Chapter 14: Viruses & Immunology
The ___ of the B cells is the binding site for helper T cells. The binding of helper T cells to B cells releases ____ (IL-2 and IL-4) and triggers the development of B cells into plasma cells and produce antibodies
MHC II interleukins
What is the purpose of a major histocompatibility complex?
MHCs are receptors on antigen-presenting cells. They bind to fragments of antigens that have been degraded by the infected cell and display it on their surface. T cells then bind to the infected cells.
Describe the nature of p53 reactivation as a cancer-fighting strategy.
Many of the early trials involved specific delivery of an active p53 gene via gene therapy. However, such delivery is impractical for human patients in many cases. Now researchers are looking for drugs that can be taken that will increase the levels of p53.
Natural killer cells (NK cells)
Member of class of leukocytes called lymphocytes Kills infected or cancerous cells Secretes cytokines that call up other cells Works with dendritic cells Helps decide whether to activate acquired immunity
T cell memory
Most of T cells generated by first infection will die 5-10% survive as memory cells. - provide higher reproductive rate even in absence of antigen - no need to go thru initial activation process
What are two components all viruses must have?
Nucleic acid and capsid
If you were going to design a drug to fight a virus, what would be likely targets for the drug design?
One good choice would be a drug that attacks one of the specific protein spikes on the virus. This may be an antibody that attacks it, or a drug that blocks its ability to attach to the host cell. Another choice would be a drug that inhibits a key viral enzyme, such as the reverse transcriptase of a retrovirus, or the enzymes involved in repackaging the viruses.
What are the components of innate immunity?
One part includes physical barriers (such as skin, mucus, and tears). The cells of the innate immune system are dendritic cells, macrophages, and natural killer (NK) cells.
First line of defense with innate immunity
Physical barriers - skin, mucous, cilia Chemical barriers - Low pH, lysozyme, and antimicrobial peptides Microbial - Host microflora
Killer T cells destroy antigen-infected cells by
binding to them, releasing protein that perforates plasma membranes of infected cells
In the presence of antigen alone, the T-cell receptor ___
binds to antigen presented on the surface of a macrophage cell by the MHC protein. - There is still no proliferation of T cells because the second signal is missing. In this way the body can avoid an inappropriate response to its own antigens.
Berlin patient is immune to aids due to ____ transplant from resistant donor. This led to efforts to develop ____ gene therapy
bone marrow, ex-vivo
Each chain in immunoglobulins has ____ domains
constant and variable domains - variable domain varies with antigen specificiy
general structure of enveloped viruses
covered with protein spikes
What types of therapy are used to fight AIDS?
creating vaccines to the virus and using antiretroviral therapy.
In the absence of antigen, proliferation of T cells ___
does not take place
two in one antibodies
engineered to recognize 2 different antigens
Killer T cells requires 2nd signal because
ensures response is appropriate
Antibody binds to ____ on antigen
epitope
How are monoclonal antibodies produced?
formation of hybridoma - B cell fused with mouse myeloma cells - B cells produce antibodies - unfused cells die and only hybridomas survive - culture individual cells and select desired clone
Macrophages
function is to phagocytose microorganisms Two functions: 1. Kill cell directly 2. Use digested fragments to alert adaptive immune cells - antigen-presenting cell - like raising the flag to alert against intruders
Characteristics of viruses
genetic material surrounded by protein coat or envelope Pathogens of bacteria, plants, and animals Any organism subject to viral infection
structure of HIV
genome surrounded by protein coat - shape of truncated cone surrounded by membrane envelope
two embedded envelope proteins
gp41 and gp120
Most common target for drugs against HIV are ___ and ___ in an attempt to prevent ____
gp41 and gp120 in an attempt to prevent entry of the virus
steps in MAP kinase signaling pathway
growth hormone binds receptor stimulates pathway leading to activation of Ras Ras activates MAPK MAPK moves to nucleus and activates transcription factors - stimulates cell growth
Mechanism of vaccines
includes weakened form of infectious agent organism produces antibodies against agent cellular memory key to vaccine success
Basic strategy for developing an AIDS vaccine
inject viral gene into muscle expressed as viral protein body develops antibodies against antigen
Importance of gene therapy
introduce good copy of defective gene (ex. cystic fibrosis)
Type 1 diabetes is an autoimmune disease in which the body attacks the insulin producing Beta-cells in the pancreas, this is possibly a result of a faulty ______ selection.
