Friday, September 13, 2013

Welcome to the Blog

Bios,

Well you have found th eMariner AP Biology blog. The blog will be used to communicate what is going on in the class and ask questions of me and your classmates. Today in class you will do the "APPLY THE CONCEPT" on page 299. Over the weekend do the "APPLY THE CONCEPT" on page 305. This is due Monday. You should also be reading chapters 15 and 16.

Welcome to the class,

Mr. Baker

Saturday, May 11, 2013

Preparing for the Exam

AP Bios,

If you have a question to ask leave it as a comment to this post. I will be checking the blog this evening, tomorrow morning, and tomorrow evening. Study on Garth.

Mr. Baker

Sunday, March 10, 2013

FRQ Test Question for HSPE Week

Explain how a hypothetical extracellular signal (like a hormone) can result in a cellular response. Your answer must include knowledge of 1) cell membrane receptor, 2) signal transduction in cell, 3) gene activiation, and 4) gene product. No specific example of a signal is required. It would help to review sections 5.5, 5.6, have knowledge of chapter 10, and parts of chapter 11. Each section, 1-4, is worth a maximum of 5 points and 20 points total. Grade reported as percent scored.

Here are some inks to DNA animations I have used in class.

http://www.hhmi.org/biointeractive/dna/DNAi_transcription_vo2.html

http://vcell.ndsu.nodak.edu/animations/regulatedtranscription/movie-flash.htm

http://www.hhmi.org/biointeractive/dna/DNAi_translation_vo2.html

http://www.hhmi.org/biointeractive/dna/animations.html

What is on Big Idea III Test b


          History of DNA research
        Griffiths
        Hershey – Chase
        Avery, MacLeod, and McCarty
        Watson and Crick / Franklin and Wilkins
          DNA structure
        Complementarity
        Nucleotide
        Antiparallel configuration
        5’ – 3’
          DNA replication
        Semiconservative, in a 5’ – 3’ direction
        Replication fork
        Leading strand, lagging strand, and Okazaki fragment
        Mutations
        Point mutations
        Chromosomal mutations
          Concept of the gene has changed
        Garrod’s observation and hypothesis
        One gene, one protein
          The Central Dogma
        Transcription
        mRNA processing
          Exons
          Introns
        Translation
          The process of translation
          The standard genetic code
          Point mutations and the genetic code
        Post translation protein modification
          Gene expression strategies
          The OPERON
        lac operon
        trp operon
        How it works and is regulated
          Eukaryotes
        Promoter structure
        Initiation of transcription
        Epigenetic changes
        Alternate splicing of mRNA

Thursday, February 14, 2013

Central Dogma Activity

5th period has informed me that I also gave them Wednesday the 20th to work on the project in class. So you have until the end of the period on the 20th to complete the assignment.

Saturday, January 5, 2013

Change in Schedule

If you are checking in to see what is on the test I have good news for you. I have decided to postpone the test until January 8th. If this is the first time you have checked in be sure to look at the post below. It tells you what you will be required to write about for the test. For those of you that are "chomping at the bit" to get going on Big Idea III please read chapter 7. I am tentatively planning on testing chapters 7 and 8 on February 4th.

See you Monday!

Friday, January 4, 2013

Wake Up Sleepy Heads! It is time to go back to school

I hope you have had a happy and restful winter break. We had the pleasure of experiencing climatological records last December. If you thought it was a bit dark, you were right. Seattle had 27 days of measurable precipitation last month, an ALL TIME RECORD for December.  The old record was 26 days. Also, December 2012 is tied for darkest December with December 2007. So December 2012 was as bad as we have seen during this century! Now for the good news. January 3, is climatologically the COLDEST DAY OF THE YEAR in Seattle.  Here is the proof, based on the period 1948-2012.  The average maximum temperature drops to 43F and the minimum temperature to 33.  Then then warming begins! This information was taken from the Cliff Mass Weather Blog. Click on the link to Cliff's blog to read the details. You will find the link on the left margin of this page.

As you recall, a written exam awaits you when you return. You will be asked to write about how mammals maintain one aspect of their homeostasis. The following is a list of topics I will accept:
  • Temperature regulation - hormonal: I am looking for you to describe how the endocrine system controls metabolism and therefore heat production and body temperature.
  • Maintenance of life during hibernation: see the chapter 29 Q and QA plus other bits through the chapter. A good paper will describe how a ground squirrel can survive the winter despite not having sufficient food or fat reserves. 
  • Temperature regulation - inputs and outputs: in total, animals regulate their body temperature by controlling the variables in the heat budget equation. For this question, write about examples of how various animals control all the components of the heat budget equation.
  • Blood oxygen/carbon dioxide balance: describe how the these are detected and how heart and respiration rates are controlled.
  • Blood glucose balance: this is not a topic we covered. But if you read section 39.4 I am confident that you will understand how it works and will be able to write a good paper.
  • Blood pressure regulation: see section 38.6 to refresh your mind. A discussion of nervous and hormonal regulation should be included.
A strong answer will describe the system in balance, out of balance, feedback mechanisms, and how the system gets back into homeostasis.

