Immunity

The immune system in general is made up of chemicals and special cells that fight infections and threats to our health. What makes up the system largely are the white blood cells, which are made in the bone marrow; the white blood cells, when in action, move through blood and tissues. Any time our body reacts to threats, a germ is defeated, and once this is done, our immune system remembers that microbe; therefore, when our system encounters the same type of microbe once more, it is able to defeat it quickly.

Firstly, I should address what exactly a threat to our bodies would be: pathogens. Pathogens are any living organisms or viruses capable of causing a disease (includes bacteria, protozoa, fungi and worms). Exposure to pathogens doesn't necessarily result in disease but depending on the conditions in which they enter and we are exposed to them there is the possibility. Most that enter our body has developed an immunity to that pathogen. Now a general way that people think of being protected from these threats are antibiotics, chemicals that take advantage of the difference between prokaryotic and eukaryotic cells. One type of antibiotic may selectively block protein synthesis in bacteria while another type may inhibit the production of a new cell wall by bacteria, blocking the ability of the pathogen to grow and divide (spread into an infection). It is important to note that antibiotics are used to treat bacterial diseases and not viral diseases because it blocks specific metabolic pathways and cell wall production in bacteria; the viruses reproduce using the host cell metabolic pathways; Viruses, contrastingly, don't have metabolic pathways, so they aren't affected by the antibiotics.

Now the problem really is what happens when the pathogen successfully enters our bodies. At first leucocytes (white blood cells) help fight off the pathogens and produce immunity for them. Macrophages, which are large white blood cells, can change their shape to surround the invader and take it in through the process of phagocytosis (process of destruction). The macrophages are able to squeeze they way in and out of small blood vessels, and when it meets a cell, it recognizes whether the cell is a natural part of the body ("self") or if its not part of the body ("not-self"). This would be a non-specific response because the identity of the pathogen has not been determined, its only response is that it should be removed.

Antibodies (protein molecules) are then produced in response to a specific/different pathogen. Each type of antibody is different because each type is produced in response to a different pathogen. The difference between a antigens and antibodies are that antigens are substances and molecules that cause antibody formations while antibodies are proteins and molecules that recognize antigens. The production of antibodies starts when the antigen stimulates an immune response. The antigen is then engulfed by macrophages, incorporated to the macrophage membrane, and presented to the T-helper cell (type of white blood cell). Once this is done the helper T-cells bind to the antigens, and when activated the B-cells are also activated by the T-cell. Next, the antibodies are produced by B-cells in response to specific antigens, and the B-cells clone. Following, it goes into the plasma cells and memory cells, where plasma cells produce specific antibodies to the antigen. Consequently, the memory cells are used as a long-term immunity because it acts faster and responds faster later on.

I think that it's important to point out different reactions of defense that our body has to different threats.

A cut:
Since the skin is opened, microbes are able to enter our body freely. The immune system, therefore, sets up a defense to the invasion. This defense would be that the white blood cells that are in the blood are alarmed chemically by the cells that are damaged. Then, it moves towards the opening (the cut) and starts eating the bacteria (not digesting). So when we see pus in our wounds, it's actually dead microbes along with dead white blood cells. Next, the B-lymphocytes attempt to identify the microbe - if it has already been detected and defeated before, the lymphocytes know what antibodies need to be used to kill the microbe. The T-lymphocytes (a variety of helper cells) help the B-lymphocytes to make the antibodies, if the microbe is not yet known. The killer cells then attack the infection to cure it.

A fever:
From my understanding, I think that a fever is simply an alarm to us that something is wrong, it's not actually the problem - which would actually be an infection. In a fever, there is a rise in body temperature; this rise in temperature can kill some microbes. A fever may also set off a repair process to the body.

A viral infection:
The immune system keeps what I see as a record of microbes that have entered the body and been defeater. So it can destroy the microbe rapidly if these microbes enter the body again before they multiply or cause any other reactions on our bodies. There are some infection that have to be fought more than once because so many viruses can cause the same disease, like the influenza and the cold. For example, catching a cold from one specific virus doesn't mean that you have immunity against other viruses that give you the cold.

