Bio Quiz

Bio Quiz

The immune system is the body's defense system. It protects the body from potentially harmful substances by locating and responding to antigens. Antigens can be proteins and/or located on the surface of cells, fungi, viruses, and bacteria, or other substances such as toxins, chemicals, drugs, and foreign particles (such as a splinter). The immune system sends out antibodies to destroy antigens, but leaving beneficial and friendly antigens alone. 

http://www.nlm.nih.gov/medlineplus/ency/article/000821.html 

(This picture illustrates antibodies attacking antigens as discussed above)

Picture from: http://www2.estrellamountain.edu/faculty/farabee/biobk/biobookimmun.html

1- An innate, or nonspecific immune response is an immediate response to any foreign antigens. Everyone is born with innate immunity, which is made up of barriers and is the first line of defense of the immune system. Examples of innate immunity include: Cough reflex, enzymes in tears and skin oils, mucus, which traps bacteria and small particles, skin, and stomach acid. 

(This picture discusses the different parts of the innate immune system, ranging from complementary proteins to phagocytes, further explained below)

http://www.nature.com/nbt/journal/v25/n11/fig_tab/nbt1342_F1.html

How does it do what it does?

If pathogens (disease-causing cells that carry antigens) are to make it past the physical barriers of the skin, they are met by complement proteins, phagocytes, and natural killer cells.

Complement Proteins

The liver produces around 20 complement proteins that work together to destroy antigens. They do this either by marking them for ingestion by other immune cells, sending out chemical signals to bring additional immune cells to join the fight, or combining together with one another and killing the invaders directly by punching holes them.

(This diagram shows complementary proteins sending signals to other complementary proteins (complement cascade) which then assist in the eventual cell burst)

http://www.niaid.nih.gov/topics/immunesystem/immunecells/Pages/complementSystem.aspx

Phagocytes

Phagocytes are white blood cells which ingest harmful foreign particles, bacteria, and dead or dying cells. Phagocytes are divided into two classes: professional, and nonprofessional. Professional phagocytes are primarily concerned with ingesting pathogens. They have special receptors embedded on them that allow them to detect foreign objects not normally found in the body. Professional phagocytes include dendritic cells, macrophages, mast cells, monocytes, and neutrophils. Nonprofessional phagocytes do sometimes ingest pathogens, but that is not their main job. Examples include: epithelial cells, endothelial cells, fibroblasts, and mesenchymal cells. For instance, fibroblasts are concerned with remolding scars, and in the process, they sometimes ingest foreign particles. 

(This illustration shows a macrophage (phagocyte) using its embedded receptor to communicate with an antigen to determine if its friend or foe. It is foe because the macrophage has called upon a antibody to assist it)

http://en.wikipedia.org/wiki/Phagocyte

Killer cells

Natural killer cells are lymphocytes (type of white blood cell) which attack tumors and body cells infected by viruses. NK cells wait in the blood stream, and in the liver and spleen which store blood, until they are needed at the site of an infection. They give off a chemical (ctyokine) which alerts nearby phagocytes for backup. They also evaluate body cells to determine whether they have been infected by a virus. Once they find infected cells, they inject those cells with enzymes that cause the body cells to self-destruct, or they signal the cell to commit suicide, destroying the pathogens.

For the entire innate response section: http://www.novimmune.com/science/innate.html  

2- T cells are lymphocytes. There are many different types of T cells, but the most important are Helper and Killer T Cells.

Helper T cell activation

Helper T cells, which carry information and decide when to give the green light to other immune cells to carry out an immune response, are activated to initiate immune reactions. This is how Helper T cells are activated: macrophages, a type of phagocyte, goes out and swallows foreign particles, but leaving behind some antigen. Helper T cells then go and read the antigen, and if it is harmful, the cells activate and signal the macrophage to finish off the antigen, then go activate other T cells and divide and produce special proteins which signal other immune cells to attack the antigen as well.

Killer T cell activation

Killer T cells are alike phagocytes except that instead of engulfing the entire pathogen, they inject enzymes which destroy the nucleus and structure of the invader. Killer T cells are activated by Helper T cells through the process described above.

