BIO101 – Cell Structure

As you may know, I have been teaching BIO101 (and also the BIO102 Lab) to non-traditional students in an adult education program for about twelve years now. Every now and then I muse about it publicly on the blog (see this, this, this, this, this, this and this for a few short posts about various aspects of it – from the use of videos, to the use of a classroom blog, to the importance of Open Access so students can read primary literature). The quality of students in this program has steadily risen over the years, but I am still highly constrained with time: I have eight 4-hour meetings with the students over eight weeks. In this period I have to teach them all of biology they need for their non-science majors, plus leave enough time for each student to give a presentation (on the science of their favourite plant and animal) and for two exams. Thus I have to strip the lectures to the bare bones, and hope that those bare bones are what non-science majors really need to know: concepts rather than factoids, relationship with the rest of their lives rather than relationship with the other sciences. Thus I follow my lectures with videos and classroom discussions, and their homework consists of finding cool biology videos or articles and posting the links on the classroom blog for all to see. A couple of times I used malaria as a thread that connected all the topics – from cell biology to ecology to physiology to evolution. I think that worked well but it is hard to do. They also write a final paper on some aspect of physiology.

Another new development is that the administration has realized that most of the faculty have been with the school for many years. We are experienced, and apparently we know what we are doing. Thus they recently gave us much more freedom to design our own syllabus instead of following a pre-defined one, as long as the ultimate goals of the class remain the same. I am not exactly sure when am I teaching the BIO101 lectures again (late Fall, Spring?) but I want to start rethinking my class early. I am also worried that, since I am not actively doing research in the lab and thus not following the literature as closely, that some of the things I teach are now out-dated. Not that anyone can possibly keep up with all the advances in all the areas of Biology which is so huge, but at least big updates that affect teaching of introductory courses are stuff I need to know.

I need to catch up and upgrade my lecture notes. And what better way than crowdsource! So, over the new few weeks, I will re-post my old lecture notes (note that they are just intros – discussions and videos etc. follow them in the classroom) and will ask you to fact-check me. If I got something wrong or something is out of date, let me know (but don’t push just your own preferred hypothesis if a question is not yet settled – give me the entire controversy explanation instead). If something is glaringly missing, let me know. If something can be said in a nicer language – edit my sentences. If you are aware of cool images, articles, blog-posts, videos, podcasts, visualizations, animations, games, etc. that can be used to explain these basic concepts, let me know. And at the end, once we do this with all the lectures, let’s discuss the overall syllabus – is there a better way to organize all this material for such a fast-paced class.

Today, we continue into biology proper – the basic structure of a (mainly animal) cell. See the previous lectures:
Biology and the Scientific Method.

Follow me under the fold:

Cell StructureSecond lecture notes from my BIO101 class (originally from May 08, 2006). As always, in this post and the others in the series, I need comments – is everything kosher? Any suggestions for improvement?

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BIO 101 – Bora Zivkovic – Lecture 1 – Part 2

The Cell

All living organisms are composed of one or more cells – the cell is the unit of organization of Life.

Most cells are very small. Exceptions? Ostrich egg is the largest cell. Nerve cell in a leg of a giraffe may be as long as 3m, but is very thin.

Basic Structure of the Cell

A cell is a small packet or bag of liquid. The liquid is cytoplasm (or cytosol), which is essentially salty water with various organic molecules suspended in it.

The cytoplasm is contained within a cell membrane. Cell membrane is a phospholypid bi-layer – this means that it is composed of two layers of tightly packed molecules of fat. Within the membrane, proteins are embedded into the bi-lipid layer and are more or less free to move around within the membrane. These proteins are important for the communication between the inside and outside of the cell.

You can see a good image here.

On the outside of the membrane, some cells may have additional structures. For instance, many bacterial and plant cells have thick cell walls that confer more rigidity to the cell as well as better defense against mechanical, chemical or biological insults.

Some cells also have hair-like cilia on the surface (e.g., a Protist called Silver Slipper), or long whip-like flagella at one end (e.g., sperm cells). Both of these structures allow the cell to move utilizing its own energy.

