Biodiversity Hotspots Lab- Mesoamerica Hotspot


This project explores biodiversity and affords the opportunity to learn what biological “hotspots” are and why they are threatened. Through research one will learn about endangered species in the selected hotpot and the awareness of human effects/impacts on biodiversity. This lab also allows one to see what is being done in regard to preservation of the selected hotspot.

The Earth’s Hotspots
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Hotpots are biologically diverse areas that contain extremely high levels of endemic (native; found only in a specific place) plant species. “To qualify as a hotspot, a region must meet two strict criteria: it must contain at least 1,500 species of vascular plants (> 0.5 percent of the world’s total) as endemics, and it has to have lost at least 70 percent of its original habitat.” (Retrieved from: on  5/06/12)

These hotspots are important as we face extinction of many species all over the world. Hotspots are places that can be considered irreplaceable, as they contain high percentages of endemic plants (and various mammal, amphibian, bird, fish, and reptile species) that can be found nowhere else. Once they are gone, they are gone forever. Already, there is an unknown decrease in the world’s amphibians. The Earth is one big interconnected web of life and ecosystems… what effects one species will ripple out and effect many, many, more.

I utilized Conservation International’s website to learn about hotspots and specifically chose the Mesoamerican hotspot to explore. This hotspot’s forests are the 3rdlargest among the world’s hotspots and contain approximately 17,000 plant species of which 17.3% are endemic. The Mesoamerican hotspot encompasses all tropical and subtropical ecosystems from central Mexico to the Panama Canal; the northern arm stretches to Sinaloa on the Pacific coast; eastern arm stretches to the middle of Sierra Madre Oriental on the coast of the Gulf of Mexico; then down south encompassing Central America; also includes many offshore and near shore islands in the Caribbean and Pacific. Within this vast expanse lie a complex mosaic of dry forests, montane forest, and lowland moist forest that range from coastal swamps on the Pacific coast to broad leafed and coniferous forests in higher lands, to rain forest east of the mountains of the Caribbean lowlands, and hardwood forests occupy steep and cloud shrouded slopes to the south.

This hotspot also yields high rates of endemic species of reptile (34.7%), fish (66.8%), and amphibians (64.5%). Endemic animals include the beautiful quetzal (a bird with emerald and crimson plumage) and the jaguar whose jaws have the strongest crushing power of all the Earth’s large cats. Chiapas and Guatemala are considered a center of origin and dispersal for tropical salamander species (120 of 160 species endemic). There are many species of endemic trees that are also considered valuable timber: Spanish cedar, Pacific Mahogany (nearly wiped clean from much of its natural range), Big Leaf Mahogany, and Rosewood. This hotspot also contains more than 300 cacti species of which approximately 85% can only be found in the Mexican portion of the hotspot.

As it only requires 1,500 species of vascular plants to be considered a hotspot, this area far exceeds this minimum with its 17,000 species. Plant endemism is highest in the mountainous regions of Southern Mexico and Guatemala. This area represents the confluence of fauna/flora from two biogeographic regions (Nearctic- North America and Neotropical-South America/Caribbean) as it has served as a land bridge for 3 million years allowing species to flow in both directions. This region is also the convergence place for 3 out of 4 major migratory bird routes in the western hemisphere!!

Jungle in Guatemala
Retrieved from: on 5/7/12

There is much poverty and some violence within the area of the Mesoamerican hotspot. Population growth rates are higher than many other hotspots around the world. This proves that much more difficult in preservation as the local people struggle to survive and provide the basic necessities of life. Areas of forest that had remained pristine and intact are opening up as the use of machinery for logging has become available. The poor people clear adjacent lands (from roads) to use for agriculture. This land has poor soil that becomes unproductive and then is sold to cattle ranchers as more trees are cleared for more agriculture and the cycle continues. Settlements border the protected areas (most parks and protected areas are only on paper as they have inadequate management/enforcement) and the locals must poach for food or clear land for agriculture to feed their families.

The largest concern in this region seems to stem from the logging and deforestation. This became most troublesome due to “technology” and the use of machinery. In the 19thcentury large scale agriculture (coffee, bananas, and oil palm) and livestock development have led to deforestation. In recent decades Mesoamerica has been the site of some of the world’s highest deforestation rates (1980-1990 1.4% annually). It is estimated that 80% of the areas original habitat has been severely modified or cleared. This is the worst in El Salvador as less than 5% of its original forest remains today! Recently, oil development and mineral extraction have increased the threat to the regions forests.

Thankfully, there people who are attempting to make efforts toward conservation. In recent decades there has been regional cooperation toward the creation/expansion of the Mesoamerican Biological Corridor. This is an initiative towards conserving biodiversity and ecosystems while promoting sustainable social/economic development. This initiative serves to protect important areas and provide connectivity between these areas through plantation forests, private reserves, and agroforestry systems. This will allow the plants/animals to disperse and move throughout the region. There are already established reserves of land that comprise this initiative: Maya Biosphere Reserve (Guatemala), Calakmul Biosphere Reserve (Campeche, Mexico), Rio Bravo (Belize), Montes Azules Biosphere Reserve (Chiapas), Guanacaste Conservation Area (Costa Rica), and the largest block of undisturbed cloud forest in Central Mexico- La Amistad International Park and Biosphere (Costa Rica and Panama- also convergence point for 75% of all migratory birds in Western Hemisphere!!!)

Ecotourism has become an important asset to nearly every country in Mesoamerica, most notably Costa Rica. This country may be the world’s best-known example of successful promotion of economic benefit from conservation. It is estimated that around 70% of the country’s tourists visit protected areas and in 2000, Costa Rica earned about $1.25 billion from ecotourism.

It is extremely important to be concerned with species extinction. Again, ecosystems are interwoven, nature is a delicate balance. What happens with one species affects another, and so on. If enough species became extinct it would eventually directly impact human beings, and one day we could be threatened with extinction ourselves. We need diversity for the health of the planet. Diversity allows the fittest to continue on to overcome natural disasters and disease. As species population shrink, so does their diversity. As their diversity diminishes, their susceptibility increases. Rapid extinction of species is also a good indicator of the health or contamination of the environment. Human beings are part of the environment, and though they might like to try, cannot separate themselves from the Earth.

A small idea of how species are interconnected
Retrieved from: on 5/7/12


This lab helped me identify what hotspots are and why preserving them is so important. The statistics I found were astonishing; its concerning how humans have negatively impacted the worlds ecosystems. In my region, 80% of the land had been drastically altered. Finding a balance with nature may be difficult when there are human lives to consider as one chooses what is necessary to feed their family. I was very pleased to learn of the Mesoamerican Biological Corridor and the knowledge that other countries are interested in preserving some of these biologically diverse gems.

Yucatan and Central America from space
Retrieved from: on 5/7/12


Bio 156 Unit 4 Compilation

Table of Contents:

The Digestive System: Nutrients into the Body

–          GI Tract Walls Are Composed of 4 Layers

–          5 Processes Accomplish Function

–          Digestive Organs/Accessory Organs

–          How Nutrients are Absorbed

–          Endocrine and Nervous System Regulate Digestion

–          Nutrition: Carbohydrates, Lipids, Proteins, Vitamins, Minerals, Fiber

–           Weight Control: Energy Consumption vs. Energy Spent

–          Digestive System Disorders

–          Eating Disorders

Nervous System

–          Neurons: Communication Cells of the Nervous System

–          Neuron Cell Structure

–          Sodium-Potassium Pump Maintains Resting Potential

–          Graded Potentials Alter the Resting Potential

–          Action Potentials are All-or-None and Self-Propagating

–          Neroglial Cells

–          Information is Transferred from Neuron to Target

–          Process of Synaptic Transmission: Neurotransmitter Release

–          Neurotransmitters Exert Excitability/Inhibitory Effects

–          Postsynaptic Neurons Integrate and Process Information

Population Growth and Human Impacts

–          Air Pollutants, Atmosphere, and Greenhouse Effects

–           Pollutants Produce Acid Rain

–          Water is Scarce and Unequally Distributed

–          Human Impacts on Water Supply and Water Pollution

–          Pollution and Overuse: Damaged Land

–          Energy: Many Options/Choices

–          Human Impacts: Creating a Biodiversity Crisis

–          Biodiversity is Healthy for Humans

–          Measuring Sustainability and Quality of Life

–          Toward a Sustainable Future

The Digestive System: Nutrients Into the Body

The digestion system comprises organs that function to get nutrients into the body. This is accomplished as food passes through a hollow tube in the body called the gastrointestinal tract (GI). 9 Organs as well as 4 accessory organs accomplish the process of breaking down food, digestion, and absorption of water and nutrients. The entire GI tract is 36 feet long as it begins as food is taken in through the mouth and expelled as waste through the anus.

Digestive System
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Digesting food takes 10% of the total daily energy requirement of the body. 70% of the energy is just spent on “idle” which maintains the functioning of the body, while 20% of energy output is utilized for activities of daily living.

GI Tract Walls Are Composed of 4 Layers

Mucosa: Innermost layer (mucous membrane) is in contact with the lumen (the space the food travels through). To enter the blood, all nutrients cross through this tissue.

Submucosa: Layer outside of mucosa that is comprised of connective tissue. The components of food that are absorbed in the mucosa enter this tissues lymph and blood vessels (this tissue also contains nerves).

Muscularis: Layer outside of submucosa that is responsible more movement. It has 2 or 3 sublayers of smooth muscle; one that is oriented in a circular fashion around the “tube” and one that is arranged lengthwise.  (Stomach has diagonal sublayer).

Serosa: The thin outermost wall of GI tract. It protects the other layers and attaches the digestive system to body cavity walls.

  • Sphincters (thick ring of smooth circular muscle) separate some of the organs from each other. They do this by contracting which closes of the passageway between organs.

    GI Tract Wall (Layers)
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  • 5 Processes Accomplish FunctionRaw materials must be broken down into a form the body can use. This is accomplished by:
    1. Mechanical processing and movement. Chewing begins the process of breaking food down. Peristalsis propels the food forward in the GI tract. Segmentation mixes the food in a back-and-forth action. Peristalsis occurs throughout the tract while segmentation occurs primarily in small intestines (this action pushes food against the mucosa so body can absorb nutrients).
    2. Secretion. Enzymes, fluid, acid, alkali, bile, and mucus are secreted at various places into the GI tract. Several hormones that regulate digestion are also secreted into the blood.
    3. Digestion. Food is broken down chemically and mechanically into smaller products, culminating in nutrient molecules.
    4. Absorption. (mostly in the small intestine) Nutrients pass into the blood or lymph by crossing the mucosal layer of the GI tract.
    5. Elimination. Undigested material (waste) is expelled out of the body.Digestive Organs/Accessory OrgansMouth : The average adult mouth contains 32 teeth that are specialized to crush, grind, cut, and tear food. The act of chewing begins the process of breaking the food down into smaller pieces. The tongue positions the food over the teeth (also assists in speech and taste).

      Salivary Glands: (Accessory Organ) the 3 pairs of glands in the mouth (near back of jaw, below lower jaw, under tongue) produce saliva that moistens and helps keep the food together and easier to swallow. The 4 main ingredients include: mucin, a protein that holds particles together for easier swallowing; salivary amylase enzyme that begins the process of digesting carbohydrates; bicarbonate that maintains pH that is most effective for amylase ; and lysozyme which helps to inhibit bacterial growth.

      Pharynx: Place where food enters after being pushed down by the tongue. Receptors in the pharynx stimulate the “swallowing reflex”. The soft plate closes off the nasal passageway (by rising) and the larynx raises a little as the epiglottis bends to close the airway (trachea) temporarily. This prevents us from choking. The food slides past the epiglottis and into the esophagus.

      Esophagus: This is a muscular tube that, through peristalsis, propels the food forward to the stomach and consists of smooth muscle and skeletal muscle. The lining produces mucus to make the food slide down easier. The esophageal sphincter prevents reflux of the contents of stomach by opening as food arrives and closing after it passes into the stomach.

      Stomach:The stomach stores food, regulates delivery, and digests protein. The stomach stores food until it can be digested and is able to expand 1-3 liters capacity when we eat. Gastric glands secrete hydrochloric acid, mucus, or primarily what becomes pepsin (protein-digesting enzyme that is created as pepsinogen is exposed to stomach acid). Muscle contractions mix all the contents together, mechanically breaking food into smaller particles. Then the stomach delivers the partially digested contents (chime) into the small intestine (stomach regulates the rate of delivery). A mucus layer protects the tissues from the acidic contents. * Peptic ulcers may occur when the mucus layer is damaged and the underlying tissue is exposed creating an open sore.

      Small Intestine: Peristalsis starts at the lower esophageal sphincter which only propels about 1 tablespoon of chime into the small intestine at a time before it closes. The small intestine contains villi, folds, and microvilli that increase the surface area of small intestine by over 500 times. This makes it ideal for the absorption of nutrients. Carbohydrates and lipids are digested here, as well as continuing of protein digestion.  The gastric juices are neutralized and digestive enzymes are added from the intestine and pancreas. The first region called the duodenum is where most of the remaining digestion takes place and the remaining 2 sections (jejunum and ileum) primarily absorb water and nutrients. As the water and nutrients are absorbed through the mucus layer, they are transported through the blood and lymph vessels to nourish the body.

      Pancreas:Organ that lies just behind the stomach and performs exocrine and endocrine functions. The pancreas produces and secretes several digestive enzymes aimed at protein, carbohydrate, and lipid digestion. Proteases, trypsin, chymotrypsin and carboxypeptidase work to digest proteins; pancreatic amylase work to finish the digestion of carbohydrates; and lipase works to digest lipids. Sodium bicarbonate is secreted to neutralize stomach acid and allow other pancreatic enzymes to work more effectively.

      Liver: The liver produces bile to facilitate digestion of lipids. The hepatic portal system (carries blood from one capillary bed to another) carries nutrient rich blood directly from digestive organs to the liver. The liver processes and stores nutrients for the body. The liver is also involved with many other functions that maintain homeostasis: stores fat-soluble vitamins; stores glucose as glycogen; manufactures plasma proteins; synthesizes and stores some lipids; inactivates many chemicals; converts ammonia into less toxic urea; and destroys worn-out red blood cells.

      Gallbladder: The gallbladder receives the bile the liver produces through ducts and then removes water to concentrate and store it. The bile is released and secreted into the small intestine after a meal.

      Large Intestine: The large intestine absorbs most of the remaining water and nutrients and stores the remainder of the material as waste until it is expelled. It begins at the cecum (a pouch that receives chyme from small intestine) and includes 4 regions: ascending colon, transverse colon, descending colon, and sigmoid colon (where feces are stored until they pass through the rectum and anus- expelled). There are multiple strains of bacteria that live in the colon, some of which create useful by-products such as vitamin K.