This entire section is from: http://sepa.duq.edu/regmed/immune/tcells.html

B cells are lymphocytes responsible for creating antibodies. They remain in peripheral tissues until they encounter an antigen and are activated. They require 2 signals for activation: The first activation signal occurs upon antigen binding to B cell receptors (BCRs), and the second signal occurs via either a thymus-dependent or a thymus-independent mechanism. Thymus dependent means Helper T cells assist in activation, and thymus-independent means the B cells are activated directly by the antigen.

This section from: http://www.rndsystems.com/molecule_group.aspx?r=1&g=3175

(This picture shows a T cell activating a B cell)

http://en.wikipedia.org/wiki/B_cell

3- "The adaptive immune system plays three primary roles. First, because the response by the innate immune system is non-specific, if it goes on too long it can also damage healthy cells in the process. Second, because microbes like bacteria and viruses continually mutate, over time they become resistant to particular drugs as well as to the effects of the immune system. To counter that, the adaptive immune system, as the name implies, can adapt itself to target very specific mutations ofantigens as they are encountered. And third, the adaptive immune system protects us against reinfection." 

The main components of the adaptive immune system are B cells and T cells (activation described above). These cells travel through the blood stream looking for antigens. "Once they encounter invaders, these B-cells and T-cells learn how to attack this one specific antigen. They then replicate in massive numbers in order to fight the invader. B-cells also create antibodies programmed to attach themselves to the particular antigen being encountered. These antibodies, in turn, can sometimes directly interfere with the functions of the antigens, they can mark the antigen for ingestion by white blood cells, or they can create a physical link between the antigen and other immune system cells allowing those immune cells to kill the antigens."

Unlike the innate response, the adaptive immune system gradually kills invaders. "However, after the foe is vanquished, some of the B-cells and T-cells remain in the body as memory cells so that the next time this particular threat is encountered, the adaptive immune system will recognize it immediately, and mount a much quicker and more efficient attack."

From: http://www.novimmune.com/science/immune.html

(This diagram shows the differences between an adaptive (gradual) and innate (immediate) system)

http://www.rikenresearch.riken.jp/eng/frontline/5028

4- Nearly every cell contains molecules that let the body know if it is self or nonself. Immune body cells normally do not attack cells with self markers. When these "troops" come across cells labeled as "foreigners," they move quickly to attack. These foreign particles are labeled by antigen markers.

The body will reject any proteins, no matter how beneficial, until they are broken down and their antigen markers disappear. An antigen announces its foreignness by means of intricate and characteristic shapes, called epitropes, which appear on its surface. Different shapes trigger different antibody responses. 

Sometimes the body accidentally labels self cells as nonself, and triggers a misdirected attack. The result is an autoimmune disease. 

(This picture depicts how antibodies examine markers to determine antigen or friend)

http://thyroid.about.com/library/immune/blimm02.htm

 

Melanoma Review Paper

From: https://docs.google.com/document/d/1WO2h55Pp2v7CffKpOTOL5QeD2XR0d7wUOP1Qkd1Mr3E/
The Surgical Role of Radiation in the Treatment of Melanoma

Joe Rode

Honors Biology

1/8/13

ABSTRACT

Radiation, specifically x-rays, is the treatment method that this paper will be focusing on. The objective of this review paper is to delve into what makes radiotherapy different from the other treatment methods of melanoma, and why and how it is used. Radiotherapy is an effective method of treating melanoma, and this paper will show how extraordinary it can be when it is used safely and correctly.

INTRODUCTION

    Cancer is when abnormal cells that have been mutated divide uncontrollably. There are several different types of cancer, but the one that will be focused on in this paper is melanoma. Melanoma is a skin cancer that begins in a certain type of skin cell called melanocytes, which provide pigment for the skin, eyes, and hair (American Cancer Society 2013). It is the deadliest skin cancer and results from unrepaired DNA damage to skin cells (Skin Cancer Foundation 2013). This occurs often from excess exposure to Ultraviolet Radiation. The damaged DNA in the skin cells then triggers genetic mutations, which cause the cells to multiply rapidly and form malignant tumors (SCF 2013). Melanoma is most commonly found on the back, chest, legs, or face areas (ACS 2013). It is mainly found in the form of oddly colored (too dark or too light) or oddly shaped (too large or too small) moles (ACS 2013).

