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The Cell (Part 1)

The Cell (Part 1)

The Cell

The Cell as a Functional Unit

The cell is the smallest living functional unit of multicellular organisms. In simpler terms, within our body, cells are the smallest living building blocks. Cells themselves are comprised of building blocks called organelles which in turn are comprised of various smaller molecules and atoms.  However these building blocks are not living or capable of self directed replication (except for the mitochondria). This distinction is crucial, and when studying the human body it is important to have a thorough understanding of its smallest living functional unit, the cell.

We have labeled cells building blocks, and we have called them functional units. Why is this important? When cells work together, like building blocks in the traditional sense, they can be more valuable than just the sum of their parts. When multiple cells of the same type are organized and form a larger group of cells with a common function, they form a tissue. The four tissue types consist of epithelial tissue, neural tissue, connective tissue, and muscle tissue. When these four types of tissue take on even greater levels of organization they can form organs. Once at the organ level, very crucial and complex tasks can be performed such as the creation and release of hormones. These complex tasks would be fruitless however without an even further level of complexity and organization. This next rung of the organizational ladder is called the system level or organ system level. Lastly, when the right systems come together, something as complex as the human body can take shape. This final level of organization is termed the organismal level.

Cellular Components and Structure

An animal cell, in this case a human cell, has three primary and distinct components. These include the nucleus, cytoplasm, and the plasma membrane. The nucleus contains the cell’s DNA. No matter which cell you examine within the human body, as long as a nucleus is present and the cell is not damaged, you will find the same copy of genetic material. This genetic material is responsible for protein synthesis, which we will examine further along with the nucleus later on. The cytoplasm represents all of the material contained within the plasma membrane, excluding the nucleus and its contents. Lastly, the plasma membrane contains the cellular contents, and carries out a multitude of crucial cellular activities that we will examine now.

The Plasma Membrane

The primary and most obvious function of the plasma membrane is to contain the cell’s contents and give the cell form. In doing so, collectively, the plasma membranes throughout the body create two distinct bodies of fluid. These fluid compartments as they are called are termed the extracellular fluid (fluid outside of the cell but within the body), and the intracellular fluid (fluid within the cell). The fact that these fluid compartments are separated from each other is vital, and creates a number of roles for the plasma membrane to carry out, such as transport between the two fluid compartments. But first lets look at the plasma membrane’s structure.

In previous classes you may have heard the terms bilayer or double layer membrane and you may have also heard the term fluid mosaic model. This refers to the membrane’s structure and composition. Primarily the plasma membrane is composed of phospholipids with polar (hydrophilic heads) and non-polar (hydrophobic) lipid tails. The polar heads are attracted to the water within the extracellular and intracellular compartments, and the lipid tails are attracted to each other. The result is the formation of a double layer of phospholipids with the fatty tails facing inwards, and the polar heads facing outwards, one layer’s polar heads attracted to the extracellular fluid, and the other layer’s polar heads attracted to the intracellular fluid. The polar and non-polar properties of the phospholipids result in a membrane structure that naturally “wants” to form a spherical continuous structure with a bilayer arrangement. The fluid mosaic model further describes the structural properties of the plasma membrane. As you know, a mosaic is an image composed of various components. Knowing this, the term fluid mosaic very accurately describes the plasma membrane. The plasma membrane consists of more than just phospholipids, it also contains a large amount glycolipids, cholesterol, lipid rafts, integral and peripheral proteins, and a sugar covering called the glycocalyx. This fits the image of a mosaic quite well. Also, due to the membrane being primarily held together by relatively weak polar forces, and also that it is only about 8 nm thin, its is very fluid like, and its components are able to move around freely, like a fluid and constantly changing mosaic. Now, lets examine the components of the plasma membrane further.


Glycolipids are found only on the outer surface of the plasma membrane and account for relatively small amount of the lipids within the membrane.  These molecules have a lipid end with attached sugar groups, forming a molecule similar to the phospholipids, with there fatty tail within the membrane, and their polar heads protruding outwards,

Lipid Rafts

The name of these structures is highly descriptive. Lipid rafts are areas of specialized lipid molecules as well as cholesterol packed into dense, stable “rafts” that float within and along the plasma membrane. These structures can sometimes include various proteins, which can be important as a staging area or for cell signaling, as is the case when the cell brings in contents from the extracellular fluid.