Inside every cell, there is hereditary material – DNA. Exceptions? Red blood cells which have a membrane and cytoplasm, but no hereditary material.

Differences between Prokaryotes and Eukaryotes:

Prokaryotes (bacteria) have a cell membrane and cytoplasm and no other organelles.

Eukaryotes (plants, animals, fungi, protista) have a number of different cell organelles.

The nuclear material in Prokaryotes is a single, circular strand of DNA.

The nuclear material in Eukaryotes is organized in multiple chromosomes contained with a nucleus.

Cell Organelles

Eukaryotic cells have organelles. Organelles are sub-cellular structures that provide internal compartmentalization and other functions.

Nuclues is a large membrane-bound organelle. Its function is to sequester the DNA from the rest of the cell. The nuclear membrane (or nuclear envelope), which is also a phospholipid bi-layer, selectively allows molecules to pass between the nucleus and cytoplasm. Inside the nucleus, DNA is organized in chromosomes. A chromosome is a tightly coiled and wound strand of DNA packaged with various proteins (e.g,. histones).

Smooth endoplasmic reticulum is a system of membranes and is involved in carbohydrate and lipid synthesis.

Rough endoplasmic reticulum is a system of membranes that possesses ribosomes. Proteins are synthesized in the rough ER.

Golgi apparatus stores and packages various molecules. When a molecule is needed elsewhere in the cell, a portion of the Golgi membrane closes off and forms a vesicle that can be transported around the cell.

Some Eukaryotic organelles contain a little bit of their own DNA: the mitochondria and the chloroplasts. These two organelles used to be inter-cellular parasites, i.e., different species of bacteria that, over time, became an integral part of a cell.

Chloroplasts are found in plant cells. Photosynthesis is the process that occurs in them.

Mitochondria are found in all Eukaryotic cells. Breakdown of glucose begins in the cytoplasm and ends in the mitochondria, where the final products of the breakdown are ATP, water, CO2 and heat. This process requires oxygen – that is why we breath: to provide the oxygen for the mitochondria and to get rid of carbon dioxide produced in the mitochondria.

ATP (adenosine triphosphate) is the energy currency of the living world. Every cellular process that requires energy gets it from ATP. Thus, mitochondria are sometimes referred to as “factories of the cell”.

The final portion of the process of glucose digestion (the Krebs cycle) is, like any process, not 100% efficient. Errors happen and not every atom of every glucose molecule ends up where it should: in ATP, water or CO2. The result of this inefficiency is production of heat and production of highly reactive small molecules called free radicals (e.g., hydrogen peroxide, H2O2). Free radicals tend to quickly react with whatever molecule they first encounter upon leaving the mitochondria. Such reactions damage those molecules, be they proteins, lipids, sugars or nucleic acids. The inter-cellular damage caused by free radicals is one aspect of the process of aging.

Some animals – birds and mammals – have harnessed the heat production by the mitochondria to keep a stable internal temperature. The efficiency of the mitochondrial “machine” is held low under the control of hormones like thyroid hormones. As a result, there is a greater production of free radicals, so warm-blooded animals evolved particularly good mechanisms for neutralizing free radicals and for repairing the damage. If a person keeps a constant low temperature or constant low-grade fever, the first thing the physician will check is the function of the thyroid gland.

The cytoskeleton, composed of filaments and microtubules, anchors the organelles and gives a cell its shape. Microtubules move organelles, including vesicles, within a cell. They also move the membrane-embedded proteins around where they are needed.

Previously in this series:

Biology and the Scientific Method

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22 responses to “BIO101 – Cell Structure

  1. I would say a tiny bit more about the plasma membrane. Introduce the idea of polar vs. non-polar and how the amphipathic phospholipids keep stuff from passing through and allows for compartmentalization. I remember being absolutely fascinated by this concept in my first biology course.

  2. I do go about it orally, while discussing it. Not sure if I should include it in the condensed notes (everything in the notes can be on the exam, and probably will be). Shall think about it. Thanks.

