The Chinese University of Hong Kong
CSS 1602 A Survey of Modern Chemistry
(2002 Summer)
End-of-course-evaluation
(Due June 27,2002)
Student name: Chan Hau
Kit
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Question 9
Describe
the chemical composition and structure of any one naturally occurring
polymer.
(A)
Introduction
What is a polymer?
A polymer is a compound consisting of very large molecules formed by
many small molecules being joined together repeatedly. These small molecules
are usually containing carbons and other elements besides hydrogen atoms in
some kinds called monomers.
Methods of the formation of a polymer
1.
Addition polymerization
2.
Condensation polymerization
The
unsaturated structure of alkenes is possible to join together to form a long
chain. These kinds of alkenes are called monomers while this reaction forming
the polymer, as a product is polymerization. It can also be concluded that
polymerization is the process of repeatedly joining together many molecules to
form very large molecules.
Addition
polymerization
In
addition polymerization, monomer molecules join repeatedly to form an addition
polymer. The monomer molecules must contain a C=C bond. No atoms are lost from
the monomer during polymerization. It is a reaction in which the monomer
molecules join to form polymer molecules. No elimination of small molecules
occurs.
Some common addition polymers
1.
Ethaneàpolythene
or poly(ethane)
2.
Styreneàpolystyrene
3.
Vinyl chloride or chloroetheneàpolyvinyl chloride or poly(chloroethene)
4.
Methyl 2-methylpropenoateàperspex
Condensation
polymerization
In
condensation polymerization, the monomer molecules must have two functional
groups (or reactive sites). The monomers react with each other and link up to
form condensation polymers. Small molecules are always eliminated during the
polymerization, which are usually water, hydrogen chloride or ammonium
molecules. In other words, it is a reaction in which the monomer molecules
join together to form polymer molecules. Small molecules are always
eliminated.
Polymers
actually can be man-made or natural. Plastics are one of the examples of
man-made polymers. Other naturally occurring polymers are wood, silk etc, some
materials using nowadays.
Polymers can also be divided into 2 broad groups: biopolymers and synthetic
polymers. Biopolymers are synthesized by organisms and are essential for
our life. Examples are DNA, RNA, proteins, and polysaccharides. Synthetic
polymers are naturally occurring polymers. Example is nylon (a polyamide, the
first synthetic fibre).
(B)
An example of naturally occurring polymer----- deoxyribonucleic acids
(DNA)
(a) Brief introduction
Deoxyribonucleic acids are one of the members of nucleic acids, which
are classified according to the nature of the sugar present. Another form of
nucleic acid is also existed, called ribonucleic acids, for short, RNA. RNAs
are found mainly in the cytoplasm of the cell, whereas DNAs are mainly found
in the nucleus.
Ribose is the pentose of yeast, liver and pancreas RNAs;
2-deoxy-D(--)-ribose occurs in the thymus DNA. Nucleic acids also occur in
plant and animal viruses.
(b) What are Nucleic acids?
Nucleoproteins are one of the classes of the conjugated proteins; the
nucleic acid part is the prosthetic group, and the protein part consists of
protamins and histones. These latter compounds are basic and form salt-like
compounds, the nucleoproteins, with the nucleic acid. On careful hydrolysis,
nucleoproteins are broken down into the nucleic acid and protein.
Information about the nucleic acids
Nucleic
acids are colourless solids, all of which contain the following elements:
carbon, hydrogen, oxygen, nitrogen and phosphorus.
Complete
hydrolysis of the purine nucleotides by dilute acids occurs relatively easily,
but the pyrimidine nucleotides usually require heating under pressure. On the
other hand, complete hydrolysis of nucleic acids may be carried out by heating
with 12N perchloric acid or with formic acid. Alkaline hydrolysis results in
the formation of ribonucleosides 2’-and 3’-phosphates. Enzymic hydrolysis
produces nucleoside 3’and 5’-phosphates, the actual product depending on
the nature of the enzyme.
(c)
The chemical composition of nucleic acid
Two
sugars have been isolated from the hydrolysates pf nucleic acids; both are
pentose: D(--)-ribose and 2-deoxy-D-(--)-ribose.
There
are two types of bases, which occur in nucleic acids: purines and pyrimidines.
The most common purine bases are adenine and guanine. Many other purine have
been isolated, for example, 1-, 2-, and 3-methyladenine, 6-methylaminopurine,
3-methylguanine, etc. The most common pyrimidine bases are uracil, thymine and
cytosine. Other pyrimidines have been isolated, for instant, 5-methylcytosine
and 5-hydroxycytosine.
DNAs, like proteins, undergo
changes in helical content under certain conditions. These changes have been
studied by the methods used in protein chemistry. Thus, when DNAs are heated
in diluted aqueous solution, they undergo helix-random coil transitions, i.e.,
they undergo thermal denaturation. The double helix separates into two
separate strands. If the solution is cooled rapidly the two strands remain
separate, but cooled slowly the original double helix is often formed
(annealing, renaturation). Extremes of pH also bring about denaturation
(irreversible). Single-stranded ring DNAs are extremely resistant to
denaturation. DNAs in the form of catenanes, by suitable treatment, can
undergo a single break in one of the strands. This broken strand can be made
to unwind and to separate from the intact strand by careful denaturation. The
single-stranded ring can be isolated.
Both
types of nucleic acids (RNA and DNA) contain adenine and guanine. On the other
hand, RNAs also contain uracil and cytosine, whereas DNAs contain thymine and
cytosine. This distribution of pyrimidines, however, is not rigid. e.g.,uracil
has been found in certain DNAs.
