In this lecture, as well as in the previous one and the next one, I tackle areas of Biology where I am really weak: origin of life, diversity of life, and taxonomy/systematics. These are also areas where there has been a lot of change recently (often not yet incorporated into textbooks), and I am unlikely to be up-to-date, so please help me bring these lectures up to standards…. This post was originally written in 2006 and re-posted a few times, including in 2010.
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.
These posts are very old, and were initially on a private-set classroom blog, not public. I have no idea where the images come from any more, though many are likely from the textbook I was using at the time. Please let me know if an image is yours, needs to be attributed or removed. Thank you.
Last week we looked at the organ systems involved in regulation and control of body functions: the nervous, sensory, endocrine and circadian systems. This week, we will cover the organ systems that are regulated and controlled. Again, we will use the zebra-and-lion example to emphasize the way all organ systems work in concert to maintain the optimal internal conditions of the body:
So, if you are a zebra and you hear and see a lion approaching (sensory systems), the brain (nervous system) triggers a stress-response (endocrine system). This is likely to happen during the day, as the biological clock (circadian system) of both animals makes them diurnal, i.e., day-active (as opposed to nocturnal, or night-active animals). If the chase occurred during the night, the lion would run slower and the zebra would take longer to mount a stress-response. Both animals would also be handicapped by lower sensitivity of their sensory systems.
Another name for the stress response is fight-or-flight response. Considering the size, strength and weaponry of the lion, the zebra’s brain is unlikely to make a decision to fight.
Flight, i.e., running away is the best course of action for the zebra.
Zebra’s great speed and the lion’s hunting tactics are a result of a co-evolutionary arms race. Let’s see what is happening in the body of the zebra once it starts running.
Running is movement. In vertebrates, the movement is accomplished by contraction and relaxation of muscles attached to the bones of the internal skeleton. The attachments of muscles to the bones are called tendons (the attachment between one bone and another is called a ligament). By the alternate contraction and relaxation of muscles located on opposite sides of the bone, the bones are moved around the joints, the hooves push against the ground and propel the body forward.
What makes the skeletal muscles contract? Muscles are composed of many muscle cells. Each cell is very long and thin and each cell receives a synaptic connection from a motor neuron. The neurotransmitter at this synapse (called the ‘neuro-muscular junction’) is acetylcholine. Release of acetylcholine into the synaptic cleft and its binding to the receptors on the surface of the muscle cell membrane triggers an influx of calcium into the cell, as well as release of calcium from intercellular stores – the endoplasmatic reticulum.
The muscle cell is divided into segments. The muscle cell is filled with long thin molecules of actin and myosin that run lengthwise along the whole length of the segment. Myosin is the thicker of the two molecules. It contains myosin heads which form cross-bridges by binding to actin filaments. ATP is necessary for detaching the myosin heads from actin, while calcium is necessary for attaching the heads again – at a new place further down the filament. In this fashion, the two kinds of molecules slide over each other. As they do so, each segment of the muscle cell shortens, thus the whole muscle cell shortens – this is contraction.
So, for the muscles to contract, it is necessary for the muscle cells to be supplied with calcium and with ATP. Calcium is regulated by a number of organs. The intake (absorption) of calcium into the body is controlled by the digestive system. Loss (excretion) of calcium is regulated by the kidney. Calcium is deposited in bones. All three of those processes (absorption in the intestine, excretion into urine, and deposition into bones) is controlled by hormones: parathormone (parathyroid gland), calcitonin (thyroid gland), estradiol (ovary and adrenal cortex) and Vitamin D (a hormone synthesized by skin). If muscle cells lack calcium, parathormone will be released, while calcitonin and estradiol will be inhibited. This will increase absorption from the gut, decrease loss via urine, and release some calcium out of the bones.
The other requirement for muscle contraction is ATP. It is synthesized during breakdown of glucose. The first several steps of the biochemical breakdown of glucose (glucolysis) do not require oxygen and result in production of just a few molecules of ATP. The last several steps of the biochemical breakdown of glucose (Krebs cycle) occur in the mitochondria (of which muscle cells have many), require the presence of oxygen, and result in production of many molecules of ATP.
Thus, in order to synthetize sufficient amounts of ATP needed for contraction, muscle cells need glucose and oxygen. Both are delivered to the muscles via blood, by the circulatory system. Oxygen in blood is bound to the molecule of hemoglobin. Hemoglobin is tightly packed inside red blood cells. In muscles, the concentration of oxygen in red blood cells is greater than in the surrounding tissue, thus hemoglobin releases oxygen which follows its concentration gradient. In lungs, the concentration of oxygen is greater in the air than in the blood, so oxygen enters the blood and binds to hemoglobin. Carbon dioxide does the opposite – it also follows its own concentration gradient, thus leaving the muscle cells and binding hemoglobin in a nearby capillary, then leaving the red blod cells and diffusing into the air in the lungs.