      How Nutrients Are Absorbed

      Carbohydrates and proteins are absorbed by active transport. Proteins are broken down into amino acids and then actively transported into the mucosal cells. Through facilitated diffusion, they eventually make their way out of the mucosal cells and into the capillaries.

      The digestion of carbohydrates begins in the mouth as salivary amylase begins the process of breaking down polysaccharides into disaccharides. The digestion is completed in the small intestine as enzymes and pancreatic amylase break down the remaining carbohydrates into monosaccharaides. Monosaccharaides use different active transport proteins, but follow similar pathways to those for amino acids.

      Lipids are broken down by bile salts into tiny fat droplets. These are then digested by intestinal and pancreatic lipases. They become fatty acids and monoglycerides and dissolve in micelles (small droplets of bile salts and lecithin). Micelles’ function is to transport monoglycerides and fatty acids to the outer surface of cells so they may be absorbed into the cell. Inside the cell they recombine into triglycerides, are given a protein coating, and released into the lymph to return to the venous blood vessels near the heart.

      Water is absorbed by osmosis due to the higher concentration of water in the lumen than in the intestinal cells (or in the blood).

      Vitamins and minerals have many paths of absorption dependent on if they are fat or water soluble. Fat- soluble follow the lipid pathway: dissolve in the micelles and absorbed by diffusion through the lipid membrane of cell layer. Water-soluble vitamins are absorbed through diffusion (through pores or channels) or active transport. (The body also digests and reabsorbs the components of digestive secretions themselves, returned to the liver, and recycled to use again).

      Endocrine and Nervous Systems Regulate Digestion

      Regulation depends on volume and content of food. As the stomach stretches the neural reflexes increase peristalsis and secretion of gastric juices. The stretching of the stomach combined with the trigger of protein release gastrin stimulates the gastric glands.

      In the small intestine, acid in chyme stimulates release of secretin which stimulates the pancreas to secrete bicarbonate (neutralizing acid).  Protein and fat stimulate release of cholecystokinin (CCK) which then stimulates the pancreas to secrete enzymes and the gallbladder to release bile. Stretching, secretin, and CCK inhibit stomach movement and stomach secretions.

      In the large intestine gastrin and stomach stretching increases movement.

      Retrieved from: on 4/23/12


      Nutrients are used or stored until needed. Depending on what molecules are in short supply and which may be in excess the body, there can be a great amount of conversion of one to another according to the body’s needs. When people consume more nutrients (and calories) than what is actually used, the body may store the excess for future use which could lead to increased body weight in time. When people consume less than what is used, the body utilizes storages of energy to make up the difference. In time (and done regularly) the person will lose weight. Eating a healthy diet may help one get the nutrients their body needs while maintaining a healthy weight. General recommendations include: consuming less than one teaspoon of salt a day and using sugar in moderation; eating plenty of vegetables, fruits, and whole-grain products; eating a variety of foods; and only drinking alcoholic beverages in moderation.


      Carbohydrates are a major source of energy and many nutritionists recommend 45%-65% of Calorie intake come from carbohydrates. Carbohydrates can be simple (sugars) that are found in natural products such as honey and fruits, or complex(starch or glycogen) found in vegetables such as potatoes and corn or grains such as rice or oatmeal. Complex carbohydrates are better because they release sugars more slowly and contribute minerals, vitamins, and fiber. Refined sugars are the least beneficial (such as corn syrup or granulated sugar) as they release sugars quickly and have had most other nutrients removed.

      Simple carbs (left), complex (right)
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      Lipids are essential for cellular structure (components) and are energy sources. Most of the cell membrane is comprised of phospholipids and cholesterol. Cholesterol also forms the backbone of steroid hormones and is used to synthesize bile. Fat cushions organs, insulates the body, stores energy, and stores vitamins. Too much fat in a diet can lead to excess weight gain and higher risk of cardiovascular disease. Most nutritionists recommend no more than 20%-35% of Calories per day should come from lipids.

      Saturated fats tend to be solid at room temperature and are found primarily in meat and dairy products. They tend to raise “bad” LDL cholesterol.

      Unsaturated fatsare oils at room temperature and are considered healthier than saturated fats because they tend to lower LDL levels. These tend to come from plants such as olive, canola, and corn.

      Trans fats are vegetable oils that are turned back into solids at room temperature by partial hydrogenation of the fatty acid tails. They may increase shelf life and are used in commercial baked goods, margarine and shortening. Trans fats also tend to raise LDL cholesterol and increase the risk of cardiovascular disease (as does saturated fats).


      Proteins make up the enzymes that direct metabolism, they build muscle fibers, serve as receptor/transport molecules, and a few are hormones. All proteins are comprised of 20 different amino acids. The body can produce 12, but 8 have to be obtained from our diet and are called essential amino acids.

      Complete proteinis a protein source that contains all 20 amino acids in the proportion the body needs. Sources include nearly all animal proteins (meat, fish, milk, yogurt, eggs), but almost all plant proteins (except soybeans) lack at least one or more of the essential amino acids. Vegetarians must be careful in selecting various foods to ensure they obtain the proper balance of amino acids (such as red beans and rice). Approximately 15% of a person’s Caloric intake should come from protein.


      A group of at least 13 chemicals that are essential for normal functioning and fall into two groups: fat soluble and water soluble. Fat soluble are absorbed and stored along with the components of fat and released from the fat tissue as needed. Water soluble vitamins are absorbed easier than fat soluble vitamins but are only stored briefly and must be consumed on a regular basis.


      Minerals are chemical compounds that are found in nature (inorganic) and are essential for normal metabolic functioning. They are found in the blood as ions (potassium, sodium, chloride), represent most of the chemical structure of bone, and contribute to the activity of muscles and nerves. There are 21 minerals that are considered essential.


      Fiber is indigestible material found in many gains, vegetables, and fruit. It is beneficial to the colon as it makes feces bulky and helps them to pass more efficiently through the colon. A diet low in fiber can cause constipation, hemorrhoids, or diverticulosis. It is recommended that a person eat 20-35 grams of fiber a day for optimum colon functioning

      Weight Control: Energy Consumed vs. Energy Spent

      Energy is measure in units called Calories. A person’s daily caloric energy needs can be determined by your basal metabolic rate (BMR). This is the energy a body needs to perform the functions of sustaining life (breathing, maintaining organ function). BMR can be influenced by several factors including: gender and body composition, age, health, stress, food intake, and genetics.

      Healthy weight control involves not consuming more calories than what you are actually burning. Physical activity is an effective way to maintain healthy weight. While a person’s BMR stays fairly constant, exercising burns extra calories. 3500 Calories must be used to lose one pound of fat.

      Healthy weight improves overall health and reduces the risk of many diseases and ailments. The government recommends a BMI (body mass index) of 18.5-25 to be healthy. BMI is a measurement of body fat that utilizes a person’s height and weight to determine percentage of body fat. A measurement of 30 or higher represents obesity.

      Digestive System Disorders

      –          Lactose intolerance: difficulty digesting milk due to loss of enzyme that digests lactose.

      –          Peptic ulcers: sores in the stomach due to erosion of mucosal lining of the stomach.

      –          Celiac disease: (also known as gluten intolerance) the immune system responds to gluten by damaging or destroying the villi in the small intestine. The results in malabsorption of all sorts of nutrients and symptoms vary but may be diagnosed by a blood test.

      –          Diverticulosis: Small sacs in the mucosal lining of large intestines which represents a weakness in the wall. It is suspected that inadequate dietary fiber may contribute to the development of diverticulosis.

      –          Colon polyps: can be cancerous or non-cancerous growth that projects from a mucous membrane.  Polyps can be detected and removed in a colonoscopy (because most colon cancer starts as polyps).

      –          Hepatitis: Generally caused by toxic substances or viruses, it is inflammation of the liver. Hep A (there is a vaccine for) is transmitted by contaminated water/food and causes a brief illness. Hep B travels in body fluids/blood and if not treated can lead to liver failure (vaccine available). Hep C is also transmitted through blood and damages the liver. Severe cases may lead to cirrhosis or liver cancer.

      –          Gallstones: Excessive cholesterol in the bile may lead to the formation of gallstones that may grow large enough to obstruct bile flow and cause intense pain. Treatments may involve dissolving the stone(s) or removal of the gallbladder.

      –          Malnutrition: Conditions where body development and function are compromised due to over nutrition (which leads to obesity) or under nutrition (insufficient diet).

      –          Obesity: The World Health Organization says obesity is a global epidemic. There is a strong link between environment and the global rise in obesity as modernization favors an imbalance between caloric intake and expenditure.

      Eating Disorders

      Eating disorders are nervous system disorders and are most prevalent in women living in industrialized Western nations. They involve intense fear of gaining weight.

      Anorexia nervosa: People with this condition stop eating or diet excessively, possibly to the point of starvation/death. Symptoms include distorted perception of body image, even when severely underweight.

      Bulimia: A binge-and-binge eating cycle where one eats (excessively) and then vomits or takes other actions to minimize the Calories ingested. This involves a lack of control over eating and a preoccupation with body weight/shape, but some bulimics may maintain a normal weight.

      Science in the News

    6. ScienceDaily (Apr. 9, 2012)

    On Monday, April 9, 2012 the first FDA approved magnetic heartburn device was inserted in a patient with GERD (gastroesophagel reflux disease). This device is called LINX and is implanted at the lower esophageal sphincter. The device addresses the source of the acid reflux by correcting the anatomy (assists in closing the sphincter) as opposed to medications that merely suppresses stomach acid. Clinical trial results have indicated that LINX is highly effective in treating GERD and the painful burning sensation that occurs with acid reflux. What makes this device even better is that it can be implanted in an outpatient setting that may only require a 20-30 minute procedure.

    1. Nervous SystemThe nervous system comprises 2 principle parts:
      1. Central Nervous System (CNS): This is made of the brain and spinal cord and functions to receive, process, and transfer information.
      2. Peripheral Nervous System (PNS): This is made of the nerves outside of the CNS.

      –          Sensory Division: carries information toward the CNS (input). Signals from the environment, skin, muscle, organs send info toward CNS.

      –          Motor Division: carries information away from the CNS (brain directs motor activation after receiving input= output). This involves control of skeletal muscle, parasympathetic, sympathetic, and automatic control.

      Neurons: Communication Cells of the Nervous System

      Neurons are specialized cells for communication that generate and conduct electrical impulses. Neurons generate and transmit action potentials that are electrical impulses. They serve as the primary means of communication throughout the nervous system. Types of neurons:

      Sensory Neurons are found in the PNS that receive stimuli and transmit information to the CNS.

      Interneurons transmit information between components of the CNS (distance between neurons).

      Motor Neurons are found in the PNS and transmit information away from the CNS.

      Neuron Cell Structure

      There are three parts of a neuron:

      Cell body- the main part of the cell where nourishment occurs, containing the nucleus and most of the cytoplasm/organelles.

      Dendrites- small slender extensions of the cell body that receive incoming information.

      Axon- slender extensions that are specialized to conduct electrical impulses away from the cell body.


      Nerve Cell
      Retrieved from: on 4/24/12

      Sodium-Potassium Pump Maintains Resting Potential

      The Sodium-Potassium Pump functions to maintain cell volume and establishes/maintains the resting potential by active transport of sodium out of the cell and potassium into the cell. The resting potential is the measurable difference in voltage across the cell membrane in a resting cell (70mv). The inside of a cell has a different (negative charge relative to exterior) than the outside of a cell, that is ready to be stimulated/altered/acted upon.

      Graded Potentials Alter the Resting Potential

      Graded Potentials are transient local changes in the resting potential that may depolarize or hyperpolarize.

      Summation: graded potentials can add up in space or time (accumulative effect of stimulus) that may reach a “trigger point” or threshold, which initiates an  Action Potential (sudden reversal of membrane voltage).

      Action Potentials occur as/when:

      –          Initiated when graded potentials reach a certain threshold/trigger point.

      –          Depolarization when sodium moves into the axon (reverses inside to a positive rather than negative charge). This causes a power surge to travel out and positives are turned to negative, negative to positive.

      –          Repolarization occurs when potassium moves out of the axon which restores the initial polarity.

      Reestablishment of the resting potential is the activity of the sodium potassium pump.

      Action Potentials are All-or-None and Self-Propagating

      Individual neuron threshold sets extent of the stimulus needed. If it achieves threshold, it fires. Once triggered, an action potential is always the same in form and voltage (all-or-none). Action potentials continue to propagate themselves in the next region of the axon, and moves like a wave down the axon (at a constant speed and amplitude).

      The number of action potentials/ unit of time encodes the strength of the stimulus. Stronger stimuli generate more action potentials/unit time. The speed of action potentials are always the same for a particular neuron.  The speed can, however, be different in different neurons based on the size of the cell membrane. In larger diameter axons, action potentials travel at a greater speed.

      Neuroglial Cells

      Neuroglial Cells support and protect axons. They make up 80% of the nervous system (Schwann cells, oligodendrocytes) and nourish, clean (some act like phagocytes to clear debris) from axons. They DO NOT transmit action potentials.

      Schwann cells form myelin sheath on neurons in the PNS. This aids in saving the neuron energy and speeds up the transmission of impulses.  Saltatory conduction (compound that insulates axon) causes a leaping pattern of action potential conduction. They help damaged or severed axons regenerate.

      Oligodendrocytes form myelin sheathes in the CNS. They do not have the same capabilities to help repair damage to axons (this is why once someone sustains spinal cord injury and are paralyzed, they do not regain movement).

      There are various disorders associated with the degeneration of myelin sheaths which causes a slowing of transmission (scattered impulse):

      –          MS (multiple sclerosis): progressive damage to the myelin sheaths in the brain and spinal cord which causes weakness, visual impairment, and incontinence.

      –          ALS (amyotrophine lateral sclerosis): progressive damage to myelin sheaths in motor area of the spinal cord which causes progressive weakening and wasting of skeletal muscle due to lack of muscle stimulation.

      Information is Transferred from Neuron to Target

      The special junction between axon terminus (axon bulb) and target cell (which can be another neuron, muscle cell, or gland) is called a Synapse. Synaptic transmission is the process of transmission of impulses from sending (pre-synaptic neuron) across the synaptic cleft to receiving (post-synaptic) target. This involves the release and diffusion of chemical neurotransmitters.

      Process of Synaptic Transmission: Neurotransmitter Release

      1. Action potential arrives at axon terminus causing calcium to diffuse into axon bulb.
      2. Calcium causes release of neurotransmitter from the vesicle.
      3. Neurotransmitter diffuses across the synaptic deficit.
      4. Neurotransmitter binds to receptor target (post-synaptic) membrane and opens gated channels.
      5. Graded potential results from sodium movement through open channels (ions go through).    

