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Po Gil 2 Enzyme Mech
Po Gil 2 Enzyme Mech
Po Gil 2 Enzyme Mech
REACTION MECHANISM
1. 2. 3.
6. 5. 4.
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Bio200 POGIL Cell Biology Activity 2 – Enzymes Schivell
CRITICAL THINKING QUESTIONS:
2. Compare panels 1 and 6 of the reaction mechanism (these contain the initial and final states
of the RNA substrate). Describe in fewer than 5 words what has changed about the RNA.
For the following questions, it is a good idea to circle or annotate the differences you see on
the model itself, or to draw arrows indicating formation of new bonds or movements of
atoms.
3. In panel 2 compared to 1, what has changed for the... (be as brief but specific as possible)
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Bio200 POGIL Cell Biology Activity 2 – Enzymes Schivell
... substrate? __________________________________________________________
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Bio200 POGIL Cell Biology Activity 2 – Enzymes Schivell
8. In panel 1, find two different types of molecular interactions that help attract and hold the
substrate in the enzyme's active site. (Choose from hydrophobic interactions, covalent bonds,
hydrogen bonds, and ionic bonds.) Write the name of each interaction and draw an example
of the atoms/groups of atoms involved in the boxes below:
b. Does the substrate in panel 2 have a higher or lower G than in panel 1? _____________
a. Describe the "job" of the two histidine (His) R-groups. Protonation site and
deprotonation site
11. a. The R-groups of the active site are in the same conformation in panels 1 and 6. Can the
enzyme catalyze another reaction after it completes this one? Why? Yes, same structure as
before.
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Bio200 POGIL Cell Biology Activity 2 – Enzymes Schivell
MODEL 2:
The wild-type enzyme and the rate at which the reaction
proceeds in its presence is shown to the right. Below are
three different enzyme mutants. For each, one aspect of
the active site's structure is slightly changed. The mutant
enzymes are mixed with RNA in solution. The reaction
rates are shown underneath each image.
WT = 1000 rxns/sec
12. How does reaction speed change when the active site is changed?
________slows_____________
13. a. Is the relative position of a specific R-group within an active site important?
___yes______
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Bio200 POGIL Cell Biology Activity 2 – Enzymes Schivell
15. Even if an R-group (that is part of the active site) does not normally accept or donate
protons or other atoms, or form covalent bonds with the substrate, can it be important?
Explain. Ionic bonds between the lys and the substrate
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Bio200 POGIL Cell Biology Activity 2 – Enzymes Schivell
On your own:
The drawing shows the first 2 steps of a 5 step
A
reaction mechanism. The enzyme's peptide backbone
is a solid line (except for some atoms shown in detail).
The two arrows (A and B) point to the two ends of the
enzyme. The two R-groups of the active site, CYS and
HIS, are shown in detail. In the first frame, the enzyme's
two substrates are shown, NAD+ and a second
substrate in the dotted line.
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Bio200 POGIL Cell Biology Activity 2 – Enzymes Schivell
10. If CYS were changed to Valine (see below), how would
the rate of catalysis change? Explain in 1-2 sentences.