During stress response, epinephrine (from adrenal medulla) and the sympathetic system speed up the heart rate, thus increasing the rate at which blood circulates through the tissues. At the same time, capillaries in the muscle dilate (open up) allowing more blood to perfuse the muscle cells.
Heart is a large muscular organ. All muscle cells in the heart are connected to each other via gap junctions so the electrical potential is spread through the heart very fast. The oxygenated blood from the lungs enters the heart via pulmonary veins into the left atrium (one of the four chambers of the heart). It flows from left atrium into the left ventricle. When the left ventricle is filled, the contraction of the heart expells the blood into aorta – the largest artery of the body. Aorta branches off into many other arteries that take blood into all parts of the body. Smaller and smaller branches of arteries finally end in capillaries.
Capillaries are blood vessels that are bounded only by a very thin single-cell layer with pores, which allows many molecules to leave the bloodstream or enter the bloodstream following their concentration gradients. Oxygen-rich blood enters the capillaries and releases oxygen.
Oxygen-poor blood moves from capillaries into small veins, which join together into large and larger veins and finally into the vena cava. Vena cava enters the heart in the right atrium. From there, O2-poor blood fills the right ventricle. When the heart contracts, the blood is expelled into the pulmonary arteries which take the blood to the lungs where the blood becomes oxygen-rich again.
The frequency and depth of respiration also increase, thus increasing the concentration of oxygen in blood. Furthermore, working muscles produce heat. Higher temperature makes it easier for hemoglobin to release oxygen into the muscle. At the same time, increased ventilation (by intercostal muscles and the diaphragm) of lungs decreases the air temperature in lungs, which makes it easier for hemoglobin to bind oxygen. All this makes more oxygen available to the working muscles.
Still, after only a few seconds of strenous work, the oxygen reserves in the muscle are depleted. The glucose is now broken down only by glucolysis (anaerobically). As a result, the final products of glucose metabolism are not water and carbon dioxide, but lactic acid – the substance that makes tired muscles hurt. The presence of lactic acid decreases the local pH in the muscle, which also makes it easier for the hemoglobin to release additonal oxygen into the muscle, but the capacity of blood to bring in more oxygen is overwhelmed by the oxygen need of the working muscle cells.
Where does the muscle get its glucose from? Most of the glucose in the body is stored in the form of glucogen in muscle cells and liver cells. Hormones like glucagon and cortisol trigger the breakdown of glucogen into glucose molecules and release of glucose out of liver into the bloodstream, thus making it available for the muscle to use.
But, where do the glucose stores come from? From food, which is ingested, digested and absorbed by the digestive system.
Digestion of food begins in the mouth, where saliva begins the process of breaking down carbohydrates, along with making the food softer for the action of teeth and tongue in breaking down the food into smaller particles that can be swallowed. The food then goes through the esophagus into the stomach. The stomach is a muscular organ. It secretes hydrochloric acid and many digestive enzymes. The movements of the stomach further turn the food into a liquid. The movements of the stomach, as in many other internal organs, is due to the activity of smooth muscles. Those are much shorter muscle cells which are, unlike skeletal muscles, not under voluntary control. The muscles of the stomach and intestine are inhibited by the sympathetic system, thus digestion slows down during the stress response – the digestive process is too slow to provide glucose to the muscles at a rate needed for escaping the lion, thus the business of digestion (which is quite energy-demanding) is postponed until after the stresful event is over.
Once the food is made completely liquid by the stomach, it passes through the pyloric sphincter into the first portion of the small intestine – the duodenum. Here, the very acidic content of the stomach is neutralized and the pH of the rest of the digestive tract is slightly alkaline. At the beginning of the duodenum, two important organs add their products into the lumen of the intestine – the liver and the pancreas. The liver produces bile which is stored in the gall bladder and secreted into the duodenum. Bile is a mix of salts that act like detergents – breaking down large globules of fats into smaller droplets, thus making fats accessible to enzymes. Pancreas produces a wide range of digestive enzymes which, together with intestinal enzymes, break down different types of food molecules: proteins, carbohydrates, lipids, nucleic acids, various minerals, vitamins, etc.
Next portion of the small intestine is the longest – the jejunum – followed by ileum. In herbivores in general, the small intestine is very long, while in carnivores (e.g, the lion), it is comparatively short. Most of digestion and absorption of nutrients is performed by the small intestine.
The small food molecules absorbed by the intestine are picked up by the hepatic portal system – a system of blood vessels that take the blood to the liver. Liver is the chemical factory of the body – it breaks down toxins as well as foods, builds new molecules out of simpler building blocks and makes those available to the rest of the body by releasing them into the main bloodstream.