  3. Hi. Love the fact that you’re requesting comments on teaching stuff! (Wish more of us did this.) I teach half of a first year Biology course (among other university Biology courses), and am a microbiologist by training. So, my comments reflect my background, and what I see as a bit of a eukaryotic bias in a lot of first year Biology textbooks, I admit.

    The prokaryote/eukaryote split is convenient … but not terribly meaningful biologically. While members of the Archaea are superficially similar to Bacteria, and share some features, they are evolutionarily quite distinct, and share some characteristics with eukaryotes (especially at the molecular level). I recognize that it can be challenging to introduce the Domains in a first year course, but I suspect that students get so focused on what appears to be an easy dichotomous split (prokaryote vs. eukaryote) that strong misconceptions are set up, making it difficult to teach more advanced concepts relating to evolution, microbiology, etc. (There is a nice, short piece by Norman Pace where he argues that we shouldn’t be using the term prokaryote in teaching at all … I originally resisted this, as I have a lot of affection for prokaryotes. But *I* know the differences between the Bacteria and Archaea – students, on the other hand, do not.)

    My second point is about organelles. Intro courses and textbooks often use the term “organelle” in a way that is inconsistent between courses/books. (I have collected glossary definitions from many different textbooks that illustrate this.) Even just referring to eukaryotic organelles, there are disputes as to how inclusionary the term should be! In the microbiological literature, there are often references to organelles in bacteria and archaea. Although these organisms are tiny, they do have some compartmentalization (albeit to a lesser extent than eukaryotic cells). There are even some bacteria that have DNA enclosed in a membrane! It’s not a true nuclear membrane, specialized in the way that we see in eukaryotes, of course, but it’s an interesting thing to show students who might wonder about how a nucleus could have evolved.

    I wandered from my point a bit, but I think it’s a good idea to explore the concept of compartmentalization with students, and perhaps even discuss how/why the term organelle is so difficult to define cleanly. In my first year course, we actually vote on what definition to use (as the students do feel more comfortable with a definition), but it’s clear that this is the “BIOL 1010 definition of an organelle”.

    Bacteria also have cytoskeletal elements (e.g., FtsZ, a tubulin homologue). Some bacteria have linear chromosomes (e.g., Streptomyces, Borrelia) and some have more than a single chromosome (Streptomyces and Borrelia are also examples for that). However, I’m not sure if that’s something to discuss in a first year course. (Microbiology students seem to accept these as exceptions to the “rule” they learned in other courses that bacteria have single, circular chromosomes.)

    I’d be happy to pass along some references, and/or my slides/notes on these points, if anyone’s interested.

    Tanya

  4. Thank you very much for this. It is always difficult to decide how many ‘exceptions to rules’ to include when teaching the rules. I do cover the Domains later in the course where I go a little bit more into differences between Archaea and Bacteria. That is the time when I refer back to these rules and teach exceptions.

    And I am always torn about the Prokaryote/Eukaryote classification, but it is so prevalent in the media (the only other place they will ever see science again in their lives) and so simple, I tend to stick with it for the purposes of the BIO101 level.

  5. I think for a biology class for non-majors, you’re pretty much hitting the target.

    I’m not sure about ostrich cell as largest—aren’t some of the algae (like Caulerpa) much larger?

    If you will eventually be getting into anything immunological with this course, I would recommend adding a statement about oligosaccharides as part of the cell membrane.

    Also, if you’re going to get into more with energy (glucose to ATP) later in the course, I might leave out the detail that you have here. It feels a little out of place with the rest of the organelle discussion.

    Would love to see you podcast your notes for students or have them build a wiki to post animations, YouTube videos, and other web resources as supplemental content. Or place an outline in a GoogleDoc and have students add the details, etc. during the session. Lots of possibilities!

  6. Great Bora, One comment (for now): Red blood cells in birds (I assume other non-mammalian vertebrates too) do not loose their nuclei.

    Have you thought about building these notes in WikiEducator? I am starting to build my content there, in the hope of creating collaborative classroom (OER) resources.

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