Chapter 2: The Chemical Level of Organization – Study Notes

Chapter 2: The Chemical Level of Organization

Atoms and Atomic Structure

The atom is the smallest stable unit of matter, composed of subatomic particles: protons (p+), neutrons (n), and electrons (e-). Protons and neutrons are similar in size and mass and are located within the nucleus, while electrons are much lighter and orbit the nucleus in an electron cloud.

• Protons: Positively charged particles found in the nucleus.

• Neutrons: Neutral particles found in the nucleus.

• Electrons: Negatively charged particles orbiting the nucleus.

• Atomic number: The number of protons in an atom, unique for each element.

• Electron cloud: The region around the nucleus where electrons are likely to be found.

Example: A hydrogen atom (atomic number 1) contains one proton and one electron.

Elements and Isotopes

An element is a pure substance composed of atoms with the same number of protons. Each element has a unique atomic number and a chemical symbol (e.g., O for oxygen, Na for sodium). Isotopes are forms of the same element with different numbers of neutrons, resulting in different mass numbers but similar chemical properties.

• Element: Substance with atoms of one type; cannot be broken down by ordinary means.

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

• Mass number: Total number of protons and neutrons in an atom.

• Radioisotopes: Unstable isotopes that emit radiation as they decay.

• Half-life: Time required for half of a radioactive isotope to decay.

Example: Hydrogen-1, Hydrogen-2 (deuterium), and Hydrogen-3 (tritium) are isotopes of hydrogen.

Additional info: PET scans use radioisotopes to detect metabolically active tissues, useful in cancer detection.

Electrons and Energy Levels

Electrons occupy energy levels or shells around the nucleus. The arrangement of electrons in these shells determines the chemical properties of an atom. The first shell can hold up to two electrons, while the second and third can each hold up to eight electrons. The outermost shell is called the valence shell, and its occupancy determines the atom's reactivity.

• Valence shell: Outermost electron shell; determines chemical reactivity.

• Stable atom: Has a filled valence shell and is chemically inert.

• Unstable atom: Has an unfilled valence shell and is chemically reactive.

Molecules and Compounds

Molecules are formed when two or more atoms share electrons. Compounds are chemical substances composed of atoms of two or more different elements. Not all molecules are compounds, and not all compounds are molecules (e.g., ionic compounds).

• Molecule: Two or more atoms held together by shared electrons (e.g., H2, O2, H2O).

• Compound: Substance composed of atoms of different elements (e.g., NaCl, C6H12O6).

Ions and Ionic Bonds

An ion is an atom or group of atoms with an electrical charge, formed by gaining or losing electrons. Cations are positively charged ions (loss of electrons), and anions are negatively charged ions (gain of electrons). Ionic bonds are formed by the attraction between cations and anions.

• Cation: Positively charged ion (e.g., Na+).

• Anion: Negatively charged ion (e.g., Cl-).

• Ionic bond: Attraction between oppositely charged ions, forming ionic compounds (e.g., NaCl).

Covalent Bonds

Covalent bonds are formed when atoms share electrons. These bonds can be single, double, or triple, depending on the number of shared electron pairs. Nonpolar covalent bonds involve equal sharing, while polar covalent bonds involve unequal sharing, resulting in partial charges.

• Single covalent bond: One pair of shared electrons.

• Double covalent bond: Two pairs of shared electrons.

• Triple covalent bond: Three pairs of shared electrons.

• Nonpolar covalent bond: Equal sharing of electrons (e.g., H2).

• Polar covalent bond: Unequal sharing of electrons (e.g., H2O).

Hydrogen Bonds

Hydrogen bonds are weak electrical attractions between the partial positive charge of a hydrogen atom in a polar covalent bond and the partial negative charge of an oxygen, nitrogen, or fluorine atom in another polar covalent bond. These bonds are important in water, proteins, and nucleic acids.