Angell
(1961) has shown, from infrared studies, that in the solid state and in the
ribose and deoxyribose nucleosides derived from these bases, adenine exists in
the form of amino form, cytosine and guanine exist in the keto-amino from and
uracil in the diketo form. Furthermore, X-ray analysis of the various bases
has shown that all are planar.
Basic components of deoxyribonucleic acids
Combination of bases (either a purine or pyrimidine) with a sugar
(ribose or deoxyribose) gives rise to a nucleoside, e.g. adenosine (ribose
+adenine), guanosine (ribose +guanine), cytidine
(ribose +cytosine), uridine (ribose +uracil), thymidine (deoxyribose +thymine).
The nucleoside derived from hypoxanthine and ribose is named inosine.
Combination of a nucleotide with phosphoric acid produces a nucleotide,
i.e., nucleotides are nucleoside phosphates, e.g., adenylic, guanylic,
cytidylic, inosinic and uridylic acid. It might be notes here that the term
nucleotide is now used to embrace a large group of compounds composed of the
phosphates of N-glycosides of heterocyclic bases, and the pyrophosphates and
polyphosphates containing one or more nucleosides.
Structure of nucleosides
Hydrolysis of nucleotides
with aqueous ammonia at 175˚C
under pressure gives nucleosides and phosphoric acid; thus in nucleosides the
bases is linked directly to the sugar. Furthermore, since nucleosides are
non-reducing, the ‘aldehyde group’ of the sugar cannot be free, i.e.,
nucleosides are glycosides.
DNAs
are natural occurring polymers
These
are polymer of the deoxyribonucleotides and hydrolysis by certain enzymes
results in a mixture of the monomers. Hydrogen-ion titrations on purified DNAs
showed the presence of phosphodiester bonds. Alkaline hydrolysis of DNAs is
very slow; this is due to the absence of the 2’-hydroxyl group in
deoxyribose, thereby preventing the formation of the cyclic 2’,
3’-phosphate, which is readily formed with RNAs. This difference towards
alkaline hydrolysis is used as a means of separating RNAs from DNAs. The
nature of the internucleotide bonds was established by means of enzymic
hydrolysis.
The
common bases in DNAs are adenine (A), guanine (G), thymine (T), and cytosine(C)
As with RNAs, the molar propostion of these bases vary considerably according
to the source of the DNA. There are, however, some important differences
between RNAs and DNAs. The following regularities (with very few exception) in
the composition of DNAs have been observed:
(a)
A=T; (b) G=C.
From this it following that:
(c)
A+G=T+C; (d) A+C= G+T
With DNAs, the sum of the keto-bases (G+T) is
equal to the sum of the amino-bases (A+C), and not roughly equal as in RNAs.
The nucleotide sequence in DNAs has been investigated by controlled
degradation with enzymes, acids, etc.
(d)
The structure of DNA
Pancreatic
deoxyribonuclease converts DNAs into a mixture of oligonucleotides (average of
about 4 nucleotides may then be subjected to the action of spleen
phosphodiesterase (deoxyribonuclease ΙΙ). This results in the formation of
the mixture of deoxyribonucleoside 3’-phosphates. These experiments have led
to the conclusion that DNAs have a linear structure of units linked by
3’—5’ bonds.
The secondary structure of DNAs
Wilkins et al. (1953), from their X-ray studies, showed that the
DNA molecule has a helical form, and suggested the helix contains two
intertwined strands. Watson and Crick, however, proposed that the secondary
structure was two DNA chains wound as right-handed helices round a common axis
but heading in opposite directions.
Furthermore, the two chains are wound in such a manner that pyrimidine
and purine bases point towards each other, and it is hydrogen bonding between
pairs of bases that holds the helices together. Also, the extremely important
made, based on steric considerations, is that pairing of bases can occur only
between a pyrimidine and a purine, and that a given pyrimidine can pair only
with its complementary purine. Such complementary pairs are A-T and G-C. The
A-T pair is held together by two hydrogen bonds and the G-C pair by three
hydrogen bonds. The ring-planes of each pair of bases lie in the same plane
and are perpendicular to the axis of the helix. The ‘backbone’ of each DNA
strand consists of deoxyribose-phosphate units. This double helix accounts for
the equivalence of A and T and of G and C.
This Watson-Crick model of DNA has been confirmed, with slight
corrections, by later work. X-ray studies have shown that the pairs are planar
and that the hydrogen bonds are almost collinear, their lengths lying between
2.8 and 2.9 °A. Each turn of the helix contains 10 nucleotide pairs, and the
diameter of the helix is about 20 °A. The spacing between adjacent pairs is
3.4 °A. It can be seen from this arrangement of the two helices that the two
DNA chains must be complementary to each other, i.e., a chain with a given
sequence of bases can pair only another chain that has the complementary
sequence of bases.
X-rays analysis has also shown that the crystalline shape of the double
helix is dependent on the amount of water present. When the water content is
about 40%, X-ray analysis shows the presence of a regular three-dimensional
crystalline structure (the A structure; repeat unit along the axis: 28°A.).
On the other hand, at higher water content (70%), the X-rays pattern shows
that the double helix are parallel and packed side by side, but not in a
regular manner (the B structure; repeat unit along the axis: 34°A.).
From 1959 onwards, it has been found that DNAs can exists as cyclic single
strands, i.e., as rings. Double helical DNAs have also been isolated in the
form of a ring. These are examples of naturally occurring catenanes, the two
rings of which are interlocked by a topological bond having a very large
winding
number.
