Chapter 2 Study Guide: Atoms, Chemical Bonds, Water, and Biological Macromolecules

Atoms and Atomic Structure

Subatomic Particles and Atomic Mass

Atoms are the fundamental units of matter, composed of three main subatomic particles: protons, neutrons, and electrons. These particles are arranged in specific ways within the atom.

• Protons: Positively charged particles found in the nucleus.

• Neutrons: Neutral particles also located in the nucleus.

• Electrons: Negatively charged particles that orbit the nucleus in electron shells.

The atomic number is the number of protons in an atom, while the atomic mass (or mass number) is the sum of protons and neutrons.

• Isotope: Atoms of the same element with different numbers of neutrons, resulting in different atomic masses.

Compounds, Molecules, and Chemical Bonds

Compounds vs. Molecules

A compound is a substance formed when two or more different elements are chemically bonded together. A molecule is two or more atoms bonded together, which may be the same or different elements.

• Example: Table salt (NaCl) is both a molecule and a compound.

• O2 is a molecule but not a compound (since it contains only one element).

Solvent and Solute

In biological systems, water is the universal solvent. A solvent is a substance that dissolves another substance (the solute).

• Example: In saltwater, water is the solvent and salt is the solute.

Octet Rule

The octet rule states that atoms tend to form chemical bonds in order to have eight electrons in their outermost shell, achieving stability similar to noble gases. This is accomplished by losing, gaining, or sharing electrons.

Chemical Bonds

Chemical bonds are the forces that hold atoms together in molecules and compounds. The main types are:

• Covalent Bonds: Electrons are shared between atoms.

  • Polar covalent bond: Electrons are shared unequally, resulting in partial charges on the atoms.

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

• Ionic Bonds: Electrons are transferred from one atom to another, creating ions (charged atoms).

  • Cation: A positively charged ion (loses electrons).

  • Anion: A negatively charged ion (gains electrons).

• Hydrogen Bonds: Weak attractions between a hydrogen atom (already covalently bonded to an electronegative atom like oxygen or nitrogen) and another electronegative atom. Hydrogen bonds are important in the structure of water and biological molecules like DNA and proteins.

Energy in Chemical Reactions

Endergonic vs. Exergonic Reactions

Chemical reactions can be classified based on energy changes:

• Endergonic reactions: Absorb energy (e.g., photosynthesis).

• Exergonic reactions: Release energy (e.g., cellular respiration).

Enzymes are biological catalysts that speed up the rate of chemical reactions by lowering the activation energy required.

Water: Properties and Biological Importance

Anabolism and Catabolism

Anabolism refers to the synthesis of complex molecules from simpler ones (requires energy), while catabolism is the breakdown of complex molecules into simpler ones (releases energy).

• Dehydration synthesis: An anabolic process that forms bonds by removing water.

• Hydrolysis: A catabolic process that breaks bonds by adding water.

Water's Polar Solvent Properties

Water is a polar molecule, meaning it has partial positive and negative charges, allowing it to dissolve many substances. When salts dissociate in water, they form ions called electrolytes.

pH, Acids, Bases, and Buffers

• pH measures the concentration of hydrogen ions [H+] in a solution.

• High [H+] = low pH = acidic.

• Low [H+] = high pH = basic (alkaline).

• Buffer: A substance that minimizes changes in pH by accepting or donating H+ ions.

Biological Macromolecules

There are four main classes of biological macromolecules: carbohydrates, fats (lipids), proteins, and nucleic acids.

1. Carbohydrates

• General chemical formula: $C_n(H_2O)_n$

• Monomers: Monosaccharides (e.g., glucose, fructose).

• Polymers: Starch, glycogen, and cellulose are polysaccharides with different structures and functions.

2. Fats (Lipids)

• Saturated fats: No double bonds between carbon atoms; solid at room temperature.

• Unsaturated fats: One or more double bonds; liquid at room temperature.

• Trans-fats vs. omega-3 fatty acids: Trans-fats are artificially hydrogenated and less healthy; omega-3s are essential and beneficial.

• Cholesterol and phospholipids are important in cell membranes, affecting fluidity and function.

3. Proteins

• Monomers: Amino acids.

• Amino acid structure: Central carbon, amino group, carboxyl group, hydrogen atom, and R group (side chain).

• Peptide bond: Covalent bond linking amino acids.

• Protein structure:

  • Primary: Sequence of amino acids.

  • Secondary: Alpha helices and beta sheets (hydrogen bonding).

  • Tertiary: 3D folding due to side chain interactions.

  • Quaternary: Multiple polypeptide chains.

• Denaturation: Loss of protein structure and function due to environmental changes (e.g., heat, pH).

• Enzymes: Proteins that catalyze biochemical reactions by lowering activation energy.

  • Cofactor: Non-protein helper (e.g., metal ion).

  • Coenzyme: Organic helper molecule (e.g., vitamins).

4. Nucleic Acids

• Monomers: Nucleotides.

• DNA vs. RNA: DNA stores genetic information; RNA is involved in protein synthesis and gene regulation.

• ATP (Adenosine Triphosphate): The primary energy carrier in cells.

• ATP releases energy when its terminal phosphate bond is broken: $\text{ATP} \rightarrow \text{ADP} + \text{P}_i + \text{energy}$

Summary Table: Types of Chemical Bonds

Bond Type	How Formed	Strength	Example
Covalent	Sharing of electrons	Strong	H2O, O2
Ionic	Transfer of electrons	Moderate (strong in crystal, weaker in water)	NaCl
Hydrogen	Attraction between H and electronegative atom	Weak	Between water molecules, DNA strands

Summary Table: Macromolecules

Macromolecule	Monomer	Main Function	Example
Carbohydrate	Monosaccharide	Energy, structure	Glucose, starch
Lipid	Fatty acid, glycerol	Energy storage, membranes	Triglyceride, phospholipid
Protein	Amino acid	Structure, enzymes	Hemoglobin, enzymes
Nucleic Acid	Nucleotide	Genetic information	DNA, RNA