My solution. I think I'm missing the point of prototypes.

/////////////Constructors/////////////

//template for questions/answers

function Question(question, choice0, choice1, correctChoice) {
  this.question = question;
  this.choice0 = choice0;
  this.choice1 = choice1;
  this.correctChoice = correctChoice;
}

//storage for Quiz questions and counters

function Quiz() {
  this.questions = [];
  this.arrayIndex = 0;
  this.correctAnswersCounter = 0;
}


////////////Instances////////////////

//  create instances of Question

var question1 = new Question("How many sides does a triangle have?", "3", "24", "choice0");

var question2 = new Question("Is Catwoman hanging from the ceiling?", "no", "yes", "choice1");

var question3 = new Question("Is this quiz awesome?", "Yes", "No", "choice0");

var question4 = new Question("Does the carpet cleaner work?", "Yes", "No", "choice1");

var question5 = new Question("Does this quiz really work?", "No", "Yes", "choice1"); 

var question6 = new Question("How many questions can I add?", "As many as I want.", "No more than 5.", "choice0");


//  create an instance of Quiz

var quiz1 = new Quiz();


////////////Prototype Methods/////////////


//Add question/answers to the quiz.

Quiz.prototype.addQuestion = function (questionAnswer) {
  this.questions.push(questionAnswer);
};

quiz1.addQuestion(question1);
quiz1.addQuestion(question2);
quiz1.addQuestion(question3);
quiz1.addQuestion(question4);
quiz1.addQuestion(question5);
quiz1.addQuestion(question6);


//changing the page


  //functions for showing and hiding elements

Quiz.prototype.sendHTML = function () {
  $("#question").html(quiz1.questions[quiz1.arrayIndex].question);
  $("#choice0").html(quiz1.questions[quiz1.arrayIndex].choice0);
  $("#choice1").html(quiz1.questions[quiz1.arrayIndex].choice1);
  var questionNumber = quiz1.arrayIndex + 1;
  $("footer").html("Question " + questionNumber + " of " + quiz1.questions.length + ".");
};

Quiz.prototype.hideQuizElements = function () {
  $("#question").addClass("hidden");
  $("#choice0").addClass("hidden");
  $("#choice1").addClass("hidden");
  $("#guess0").addClass("hidden");
  $("#guess1").addClass("hidden");
  $("footer").addClass("hidden");
};

Quiz.prototype.showQuizElements = function () {
  $("#start").addClass("hidden");
  $("#question").removeClass("hidden");
  $("#choice0").removeClass("hidden");
  $("#choice1").removeClass("hidden");
  $("#guess0").removeClass("hidden");
  $("#guess1").removeClass("hidden");
  $("footer").removeClass("hidden");
};

Quiz.prototype.showNextButton = function () {
  $("#nextButton").removeClass("hidden");
};

Quiz.prototype.hideNextButton = function () {
  $("#nextButton").addClass("hidden");
};

Quiz.prototype.showFinalButton = function () {
  $("#finalButton").removeClass("hidden");
};

Quiz.prototype.hideFinalButton = function () {
  $("#finalButton").addClass("hidden");
};

Quiz.prototype.activateAnswerButtons = function () {
  $("#guess0").on("click", quiz1.checkAnswer);
  $("#guess1").on("click", quiz1.checkAnswer);
};

Quiz.prototype.clearButtonClasses = function () {
  $("#guess0").removeClass("btn--success btn--error").html("Select Answer");
  $("#guess1").removeClass("btn--success btn--error").html("Select Answer");
};

  //Adding and removing from DOM

Quiz.prototype.firstLoadQuestionsPage = function () {
  quiz1.addNextButton();
  quiz1.hideNextButton();
  quiz1.sendHTML();
  quiz1.showQuizElements();
  quiz1.activateAnswerButtons();
};

//quiz mechanics

//  checking the answers

Quiz.prototype.checkAnswer = function () { //what happens when you click on one of the quiz answers
  $("#guess0").off();
  $("#guess1").off();
  var correct = quiz1.questions[quiz1.arrayIndex].correctChoice;
  if ($(this).prev().attr("id") === correct) {
    $(this).addClass("btn--success").html("Right!");
    quiz1.correctAnswersCounter += 1;
  } else {
    $(this).addClass("btn--error").html("Bummer! That's the wrong answer.");
  }
  quiz1.showNextButton();
};


Quiz.prototype.loadNextSetOfQuestions = function () {
  console.log("click is working");
  quiz1.arrayIndex += 1;
  if (quiz1.arrayIndex < quiz1.questions.length) {
    quiz1.clearButtonClasses();
    quiz1.activateAnswerButtons();
    quiz1.sendHTML();
  } else {
    quiz1.hideQuizElements();
    quiz1.addFinalPageButton();
  };
  quiz1.hideNextButton();
};

// method to hide the quiz and load a summary page
Quiz.prototype.loadFinalPage = function () {
  quiz1.addTryAgainButton();
  quiz1.hideFinalButton();
  $("#score").html("You got " + quiz1.correctAnswersCounter + " right out of " + quiz1.questions.length + " questions.");
  console.log("We've reached the end");
};

// method to start the quiz over again
Quiz.prototype.takeAgain = function () {
  window.location.reload();
};

//adding buttons

Quiz.prototype.addStartButton = function () {
  var p = '<p></p>',
    start = '<button id="start" class="btn--default">Start quiz</button>';
  $("#quiz").append(p, start);
  $("#start").on("click", quiz1.firstLoadQuestionsPage);
};

quiz1.hideQuizElements();
quiz1.addStartButton(); //to have a start button on the page to start with.

Quiz.prototype.addNextButton = function () {
  var p = '<p></p>',
    nextButton = '<button id="nextButton" class="btn--default">Next</button>';
  $("#quiz").append(p, nextButton);
  $("#nextButton").on("click", quiz1.loadNextSetOfQuestions);
};

Quiz.prototype.addFinalPageButton = function () {
  var p = '<p></p>',
    finalButton = '<button id="finalButton" class="btn--default">See how you did</button>';
  $("#quiz").append(p, finalButton);
  $("#finalButton").on("click", quiz1.loadFinalPage);
};

Quiz.prototype.addTryAgainButton = function () {
  var p = '<p></p>',
    restart = '<button id="restart" class="btn--default">Try again?</button>';
  $("#quiz").append(p, restart);
  $("#restart").on("click", quiz1.takeAgain);
};