Chemical Reactions

Chemical reactions involve the formation or breaking of bonds between atoms. They are represented by chemical equations, with reactants on the left and products on the right. Types of reactions include decomposition, synthesis, exchange, and reversible reactions.

• Decomposition reaction: $AB \rightarrow A + B$

• Hydrolysis: $AB + H_2O \rightarrow AH + BOH$

• Synthesis reaction: $A + B \rightarrow AB$

• Dehydration synthesis: $AH + BOH \rightarrow AB + H_2O$

• Exchange reaction: $AB + CD \rightarrow AD + CB$

• Reversible reaction: $A + B \rightleftharpoons AB$

pH and Homeostasis

pH measures the concentration of hydrogen ions in a solution. A pH of 7 is neutral, below 7 is acidic, and above 7 is basic (alkaline). The pH of blood is tightly regulated between 7.35 and 7.45. Deviations can cause acidosis (pH < 7.35) or alkalosis (pH > 7.45), which can be life-threatening.

• Acidosis: Low blood pH, can lead to coma.

• Alkalosis: High blood pH, can cause sustained muscle contractions.

• Homeostasis: Maintained by negative feedback mechanisms involving respiration and kidney function.

Macromolecules

Macromolecules are large, complex molecules essential for life. There are four main types: carbohydrates, lipids, proteins, and nucleic acids. Each is composed of smaller subunits called monomers, which join to form polymers via dehydration synthesis and are broken down by hydrolysis.

• Carbohydrates: Energy sources; monomer is monosaccharide (e.g., glucose).

• Lipids: Energy storage, insulation, and membrane structure; monomers include fatty acids and glycerol.

• Proteins: Structure, enzymes, transport, defense; monomer is amino acid.

• Nucleic acids: Information storage and processing; monomer is nucleotide.

Carbohydrates

Carbohydrates contain carbon, hydrogen, and oxygen in a 1:2:1 ratio. They serve as energy sources and structural components. Types include monosaccharides (simple sugars), disaccharides (two monosaccharides), and polysaccharides (many monosaccharides).

• Monosaccharide: Simple sugar (e.g., glucose).

• Disaccharide: Two monosaccharides joined (e.g., sucrose).

• Polysaccharide: Many monosaccharides (e.g., starch, glycogen, cellulose).

• Isomers: Molecules with the same formula but different structures (e.g., glucose and fructose).

Lipids

Lipids are hydrophobic molecules with a high carbon-to-hydrogen ratio. Types include fatty acids, glycerides, steroids, and phospholipids. Fatty acids can be saturated (no double bonds) or unsaturated (one or more double bonds). Triglycerides are important for energy storage, insulation, and protection. Steroids (e.g., cholesterol, hormones) and phospholipids are key components of cell membranes.

Proteins

Proteins are polymers of amino acids and are the most abundant macromolecules in the body. They serve structural, functional, and regulatory roles. Protein structure has four levels: primary (amino acid sequence), secondary (alpha helix, beta sheet), tertiary (3D folding), and quaternary (multiple polypeptides). Denaturation disrupts protein function. Many proteins are enzymes that catalyze biochemical reactions.

Nucleic Acids

Nucleic acids (DNA and RNA) store and process genetic information. They are polymers of nucleotides, each consisting of a pentose sugar, phosphate group, and nitrogenous base (A, G, C, T, U). DNA encodes protein instructions; RNA helps build proteins. DNA is double-stranded (A-T, C-G base pairs), while RNA is single-stranded (A, C, G, U).

High-Energy Compounds

Cells use high-energy compounds, such as ATP, to perform work. ATP is formed by adding phosphate groups to adenosine (AMP, ADP, ATP). The enzyme ATPase catalyzes the breakdown of ATP to ADP, releasing energy for cellular processes.

• ATP hydrolysis: $\text{ATP} + \text{H}_2\text{O} \rightarrow \text{ADP} + \text{phosphate group} + \text{energy}$