Large intestine – the coecum, the colon and the rectum – is primarily involved in reabsorption of water so it is not lost via feces. In some animals, various portions of the digestive tract are enlarged and contain chambers full of bacteria and protista that are capable of breaking down food substances (e.g., cellulose) that the animal itself is incapable of digesting. In ruminants (e.g., cows, sheep, camels, giraffes), it is the stomach that serves this function – it is divided into four large chambers. In horses and zebras, the coecum serves the same function. In humans, coecum is a rudimentary organ – all that is left is the non-functional appendix.
If you paid attention so far, you may have noticed a pattern. During stress reponse – running in this case – the most important organ system is the system for locomotion – the skeletal muscles. Every other organ system that is involved in providing the muscles with the optimal internal environment for maximal function, i.e., the systems that control calcium, or provide glucose and oxygen to the muscles, are stimulated by the control and regulatory mechanisms. All other systems are inhibited or even completely shut down – they consume precious energy. If the muscles perform their function succesfully and the zebra escapes, the normal function of these systems can resume.
However, using up energy by non-essential systems can lead to the zebra not having enough energy for running at the maximum speed for sufficiently long time to evade the lion. Being eaten by the lion is certainly not good for zebra’s homeostasis!
Along with the digestive system, other systems that are inhibited during stress response are the immune system (which we will not cover in this course), the excretory system (kidney) and the reproductive system. Compared to the lion, fighting off bacteria is not so important – this can wait for a couple of minutes. Having to stop to pee is not a good idea while running away from the lion as well. It goes without saying that engaging in reproductive functions is out of question during the flight from the ferocious predator – but the survivors will have the opportunity to breed later, passing on their genes to the next generation – genes that contain information about building the body that is capable of effectively allocating resources in order to escape a lion’s attack.
So, now that you – the zebra – have successfully run away from the lion, all the functions are coming back to normal – the breathing and heart-rate slow down, the glucose gets redeposited as glucagon in the liver and muscles (under the influence of insulin), the digestion restarts and the immune system re-engages. Let’s now look at the remaining two systems – excretion and reproduction.
The main organ of the excretory system is the kidney. Kidney is built of billions of little tubes called the nephrons. At the beginning of each nephron, a web of capillaries releases much water and other molecules into the nephron. Then, along the length of the nephron, there is exchange between the nephron, the neighboring capillaries and the space between them. Some substances, e.g, glucose, get completely reasborbed out of the nephron and back into the bloodstream. Toxic and waste materials are actively secreted from the blood into the nephron. Many ions are also exchanged, leading to regulated changes in pH. Finally, most of the water gets reabsorbed as well, under control of antidiuretic hormone and aldosterone. Control of how much water gets excreted in the urine and how much is reabsorbed back into the bloodstream is important not just for preventing water loss, but also in controlling blood pressure. The urine is collected in the urinary bladder and, when it fills up, it is excreted via urethra into the outside environment.
Testis is the main organ of the male reproductive system. Apart from being an endocrine gland – secreting testosterone – this is the site where sperm cells are continuously produced out of their stem cells within long convoluted tubes of the testis. The mature sperm cells – spermatozoids – are collected in the epidydimis on the surface of the testis. At the end of copulation, during orgasm, the sperm cells are ejected via sperm duct (vas deferens) and urethra (housed within the penis) into the female’s vagina. On the way out, the sperm cells are mixed with secretions of three glands – the prostate, the seminal vesicles and the bulbourethral glands whcih provide the optimal environment (e.g, pH, sugars) for the survival of sperm cells in the inhospitable regions of the acidic female genital tract.
In the female, the ovary is the organ which produces hormones estradiol and progesterone. All the egg cells are stored in the ovary before birth, i.e., no new eggs are produced after birth. In every cycle, one of the egg cells matures – it builds around itself a large follicle. Ovulation is the moment at which the follicle bursts and the egg is released into the oviduct. If no fertilization occurs, the egg, together with the lining of the uterus, gets shed out of the body (menstruation). If fertilization does occur in the oviduct, the zygote moves into the uterus and implants itself into its wall. The empty follicle left behind in the ovary turns into the yellow body which secretes progesterone throughout pregnancy. The fertilized egg starts developing. A part of it develops into placenta and the other part into an embryo.
Previously in this series:
BIO101 – Biology and the Scientific Method
BIO101 – Cell Structure
BIO101 – Protein Synthesis: Transcription and Translation
BIO101: Cell-Cell Interactions
BIO101 – From One Cell To Two: Cell Division and DNA Replication
BIO101 – From Two Cells To Many: Cell Differentiation and Embryonic Development
BIO101 – From Genes To Traits: How Genotype Affects Phenotype
BIO101 – From Genes To Species: A Primer on Evolution
BIO101 – What Creatures Do: Animal Behavior
BIO101 – Organisms In Time and Space: Ecology
BIO101 – Origin of Biological Diversity
BIO101 – Evolution of Biological Diversity
BIO101 – Current Biological Diversity
BIO101 – Introduction to Anatomy and Physiology
BIO101 – Physiology: Regulation and Control