August 13, 2011 | 1
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:
Second 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?
BIO 101 – Bora Zivkovic – Lecture 1 – Part 2
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 animal cell. There are some algae (like Caulerpa) with even larger cells. A nerve cell in a hind leg of a giraffe may be as long as 3m, but is very thin. There are some important differences between animal, plant and microbial cells, but ss this is a BIO101 speed course, we do not have time to cover all the nuances, so we’ll focus on the animal cell for the most part.
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. The molecules that make the membrane are polar, thus one end of the molecule repels water while the other one attracts it: this prevents many substances from passing through the membrane – their passage is thus controlled and facilitated by proteins. 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 of mammals which have a membrane and cytoplasm, but no hereditary material.
Differences between Prokaryotes and Eukaryotes:
Prokaryotes (bacteria, archaea) have a cell membrane and cytoplasm and no other organelles.
Eukaryotes (plants, animals, fungi, protista) have a number of different cell organelles.
Later in the course, when we cover diversity, you will see that this division is arbitrary and somewhat out-dated, but we’ll temporarily use it here as it helps with the organization of the topic.
The nuclear material in Prokaryotes is a single, circular strand of DNA (though there are exceptions).
The nuclear material in Eukaryotes is organized in multiple chromosomes contained within a nucleus.
As a rule, Eukaryotic cells have organelles. Some Prokaryotic cells may have some of the organelles, or some internal organization, though, so use this only as a “rule of thumb”. Organelles are sub-cellular structures that provide internal compartmentalization and other functions.
Internal compartmentalization – it is important for a complex cell to a) place all the chemicals involved in a particular biochemical reaction in close proximity to each other, enclosed in a smaller space, and b) separate from each other chemicals that would otherwise react with each other, yet it is important for the cell they do not.
Thus, organelles are for the most part internal structures that accomplish this: providing separate spaces within a cell, so different chemical reactions can occur in different places without any cross-reactions. The cell, as it synthesizes the molecules, transports each into the appropriate compartment. This is called spatial compartmentalization as the biochemical reactions are separated in space. Cells also use temporal compartmentalization by producing different chemicals at different times (e.g., time of day, time of year, or stage of life), so some biochemical processes may, for example, occur only during the day and others only during the night, and the two do not interfere with each other. This is more energy-efficient (no need to keep producing all the chemicals all the time) and also helps in coordinating and synchronizing biological processes between the cells in a tissue.
Nucleus 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 are essential for making sure that the right molecules end up in the right compartments within the cell. They also move the membrane-embedded proteins around where they are needed.
Previously in this series:
Images: they come from the textbook I used before, I think. These posts are several years old I and I lost the image sources in the meantime – help me by letting me know if you know the sources so I can properly acknowledge them.
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