Download What are enzymes and how do they work

Bio200 POGIL Cell Biology Activity 2 – Enzymes TA KEY KEY KEY KEY
How do enzymes work?
Schivell
NOTES:
- His 12, Lys41, and His119 are key parts of the
active site (shown in the gray box and expanded
below), which is a small part of the enzyme.
MODEL 1:
Substrate
- The substrate is RNA (ribonucleic acid).
Enzyme
- Phosphorus (P) is most stable with 5 bonds and has
about the same electronegativity as C and H.
- This enzyme "catalyzes" the reaction shown.
REACTION MECHANISM
1.
2.
3.
6.
5.
4.
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Bio200 POGIL Cell Biology Activity 2 – Enzymes TA KEY KEY KEY KEY
CRITICAL THINKING QUESTIONS:
Schivell
1. What biological macromolecule is the enzyme made of? Protein
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.
RNA is cleaved
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)
... substrate? New bond btwn O and P, H+ lost
... enzyme? H+ from substrate received on His12
4. In panel 3 compared to 2, what has changed for the...
... substrate? Bond broken between P and O, H+ received from His119
... enzyme? His119 lost H+
5. a. In panel 4 compared to 3, what has changed for the...
... substrate? Nothing, but half of it has left the active site and water has entered
... enzyme? No difference in enzyme structure
b. What new molecule is introduced in panel 4? water
6. In panel 5 compared to 4, what has changed for the...
... substrate? Water lost a H+ to His119, new bond btwn OH from water and P
... enzyme? His119 received an H+ from water
7. In panel 6 compared to 5, what has changed for the...
... substrate? Bond broken between O and P, H+ received from His12
... enzyme? H+ lost from His12
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Bio200 POGIL Cell Biology Activity 2 – Enzymes TA KEY KEY KEY KEY
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:
(Example of Hydrogen Bond)
(Example of Ionic Bond)
9. a. In panel 2, which atom has an unusual number of bonds? Phosphorus
b. Does the substrate in panel 2 have a higher or lower G than in panel 1? Higher G
10. Consider the enzyme's role in the reaction mechanism:
a. Describe the "job" of the two histidine (His) R-groups.
The histidines donate or accept protons to or from the substrate to facilitate the changes in the
substrate's chemical structure.
b. Describe the "job" of the lysine (Lys) R-group.
The lysine is helping keep the substrate in the active site through an ionic bond with phosphate.
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, because the enzyme has exactly the same conformation when it begins the catalysis, so a new RNA
molecule could bind and go through the same steps.
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Bio200 POGIL Cell Biology Activity 2 – Enzymes TA KEY KEY KEY KEY
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
(His12 shifted "up"
slightly)
(Lys41 is now Met41)
Mut1 = 10 rxns/sec
Mut2 = 1 rxn/hour
(His119 is now Val119)
Mut3 = 1 rxn/millenium
12. How does reaction speed change when the active site is changed? It slows down
13. a. Is the relative position of a specific R-group within an active site important? Yes
b. Which mutant helps to answer this question? Mut1
14. When the transfer of a proton between the enzyme and
substrate is prevented, is the reaction rate changed slightly or dramatically? dramatically
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.
Yes, it can be important. For example, even though Lys42 does not do any of those things, it is
important for holding the substrate in the enzyme active site. If Lys41 isn't there, the substrate doesn't
stay in the active site as long and not as many reactions are catalyzed.
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Bio200 POGIL Cell Biology Activity 2 – Enzymes TA KEY KEY KEY KEY
On your own:
A
The drawing shows the first 2 steps of a 5 step
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.
1. What type of biological macromolecule
is the second substrate (ignore phosphate)?carbohydrate
2. Which end (A or B) is the amino
terminus of the enzyme? B
B
3. Which of the following R-groups would be best
suited to be in the "X" location shown in the first
diagram? (Circle ONE)
Step 1
4. Which terms describe the reaction catalyzed
by this enzyme?
(Circle ALL that apply)
- spontaneous
5. In Step 1, how does HIS participate in the reaction?
(1 sentence or less)
HIS accepts a proton from Cys to facilitate its new bond
with the substrate.
6. What is transferred between the two substrates
during Step 2?a hydrogen
7. Can the enzyme catalyze another reaction after Step 2? No
9. Using the enzyme to catalyze the reaction changes which
of the following? (Circle ALL that apply)
G‡ (EA)
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Step 2
Schivell
Bio200 POGIL Cell Biology Activity 2 – Enzymes TA KEY KEY KEY KEY
10. If CYS were changed to Valine (see below), how would
the rate of catalysis change? Explain in 1-2 sentences.
If Cys were changed to valine, the reaction
would slow because valine would not be able
to form a covalent bond with the substrate.
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Schivell