Tutorial 2 Solutions

There are four important molecules classes in chemical biology: nucleic

acids, proteins, glycans, and lipids.
1. Compare the homopolymers cellulose and glycogen with respect to their
stereochemistry, their physical properties, and their intramolecular
interactions.
Glycogens Cellulose
energy storage (animals, fungi, cell wall rigidity (plants)
bacteria) glucose β 1->4 linked
glucose α 1->4 linked linear
(occasionally 1->6) stiG fibres
branched sheet structure, layered
gel-like (crystalline)
spiral insoluble in water
soluble in water indigestible (dietary fibre)
broken down by human enzymes

2. Discuss what roles glycosylation plays in biology. Give some examples

from the lectures. Many drugs are protein based; why is it hard to make
glycoprotein-based drugs?
Add complexity to surface of proteins. Protect from proteases. Used for
interprotein signalling. Can be important to protein folding.
Eg. ABO blood type system. The presence or absence of
glycosyltransferases dictates which blood group antigens are present. A
type has a gene for a glycosyltransferase that adds GalNAc. B type has
one that adds galactose. O has no gene for either enzyme.
DiGiculties: they are not templated like DNA or proteins. Can’t feed
genetic information to a bacteria like we can for proteins. Hard to attach
to glycans to specific protein sites synthetically – glycans are
heterogenous.

3. Lipids are amphiphilic – explain what this means, and why lipids have this
property in relation to the below structure

Glycerol backbone (red), saturated acyl chain (green), unsaturated acyl

chain (blue), hydrophilic head group (purple)
4. What is the key diGerent between the higher order structure of lipids, vs
protein, DNA, and glycans?
Lipids form bilayers or micelles through non-covalent bonds. Higher order
protein, DNA and glycan structure is through covalent and non-covalent
bonds. ie. DNA or protein chains.

5. Detergents and lipids are chemically and structurally similar; but what is their
key diGerence?
Detergents form micelles, whereas lipids can form bilayers.

6. What structural diGerence determines whether a micelle or a bilayer are formed?

The size and shape of the hydrophobic chain and the polar head group. For lipids
with a single alkyl chain, packing favours a curved shape, because of the space
taken up by the polar head. When a lipid has 2 alkyl chains, side-by-side packing
tends to be mostly linear in cross sectional shape.

7. Lipid bilayers are often drawn as highly ordered structures (see below). Is this an
accurate representation of a bilayer structure? What’s an experiment we could
do to prove this?

Bilayers are drawn as highly ordered planes of lipids; but in reality, they are very
fluid and move around a lot. Each individual lipid takes on a variety of
conformations. There is variation to how much water solvates the head groups.
The alkyl chains undergo rapid rotation around their C-C bonds. Although the
spacing between lipids is fairly uniform, there is no position order for each lipid
molecule, and molecules diGuse rapidly. We can view this diGusion using
fluorescent tags; lipids tagged with fluorescent molecules can be bleached in a
very small region, causing them to stop fluorescing. Within a short time, these
bleached lipids diGuse back throughout the membrane, and overall fluorescence
is restored.

8. What is the equation to calculate the dissociation constant of a binding event,

and therefore what is the equation to determine the association constant. For
each, what does a high and low value mean?
 𝐾𝑑 = 𝑘𝑜𝑓𝑓/𝑘𝑜𝑛

𝐾 = 𝑘𝑜𝑛/𝑘𝑜𝑓𝑓

For Kd a low value means strong binding.

For K a high value means strong binding.

9. Collision frequency is proportional to ______.

Reactant concentration.

10. What is the half life of a reaction?

The point at which half of the reactants have been used, is given as a measure of
time e.g. seconds.

11. A reaction with three steps has rate constants of 8 s-1, 10 s-1, and 6 s-1. What
will be the rate constant for the entire reaction.
6 s-1. The reaction always depends on the rate determining step, which is the
slowest step.