      Neurotransmitter Exert Excitability/Inhibitory Effects

      The response of postsynaptic target cells depends on several factors. First off, the response depends on the type of neurotransmitter, as there are 750 types. Response also depends on type of receptors and type of gated ion channels (the gates allow or don’t allow a particular molecule to pass through).

      Excitatory neurotransmitters depolarize the postsynaptic cell, approaching or exceeding threshold. Inhibitory neurotransmitters hyper-polarize the postsynaptic cell (prevents from receiving charges).

      Postsynaptic Neurons Integrate and Process Information

      Response in postsynaptic cells depends on how many neurons are forming synapses with it and whether the neurons forming synapses with it are excitatory or inhibitory. Convergence occurs when one neuron receives input from many others (spinal cord receives sensation from skin). Divergence occurs when one neuron sends action potentials to multiple other neurons.

      Population Growth and Human Impacts

      Air Pollutants, Atmosphere, and Greenhouse Effects

      Pollutants impair air quality (air pollution) and create many concerns: global warming, destruction of the ozone layer, acid precipitation, and smog production.

      The sun supplies the Earth with abundant energy (especially at the equator) and the atmosphere captures it selectively. 25% of the energy is reflected by clouds and atmospheric gasses; 25% is absorbed by carbon dioxide, water vapor, ozone, methane (and a few other gasses); and 50% of incoming solar radiation (insolation) actually reaches the Earth’s surface.

      The Greenhouse Effect has to do with the second law of thermodynamics= high quality solar energy entering Earth’s atmosphere is re-emitted as lower-quality heat energy. The idea is that energy is not created/destroyed but is transformed. The atmosphere close to Earth (troposphere) is loosely comparative to the glass of a greenhouse because it lets sunlight through but traps heat from radiating back outward. This maintains the heat needed for liquid water on Earth.

      The Greenhouse Effect is responsible from global warming. Human activities have increased levels of carbon dioxide which is a major greenhouse gas through deforestation and usage of fossil fuels. Other examples of Greenhouse gasses include: methane, nitrous oxide, chlorofluorocarbons (CFCs), and halons. The effect is that some areas of the Earth warm and others cool as a result of change in ocean temperatures (which have a major role in climate system).

      CFCs deplete the ozone layer (divided into 2 atmospheric locations troposphere and stratosphere). Pollutants in the troposphere (closest to Earth’s surface) cause respiratory difficulties. The stratosphere is the shield that protects Earth’s surface from UV light. The stratospheric ozone layer has been (and continues to be) depleted by reactions with CFCs. This has created concerns about excess UV radiation and exposure. CFCs come from refrigerants and aerosol sprays, and their use has decreased due to international agreements.

      Smog (smoke+fog) production comes from industry and the burning of fossil fuels. Smog constituents are: nitrogen oxides, hydrocarbons, small oil droplets, wood particles, coal ash, asbestos, lead, animal waste, and dust. This makes for a cocktail of irritants for eyes and the respiratory system. Thermal inversion refers to atmospheric conditions that trap smog and prevent its dispersal as cold air above traps warm air and holds it down close to the Earth’s surface (makes me think of the brown haze I have witnessed in PHX).

      Pollutants Produce Acid Precipitation

      Sulfur dioxide from high sulfur coal and oil (once trapped in the Earth) is released in to the air along with nitrogen oxides from car exhausted. Once the sulfur dioxide and nitrogen oxide mix with water vapor they become sulfuric acid and nitric acid. When the rain comes down the acid precipitation causes damage to the Earth including: corrosion of metal and stone, and the disruption of forest and aquatic ecosystems. This occurs as a result of lowering pH levels of the ecosystems which maintain a delicate balance and can’t tolerate the disturbance. Acid precipitation is on the decline due to pollution abatement measures, but in North America the north east and parts of Canada are most affected.

      Water is Scarce and Unequally Distributed

      Less than 1% of the Earths total water supply is fresh water. Salt water ocean accounts for 97%, and water frozen in glacier and polar ice caps accounts for the remaining 2% (which are melting).

      Industrialized nations use 10-100 times more water than less industrialized countries. It requires more water to make things, and indoor plumbing makes water more accessible. Some desert and semi-desert countries have reached their water supply carrying capacity and must transport water in. When this happens, diversion of water impacts other human populations and species.

      Human Impact on Water Supplies and Water Pollution

      Human beings as a whole use tremendous amount of water, depleting freshwater supplies. Think about the daily activities of laundry, dishes, showers, toilets, drinking, watering your garden, washing your car, not to mention industry and construction demands.

      –          Urbanization increases storm water runoff as the water from roads, parking lots, and buildings rush into streams. The runoff doesn’t allow the water to be absorbed into the ground (and causes erosion) and the aquifer stores don’t have the opportunity to be replenished. Groundwater pollution contaminates drinking water supplies. There is a very slow exchange of the groundwater pool, it “cleans” slowly but cannot filter pollutants out the runoff also prove harmful as it may combine with sewage as overflow. This leads to possible spreading of diseases and poses a health hazard.

      .-          Human activities pollute freshwater with organic and inorganic pollutants. Organic pollutants are a result of sewage and industry, but the inorganic pollutants include: nitrates; phosphate fertilizers; and sulfates from detergents. Nitrates and phosphates wash off fields and in to the ecosystem where they alter the natural balance. Introduction of fertilizer may result in eutrophication which is rapid growth of plant life leading to death of animal life result from excessive inorganic/organic nutrients. This could present itself as an overgrowth of algae that eventually eliminates fish that can no longer breathe.

      –          Toxic pollutants include: polychlorinated biphenyls (PCBs); oil and gasoline; pesticides; herbicides; and heavy metals. These pollutants bring the issue of biological magnification: the concentration of toxic pollutants in the tissues of organisms higher on the food chain. The toxic substances accumulate in the flesh of the animal (think accumulation of mercury in fish). I also remember watching a program about the Eskimo in Alaska who are eating large mammals that contain high levels of heavy metals in their blubber. There are issues with birth defects as the mothers are ingesting the toxic flesh.

      –          Oil is another pollution concern. Sources include: 20% accidents at sea; 30% from runoff of the land; 50% seepage. The percentage for accidents at sea has most likely risen as a result of the 2010 Deepwater Horizon explosion and “spill”. Another unknown percentage comes from cruise liners. The oil pollution causes significant damage to shoreline ecosystems as 25% of the oil spilled at sea ends up in the sediment. The remaining 75% ends up in evaporation (25%) or degraded by bacteria (50%).

      Pollution and Overuse: Damaged Land

      One third of Earths land mass has been altered by human beings. This includes the fact that 50% of the world’s forests have been removed, often times for agriculture. As cities expand productive land is consumed and the urbanization increases water use and runoff issues. Desertificationis the transformation of marginal land into near desert conditions due to over use, making it unusable for future agriculture. Land is also damaged as we use it to bury our garbage in dumps and may be contaminated through war.

      Risk of Human Induced Desertification
      Retrieved from/: on 4/28/12

    2. Its interesting to note that while there are over 80,000 potentially edible plants, human beings only consume aproximately 30 of them which comprise 90% of our caloric intake. Only about 1% of plants have been tested for their medicinal value, yet plant products constitue 50% of medication ingredients.

    Energy: Many Options/Choices

Nonrenewable resources include fossil fuels such as coal, oil, and gas. These products are limited in that there are only so much of these

in the world. Renewable resources include:

  • Nuclear energy- but then there are safety concerns and disposal issues
  • Hydroelectric power- yet the dams used to capture water alter ecosystems
  • Wind farms- but these have created problems for some species of birds/bats
  • Biomass fuels – which have created concern over usage of land (fuel or food) as well as usage of plants for food or for energy
  • Solar energy- utilizing the abundant source of light from the sun to harness energy- yet at the moment aren’t efficient enough to need all the world energy demands

    Retrieved from: on 4/28/12

Human Impacts: Creating a Biodiversity Crisis

Human beings are creating a misbalance in ecosystems all over the world. We are accomplishing this through the various sources of pollution and habit destruction as there is a worldwide shift in people moving into cities. As people destroy habitat there is less plant and animal diversity. Diversity is essential to species surviving natural disasters and increase in global temperature.

Humans also over exploit natural resources, taking and using at a rate that nature can’t keep up with. The land is over farmed, the oceans are overfished which and doesn’t allow enough time for the species to regenerate fast enough to keep up with human demand. There is much exploitation of scarce forest resources as logging and deforestation wipe our forests out. As the forest (specifically referring to South America) is cut down and cattle are introduced, the soil is initially great for grazing, yet the soil is very delicate. Eventually, the soil cannot sustain the cattle and becomes useless as more forest must be cut down to feed the cows (which also accounts for a surprising amount of methane in the atmosphere).

Retrieved from: on 4/28/12

Worldwide, cities create 78% of carbon emissions, 60% of residual water use, and 76% of wood is used for industry. The ecological damage that a city causes is much larger than the size of the city itself.

Biodiversity is Healthy for Humans

There are 895 separate ecological regions on the Earth that human beings benefit from.  Plants (through photosynthesis) recycle carbon dioxide and provide us with oxygen. Plants are also sources of food for us and the animals we eat, in addition to providing humans with medicines. A variety of plant life provides stability to all ecosystems. No matter how much man would like to see himself apart from nature, we depend on the Earth’s animals/plants/ecosystems everyday for the necessities of life. We are a part of the web, not outside of it.

Measuring Sustainability and Quality of Life

Gross Domestic Product (GDP) refers to the total market value of all goods and services produced within a country per year. This is the standard indicator of economic progress. Genuine Product Indicator (GPI) is the measurement of the market value of goods and services PLUS the environmental costs of production (of the goods and services), social costs, and the overall quality of life. This reminds me of a saying I heard recently, “What are we going to tell our kids when we have done so much harm to this Earth.. that it was good for the economy?!”

Retrieved from: on 4/28/12

Toward a Sustainable Future

People must take action if we are to live in harmony with the delicate balance of ecosystems. By exterminating other species life on Earth, we threaten exterminating ourselves in time. Some ideas include:

  • Consume less. Industrialized nations in particular tend to use more than what they need.
  • Recycle more. There are many daily products that can be recycled or reused.
  • Support sustainable agriculture.
  • Support green roofs.
  • Lower worldwide fertility rate- over population is the concern here.
  • Reduce rural world poverty.
  • Conserve energy at home- afterall that’s where it starts- in your own home.
  • Use environmentally preferable products- less garbage, possibly less contamination.
  • Protect ecosystems that provide ecoservices

We only have one beautiful planet. As human beings look forward into the future, I hope people recognize that change must occur if we are to survive on this planet. The Earth has always provided the balance needed for regeneration, it is human beings that have altered and created imbalance through our actions. We must learn to live with the Earth, instead of merely exploiting the resources at will.


Bio 156 Lab: Chicken Leg Dissection


This lab assignment will involve dissecting a chicken leg so that we may recognize and view a three dimensional muscle/bone structure and how they function. This allows experience and physical application in addition to reading from the textbook.

Objective: To utilize a hands-on approach to view, identify, and describe the structure and function of tendons, ligaments, and cartilage; identify muscles and their function; observe bone and its components; gain experience dissecting fresh biological material.


Materials Used

  1. Gather materials necessary for the dissection: one chicken leg quarter; gloves; cutting board; scissors; knife; paper towels; soap.
  2. Put on gloves.
  3. Wash and dry (using paper towel) one chicken leg quarter. Place on cutting board.
  4. Examine the outside skin tissue.
  5. Using scissors and a sharp knife, begin to work slowly and carefully to cut the skin and peel it away from the muscle below. Cut away some of this connective tissue as needed. Work slowly and carefully with scissors and knife until all skin is removed.
  6. Notice the fat, connective tissue, and pink muscle.
  7. Manipulate the tissue to view a white shiny tendon.
  8. Remove a single muscle by cutting the tendons and peeling the muscle away from the bone.
  9. Remove all remaining muscle to expose the bones of the chicken leg.
  10. Operate the leg joint to verify type of movement.
  11. Find any ligaments. Cut the ligaments at the joint between the upper and lower leg. Examine how the bones fit into each other.
  12. Using warm water and soap, thoroughly wash all tools and materials, including your hands and the surface you worked upon.


As I cleaned and placed the chicken leg quarter on the cutting board I took a moment to view the skin tissue. What I observed was a fairly thick skin that was covered in “goose bumps” which still contained a few tiny feathers. The skin was tinted yellow in places where fat was underneath, and pinkish were lean muscle was underneath.

Cutting the skin away from the muscle I observed a thin film that reminded me of saran wrap. This connective tissue adhered to the muscle and skin which required me to tear/cut it away from the muscle. It didn’t seem to me that this connective tissue was found where the fat met the skin. This makes me certain that what I was viewing was fascia as it was clear but strong.

The fat was found in yellowish clumps. It wasn’t marbled throughout the muscle, but was separate or found on the inner edges of the muscles. I found a few small red blood vessels in the fat globs. Fat provides many functions in the body. Phospholipids are an important component of cell membranes. Fat provides warmth (insulation) for the body and is stored in Adipose tissue as an important source of stored energy (triglycerides).

View of muscle and fat; note the "lines" in the muscle

Upon observing the bundles of pink muscle tissue, it is obvious that several individual muscles are present. This is obvious by observing both the shape of the muscles as well as viewing the “lines” or direction of muscle fibers. There are many faint parallel lines in each muscle and some have a slight white series of parallel lines over the surface. This makes a distinct visual of where one muscle ends or runs close to another as the series of lines may be running in an opposite direction.

As I manipulated the chicken to view a tendon, I noticed how white and shiny it appeared. Tendons connect muscle to bone and it was interesting to note how the individual tendon fibers fanned out over the bottom portion of the muscle and then condensed to form a strong white “rope” as it attached to the bone. The tendon was strong but felt more flat than round between my fingers and reminded me of plastic or synthetic (possibly nylon) “rope”.

Tendons join muscle to bone

Skeletal muscles are very large muscles in the body that are attached to the skeleton. Their multi-nucleated cells are arranged in parallel bundles and their primary function is to produce or prevent movement of the body. They are very fast in initiation of contraction by a nerve cell.

As I initially removed a single muscle from the leg bone, and then the subsequent muscles, I was amazed to witness the many tendons present. There were more individual muscles than I had realized and cutting the muscle away from the bone involved severing many tendons.

Various muscles pulled away from bone

Many tendons I had to sever to reveal bone

Next, I operated the leg joint to witness the motion. What I observed was flexion/extension movement. Flexion increases the angle of a joint while extension increases the angle of a joint.

Ligaments are found where two bones come together and connect bone to bone. I found the ligaments between the bones of the chicken’s upper and lower leg and cut the ligaments to view the ends of the bones at the joint.  What I observed was a smooth, white, glassy cartilage that covered the end of the bones. This type of cartilage is called Hyaline Cartilage which creates a smooth and low-friction surface. What I was observing was a hinged synovial joint as it allows movement in one direction as the hinges on a door.