Immunization:
This works like copying/ acting out the body's natural immune response. Immunization is basically referred to vaccines, where a small amount of the specially treated virus, bacterium, or toxin is injected into our bodies. Once this is done, our bodies create antibodies. So the next time that the body of the individual encounters and is exposed to the actual virus, bacterium, or toxin, they're bodies will destroy them and their health won't be affected.

Defenses of our physical body:
Our skin itself is a barrier of infection once it is intact and protects pathogens to enter living tissues. The acidity and oiliness of our skin prevents the entering of pathogens as well. Also, the acidic environment of our stomach helps kill any pathogen that we may ingest. Thirdly, all our "openings" - the trachea, nasal passages, urethra, and vagina, are lined with mucous membrane. The cells of the membrane produce and secrete mucus, the mucus then traps the incoming pathogens. Another point regarding the mucus which is important is that it secretes lysozyme, therefore, it chemically damages the pathogens. Lastly, the cilia serves as defense as well; the cilia is a hair-like extension capable of wave-like movement, the movement of the cilia removes the mucus, excreting the pathogens.

Now I will give a general summary of the immune response process to make everything more clear. The immune response, in itself, begins when a pathogen enters the body. The macrophages that encounter the pathogen ingest, process, and display the antigen fragments on their cell surfaces (antigen-presenting cells). These cells then interact with the T-helper cell to recognize the same antigen. During this "communication" the macrophage releases a chemical alarm (interleukin 1), which stimulates the T-helper cell to secrete interleukin 2, causing proliferation of some cytotoxic B cells and T cells. At this point the process has two directions to go in, one through the B cell and one through the T cell. Since normal cells can also be affected by the pathogens, so the T cells recognizes a particular antigen. Once they are recognized, the T cell binds to the infected cell and releases a chemical to kill the infected cell, resulting in the destruction the pathogen. B cells which are in a wide variety, each recognizes particular antigens. When the B cells are activated by the T-helper cells they are differentiated into plasma cells, which become anti-body producing "centers", sending out antibodies that can bind to the antigen involved in the infection to the blood stream. The antibodies bind to the antigens on the surfaces of the pathogens, marking them for destruction, which is done by macrophages. The remainder of the B cells that don't produce anti-bodies, become memory cells; these memory cells are what trigger an immune response in a future infection by the same pathogen in a faster and more powerful way. This response is what gives our bodies immunity to diseases you have already had or have been vaccinated with.

To end on a different note, I will comment on HIV/AIDS to show how it is an important subject when regarding the immune system. HIV is the human immunodeficiency virus (which leads to AIDS). HIV damages a person's body by destroying specific blood cells - the T cells - which are crucial in helping the body fight diseases. AIDS is caused by HIV, since it is the last stage of HIV infection; it is when a person's immune system is severely damaged and has difficulty fighting diseases and certain cancers. HIV (the virus, not AIDS) can be transmitted from man to woman, woman to man, man to man, or mother to fetus. The man to man, woman to woman, and man to man contamination is during sexual relations with no protection (condoms). It can also be transmitted through breast milk, saliva, or other body fluids. Another physical from it is transmitted in is through contaminated needles and blood transfusions. HIV/AIDS causes many social implications. Firstly, it may cause social stigma and discrimination to the contaminated individuals. Secondly, it may affect their chances of obtaining employment and life insurance. Thirdly, it impacts the costs on health systems to treat contaminated individuals. Furthermore, early deaths reduces number of adults, therefore the workforce, and consequently the family income. Another important problem to the contaminated individuals is that the expense of the drug treatment is very high.


Below are two quizzes that I found on the immune system which is a good way to practice and become more familiar with the topic. The first quiz is on HIV/AIDS and the second quiz (includes an animation) is on the immune system in general.

1.http://www.thebody.com/content/art33136.html
2.http://highered.mcgraw-hill.com/sites/0072495855/student_view0/chapter24/animation__the_immune_response.html

Below is a video I found regarding a research scientists at Cambridge University did which claims that the immune system's main assault on viruses take place inside infected cells and not outside as it was thought to (came out in 2010).
http://www.guardian.co.uk/science/video/2010/nov/01/immune-system-viruses-cells

Below is a brief video I found explaining the basics on immunity.
http://www.youtube.com/watch?v=IWMJIMzsEMg

Transport System

The first thing I think should be addressed regarding the circulatory system is the blood, since it's basically what delivers most things we need throughout our body. Blood is made of 45% solids (which would be cells) and 55% fluids (which would be plasma); among these fluids are dissolved waste products, proteins, water, hormones, antibodies, and nutrients. It's important to mention that platelets are also in the blood, which are cell fragments with no nucleus and is involved in clotting. There are also two types of blood cells, the red blood cell and the white blood cell. The red blood cell is erythrocyte and is responsible for transporting oxygen and carbon dioxide to and from tissues. The white blood cell is leukocyte and is responsible for counteracting foreign substances and disease.