negative
if the cell's receptors encounter self-antigens that are recognized with high affinity, it undergoes a process called ___ selection and is programmed for ____.
negative apoptosis, or cell death
proto-oncogenes
normal eukaryotic genes that are very similar in sequence to a cancer causing gene
Monoclonal antibodies
only one clone that produces only one type of antibody enable large production of antibodies with designed specificity
Describe different techniques that might restore p53 to a cell lacking it.
p53 can be restored in several ways. One way would be through gene therapy to give the patient functioning copies of the p53 gene if he or she lacks it. Another is to neutralize molecules that naturally inhibit p53. Another is to give the patient drugs that stimulate the production of p53 by stimulating the transcription of the p53 gene. Finally, one could use drugs that would inhibit the transcription of molecules that act as inhibitors of p53.
If the receptors recognize self-antigens or MHC but with low affinity, then the cell undergoes ___ selection and differentiates into a ____
positive killer T cell or a helper T cell
B cells function
produce antibodies
General characteristics of a retrovirus
replication "backward" compared to central dogma - DNA made from RNA template ssRNA genome - RNA used as template to make dsDNA, after infection DNA product incorporated into host DNA - facilitated by long terminal repeats (LTRs)
What happens if a tumor suppressor is mutated
replication and division become uncontrolled and tumors result.
polyclonal antibodies
result from polyclonal expansion Organism infected with antigen Many B cell clones respond - poly clonal expansion - Each produces only one antibody - binds one epitope
What enzyme is responsible for the production of viral DNA from a retrovirus?
reverse transcriptase
A common method of attachment of a virus to a host cell involves the binding of one of the ____ on the envelope of the virus to a specific receptor on the host cell.
spike proteins
composition of HIV
ssRNA genome + proteins
antigens
substances that trigger an immune response (T cells have T-cell receptors (TCRs) on their surfaces that recognize and bind to antigens)
Virotherapy
the use of viruses to kill cancer cells adenovirus the main choice must be specific for cancer cells
Steps in HIV infection
virus binds cell surface receptor viral core enters into cell and disintegrates reverse transcriptase converts ssRNA into dsDNA viral DNA integrated into host genome viral DNA transcribed when host cell activated then goes through life cycle and produces more viral particles
general steps of transcriptional targeting
virus engineered to be more active in cancer cell promotors for viral replication triggered more often
What is the difference between the lytic pathway and the lysogenic pathway?
In the lytic pathway, the viral nucleic acid is replicated in the host cell and packaged into new virus particles that lyse the host cell. In the lysogenic pathway, the viral DNA is incorporated into the host DNA.
Two main branches of the immune system
Innate - Always present, first line of defense Acquired - Developed over time
What is innate immunity? What is acquired immunity?
Innate immunity refers to a variety of protective processes, including skin, mucus, and tears as a first line of defense, and dendritic cells, phagocytes, macrophages, and natural killer cells as a second line of defense. These are always present, and the innate-immunity cells are always circulating in the body. Acquired immunity refers to the processes involving B cells and T cells, in which specific sets of them are activated in response to an antigen challenge, and these subsets then multiply.
Steps of lytic pathway
Involves virus lysing infected cell: -Virus binds to cell membrane and releases genome (like DNA) into cell - DNA is replicated by host DNA polymerases and transcribed by host RNA polymerases - mRNA translated into protein - New virions produced and released from cell
What are two ways that viruses disrupt their hosts? Compare and contrast these two pathways.
