Biocatalysis: Science and Technology

Vakinformatie

Voor 2021 heette het vak Advanced Enzymology.

Question 1

What drives protein folding? Which mechanisms are involved?
Why do we say that the structure of a protein is encoded in the primary sequence?
How do AlphaFold and related algorithms work?

Question 2

Why do proteins need cofactors? Explain with examples.

Question 3

Figure of Ohno and IAD model is given.

What does neofunctionalization mean in the scheme below?
What does specialization mean?
Why does the IAD model, which is thought to be more correct than the Ohno model, indicate that neofunctionalization happens first?
What does this mean for the specificity of natural enzymes?

PART 1. Oral examination by prof. Peter Dedecker

Given a kinetic scheme with product feedback, compose the differential equations that govern this system.
Explain the value of k' = k1 (1+([S2]/K)^n) [S1].
Explain the concept and the procedure of numerical integration for a simulation of a product feedback scheme.
Given data of real, in vitro experiment of [Ca2+]i by Fura-2 and [cAMP] by IUCP, list the problems that may arise in such an experiment and how to surmount them. How does an experiment like this work practically?

PART 2. Written examination by Dr. Fabian Hertel

Sketch an acid-base, electrophilic or nucleophilic catalysis pathway using a correct amino acid of choice.
Give the correct action mechanism for two different amino acids.
What role do metal ions play in enzymatic catalysis?
Sketch a 2D folding funnel. Mark where the completely folded enzyme, and a unfolded intermediate are located. What mechanisms exist in nature to make the folding process more efficient?
Your research requires an enzyme that is capable of converting MDMA to the non-pyschoactive compound benzaldehyde. There exists a catalytic antibody that is capable of this reaction. How do these catalytic Abs work? Is further optimisation necessary? Describe one method to design an artificial enzyme.