Melanoma is usually curable when recognized and treated in Stage 1, but is extremely dangerous when neglected and can spread quickly to other parts of the body, where it can then be tough to treat or even fatal. There are four main treatment choices for melanoma: Surgery, Chemotherapy, Biological Therapy, or Radiation Therapy. Surgery is the most commonly used melanoma therapy, and consists of cutting out the melanoma and the surrounding tissue to ensure no cancer cells remain. Surgery is used in nearly every occasion but when it cannot completely kill the cancer cells, the other choices must be used. If the melanoma is in Stage 3 or 4, chemotherapy can be used because although melanoma does not normally respond well to chemo, the cancer has already transferred to other parts of the body and cannot be taken out by surgery. Chemotherapy is the use of drugs to kill cancer cells, and can either be taken through the mouth or injected into the bloodstream. Another alternative is biological therapy, or immunotherapy, which is a form of treatment that uses the body’s immune system to prevent the melanoma from coming back after surgery. The final treatment method is radiation. Radiation or radiotherapy, uses high energy waves, such as x-rays or gamma rays to kill cancer cells. Radiotherapy is used to control melanoma that has spread to the brain, bones or other parts of the body. Radiation kills the cancer cells so that they cannot divide or reproduce, preventing DNA Replication.

(Cancer Compass 2013).

TYPES OF RADIATION

External Radiation

External beam radiation therapy (EBRT) is a type of radiation therapy that directs a beam of radiation from outside the body at cancerous tissues inside the body

    EBRT delivers high-energy rays to tumors, using a special X-ray machine called a linear accelerator. This machine allows radiation to be delivered from any angle and shapes radiation beams to the contour of the tumor. Radiation oncologists use EBRT to target a tumor with higher, more precise doses of radiation, while minimizing damage to healthy tissue and nearby organs. As a result, EBRT can reduce the risk of side effects typically associated with radiation treatment

EBRT is an outpatient procedure. This technique does not carry the standard risks or complications associated with major surgery for melanoma, which can include surgical bleeding, post-operative pain or the risk of stroke, heart attack or blood clot. The procedure itself is painless. EBRT poses no risk of radioactivity to the patient or others with whom the patient have contact.

    (Cancer Treatment Centers of America 2001).

Internal Radiation

Internal radiation therapy (also known as brachytherapy) delivers radioactive material to a location very close to the tumor from a source placed inside the body. Methods of delivery include injection, ingestion, or implantation. Radioactive materials are delivered to melanoma cells via monoclonal antibodies (cloned antibodies from a single parent cell), and laboratory-produced, infection-fighting proteins that can attach to targeted cancer cells. Cancer cells, including melanoma cells, have special marker substances on their surface, known as antigens. Monoclonal antibodies circulate through the bloodstream until they find melanoma cells with the target antigen. The antibodies then bind to the melanoma cells and signal other immune cells to help destroy or contain the tumor. When radioactive material is attached to the antibody, radiation is released directly into the tumor to kill melanoma cells. The effectiveness of monoclonal antibodies as a stand-alone treatment or when coupled with radiation or chemotherapy is currently being investigated in clinical trials.

(Melanoma Center 2010).