Chicken leg joint after ligament was cut

Osteoarthritis occurs as the cartilage wears away. This happens because joints are exposed to high compressive forces and prone to continual wear caused by friction. Synovial joints are designed with fluid-filled cavities to help with lubrication. Synovial membranes secrete synovial fluid to aid in lubrication and to cushion the joint. Hyaline cartilage covers the ends of the bones in these joints to reduce the friction even further.

If you could look inside the bone you would find many cells and structures. Inside the central cavity you would find yellow bone marrow and blood vessels. Inside spongy bone you would find red bone marrow.  Within the compact bone you would find various cells such as osteons, osteocytes, and osteoblasts. Yellow bone marrow can be used for stored energy while red bone marrow produces red/white blood cells and platelets. Osteoblasts assist in the formation of new bone.

BIO 156 Unit 3 Compilation

Table of Contents

The Skeletal System

–          Bones

–          Types of Bones by Shape

–          Cells Involved in the Development and Maintenance of Bone

–          Mature Bone Remodeling and Repair

–          Cartilage, Ligaments, and Joints

–          Vocabulary Related to Motion

The Muscular System

–          Muscle Structure

–          Nerve Activation/Calcium Initiates the Sliding Filament Mechanism

–          Muscle Relaxation and ATP Energy


–          Red Blood Cells

–          Stem Cells Form Various Specialized Cells

–          Homeostasis and Platelets

–          Antigens, Rh, and Blood Typing Concepts

Blood Vessels

–          Purpose of Circulation

–          The Pulmonary Circuit

–          The Systemic Circuit

The Heart: Layers and Structure                                                                                

–          Reducing the Risk of Cardiovascular Disease

Science in the News

The Immune System

–          Overview

–          Pathogens, Bacteria, Viruses, and Prions

–          Determination of Health Risk

The Lymphatic System Defends the Body

–          The First Line of Defense (Keeping Pathogens Out)

–          The Second Line of Defense: Nonspecific Defenses

–          The Third Line of Defense: Specific Defense Mechanism

–          Immune Memory, Immunity, and Secondary Immune Response

–          Medical Assistance Against Pathogens: Immunizations, Monoclonal Antibodies, and Antibiotics

Inappropriate Immune System Activity: Allergies

–          Autoimmune Disorders

Respiratory System

–          Upper Respiratory Tract

–          Lower Respiratory Tract

–          The Lungs Exchange Gas

–          Breathing and Pressure Gradient

–          Lung Volume/Capacity and Related Terms

–          Gas Exchange/Transport Occur Passively: Partial Pressure

–          External Respiration: Gas Exchange Between Air/Blood

–          Oxygen/Carbon Dioxide Transport

–          Nervous System Regulates Breathing

The skeletal system is comprised of connective tissue: bone, ligaments, and cartilage.

Science in the News


Bones are comprised of a hard inorganic matrix of calcium salts and serve 5 important functions in the human body: support, protection of organs, movement, blood cell formation, and mineral storage for calcium and phosphate. Some bones are compact containing marrow; others are “spongy” which provides less weight while maintaining strength. Bones regenerate and change shape over the course of a lifetime. They contain blood vessels and nerves and will bleed when cut.

Spongy Bone
Retrieved from: on 4/4/12

The human skeleton contains 206 bones which can be divided between the axial skeleton and the appendicular skeleton. The axial skeleton includes the skull, vertebral column (cervical, thoracic, lumbar, sacral, coccyx vertebrae; and discs that cushion and assist with movement and flexibility), 12 pairs of ribs (bottom 2 are “floating” and not attached to cartilage), and the sternum (3 bones fused together referred to as “breast bone”). The appendicular skeleton include the left and right pectoral girdle (shoulder, clavicle, and scapula’s), the left and right pelvic girdle (hip, coaxial bones, sacrum, pubic symphysis), and the limbs (all leg and arm bones).

Types of Bones by Shape

Long Bones: These bones are connected with large movement. They are long and cylindrical with growth heads (epiphyses) at both ends. The epiphyses are covered by articular cartilage.

Short Bones: These bones are associated with smaller and more complex movements. They are almost cubed shaped as in the carpals in the base of the hand or tarsals in the feet.

Flat Bones: These bones protect the internal organs. The skull, ribs, shoulder blades, sternum and pelvic girdle all protect internal organs.

Irregular Bones: These bones are irregular in shape and include the vertebrae (7 cervical, 12 thoracic, 6 lumbar) and some facial bones.

Sesamoid Bones: These are small bones held within tendons and include the knee cap (patella). Cartilage acts as a shock absorber between the femur and patella.

Cells Involved in the Development and Maintenance of Bone

There are several types of cells involved in the development and maintenance of bone. Osteoblasts are young bone-forming cells. Osteocytes are mature bone cells and osteoclasts are cells that can break down bone which releases calcium and phosphates needed for the body. Once the hydroxyapatite (calcium/phosphate) is released, osteoblasts move in to form bones. Bones have an osteon/haversian system which is a concentric circle cellular arrangement (reminds me of tree rings). Haversian canals are called central canals. The periosteum is a connective tissue covering. Chondroblastsare cartilage forming cells that are a precursor to bone development in a fetus.

Mature Bone Remodeling and Repair

Bones change in size, strength, and shape throughout a person’s lifetime. This is dependent on exercise (weight-bearing), diet, and age.  Bone cells are regulated by hormones such as the parathyroid hormone which removes calcium from bone. Calcium is used in the body for muscle contraction, and the hormone ensures availability of the mineral in the blood so the body can perform its needed functions. Calcitonin adds calcium to the bones as needed. Electrical currents can stimulate the bone to change shape due to compression force. The bone will change shape as needed to make up for the downward forces on the bone.

When a bone is broken a hematoma forms first, and then as the break is repaired, it forms a callous ring- shaped formation that is stronger than the rest of the bone. This is why it is unlikely that a bone would break more than once in the same place.

Cartilage, Ligaments, and Joints

There are 3 types of cartilage (fibrocartilage, hyaline, elastic cartilage) all of which serve as support to the skeleton. Ligaments are dense fibrous connective tissue that attach bone to bone. Tendons join bone to muscle. These connective tissues add support and allow various ranges of movements in the body (such as arm and leg movements).

Joints are classified by degree of movement:

Fibrous joint: Immovable joints as found in the plates of the skull (fontanels).

Cartilaginous joint: Slightly movable as in cartilage connection in the backbone.

Synovial joint: Freely movable joints as in knee and shoulder.

Synovial joints are the most flexible in the body. They are comprised of a joint capsule (synovial membrane and hyaline cartilage). The synovial membrane secretes synovial fluid as a lubricant to reduce friction, while hyaline cartilage acts as a cushion as its surface is smooth and shiny. Types of synovial joints include: hinge joint (knee) and ball and socket joint (shoulder).

Vocabulary Related to Motion

Abduction: Movement of a limb away from the body’s midline (outward).

Adduction: Movement of a limb toward the body’s midline (inward).

Rotation: Movement of a body part around its own axis.

Circumduction: Movement of a limb so that it describes a cone.

Extension: Increases the angle of a joint (hyperextension occurs as it is over extended).

Flexion: Decreases the angle of a joint (think of flexing your bicep).

Supination: Rotation of the forearm so palm faces anteriorly (palm faces upward).

Pronation: Rotation of the forearm so palm faces posteriorly (downward).

Flexion decreases the angle of a joint
Retrieved from:

The Muscular System

The primary functions of the muscular system are to produce movement or to generate tension. Muscle contractions result in shortening the distance between bones through action of skeletal muscle or in smaller movements that do not act on bones.

Muscle groups are labeled as synergistic (groups work together) or antagonistic (groups oppose each other). Antagonistic muscles produce opposite movements. A great example is the muscles in the arm. The forearm bends when the biceps contract and the triceps relax. The forearm straightens when the biceps relax and the triceps contract.

Muscles are recognized to have a point of origin and point of insertion. The point of attachment of a muscle to the stationary bone is its point of origin. The point of attachment to the moveable bone is its insertion.

Muscle Structure

Muscles are comprised of myofibrils, muscle fibers, and fascicles. Myofibrils containing the proteins actin and myosin are found in large quantities within the individual muscle cells (fibers). The muscle cells are long and tube shaped, which are multinucleated (arising from fused embryonic cells). The muscle fibers are bundled together in fascicles that are wrapped in a thin connective called fascia. Many, many of these fascicles combine to form the whole muscle which is attached to the bone by a tendon.

The skeletal muscle’s main contractile units are the sarcomeres. Sarcomeres contain myosin (thick filaments) and actin (thin filaments). At magnified views, one may witness a “Z Line” in the surface of the muscle which is the attachment points for sarcomeres. The arrangement of filaments also gives rise to striated appearance on skeletal muscle.

Muscle Structure
Retrieved from: on 4/5/12

Nerve Activation/Calcium Initiate the Sliding Filament Mechanism

To produce muscle movement, there are a series of events that must occur:

  1. A stimulus must occur. Acetylcholine is released form the motor neuron at the neuromuscular joint.
  2. Electrical impulses are transmitted a long T tubules which causes step 3:
  3. Calcium is released from sarcoplasmic reticulum (hold calcium until ready to be released and used).
  4. Calcium binds to troponin.
  5. Troponin becomes tropomyosin complex which shifts position which creates step 6:
  6. Myosin binding site is exposed as a result of the above shift.
  7. Myosin heads form cross-bridges with actin.
  8. Actin filaments are pulled toward center of sarcomere= muscle contraction.

The above steps describe the sliding filament mechanism which is initiated by calcium. Essentially, the contraction results from the formation of cross-bridges between the thick and thin filaments (myosin and actin).

Muscle Relaxation and ATP Energy

As nerve contractions end, the contraction ends. Calcium is then pumped back to the sarcoplasmic reticulum as calcium is removed from the troponin. Myosin binding site is then again covered and myosin heads do not make contact with actin. No calcium= no cross-bridges.

ATP energy is required for both contraction and relaxation. Energy is required to change the shape of the myosin head as the muscle is flexed and to release the head from filaments. Rigomortis occurs as the muscles are “locked” into position because there is no availability of ATP to release the myosin heads.

ATP is replenished by a variety of means: creatine phosphate, stored glycogen (chain of glucose), and aerobic metabolism of glucose, fatty acids, and other high-energy molecules.

Creatine phosphates are proteins containing an extra phosphate. Adenosine triphosphate can be anaerobically generated from adenosine diphosphate.  In the metabolism of creatine phosphate, a phosphate group is donated with creatine kinase acting as a catalyst. The resultant product is creatine and the reaction is reversible.


Blood serves 3 primary functions:

  • Transportation of nutrients, oxygen, wastes, and hormones.
  • Regulation (homeostasis) of temperature, water volume, and pH. The breaking down of molecules generates energy which is converted into heat which is essential to molecule functioning and maintaining their particular shape.
  • Defense against infections and bleeding.

Blood is 45% plasma and 55% formed elements. The plasma is a conglomeration of water, electrolytes (such as calcium and potassium), proteins (globulins, albumins, clotting proteins), hormones, gasses, nutrients, and wastes. The formed elements include: red blood cells (transports oxygen and carbon dioxide), white blood cells (protect from infection), and platelets (aid in clotting).

Red Blood Cells

Red blood cells transport oxygen into the body and carbon dioxide out of the body. Red blood cells contain no nucleus and originate in stem cells of the bone marrow. Their lifespan is approximately 120 days in a human. The cells are composed of 4 heme chains and 4 iron molecules and are shaped in a concaved disc which allows the most beneficial binding for oxygen.

Red blood cell production is controlled by the hormone erythropoietin. This is due to a negative feedback control loop (cells detect amount of oxygen) that maintains homeostasis. The number of cells themselves are not counted, only their effect as a whole as witnessed by the oxygen level. Cells in the kidney monitor the availability of oxygen and secrete erythropoietin  (if levels fall), which is transported in the blood to the red bone marrow where it stimulates the stem cells to produce more red blood cells.

Stem Cells Form Various Specialized Cells

The specialized cells labeled as white blood cells:

Erythroblasts: the nucleus is lost and become red blood cells

Myloblasts: become neutrophils, eosinophils, or basophils

Monoblasts: become monocytes

Lymphoblasts: become lymphocytes

Megakaryoblasts: become megakaryocytes whose fragments become platelets

White blood cells protect the body from infection and regulate the inflammatory reaction. Granular Leukocytes (white blood cells):

Neutrophils are the most abundant white blood cells (60% of circulating WBC) and are also the first to attack intruders. They engulf microorganisms.

Eosinophils account for 2-4% of circulating WBC and defend against large parasites such as worms. They are responsible for moderate severity of allergic reactions.

Basophils only account for .5% of circulating WBC. They release the chemical histamine in response to specific pathogens and play a role in inflammation.

Agranular Leukocytes white blood cells: lymphocytes and monocytes.

Lymphocytes account for 30% of circulating WBC. There are two types: B lymphocytes and T lymphocytes that play a large role in immune response.

Monocytes account for 5% of circulatory WBC and leave the blood to transform into macrophages.

Homeostasis and Platelets

When a blood vessel is penetrated there are 3 stages that occur to stop the bleeding:

  1. Vascular spasm: The blood vessels constrict to reduce blood flow. Chemicals are sent out that attract platelets to the area.
  2. Platelet plug formation: sealing off the ruptured vessel. Platelets are small cell fragments that derive from megakaryocytes. They play an important role in homeostasis as they prevent severe blood loss and in turn heat loss.
  3. Coagulation: formation of blood clot thru a complicated process of reactions involving fibrinogen, where fibrin sticks together with platelets forming a clot which eventually dissolves.


Antigens, Rh, and Blood Typing Concepts

Antigens are molecules or proteins on the outside of a cell that flag to identify “self”.  In blood typing, a person who has type A blood would have the antigen A but antibodies for B blood. A person who has type B blood would have B antigens, and would then have antibodies against type A. Type O blood carry no antigens but have antibodies to A and B. AB blood contain both antigens, therefore no antibodies. Antibodies are immune system proteins that are directed against antigens and attack foreign cells not flagged as “self”. As a result, if one needed a blood transfusion and received an incompatible blood type, the results could be fatal. Antibodies could attack and clump the cells together forming “clots” and restricting blood flow.

Another genetic condition to consider is a person’s Rh factor. A positive Rh factor represents antibodies to Rh factor; a negative Rh requires that both alleles are negative for Rh.  This is important to know for women who become pregnant. If a woman who is Rh negative becomes pregnant with a fetus that is Rh positive (from father), the woman’s body could recognize the fetus as “not self” and attack the baby. A small amount of fetal blood comes into contact with the mother’s blood (typically at child birth). The first baby would be out of the womb before the mother’s body had time to detect and inflict harm on the baby, but with any future pregnancies there would be risk. If the mother’s body detected in an Rh positive future pregnancy, it would attack the baby as “foreign”.

