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Look up published modes of inhibition for the three inhibitors and compare with your conclusions. Explain why your results might suggest a different mechanism vs. published mechanisms. Provide references for published sources.

Sodium phosphate competitive

L-phe inhibitor

D-phe

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Lelia Lubowitz
Lelia LubowitzLv2
28 Sep 2019

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Related questions

Article: Basal forebrain degeneration precedes and predicts the cortical spread of Alzheimer’s pathology

https://bbl.westfield.ma.edu/bbcswebdav/pid-1058990-dt-content-rid-12869706_1/courses/wsu_BIOL0333001_2018fall/Alzheimers.pdf

-Please do not use direct quotes from the article-

2. Hypotheses:

a) What are the hypotheses? (list all hypotheses proposed)

b) Is the reasoning behind the hypotheses explained? What is the logic behind each hypothesis?

3. Introduction:

a) Does the introduction provide appropriate background for the study? Why or why not?


b) Is the introduction missing useful information that would have been helpful? If so, explain. For example, did you have to look up any additional information?

c) Is the relevance of the work clear? What is the relevance of the work?

4. Methods:

a) Summarize the methods that were used.

b) Were the methods appropriate? {Was this the best way to test the hypotheses? Were there problems with the methodology (if so describe them)?}

5. Analysis:

a) Were there any problems with the data analysis, including use of statistics?

b) Did the authors present quantitative data in a clear way (use of graphs/tables)?

6. Your OWN assessment of the results:

a) List YOUR conclusions from the DATA presented?

b) Do you feel that the author's conclusions are reasonable and justified? If there are any problems with the author’s conclusions, explain them.

c) Does the author ignore any aspects of the results?

7. Discussion:

a) Did the authors compare their results with previous published papers? If so, provide at least 1 example.

b) Are the implications of the results properly discussed (how do these results relate back to the “big picture” of what is being studied)? What are the implications?

c) Are the conclusions clearly stated? If so, what are they?

d) In addition to what the authors discussed, what further studies would YOU find interesting to pursue?

8. Abstract (if there is one):

a) Does the Abstract really give an appropriate summary of the paper?

describe the definitions of substrate, enzyme active site and its general characteristics, and apoand

holo-enzymes.

· describe the fact that enzyme catalysis is specific in terms of the type of reaction and the exact

substrate structure.

· Explain the difference in the “lock-and-key’ model and the induced fit model of enzyme

substrate interaction.

· describe that reaction rate constant thus reaction rate is dependent on the activation energy.

· describe the relationship between the energy of the transition state and the activation energy.

· describe the relative binding affinity of a substrate and its transition state to the enzyme.

· Explain how enzymes speed up reaction rate, i.e., how do enzymes lower the activation

energy. Note: Factors other than preferential stabilization of transition state also contribute to increased

reaction rate. They include 1) enzymes placing one substrate (reactant) next to the other substrate (reactant)

so that the reaction is no longer dependent on the collision rate of the two substrates; 2) enzymes sequester the

substrate(s), minimizing solvent competition thus speeding up the reaction; 3) in enzyme complexes with each

enzyme catalyzing one step in a multi-step reaction sequence, the product of one reaction is fed to the active site

of another enzyme for the next step without the product diffusing away from the enzyme complex thereby

increasing reaction rate.

· describe the Michaelis-Menten equation relating the initial velocity to total substrate

concentration.

· describe the assumptions that went into the derivation of the Michaelis-Menten equation. ([E]

is constant, steady state assumption, etc)

· describe the relationship between Vmax and kcat and the fact that kcat is a constant for a given

enzyme and substrate at a given temperature and solution condition; whereas Vmax can differ

for a given enzyme and substrate at a given temperature and solution condition, depending

on the enzyme concentration.

· describe the definition of Kd (equilibrium dissociation constant for ES into E and S).

· describe the relationship between Kd and the affinity of substrate for the enzyme, i.e., the

higher the Kd, the weaker the binding between E and S.

· describe the relationship between Kd and Km, i.e., in general, the higher the Kd, the higher theKm.

· Use the Michaelis-Menten equation and the relationship between Vmax and kcat to do

calculations.

· describe the other names for the catalytic rate constant, kcat (i.e., the turn over number; also

called krelease) and why it is so called (kcat reports on per unit time per enzyme molecule the

number of product molecules formed/released, thus the name turnover number or krelease).

