1.1 What is biology?

Biology is the study of life at all levels of organization, ranging from molecules to the biosphere.

The cell theory states that all life consists of cells, and all cells come from preexisting cells.

All living organisms are related to one another through descent with modification. Evolution by natural selection is responsible for the diversity of adaptations found in living organisms.

The instructions for a cell are contained in its genome, which consists of DNA molecules made up of sequences of nucleotides. Specific segments of DNA called genes contain the information the cell uses to make proteins. Review Figure 1.4

Cells are the basic structural and physiological units of life. Most of the chemical reactions of life take place in cells. Living organisms control their internal environment. They also interact with other organisms of the same and different species. Biologists study life at all these levels of organization. Review Figure 1.6, Web/CD Activity 1.1

Biological knowledge obtained from a model system may be generalized to other species.

1.2 How is all life on Earth related?

Biologists use fossils, anatomical similarities and differences, and molecular comparisons of genomes to reconstruct the history of life. Review Figure 1.9

Life first arose by chemical evolution. Biological evolution began with the formation of cells.

Photosynthesis was an important evolutionary step because it changed Earth's atmosphere and provided a means of capturing energy from sunlight.

The earliest organisms were prokaryotes; organisms with more complex cells, called eukaryotes, arose later. Eukaryotic cells have discrete intracellular compartments, called organelles, including a nucleus that contains the cell's genetic material.

The genetic relationships of species can be represented as an evolutionary tree. Species are grouped into three domains: Archaea, Bacteria, and Eukarya. The domains Archaea and Bacteria consist of unicellular prokaryotes. The domain Eukarya contains the microbial eukaryotes (protists), plants, fungi, and animals. Review Figure 1.11, Web/CD Activity 1.2

1.3 How do biologists investigate life?

The scientific method used in most biological investigations involves five steps: making observations, asking questions, forming hypotheses, making predictions, and testing those predictions.

Hypotheses are tentative answers to questions. Predictions made on the basis of a hypothesis are tested with additional observations and two kinds of experiments: comparative and controlled experiments. Review Figure 1.13 and 1.14

Statistical methods are applied to data to establish whether or not the differences observed are significant or whether they could be expected by chance. These methods start with the null hypothesis that there are no differences.

Science can tell us how the world works, but it cannot tell us what we should or should not do.

1.4 How does biology influence public policy?

Wise public policy decisions must be based on accurate scientific information. Biologists are often called on to advise governmental agencies on the solution of important problems that have a biological component.

2.1 What are the chemical elements that make up living organisms?

Matter is composed of atoms. Each atom consists of a positively charged nucleus made up of protons and neutrons, surrounded by electrons bearing negative charges. Review Figure 2.1

The number of protons in the nucleus defines an element. There are many elements in the universe, but only a few of them make up the bulk of living organisms. Review Figure 2.2

Isotopes of an element differ in their numbers of neutrons. Radio­isotopes are radioactive, emitting radiation as they decay.

Electrons are distributed in shells, which are volumes of space defined by specific numbers of orbitals. Each orbital contains a maximum of two electrons. Review Figure 2.6, Web/CD Activity 2.1

In losing, gaining, or sharing electrons to become more stable, an atom can combine with other atoms to form molecules.

2.2 How do atoms bond to form molecules?

See Web/CD Tutorial 2.1

A chemical bond is an attractive force that links two atoms together in a molecule. Review Table 2.1

A compound is a molecule made up of atoms of two or more elements bonded together in a fixed ratio, such as water (H2O) or table sugar (C6H12O6).

Covalent bonds are strong bonds formed when two atoms share one or more pairs of electrons. Review Figure 2.7

When two atoms of unequal electronegativity bond with each other, a polar covalent bond is formed. The two ends, or poles, of the bond have partial charges ( δ+ or δ-). Review Figure 2.9

Ions are electrically charged bodies that form when an atom gains or loses one or more electrons. Anions and cations are negatively and positively charged ions, respectively.

Ionic bonds are electrical attractions between oppositely charged ions. Ionic bonds are strong in solids (salts), but weaken when the ions are separated from one another in solution. Review Figure 2.10

Hydrogen bonds are weak electrical attractions that form between a δ+ hydrogen atom in one molecule and a δ- atom in another molecule (or in another part of a large molecule). Hydrogen bonds are abundant in water.

Nonpolar molecules interact very little with polar molecules, including water. Nonpolar molecules are attracted to one another by very weak bonds called van der Waals forces.

2.3 How do atoms change partners in chemical reactions?

In chemical reactions, atoms combine or change their bonding partners. Reactants are converted into products.

Some chemical reactions release energy as one of their products; other reactions can occur only if energy is provided to the reactants.

Neither matter nor energy is created or destroyed in a chemical reaction, but both change form. Review Figure 2.13

Some chemical reactions, especially in biology, are reversible. That is, the products formed may be converted back to the reactants.

In living cells, chemical reactions take place in multiple steps so that the released energy can be harvested for cellular activities.

2.4 What properties of water make it so important in biology?

Water's molecular structure and its capacity to form hydrogen bonds give it unique properties that are significant for life. Review Figure 2.14

The high specific heat of water means that water gains or loses a great deal of heat when it changes state. Water's high heat of vaporization ensures effective cooling when water evaporates.

The cohesion of water molecules refers to their capacity to resist coming apart from one another.

Solutions are produced when solid substances (solutes) dissolve in a liquid (the solvent). Water is the critically important solvent for life.