Blood Vessels

There are 3 types of blood vessels that transport blood:

–          Arteries carry oxygenated blood AWAY from the heart under high pressure. They are structured in 3 thick walled layers. The endothelium is the innermost layer. The middle layer consists of smooth muscle, and the outer layer is comprised of connective tissue.

  • Arterioles are the smallest arteries.

–          Capillaries are the smallest blood vessels and serve as points of exchange between solutes and water within the cells of the body. The walls are only once cell layer thick, which makes for an extremely thin and porous wall. This makes the wall “leaky” where fluids can squeeze out between cells and gasses can exchange.

  • Capillary beds are extensive networks of capillaries that provide oxygen and remove carbon dioxide from cells as well as nutrients and raw materials. This allows for exchange of substances with the interstitial fluid.
  • Precapillary sphincters control blood flow into the capillaries.
  • Vasodilation increases blood flow to capillaries.
  • Vasoconstriction decreases blood flow to capillaries

–          Veins return the deoxygenated body up toward the heart. While the veins also have 3 layered walls, they are thin and stretchy with a larger lumen (opening) than arteries. They can distend and serve as blood volume reservoirs.

  • Mechanisms to assist in venous return to the heart include: contraction of skeletal muscles, especially in the legs; one way valves keep blood from moving backward (down); and pressure change associated with breathing acts as a syphon.

Note: varicose veins occur because the leaflets of the valves no longer meet properly and valves don’t work. This allows blood to flow backward and pool in veins, which enlargens them.

Retrieved from: http://www.abacom./dia/exphys/six.html on 4/5/12

Blood flow> heart> arteries> arterioles> capillaries> venules> veins> heart

Purpose of Circulation

The circulatory system distributes materials to the cells and organs. These materials include: heat, water, oxygen, carbon dioxide, immune system related cells, nutrients, hormones, and wastes. The pulmonary and systemic circuits serve these purposes.

 The Pulmonary Circuit                                   

The pulmonary circuit is the cycle of oxygenating the blood. It begins as the deoxygenated blood from the body travels thru the vena cava to the right atrium. It moves thru the right atrial ventricular valve to the right ventricle. Next it moves thru the pulmonary semilunar valve to the pulmonary trunk and lungs. Blood is then oxygenated within pulmonary capillaries. The oxygenated blood travels thru the pulmonary veins to the left atrium, then thru the left atrial ventricular valve to the left ventricle.

The Pulmonary Circuit
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The Systemic Circuit

The systemic circuit delivers oxygenated blood to tissues.  Oxygenated blood travels from the left ventricle thru the aortic semilunar valve to the aorta. It travels through the branching arteries and arterioles to tissues, through the arterioles to capillaries. From the capillaries it moves into verules and veins and then to the vena cava and into the right atrium.

The Heart: Layers and Structure

The heart is an organ comprised mostly of cardiac muscle.  The inner layer (endocardium) is made of epithelial tissue. The middle layer (myocardium) is a thick layer of cardiac muscle, and the outer layer (epicardium) is made of a thin layer of epithelial and connective fat tissue, and nervous tissue that functions to regulate the heartbeat (not initiate it, but maintain it). The heart is surrounded by a fibrous sac called the pericardium.

The heart has 4 chambers: 2 atria and 2 ventricles. There are 4 valves that prevent backflow: tricuspid and bicuspid/mitral (atrioventricular valves) and pulmonary and aortic (semilunar valves).

Reducing the Risk of Cardiovascular Disease

There are many steps a person can take to reduce the risk of developing cardiovascular disease. One of the most important is not smoking. Monitoring cholesterol levels (blood lipids) is recommended. Engaging in regular and moderate exercise is very beneficial to the cardiovascular system, as well as the entire body. People who have hypertension need to treat it. Maintaining a healthy weight is beneficial as being overweight increases the risk of heart attack and stroke. Controlling diabetes is essential because early diagnosis and treatment can delay the onset of related problems. Although it may be difficult in our busy lifestyles, it is suggested that people avoid chronic stress.

Science in the News

Science Daily (March 26, 2012)

New research has found that a sharp rise in blood pressure in mid-life can increase a person’s risk of heart disease in later life. The study also found that blood pressure medications don’t fully reverse heart damage from high blood pressure. This suggests that early detection and treatment of rapidly rising blood pressure in midlife (as opposed to the current wait-and-see method) may be necessary to prevent long term damage to the heart. People with pre-hypertensive blood pressures of 120 or higher (systolic) or 80 or higher (diastolic) in their thirties should monitor their blood pressure to watch for any rapid elevation.

The Immune System


The human body has several defense mechanisms to ward off pathogens (agents that cause disease):

  1. There are barriers such as the skin, stomach acid, and tears that make entry of pathogens difficult.
  2. There are nonspecific defense mechanisms such as phagocytosis (inflammation) to ward off invaders.
  3. If the invader does manage to get through the first two barriers, then we can count on a third line of defense: specific defense mechanisms such as the immune system response. This involves antibodies and T cells that specifically seek out and destroy the intruder.

Pathogenscan fall into many categories since the term refers to a broad scope of agents that cause disease. Pathogens that are living organisms include: bacteria, fungi, and parasites. Pathogens may also be non-living infectious “particles” such as viruses and prions.


Bacteria are unicellular (single celled) prokaryotes. They have developed to use a variety of resources for growth and reproduction. Antibiotics are given to treat bacterial infections such as: pneumonia, tonsillitis, tuberculosis, botulism, and syphilis.


Viruses are tiny infectious agents that seem to be non-living particles. There are no signs of metabolic activity and they are unable to reproduce outside of the host cell. Once they are within the cell, they take it over and use the host cells “hardware” to manufacture move viruses. Without the host cell, there are no observable signs of life. Viruses contain DNA OR RNA in nucleic acid that is surrounded by a protein coat. Some diseases caused by viruses are: AIDS, hepatitis, encephalitis, rabies, flu, colds, and warts (antibiotics don’t work on viruses).


Prions are infectious agents that originate in our own bodies. Prions are normal brain proteins that are not folded correctly. The misfolding induces other proteins to misfold in a domino effect. Once this has occurred enough times, they fill and disable the nerve cells with protein debris and block nerve transmissions killing nerve cells. Unfortunately, they resist cooking, freezing, and drying. Diseases associated with prions are: Mad Cow Disease and Creutzfeldt – Jakob disease.

Prion misfolding
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Determination of Health Risk

-Transmissibility: How easy a pathogen is passed from person to person?

-Mode of transmission: How it is passed (airborne, fecal-oral, body fluids).

-Virulence: How much damage the pathogen causes by infection.

The Lymphatic System Defends the Body

The lymphatic system could be considered “the other circulating system”. It functions to maintain blood volume in the cardiovascular system, filters foreign material to defend against infection, and transports fats and fat-soluble material from the digestive system. The lymphatic system comprises the lymphatic vessels (transports lymph), lymph nodes (cleanses the lymph), spleen (cleanses the blood), thymus gland (maturation of T lymphocytes), and the tonsils and adenoids (protect the throat).

The First Line of Defense (Keeping Pathogens Out)

The human body has many defense mechanisms to keep pathogens out. Skin is an effective deterrent as it serves as a barrier and provides acidic secretions. Tears and saliva contain antibacterial enzymes called lysozymes. Earwax entraps microorganisms in the ears while mucus entraps microorganisms in the nose. The stomach is extremely acidic which inhibits microorganisms (that we have ingested) from growing. The vagina also has a slightly acidic quality which inhibits some microorganisms. Urination, defecation, and vomiting are other ways microorganisms are removed/released from the body.

While the body works to keep invaders out, the human body contains various “resident bacteria” These bacteria live with us and in us. They may produce vitamin B and vitamin K or just serve to out-compete other dangerous pathogens.

The Second Line of Defense: Nonspecific Defenses

The second line of defense is produced by the body thru defensive mechanisms that develop INSIDE the body without singling out a specific pathogen:

Phagocytic cells: Neutrophils and macrophages are white blood cells that surround, engulf, and digest foreign cells. They do this by engulfing the foreign cell and surrounding it in a vesicle while bombarding it with enzymes that create holes in the cell wall. This causes the cell to burst as water and salts rush in. Eosinophils are white blood cells that bombard large parasites with digestive enzymes.

Inflammation: Inflammation can be witnessed as redness, warmth, and swelling to the infected/injured area and may be accompanied by pain. The redness and swelling occur as more blood rushes to the area providing nutrients and healing agents as well as additional fluid to wash the pathogens away. The rise in temperature creates an environment that is less suitable for bacteria growth and the pain is felt as chemicals are released by cells dying and a signal for other cells to come in to the area.

Natural Killer Cells: These cells are a type of lymphocyte that attack virus-infected cells and tumor cells by releasing chemicals that disintegrate the cell membrane.

Compliment System: This is comprised of a group of proteins that assist other defense mechanisms. They may kill pathogens or enhance inflammation or phagocytosis.

Interferon’s: Antiviral proteins that interfere with viral reproduction.

The Third Line of Defense: Specific Defense Mechanism

The third line of defense is also known as the immune system.  The immune system recognizes and targets specific foreign substances and pathogens. It has a “memory” which “remembers” previous exposure and responds more aggressively and quickly on subsequent exposures. The immune system is able to distinguish between healthy cells and tumor (abnormal) cells as well as “self” cells and foreign cells.

  • The Immune Response Targets Antigens

Antigensare any substances that trigger an immune response but are usually a protein or polysaccharide (sometimes a combination of the 2) on the outer surface of an invading cell or virus.

The immune system is able to distinguish “self” from “nonself” by recognition of MHC (major histocompatibility complex) proteins.  These proteins are self-antigens that are on human cell surfaces.  (Example: A non-self RBC blood type antigen would elicit an immune response from our body)

  • Lymphocytes Are Central to Specific Defenses

B Lymphocytes:  provide antibody-mediated immunity that is active against bacteria, viruses, and soluble foreign molecules (such as protein from pollen) in blood and lymph. Antibodies are proteins that bind with and neutralize specific antigens and are specifically made by B Lymphocytes.

B cells originate from stem cells in bone marrow and mature there. They are activated only when they recognize an antigen, they “dock” with the antigen and that is what actually activates them. After this occurs they rapidly divide into 2 cell types: memory cells store information for future immune responses or plasma cells that actively secrete antibodies which eventually destroy the invader.

–          5 Specific Classes of Antibodies (also known as immunoglobulin’s ):

–          IgG = Antibodies that are most prevalent in the blood.

–          IgM= These are the first antibodies produced in an immune response.

–          IgA= Antibodies that are found in body secretions, including breast milk.

–          IgD= The function of these antibodies are as of yet unclear.

–          IgE= These antibodies play a pivotal role in allergic reactions.

T Lymphocytes: provide cell-mediated immunity by directly attacking foreign cells or coordinating the immune response from other cells. This type of immunity protects against parasites, fungi, viruses, intracellular fungi, cells with “non-self” MHC, and cancer cells. T cells can target and kill infected cells before they have a chance to release new viruses/bacteria into the blood.

T cells originate from stem cells in the bone marrow but mature (learn to distinguish cells as being self or non-self) in the thymus (hence “t” cell). T cells cannot recognize whole antigens, only small fragments of them. They must be presented with antigen in a form they can recognize by antigen-producing cells (APC’s) such as macrophages and B cells.

–          Types of T cells:

–          CD4 T cells become Helper T and Memory T cells. Helper T cells secrete cytokines, which stimulate other immune system cells. They play a role in directing immune responses and are a target of HIV infection. Memory T cells are reactive during later exposures.

–          CD8 T cells become Cytotoxic T cells and Suppressor T cells. Cytotoxic T cells directly attack ad destroy abnormal cells (tumor or viral-infected) and foreign cells. They accomplish this by: 1. Attaching to the antigen or MHC complex, 2. Inserting perforin causing the cell to burst by creating a pore in the cell membrane, and 3. Inserting granzyme into the cell to poison it and ensure the target cell dies. Suppressor cells suppress immune response to moderate it in such a way as to avoid harming the self as a whole.

–          Clonal Expansion:

The foreign antigen-MHC complex on the surface of an antigen-presenting cell is scanned by the millions of T cells present in the lymph node. If the T cell is able to bind to the complex, this triggers activation and begins a number of mitotic cell divisions. This process is referred to as clonal expansion and provides a significant increase of the number of T cells that recognize the antigen.

Immune Memory, Immunity, and Secondary Immune Response

The primary immune response occurs on the first exposure to a particular antigen. This creates a lag time of 3-6 days for antibody production and peaks at around 10-12 days after initial exposure. Immune memory is what actually creates immunity. The secondary immune response occurs on the second and subsequent exposures/encounters to a particular antigen. It is the history of infection the immune system can remember and respond to. Secondary immune response is characterized by lag time of mere hours and peaks within days.

Medical Assistance Against Pathogens: Immunization, Monoclonal Antibodies, and Antibiotics

Immunizations are utilized as a strategy for causing the body to develop immunity to a specific pathogen.

Active immunization: This strategy intentionally exposes an individual to a form of the antigen that doesn’t produce disease but does activate cells to produce antibodies. It may utilize the protein coat of a virus, for example. (This is known as vaccination)

Passive immunization: Instead of administering a form of the antigen itself, the protective antibodies are administered to an individual.

Monoclonal antibodies are produced in a lab. These antibodies attach to a cell or virus and are used in commercial applications as well. Home pregnancy tests work utilizing these antibodies to bind with human chorionic gonadotropin hormone as well as an indicator (such as a dye). The antibody will only bind to HCG; other hormones will not give a positive test result. The same technology is used in prostate cancer screening tests and diagnostic testing for hepatitis, influenza, and HIV.

Antibiotics are used to kill or inhibit growth of bacteria and are not effective against viruses. Bacteria cells are different than eukaryotic cells (such as in the construction of their cell wall). The antibiotics selectively target these features to kill bacteria.

Inappropriate Immune System Activity: Allergies

Allergies are hypersensitivity reactions which are an inappropriate response to an allergen. Allergens can be any substances (antigens) that cause an allergic reaction. The body reacts as though the allergen is a pathogen, but it not. Allergens may be: foods, pollen, bee venom, etc…

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The excessive inflammatory response is mediated by Ige which sends out the alert to basophils and mast cells which proliferate. Histamine is released in an attempt to eliminate the allergen and causes the “itchy” sensation. These types of reactions may be localized to a particular area or systematic. Localize reactions affect only the area that is exposed to the allergen while systematic reactions affect several organ systems. Anaphylactic shock may occur in severe systematic reactions which may prove life-threatening. This sort of reaction may cause the patient difficulty in breathing, circulatory collapse, and drop in blood pressure.