The second "member" of the circulatory system that should be mentioned is the heart which is the muscular organ that pumps the blood through the system by contraction and dilation. The heart has four chambers, two atria, and two ventricles. The right side of the heart (right atrium and right ventricle) is responsible for pumping and controlling the oxygenated blood while the left side (left atrium and left ventricle) is responsible for deoxygenated blood.

Blood vessels are also an important component to call attention to in the circulatory system. The blood vessels are divided into three types: arteries, veins, and capillaries. There are structural and functional differences between the these three vessels. Arteries have a thick elastic wall that helps withstand the high pressure, an outer fibrous coat to prevent from rupturing under high pressures, a small lumen compared to the wall thickness to maintain high pressure, layer of smooth muscle - which allows them to contract. It is important to note that the only large lumen (as an artery) is near the heart, used to conduct a large volume of blood. Veins, on the other hand always have a large lumen in relation to the diameter to facilitate blood flow, it has a thin wall, more collagen and fewer elastic fibres than arteries because the pressure is low. It also have very little muscle since its not needed for constriction, and the valves are used to prevent back flow between pulses. Capillaries, in my perspective, is the smallest form of blood vessel since it has no muscle and elastic tissue once the pressure is very low and the endothelial layer on the cell is thick to allow permeability, diffusion of chemicals, or tissue fluid. Furthermore, the diameter is small, which leads exchanged to occur, there are pores to allow rapid diffusion, and there are no valves since the pressure is very low.

I think that the lab done in class was very helpful for us to understand the heart. When I started to learn the events that occur within the heart that causes the blood to move throughout the whole body, I got kind of stuck. This happened mostly in part because of the names and the constant opening and closing of something. But after seeing the heart and actually seeing the venrticles, atrium, arteries, etc. I became more familiar with the process and the relation between all parts. Firstly, the blood is collected in the atria and it is pumped into the ventricles. Then, the opened atrio-ventricular valves allow the flow from the atria to the ventricles (right atrium ⇒ right ventricle + left atrium ⇒ left ventricle). The closed semi-lunar valves (which I see as the "end points" of the pulmonary artery and the aorta) prevent the backflow from the arteries to the ventricles. Next, the blood is pumped from the ventricles to the arteries and the opened semi-lunar valves allow this flow. The now closed atrio-ventricular valves prevent backflow to the atria. The pressure is then generated by the heart, causing the blood to move through the body; the pumping of the blood occurs from the beginning of one heart beat, which is initiated by the SAN (sino atrial node).

This now leads me to the mechanisms that control the heartbeat. The heartbeat is the myogenic which is the muscle contraction of the heart. Then, the SAN (mentioned above) generates an electrical impulse on its own with a regular frequency, known as pacemaker. This impulse is spread to both atria, causing the two to contract in unison. The AVN (atrio ventricular node) picks this impulse that was spread in the right atrium septum and conduces it to the ventricles through fibers, causing the heart to contract and "relax" - the heart beat.

