms can form new shapes, such as tetrahedral or planar structures, which affect the molecule's properties and reactivity.

Shape: The three-dimensional arrangement of atoms in a molecule, determined by the number of electron pairs around the central atom.
Example: Methane (CH4) has a tetrahedral shape due to sp3 hybridization.

Importance of Molecular Shape

Shape determines function: The shape of a molecule affects how it interacts with other molecules, including biological recognition and chemical reactivity.
Example: The bent shape of water (H2O) leads to its polarity and unique properties.

Examples of Molecules and Compounds

Hydrogen gas (H2): Nonpolar covalent molecule.
Oxygen gas (O2): Nonpolar covalent molecule.
Water (H2O): Polar covalent molecule with hydrogen bonding.
Methane (CH4): Nonpolar covalent molecule with tetrahedral geometry.

Uses of Radiation in Biology

Medical imaging: X-rays, PET scans, and other techniques use radiation to visualize structures inside the body.
Radioisotopes: Used as tracers in biochemical research and for cancer treatment.

Summary Table: Types of Chemical Bonds

Bond Type	Mechanism	Example	Strength
Ionic	Transfer of electrons	NaCl	Strong (in solid state)
Covalent	Sharing of electrons	H2O, CH4	Strong
Hydrogen	Attraction between H and electronegative atom	Between water molecules	Weak
Van der Waals	Transient charge interactions	Between nonpolar molecules	Very weak

Key Equations

Atomic Mass Calculation:

Number of Neutrons:

Electron Shell Capacity:

(where n = shell number)

Additional info: This guide expands on the original notes with definitions, examples, and academic context for clarity and completeness.