Allergies may be treated with antihistamines for mild or moderate symptoms and epinephrine injections for people experiencing anaphylactic shock. Epinephrine works by constricting the blood vessels and redirecting the blood to essential organs such as the heart and brain. This effect also counteracts the swelling that commonly occurs as a result of the allergic reaction. Epinephrine dilates the air passages making breathing easier.

Autoimmune Disorders

These types of disorders are characterized by the immune systems inability to distinguish “self” from “nonself”. Essentially, the body attacks itself. Autoantibodies and cytotoxic T cells target the body’s own tissues. Some examples include: Lupus (inflamed connective tissue) and rheumatoid arthritis (inflamed synovial tissue).

Respiratory System

Respiration takes place throughout the body as ventilation moves air in and out of the lungs. External respiration involves gas exchange between air and blood in the lungs. Internal respiration involves the gas exchange between blood and tissues. Cellular respiration involves oxygen use to produce ATP and produces carbon dioxide as a waste product.

The respiratory system consists of upper and lower tracts:

Upper: nose, nasal passages, and pharynx

Lower: larynx, trachea, bronchi and bronchioles, lungs and alveoli

Upper Respiratory Tract

The upper respiratory tract serves as a passageway for respiration from the outside. It has receptors for smell and filters larger foreign material from in-coming air. Inhaled microorganisms are entrapped in mucus. The nasal passages moisten and warm incoming air and contain resonating chambers for voice.

Lower Respiratory Tract

The larynx serves main functions: it maintains an open airway; assists in sound production; and routes food and air appropriately so no food may enter the trachea. The larynx includes the epiglottis, vocal cords, and glottis (opening).

The trachea transports air to and from the lungs through its cartilagous rings. Bronchi branch into the lungs which transport air to alveoli for gas exchange. The lungs are made of connective tissue, bronchi, and alveoli and are attached to the diaphragm by a double membrane.

Besides mucus, the respiratory tract also has other specific defenses to keep microorganisms out. Cilia sweep and push mucus and microorganisms up and out of the respiratory tract. The cough reflex serves the same purpose. If a person smokes, they will eventually damage the cilium which in turn impairs this defense mechanism and may result in a “smoker’s cough”.

The Lungs Exchange Gas

The lungs are located within the thoracic cavity and are surrounded by pleural membranes. The two layers are connected by thin layers of water that create a surface tension. Within the lungs, bronchioles terminate in clusters of alveoli. Alveoli are tiny air-filled sacs with a super thin membrane, where gas exchange occurs. Pulmonary capillaries in alveolar walls bring blood and air into close contact (only 1-2 cells separate blood from air in alveolus). Gases (oxygen and carbon dioxide) are exchanged thru a concentration gradient (oxygen moves to areas of lower concentration). The left lung is comprised of 2 lobes and right lung is comprised of 3.

Breathing and Pressure Gradient

The process of breathing (inhalation/expiration) involves a pressure gradient. In the relaxed state, the diaphragm and intercostal muscles relax. On inhalation the diaphragm contracts, pulling muscles down while the intercostal muscles contract. This elevates the chest wall and expands the volume of the chest, lowering pressure in the lungs which pulls air inward.

On expiration, the muscles relax and the diaphragm resumes its dome shape. The intercostal muscles allow the chest to lower resulting in an increase of pressure in the chest and expulsion of air. The lungs stay “attached” to the chest because of 2 thin sheets of membranes and water that provides a surface tension. This allows the lungs to expand with the chest.

Lung Volume/Capacity and Related Terms

Tidal Volume: The volume of air inhaled and exhaled in a single normal breath.

Dead space Volume: The volume of air that remains in the airways and doesn’t participate in gas exchange.

Vital Capacity: The maximal volume that can be exhaled after maximal inhalation.

Inspiratory Reserve Volume: The volume of air that can be inhaled beyond the tidal volume.

Expiratory Reserve Volume: The volume of air that can be forcibly exhaled beyond the tidal volume.

Residual Volume: The volume of air remaining in the lungs, even after a forceful maximal expiration.

Gas Exchange/Transport Occur Passively: Partial Pressure

Partial pressure is the pressure exerted by one particular gas in a mixture of gases. Partial pressure of a gas is proportional to its percentage of the total gas composition. A gas always diffuses down its partial pressure gradient. It moves from higher to a lower partial pressure.

External Respiration: Gas Exchange Between Air/Blood

Oxygen diffuses from alveoli into blood (down its partial pressure gradient). Carbon dioxide diffuses from blood into alveoli down its partial pressure gradient. Oxygen diffuses down the pressure gradient from capillaries into interstitial fluid, and then into cells. Carbon dioxide diffused down its pressure gradient from cells to interstitial fluid and then into the capillaries.

Oxygen/Carbon Dioxide Transport

Hemoglobin in red blood cells carries 98% of oxygen in blood. Hemoglobin + Oxygen = Oxyhemoglobin. Only 2% of oxygen is dissolved in to the plasma.

Most carbon dioxide is transported in plasma bicarbonate. 70% of carbon dioxide is converted to and transported in the plasma as bicarbonate. Here it is used as a buffer which absorbs and releases hydrogen to moderate pH levels. 10% of carbon dioxide is dissolved in plasma and 20% binds to hemoglobin for transport.

Nervous System Regulates Breathing

The respiratory center is located in the medulla oblongata. This is where the basic breathing pattern is established (unconscious breathing). Neurons in the medulla generate impulses every 4-5 seconds that stimulate the intercostal muscles and diaphragm to contract/relax.

Chemical receptors monitor oxygen, carbon dioxide, and hydrogen levels (build-up of cell metabolism products). Receptors monitor hydrogen ions in cerebrospinal fluid and receptors in the medulla oblongata monitor carbon dioxide levels directly. An increase in partial pressure of oxygen in arterial blood will cause an increase in hydrogen in cerebrospinal fluid, which will signal the medulla oblongata to increase the respiratory rate.

The aortic and carotid bodies monitor partial pressure of oxygen. They become activated if the pressure falls by at least 20% and will increase rate of depth of breathing in response to sufficiently reduce arterial partial pressure of oxygen. The rate and depth of normal breathing is determined by the need to get rid of carbon dioxide rather than the need to obtain oxygen.

Conscious control of breathing resides in the cerebral cortex. People are able to modify breath to speak and sing, but are unable to hold their breath for a prolonged length of time. The automatic controls in the medulla oblongata will override our conscious effort.

Science in the News

Science Daily (April 5, 2012)

Harvard stem cell researchers have taken the next critical step in cystic fibrosis research which could lead to a drug that controls the disease. Researchers have successfully created induced pluripotent stem cells (iPS) and used them to create human disease-specific functioning lung epithelium (the tissue lining airways). Cystic Fibrosis claims about 500 lives per year in the US, and cause irreversible lung disease and respiratory failure.

With this new ability comes the possibility of producing actual cells to utilize for drug screening. This is the first time actual patients cells could be used as the target. While this isn’t a cure for the disease, this has the significant opportunity to lead to the creation of a drug that hits the major complication of the disease. This concept seems to be a near future reality that could develop useful drugs within the next several years.

BIO 156 Unit 2 Compilation

Cell Reproduction and Differentiation
– Mitotic Cell Cycle
– Interphase
– Prophase
– Metaphase
– Anaphase
– Telophase
– Cytokinesis
Meiotic Cell Division
– Prophase 1
– Metaphase 1
– Anaphase 1
– Telophase and Cytokinesis
– Sex Differences in Meiosis

Science In The News

The Cell Cycle Creates New Cells
– Replication, Transcription, and Translation: An Overview
– Process of Replication
• Mutations
– Transportation: Converting Gene’s Code Into mRNA
• Genetic Code
• Codon “Punctuation”
– Translation: Making a Protein from RNA
– Normal Cells and Regulatory Mechanism
The Cell Cycle and Cancer
– Cancer Terminology
– How Cancer Develops
Genetics Terminology
Gregor Mendel Developed Basic Rules of Inheritance
– The Law of Segregation
– The Law of Independent Assortment
Traits Can Be Inherited Many Ways
– Maternal Inheritance
– Incomplete Dominance
– Co-Dominance
– Sickle-Cell Gene
– Polygenic Inheritance
– Sex-Linked Inheritance: X and Y Chromosomes Carry Different Genes

Chromosomes May Be Altered in Number

Chromosomes May Be Altered in Structure

Inherited Genetic Disorders

Genes and Behavior
DNA Technology and Genetic Engineering
– Recombinant DNA Technology
– Cloning DNA Fragments
– Identifying the Source of DNA
– Transgenic Organisms
• Transgenic Concerns
– Gene Therapy and Hope for the Future
• Vectors Transfer Genes to Human Cells
• Gene Therapy Success

Science In The News

Cell Reproduction and Differentiation (one become two)

There are 2 kinds of cell reproduction processes in Humans. These are the mitotic cell cycle which generates new diploid cells (containing chromosomes in pairs), and meiotic cell division which generates haploid gametes (containing chromosomes not in pairs).

All cells in the body divide by mitosis except for the cells that form sperm and eggs which are present in the ovaries and testes. All body cells other than the sperm and egg have 46 chromosomes. Gametes (sperm, egg) are haploid cells that only contain 23 chromosomes. The reduction in chromosome number from diploid to haploid cell is accomplished by meiosis, a special cell division process that occurs in ovaries and testes.

Mitotic cell cycle

The mitotic cell cycle produces daughter cells that are identical to the parent cell. This is accomplished through mitosis (nuclear division) where the DNA is duplicated and distributed between 2 daughter nuclei which results in the nucleus dividing. This is then followed by cytokinesis (cytoplasmic division) which creates 2 new daughter cells. This is accomplished through a series of 6 phases: interphase (long period of synthesis), prophase, metaphase, anaphase, telophase, and cytokinesis. The complete cell cycle takes 18-24 hours to complete, however, mitosis and cytokinesis takes less than one hour of the cycle. It is also interesting to note that some cells enter a non-dividing state, either temporarily or permanently (neurons, osteocytes after adolescence).


This is the longest period where growth and synthesis occur. In the G1 phase small cell actively grows to become large. Then S phase is where DNA synthesis occurs. G2 phase allows continued growth and synthesis of larger enzymes.


In this phase the mitotic spindle is formed out of microtubules in the cytoskeleton. The duplicated DNA and proteins are moved to the “right place” as centrioles migrate to cell poles. Chromatin condenses (coils up) into visible chromosomes and the nuclear membrane dissolves. At this point metabolic activity decreases and no proteins are made as the concentration then becomes on dividing.


At this point, the duplicate chromosomes form a single line at the equator (center) between centriole poles.


The duplicate chromosomes separate and “pop apart” at the centromere. This happens as daughter chromosomes are pulled toward poles by the microtubules (spindle).


The mitotic spindle disintegrates and the process is essentially the reverse of prophase. The nuclear membrane reforms and the chromosomes uncoil, reverting back to chromatin.


A contractile ring of filaments forms at the midsection of the cell (almost like a drawstring) and tightens, forming a cleave furrow. 2 Daughter cells are formed as the contractile ring pinches them apart resulting in 2 identical daughter cells (diploid).

Meiotic Cell Division (Preparing for sexual reproduction)

Meiotic cell division includes 2 successive cell division processes: Meiosis 1 (prophase 1, metaphase 1, anaphase 1, telophase 1, and cytokinesis) and Meiosis 2 (prophase 2, metaphase 2, anaphase 2, telophase 2, and cytokinesis). Meiosis reduces chromosome number by half (23) resulting in haploid daughter cells.

Prophase 1:

Duplicated homologous chromosomes pair up and swap segments in synapse (crossing over), resulting in the chromosomes being reshuffled.

Metaphase 1:

The homologous pairs of chromosomes line up forming a double line of chromosome pairs. (none of the haploid daughter cells are exactly alike).

Anaphase 1:

Pairs of chromosomes are separated, but duplicated chromosomes stay intact.

Telophase and cytokinesis:

This marks the end of meiosis 1. 2 haploid daughter cells are created, but chromosomes are still in duplicated state (2 arms, 2 legs).

  • Both of the 2 daughter cells from meiosis 1 go through meiosis 2, a similar process: prophase 2, metaphase 2, and anaphase 2 (where duplicated chromosomes separate), and telophase/cytokinesis (nuclei have the haploid chromosome number). This results in the creation of 4 haploid daughter cells.
  • Sex Differences in Meiosis

    For males, 4 sperm are produced from each cell entering meiosis. All sperm are viable and functional, but sperm aren’t regularly produced until puberty.

    In females, unequal cytokinesis occurs during meiosis 1 and 2. Only one egg with a lot of cytoplasm is produced, along with 3 polar bodies, from each cell entering meiosis. So, only one egg is viable and the remaining 3 polar bodies are reabsorbed into the body. Females are born with a certain amount of eggs, but they are released starting at puberty with the most mature egg being released first.

    Sexual reproduction may increase success of species by adding variation to the population. Since genes from 2 separate individuals are combined, this may result in resilience to a specific population and perhaps reduce susceptibility to a specific disease.

  • Science In The News
  • from Science Daily (Feb.16 2012)
  • New research has found the (TFF3) protein found in normal breast tissue to possibly contribute to breast cancer metastasis. This protein helps maintain integrity and protects breast tissue. On the flip side, with loss of tumor cell differentiation, its it functions to promote the development and infiltration of tumors and lymph node metastasis. “A positive association between the protein expression and microvessell density suggesting that it stimulates angiogenesis in breast tumors.” While the findings require further evaluation, this protein has the potential of being a biomarker of specific metastasis and a predictive marker of response to therapy.
  • The Cell Cycle Creates New Cells         Interphase is the long growth period between all divisions and can be divided into 3 sub phases. G1 (gap 1) is the primary growth phase (very active growth). S (synthesis) is the phase of synthesis of DNA for next cell division. G2 (gap 2) is the final growth phase before cell division.

  • Replication, Transcription, and Translation: An OverviewHuman DNA is organized in 46 separate chromosomes. DNA replication is the process of coping DNA prior to cell division. This involves making exact copies of all 46 chromosomes. Genes are short segments of DNA that contains the code or recipe for a specific protein. Genes are the smallest functional unit of DNA.Transcription is the process of copying DNA of a gene into mRNA (messenger ribonucleic acid). Transcription occurs within the cell of the nucleus and converts the double DNA strand to a single strand of mRNA.Translation is the process of converting the mRNA template into 1 or more proteins. This occurs in the cytoplasm at ribosomes.
  • Process of ReplicationDNA strands uncoil and “unzip” which involves many enzymes “unzipping” at the hydrogen bonds. Each single strand serves as a template for the creation of a new complimentary strand. DNA nucleotides are positioned and linked by DNA polymerase (enzyme). Precise base-pairing (A-T, C-G) assures that an exact copy is made. Centromeres hold duplicate daughter chromosomes (sister chromatids) together.
  • Mutations

    Mutations are alterations or “mistakes” in the DNA code and occur most frequently during DNA replication. There are chemical and physical forces that can cause a mutation. Some mutations are “silent” and seem to have no effect. Many mutations are harmful and may result in cell death or cancer. There are instances where a mutation may be beneficial, such as an advanced response to the environment. Repair enzymes may repair some mutations.