Acids are solutes that release hydrogen ions in aqueous solution. Bases accept hydrogen ions.

The pH of a solution is the negative logarithm of its hydrogen ion concentration. Values lower than pH 7 indicate a solution is acidic; values above pH 7 indicate a basic solution. Review Figure 2.16

Buffers are mixtures of weak acids and bases that limit the change in the pH of a solution when acids or bases are added.

3.1 What kinds of molecules characterize living things?

See Web/CD Tutorial 3.1

Macromolecules are polymers constructed by the formation of covalent bonds between smaller molecules called monomers. Macromolecules in living organisms include polysaccharides, proteins, and nucleic acids.

Functional groups are small groups of atoms that are consistently found together in a variety of different macromolecules. Functional groups have particular chemical properties that they confer on any larger molecule of which they are a part. Review Figure 3.1, Web/CD Activity 3.1

Structural and optical isomers have the same kinds and numbers of atoms, but differ in their structures and properties. Review Figure 3.2

The many functions of macromolecules are directly related to their three-dimensional shapes, which in turn is the result of the sequences and chemical properties of their monomers.

Monomers are joined by condensation reactions, which release a molecule of water for each bond formed. Hydrolysis reactions use water to break polymers into monomers. Review Figure 3.4

3.2 What are the chemical structures and functions of proteins?

Web/CD Activity 3.2

The functions of proteins include support, protection, catalysis, transport, defense, regulation, and movement.

Amino acids are the monomers from which proteins are constructed. The properties of the amino acids depend on their side chains, or R groups, which may be charged, polar, or hydrophobic. Review Table 3.2

Peptide bonds covalently link amino acids into polypeptide chains. These bonds form by condensation reactions between the carboxyl and amino groups. Review Figure 3.6

The primary structure of a protein is the order of amino acids in the chain. This chain is folded into a secondary structure, which in different parts of the protein may be an α helix or a β pleated sheet. Review Figure 3.7A-C

Disulfide bonds and noncovalent interactions between amino acids cause the polypeptide chain to fold into a three-dimensional tertiary structure and allow multiple chains to interact in a quaternary structure. Review Figure 3.7D, 3.7E

The specific shape and structure of a protein allows it to bind non- covalently to other molecules, often called ligands.

Heat, alterations in pH, or certain chemicals can all result in protein denaturation, which involves the loss of tertiary and/or secondary structure as well as biological function. Review Figure 3.11

Chaperonins assist protein folding by preventing binding to inappropriate ligands. Review Figure 3.12

3.3 What are the chemical structures and functions of carbohydrates?

Carbohydrates contain carbon bonded to hydrogen and oxygen atoms in a ratio of 1:2:1, or (CH2O) n.

Monosaccharides are the monomers that make up carbohydrates. Hexoses such as glucose are six-carbon monosaccharides; pentoses have five carbons. Review Figure 3.14, Web/CD Activity 3.3

Glycosidic linkages , which have either an α or a β orientation in space, covalently link monosaccharides into larger units such as disaccharides, oligosaccharides, and polysaccharides. Review Figure 3.15

Starch stores energy in plants. Starch and glycogen are formed by α-glycosidic linkages between glucose monomers and are distinguished by the amount of branching they exhibit. They can be easily broken down to release stored energy.

Cellulose, a very stable glucose polymer, is the principal component of the cell walls of plants.

3.4 What are the chemical structures and functions of lipids?

Fats and oils are triglycerides, composed of three fatty acids co­valently bonded to a molecule of glycerol by ester linkages. Review Figure 3.18

Saturated fatty acids have a hydrocarbon chain with no double bonds. The hydrocarbon chains of unsaturated fatty acids have one or more double bonds that bend the chain, making close packing less possible. Review Figure 3.19

Phospholipids have a hydrophobic hydrocarbon "tail" and a hydro­philic phosphate "head." In water, the interactions of the hydrophobic tails and hydrophilic heads of phospholipids generate a phospholipid bilayer that is two molecules thick. The heads are directed outward, where they interact with the surrounding water. The tails are packed together in the interior of the bilayer. Review Figure 3.20

3.5 What are the chemical structures and functions of nucleic acids?

The unique function of the nucleic acids—DNA and RNA—is information storage; they form the hereditary material that passes genetic information to the next generation.

Nucleic acids are polymers of nucleotides. A nucleotide consists of a phosphate group, a pentose sugar (ribose in RNA and deoxyribose in DNA), and a nitrogen-containing base. Review Figure 3.23, Web/CD Activity 3.4

In DNA the nucleotide bases are adenine, guanine, cytosine, and thymine. Uracil substitutes for thymine in RNA. The nucleotides are joined by phosphodiester linkages between the sugar of one nucleotide and the phosphate of the next.

RNA is single-stranded. DNA is a double helix in which there is complementary base pairing based on hydrogen bonds between adenine and thymine (A-T) and between guanine and cytosine (G-C). The two strands of the DNA double helix run in opposite directions. Review Figure 3.24 and 3.26, Web/CD Activity 3.5

The information content of DNA and RNA resides in their base sequences.

3.6 How did life on Earth begin?

Chemical evolution proposes that conditions on early Earth could have produced the macromolecules that distinguish living things. Review Figure 3.28, Web/CD Tutorial 3.2

Because it can form a three-dimensional shape, RNA could act as a ribozyme, an RNA surface on which chemical reactions proceed at a faster rate. Review Figure 3.29

Experiments have ruled out the continuous spontaneous generation of life. Review Figure 3.30, Web/CD Tutorial 3.3

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