Chapter Capsule

A. Atomic Structure

1. All matter in the universe is composed of minute particles called atoms—the simplest form of matter not divisible into a simpler substance by chemical means. Atoms are composed of smaller particles called protons (p¹), positive in charge; neutrons (n⁰), uncharged; and electrons (e²), negative in charge. Protons and neutrons comprise the nucleus of an atom, and electrons move about the nucleus in orbitals arranged in shells.

2. Atoms that differ in numbers of protons, neutrons, and electrons are elements. Elements can be described by mass number (the total number of protons and neutrons in the nucleus) and atomic number (the number of protons alone), and each is known by a distinct name and symbol. An unreacted atom is neutral because electron charge cancels out proton charge. Elements may exist in variant forms called isotopes, which differ in the number of neutrons.

3. Electrons fill the orbitals in pairs: The first orbital (shell) holds 2 e², the second shell can hold 8 e² (4 pairs), and the third shell can hold 18 e² (9 pairs). The electron number of each element dictates orbital filling; the outermost shell becomes the focus of reactivity and bonding. In general, atoms with a filled outermost shell are less reactive than atoms with unfilled ones.

B. Chemical Bonds and Molecules

1. Atoms interact to form chemical bonds and molecules. Member atoms of molecules may be the same element or different elements; if the member elements are different, the substance is a compound.

2. The type of bond is dictated by the electron makeup (valence) of the outer orbitals of the atoms.

3. With covalent bonds, the electrons are shared and orbit within the entire molecule. This molecule can be polar, due to an imbalance of charge, or nonpolar.

4. With ionic bonds, an atom with a low number of valence electrons loses them to an atom that has a nearly filled outer orbital. When ionic bonds are broken, the atoms ionize into charged particles called ions. Ions that have lost electrons and have a positive charge are cations (Na¹), and those that have gained electrons and have a negative charge are anions (Cl²). Ions of the opposite charge are attracted to each other, and those with the same charges repel each other.

5. Hydrogen bonds are caused by weak attractive forces between covalently bonded hydrogen and negatively charged oxygen or nitrogen on the same or nearby molecules.

C. Redox Reactions

Chemicals may participate in a transfer of electrons, called an oxidation-reduction (redox) reaction, between pairs of atoms or molecules. Oxidation is a reaction in which electrons are released, and reduction is a reaction in which these same electrons are received. Any atom or molecule that donates electrons to another atom or molecule is a reducing agent, and one that picks up electrons is an oxidizing agent.

D. Chemical Formulas, Models, and Equations

1. Chemical formulas may be presented as simple molecular summaries of the atoms or expressed as structural formulas that give the details of bonding.

2. Chemical equations summarize a chemical reaction by showing the reactants (starting chemicals) and the products (end results), and can indicate synthesis reactions, decomposition reactions, exchange reactions, and reversible reactions.

E. Solutions, Acids, Bases, and pH

1. A solution is a combination of a solid, liquid, or gaseous chemical termed a solute dissolved in a liquid medium called a solvent. Water-soluble solutes are either charged or polar. The dissolved solute will become hydrated due to electrostatic attraction. Chemicals that attract water are hydrophilic; those that repel it are hydrophobic. The concentration of a solution is defined as the amount of solute dissolved in a given amount of solvent.

2. Acidity and basicity of solutions are represented by the pH scale, based on a standardized range of hydrogen ion concentration [H¹]; an acid is a solution that contains a concentration of [H¹] greater than 0.0000001 moles/liter (10²⁷), and a base is a solution that contains a concentration of [H¹] below that amount. When a solution contains exactly that [H¹], it is considered neutral (pH 7). The working pH scale ranges from the most acidic reading of 0 to the most basic (alkaline) reading of 14. Acidic and basic ions in aqueous solutions may interact to form water and a salt through neutralization.

A. Organic compounds contain some combination of carbon and hydrogen covalently bonded. Carbon can also bond with other carbons and with oxygen, nitrogen, and phosphorus to create the diversity of biological molecules. Organic compounds constitute the most important molecules in the structure and function of cells. Inorganic compounds are composed of some combination of atoms other than carbon and hydrogen.

B. Functional groups are special accessory molecules that bind to carbon and provide the diversity and reactivity seen in organic compounds.

C. Biochemistry and Macromolecules

1. Organic compounds that function in living things are biochemicals. Many of them are macromolecules (very large compounds). Levels of structure are monomers (single units) and polymers (long chains of single units) assembled by polymerization.