Cholesterol, like the phospholipids discussed earlier, has a polar and a non-polar region. Cholesterol contributes to the stability of the plasma membrane and decreases its flimsy, fluid like nature. Its large presence in lipid rafts may explain why lipid rafts are so stable.

Integral Proteins

Integral proteins are structures comprised of amino acids that are embedded within the plasma membrane. Some poke out of the extracellular surface, but most span the entire membrane and are termed transmembrane proteins. Again we see the pattern that most membrane components share, and that is the presence of both hydrophobic and hydrophilic regions, this allows the proteins to remain within the membrane bilayer while simultaneously interacting with the intra and extracellular compartments. We will see that it is proteins that carry out the various roles that cells perform. Transmembrane proteins can serve as pumps or carriers, they can create pores allowing substances to enter and exit the cell, and they can even serve as receptors triggering chemical cascades within the cell.

Peripheral Proteins

Peripheral proteins are attached on the internal plasma membrane layer and lie within the intracellular fluid. They are not embedded in the lipid layer and serve primarily to add support to the cell’s cytoskeleton and provide motors for cellular movement required during activities like cellular division.

The Glycocalyx

The glycocalyx is a term describing the sugar coating on the exterior of our body’s cells.  This coating is comprised of the various glycolipids and glycoproteins embedded within the plasma membrane with their polar “sugar” ends facing outwards into the extracellular fluid. This coating serves as a unique identifying feature for cells. Its role is similar to a barcode or fingerprint and serves to allow certain cells to recognize other cells or invading bodies.

Cellular Junctions

Cells forming tissues require some type of structure to remain anchored together and function as a cohesive unit. Also some type of mechanism is required to allow chemicals to travel freely between cells. This is accomplished through intrinsic properties of cells such as their sticky exterior and also through the utilization of cell junctions which we will discuss in detail below and include desmosomes, tight junctions, and gap junctions.


Desmosomes are purely a structural cell junction. Filaments extend into the cytoplasm of two neighboring cells and are bound together in the extracellular space. This creates a very strong bond betwwen cells. Additionally the filaments within the cytoplasm entwine with the cytoskeleton within the cells forms a rigid and stable cellular junction.

Tight Junctions

Tight junctions like desmosomes provide structure and anchor adjacent cells together. Additionally, tight junctions prevent molecular and ion flow between adjacent cells.

Gap Junctions

Gap junctions provide a passageway for simple molecules between cells. This is import in tissue where it is imperative that chemical messages or potentials (refer to membrane potential section) pass freely between cells unhindered.

Membrane Transport

Transport between cells is achieved through the utilization of gap junctions. However, it is also necessary for transport to occur between the cell and the extracellular fluid. The portion of extracellular fluid that comes in direct contact with, and bathes the cells is referred to as interstitial fluid. This fluid is filled with nutrients and ions vital to cellular function, but not necessarily at appropriate concentrations to support all cellular activities. This is why it is important to either passively or selectively transport various molecules and ions either into or out of the cell.  Membrane transport can either be an active, or a passive process and both types of transport are described below.

Passive Membrane Transport

Passive membrane transport is transportation of a molecule or ion across the plasma membrane without the use of ATP to fuel the process. The different types of transport are all variations of a process known as diffusion. Diffusion when related to cells is simply the process of substances (molecules/ions) suspended in fluid to move down their concentration gradient. When this substance is water, the process is termed osmosis.

  • Simple diffusion: Substances without an inherent polarity can pass directly through the lipid bilayer because they are hydrophobic and will not be rejected by the lipid tails within the membrane. This allows substance such as oxygen, which has a higher concentration within arterial blood than within the cell, to diffuse passively into the cells without any sort assistance other than simple diffusion of the gas through the plasma membrane.

