Immune System & Disease
Reading
OpenStax orange book: Read Ch. 17 - "The Immune System and Disease", and section 13.1 - "Prokaryotic diversity" (bacteria)
BJU: Read Ch. 10 - "Bacteria and viruses", and section 22B - "The lymphatic system and immunity"
AP students planning to take the AP exam need to be doing practice exam questions during this time
Topics
Labs
Memo: 2020-2021 labs will include hands-on and virtual, and may vary as the Covid-19 situation changes.
Here is a list of possible labs for this lesson. I will choose from this list when we get here.
OpenStax orange book: Read Ch. 17 - "The Immune System and Disease", and section 13.1 - "Prokaryotic diversity" (bacteria)
BJU: Read Ch. 10 - "Bacteria and viruses", and section 22B - "The lymphatic system and immunity"
AP students planning to take the AP exam need to be doing practice exam questions during this time
Topics
- Viruses
- Immune system
- Lymphatic system
Labs
Memo: 2020-2021 labs will include hands-on and virtual, and may vary as the Covid-19 situation changes.
Here is a list of possible labs for this lesson. I will choose from this list when we get here.
- HHMI Virus Explorer weblab
- Bio-Rad Microbes and Health lab (Yogurtness lab)
A virus invading a cell
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A bacterium in all its glory
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Lecture outline
Viruses are not considered alive. They have no cell membrane, or internal organelles; and they do not divide. Instead, they invade a host cell, inject their DNA or RNA, and take over the machinery of the host cell to make copies of themselves. Viruses infect all types of organisms - animals, plants, bacteria, etc.
Bacteria are living, single-celled organisms, about 1/1000ths the size of a human cell, but huge compared to viruses! All bacteria are prokaryotes (no nucleus, no organelles, divide by binary fission), but they are divided into two kingdoms - Archaebacteria and Eubacteria.
A breakdown of the immune system:
Type 1: Innate immunity (innate = what you're born with)
A) Physical barriers
Type 2: Adaptive immunity (also known as specific or targeted or acquired immunity)
Your adaptive immune response kicks-in if your innate immune response (above) is insufficient.
The adaptive immune system responds to an antigen; antigens are foreign substances that provoke an immune response.
Antigens are typically organic molecules not normally found in the body
B-cells and T-cells are types of white blood cells called lymphocytes
B-cells produce specific antibodies which circulate throughout the body and bind to antigens to 'tie them up' - so they can't bind to their target, and a macrophage can come along and eat it up.
Helper T-cells release chemicals that help other white blood cells recognize and destroy antigens
Cytotoxic T-cells release toxic chemicals that destroy target cells
Viruses are not considered alive. They have no cell membrane, or internal organelles; and they do not divide. Instead, they invade a host cell, inject their DNA or RNA, and take over the machinery of the host cell to make copies of themselves. Viruses infect all types of organisms - animals, plants, bacteria, etc.
Bacteria are living, single-celled organisms, about 1/1000ths the size of a human cell, but huge compared to viruses! All bacteria are prokaryotes (no nucleus, no organelles, divide by binary fission), but they are divided into two kingdoms - Archaebacteria and Eubacteria.
A breakdown of the immune system:
Type 1: Innate immunity (innate = what you're born with)
A) Physical barriers
- Skin
- Mucous (in nose, throat, etc)
- Cilia (sweeping action)
- Stomach acid
- Tears
- Saliva
- Urine
- Other secretions
- White blood cells (leukocyte = white + cell)
- Neutrophils and macrophages migrate to area of infection and engulf and destroy invaders - known as phagocytosis
- Eosinophils produce toxins
- Natural killer cells police the blood and lymph, cause cell lysis of virus-infected cells
- Inflammatory response - redness, heat, swelling
- Fever - speeds up repair
- Blood vessels dilate, become more permeable, allow soldiers, chemicals, clotting factors to move to the area
Type 2: Adaptive immunity (also known as specific or targeted or acquired immunity)
Your adaptive immune response kicks-in if your innate immune response (above) is insufficient.
The adaptive immune system responds to an antigen; antigens are foreign substances that provoke an immune response.
Antigens are typically organic molecules not normally found in the body
- Toxic molecules attached to the cells of bacteria, fungi, etc.
- Various molecules which present on the surface of virus-infected cells
- Chemicals in poison ivy, animal dander, detergents, cosmetics, etc.
- Foreign molecules on pollen
B-cells and T-cells are types of white blood cells called lymphocytes
B-cells produce specific antibodies which circulate throughout the body and bind to antigens to 'tie them up' - so they can't bind to their target, and a macrophage can come along and eat it up.
- Antibodies are large Y-shaped proteins with two 'crab arms' that bind up antigens and clump them together. Your body has one billion(!) different antibodies, each with a unique shape, and each targeted to a different potential antigen.
- Antibodies are found in blood, lymph fluid, tears, saliva, breast milk, and other body fluids.
