when they are not linked by a covalent bond (Figure B14.1d and Figure B14.2b).

• Ribbon models are very schematic (Figure B14.2c). They are commonly used to highlight a few major features of protein structure. For example, α-helices are depicted as spring-like coils, β-pleated sheets as flat arrows, and loops as simple lines (see Chapter 3).

BioSkill 14 Reading Chemical StructuresIf you haven’t had much chemistry yet, learning basic biologi-cal chemistry can be a challenge. One stumbling block is simply being able to read chemical structures and understand what they mean. This task will become much easier once you have a little notation under your belt and you understand some basic symbols. Atoms are the basic building blocks of everything in the universe, just as cells are the basic building blocks of your body. Every atom has a one- or two-letter symbol.

Table B14.1 shows the symbols for most of the atoms you’ll encounter in this book. You should memorize these symbols. The table also offers details on the number of bonds each atom can form, as well as how the atoms are represented in some visual models.

When atoms attach to each other by covalent bonding, a molecule forms. Table B14.1 also includes atoms such as chlo-rine and potassium that are joined by ionic bonds to form ionic compounds (see Chapter 2), but the focus here is on atoms that form molecules. Biologists have a couple of different ways of representing molecules—you’ll see each of these in the book and in class.

• Molecular formulas like the one for the amino acid glycine (see Chapter 3) in Figure B14.1a simply list the atoms present in a molecule. Subscripts indicate how many of each atom are present. If the formula has no subscript, only one atom of each type is present. A methane (natural gas) molecule, for example, is written as CH4. It consists of one carbon atom and four hydrogen atoms.

• Structural formulas like the one for glycine in Figure B14.1b show which atoms in a molecule are bonded to each other. Each bond is indicated by a dash. Single covalent bonds are symbolized by a single dash, as in the bonds between the hydrogen atoms and the nitrogen atom in glycine. Double bonds are indicated by two dashes, as in the covalent bond between a carbon atom and an oxygen atom in glycine. Triple bonds are indicated by three dashes, as in the structural for-mula for molecular nitrogen (N2), which is written as N≡N.

Even simple molecules have distinctive shapes, because dif-ferent atoms make covalent bonds at different angles. Ball-and-stick and space-filling models show the geometry of the bonds in a molecule accurately, while ribbon models are used to depict the way large molecules fold.

• Ball-and-stick models are not as realistic as space-filling mod-els, but they make the bonding arrangement of atoms easier to see because the bonds are represented as sticks. Ball-and-stick models provide information on the three-dimensional shape of molecules and, in some cases, they show the relative sizes of the atoms (colored balls) involved (Figure B14.1c and Figure B14.2a on page 50).

• Space-filling models are the most realistic, with a sphere drawn around each atom to show its relative size. The models depict the spatial relationship between atoms—for example, how closely two atoms can approach each other

Figure B14.1 A Molecule Can Be Represented in Several Different Ways. The amino acid glycine consists of one nitrogen atom, two carbon atoms, five hydrogen atoms, and two oxygen atoms.

MODEL Carbon dioxide consists of a carbon atom that forms a double bond with each of two oxygen atoms, for a total of four bonds. It is a linear molecule. Write carbon dioxide’s molecular formula and then draw its structural formula, a ball-and-stick model, and a space-filling model.

(a) Molecular formula:

(b) Structural formula:

(c) Ball-and-stick model:

(d) Space-filling model:

NH2CH2COOH(glycine)

H

C

OHH

OH

CN

H

Table B14.1 Some Attributes of Atoms Found in Organisms

Atom SymbolNumber of Bonds It Can Form

Standard Color Code*

Hydrogen H 1 white

Carbon C 4 black

Nitrogen N 3 blue

Oxygen O 2 red

Sodium Na 1 —

Magnesium Mg 2 —

Phosphorus P 5 orange or purple

Sulfur S 2 yellow

Chlorine Cl 1 —

Potassium K 1 —

Calcium Ca 2 —

*In ball-and-stick or space-filling models.

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To learn more about a molecule when you look at a chemical structure, ask yourself three questions:

1. Is the molecule polar—meaning that some parts are more negatively or positively charged than others? Molecules that contain nitrogen or oxygen atoms are often polar because these atoms are very electronegative (see Chapter 2). This trait is important because polar molecules dissolve in water.

2. Does the structural formula show atoms that might participate in chemical reactions? For example, are there charged atoms or amino (–NH2) or carboxyl (–COOH)

functional groups that might make the molecule act as a base or an acid?

3. In ball-and-stick and especially space-filling models of large molecules, are there interesting aspects of overall shape? For example, is there a groove where a protein might bind to DNA, or a cleft (as shown in Figure  B14.2) where a substrate might undergo a reaction in an enzyme?

Figure B14.2 Three Different Models of an Enzyme. The enzyme phosphoglycerate kinase catalyzes step 7 in glycolysis (see Chapter 9). The active site appears as a deep cleft.

(a) Ball-and-stick model (b) Space-filling model (c) Ribbon model

Activesite

Activesite

Activesite

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