  • Facilitated Diffusion: The cell must also transport polar molecules such as proteins and sugars. This task cannot be performed using simple diffusion because these polar molecules cannot traverse the lipid portion of the plasma membrane. Therefore another mechanism must perform this task, this mechanism is facilitated diffusion. There are two types of facilitated diffusion, one is known as Carrier mediated diffusion, and the other channel mediated diffusion. In carrier-mediated diffusion the substance to be transported binds to a transmembrane protein. Once this binding occurs the shape of the transmembrane protein undergoes a change in shape, thus enveloping and releasing the substance into the cytoplasm. Or interstitial fluid. In channel mediated diffusion, hydrophobic substances move through channel proteins within the membrane according to their concentration gradient.  Some channels are always open and others are gated, also these channels are selective and only allow molecules of the right size to diffuse across the membrane.


Another type of diffusion as mentioned earlier, is called osmosis. Osmosis is the diffusion of water or any other solvent across a membrane as dictated by the solvents concentration gradient. It is not clearly understood why a polar substance such as water can passively diffuse across a lipid bilayer. One hypothesis is that as the bilayer moves, small momentary gaps form allowing the water to seep through passively. As mentioned early this diffusion of water across a membrane is dependent upon a concentration gradient. Water, or any solvent, moves down its concentration gradient just like a solute. Say for example the interstitial fluid around a cell has a high concentration of various ions and molecules, or in other words contains a high concentration of solute. Also, the cell’s interior has a very low concentration of solute. The solvent concentration is relatively low outside the cell compared to inside the cell, thus osmosis will occur and water will move down its concentration gradient out of the cell. What is important, is that these substances that are in varying concentrations on either side of the membrane are non permeable across the membrane. When the substances are unable to move down their concentration gradient through the membrane, water must move down its concentration gradient, or towards the area of higher solute concentration. In this way, the solute concentration gradient is neutralized without the solute having to be actively transported across the membrane.  The conditions that lead to net flow of water into or out of a cell are called tonicity.



  • Hypotonic Solutions: Solutions containing a lower concentration of nonpenetrating solutes than within the cell. The result is a net movement of water into the cell down its concentration gradient. As this occurs, intracellular volume increases, and also intracellular hydrostatic pressure increases. The result is a swollen cell. This process will continue until the forces pulling water within the cell (the relatively high solute concentration within the cell) are neutralized, or until the hydrostatic pressure within the cell prevents more water from entering the cell.

  • Isotonic solutions: Solutions having the same concentration of non-penetrating solute as within the cell’s intracellular fluid. This results in an equal net movement of water into and out of the cell, allowing the cell to maintain its optimum size and shape.

  • Hypertonic solutions: Solutions containing an increased solute concentration relative to the intracellular fluid. This causes a net flow of water out of the cell causing the cell to shrink.

Active Transport

Active transport much like facilitated diffusion utilizes transmembrane proteins to transport substances across the plasma membrane. Unlike facilitated diffusion however active transport moves substances against a concentration gradient and is divided into two distinct types.

  • Primary Active Transport: In this type of active transport an ATP molecule binds with a “pump” made from amino acids within the plasma membrane. This causes a conformational change in shape within the protein that “pumps” the substance either into or out of cell against the substance’s, (typically an ion’s,) concentration gradient.

  • The most studied example of a primary active transport pump is the sodium potassium pump. In our bodies, the concentration of potassium is much higher in the intracellular fluid than in the interstitial fluid. The same is true in reverse for sodium, which is found in much higher concentrations in the interstitial fluid than in the intracellular fluid. This arrangement is essential for cells that rely on membrane potentials, which we will discuss later, to function normally. Although necessary, this gradient is unsustainable without the NA-K pump. Why? Well, as we learned earlier ions like NA and K can passively diffuse through the plasma membrane by way of channel mediated diffusion. The steep concentration gradients force Na into the cell and K out of the cell. In order to maintain the ideal concentrations on either side of the plasma membrane the sodium potassium pump must continuously work to pump potassium into the cell, and sodium out of the cell thus preventing the concentrations of NA and K from equalizing both within and outside of the plasma membrane.

