Chemistry - A Molecular Science

Chapter 13 Organic Chemistry

311

is emphasized in Figure 13.35 by the bonds show

n in red. As we shall see in the next

section, the overall structure (shape) of proteins is often represented as a ribbon diagram. Ribbon diagrams emphasize the secondary structure of a protein by superimposing a ‘ribbon’ on the atoms of the polypeptide backbone. SECONDARY STRUCTURES Interactions such as hydrogen bonding and di

polar interactions that occur between groups

within a polypeptide or protein are responsible

for certain features of its three-dimensional

shape known as its

secondary structure

. An example of secondary structure is the

• α

helix

. The

-helix is adopted in order to optimα

ize hydrogen-bonding interactions between

different monomer units. The strongest interaction occurs when each amide N-H group forms a hydrogen bond to the C=O group of the amide four units away in the peptide sequence (Figure 13.36 below). The resulting

-helix is shown in Figure 13.37. The α

relatively short hydrogen bond between the

first and fourth amino acids causes the

intervening amino acids to form a loop. Multiple loops (four are shown in Figure 13.37) form an

-helix. In biology, specific amino acids can be placed at distinct positions around α

the core of the

-helix to give a protein its specific function. α

The three-dimensional shapes

associated with secondary structures, like the

-helix, are essential for the biological α

function of proteins.

N

N

N

N

N

N

H

O

H

H

O

O

O

H

H

H

O

Figure 13.36 Hydrogen bonds responsible for the

α-helix structure

Each amide linkage is highlighted with red or blue bonds. Green arrows indicate two of the hydrogen bonds responsible for the

α-helix structure as the molecule bends and twists to bring the O and H

atoms close enough to interact.^ DNA STRUCTURE: THE DOUBLE HELIX A nucleotide consists of a phos

phate, a sugar*, and a N-contai

ning base. A nucleic acid is

a polymer formed from nucleotide residues (Figure 13.38). If the sugar is deoxyribose, the nucleic acid is

Deoxyribose

Nucleic

Acid or DNA. Only four nitrogen-containing bases

are found in DNA: adenine (

A), thymine (

T), cytosine (

C), and guanine (

G).

(a) (b) (c)

Figure 13.37 Portion of an

α-helix

Color code: red = oxygen; blue = nitrogen; grey = carbon; white = hydrogen; yellow = sulfur. Note only those hydrogen atoms involved in hydrogen bonding are shown. (a) Space-filling model (b) Ball-and-stick model with green ribbon to show polypeptide

backbone

(c) Ball-and-stick model in which the side chains have been

removed, and hydrogen bonds are shown as dashed lines.

* Sugars are carbohydrates with the formula C

(Hx

O) 2

, where x is an x

integer greater than three. Ribose is a sugar with the formula C

H 5

O 10

, 5

but, as its name suggests, deoxyribose has one less oxygen.

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