USES OF RADIATION

Radiotherapy as a Primary Method of Treatment

Radiotherapy is rarely used as a primary treatment instead of surgery, which is the curative treatment of choice for all types of primary melanoma incisions. Poor performance status of the patient with severely low pain tolerance or refusal of proposed surgery are potential but less plausible motives in clinic for replacing surgery with radiotherapy. More frequent indication for upfront radiotherapy is lentigo maligna melanoma (LMM). Particularly when LMM is extensive and located on the face of elderly patient, radiotherapy is a good alternative to surgery. An experiment was conducted with a total of 107 patients. Of those 107, 3 local recurrences were observed 13-44 months after radiotherapy

Time to complete regression of the lesion (incision) after irradiation took up to 24 months. Regional node (organizer tissue) metastases (spread of cancer to different organs) developed in 3 patients 6, 8 and 18 months after therapy, respectively, whereas in one patient, pulmonary (lung) metastases occurred 44 months after treatment. All theses patients had their primaries (original tumor area) controlled. Thus, whenever surgery attempting to achieve clear margins would result in excessive mutilation, either cosmetic or functional, or in elderly patients, it should be replaced with radiotherapy, which is effective and has curative potential in LMM. Because the incidence of regional metastases is extremely low, no elective irradiation of regional lymphatics is required

Primary curative radiotherapy should be attempted also in localized inoperable mucosal melanoma (MM) where it is considered the most effective treatment modality. 70% of the melanoma can be controlled by radiotherapy alone in MM, which could be then further improved by utilizing high-linear energy transfer (LET) radiation.

(Strojan 2010).

Adjuvant Radiotherapy

Adjuvant radiotherapy is radiation that is used after surgery to significantly reduce the risk of recurrence. Postoperative radiotherapy depends on the risk estimate for recurrence, treatment related side-effects and the possibility for successful salvage when recurrence occurs. The risk for serious complications after post-op radiotherapy is low. Factors that influence control are close or positive margins, early and/or multiple recurrences, extensive satellitosis (build up of neuroglial cells, which protect neurons) desmoplasia (growth of fibrous tissue) or neurotropism (attacking of tissue), and MM primaries (aggressive neoplasm, or build up of tissue). Recurrence may be related to the presence of neurotropism and inadequate surgical margins. Radiotherapy adds significant control after surgery. A study showed that after lymphadenectomy (cutting out of the lymph nodes) for recurrence of melanoma, less than 25% of patients considered to be at high risk of recurrence

The factors contributing to an increased recurrence are the presence of residual disease after surgery, tumor extension outside of a joint, nodes measuring ≥3 cm in the largest diameter, multiple nodal involvement or recurrence after previous lymph node (tissue that helps recognize and fight germs) dissection (See Below). Comparison of studies using surgery alone or surgery plus radiotherapy provides a strong argument for the effectiveness of adjuvant irradiation. Tumor control is roughly 90% in adjuvantly irradiated patients.

(Strojan 2010).

(Right) Residual disease triggers recurrence in melanoma (The Scientist 2011).

Palliative Radiation

Palliative radiotherapy is radiation used to reduce signs and symptoms related to melanoma and improve quality of patients’ life, prolonging her/his lifespan. Palliative RT is to be introduced whenever surgery is not possible (i.e. tumors that cannot be cut out or poor general condition of the patient) or is deemed ineffective (i.e. multiple metastases).

In general, all types of metastases or metastatic sites can be irradiated, including skin, lymphatic, brain, bone, and visceral incisions. The effectiveness of radiotherapy in palliative setting is primarily dependent on tumor burden and site. Cells from metastatic lesions (incisions) are more radioresistant than those from primary tumors (tumors remaining in their original site). Thus, the symptoms are ridden easier and more effectively when radiotherapy is done on metastatic tumors. Combined treatment, or the use of radiotherapy and another form of cancer treatment, offers good chance for pain relief and restoration of affected neurological functions as well as delay in tumor regrowth and prolongation of symptoms-free period

(Strojan 2010).

SIDE EFFECTS OF RADIATION

    Recovery from radiotherapy depends on the tumor site, the stage and grade of the

cancer, and the amount of healthy tissue that is affected during treatment. Damage to normal cells during radiation therapy may cause side effects.

Skin Changes

Skin changes are common with radiation therapy. The skin in the area of your body that is getting radiation may turn red and tender, itch, peel, or blister. Toward the end of treatment, the skin may become moist and "weepy." These effects are temporary, and the area will gradually heal when treatment is completed. The patient may notice a slight change in the color of the skin. (Web MD 2001).

(Right) An example of skin damages after radiotherapy (Fashion-Era 2007).

