21. Quaternary structure

Many proteins don’t have a __ structure

Quaternary

Give examples of two quaternary proteins:

• haemoglobin

• Restriction enzymes homodimers (cleave sections of DNA at palindromic sequences)

What is GAPDH?

A glycolytic enzyme. The monomer is catalytically inactive but has other cellular functions. BUT the main function is when it is a tetramer and it is catalytically active.

Collagen is a trimmer because: (describe more too)

It is made up of 3 polypeptides wound into a rope structure (tighter than an alpha helix). It has the repeating unit Gly-X-Y.

He also added Beta-mercaptoethanol which…

Reduces disulphide bonds. This is because it has an -SH group (Mercapto group) which is very chemically active.

Both of these things cause the protein to…

- After this, he removed urea and Beta-mercaptoethanol through dialysis and what happened?

Unfold and the disulphides to break.

- protein refolds

What does this experiment tell us?

Protein folding is spontaneous and doesn’t require energy.

Proteins don’t fold through random exploration

Protein folding is an ordered process. This process has 3 sections. What are these processes?

1. Nucleation - Hydrophobic regions condense (hydrophobic collapse). Short stretches of secondary structure

2. Aggregation - Motifs, domains and a molten globule. Extensive secondary structure, no tertiary structure

3. Compaction - tertiary structure is obtained.

If there are a high concentration of amino acid chains ready to be folded why is this a bad thing?

Folding is favoured in low concentration because at high, aggregation is caused. This is where hydrophobic regions clump together from different chains as unfolded regions of proteins are ‘sticky’ due to hydrophobic surfaces.

This is combatted with chaperones which are proteins that do what?

Looks after other proteins when not fully folded. Most prevent aggregation but some directly assist the folding.

How do the ones that prevent aggregation work?

They hold onto individual chains to keep overall protein conc low and release the chain when it is ready to be folded. This binding and release requires conformational change in chaperone and therefore ATP hydrolysis.

The chaperones that assist folding are called chaperoning. They were discovered by prof john Ellis and work by…

Trapping the partly folded polypeptide in its hollow inside and trap it in with a cap until it is fully folded and the cap is removed and allows another protein to fold. This physically stops aggregation.

How does disulphide isomerase help fold proteins?

It catalyses the oxidation and isomerisation of disulphide bonds. PDI then checks over this process and if it is wrong, it recatalyses the oxidation and isomeristion of disulfide bonds in proteins correctly.

What is the only amino acid that does need an enzyme to fold?

Proline, because it has a cis and trans form and so the conversion of one to the other is slow a

Sickle cell Anemia is caused by protein misfolding. How is this caused?

Haemoglobin aggregates to form long chains that distort the shape of the cell. It affects around 300,000 people worldwide but mostly in sub-Saharan Africa.