Lytic cycle vs lysogeny ■ Lytic cycle - virus binds and releases genome, genome is replicated and transcribed, new virions produced and released from cell, host destroyed ■ Lysogenic cycle - same entry as lytic cycle, viral DNA integrated into host DNA without lysing cell, eventually becomes lytic
problem with monoclonal antibodies
b cells dont survive in culture
What are leukocytes?
(white blood cells) Lymphocytes that kill infected or cancerous cells through secretion of cytokines Circulate in lymphatic system
Different types of cells associated with innate immunity and their functions
*Dendritic cells* - first to encounter viruses or bacteria *Macrophages* - Cells that digest cellular debris and pathogens *Natural killer cells* - Kill infected or cancerous cells
Acquired immunity depends on two types of lymphocytes
*T cells* - mature in Thymus *B cells*- mature in Bone marrow
What do T cells and B cells do? To which branch of immunity do they belong to?
*T cells* can destroy infected cells or controls the differentiation or activity of other cells of the immune system and *they belong mainly to acquired immunity*. *B cells* are involved in the production of antibodies and are mainly involved with the molecular aspect of the immune system.
Describe the relationship between the innate immunity system and the acquired-immunity system.
*The cells of the innate system* initially attack a pathogen, such as a virus, bacteria, or even a cancerous cell. They then present antigens from the pathogen on their surfaces via their MHC proteins. *The acquired immunity cells* then recognize the MHC/antigen complex, bind to it, and begin the involvement of the acquired immunity system.
each antibody can bind ___
2 antigens
What is unique about the life cycle of a retrovirus?
A retrovirus has an RNA genome that must pass through a stage in which it is reverse-transcribed to DNA, and this DNA must recombine with the host's DNA.
What is a tumor suppressor? What is an oncogene?
A tumor suppressor is a molecule that restricts the ability of a cell to grow and to divide. An oncogene is a gene whose product stimulates a cell to grow and to divide.
Describe the difference between a tumor suppressor and an oncogene with respect to the actual causes of cancer.
A tumor suppressor is a protein that helps control cell growth and division. It is like the brakes on a car, trying to slow down a process. Many cancers are related to mutation of tumor suppressors. An oncogene produces something that stimulates growth and division. This is like the accelerator of the car. Many other cancers are caused ultimately by overactivation of an oncogene.
What health conditions are linked to malfunctioning immune systems?
AIDS is the most well-known problem of a malfunctioning immune system. SCID is also high on the list. All allergies are immune system problems, as are autoimmune diseases. Many forms of diabetes are caused by an autoimmune disease in which a person's pancreatic cells are attacked by the immune system.
How and why are vaccines helpful for the immune system?
Allow antibodies to be produced against the infectious agent without causing disease, provide memory for immune system which generates a quick response for future infections
What health conditions linked to malfunctioning immune systems?
Autoimmune disease - immune system attacks body's own tissues Allergies
Th cells stimulate ______
B cells
What are the components of acquired immunity?
B cells, which make antibodies, killer T cells, which attack infected cells, and helper T cells, which help activate B cells.
When an infection takes place, a ___ protein is produced in response to the infection. which is presented on the surface of the infected cell and binds to a ____ protein on the surface of the immature T cell. - Giving the second signal that allows it to grow and proliferate
B7 CD28
B cells mature in ___
Bone marrow
How do Th cells bind to target cells
CD4 receptor recognizes MHC II on APC
What characteristics are shown by cancer cells?
Cancer cells continue to grow and divide in situations in which normal cells do not, such as when they are not receiving growth signals from surrounding cells. They also continue to grow even if surrounding tissues are sending out "stop growth" signals. Cancer cells can co-opt the body's vascular system, causing the growth of new blood vessels to supply the cancerous cells with nutrients. Cancer cells are essentially immortal. They can continue to grow and to divide indefinitely. Cancer cells can break loose, travel to other parts of the body, and create new cancerous areas, a process known as metastasis.
What is clonal selection?