If you have a question about this post leave a comment. I will monitor the blog form time to time.

Be sure to tell the others about this post so they are ready.

See you Monday.

Wednesday, December 19, 2012

Answers to Chapter 31 DYUC and ATC


Do You Understand Concept 31.1?
                           
List the differences between innate and adaptive immunity.

Answer:
Innate immunity is nonspecific. It may be present all the time or activated in response to an injury or invasion. Innate systems include the skin and toxic molecules, which provide a rapid first line of defense, and phagocytic cells that ingest foreign particles. Adaptive immunity is specific and distinguishes between substances as self or nonself. Found only in vertebrates, adaptive immunity is slow to develop and involves proteins such as antibodies and T cell receptors that can recognize and destroy foreign particles.

Rarely, a person is born with a genetic disease and has no lymphocytes. What would be the consequences of this situation for the immune system? Explain why such a person would have to be very careful about going outdoors.

Answer:
Lymphocytes include both B cells and T cells and are involved in adaptive immunity. A person without them would not develop immunity over time to pathogens in the environment, and thus would be at risk for infections when going outdoors. The immune system would have to rely on less-specific innate responses, which might not be as effective.

Do You Understand Concept 31.2?

Outline the sequence of innate defenses encountered by a pathogenic bacterial cell if it is ingested in food. Similarly, outline the defenses encountered by a bacterial cell that lands in the nose.

Answer:
A bacterial cell that is ingested in food will encounter mucus in the body cavities, which may trap it. In the stomach it will also be exposed to gastric juices containing hydrochloric acid and proteases. A bacterial cell that lands in the nose will encounter mucus, lysozymes that can cleave bacterial cell walls, and defensins. Defensins can insert themselves into the bacterial membrane and increase its permeability to water and all solutes.

Antihistamines are used to treat the symptom of sneezing due to inflammation caused by irritants in the airways. How do you think antihistamines might work?

Answer:
Antihistamines block the action of histamine, a substance that increases permeability of blood vessels to white blood cells and other molecules and allows these to move into tissues that are challenged. If these cells and molecules are blocked they will not be able to initiate the responses of inflammation and sneezing.

A massive inflammation due to a food allergy can be treated with an injection of epinephrine. Refer to the description of epinephrine’s effects in Concept 30.2. How do you think this hormone relieves the inflammation symptoms?

Answer:
Epinephrine is involved in the fight-or-flight response. Some of its effects include increased heart rate and blood flow, and increases in fuel in the blood. These responses can combat the inflammation caused by a food allergy. Epinephrine also constricts blood vessels. This results in less flow in the capillaries and a reduction of inflammation.

Do You Understand Concept 31.3?

Make a table describing the four key features of the adaptive immune system.

Answer:

Specific
Focuses responses on pathogens that are actually present
Diverse
Responds to novel pathogens
Distinguishes self from non-self
Doesn't destroy self-cells
Has immunological memory
Responds effectively to the same pathogen in later exposures

 
In 2009, the H1N1 strain of influenza was a worldwide epidemic. Notably, very old people, who had been alive during the 1918 flu outbreak, had low rates of H1N1 infection. Explain this in terms of immunological memory.

Answer:
The immune system remembers a pathogen after an earlier exposure through the adaptive immune response. Older people who had been exposed to that pathogen in the first epidemic and survived would have mounted a stronger and more rapid immune response to the subsequent exposure.

Insulin-dependent diabetes (Type 1) results from a destruction of the cells in the pancreas that make the hormone insulin (see Concept 39.4). One hypothesis for this disease is that it is caused by an autoimmune reaction. Explain how this might happen and how you would investigate your hypothesis.

Answer:
During development, B cells that fail to recognize self-cells usually undergo apoptosis, called clonal deletion. If clonal deletion doesn't occur, it can lead to an autoimmune disease, in this case destruction of the pancreatic cells that make insulin. One way to test this would be using molecular mimicry to see if exposure to an antigen very similar to the suspected self antigen, the pancreatic cells, would lead to an immune response.

Do You Understand Concept 31.4?

Sketch an IgG antibody, identifying the variable and constant regions, light and heavy chains, and antigen-binding sites.

Answer:
Refer to textbook Figure 31.7A.
 
The bacterium that causes diphtheria (refer to textbook Figure 31.4) synthesizes a toxic protein. You have probably not been exposed to this bacterium or its toxin. At the present time, are you making B cells and antibodies that bind specifically to diphtheria toxin? Explain your answer.

