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Exam Protein Science 2022
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What does the term “electronegativity” mean?
With regard to electronegativity, explain the differences in electron distribution between a C-C, a C-H, and a C-O single bond
What does the term “electronegativity” mean?
With regard to electronegativity, explain the diffe...
Electronegativity describes the ability to attract electrons within a chemical bond.
C-H slightly polar, partial negative charge at C
Strongly polar, partial negative charge at O
C-C unpolar, no difference in electronegativity
The equilibrium constant describing a chemical reaction is related to the free energy change of this reaction. How exactly does the equilibrium
constant depend on the free energy change (not at all, linearly, exponentially, logarithmically,…..) and what is an important consequence of this
dependency?
The equilibrium constant describing a chemical reaction is related to the free energy change of this...
The equilibrium constant depends exponentially on the free energy of the reaction. As a consequence, small energy changes can drastically change the equilibrium.
Several algorithms are available for predicting the secondary structure of a protein based on its known primary amino acid sequence, e.g. the
Chou-Fasman approach.
Explain the principle of how this approach works.
Several algorithms are available for predicting the secondary structure of a protein based on its kn...
Each residue has its characteristic likelihood to be located in a helix/sheet/loop etc (calculated based on information from known structures).
For a chosen stretch of amino acid residues in the new sequence (10-20 residues) these probabilities are summed up and normalized. This
procedure is repeated for the next stretch of residues and so on.
Does a hydrophobic (as compared with water) environment increase or decrease the pKa value of a basic amino acid side-chain? Give reasons
for your answer.
Does a hydrophobic (as compared with water) environment increase or decrease the pKa value of a basi...
In a hydrophobic environment charges are disfavored, therefore the protonated/deprotonated equilibrium of a basic reside will be shifted
towards the deprotonated state. Consequently, the pKa will decrease.
Interactions between an inhibitor and a protein can be characterized by the KI
value. What is a KI
value? Give an equation and explain in words.
The inhibitor I binds to the enzyme E in a 1:1 ratio. You know the KI
value, 10^-5 M. What percentage of enzyme molecules has the inhibitor bound
if [I] = 10^-4 M or 10^-7 M, respectively?
Interactions between an inhibitor and a protein can be characterized by the KI
value. What is a KI
...
KI
= [I[E]/[IE]
It represents the equilibrium dissociation constant of the inhibitor.
With [I] = 10^-4 90 % of the enzyme molecules have the Inhibitor bound
With [I] = 10^-7 1 % of the enzyme molecules have the inhibitor bound
Explain the molecular mechanism of the reversible switch employed by G-proteins.
Explain the molecular mechanism of the reversible switch employed by G-proteins.
These proteins switch back and forth between a GTP and a GDP bound state. If GTP is bound the terminal phosphate forms hydrogen bonds
that move a protein domain, if GTP is hydrolyzed and replaced by GDP then this phosphate is not present, the hydrogen bond not formed and
the domain moves back. This structure change can be used for signal transduction.
Foerster/Fluorescence Resonance Energy Transfer (FRET) is a frequently used technique for investigation of proteins. Briefly describe the
principle of FRET and mention two factors that strongly determine FRET efficiency.
Foerster/Fluorescence Resonance Energy Transfer (FRET) is a frequently used technique for investigat...
Energy transfer between two fluorophors.
Fluorophore 1 (donor) absorbs light, but the energy is not emitted as fluorescence. Instead, the energy is transferred to fluorophore 2
(acceptor) whose absorption spectrum overlaps with the emission of the donor. The acceptor then emits the fluorescence.
Two parameters:
1. distance between fluorophores
2. Orientation of the fluorophores.
Gel filtration chromatography is a frequently used method to purify proteins. Often, this method is used after an initial affinity chromatography
step. Describe the working principle of gel filtration chromatography and explain why performing a gel filtration step, even after affinity
chromatography, can be very useful for protein purification.
Gel filtration chromatography is a frequently used method to purify proteins. Often, this method is ...
In this type of chromatography, proteins are separated according to size. The sample flows through a column filled with beads that have pores
on their surface. The smaller the proteins are, the higher the chance that the proteins will enter the pores. Proteins that enter the pores will be
retarded and will eluted later. Therefore, with this technique large proteins are eluted first and small proteins elute later.
This step is often used as final purification step, after intial affinity chromatography as gel filtration seperates monomers from oligomers, from
potentially degraded proteins or from proteins that have lost subunits.
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