3 - Macromolecules

Question 1

What are the three classes of tertiary structure?

Answer 1

Globular (spheroid)
Prolate (rod-like)
Oblate (disc-shaped)

Question 2

What is relative molar mass?

Answer 2

A dimensionless quantity found simply by dividing the molar mass by 1gmol‾¹.

Question 3

What are the two categories of macromolecule solutions?

Answer 3

Monodisperse and Polydisperse.

Question 4

What are monodisperse solutions?

Answer 4

Ones where all solutes have the same RMM.

Question 5

What are polydisperse solutions?

Answer 5

Ones where the solute does not have a uniquely defined RMM.

Question 6

What is ‘Effective molecular mass’?

Answer 6

The average RMM of a polydisperse solution, calculated in various ways.

Question 7

What three ways can effective molecular mass be defined?

Answer 7

Number Weighted Average (Mn)
Mass Weighted Average (Mm)
Double Mass Weighted Average -AKA Z-averaged (Mz)

Question 8

How are number weighted averages be determined?

Answer 8

From experiments concerning colligative properties, often osmometry.

Question 9

How can Mass Weighted Averages be determined?

Answer 9

Light Scattering experiments.

Question 10

How can Double Mass Weighted Averages be determined?

Answer 10

From Sedimentation rate measurements.

Question 11

What is a heterogeneity index?

Answer 11

The ratio of Mm to Mn. Also known as polydispersivity. Higher values indicate higher polydispersivity.

Question 12

What is the heterogeneity index of a monodisperse solution?

Answer 12

1, though anything less than 1.1 is generally counted as monodisperse.

Question 13

Why are RMM averages of macromolecule solutions useful?

Answer 13

When producing polymers such as polythene, the chain length can vary hugely between the molecules which may effect the properties.

Question 14

Why are three types of macromolecular solution RMM average used?

Answer 14

Practically because different experiments yield results that correspond to different types of average. However the averages have the use that that respond to different types of impurity differently.

Question 15

How do low molecular weight impurities affect Mn and Mm comparatively?

Answer 15

Makes Mn far lower than the true RMM of the macromolecule, only has a very small effect on Mm.

Question 16

How do high molecular weight impurities affect Mn and Mm comparatively?

Answer 16

Very little effect on Mn, but cause a large increase in Mm.

Question 17

What RMM averages can be found from MALDI-TOF mass spectrometry?

Answer 17

Mn and Mm, and hence also the heterogeneity index.

Question 18

What does MALDI-TOF stand for?

Answer 18

Matrix Assisted Laser Desorption/Ionisation Time-Of-Flight.

Question 19

When measuring the average molar mass of a solution, what problem do polyelectrolyte solutions pose?

Answer 19

Molecules (like proteins) with multiple ionisable/dissociating groups can present an issue as a single of the macromolecules may cause itself to be outnumbered hugely by its own dissociating groups. This is a particular issue in osmometry, as relying on colligative properties (independent of solute nature) it cannot distinguish between molecule sizes.

Question 20

How are polyelectrolytic macromolecule solutions made to be measurable by osmometry?

Answer 20

By using a swamping electrolyte of whatever the dissociating group on the macromolecule is, preventing dissociation and so preserving molecular mass. An osmotic membrane that is permeable to small ions but not to macromolecules must be used to prevent all the extra ions from having an effect.

Question 21

The effects of the proteins weight and structure affect what processes utilised in ultracentrifugation sedimentation?

Answer 21

Heavier molecules tend to sink due to gravitational effect, which competes with the thermal motion of the liquid which prevents them from forming rigid structure and keeps them suspended in the solution.

Question 22

What does the equilibrium molecule distribution indicate about their properties?

Answer 22

Larger and heavier molecules towards the bottom, smaller and lighter towards the top on a distribution that relies mostly on molecular mass but also on shape - globular tending to sediment faster than prolate proteins for example.

Question 23

What does the ultracentrifuge provide in the process?

Answer 23

The rate of sedimentation would be incredibly slow due to gravity alone, by spinning the container at very high angular velocities they can provide up to 100,000x the force of gravity.

Question 24

What coefficient is measured in ultracentrifugation?

Answer 24

S, the sedimentation coefficient. It is related to the drift speed of the solutes and the angular velocity pf the centrifuge.

Question 25

What factor noted as D must be known in order to calculate Mn from a sedimentation coefficient, and how is it found?

Answer 25

The diffusion constant, related to frictional force between the solute and solvent (frictional coefficient, f). This is determined in a tricky light scattering experiment that can introduce a lot of accuracy.

Question 26

What factor noted as b must be known in order to calculate Mn from a sedimentation coefficient, and how is it found?

Answer 26

Buoyancy of the solvent, which depends on the density and specific volume of the solvent. Determined by calibration experiments.

Question 27

When calculating Mn from a sedimentation experiment, how can the issue of finding an accurate value for the diffusion coefficient be avoided?

Answer 27

Measure the relative concentration of the macromolecule at two radii across the tube instead of the absolute sedimentation rate. This gives a direct value of Mn, and can also be used to derive Mz.

Question 28

How is the viscosity of a macromolecule measured?

Answer 28

An Ostwald Viscometer is used to compare the time taken for a variety of concentrations of the macromolecule solution to pass through a capillary tube with that of a pure solvent with known viscosity.

Question 29

What can be determined from a Viscometer measurements?

Answer 29

The instrinsic viscosity of a macromoolecule, and from this the molar mass using the Mark-Houwink equation.

Question 30

Why do macromolecular solutions often appear cloudy?

Answer 30

Because the molecules are of the right size to scatter visible light.

Question 31

What information about a macromolecule solution can be determined from a light scattering experiment?

Answer 31

Absolute Mm values are very difficult to obtain and require lots of assumption/approximation. Usually measured relative to other samples or related macromolecules with known Mm. Sophisticated treatments can give some idea of shape.

Question 32

How does the concentration of a macromolecule solution affect its use in light scattering experiments?

Answer 32

The theory behind the information derivation breaks down at high concentrations, so like with osmometry multiple concentrations are used and the results are extrapolated back to ‘infinite dilution’.

Question 33

What are the advantages of using light scattering experiments on macromolecular solutions?

Answer 33

Despite the complex analysis, the methods themselves are fast and reliable.

Question 34

What is end group labelling used for?

Answer 34

Quantifying the number of macromolecules in a solution, and if using a known mass the molar mass can be derived.

Question 35

What are the principles that underpin end group labelling?

Answer 35

A known mass of dissolved macromolecules are reacted with an excess of a specifically labelled (often radio-) that attaches only to one end of the macromolecule. By then isolating the ‘doped’ macromolecules the end labelling groups can be counted thus giving the number of macromolecules present.

Question 36

What sort of macromolecule is end group labelling particularly useful for?

Answer 36

DNA.