Helper T-cells release chemicals that help other white blood cells recognize and destroy antigens
Cytotoxic T-cells release toxic chemicals that destroy target cells
| Immune System lecture slides |
We will watch the following video clips on bacteria, viruses, and the immune system.
pGLO Bacterial Transformation lab (AP Bio lab #9) - part 1
In this 2-part lab we will insert foreign DNA from a glowing jellyfish into some bacteria, and use the bacteria's genetic machinery to express the foreign DNA. The bacteria will then glow bright green under UV light. This is the same technique used in Biomedical Research to make modern drugs
Objectives: learn the techniques of recombinant DNA and gene splicing
2018-2019 class: We will be trying a new lab protocol which results in Pink, Purple, and Blue transgenic bacteria. (Rainbow Transformation - see handout below)
In this 2-part lab we will insert foreign DNA from a glowing jellyfish into some bacteria, and use the bacteria's genetic machinery to express the foreign DNA. The bacteria will then glow bright green under UV light. This is the same technique used in Biomedical Research to make modern drugs
Objectives: learn the techniques of recombinant DNA and gene splicing
2018-2019 class: We will be trying a new lab protocol which results in Pink, Purple, and Blue transgenic bacteria. (Rainbow Transformation - see handout below)
| pglo_bacterial_transformation_lab__rainbow_transformation__-_student_handout.pdf |
Background to the pGLO/molecular cloning lab:
- RECOMBINANT-DNA is where we take a piece of DNA from one organism and introduce it into the DNA of another host organism. In this case, we are taking a piece of jellyfish DNA and inserting it into the DNA of a bacteria. The bacteria serves as the HOST organism. The piece of jellyfish DNA is called the GENE-OF-INTEREST. In this case, the section of jellyfish DNA is comprised of a GENE which encodes for a PROTEIN in the jellyfish which causes it to GLOW GREEN in its natural environment (the ocean). The jellyfish manufactures this "green" protein perhaps to defend against predators, or maybe to attract things - we don't really care for purposes of this lab. What we care about is using the MOLECULAR MACHINERY of the bacteria to start cranking-out foreign proteins which could be an important BIOLOGIC DRUG we are trying to mass-produce, let's say.
- GENE SPLICING is the process of taking carefully-chosen molecular scissors - or RESTRICTION ENZYMES - and cutting out the jellyfish "glowing protein" gene and inserting it exactly where we want it on the bacterial DNA. For our lab, the Bio-Rad company has already done this for us. In a real project, you the Bioengineer would select an appropriate restriction enzyme to use as the "molecular scissors" based upon the gene map of the DNA VECTOR you were using
- MOLECULAR CLONING describes the whole process of using E. Coli bacteria as your "host" factory, to manufacture millions & millions of copies (CLONES=COPIES) of your gene-of-interest, and then to crank out large quantities of the protein you are trying to manufacture. Bacteria makes a good factory because it replicates very fast - every 20 minutes.
- This lab exercise illustrates how modern Biopharmaceuticals are made! Instead of making lots of green protein which is a really cool trick, you the Bioengineer would be making lots and lots of Insulin, or Monoclonal Antibodies, or some other biologic drug in order to cure diseases and improve the lives of millions of people.
Lab report
Write a 2 page lab report on the pGLO lab, using 1.2 spacing. Submit a professional-looking report with an appropriate title header, name, date, etc. Address the following questions:
1. What is molecular cloning?
2. What are we doing in this lab? Don't try to outline the whole procedure in your report - I just want to know "what we are doing". What are we trying to accomplish in your own words?
3. We labeled 4 plates as follows: 1) LB, -pGLO, 2) LB, ampicillin, -pGLO, 3) LB, ampicillin, +pGLO, and 4) LB, ampicillin, arabinose, +pGLO. Question: What ends up growing on each plate? Describe what should appear on each plate after incubation.
4. What is the purpose of the LB broth?
5. Why do we use ampicillin in the experiment?
6. What is the purpose of the arabinose sugar in the experiment?
7. What is meant by a "plasmid vector"?
8. The bottom line: why does this bacteria glow green? Explain this in "biology" terms.
9. List 4 or 5 common Biopharmaceuticals or "Biologic drugs" which are produced in this manner, and what do they do? Hint: search "Biologic drugs list" for starters.
Write a 2 page lab report on the pGLO lab, using 1.2 spacing. Submit a professional-looking report with an appropriate title header, name, date, etc. Address the following questions:
1. What is molecular cloning?
2. What are we doing in this lab? Don't try to outline the whole procedure in your report - I just want to know "what we are doing". What are we trying to accomplish in your own words?
3. We labeled 4 plates as follows: 1) LB, -pGLO, 2) LB, ampicillin, -pGLO, 3) LB, ampicillin, +pGLO, and 4) LB, ampicillin, arabinose, +pGLO. Question: What ends up growing on each plate? Describe what should appear on each plate after incubation.
4. What is the purpose of the LB broth?
5. Why do we use ampicillin in the experiment?
6. What is the purpose of the arabinose sugar in the experiment?
7. What is meant by a "plasmid vector"?
8. The bottom line: why does this bacteria glow green? Explain this in "biology" terms.
9. List 4 or 5 common Biopharmaceuticals or "Biologic drugs" which are produced in this manner, and what do they do? Hint: search "Biologic drugs list" for starters.
| pGLO_lab__intro PowerPoint |
Homework
| 16._immune_system_questions_part_1.docx |
| 16._immune_system_questions_part_2.docx |