## TITLE('Biochemistry: Identify Allosteric Enzyme Model by Description')
## DESCRIPTION
## Algorithmic MC question that randomly presents a description of either
## the concerted (MWC) or sequential (KNF) allosteric model and asks
## students to identify which model is being described. Covers the key
## distinction: concerted requires all subunits in the same state while
## sequential allows mixed T/R states. Wrong answers are drawn from a
## larger distractor pool with fake abbreviations and vary per seed.
## ENDDESCRIPTION
## KEYWORDS('allosteric','concerted model','sequential model','MWC','KNF')
## DBsubject('Biochemistry')
## DBchapter('Enzymes')
## DBsection('Allosteric Regulation')
## Level(1)
## Date('2026-03-27')
## Author('Dr. Neil R. Voss')
## Institution('Roosevelt University')
## Language(en)
# https://github.com/vosslab
# https://bsky.app/profile/neilvosslab.bsky.social
# This work is licensed under CC BY 4.0 (Creative Commons Attribution 4.0
# International License).
# https://creativecommons.org/licenses/by/4.0/
# Source code portions are licensed under LGPLv3.
DOCUMENT();
# ----------------------------
# 1) Preamble
# ----------------------------
loadMacros(
'PGstandard.pl',
'MathObjects.pl',
'PGML.pl',
'parserRadioButtons.pl',
'PGcourse.pl',
);
$showPartialCorrectAnswers = 0;
# ----------------------------
# 2) Setup
# ----------------------------
# ----------------------------
# 2a) Deterministic local RNG
# ----------------------------
my $local_random = PGrandom->new();
$local_random->srand($problemSeed);
# ----------------------------
# 2b) Question pool: [question_html, correct_answer, explanation]
# ----------------------------
# Each entry builds a full sentence with an HTML blank for the model name.
# Two variants testing the concerted vs sequential model distinction.
# emphasized key phrases: dark blue bold for critical distinction
my $emph_style = "font-weight:700; color:#1a3a6e; font-size:1.05em;";
# blank-line style for the missing model name
my $blank = " ";
my @question_pool = (
[
"The ${blank} model states that "
. "all subunits "
. "in an allosteric enzyme must be in either the T or the R state; "
. "there cannot be hybrids.",
'concerted (MWC)',
"The concerted (MWC) model, proposed by Monod, Wyman, and Changeux, "
. "requires that all subunits of an allosteric protein undergo the "
. "conformational change simultaneously. The entire oligomer exists "
. "in either the T (tense) state or the R (relaxed) state, with no "
. "mixed intermediates allowed.",
],
[
"The ${blank} model allows a "
. "mixture of states "
. "in an allosteric enzyme and "
. "each individual subunit "
. "can be in either the T or the R state.",
'sequential (KNF)',
"The sequential (KNF) model, proposed by Koshland, Nemethy, and "
. "Filmer, allows each subunit to change conformation independently. "
. "Ligand binding to one subunit induces a conformational change in "
. "that subunit, which then influences neighboring subunits. This "
. "permits hybrid states where some subunits are in T and others "
. "are in R.",
],
);
# ----------------------------
# 2c) Select one random question from the pool
# ----------------------------
my $q_idx = $local_random->random(0, $#question_pool, 1);
# package-scoped so PGML can access them
$question_html = $question_pool[$q_idx][0];
$correct_answer = $question_pool[$q_idx][1];
$explanation = $question_pool[$q_idx][2];
# ----------------------------
# 2d) Build answer choices with varied distractors
# ----------------------------
# The other model is always included as a strong distractor.
# Additional wrong answers drawn from a larger pool with fake abbreviations.
my $other_model;
if ($correct_answer eq 'concerted (MWC)') {
$other_model = 'sequential (KNF)';
} else {
$other_model = 'concerted (MWC)';
}
# Pool of plausible wrong answers with fake abbreviations in parentheses
# Abbreviations vary in length (2-4 letters) for realism
my @distractor_pool = (
'induced fit (IF)',
'cooperative (COOP)',
'equilibrium (EQ)',
'Michaelis-Menten (MM)',
'lock and key (LK)',
'competitive (CI)',
'allosteric (ALLO)',
'Hill (HC)',
);
# Fisher-Yates shuffle the distractor pool
for my $i (reverse 1 .. $#distractor_pool) {
my $j = $local_random->random(0, $i, 1);
@distractor_pool[$i, $j] = @distractor_pool[$j, $i];
}
# Take 3 random distractors from the shuffled pool
my @wrong_choices = ($other_model, @distractor_pool[0..2]);
# Combine correct answer with wrong choices
my @all_choices = ($correct_answer, @wrong_choices);
# Fisher-Yates shuffle the final choice list
for my $i (reverse 1 .. $#all_choices) {
my $j = $local_random->random(0, $i, 1);
@all_choices[$i, $j] = @all_choices[$j, $i];
}
# ----------------------------
# 2e) Build RadioButtons
# ----------------------------
$radio = RadioButtons(
[[@all_choices]],
$correct_answer,
labels => 'ABC',
displayLabels => 1,
separator => '',
);
# ----------------------------
# 3) Statement (PGML)
# ----------------------------
BEGIN_PGML
Allosteric enzymes are regulated by conformational changes between the T (tense, low-affinity) and R (relaxed, high-affinity) states. Two classical models describe how these transitions occur across subunits.
[$question_html]*
[_]{$radio}
END_PGML
# ----------------------------
# 4) Solution
# ----------------------------
BEGIN_PGML_SOLUTION
The correct answer is [$correct_answer].
[$explanation]*
The two models differ in a key way:
1. Concerted (MWC) model: All subunits switch states together. The protein is either all-T or all-R with no hybrids.
2. Sequential (KNF) model: Each subunit can change state independently upon ligand binding, allowing mixed T/R conformations.
Common distractors: "induced fit" describes substrate-induced changes in enzyme shape at the active site (not allosteric subunit transitions). "Lock and key" is the rigid active-site model. "Michaelis-Menten" describes simple enzyme kinetics without cooperativity. "Cooperative" describes binding behavior, not a specific model. "Hill" refers to the Hill equation for cooperativity measurement. The abbreviations on the wrong answers are fictional.
END_PGML_SOLUTION
ENDDOCUMENT();