    Transcription: Converting Gene’s Code Into mRNA

    DNA within the region of a gene unwinds. RNA polymerase (enzyme) assists in copying the base sequence in RNA nucleotides. The primary transcript is folded many times and is made into introns (intervening sequences) and exons. Introns are edited out and removed by enzymes. Exons, which carry the genetic info, are spliced appropriately. The messenger RNA is then produced.

  • Genetic CodeIn the nucleus of each cell is a reference library, the DNA molecule. The reference information stays in the library, but the information contained in them can be copied and carried outside by the RNA. The “books” in the library are written in a language called “the genetic code” which is a sequence of nucleotide bases. The genetic code is written in 3 letter words, each 3 base word gives instructions for 1 amino acid. Each of these words makes sentences with certain meanings (amino acids build into polypeptides) and may mature into proteins. Redundancy of the genetic code means that there are 64 different codons (3 units) but only 20 different amino acids. This means that several different codons encode each amino acid with the exception of methionine(AUG), which is the “start” codon.Codon “Punctuation”The “start” codon always begins with (AUG) in the genes of RNA. DNA is started with (TAC). The “stop” codon is one of the 3: (UAA), (UAG), (UGA).

  • Translation: Making a Protein from RNAComponents: Messenger RNA (mRNA) which is essentially the copy of the recipe. Transfer RNA (tRNA) which is a relatively small RNA molecule that escorts amino acids to the ribosome (site of translation).Ribosomes are made of ribosomal RNA (rRNA) and protein. They contain sites for mRNA and incoming amino acid tRNA. Ribosomes provide structural support for a protein and contain the enzyme/factors that catalyze the peptide bond formation.The translation process begins with initiation. Initiator tRNA (carrying methionine) starts codon on mRNA and ribosomal subunits form an initiation complex. Elongation occurs as tRNA brings specific amino acids to the developing protein chain. The chain elongates one amino acid at a time. Termination occurs as the stop codon terminates the developing chain and the protein is released from the ribosome. (polypeptide isn’t protein until further processed)Normal Cells and Regulatory MechanismsNormal cells have regulatory mechanisms that maintain an appropriate rate of cell division. A cell has an internal “clock” which is a schedule that manages when proteins are released and regulates size. There are hormones as well as inhibiting signals from nearby cells (when a cell bumps into another cell)and various check-points that are all in place to help regulate cell division. In general, cells remain in one location throughout their entire lifespan.

    Internal cell cycle signals are signals that come from inside a cell. Cyclins are present only during certain stages of the cell cycle and are destroyed at the appropriate time. This is necessary for normal cell cycle progression.

    There are also external cell cycle signals. Epidermal Growth Factor (EGF) stimulates skin near an injury to finish cell cycle and repair the injury. Another example is the hormone estrogen stimulating the lining of the uterus to divide and prepare for egg implantation. Cells also stop dividing when they touch (contact-inhibitor). Cells divide about 70 times in culture and die due to shortening of telomeres. (Telomeres are a repeating DNA sequence at the end of a chromosome).

  • Apoptosis is a programmed cell death and is unleashed by internal or external signals. This process helps keep numbers of cells at appropriate levels and is balanced with cell reproduction. The remaining cell fragments are engulfed by white blood cells which recycle the materials. Apoptosis is a normal part of growth and development.Cell Cycle and CancerThe cell cycle is regulated by signals that inhibit or promote the cell cycle. Cancer may result from an imbalance due to a mutation in the DNA of the cell. Cancer is a disease of the cell cycle in which cellular reproduction occurs repeatedly without end. Cancers are classified by location:
    • Carcinoma: cancer of epithelial tissues lining organs.
    • Sarcoma: cancer arising in muscle or connective tissue.
    • Leukemia: cancer of the blood (connective tissue).

    • There are many characteristics of cancer cells.  First, they lack differentiation and do not contribute to bodily function, but interfere with function. They may be immortal and divide repeatedly (rather than the norm up to 70 times). They have abnormal nuclei with an abnormal number of chromosomes. The cells have the ability to form tumors because they do not respond to inhibitory signals and there is no apoptosis (programmed death). The cells may travel to start new tumors and form new blood vessels to nourish themselves. Carcinogenesis is the development of cancer.Some Cancer Terminology:Tumors may be benign or cancerous.Hyperplasiais a substantial increase in cell division.Dysplasiais an abnormal change in cell structure that is considered to be a pre-cancerous state.Tumor, also known as neoplasm, is a discrete mass of cells resulting from hyperplasia.

      Cancerous tumors have abnormal cell structure and loss of regulation of cell growth.

      Benign tumors are non-cancerous and remain in one location in the body. They are a single, well-defined mass that may be surrounded by connective tissue.

      In situ cancer is a cancer that stays in one place.

    • Malignant tumors invade normal tissue and compromises organ function. They may undergo metastasis, a spreading of the cancer, to another organ or body region. This may result in secondary, malignant tumors developing at other locations in the body. These secondary tumors are often genetically different than the primary tumor.

      How cancer develops

      • Through mutated or damaged proto-oncogenes, which would regulate and promote normal cell growth, differentiation, or adhesion. Mutated proto-oncogenes are called oncogenes.

    • Genetics Terminology

      Genes: DNA sequences that contain instructions for building proteins or RNA molecules with enzymatic functions.

      Chromosomes: Structures within a nucleus that are composed of DNA and protein. In humans there are 23 pairs of chromosomes. 22 of these pairs are known as homologous chromosomes (known as autosomes). There is 1 pair of sex chromosomes that determine gender.

      Homologous chromosomes: One member of each pair of chromosomes is inherited from each parent. They look alike in size, shape, pattern, but are not identical. The may have different alleles of particular genes.

      Alleles: Alternative forms of a gene that originated from mutation.There are 2 alleles for every 1 gene.

    • Homozygous chromosome: These chromosomes contain 2 identicalalleles at a particular location (locus). (AA or aa)Heterozygous chromosome: These chromosomes contain 2 differentalleles at a particular locus. (Aa)Genotype: An individual’s complete set of alleles. Genotype is the genetic basis of phenotype.Phenotype: The observable physical and functional traits such as hair or eye color. Phenotype is determined by inherited alleles and environmental factors. Environmental factors can profoundly influence phenotype: nutrition affects height and body size.Punnett square analysis predicts patterns of inheritance.

      Retrieved from: on 3/3/12

    • Gregor Mendel Developed Basic Rules of InheritanceGregor Mendel can be viewed as “the father of genetics”. He experimented with pea plants in Austria in the 1850’s. Mendel composed multiple genetic experiments to develop basic rules of inheritance. These include: the law of segregation and the law of independent assortment. He also was the first to use the phrase “dominant” or “recessive” in explaining how an allele is expressed.The law of segregation: Gametes (sperm and egg) carry only 1 allele of each gene.The law of independent assortment: The alleles of different genes are distributed to gametes independently during meiosis.2 trait crosses: independent assortment. This law applies only if the 2 genes in question are on different chromosomes.Dominant alleles mask or suppress the expression of its complimentary allele. A dominate gene will always be expressed, even in heterozygous (Aa). Dominant alleles are not always more common than recessive; sometimes they may be rare in a population.

    • Recessive alleles will not be expressed if paired with a dominant allele and will only be expressed if it is homozygous (aa) for the recessive allele.Traits Can Be Inherited Many Ways-autosomal dominant                    – autosomal recessive                 – sex linked-co-dominant                                  – incompletely dominant            – polygenic- multiple alleles                             – epistatic                                      – linked- maternal genes…            AND MORE…

      Maternal Inheritance

      Mitochondria, which are structures in each cell that convert molecules into energy, contain a small amount of DNA. They divide independently of other cells. Because only egg cells contribute mitochondria to the developing embryo, only females can pass on mitochondrial mutations to their children. Disorders resulting from mutations in mitochondrial DNA can appear in every generation of a family and can affect both males and females. Fathers do not pass these disorders to their children. Females may be carriers even if they themselves aren’t directly affected.

      Incomplete Dominance                                                        

      Heterozygous phenotype is intermediate between that of either homozygote. If one parent had straight hair (HH) and the other parent had curly hair (hh), then the intermediate would be wavy hair (Hh). Familial hypercholesterolemia is another example of incomplete dominance.


      Products of both alleles are expressed. An example would include genes for ABO blood type. O is recessive but A and B are dominant. An individual heterozygous for the A and B genes will be blood type AB. This is also true of the sickle cell gene.

    • Sickle-Cell geneThis gene involves 2 different alleles of hemoglobin gene. HbA encodes for normal hemoglobin while HbS encodes for sickle cell hemoglobin. For a person to develop sickle cell anemia, they would have to have (HbS HbS) which is homozygous. One may carry the sickle cell trait if they are heterozygous (HbS HbA). A person affected with the trait would make both types of hemoglobin.Oxygen is a key factor for people who have sickle cell anemia. If the air has even a slightly less oxygen concentration the HbS hemoglobin will crystallize within the red blood cell, which is what creates the crescent shape of the cell. This sickle cell results in oxygen deprivation of tissues and organs produce symptoms of fatigue, bodily pains, swollen extremities, and visual problems.

    • Polygenic InheritanceThis is the inheritance of phenotypic traits that depend on 2 or more genes. There are many traits that are acquired through multiple genes acting simultaneously. An example would be eye color. The colors of a person’s eyes are controlled by at least 3 genes. Other examples include height and body shape. Polygenic traits are usually distributed within a population as a continuous range of values (visually resembling a bell curve).Linked alleles are physically located on the same chromosome. They may be inherited together (travel together). They may also be “shuffled” during crossing over in meiosis. They may be unlinked in the process of crossing over in meiosis also.Sex-Linked Inheritance:  X and Y Chromosomes Carry Different GenesThe sex chromosomes comprise 1 pair of genes. The X and Y carry different genes that do different work. Males have (XY) which are not homologous. Females have the (XX) heterozygous. In males, the Y chromosome has to do with all things male, but does have some aspects of “housekeeping”. The X gene does the majority of the “housekeeping” and work associated with maintaining life and is much larger than the Y. Males produce approximately 50% X carrying, and 50% Y carrying gametes. The male parent contributes the determining gender of their offspring.

    • Sex-linked inheritance depends on genes located on sex chromosomes. Sex-linked genes are located on sex-chromosomes. They may have an X-linked inheritance. In this case, more males than females would express the disease. Females have another X chromosome as a backup file so if something were to go wrong, there is another X copy to refer to. Men don’t have this ability and makes them more susceptible for diseases associated with recessive alleles on the sex chromosomes. Fathers cannot pass the gene to sons, but mothers can pass it to sons. Examples include: color blindness, hemophilia, and Duchenne muscular dystrophy.Sex-influenced traits are encoded in the autosomes, not in the sex chromosomes. The expressions of these traits are affected by the presence of testosterone or estrogen. Example: baldness. Several genes influence hair patterns but is also influenced by the presence of hormones testosterone/estrogen.
    • Chromosomes May Be Altered in NumberNon-disjunction during meiosis is the failure of homologous chromosomes or sister chromatid to separate. Examples: Down Syndrome= trisomy (3) chromosome 21.


    • Alterations of number of sex chromosomes can create:XYY= Jacob Syndrome    Tall males with some impaired mental functions.XXY= Klinefeter Syndrome    Tall male phenotype, sterile, may develop enlarged breasts (X chromosome)XXX= Trisomy Syndrome   Female phenotype tendency toward mild mental retardation.XO= Turner Syndrome (no Y)   Phenotypically female but tend to be short with slightly altered body form.Chromosomes May Be Altered in Structure

      Deletions occur when pieces of a chromosome break off. Translationsoccur when pieces of a chromosome breaks off and attaches to a different chromosome. (Interact in pairs, if nothing to interact with, product will be different and shifted to a different product).

      Inherited Genetic Disorders

      Many genetic disorder involve recessive alleles. For a person to develop these diseases, 1 recessive allele is inherited from each parent, who are usually carriers (Aa).

      (PKU) Phenylketonuria is an autosomal disorder  where the person lacks an enzyme to metabolize phenylalanine. If not treated, this may cause mental retardation. A patient would have to limit phenylalanine from their diet.

      Tay-Sachs is a disease where a person lacks the enzyme to metabolize a brain lipid. Lipid builds up in the brain over time and leads to brain dysfunction. There is no current cure and leads to death by age 4.

      Huntington Disease is not common but is caused by a lethal dominant allele. It is always expressed in heterozygote but not until mid-life. Since the symptoms do not present themselves until midlife, most people do not realize they have the disease and have already procreated. Each child of an infected individual has a 50% chance of inheriting the gene which is always lethal.

      Genes and Behavior

      Genes encode for specific proteins, not for specific behaviors. Proteins have specific functions leading to phenotypes and may affect mood overall. No specific actions can be linked to genes, however. Proteins functions have to do with: hormones, enzymes, structure, and neurotransmitters. Genes may provide pre-disposition but there are too many variables to account for specific behaviors.

    • DNA Technology and Genetic EngineeringBiotechnology: The technical application of biological knowledge for human purposes.Genetic Engineering: Manipulation of the genetic makeup of cells or whole organisms.Recombinant DNA Technology: Applied science that explores applications of cutting, splicing, and creating DNA (creating DNA in combinations).Polymerase Chain Reaction: Used to rapidly amplify DNA to obtain millions of copies.DNA Fingerprinting: A scientific process that can identify the source of DNA.

      Retrieved from: on 3/3/12

    • Recombinant DNA TechnologyDNA can be cloned in the laboratory thru recombinant DNA technology. First the DNA plasmids (plasmids are small circular pieces of DNA to which desired genes can be inserted into bacteria for amplification) and human DNA of interest are isolated. Then both DNAs are cut with the restriction enzyme which cuts only at specific sites. The DNA fragments are joined together with assistance of DNA ligase. Once this is complete, the new plasmid is introduced into the bacteria and allowed to reproduce.

      Cloning DNA Fragments

      A technique called polymerase chain reaction is used to make millions of copies of a small fragment of DNA. DNA to be amplified, primers, and heat –stable DNA polymerase are combined. Many cycles of repeated heating and cooling allow for rapid amplifications of a sequence of DNA defined by the primers as they double in number for each cycle.

