BISC 122 P1/T1 CELL AND MOLECULAR BIOLOGY

STRUCTURAL BIOLOGY of PROTEINS

Molecular Model Building

The important features of biomolecules usually reside in their 3-dimensional structure - features that are not at all obvious from 2-dimensional representations. You are provided with components from which you can construct models of a series of amino acids and link these into short peptides. These models will give you an insight into certain stereochemical and conformational problems.

Please treat the models and their components with respect and ensure that the kit is complete, including instruction sheet, before you leave the laboratory.

Work through each exercise in order. There is no written work to be handed in but a member of will staff check your models at defined stages to make sure that you understand the principles involved

When you have made a model, get it checked by a member of staff before moving on to the next part of the exercise

The Models

The models that you will be using are of the skeletal "open" type in which the atoms are joined by semi-stiff rods. They are marketed by the firm of Spiring Enterprises under the name of Molymod. All single covalent bonds are of the same length in these models. The information sheet supplied by Spiring, amended and reproduced with permission is available on the Learn server and is included in each kit. Note the code given to each atom type in the contents table: this will be used in the diagrams for the laboratory exercise. Where double bonds are delocalised, as with aromatic ring compounds, there is no point in attempting to distinguish them by using double bonded atomic centres as the rings will be planar. Only use such double bonds when necessary to draw attention to a particular double bond.

Model Building

For this practical you will work in pairs. Ensure that you are familiar with all the ideas and play a full part in constructing the models. At suitable junctures, models may be made by both members of the team and brought together to make more complicated structures for comparison. Check your structures with the demonstrator at the end of each exercise.


PROTEIN BUILDING BLOCKS

ONE basic building block (the α Amino Acid) with twenty variations. The building blocks join together in a long chain. The number of building blocks in a protein may be as low as 50 or as high as 2500 or more.

Join now!

  • The ORDER of the building blocks in the chain determines the character and function.

  • The Amino Acid is a very simple small molecule built from an acidic (carboxyl) group and a basic (amino) group linked by a carbon (called Cα) atom.

  • The carboxyl group is a weak acid and the amino group is a weak base. In the pH range 4-9 both the basic and acidic groups are ionised and the amino acid is a zwitterion (provided there is no charge on the side chain R!).  A zwitterion is an ionic molecule with no net charge.
...

This is a preview of the whole essay