General Biology: Atomic Structure, Chemical Bonds, and Properties of Water

Atomic Structure and Elements

Atoms and Molecules

Atoms are the basic units of matter, composed of protons, neutrons, and electrons. Molecules are formed when atoms bond together chemically.

• Atom: The smallest unit of an element, retaining its chemical properties.

• Molecule: Two or more atoms bonded together.

• Element: A substance made of only one type of atom.

• Atomic Number: Number of protons in the nucleus of an atom.

• Mass Number: Sum of protons and neutrons in the nucleus.

• Isotope: Atoms of the same element with different numbers of neutrons.

• Ion: An atom or molecule with an electrical charge due to loss or gain of electrons.

Example: Carbon-12 and Carbon-14 are isotopes of carbon, differing in neutron number.

Subatomic Particles

• Proton: Positively charged particle in the nucleus; defines the element.

• Neutron: Neutral particle in the nucleus; contributes to atomic mass.

• Electron: Negatively charged particle orbiting the nucleus; involved in chemical bonding.

Example: Hydrogen has 1 proton, 0 neutrons, and 1 electron.

Electron Shells and Energy Levels

Electrons occupy energy levels (shells) around the nucleus. The arrangement of electrons determines chemical reactivity.

• First shell: up to 2 electrons

• Second shell: up to 8 electrons

• Third shell: up to 8 electrons (for main group elements)

Valence electrons are electrons in the outermost shell and are crucial for chemical bonding.

Chemical Bonds and Interactions

Types of Chemical Bonds

Chemical bonds form when atoms share or transfer electrons to achieve stability.

• Ionic Bond: Formed when one atom donates an electron to another, resulting in oppositely charged ions.

• Covalent Bond: Formed when atoms share pairs of electrons.

• Polar Covalent Bond: Unequal sharing of electrons, resulting in partial charges.

• Nonpolar Covalent Bond: Equal sharing of electrons.

• Hydrogen Bond: Weak attraction between a hydrogen atom (partially positive) and an electronegative atom (such as oxygen or nitrogen).

Example: Sodium chloride (NaCl) forms an ionic bond; water (H2O) has polar covalent bonds and hydrogen bonds between molecules.

Bond Properties and Electronegativity

• Electronegativity: The tendency of an atom to attract electrons in a bond.

• Large differences in electronegativity lead to ionic bonds; small differences lead to covalent bonds.

Example: Oxygen is more electronegative than hydrogen, making water a polar molecule.

Properties of Water

Water Structure and Polarity

Water is a polar molecule due to the unequal sharing of electrons between oxygen and hydrogen.

• Polarity: Water has a partial negative charge near oxygen and partial positive charges near hydrogens.

• Hydrogen Bonding: Water molecules form hydrogen bonds, leading to unique properties.

Unique Properties of Water

• Cohesion: Water molecules stick to each other.

• Adhesion: Water molecules stick to other surfaces.

• Surface Tension: Water has a high surface tension due to hydrogen bonding.

• High Specific Heat: Water resists temperature changes.

• Solvent Properties: Water dissolves many substances due to its polarity.

Example: Water rises in a plant stem due to cohesion and adhesion (capillary action).

Acids, Bases, and pH

Definitions and Properties

Acids and bases are substances that affect the concentration of hydrogen ions (H+) in solution.

• Acid: Substance that increases H+ concentration; pH < 7.

• Base: Substance that decreases H+ concentration (or increases OH-); pH > 7.

• pH Scale: Measures acidity or basicity; ranges from 0 (most acidic) to 14 (most basic).

Formula:

$pH = -\log_{10}[H^+]$

Example: A solution with [H+] = 1 x 10-7 M has a pH of 7 (neutral).

Buffers

Buffers are substances that minimize changes in pH by absorbing or releasing H+ ions.

• Important for maintaining homeostasis in biological systems.

Macromolecules and Functional Groups

Macromolecules

Large molecules essential for life, formed by joining smaller units (monomers).