      Identifying the Source of DNA

      DNA fingerprinting is a technique for identifying the source of DNA. Often a DNA sample must be amplified by polymerase chain reaction first. The DNA is then cut with restrictive enzymes. Next it is separated by gel electrophoresis and the fragment pattern is compared.  Every individuals DNA looks different because we have different lengths of DNA between restriction sites.

    • Gel electrophoresis separates DNA strands by size. This is possible because the restrictive enzymes find the sequences that differ between individuals, and cut the molecules in these places. Although we are almost identical, each individual will have variances in sequences.Transgenic OrganismsTransgenic organisms carry one or more genes from a different species. Transgenic bacteria have been developed to produce insulin, human growth vaccine, erythropoietin, and vaccines. Transgenic plants have produced vaccines, resist freezing which may lead to more dependable crops, synthesize hormones, and may improve nutrition. Transgenic animals have been developed to participate in medical research. They have been used to make (prescription) drugs from the animal’s milk.Transgenic ConcernsThere seem to be valid reasons for concern about transgenic plants. Since genetically modified (GM) plants are genetically similar to each other, they would all be susceptible to a particular disease. If a disease affects a certain group of plants it could eventually lead to crop failure. There would be no built-in internal resistance.Another concern is the idea that GM crops hybridizing with natural crops would devalue the natural ones. This could make native seeds sterile if they combined with the GM. Some people just don’t like the idea of eating “frankenfoods” that are unnatural and altered.

    • There are many concerns and challenges regarding transgenic animals. Cloning is more difficult in animals and requires more chemicals and provides more room for errors. It is more difficult to introduce foreign DNA into animal cells and costs significantly more money and time.Others are concerned that we are just getting too close to cloning a human. Now that the threshold has been reached for cloning animals, will humans be next? At present there is no governmental funding for cloning a human. If someone where wealthy enough to try, however, there is no U.S. law against it.
    • Gene Therapy and Hope for the Future
    • Gene therapy involves the introduction of human genes into human cells with the intent of treating or correcting a disease. The great hope for the future is that thru gene therapy we may fix mutations and correct diseases. There are many obstacles to overcome before we can achieve this dream.One such obstacle is the fact that it is difficult to introduce genes into the exact or “right” cells where the genes would normally be expressed. For gene therapy to be successful we would need an effective means of delivery of genes. No such delivery system exists yet.Even if we are successful at correcting a specific disease or disorder in a person, it is not to say that the disease would be corrected in the person’s offspring. Can corrective genes be introduced into reproductive cells to stop passing of defective genes to future children?

      Vectors Transfer Genes to Human Cells

      Human genes can be packaged in retroviruses which can introduce genes to human cells. They tell the human cell to make something it wouldn’t normally make. There are problems with retroviral vectors because it is hard to target and insert genes into dividing cells. The insertion sites are random which leaves more room for error or ineffectiveness.

      Some other experimental methods include: utilizing liposomes to coat pharmaceuticals so they may cross into the cell membrane easier, and injecting naked DNA directly into the cell of interest.

      Gene Therapy Success

      There has been some success with gene therapy for people with Severe Combined Immunodeficiency (SCID). SCID is a genetic disorder of the immune system that occurs when the T-lymphocyte system doesn’t function properly. T-lymphocytes have the ability to recognize specific proteins thru receptors on their cell surface (cells that produce antibodies).

      There has also been some successful improvement with cystic fibrosis utilizing the liposome technique which delivers gene into cell membrane (defect). There has also been some success in treating blindness with retinal cells that are not operating properly and utilizing this technology for cancer research.

    • Science In The News
    • from Science Daily (Mar.8 2012)
    • Researchers at Weill Cornell Medical College have engineered cells to express a modified RNA to view metabolics (products of individual cell metabolism) in living cells. This allowed the researchers to observe how their levels changed over time and may be used to recognize a cell gone metabolicly awry, as in cancer. This new tool could be used to find treatments associated with restoring metabolite levels back to normal.

Bio 156 Lab 2: DNA and RNA


Transcribe a sequence of DNA into mRNA  and translate it into a polypeptide (a chain of amino acids that are linked together). DNA contains the instructions for producing RNA which contains the instructions for making proteins. Proteins facilitiate most of life’s processes. Then I will build a model of DNA. I will copy just one line from the base code for the Y chromosome and will transcribe the DNA code into mRNA. The mRNA will be further broken down into amino acids (organic building blocks from which proteins are constructed- there are 20 in the human body).


Part 1: Translate DNA into RNA

First I visited the DNAi website to obtain one line from the base code for the Y chromosome. I cut and pasted one line to this blog and began the business of translating the DNA to RNA.

DNA is comprised of four base molecules: adenine, thymine, cytosine, and guanine. There are two strands to DNA. One strand determines the sequence of the other because they are complimentary to each other. Adenine can only form bonds with thymine and cytosine can only form bonds with guanine. The specific “code” for a protein resides in the exact sequence of base pairs in one strand of the DNA. To obtain the sequence for the RNA, I need to figure out the complimentary base to each molecule.  RNA does not contain thymine, and instead contains uracil. Knowing this means that cytosine(C) will always match-up with guanine(G) (C = G). On the RNA strand however, if the DNA reads adenine (A) I will replace what normally would be thymine(T) with uracil (U). So, DNA = T then RNA= A. If DNA= A then RNA= U.
Part 2: Build a Model of DNA

1. I gathered the supplies needed to construct a 3-D DNA. I chose styrofoam craft balls for the outer structure of the helix. Toothpicks will help for stability, popsicle sticks, and markers.

Lab Materials

2. Each of the four base molecules will have a different color assigned to represent it on the DNA strand. Color the popsicle sticks to match the DNA above: yellow= (T) thymine, green= (A) adenine, blue= (C) cytosine, and orange= (G) guanine.

3. Insert each end of the popsicle stick into a styrofoam ball.

4. Utilizing the DNA sequence above, coordinate the molecules (styrofoam and popsicle sticks) to parallel the same sequence.

5. Using toothpicks for stability, attach 2 styrofoam balls together (in correct order) by piercing them both with the toothpick. Repeat the same on the other end of the “molecule”.

6. Repeat step 5 building and slightly twisting or angling in a way that forms a spiral. Puncture and insert toothpicks into styrofoam as needed for support/stability.

Approx half way thru the building

After completing my DNA model, I found myself not satisfied with the end result. It lacked some of the detail of a DNA strand. I made another model out of paper:

1. Gathered 1 sheet each of purple, yellow, orange, blue, brown, and black construction paper; scissors, tape, a ruler, and markers.

Lab Materials

2. Take a piece of purple construction paper (will represent the outer helix) and cut 6 strips of paper measured in equal lengths and widths. Tape 3 strips of paper together, end on  end, to form a “line” of one purple strand of paper. Repeat with the 3 remaining strips. This will yield 2 long strands of paper.

3. Measure 7 strips of each color (orange, green, blue, and brown) 6mm wide and cut. Then cut  into 1.5 inch long pieces.This will represent the base molecules.

4. Take the an orange strip of paper (representing thymine) and cut a triangular piece out of one end. Then take one piece of green paper (representing adenine) and tape the cut edge of orange paper with the green paper. Repeat step 4 fifteen times.

5. Take a blue strip of paper (representing cytosine) and cut a rounded half-circle into one edge. Then take a brown piece of paper (representing guanine) and tape the cut edge of blue paper with the brown paper. Repeat step 5 thirteen times.

Strips of Base Pairs

6. Utilizing a dime as a stencil, draw 56 circles on yellow paper and cut them out to represent the phosphate group.

7. Cut 2 strips of 1cm wide black construction paper. Cut these strips into approximately .5 inch long pieces. To make a 5-sided shape that represents the sugar in DNA, cut the corners off of the square. The first two cuts should meet to create a point. The second two cuts shouldn’t meet and allow for one flat edge.

8. Assemble:  Utilizing the DNA code I match up the first base code (T) and (A) and tape the orange/green paper to both strips of purple paper. DNA when flattened out looks like a ladder. The base codes fit into the DNA as the rungs of a ladder do. Then take one black 5-sided paper and tape it to the space where the base pair meets the purple paper, this represents the sugar. Next, I tape a yellow circle representing the phosphate group, onto the purple paper directly below base pair. One circle is taped onto both purple papers repeat all the same steps above, but utilizing the DNA sequence found on the website.




Each RNA 3 letter sequence above is a codon for a specifc amino acid. Below I have listed the first 10:

Amino Acid 1: Asparagine (Asn)  =AAU

Amino Acid 2: Valine (Val)  = GUG

End Result of Styrofoam DNA

Amino Acid 3: Glycine (Gly)   = GGG

Amino Acid 4: Isoleucine (Ile)   = AUU

Amino Acid 5: Asparagine (Asn)  = AAU

Amino Acid 6: Threonine (Thr)   = ACC

Amino Acid 7: Valine (Val)   = GUA

Amino Acid 8: Leucine (Leu)   =UUG

Amino Acid 9: Aspartic acid (Asp)   = GAC

Amino Acid 10: Glycine (Gly)   = GGG

The model represents the physical appearance of a strand of DNA and this experiment represents the Central Dogma. There are three major stages to this process: DNA replication, transcription, and translation.

Before every cell division replication occurs which produces an exact copy of DNA. Transcription occurs in the nucleus and converts one side of the DNA strand into a single strand of (m)RNA. This RNA is the message or code that, through the process of translation, will convert into one or more proteins. This takes place in the cytoplasm of the cell. Proteins are comprised of at least one polypeptide chain (must contain at least 100 amino acids to be considered a polypeptide). Proteins are what ultimately direct life’s processes.

Result: the appearance of a DNA if it were flattened out



This experiment demonstrated the complexities and processes involving DNA and the instructions that direct all  cell  functions. Converting DNA (reference library) to RNA (copied information/message) was rather easy once I realized the pattern, but what was amazing is realizing how the 4 base molecules could form so many combinations of codons (3-base sequence of RNA provides the code for a specific amino acid) and amino acids. To realize these products, these proteins,direct all of life’s functions is remarkable!

Beyond everything else, I feel that this experiment has given me such an attitude of marvel toward the human body. These processes go on everyday, every moment, and with such detail and precision. The body has so many control measures and DNA repair enzymes that work to correct errors, all of which originate from genes which code for the enzymes.

Discovering Chromosome 17

Objective: Appreciate complexity of the Human Genome and interpret information relating to what information genes hold. There are approximately 22,000 genes on the 23 sets of chromosomes (genetic material) of human beings. Exploring a specific chromosome will enable me to witness the broad and complex information that genes contain by viewing a list of some of the genes/proteins and their related functions in the body.

Results: I was assigned chromosome number 17. Below is a list of 8 interesting genes contained on the chromosome and how they relate to body functions:

BIRC5 (baculoviral IAP repeat containing 5):

This gene has to do with inhibiting apoptosis (a programmed cell death in damaged cells). Negative regulatory proteins ( proteins pass along information as a system of communication and control mechanism) are encoded that prevent apoptotic cell death. Gene expression is low in adult tissue and high during fetal development and in most tumors.

GH1(growth hormone 1):

The protein encoded by this gene plays an important role in growth control. This gene is part of a family of hormones and is expressed in the pituitary, not in the placental tissue (as is the case of 4 other related genes). Mutations or problems with this gene lead to short stature (growth hormone deficiency).

ACE (angiotensin 1 converting enzyme (peptidyl-clipeptidase A) 1):

This gene encodes for an enzyme catalyzed reaction. Enzymes act as a catalyst to speed up a chemical reaction in the body and are essential to life. Without enzymes, most chemical reactions in the body would occur too slowly to maintain life. The enzyme converts Angiotensin 1 to Angiotensin 2 which ultimately assists in controlling blood pressure and fluid-electrolyte balance.

COL1A1(collagen, type 1, alpha 1):

This gene encodes for a specific type of collagen (a fiber made of protein that is slightly flexible but strong) with a triple helix (a 3 diminsional spiral structure). This type 1 collagen is found in most connective tissues, bone, cornea, tendon, and dermis (skin). There are several syndromes or diseases associated with mutations of this gene, one is idiopathic osteoporosis. Osteoporosis is the loss of bone mass resulting in brittle bones. The U.S. National Library of Medicine, National Institutes of Health defines idiopathic osteoporosis to be: “the development of osteopenia and fractures with minimal or no trauma in otherwise young, healthy individuals who are not postmenopausal or have other, identifiable secondary causes of osteoporosis. ” This type of osteoporosis is rare.

BRCA1(breast cancer 1, early onset):

This gene plays a role in maintaining genomic stability and acts as a tumor suppressor. The gene product plays a role in transcription, DNA repair of breaks, and recombination. In other words, this gene plays a big role since it is closely involved with DNA, DNA repair, and sending out the “message” or “recipe” that instructs cellular functions. Approximately 40% of inherited breast cancer and more than 80% of inherited breast and ovarian cancers are responsible from mutation of this gene.

SLC6A4 (solute carrier family 6 (neurotransmitter, transporter, seratonin) number 4)

This gene encodes for a protein that transports serotonin (a neurotransmitter) from synaptic spaces into the presynaptic neurons. The protein then terminates the action of seratonin and recycles it. A repeat length  in the gene may play a role in sudden infant death syndrome, aggressive behavior in Alzheimer’s patients, and depression- susceptibility. As found on the definition of neurotransmitter is: “any of several chemical substances…that transmit nerve impulses across a synapse to a postsynaptic element, as another nerve, muscle, or gland.” Synapses are also defined on the same site as: “a region where nerve impulses are transmitted and received, encompassing the axon terminal of a neuron that releases neurotransmitters in response to an impulse, an extremely small gap across which the neurotransmitters travel, and the adjacent membrane of an axon, dendrite, or muscle or gland cell with the appropriate receptor molecules for picking up the neurotransmitters.

CCL2 (chomokine (C-C motif) ligand 2)

This gene is one of several related on chromosome 17 that is secreted protein involved in regulating the immune system and inflammatory processes. It has been implicated in the production and development of diseases such as psoriasis, and rheumatoid arthritis.

MAPT (microtubule-associated protein tau)

This gene encodes for a protein whos transcript undergoes complex splicing creating several mRNA species, which are differentially expressed in the nervous system. This gene mutation has been associated with many neurodegenerative disorders such as Alzheimer’s.

The gene I found personally so interesting was BRCA1. I do not know of breast cancer being an issue in my family, but it is something that affects so many people. To understand that the mutation of this single gene accounts for such a large percentage of inherited breast/ovarian cancers  is astounding! It is truly amazing how just one small gene (or its mutation) can have such an effect on the body.


This lab/investigation truly gave me an opportunity to see how vast, complex, specific, and amazing our bodies are. I merely scratched the surface in exploring #17, as there are a total of 1773 genes on this chromosome! With all the genes and proteins associated with all the various body processes, its amazing that most of us are relatively healthy without too much going wrong!

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