Sugars

In this step we will analyze sugars. Unfortunately, it is very difficult to solve the structure of poly-saccharides (Question: Why?). So we cannot see much about this in 3D. Most cells consist for about 90% of water. The other ten percent is divides as follows:

• 5% protein
• 1.5% carbohydrate
• 1.5% nucleic acid
• 1% lipid
• 1% miscellaneous (metabolites, hormones, poly-phenol, terpenes, etc., etc.)

So, it makes sense to spend a bit of time on sugars too...

• Which roles do sugars have in the living cell?
• Draw the structure of sucrose.
• Mention ten classes of enzymes that act on sugars.
• What does H5N1 mean to you? And what are the H and the N for in the name?
• Which sugar cleaving enzyme is an essential part of the flu-virus and why is it needed?

Now, lets look at a sugar cleaving enzyme. First download 7taa.pdb from the PDB.

Figure 44. Taka amylase. A oligo saccharide is shown in yellow.

Question 41: Why is it so difficult to solve the structure of poly-saccharides?

Taka amylase question(s)

Question 42:

• Describe the fold of Taka amylase (in terms of domain structure).
• Is the location of the oligo-saccharide relative to the TIM-barrel a surprise to you? And why (not)?
• Why is the oligo saccharide not cleaved?
• Look at the tyrosines 75 and 82. How are they packed against the sugar?
• Which are the active site residues?

Chitinase question(s)

Question 43:

• What is the main role of chitin in nature?
• Which residues bind the sugars in the 1hkk chitinase? And what is striking about this binding?
• There are two Zinc ions bound to the chitinase. What role do these Zincs have?