Chapter 2: The Chemical Context of Life

Elements and Compounds

All matter is composed of chemical elements, which can exist in pure form or combine to form compounds. Four elements—carbon (C), hydrogen (H), oxygen (O), and nitrogen (N)—make up about 96% of living matter.

• Element: A substance that cannot be broken down to other substances by chemical reactions.

• Compound: A substance consisting of two or more elements in a fixed ratio.

Atoms and Atomic Structure

An atom is the smallest unit of matter that retains the properties of an element. Atoms are composed of protons (positive charge), neutrons (no charge), and electrons (negative charge).

• Atomic number: Number of protons in the nucleus.

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

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

• Radioactive isotopes: Unstable isotopes that decay spontaneously, emitting particles and energy.

Electron Configuration and Chemical Bonds

The behavior of an atom is determined by the distribution of electrons in its electron shells. Atoms interact through chemical bonds to achieve stable electron configurations.

• Covalent bond: Sharing of a pair of valence electrons by two atoms.

• Ionic bond: Attraction between oppositely charged ions (atoms or molecules that have gained or lost electrons).

• Hydrogen bond: Weak bond formed when a hydrogen atom covalently bonded to one electronegative atom is attracted to another electronegative atom.

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

Molecular shape is crucial to a molecule's function, and chemical reactions are generally reversible.

Water and Life

The unique properties of water arise from its polarity and ability to form hydrogen bonds. These properties make water essential for life.

• Cohesion: Water molecules stick together due to hydrogen bonding.

• Adhesion: Water molecules stick to other substances.

• High specific heat: Water can absorb or release a large amount of heat with only a slight change in its own temperature.

• Solvent properties: Water dissolves many substances, facilitating chemical reactions in cells.

Acids, Bases, and pH

Acids and bases affect the concentration of hydrogen ions (H+) in a solution, which is measured by the pH scale.

• Acid: Substance that increases the H+ concentration of a solution (pH < 7).

• Base: Substance that reduces the H+ concentration of a solution (pH > 7).

• pH: Defined as the negative logarithm of the H+ concentration:

• At 25°C, the product of H+ and OH- concentrations is constant:

• Buffer: Substance that minimizes changes in the concentrations of H+ and OH- in a solution.

Chapter 3: Carbon and the Molecular Diversity of Life

Organic Chemistry and Carbon Compounds

Organic chemistry is the study of carbon-containing compounds. Carbon's ability to form four covalent bonds allows for a vast diversity of organic molecules, which are the basis of life.

• Major elements in organic molecules: C, H, O, N, S, P.

• Carbon can form single, double, or triple bonds, and can bond with many elements.

• Common bonding partners: hydrogen, oxygen, nitrogen.

Valences of Major Elements in Organic Molecules

The valence of an element is the number of covalent bonds it can form. This determines the structure and shape of organic molecules.

Diversity in Carbon Skeletons

Carbon skeletons form the backbone of organic molecules and can vary in several ways, contributing to molecular diversity.

• Length: Carbon chains can be short or long.

• Branching: Chains may be unbranched or branched.

• Double bond position: Double bonds can be in different locations.

• Presence of rings: Carbon skeletons may form rings.

Example: Ethane (C2H6) vs. Propane (C3H8); Cyclohexane (ring structure).

Hydrocarbons and Isomers

Hydrocarbons are organic molecules consisting only of carbon and hydrogen. Isomers are compounds with the same molecular formula but different structures and properties.

• Structural isomers: Differ in covalent arrangements of atoms.

• Cis-trans isomers: Differ in arrangement around a double bond.

• Enantiomers: Mirror images of each other.

Chemical Groups and Molecular Function

Functional groups are specific groups of atoms attached to carbon skeletons that determine the chemical properties of molecules.

• Hydroxyl group (-OH): Alcohols

• Carbonyl group (C=O): Aldehydes and ketones

• Carboxyl group (-COOH): Carboxylic acids

• Amino group (-NH2): Amines

• Sulfhydryl group (-SH): Thiols

• Phosphate group (-OPO32-): Organic phosphates

• Methyl group (-CH3): Methylated compounds

Example: Estradiol and testosterone are steroids with similar carbon skeletons but different functional groups, resulting in different biological functions.

ATP: An Important Source of Energy

Adenosine triphosphate (ATP) is the primary energy carrier in cells. Hydrolysis of ATP releases energy for cellular processes.

• ATP consists of adenosine (adenine + ribose) and three phosphate groups.

• Hydrolysis reaction:

Macromolecules: The Molecules of Life

Polymers and Monomers

Most biological macromolecules are polymers, long chains of monomers joined by covalent bonds.

• Dehydration reaction: Joins monomers by removing a water molecule.

• Hydrolysis: Breaks polymers into monomers by adding water.

Carbohydrates

Carbohydrates serve as fuel and building material. They include sugars and polymers of sugars.

• Monosaccharides: Simple sugars (e.g., glucose, C6H12O6).

• Disaccharides: Two monosaccharides joined by a glycosidic linkage (e.g., sucrose).

• Polysaccharides: Polymers of many monosaccharides (e.g., starch, glycogen, cellulose, chitin).

Example: Starch (plant storage), glycogen (animal storage), cellulose (plant cell walls), chitin (arthropod exoskeletons).

Lipids

Lipids are hydrophobic molecules that include fats, phospholipids, and steroids.

• Fats: Constructed from glycerol and fatty acids. Used for energy storage.

• Saturated fats: No double bonds; solid at room temperature (animal fats).

• Unsaturated fats: One or more double bonds; liquid at room temperature (plant oils).

• Phospholipids: Two fatty acids and a phosphate group attached to glycerol; form cell membranes.

• Steroids: Lipids with four fused carbon rings (e.g., cholesterol).

Proteins

Proteins are polymers of amino acids and perform a wide range of functions, including catalysis, defense, storage, transport, cellular communication, movement, and structural support.

• Amino acids: Organic molecules with amino and carboxyl groups; differ in side chains (R groups).

• Peptide bond: Covalent bond joining amino acids.

• Polypeptide: Polymer of amino acids.

Levels of Protein Structure

• Primary structure: Sequence of amino acids.

• Secondary structure: Coils and folds (α-helix, β-pleated sheet) due to hydrogen bonding.

• Tertiary structure: Overall 3D shape due to interactions among R groups.

• Quaternary structure: Association of multiple polypeptides.

Denaturation: Loss of protein structure due to changes in pH, temperature, or other environmental factors.

Nucleic Acids

Nucleic acids store, transmit, and help express hereditary information. The two types are DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).

• Nucleotide: Monomer of nucleic acids; consists of a nitrogenous base, a pentose sugar, and a phosphate group.

• DNA: Double helix; bases are adenine (A), thymine (T), guanine (G), cytosine (C).

• RNA: Single-stranded; uracil (U) replaces thymine.

• Phosphodiester linkage: Joins nucleotides in a polynucleotide chain.

• Antiparallel: The two strands of DNA run in opposite 5' to 3' directions.

Complementary base pairing: In DNA, A pairs with T (2 hydrogen bonds), and G pairs with C (3 hydrogen bonds). In RNA, A pairs with U.

Central Dogma: Genetic information flows from DNA to RNA to protein.