Chemguide: Support for CIE A level Chemistry


Learning outcome 21.3(d)

This statement is about the structure of proteins.

Before you go on, you should find and read the statement in your copy of the syllabus.


Introduction

Unless you have been learning about amino acids recently, before you do anything else, follow this link and read the first section headed "What are amino acids?"

You don't need to go any further than this for the present topic.


Main page to read

Now read the page about the structure of proteins.

In common with most people, CIE count sulphur bridges as a part of the tertiary structure of the protein.


Points to notice for CIE exam purposes

This isn't a new statement, and so you can look back at older exam papers. But be careful! There was much more about proteins and enzymes on the previous syllabus. There will be bits of older questions that you won't be able to do.

A relatively common question asks you for diagrams (or an explanation) showing the types of bonds which contribute to the primary, secondary and tertiary structures. This is easy stuff, and you can't afford to waste marks by getting it wrong.


For primary structures

You should realise that the bonds which make up the primary structure are all covalent, and you should be confident that you can draw a short length of protein (or other polypeptide chain), showing the exact bonding in the peptide link.


For secondary structures

You should know that secondary structures are held together with hydrogen bonds involving the atoms in the peptide links.

A lone pair on the double bond oxygen is attracted to the hydrogen attached to the nitrogen atom in a second peptide link in a different part of the chain. If you aren't clear about this, go back and read the protein structure page again.

Repeating the essential diagram from that page:

Both alpha-helices and beta-pleated sheets result from hydrogen bonds between these two groups. But it is important to realise that the detailed arrangements are different in the two structures.

So how might this be asked in an exam?

One CIE question gave you the structure of a bit of protein chain in a beta-pleated sheet, and asked you to draw the bit of chain that this was attached to, showing the bonds that are formed between the two. As long as you understand what a beta-pleated sheet is, that isn't too difficult.

In another question, you were asked to name the two forms of secondary structure for a mark each. That's easy, of course.

The question then went on to ask you to draw a diagram to show one of these, and that was worth another 2 marks. The mark scheme and examiner's report weren't clear about how much of the structure you were expected to show. The marks went for:

  • showing the helix or two parallel zig-zag strands in the beta-pleated sheet

  • showing C=O- - -H-N hydrogen bonds between the turns in the helix or the strands in the beta-pleated sheet

Based on the marks available, you have only got about 2 minutes to do this. I would suggest you keep it simple.

For the helix, draw a helix shape as shown in green on the page you have just read. Draw just enough of the chain on the top two coils to show perhaps two of the hydrogen bonds.

For the beta-pleated sheet, draw the pleated sheet as shown in green on that page. Then on just two of the strands, draw enough of the chain to be able again to show a minimum of two of the hydrogen bonds.

If you spend a bit of time working out how to do this, it should help you to learn how both of these structures fit together.


For tertiary structures

The tertiary structure involves interaction between side groups on the protein chain - NOT between atoms in the peptide links.

You must know the four ways in which the tertiary structure is held together. They are:

Sulphur-sulphur bridges

These are simple covalent bonds formed between two cysteine residues. Cysteine has a side group containing the -SH group. These react together with the loss of the hydrogen (this is an example of oxidation - CIE asked this once).

Sulphur-sulphur bridges consist of single bonds holding two bits of the chain together via the link -S-S-.

Try to tie together the words cysteine and sulphur-sulphur bridge in your mind, so that whichever one you see, you immediately think of the other one.

Ionic interactions

These come from ionic groups on side chains - between -NH3+ in one side group and -COO- in another one.

Look for the presence of -NH2 and -COOH groups in side chains. If they get close together, there will be a transfer of a hydrogen ion from one to the other to give these ionic groups.

Hydrogen bonds

Take care not to confuse these with the hydrogen bonds that hold secondary structures together - those involve atoms in the peptide links. What we are talking about now are hydrogen bonds involving the side groups.

This will involve typical hydrogen bonding groups like -OH or -COOH or -NH2 groups. (But don't forget that -COOH or -NH2 groups close to each other will transfer a hydrogen ion, and give you ionic attractions rather than a hydrogen bond.)

Van der Waals dispersion forces

These are most important where you have reasonably big hydrocarbon groups in the side chains - but they will be there to some extent in the interactions between every side group.


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© Jim Clark 2011 (last modified July 2014)