Download Supplement 5.1: Polymers and Biopolymers. Proteins. Polymers are

Supplement 5.1: Polymers and Biopolymers. Proteins.
Polymers are large molecules that consist of repeating units. The simplest view of a polymer is
that the repeating units are joined end-to-end to form a long chain; but in some polymers,
branching can occur. For now, we’ll restrict ourselves to the simple end-to-end concept of a
polymer. In a homopolymer, the repeating units are identical. In a heteropolymer, there is some
variation in the units superimposed on a common structural motif. For example, polyethylene is a
homopolymer; is consists of repeating, identical, two-carbon alkane fragments. A typical
polyethylene molecule might contain thousands of units.
(1)
(You might think it should be called polyethane because it has only single bonds; the name comes
from the fact that it is made from ethylene, as Sec. 5.7 in your text shows.)
Proteins are examples of heteropolymers. There is a fundamental structural motif in each
repeating unit (the peptide backbone), but there is variability in the “R” groups that constitute the
side chains. Each repeating unit is called a residue.
(2)
An analogy to a homopolymer is a long railroad train that consists of identical boxcars. An
analogy to a heteropolymer is a long railroad train that consists of different types of cars. They all
have common repeating elements—the wheels and couplings, for example—but the types of cars
vary. For example, the train may consist of tank cars, boxcars, cattle cars, etc.
Although we represent polymers simplistically as repeating units, some have terminating
groups on the ends that are different from the repeating units. Again, the analogy to a railroad train
is apt. While we might say that a train consists solely of boxcars and represent it in abbreviated
form as
(3a)
we understand that there is an engine at one end and a caboose at the other.
(3b)
In polyethylene, for example, there might be a fragment derived from the initiator at one end and
perhaps an alkene at the other:
(4)
Supplement 5.1, p. 2
Because these terminating groups make a negligible contribution to the properties of the polymer,
they are usually ignored.
In proteins, the most common terminating groups are a protonated amino group (that is, an
ammonium group) and an ionized carboxylic acid group (that is, a carboxylate ion), but in some
cases these are chemically modified. We won’t consider these chemical modifications here, but
when they occur they typically serve an important role in the biological properties of the protein.
(5)
Polymers are usually made by the repeated chemical linkage of small molecules, called
monomers. Ethylene is the monomer from which polyethylene is formed. (See Sec. 5.7 of your
text for a mechanism of free-radical polymerization.) When the polymerization process produces
no small-molecule by-products at each step of the reaction, the resulting polymer is called an
addition polymer. Polyethylene is an example of an addition polymer.
When the combination of monomer units at each step liberates a small-molecule by-product,
the polymer is called a condensation polymer. Peptides and proteins are condensation polymers
because, when they are formed from a-amino acids (the monomers), a molecule of water is
liberated for each amide bond formed.
(6)
Note that this is not a chemical mechanism. But it does show the overall result.
Biopolymers. Biopolymers are naturally-occurring polymers that play important roles in living
systems. There are three especially important classes of biopolymers, all of which are
condensation heteropolymers.
1.
2.
3.
Proteins
Nucleic acids
Polysaccharides
The goal of this section is merely to characterize the covalent structures of these biopolymers. As
the course goes on, we’ll learn more details about their conformations and, to some extent, their
functions.
Proteins. As we’ve seen already, proteins are condensation heteropolymers of the a-amino acids.
There are 20 commonly occurring amino acid residues in proteins. The structures of these are
given in Table 27.1, pp. 1376–1377 of your text. (There is one cyclic amino acid, proline, that
doesn’t fit the simple structure in (2), but we’ll gloss over that for now. We’ll ask you to think
about proline and how it affects protein structure in Problem 3 at the end of this supplement.) You
don’t need to learn the structures of the a-amino acids now.
Proteins serve many roles in living systems. Some proteins serve structural roles. Drug
receptors are proteins. Hemoglobin, which transports oxygen and CO2 in the blood, is a protein.
Supplement 5.1, p. 3
Antibodies are proteins. Snake venoms are proteins. Almost all enzymes are proteins. Because our
goal is to understand the chemistry of living systems, and because enzymes are the biological
catalysts that make this chemistry possible, we will be developing a particularly detailed
understanding of enzymes and how they function as the course progresses.
Nucleic Acids. The nucleic acids include ribonucleic acid (RNA), a condensation heteropolymer
of ribonucleotides, and deoxyribonucleic acid (DNA), a condensation heteropolymer of 2-deoxy–
ribonucleotides. As you may already know, there are several types of RNA, but we’re going to
focus solely on the covalent structures that they all have in common.
(7a)
(7b)
The variable parts of the structures of nucleic acids are called bases. These are nitrogen-containing
cyclic entities whose structures can be found in your text on p. 1354. Don’t try to learn these now.
Nucleic acids are involved in the storage and transmission of genetic information.
Polysaccharides. Polysaccharides are condensation polymers of various sugars, which themselves
are cyclic ethers that contain, typically, many hydroxy (—OH) substituents and in some cases
other substituents, such as amines and carboxylic acid groups. There are so many sugar
monomers, and the heterodiversity of polysaccharides is so broad, that it isn’t possible to write a
single general structure as we did for proteins and nucleic acids. However, as specific examples,
examine the structures of two important polymers of the sugar glucose, cellulose and starch, on
pp. 1273–1274 of your text. The relationship of cellulose, the polymer, to the monomer glucose is
shown in (8):
(8)
Polysaccharides are used as sources of stored energy, for cellular recognition (as in blood
typing), for cell walls of certain bacteria, for the shells of arthropods. Cellulose is the primary
structural material of plants and is the most abundant organic compound on the face of the earth.
Supplement 5.1, p. 4
Problems (For the solutions to these problems, click HERE.)
1.
Polyester is a condensation polymer that is formed from the reaction of ethylene glycol and
terephthalic acid. Two molecules of water are formed for each polymer unit produced. Propose a
general structure for polyester and explain your reasoning.
2.
Artificial skin is an addition homopolymer used to close skin wounds without sutures. The general
structure is shown below. Give the structure of the monomer, which is an alkene.
3.
Using Table 27.1, pp. 1376–7, for the structures and abbreviations of the amino acids, draw a
structure of the peptide Gly-Ser-Pro-Val, where Gly is at the amino end of the peptide, and Val is
at the carboxy end. Use the general structure in (5) to guide you. However, Pro ( = proline) is an
unusual cyclic amino acid. You’ll have to decide how this alters the general structure shown in (5).
4.
Nylon-6 is a homopolymer used in artificial fibers. Although Nylon-6 could be conceived as a
condensation polymer derived from an amino acid, it is actually produced as an addition polymer.
Suggest a structure for the monomer. (Hint: This type of addition polymerization is sometimes
called ring-opening polymerization.)