Enzymes II Flashcards
What is a perfect enzyme?
It’s an enzyme that catalyses a reaction so efficiently that the rate-limiting step is that of substrate diffusion into the active site.
RECAP: What is the turnover number?
The turnover number is the maximum number of chemical conversions of substrate molecules per second that a single catalytic site will execute for a given enzyme concentration. The equation is: TURNOVER NUMBER = Vmax/[enz]total
Give an example of a ‘perfect’ enzyme.
An example of a perfect enzyme would be Triosephosphate isomerase (TIM). It catalyses the conversion of Dihydroxyacetone Phosphate & Glyceraldehyde 3-Phosphate (the two 3C intermediates in glycolysis)
How does Triosephosphate isomerase work (or a perfect enzyme, in general)?
It makes it so that, instead of there being a big energy change and the reaction happening by conversion of A to Z, it happens via intermediates that don’t have a high energy change between them, making the conversion easier. The reaction is limited by E + S (substrate diffusion into the enzyme), so decreasing the energy levels doesn’t increase the efficiency/rate of reaction.
Give an example of a serine protease and how it works.
Chymotrypsin has a very reactive serine group which attacks the peptide bond to form an acyl-enzyme. Chymotrypsin (and Trypsin) are made in the pancreas.
Describe the catalytic triad.
- A catalytic triad is a set of three coordinated amino acids that can be found in the active site of some enzymes.
- Ser 195 may get its reactivity due to its positioning next to His 57 and Asp 102.
- This is a catalytic triad, which makes the serine much more electronegative.
- This triad is found in all proteases.
Give specific examples of three serine proteases, and describe how they work.
- TRYPSIN: cleaves after Lys, Arg (which are positively charged), thanks to its negative pocket/cleft - CHYMOTRYPSIN: cleaves after Phe, Trp, Tyr (which are aromatic and hydrophobic) thanks to its hydrophobic pocket/cleft - ELASTASE: cleaves after small amino acids (with a small R group) thanks to its narrow pocket/cleft.
How does ATP synthesis occur in a mitochondrion?
It occurs via a proton-driven rotary ATP Synthase. It has to do so, as the inner membrane of the mitochondrion is impermeable to ATP.
Describe how ATP Synthase synthesises ATP.
1) ATP Catalysis begins when protons pass through the part of the enzyme that lies in the cell membrane, causing it to turn. 2) The central core then rotates inside the top half of the enzyme. 3) This region holds an ATP molecule and pulls in ADP and an inorganic phosphate group in the neighbouring subunit. 4) As the core rotates, the subunit with ATP loosens, and the section holding ADP closes. 5) The original ATP molecule is released, and a new one is formed from the ADP. 6) The cycle repeats.
What is Topoisomerase II?
It is a molecular clap that unlinks tangles chromosomes.
Describe how Topoisomerase II works.
1) The G-segment (gate segment) of the chromosome binds to the Topoisomerase II. 2) ATP is used to clamp the T-segment (target segment) of the chromosome. 3) The G-segment is broken, and the T-segment is pulled through. 4) The G-segment is resealed and released via ATP hydrolysis.