· Determine Vmax and Km using both the Michaelis-Menten plot (initial velocity versus [S]) and

the Lineweaver-Burk Plot (the double reciprocal plot), given the data of initial velocity and

[S].

· Draw the Michaelis-Menten plot AND the double reciprocal plot (Lineweaver Burk), given

the Vmax and Km values.

· describe the fact that the term kcat/Km is the best parameter for measuring the catalytic

capability (efficiency) of an enzyme.

· describe the existence of irreversible enzyme inhibition and the general mechanisms of

irreversible inhibition.

· describe the different types of reversible inhibitions, namely the competitive, uncompetitive,

and mixed inhibitions (noncompetitive inhibition is a special case in which the inhibitor

binds E and ES with equal affinity therefore α is equal to α’ – Km is not affected).

· Describe each type of inhibition in terms of inhibitor binding site (active site or other than

the active site), how the inhibitor affects vmax and Km and the quantitative relationship of

each parameter with and without the inhibitor present and their relationship with [I] and KI

or KI

’

.

· Show the characteristics of each type of inhibition on a Michaelis-Menten plot (initial

velocity versus total substrate concentration), i.e. draw the curves with and without the

competitive inhibitor.

· Show the characteristics of each type of inhibition on a double reciprocal plot (LineweaverBurk

Plot) by drawing the lines with and without the competitive inhibitor.

· Given the Michaelis-Menten or double reciprocal plot with and without the inhibitor,

determine the type of inhibitor.

· describe the fact that transition state analogs are potent inhibitors.

· Explain why transition state analogs are potent inhibitors.

· describe that not all enzymes obey Michaelis-Menten kinetics.

· describe situations when an enzyme will not obey Michaelis-Menten kinetics (when the enzyme

catalyzes reactions with multiple substrates or when the enzyme is allosteric, i.e. binding of

the substrate at one active site affects the other active site(s) for the same substrate).

· Name the four types of catalytic mechanisms. (electrostatic catalysis, general/specific acid

base catalysis, metal ion catalysis, covalent catalysis)

· Contrast acid/base catalysis to general acid/base catalysis, i.e., comment on their similarity

and difference.

· Name the eight common general acid/base pairs in proteins and write the formula of the

acid and base form for each pair (hint: consider the eight amino acids that have ionizable

side chains…)

· describe the meaning of covalent catalysis.

· describe the reaction catalyzed by chymotrypsin and the three catalytic residues in

chymotrypsin.

· Draw the interactions among the three catalytic residues (catalytic triad).

· State the catalytic role of each of the catalytic residues and how they accomplish that.

· describe the steps in the formation of the acyl-enzyme intermediate, and the substrate and

products in this first part of the chymotrypsin mechanism.

· Draw the transition state structure for the formation of the acyl-enzyme intermediate and

indicate by drawing how it is preferentially stabilized.

· describe the steps in the regeneration of chymotrypsin (deacylation), the substrates and

product of this second part of the chymotrypsin mechanism.

· Draw the transition state for deacylation and explain how it is preferentially bound to or

stabilized by the enzyme.

· Explain what general acid and base catalysis refers to and what groups act as the general acid

and base in the chymotrypsin mechanism.

· Explain what covalent catalysis refers to in the chymotrypsin mechanism.

· Explain the basis for the substrate specificity of chymotrypsin (consider the composition of

the active site – chymotrypsin specifically cleaves peptide bonds adjacent to aromatic

residues)

· Explain the term “serine protease”. Answer: these are proteases (enzymes that

hydrolyze peptide bonds) that have serine as a catalytic residue (that acts as a

nucleophile, which can attack the carbonyl carbon of the peptide bond).

· Key features of Hexokinase, enolase and lysozyme mechanisms that were discussed in class

(specific methods of catalysis utilized by these enzymes; general description of overall

catalytic transformation)

· describe the four regulatory strategies of enzyme catalysis

· describe the definition of feedback inhibition (mechanism of cellular regulation that regards an

enzyme that catalyzes the production of a given substance that then inhibits the cell when

concentration of that substance has reached an appropriate level – this balances/regulates

amount of product provided with amount needed)

· describe the most common type of covalent modification and the types of enzymes

responsible for the addition and removal of the chemical group in this covalent

modification.

· Explain the general mechanism of phosphorylation in regulating enzyme activity.