Fatigue

Fatigue is another common side effect of radiation therapy. It is a sense of tiredness that doesn't seem to go away, even with rest or sleep. Some people may only have mild fatigue. For others, fatigue may be a bigger problem. It may last from 6 weeks to a year after your last radiation treatment.

(Web MD 2001).

Others

    In a study done with patients after receiving radiotherapy, 46% experienced

headaches, making that the most frequent side effect of radiation. However, in

only one patient was the headache debilitating enough to result in a treatment

delay of one week. Other less frequent side effects were nausea and vomiting.

Dermatitis (inflammation of the skin) developed in two patients, and chills were noted in one patient. In no instance was therapy discontinued as a consequence of

side effects

(Vlock et. al. 1982).

CONCLUSION

    Radiation, while not normally used as a primary method of treatment, is an integral part of melanoma treatment. Through technological advances, however, it could soon become even more important in the treatment process of Melanoma. In the near future, it may be possible for x-ray machines to locate only abnormal cells and leave the normal cells alone, eliminating possible side effects. As technology continues to progress, the different treatment methods of cancer are continuously interweaving, and this is making treatment less painful and more effective. One can only imagine how soon cancer will be curable with the aid of technology.

Works Cited

DiChiara, Timothy. "Moles Versus Melanoma Skin Cancer: Learn to Tell the Difference

with Pictures."

. N.p., 09 Nov. 2000. Web. 16 Jan. 2014.

"EBRT for Melanoma."

. N.p., 01 Jan.

2001. Web. 16 Jan. 2014.

“Melanoma."

. N.p., n.d. Web. 16 Jan. 2014.

"Pauline's Diary - Page 7."

. N.p., n.d. Web. 17 Jan. 2014.

"Radiation Treatment for Melanoma." WebMD. WebMD. 03 Jan. 2001. Web. 17 Jan. 2014.

Restifo, Nicholas P. and Megan Bachinski. "The Scientist." The Scientist. N.p., 11 Apr. 2011.

Web. 17 Jan. 2014.

"Skin Cancer Foundation."

. N.p., 2013. Web. 14 Jan. 2014.

Strojan, Primoz. “Role of Radiotherapy in Melanoma Management.”

. 44.1 (2010): n. pag. Web. 17 Jan. 2014.    

“Types of Treatment.”

N.P., n.d. Web. 16 Jan. 2014.

"What Is Melanoma Skin Cancer?"

N.p., 29 Oct. 2013. Web.

16 Jan. 2014.

Vlock, Daniel R., et. al. “High-dose fraction radiation therapy for intracranial metastases of

malignant melanoma: A comparison with low-dose fraction therapy.”

49.11.

(1982): pages 2289–2294. Web. 17 Jan. 2014.      

   

   

Cell Respiration Yeast Lab

From: https://docs.google.com/document/d/1k4orKQXzhQ81XhFNIgAde5Sn81qJz5MMDFO74URJ-S4/edit


Joe Rode

2/16/14

Hon Bio Lab Report

The Effect of Water Levels on Cell Respiration

ABSTRACT

In this lab, we mixed yeast, sucrose, and salt with four different water levels to determine how different amounts of water affect the amount of carbon dioxide produced in cell respiration, specifically fermentation.

After viewing the results, we found that only small amounts of carbon dioxide were produced by too much or too little water, while large amounts of carbon dioxide were produced by moderate water levels in between.

INTRODUCTION

To achieve these results, we plugged the test tubes that the substances were in to restrict oxygen from entering, causing fermentation to occur. Fermentation is a form of cell respiration that does not need oxygen and is also known as anaerobic respiration. Cell respiration is the process by which glucose is broken down and ATP is produced.

Fermentation contains the same first step as aerobic respiration, but then takes different routes from there. The first step is known as glycolysis. In glycolysis, the six carbon glucose is broken down into two pyruvates. Essentially what happens is the six carbons are split into two three carbon groups, each called pyruvates. Then, what happens in aerobic respiration is the pyruvates are oxidized, diffused through the outer membrane of the mitochondria, and ultimately, oxygen acts as the final electron acceptor to form water.