Answer:
There are millions of naïve B cells in circulation, each one specific to a particular antigen, even if not previously exposed. A small number of the B cells make an antibody on their cell surface that binds to the diphtheria toxin. Once a B cell is activated by antigen-binding (exposure) only then will it begin antibody production.

When an antigenic protein such as diphtheria toxin (see above) enters the bloodstream, numerous clones of B cells are activated. Explain.

Answer:
The original antigen binding stimulates the B cell to divide and create a clone of cells. These are genetically identical to the B cell and will all produce or secrete antibodies with the same specificity as the B cell and will bind to the free antigen in the bloodstream. Because an antigen, such as a protein, usually has several groups of atoms that themselves are antigens (antigenic determinants), there will be numerous B cell clones activated.

Do You Understand Concept 31.5?

Compare the T cell receptor and B cell receptor in terms of structure, diversity, and function.

Answer:
T cell and B cell receptors are similar in structure, each with a variable and a constant region, though the T cell receptors are smaller and are glycoproteins instead of immunoglobulins. The two types are equally diverse and specific to a particular antigen. B cells function as part of the humoral response to produce antibodies. T cells are of two types: TH and TC. TH cells can bind to an antigen and stimulate other immune cells, including B and TC cells, to divide. TC cells bind to and destroy cells that bear the antigen on their surface.

What are the similarities and differences in function between class I and II MHC proteins?

Answer:
Class I MHC proteins are present on the surfaces of nucleated mammalian cells. They present fragments of antigens to TC cells. Class II MHC proteins are on the surfaces of macrophages, B cells, and dendritic cells. They ingest antigens and bind fragments for presentation to TH cells.

What are the roles of TH cells in cellular and humoral immunity?

Answer:
TH cells with specific receptors bind to antigen-presenting cells and then release cytokines, which stimulate B cells to divide in the humoral immune response and TC cells to divide in the cellular immune response.

Since MHC proteins are highly variable and almost always differ between unrelated people, an organ transplant between such people will generally provoke a cellular immune response, and the organ will be rejected. Patients receiving organ transplants are treated with cyclosporin, a drug that inhibits T cell development. How do you think cyclosporin prevents rejection? What side effects might you expect in treated people?

Answer:
Blocking the production of T cells would interfere with the immune responses at several stages immediately following recognition. Without T cell activity, the transplanted organ would not be treated as an antigen or be subject to rejection or attack. However, the patient would also not be able to mount an immune response to real pathogens and so would be susceptible to disease.


Apply the Concept for Chapter 31

Concept 31.1 The Adaptive Immune Response Is Specific, p. 629

1.

Mother
Mother
Fetus
Fetus
Result
Genotype
Phenotype
Genotype
Phenotype
 
Dd
Rh+
Dd
Rh+
Compatible
dd
Rh
Dd
Rh+
Incompatible

2. An immune response is mounted in the mother to the Rh+ fetal cells. But the fetus has been born and so is not affected. After the mother’s response, immune cells specific for Rh+ remain as memory cells. The next time a fetus carries the Rh+, there is a massive response by the mother, only this time the fetus has not yet been born and hemolytic disease can result.

3. Antibodies against Rh+, given to the mother, “tie up” antigens that may pass to the mother, and shield the mother’s immune system, with its memory cells, from the antigen so an immune response is not mounted.

 

Answers to Chapter 38 DYUC and ATC


Do You Understand Concept 38.2?

Draw sketches of circulatory systems showing a single and a double circuit design. Label all of the parts.

Answer:
Refer to textbook art on pages 748 and 750.

Why can a mammalian circulatory system have different pressures in the pulmonary and the systemic circuits, and why do you think this is important?

Answer:
Although the pulmonary and the systemic circuit are in series, they are separated by the heart, which provides a separate pump for each. The right ventricle pumps blood through the pulmonary circuit, and the left ventricle pumps blood through the systemic circuit. This anatomy enables the heart to create a higher pressure in the aorta than in the pulmonary artery, which is important because the total length of blood vessels, and hence the total resistance, is greater in the systemic circuit.

Do You Understand Concept 38.3?

A red blood cell is flowing through the superior vena cava. List all of the heart chambers, valves, vessels, and organs it will pass through before it leaves the heart in the aorta.

Answer:
The blood cell will enter the right atrium, flow through an atrioventricular valve into the right ventricle and be pumped through the pulmonary valve into the pulmonary artery, flowing to the lung. After oxygenation, the blood cell will return to the heart via the pulmonary vein and enter the left atrium. It will pass through another atrioventricular valve into the left ventricle and be pumped into the aorta, passing through the aortic valve.