· describe the general naming scheme for active and inactive proteases.

· describe that protease inhibitors exist to inhibit protease.

· describe that enzymes are regulated through covalent and non-covalent processes.

· Noncovalent regulation

o Describe noncovalent modification in general terms. Elaborate on the relation

among enzyme activity, allostery, effector molecules (small molecules) and control

proteins.

o Concerning allosteric regulation, some enzymes have multiple active sites for the

same substrate and the binding of the substrate increases the activity of the enzyme

by stabilizing the R (more active) state over the T (relatively inactive) state. (Lecture

13: “Noncovalent Modification: Allosteric Regulators”)

ß Draw a curve for the initial reaction velocity versus substrate concentration.

ß describe and explain the specific shape of the v0 vs. [S] plot.

ß Draw on the same graph above a v0 vs. [S] curve for the enzyme in the

absence of allostery. and how th i.e., in the absence of conformational change

upon substrate binding. Comment on the shape of this curve.

ß Comment on the benefit of allosteric activation.

ß When an inhibitor is present for such an allosteric enzyme, the v0 versus [S]

plot will shift. Draw a v0 vs. [S] curve with and without the inhibitor.

ß When an activator is present for such an allosteric enzyme, the v0 versus [S]

plot will shift. Draw a v0 vs. [S] curve with and without the inhibitor.

ß When an activator is present for such an allosteric enzyme, the v0 versus.

ß describe the relationship between feedback inhibition and allosteric regulation

and the reason behind the term “feedback inhibition”.

· Covalent regulation

o describe the most common covalent modification, the enzymes that catalyze the

modification and the removal of that modification, respectively and the amino acid

residues that tend to be the site of this modification.

o Write the structure of the added group bonded to those residues and the reaction for

this covalent modification.

o Rationalize the effectiveness of phosphorylation on altering the activity of an

enzyme.

o describe the mechanism of chymotrypsinogen activation to chymotrypsin (cleavage of

zymogen by trypsin).

QUESTION SET 3

Sexual Selection, Developmental Thresholds, and Ornamentation

INTRODUCTION

In Chapter 10 you read about how sexual selection can drive the evolution of bizarre and sometimes costly ornamentation or weaponry in animals, often in males. This paper reveals a situation where sexual selection is the driver, but the result is more complex than might be expected at first glance. The authors describe some beetle species where different thresholds encountered as larvae result in different levels of ornamentation, and consequently different reproductive strategies.

The authors show that in one family of beetles (the Scarabeidae [dung beetles]), two different threshold mechanisms have independently evolved. Each of these thresholds has a different effect on horn development in the males of these beetles. Both mechanisms are triggered by body size in larvae. For one mechanism, if a larva attains the threshold size its adult morphology (the phenotype it will have after it pupates) switches from being hornless to being horned. The second threshold, also based on larval body size, similarly results in either having a short or a long horn (see Figure 2).

This discovery led the authors to look more closely at other beetle species where male polymorphism was known to occur, and they found two other examples where this double threshold mechanism was operating (see Figure 1). In the family Lucanidae (stag beetles), they found that male trimorphism was characterized by differences in the mandibles, with male mandibles exhibiting three increasing sizes moderated by the thresholds. In the family Curculionidae (weevils), the thresholds controlled the development of ventral body spines. Here, the beetles either lacked spines (and thus resembled females), had short spines, or had long spines.

The authors suggest that this multiple-threshold system may be more prevalent than previously thought, and anticipate more examples coming to light.

QUESTIONS

Question 1

What are polyphenic regulatory developmental mechanisms?

Answer:

Question 2

Can you think of an example of polyphenic regulatory developmental mechanisms besides the beetles mentioned in this paper.

Answer:

Question 3

The authors use the “rock-paper-scissors” analogy to describe the potential result of this two threshold system when it comes to reproductive success in dung beetles. As in the game of rock-paper-scissors, each possible pair-wise comparison has a clearly defined winner. Give a hypothetical example of what this might look like in the context of dung beetle mating success.

Answer:

Question 4

What is the difference between the systems described in this paper and the other examples of male trimorphism cited by the authors (in isopods, lizards, and birds)?

Answer:

Question 5

Why might a trimorphic system such as this evolve? Why wouldn’t natural selection just drive all males to have the biggest possible horn, spine, or whatever the ornament involved is?

Answer:

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