  • Secondary Active Transport: This type of transport utilizes the concentration gradient maintained by the previous type, primary active transport. This concentration gradient acts as a source of potential (stored) energy that when utilized can drive one of two systems, a symport or antiport system. Think back to the concentration gradient maintained by the sodium potassium pump. Sodium “wants” to enter the cell because the sodium concentration is much lower there. In a symport system this gradient is utilized by allowing sodium to flow into the cell along with a desirable substance. In this manner the desirable substance, say glucose, is cotransported into the cell by sodium through a carrier protein. An antiport system works in a very similar manner. In this system however a substance is ejected from the cell as sodium enters. In both systems, in fact in all active transport systems, substances are moved against their concentration gradients, thus the term “active” transport.

Vesicular Transport


A vesicle is a membranous sac that is actually a portion of the plasma membrane or a membranous organelle membrane that has been pinched off forming a spherical sac which can transport substances into, out of, within, and across the cell. These processes are termed endocytosis, exocytosis, transcytosis, and vesicular trafficking.


  • Endocytosis: Endocytosis is the method used to bring in substances that the cell cannot transport across the membrane through other methods. Endocytosis is a 6 step process and is outlined below


  • Step 1: A portion of the plasma membrane begins to form a pit and enclose the substance to be brought into the cell. The protein on the cytoplasmic side of the vesicle (clathrin) both identify the appropriate substance to be ingested and perform the process of deforming the membrane and enclosing the selected substance.

  • Step 2: After the vesicle is completely formed and it detaches from the plasma membrane

  • Step 3: The clathrin proteins detach and are returned to the cell’s plasma membrane.

  • Step 4: The uncoated vesicle fuses with a sorting vesicle termed an endosome

  • Step 5: A portion of the vesicle may detach and be recycled back into the plasma membrane

  • Step 6: The remaining vesicle and its contents can either combine with a lysosome for digestion, or travel to the opposite side of the cell to be released by exocytosis (transcytosis)


  • Phagocytosis: Phagocytosis, a type of endocytosis is the process by which the cell engulfs a large substance or foreign debri. Once the vesicle, or in this case the phagosome is taken into the cell containing the foreign material it fuses with a lysosome for digestion. Some cells are specially designed for phagocytosis and make it their duty to creep along and phagocytize dead cells, debris, and foreign invaders.


  • Pinocytosis: In this form of endocytosis a small bit of extracellular fluid containing dissolved substances is taken into the cell. This is an especially important process in cells that absorb nutrients such as though lining the intestines.


  • Exocytosis: A process in which substances are removed from the cell after being engulfed by vesicles, transported to the plasma membrane, and ejected into the extracellular fluid.

Resting Membrane Potential 

Think back to the steep ion concentration gradients maintained by active transport. Remember that these ions have charge. This creates a situation where charged particles want to, or more accurately have the potential to travel across the plasma membrane if allowed thus creating current. This potential for current flow across the membrane is known as membrane potential. During their resting state all of the cells in the body, or more specifically the plasma membranes of all cells in the body, have a resting membrane potential of between -50 and -100 millivolts. This creates a charge separation between the cells negative interior, and the relatively positive charge of the extracellular fluid, giving the cell polarity. It is important to realize that this charge separation exists only at the plasma membrane and if we averaged the charge of all regions of the cell we would find that it is electrically neutral.

The Cytoplasm

The cytoplasm consists of all of the material contained within the cell’s plasma membrane excluding the nucleus and its contents. The three components of the cytoplasm are the cytosol, organelles, and inclusions.


  • The Cytosol: The cytosol is the fluid which suspends the other elements of the cytoplasm and consists mostly of water, as well as macromolecules and ions.


  • The Organelles: The organelles are the machinery of the cell. They perform a multitude of cellular activities ranging from production of energy packed molecules to protein synthesis.


  • Inclusions: Inclusions are not present in all cells, but they consist of chemical substances stored within a cell. Some examples include lipids stored in fat cells and glycogen stored in liver cells.


