Protein structure (6)

Question 1

When does a sigma bond occur?

Answer 1

e.g when an anion + cation encounter one another

Question 2

What are nucleophiles + electrophiles?

Answer 2

-nucleophiles supply electrons
-electrophiles accept electrons

Question 3

When does the simultaneous making + breaking of sigma bonds occur?

Answer 3

When a nucleophile approaches a carbon atom having a leaving group (L) in a direction anti + rearward to the leaving group

Question 4

Describe the process of simultaneous making + breaking bonds

Answer 4

1. nucleophile substitutes for L group - and SN2 reaction (substitution nucleophilic bimolecular reaction)
2. the attack by the nucleophile doesn’t have to be at carbon

Question 5

What is the sigma bond making and Pi bond breaking reaction?

Answer 5

Condensation of a molecule + and an ion into a single ion

Question 6

What are lysozymes?

Answer 6

Enzymes involved in the first line of defence against bacterial attacks that cleave peptidoglycan

Question 7

What is peptidoglycan?

Answer 7

A polysaccharide complex in walls of gram-positive bacteria

Question 8

What do lysozymes cut?

Answer 8

-a glycosidic bond
-between NAM and NAG sugars in bacterial peptidoglycan

Question 9

What are the differences in structure of NAG and NAM and what does this control?

Answer 9

-have very similar structures
-differ at position C3 on the ring
-NAM is larger
-difference controls the site at which they can bind to lysozyme

Question 10

Describe the structure of lysozymes

Answer 10

-2 lobes separated by a deep cleft
-left lobe is a small beta sheet of mainly hydrophilic residues
-right lobe is a hydrophobic core surrounded by short helices

Question 11

What is the substrate for lysozymes and where do they bind?

Answer 11

-triNAG
-observed binding to top half of cleft, the binding site

Question 12

What does the active site of the lysozyme bind to?

Answer 12

6 sugars - ABCDEF

Question 13

What bond is broken and where when the substrate binds to the lysozyme?

Answer 13

-glycosidic bond
-between the 4th + 5th sugars (D-E)

Question 14

Why does the lysozyme bond to the peptidoglycan carbohydrate polymer?

Answer 14

So that a NAM ring is at site D + a NAG ring is at site E in the binding site

Question 15

What is the D-E glycosidic bond close to?

Answer 15

The side chains of Glu 35 and Asp 52 - both have carboxylic acid side chains

Question 16

At pH 6, what form is Asp 52 in?

Answer 16

The carboxylate form as expected - optimum temp for lysozyme

Question 17

What form is Glu 35 in at pH 6?

Answer 17

The carboxylic acid form

Question 18

Describe the pKa of Glu 35 at pH 6

Answer 18

-unusually raised
-due to hydrophobic microenvironment

Question 19

Describe the lysozyme mechanism

Answer 19

-nucleophilic attack by Asp 52 forms covalent acyl-enzyme intermediate
-Glu 35 donates proton + sugars E-F diffuse away (1st product)
-attach by water: OH added to C1 of D + a proton to Glu 35
-sugars A-B-C-D are 2nd product