I've explained basic functions and concepts present in the transport system, and now the basic process of the blood flow throughout the whole body will be outlined. To begin with the right atrium receives blood from the body through the vena cava, the blood then passes through the right atrioventricular valve, which is closed when contracted, keeping the blood from re-entering the atrium. Following, the blood goes into the right ventricle (the wall of the right ventricle is thinner than the left ventricle and it only pumps blood to the lungs). Then, the blood goes to the right semilunar valve (beginning of artery) and it closes to prevent the blood from flowing back to the ventricle. The blood goes into the pulmonary artery, which takes the deoxygenated blood to the lungs. Once it is taken, the blood goes to both the left and right lungs. In the lungs, the capillaries that are present are in close contact with the alveoli so the blood can release CO2 and pick up O2. The alveoli (even though it's more relevant in the respiratory system) has a large surface area (because it's round), has a short diffusion distance from the blood, has a dense capillary network, and has a moist solution of gases - all of which facilitate the exchange of CO2 and O2. Next, from the lungs, the pulmonary vein carries the now oxygenated blood back to the heart, which is received from the left atrium. The blood then passes through the left atrioventricular valve and enters the left ventricle (the wall of the left ventricle is is thicker than the right ventricle and it pumps blood to the whole body). After this, the blood passes through the left semilunar valve which is at the start of the aorta. The aorta is the main and largest artery of the body; from the artery, the coronary artery branches off, which supplies blood to the heart muscle so it can pump. If the coronary artery is blocked, it can cause parts of the heart to die if they don't get the nutrients and oxygen. At last, the aorta also branches off into arteries that distributes blood tho the whole body, marking this as the last step in the transport system as the process begins all over again.


Below is a short video that I found on circulation. I chose this brief video because it's easy to understand and underlines the basic process of circulation.


Below is the concept map I did for the transport system. It's pretty big but contains important aspects to be studied.

Digestion

Digestion is the breaking down of macro food molecules into smaller components, to a form that can be, for example absorbed, into the blood stream. There are two types of digestion: mechanical digestion and chemical digestion. First, I will explain the mechanical digestion, which is the first process that happens in the overall all digestion activity.

It is important to note that mechanical digestion isn't just another process we need to complete, there is a specific and important purpose for it; the purpose of mechanical digestion is essentially to improve the access of digestive enzymes. In mechanical digestion the food goes into the mouth, which is broken down into molecules by the teeth. After this happens, the broken down food goes through the esophagus, that uses the peristalsis (muscle) which contracts and pushes the food into the stomach. Inside the stomach, muscles work to transform the food into chyme (partly digested food).

During and subsequent to mechanical digestion, chemical digestion takes place. I say during mechanical digestion because at the same time the food is being chewed in the mouth, the salivary glands produce saliva, in the saliva, salivary amylase is present; the salivary amylase serves to catalyze the hydrolysis of starch into simpler compounds, like the disaccharide maltose. Also, at the same time the muscles of the stomach contract to make chyme, the lining produces HCI and pepsin to digest the proteins into polypeptides. Proceeding, the chyme is moved into the small intestine. In the small intestine numerous tasks occur; to make it easier I will list them.

1. The CCK produced in the lining of the small intestine goes into the pancreas. In doing so, the pancreas releases pancreatic amylase, pancreatic lipase, and pancreatic trypsin. Each of these three substances released have a task. The pancreatic amylase cuts starch into disaccharides, the pancreatic lipase cuts triglycerides, and the pancreatic trypsin cuts the polypeptides into dipeptides.

2. The intestinal lining produces sucrose, maltase, and lactase. These released substrates are then digested into monosaccharides (fructose, glucose, galactose).

3. The CCK produced in the lining of the small intestine goes to the gallbladder (in the liver); the gallbladder stores bile, so as the CCK reaches it, bile is released. Then, when the bile is released into the small intestine, the bile emulsifies the fats to act (work/ react) on the triglycerides to become fatty acids and glycerol.

4. The blood flowing along the lining of the small intestine absorbs fatty acids with the help from the lacteals. This blood is flowing in villi, which absorbs amino acids and monosaccharides (and some mineral and vitamins). What helps the function of absorption is that the villus intestinal wall has many folds, increasing the surface area, the surface of villus is close to the blood vessels so materials can easily diffuse, and the villus wall consists of single layer of cells.

Once all these processes occur in the small intestine, the digested food is moved into the large intestine. In the large intestine the following happens:

1. Blood absorbs some water, vitamins, and minerals

2. The rectum stores the rest of water, cellulose, and enzymes that weren’t absorbed

And finally…the rest is released through the anus!

I personally had a very hard time in understanding the whole digestion process in terms of chemical actions that occur, like the breaking down amylase, protease, and lipase. After going back to my notes to write this blog post I believe I have a more clear understanding on what happens chemically in digestion. However, I still think that I have to commit myself into studying this aspect because I know I don't have a full understanding and comprehension.

Underneath is a mind map that I made to make the whole digestive process something more visual and most likely easier to understand.

How do I evaluate my performance in Bio I and what are my goals for this year?