The mitochondria produce the majority of ATP for the cell. The ribosomes are responsible for protein production. Nucleic acids are generated and stored in the nucleus. The lysosomes are the responsible for digestion of cellular wastes.

Both the citric acid cycle and the electron transport chain take place in the mitochondria.

An active mitochondrion is simultaneously running the citric acid cycle in the matrix, as well as the electron transport chain along the inner membrane. In order to create ATP, mitochondria are responsible for creating a proton gradient by sending protons into the intermembrane space. By using this proton potential gradient ATP synthase is able to create ATP from a molecule of ADP and a molecule of phosphate. The pH will thus be lower in the intermembrane space than in the matrix. The pH will not, however, drop nearly as acidic as a pH of 2.0, which only occurs in the body in certain parts of the digestive system due to gastric acid.

This question tests your ability to integrate information about a fictional organism, which you are told has a number of structural and functional similarities to humans, and apply that to answer a question about this organism's cellular functions. In this question, you are told that tissue from organs highly similar to human muscles are being analyzed at the cellular level, and you are asked to choose the function carried out by the organelle that would be very highly expressed in this organ. As we are talking about an organ that is highly similar to the human muscle, we can assume that the organelle of interest here is mitochondria, as mitochondria are responsible from producing a majority of the energy for cells in the human body. Tissues with high energy demand, like muscle in active organisms, tend to have higher levels of mitochondria such that adequate amounts of energy can be supplied to the tissue. The answer that best describes the function of the mitochondria is, "energy production and metabolism." The mitochondria are the sites of numerous metabolic processes including the citric acid cycle and oxidative phosphorylation. 

"Structural integrity of the cell" and "permeability regulation" are both functions served by the plasma membrane, not the mitochondria.

"Translation" takes place at the site of the ribosomes, not the mitochondria. 

"Intracellular transport" is a function that takes place largely by the cytosol, also known as the cytoplasm.

Zona occludens block transport between cells by forming a zipper like boundary toward the apical surface of neighboring cells. These are also known as "tight junctions."

Zona adherens are also called adherens junctions or desmosones, and are designed to join cells together rather than to block transport between cells. Hemidesmosomes serve to link cells to an extracellular matrix or basement membrane, and gap junctions allow signal transduction between cells.

Desmosomes directly attach cells to one another by connecting their cytoskeletons. These aggressive junctions are found in cells that experience large amounts of stress, such as the skin. Cadherin proteins on adjacent cell membranes bind to one another in the extracellular space, and bind to intermediate filaments of the cytoskeleton in the cytosol.

Tight junctions blockade gaps between cell membranes, increasing the selectivity of an internal cavity by creating a strong barrier against fluids and ions. The blood brain barrier is formed from tight junctions. Gap junctions serve the opposite function, creating small perforations to connect adjacent cell cytosols. This allows for rapid transmission of cell signals and communication. Intercalated discs are specialized gap junctions found in cardiac muscle cells.

An action potential is a process that involves the rise and fall of membrane potential of a cell. The changes in membrane potential is associated with the movement of ions (especially sodium and potassium ions) into and out of the cell. Recall that gap junctions are a type of intercellular connections that create gaps (tunnels) between adjacent cells and facilitate movement of ions; therefore, cardiac cells must possess gap junctions to propagate action potentials.

Gap junctions do facilitate movement of fluid; however, fluid movement is irrelevant to action potential. Tight junctions are another type of intercellular connections that form a tight seal between adjacent cells. These tight seals do not allow movement of ions, molecules, or fluid.

There are two main characteristics that distinguish desmosomes from other cell junctions. First, a desmosome forms a connection between the cells’ cytoskeletons. A cell’s cytoskeleton is mostly made up of microfilaments, intermediate filaments, and microtubules. Adherens junctions form connections between the actin microfilaments of adjacent cells, while desmosomes form connections between the intermediate filaments. Second, desmosomes look like a patch and occur only at a single location. Other junctions, such as gap junctions and tight junctions, occur at multiple locations along the extracellular space; therefore, the researcher must have observed the connection at a single location.

Prevention of fluid exchange is not a characteristic of desmosomes; it is a characteristic of tight junctions. Tight junctions are tight seals that prevent the flow of water, molecules, and ions between cells.

There are four major types of connections between cells that facilitate intercellular communication and interaction: gap junctions, desmosomes, adherens junctions, and tight junctions.

Gap junctions are tunnels between cells, formed by perforations in the plasma membrane, that allow ions and molecules to pass between cells. Desmosomes connect the cytoskeletons of adjacent cells, assisting in force transduction. Adherens junctions use specialized proteins called cadherins and catenins to create a strong adhesion between adjacent cells. They are similar to desmosomes, but have different molecular components. Finally, tight junctions, as the name suggests, are sealed connections that do not permit exchange of fluid between cells. The question states that there is no exchange of water and ions between the cells; therefore, the connection between the cells must be a tight junction.

Plasmodesmata are similar to gap junctions, but they are only found in plant cell walls. They connect adjacent plant cells and facilitate intercellular communication and movement of nutrients between cells.

A cellular junction is made up of cytoskeletal filaments and cell adhesion molecules, which connect cytoskeletal elements between adjacent cells. There are three types of cytoskeletal filaments: microfilaments (actin filaments), intermediate filaments, and microtubules. A cellular junction usually utilizes connections with either actin filaments or intermediate filaments. Desmosomes and hemidesmosomes use intermediate filaments (particularly keratin) whereas tight junctions, adherens junctions, and focal adhesion junctions use actin filaments.

The question states that the autoimmune disease attacks occludin proteins. Recall that the occludin proteins are cell adhesion molecules found in tight junctions. Tight junctions, as the name implies, form sealing junctions that restrict the passage of molecules between adjacent cells. A lack of occludin proteins will decrease the amount of tight junctions and, subsequently, will increase the exchange of molecules between cells.

Cadherin proteins are also cell adhesion molecules, but they are found in adherens junctions. They do not depend on occludin proteins and, therefore, will not be affected by this disease. Tight junctions do require actin filaments and will be affected by this autoimmune disease; however, other actin utilizing junctions, such as adherens junctions and focal adhesions, don’t use occludin proteins and will not be affected.