Instead of oxygen, yeast fermentation creates ethyl alcohol, which also acts as an electron acceptor, making up for the lack of oxygen. Fermentation also regenerates NAD+, which allows for the process to become a cycle and continue to produce more ATP.

While we didn’t let the substances sit long enough to become alcohol, we let them sit long enough to be able to study the amounts of carbon dioxide produced through this process.

HYPOTHESIS

If the sucrose, yeast, and salt are placed at water levels of 20 ml, 10 ml, and  5 ml, then more carbon dioxide will be released than in the control (35 ml).

MATERIALS

4 graduated cylinders, 4 pieces of paper, 4 test tubes, 4 g of yeast, 4 g of table sugar, .4 g of salt, 70 ml of water, 4 stoppers with syringes attached, 4 stoppers, and a scale.

PROCEDURE

1.    We put 35 ml of water into one graduated cylinder, making this the control.

    2.    We placed 20, 10,  and 5 ml of water into three separate cylinders.

    3.    Next, we poured the water from each of the four graduated cylinders into four test tubes.

    4.    Using folded pieces of paper, we placed 1 g of yeast, 1 g of sucrose (table sugar), and 0.1 g of salt into each of the four test tubes at the same time for accuracy.           

    5.    We then put stoppers on the test tubes, shook them, switched the stoppers with stoppers with syringes, and let the mixtures sit for 5 minutes.    

    6.    When the 5 minutes was up, we immediately pressed on each of the syringes to study the amounts of  carbon dioxide created.

    7.    From there, we waited one minute, studied the carbon dioxide levels, and then pressed the syringes again.

    8.    We took three more data points using the method described in     Step 7, finishing with a total of  five data points.

RESULTS

       

Water Levels	Carbon dioxide produced after 0 min	Carbon dioxide produced after 1 min	Carbon dioxide produced after 2 min	Carbon dioxide produced after 3 min	Carbon dioxide produced after 4 min
5 ml	1.6 ml	1.9 ml	2 ml	3 ml	4 ml
10 ml	5 ml	5.1 ml	6.3 ml	7.4 ml	8.6 ml
20 ml	1.6 ml	1.8 ml	3.2 ml	4.5 ml	6.2 ml
35 ml	1.8 ml	1.9 ml	2 ml	2.2 ml	2.4 ml

The table above shows the amounts of carbon dioxide produced in the different water volumes and at the different times the syringe was pressed down.

The above graph displays the carbon dioxide produced after the allotted times. The different colored lines represent the different water levels (See key). Note: the 10 ml line is in pen, which is easy to see on paper and somewhat tough to see in a picture. The 10 ml line is slightly darker than the 5 ml line and is the highest line.

CONCLUSION

It is clear to see in the graph above that the moderate volumes of water- at 10ml and 20 ml- were the optimal levels for cell respiration. These volumes also experienced the steepest increase in carbon dioxide production. This is evident in observing that the slopes of 10 ml and 20 ml lines are much greater than the slopes of the 5 ml and 35 ml. While the 5 ml level had some increase in production, it still failed to reach close to the 10 ml and 20 ml. The control, the 35 ml volume, had the least carbon dioxide production and increase over time.

The reason water was used in this experiment was to hydrate the yeast and and allow yeast molecules to move freely through the liquid and react to the sugar. This makes the results unexpected and rejects our hypothesis because we thought that more water meant more reaction and thus more carbon dioxide, but instead, too much water, in the case of the 35 ml control, meant less production and slower increase in carbon dioxide. A similar result came with the 5 ml volume, but at least there was some increase and higher production at that level, allowing us to make the assumption that too much and too little water make for little production of carbon dioxide in fermentation.

Two constants were the sugar and yeast levels, and two potential sources of error were putting the different ingredients in at different times and having slight gaps in the stoppers for oxygen to escape and enter.

CITATION

    Helmenstine, Anne Marie. "What Is Fermentation?" About.com Chemistry. N.p., n.d. Web. 18 Feb. 2014.