The Cytoplasmic Organelles


The Mitochondrion

The mitochondrion is often referred to as the cell’s powerhouse, however this can be a bit misleading. In reality the mitochondrion is a cellular fuel factory. To use an analogy it would be better likened to an oil refinery that produces gasoline than a car’s engine that burns it. In the cell, the gasoline is ATP or adenosine tri-phosphate, and theres a multitude of engines within the cell that use this fuel. The Mitochondria are some the most complex organelles in the cell. Not only do they have two membranes, with the inner membrane being folded, but they even have their own DNA, RNA, and ribosomes. These structures allow the mitochondria to produce some of the proteins required for their own function and allow the organelles to reproduce themselves independently. This is a valuable capability when the demand on mitochondria can vary from very low in a resting cell to very high in an active cell. As cellular activity and demand for fuel increase, so too can the number of mitochondria. These many features and abilities distinguish the mitochondria from all of the other organelles within the cytoplasm. In fact the mitochondria more closely resemble certain types of bacteria than they do other organelles. For this reason, and reasons related to mitochondrial dna and its inheritance, it is believed that mitochondria are actually distant descendants of early bacteria that invaded early animal and plant cells. It is theorized that somehow these bacteria merged with the cell and became the mitochondria that we know today. Additionally, it is widely believed that this merger is what allowed for the development of more advanced and complex cell and tissue types.



The ribosome is the cell’s site of protein sythesis. It is composed of two subunits which are made of protein and ribosomal ribosomal RNA. Ribosomes can be either free floating in the cytosol, or bound to the rough endoplasmic reticulum. Ribosomes suspended in the cytosol produce proteins necessary for the function of various organelle activities, while those bound to the rough ER produce proteins to be used in the plasma membrane, lysosome membrane, or can be exported from the cell.


Endoplasmic Reticulum

Divided into two subtypes, smooth and rough, the endoplasmic reticulum is a of tubes and flattened membranous sacs called cisterns. This system is connected to the nucleus and its distinction as being separate from the nucleus is only academic. The endoplasmic reticulum is so extensive that its membranes  account for around half of the cell’s total membrane amount.


  • Rough endoplasmic reticulum: This portion of the endoplasmic reticulum receives its name from the many ribosomes attached to its exterior membranous surface. These ribosomes produce proteins that enter the rough ER for modification and processing. Once these proteins are complete they are packaged in vesicles for transport to the golgi apparatus for export from the cell. This arrangement makes for a very efficient protein export system that is highly developed in cells whose primary role is to release proteins such as many liver cells and cells that produce antibodies that fight infection. The Rough ER serves another very important function, the production of membrane. When the cell grows it requires more plasma membrane, this membrane is produced by the rough ER.


  • Smooth endoplasmic reticulum: Although continuous with the rough ER, no protein synthesis occurs here. Instead the smooth ER is the site of lipid metabolism and hormone synthesis. Also the smooth ER breaks down the complex glycogen molecules to form free glucose which fuels cellular metabolism (ATP production), and is the site of drug detoxification. The smooth ER is especially abundant in liver cells, which produce glucose, detoxify drugs, synthesize cholesterol, and metabolize lipids.


Golgi Apparatus: The golgi apparatus is comprised of membranous sacs that have been flattened into a stack resembling a stack of hollow pancakes. On one side of the apparatus incoming vesicles from the rough ER fuse with the golgi apparatus, on the other side vesicles filled with proteins or lipids detach for export from the cell or variety of other destinations. The receiving side of the golgi apparatus is called the cis face, the side that releases vesicles for protein export is called the trans face. An easy way to remember this arrangement is to associate the cisterns of the rough ER with the cis face of the golgi apparatus and to associate the trans face with transport out of the cell.  Once detached from the trans face the outgoing vesicles have three possible destinations


  • Vesicles containing material destined for export out of the cell (secretory vesicles) travel to the plasma membrane and release their contents into the extracellular fluid.

  • Some vesicles contain lipids and proteins that need to be transported to the plasma membrane or other organelles for integration into their membranes

  • Some vesicles leaving the trans face are packed with digestive enzymes and remain in the cell to function as the organelle of cellular digestion, the lysosome.


Lysosomes: Lysosomes serve as the site for safe cellular digestion and are packed with activated digestive acids. Lysosomes are organelles that are produced at the golgi apparatus, and are particularly abundant in cells that destroy invaders through phagocytosis such as macrophages. Targets for lysosomal digestion are ingested bacteria, viruses, toxins, nonfunctional organelles, glycogen, non useful tissues, and bone tissue when blood calcium concentration is low.