• Polymer: Large molecule made of repeating monomers.

• Monomer: Small unit that joins to form polymers.

• Examples: Proteins (amino acids), nucleic acids (nucleotides), carbohydrates (sugars), lipids (fatty acids).

Functional Groups

Groups of atoms attached to carbon skeletons that determine chemical properties.

• Hydroxyl (-OH): Found in alcohols.

• Carboxyl (-COOH): Found in acids.

• Phosphate (-PO4): Found in nucleic acids.

• Amino (-NH2): Found in amino acids.

• Sulfhydryl (-SH): Found in proteins.

• Carbonyl (C=O): Found in sugars.

Functional groups affect solubility, reactivity, and interactions of molecules.

Energy and Thermodynamics

Types of Energy

• Energy: Capacity to do work.

• Entropy: Measure of disorder in a system.

• Kinetic Energy: Energy of motion.

• Potential Energy: Stored energy due to position or structure.

Thermodynamics

• First Law: Energy cannot be created or destroyed, only transformed.

• Second Law: Entropy increases in any energy transformation.

Spontaneous reactions occur when products have lower energy and higher entropy than reactants.

Tables and Data

Table 1: Characteristics of Select Elements

Element	# Electrons	# Protons	# Neutrons	# Valence Electrons
Hydrogen	1	1	0	1
Helium	2	2	2	2
Sodium	11	11	12	1
Chlorine	17	17	18	7
Carbon	6	6	6	4
Oxygen	8	8	8	6
Nitrogen	7	7	7	5

Table 2: Bonding Characteristics of CHNOPS Elements

Abbreviation	Atom	# Electrons in Outer Shell	# Empty Slots	# Bonds Formed
C	Carbon	4	4	4
H	Hydrogen	1	1	1
N	Nitrogen	5	3	3
O	Oxygen	6	2	2
P	Phosphorus	5	3	3
S	Sulfur	6	2	2

Table 3: Bond Classification

Elements	Difference in Electronegativity	Bond Type
Ca and Br	Large	Ionic
O and O	None	Nonpolar Covalent
H and S	Moderate	Polar Covalent
Ca and O	Large	Ionic
Si and Cl	Moderate	Polar Covalent
As and P	Small	Nonpolar Covalent
C and O	Moderate	Polar Covalent
H and H	None	Nonpolar Covalent
Additional info: Entries inferred based on standard electronegativity values.

Electron Configuration

Writing Electron Configurations

Electron configuration describes the arrangement of electrons in an atom's shells and subshells.

• Hydrogen (H): 1s1

• Beryllium (Be): 1s2 2s2

• Oxygen (O): 1s2 2s2 2p4

• Sodium (Na): 1s2 2s2 2p6 3s1

• Magnesium (Mg): 1s2 2s2 2p6 3s2

• Sulfur (S): 1s2 2s2 2p6 3s2 3p4

Diagrams and Models

Bohr Models of Atoms

Bohr models show electrons in discrete energy levels around the nucleus.

• Helium: 2 electrons in first shell

• Carbon: 2 electrons in first shell, 4 in second shell

• Sulfur: 2 electrons in first shell, 8 in second shell, 6 in third shell

Example: See diagram for electron placement in shells.

Summary Table: Key Terms and Definitions

Term	Definition
Atom	Smallest unit of matter retaining chemical properties
Element	Substance made of one type of atom
Isotope	Atoms of same element with different neutron numbers
Ion	Atom or molecule with net electrical charge
Covalent Bond	Bond formed by sharing electrons
Ionic Bond	Bond formed by transfer of electrons
Hydrogen Bond	Weak attraction between polar molecules
pH	Measure of hydrogen ion concentration
Buffer	Substance that stabilizes pH
Polymer	Large molecule made of monomers
Functional Group	Specific group of atoms affecting molecule's properties

Additional info:

• Some table entries and bond classifications were inferred based on standard chemistry knowledge.

• Electron configurations and Bohr models are expanded for clarity.

• Functional group examples and definitions are provided for completeness.