Why do the atria contract before the ventricles? What would happen if they contracted at the same time?

Answer:
The atria contract when an action potential spreads through gap junctions. They are not coupled through these junctions to the ventricles. Instead, the atrioventricular node generates another action potential when its cells are depolarized and conducts it via the bundle of His to the ventricles. If the chambers contracted at the same time it would be possible for blood to flow in the wrong direction.

Do You Understand Concept 38.4?

List the major components of blood (liquid and cellular) and state their functions.

Answer:
Plasma is the liquid, extracellular matrix of blood and contains water and solutes, such as nutrients, ions, waste products, hormones, gases, and clotting proteins. Cellular components of blood include: erythrocytes, or red blood cells, which carry respiratory gases; leukocytes, or white blood cells, of the immune system; and platelets, which are involved in blood clotting.

Some competitive cyclists have admitted using erythropoietin as an illegal performance-enhancing drug. How can erythropoietin enhance performance?

Answer:
Erythropoietin enhances the blood's capacity for carrying oxygen by extending the life of existing red blood cells as well as by stimulating development of new ones in the bone marrow.

Do You Understand Concept 38.5?

In which vessels of the circulatory system does the blood move most rapidly? In which does it move most slowly? Why?

Answer:
Blood moves most rapidly through the arteries due to higher pressure after ventricular contraction and the elastin and smooth muscle fibers that can stretch and withstand this pressure. Blood moves most slowly through capillaries due to their tiny size and the huge quantity of capillaries, resulting in both lower blood pressure and allow for exchange of material with the interstitial fluid.

Compare and contrast the structure of the walls of arteries, capillaries, and veins. How does the structure of the wall relate to each vessel’s function?

Answer:
Arterial walls contain elastin fibers and smooth muscle fibers that accommodate the high pressure and also propel the blood forward through elastic recoil. Capillaries are very permeable to allow for exchange with the interstitial fluid. Veins have no elastin layer due to the low pressure and rate of flow through them, but may have one-way valves to prevent backflow of blood.

Certain parasitic worms can block lymph vessels. Suppose the lymph vessels draining a leg were completely blocked by a parasite infestation. What do you think would happen to the leg? Explain your answer.

Answer:
Lymph capillaries take up excess fluid in the capillary beds and then pass the fluid into larger lymphatic vessels that return it to the heart.. If this system were blocked, the lymph would remain in the capillary beds, and the leg would swell as the fluid accumulated.

Occasionally soldiers or guards standing at attention and not moving will faint. Why do you think that occurs? How could they avoid that embarrassing situation?

Answer:
Fainting can be due to not enough oxygen circulating in the blood. Soldiers who don't move might increase blood flow returning to the heart by flexing skeletal muscles in their legs to compress the veins. They also might exhale completely and inhale deeply to take in more highly oxygenated air.

Do You Understand Concept 38.6?

What three factors determine the mean arterial pressure?

Answer:
Mean arterial pressure is equal to the product of the heart rate, the stroke volume, and the total peripheral resistance.

If blood pressure gets too high, will angiotensin levels go up or down? What about ADH levels? Explain your answer.

Answer:
If blood pressure becomes elevated, angiotensin levels will fall because its function is to raise MAP and blood flow to some organs by constricting arterioles throughout the body. ADH levels would also fall so that kidneys would lower their reabsorption of water, decreasing blood volume and thus pressure.

Apply the Concept for Chapter 38

Concept 38.1 A Beating Heart Propels the Blood, p. 752
 
1. Systole is the duration of contraction of the ventricles, and it would extend from point B to point D.

2. Diastole is when the ventricles are relaxing and filling, and it would extend from point D through B.

3. The blood pumped each cycle is the difference between the end systolic volume and the end diastolic volume—or 70 ml.

4. The first heart sound occurs when the atrioventricular valves shut at the beginning of systole—point B. The second heart sound is when the aortic valve shuts at the end of systole, at point D.

5. The aortic valve would open at point C, when the pressure in the ventricle exceeds the back pressure in the aorta.

Concept 38.2 Blood Circulates in Arteries, Capillaries, and Veins, p. 758

1. There is no sound at the high cuff pressure because the arteries into the arm are totally occluded by the pressure. As the cuff pressure falls, it will eventually fall below the maximum arterial pressure, and at that time the arterial pressure will squeeze some blood into the artery. The sound is due to the starting and stopping of that flow.

2. When the cuff pressure falls below the lowest arterial pressure, the blood will flow continuously through the artery and no periodic sound will be heard.

3. The cuff pressure at which the tapping sounds are first heard (120 mm Hg) is closest to the systolic pressure and the cuff pressure at which the periodic sounds cease (60 mm Hg) is closest to the diastolic pressure.