Peroxisomes: Peroxisomes are very similar in structure to lysosomes, however they serve a different function. Like lysosomes, peroxisomes are membranous sacs. Peroxisomes however containing powerful enzymes such as oxidases and catalases. These enzymes neutralize and detoxify harmful substances that find their way into the cell such as alcohol and most importantly free radicals. It makes sense then why peroxisomes are found in such great number in liver cells.


Cytoskeleton: The cytoskeleton, like the human body’s skeleton, provides structure and support. This structure helps the cell maintain its form, as well as also providing machinery (motor proteins) to produce cellular movement and activities. We’ve talked a great deal about various organelles moving about the cytoplasm, such as vesicles, but we haven’t talked about how this is accomplished. The cell’s skeleton, or cytoskeleton, provides the necessary structure and motor proteins to accomplish this movement, as well as accomplish cellular propulsion through the use of cilia, flagella, and microvilli. The cytoskeleton is composed of three types of tubes or rods as well as various proteins which are identified below


Microfilaments: These are the thinnest filaments of the three rods composing the cytoskeleton and are composed of actin. Although no two cells have the same microfilament structure, almost all cells have an interconnected web on the interior of the cells membrane, or cytoplasmic side of the membrane. This web is semiflexible giving the cell form without making it excessively brittle when deformed. Additionally this web, with the help of motor proteins, gives rise to cellular movement, the ability to deform the plasma membrane during endocytosis, and performs the splitting of the cell during cellular division.


Intermediate Filaments: These filaments are larger in size than microfilaments and smaller in size than the next class of cytoskeletal rods or microtubules, thus giving rise to the name “intermediate” filaments. These filaments are the strongest of the three cytoskeletal elements, and thus resist the many tensile forces placed on various cells.


Microtubules: The largest cytoskeletal element, microtubules are incredibly dynamic. develop like spokes of a wheel eminating from the cells center, or centrosome. Howeveer they can rapidally dissasemble and reassemble at various sites to serve various purposes. Microtubules are very stiff however can deform under stress making them an ideal structure to serve as the primary determinants of cellular shape. They also serve as tracks that lysosomes and mitochondria are anchored to and ferried around the cell on. Their origin, the centrosome, isn’t just a location within the cell, it is the production site of microtubules and contains two small organelles called centrioles.

7 comments on “The Cell (Part 1)

  1. Missy
    September 26, 2013

    Hi I was just wondering where part 2 is?

    • tlohman2
      September 26, 2013

      In my brain unfortunately. I’m a bit behind on writing this stuff… Forgive me, I am trying to keep up! If you have any particular questions about the second half of the chapter please ask and I will do my best to give a detailed explanation.


  2. Raluca A.
    September 27, 2013

    Is the second part coming up ?

    Thank you .

    • tlohman2
      September 27, 2013

      Sorry, I don’t think I will be able to write it. I am trying to get ahead for next weeks materials. Use the lecture text book and if there is anything you would like further explanation on just let me know.

  3. Pam U.
    September 27, 2013

    Hello! I was wondering if you could explain a bit more about what causes the concentration gradient when talking about resting membrane potential? Also, could you explain what you mean regarding the following questions from the study guide:

    “what are the concentration gradients (sodium is of 10 times concentration in extracellular fluid etc) where is this charge difference located?)”

    Thank you!

    • tlohman2
      September 27, 2013


      For the first part of your question please refer to the quick review section on membrane potential. If you still have a question I will try again because I am sure the fault is mine and not yours.


      For the second part:

      I want you to know the relative concentrations of sodium and potassium (the two most important ions in terms of establishing the resting membrane potential(K+ is the most important)) For example, is potassium more highly concentrated in the intracellular or extracellular fluid and vice versa for sodium.

      Now the last part

      I want you to know whether or not the charge separation (resting membrane potential) is located only in close proximity to the cell membrane, or is the entire intracellular fluid more negative than the entire extracellular fluid compartment. Again check the quick review page on membrane potential for this one.

  4. Pingback: The Cell, Tissues, Integumentary system, and Skeletal Tissues Study Guide | A & P Source

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