Question

6. You notice one day a slimy patch of goo on your carpet. It seems as Being an awesome biologist, you figure out it's bacteria feeding off you of nylon! How can this be? Perhaps the landfill and nuclear power plant next to your no do with it... Boo on your carpet. It seems as if the goo is eating away at your carpet. gure out it's bacteria feeding off your carpet. But wait, your carpet is made id nuclear power plant next to your house has something to You set out to determine how the bacteria can live off of nylon since nothing known can. To off of nylon since nothing known can. You scrape some off Dub-intested carpet and take it to your lab, You culture large quantities of the bacteria and painstakingly purity a protein with the ability to cleave the nylon. You name the newly discovered enzyme Leggsase. Nyom denzyme legesase. Nylon is a polymer made up of many repeating subunits (like the polysaccharides). It looks like this: O H H H H H H H H H H w e - - -C- C-E N -C-0-0-0-0-0-NW H H H H H H H H H H The squiggly lines at the ends indicate that this same unit is repeated many times in both directions. The arrow points to the bond that is cleaved to break up the nylon polymer. a) Just how good is the enzyme? If we just put nylon in water, the rate at which this bond will cleave is about 1 per year. In the presence of the enzyme, it's about 100 per second. What is the increase in the rate of the reaction? ENZYME INCREASES THE RATE OF CHEMICAL REACTION BY LOWING THE REACTION'S ACTIVATION ENERGY b) Since the world probably wouldn't like to have this bacteria eating up all the nylon around, you decide to make a bunch of money by discovering an inhibitor to it. You discover that a dipeptide, Glycine-Glycine, is a fair inhibitor of Leggsase. i) Draw the structure of the dipeptide and explain why it would inhibit Leggsase. ii) Is this likely to be a competitive or non-competitive inhibitor? Explain.

Answer 1

The cleavage of the nylon by the enzyme Leggsase is a chemical reaction. Every chemical reaction has a rate. Enzyme increases the rate of the chemical reaction, they usually act in one direction thereby favoring or directing the reaction. The rate of the reaction is defined as the number of product units formed or the number of substrate units consumed per unit time.

a) In water, the cleavage of nylon has a rate:

Tw = 1/year

When the enzyme is present, however, the cleavage of nylon has a rate:

rn = 100) second = 100 x 60 minute = 100 x 60 x 60/hour

..r = 3.6 x 105/hour = 3.6 x 105 x 24/day = 3.6 x 108 x 24 x 365.25/year

rn = 31557.6 x 10/year 3.16 x 10°/year

The above calculation follows from 1 minute = 60 seconds, 1 hour = 60 minutes, 1 day = 24 hours and 1 year = 365.25 (averaged with taking into consideration leap year after each four years).

Thus, the increase in the rate of increase is

In -rw 3.16 x 10°/year – 1/year * = 3.16 x 10= 3.16 x 101% 1/year

b) Glycine-glycine dimer is formed by peptide bond formation between two glycine molecules. The structure is as follows:

но и HN- С – С – – С. — со ни Glycine - Glycine

Since the cleavage site of the enzyme is CO-NH bond, the glycine-glycine can also be cleaved by the enzyme. Additionally, the milieu of glycine-glycine is similar to the CO-NH bond in nylon. Hence this dipeptide will be able to bind to the inhibitor.

The binding pocket of the inhibitor is the same as that of the substrate. Hence this is an instance of a competitive inhibitor.

Active Site SUBSTRATE ENZYME INHIBITOR