2. Carbohydrates are composed of carbon, hydrogen, and oxygen (CH₂O) and contain aldehyde or ketone groups.

3. Monosaccharides (glucose) are the simplest sugars. When two sugars are joined by the 2OH group and carbon through dehydration synthesis, a glycosidic bond occurs.

4. Disaccharides are composed of two monosaccharides (lactose, sucrose). Polysaccharides are chains of five or more monosaccharides; examples are cellulose, peptidoglycan, starch, and glycogen. Di- and polysaccharides are digested by specific enzymes that break the bond through hydrolysis.

5. Lipids are not soluble in water and other polar solvents due to their nonpolar, hydrophobic chains. Triglycerides, including fats and oils, consist of a glycerol molecule bonded to 3 fatty acid molecules. They are important storage lipids. Phospholipids are composed of a glycerol bound to two fatty acids and a phosphoric acid–alcohol group; the molecule has a hydrophilic head and long hydrophobic fatty acid chains; they form single or double lipid layers in the presence of water and are important constituents of cell membranes.

6. Proteins are highly complex macromolecules assembled from 20 different subunits called amino acids (aa). Amino acids are combined in a certain order by peptide bonds:

	O O
aa ± N ± C ± aa
		W H

a. A peptide is a short chain of aa’s; a dipeptide has two, and a tripeptide has three; a polypeptide is usually 20–50 aa’s; a protein contains more than 50 aa’s. Larger proteins predominate in cells.

b. The chain of amino acids is a protein’s primary structure. Interactions between functional groups result in additional levels of structure. Hydrogen bonds within the chain fold it first into a helix or sheet called the secondary structure. This folds again, forging stronger disulfide bonds on nearby cysteines and producing a three-dimensional tertiary structure. Proteins composed of two or more polypeptides exist in a quaternary state. Variations in shape provide specificity and give rise to the diversity in enzymes, antibodies, and structural proteins.

7. Nucleic Acids

a. Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are very complex molecules that carry, express, and pass on the genetic information of all cells and viruses. Their basic building block is a nucleotide, composed of a nitrogen base, a pentose sugar, and a phosphate. Nitrogen bases are the ringed compounds: adenine (A), cytosine (C), thymine (T), guanine (G), and uracil (U); pentose sugars may be deoxyribose or ribose. The basic design is a polynucleotide, with the sugars linking up in an alternating series with phosphates to make a backbone, and the bases branching off the sugars.

b. DNA contains deoxyribose sugar, has all of the bases except uracil, and occurs as a double-stranded helix with the bases hydrogen-bonded in pairs between the helices; the pairs mate according to the pattern A–T and C–G. DNA is the master code for a cell’s life processes and must be transmitted to offspring. During cell division, it is replicated by separation of the double strand into two single strands, which are used as a template to form two new double strands. RNA contains ribose sugar, has all of the bases except thymine, and is a single-stranded molecule. It expresses the DNA code into proteins.

8. Adenosine triphosphate (ATP) is a nucleotide involved in the transfer and storage of energy in cells. It contains adenine, ribose, and three phosphates in a series. Splitting off the last phosphate in the triphosphate releases a packet of energy that may be used to do cell work.

A. Cells are huge aggregates of macromolecules organized to carry out complex processes described as living. All organisms consist of cells, which fall into one of two types: procaryotic, which are small, structurally simple cells that lack a nucleus and other organelles; and eucaryotic, larger cells with a nucleus and organelles, found in plants, animals, fungi, and protozoa. Viruses are not cells and are not generally considered living because they cannot function independently.

B. Organisms demonstrate several essential qualities of life.

1. Growth and reproduction involve producing offspring asexually (with one parent) or sexually (with two parents).

2. Metabolism refers to the chemical reactions in cells, including the synthesis of proteins on ribosomes and the release of energy (ATP).

3. Motility originates from special locomotor structures such as flagella and cilia; irritability is responsiveness to external stimuli.

4. Protective external structures include capsules and cell walls; nutrient storage takes place in compact intracellular masses.

5. Transport involves conducting nutrients into the cell and wastes out of the cell.

C. Membranes surround the cytoplasm and may occur internally in organelles. The cell membrane is a continuous ultrathin bilayer of lipids studded with proteins that controls cell permeability and transport. Proteins also serve as sites of recognition and cell communication.