Glycoconjugates

A glycoconjugate is a carbohydrate (glycan) covalently linked with another

compound. We only briefl y summarize them here. The fi rst type of
glycoconjugate
we consider are glycoproteins, which are proteins with monosaccharides,
disaccharides, oligosaccharides, or polysaccharides (or a carbohydrate
derivative)
attached. These include carbohydrate chains that are between 1 and 30 base
units
in length. If the carbohydrate is bonded to the OH group of serine or threonine,
we say that the molecule is O-linked. If it is linked to an asparagine, then we say
it is N-linked. Glycoproteins play a role in many important biological processes
in eukaryotic cells. For example, they can form the basis of structural proteins,
enzymes, or hormones.
A proteoglycan is a complex molecule consisting of polysaccharides together
with glucosaminoglycans and proteins. A glucosaminoglycan is an unbranched
polysaccharide
with alternating hexosamine and uronic acid residues. These substances
form a gel-like matrix and are used in cartilage and synovial fl uid. Examples
include
chondroitin-6-sulfate and hyaluronic acid.
Carbohydrates are the most abundant biomolecule playing diverse roles in
nature
including structure, playing a role in DNA, and, most importantly, forming the
basis of
energy storage and metabolism. Large carbohydrates are constructed from
fundamental
units called monosaccharides. Monosaccharides come in different isomers, the
most
important of which are D and L isomers that react differently to light. Most
biomolecules
are D isomers but it is possible to have biologically active L isomers of some
compounds.
The most important monosaccharide in biological processes is glucose.
More complex molecules can be constructed by linking monosaccharides
together.
Two monosaccharides can be joined together with a glycosidic bond. The most
familiar such compound is sucrose, which consists of a glucose and fructose
molecule
joined together. Polysaccharides are large carbohydrates built out of glucose
molecules.
Plants use starch, which consists of amylose and amylopectin, to store energy.
Animals
also store energy in the form of carbohydrates in glycogen. Cellulose is a longchain
molecule of glucose units that gives plants their structure.
Derivatives of carbohydrates also play an important role in biological processes.
For example, a deoxycarbohydrate is derived from a carbohydrate by the
removal of
an oxygen. Ribose and deoxyribose are components of RNA and DNA,
respectively.
Carbohydrates can form complex molecules with other constituents such as

proteins. When this occurs, the resulting compound is called a glycoconjugate.

Cot curve. A curve that indicates the rate of DNA-DNA annealing as a function
of DNA concentration and time.

Cot curves. Data from genomic Cot analysis are

usually plotted as IOQ1oCoto.s against the fraction of
reassociated DNA (1 - C/C0) to give a Cot plot or
Cot curve. For the simple genomes of bacteria and
viruses, reassociation occurs over two orders of
magnitude of Cot values. and Co\ curves are linear
over approx. 80% of their lengths. As the complexity
of the genome increases, Coto.s increases
and curves are displaced to the right. The Cot plots
of E. coli and bacteriophage A. DNA are shown
below, together with polyuridilatelpolyadenylate, an
artificial 'genome' with the minimum complexity of
1. Eukaryotic genomes subjected to similar analysis
show reassociation over a much broader range of
Cot values. The eukaryotic Cot plot can often be
resolved into three overlapping curves, representing
genome fractions with different sequence complexities.
These are sometimes termed the fast, Intermediate
and slow components, and correspond to
highly repetitive, moderately repetitive and unique
sequence DNA. The slow component gives the best
estimate of true genome complexity, because most
genes are found in unique sequence DNA. A
proportion of DNA also reanneals immediately. This
zero time binding DNA is also known as snapback
or fold-back DNA because it represents
regions of dyad symmetry which can hybridize by
intramolecular base pairing. The Cot plot of a typical
mammal is superimposed over those of the three
simple genomes below.
Cot analysis. Before genome analysis by sequencing
was feasible, reassoclation kinetics (the analysis of
the behavior of single-stranded nucleic acids annealing
in solution) was used to investigate genome
properties. Although this technique is now mainly of
historical interest, the principles remain useful for
understanding genome architecture and nucleic acid
hybridization in general (q.v.). Double-stranded DNA
can be denatured or melted (separated into single
strands) by heating, and if gradually cooled, will reassociate
(renature, reannea~ to form duplex molecules.
The reassociation of single-stranded DNA in solution
follows second-order kinetics because there are two
strands, and the rate at which this occurs can be
expressed as shown in Equation 12.1 , where C is the
concentration of single-stranded DNA at timet, and k
is the reassociation rate constant. The proportion
of single-stranded molecules remaining at any time,
given a starting concentration of Co. can thus be
determined by integration, as shown in Equation
12.2. This identifies the product of Co and t as the
parameter which controls the rate of reassociation.
dC :::--kC2

dt

C0 "'1+kC0t
(12.1)
(12.2)
The point at which half the DNA has reassociated

(f0.5) is chosen as a reference. At this point, C/Co =

0.5, and by rearranging Equation 12.2, it can be

shown that Coto.5 = 1/k. Coto.s is described as the
Cot value, and is proportional to genome complexity.
This is because as complexity increases, the
relative concentration of any individual sequence
decreases and takes longer to find a complementary