Clonal selection refers to the process in which a particular T cell or B cell is stimulated to divide. Only the one bearing the correct receptor for the antigens being presented is selected.
two types of T cells
Helper T cells (Th) - involved in process of B-cell maturation and Cytotoxic T cells (killer Tcells, Tc) - destroy infected cells
Reactivating p53 to treat cancer
Drugs to help it fold and increase levels Drugs to disrupt inhibitors of p53
What are the two types of gene therapy?
Ex vivo gene therapy, in which the cells are removed from the patient before being infected with the virus carrying the therapeutic gene, and in vivo gene therapy, in which the patient is directly infected with the virus carrying the gene.
Dendritic cells
Found in skin, mucous membrane, lungs, and spleen Use suction-cup-like receptors to grab invaders and engulf them via endocytosis Travel through lymph to spleen, where they present antigens to helper T cells (Th cells) Display antigens on surface and activate acquired immune system
Way B cells produce antibodies with unique specificities
Gene rearrangement for both H and L chains Each B cell produces only one type of antibody
What is HAART?
HAART stands for highly active antiretroviral therapy. It is based on using a combination of drugs to attack multiple parts of the HIV life cycle.
How does HIV confound the human immune system?
HIV is difficult to kill because it is difficult to find. The reverse transcriptase of HIV is very inaccurate in replication. The result is rapid mutation of HIV. There is also a conformational change of the gp120 protein when it binds to the CD4 receptor on a T cell making it difficult to create antibodies that will mount a useful attack. HIV is also adept at evading the innate immunity system. Lastly, HIV hides from the immune system by cloaking its outer membrane in sugars that are very similar to the natural sugars found on most of its host's cells, rendering the immune system blind to it.
Which cells are attacked by HIV?
Helper T cells
What's the difference between positive selection and negative selection?
Positive selection - receptor of DP cell recognizes self-antigens/MHC with low affinity ■ Differentiation into killer or helper T cells ■ Requires 2nd signal for activation Negative selection - receptor recognizes self-antigens with high affinity ■ DP cell reacts to self antigens and is programmed for apoptosis
How are viruses differentiated
Presence of an envelope Nature of genome - DNA or RNA, - Linear vs. circular - small vs. large - single-stranded vs. double Mode of incorporation - nucleic acid remains separate or inserts into host chromosome
MHC molecules and their role in presenting antigen
Responsible for transplant (histo = tissue) rejection MHC is the flag pole and antigen is the flag - present the antigen so the body can see
What is the genetic material of a virus?
Some viruses have DNA and some have RNA. In some cases, a viral genome is single-stranded and in others it is double-stranded.
What is the role of each T cell in the immune response? What issues could arise in the case that either T Cell is malfunctioning?
T cells - ■ Helper T cells - help cell dock to MHC II of antigen-presenting cell by recognizing MHC II, stimulate B cells ■ Memory T cells - remember infection so in future don't have to go through initial activation process Issues - ■ Helper T cells: if malfunctioning it could leave killer T-cells and B-cells inactive and there could be no immune response ■ Killer T cells: if malfunctioning they might attack the incorrect cell or allow the infected cells to live and replicate
Compare and contrast the structures of T4 bacteriophage and TMV.
T4 - hexagonal capside with rod sticking out of it (looks like a robot) TMV - rod shaped virus (looks like a tampon)
Killer T cell function surface receptors
TCRs - recognize and bind antigen on surface of APC (antigen-presenting cells)
Th cells help in clonal expansion of ____
Tc cells
How is the gp120 protein important to HIV and its ability to confound the immune system?
The gp120 protein on the HIV virus is the molecule that docks with the CD4 receptor on the helper T cell, so it is very important to the action of HIV. The problem is that the gp120 protein changes conformation when it binds, making the attempt to use purified gp120 to make antibodies ineffective. There is also a high mutation rate of the gp120 protein.
Describe the positive and negative effects of the innate immune system on cancer cells.
The innate immune system is instrumental in fighting cancer cells. Cells that turn cancerous display antigens on their surfaces that act as a help signal. Cells of the innate immune system such as macrophages and natural killer cells attack cells that display these cancer-linked antigens on their surfaces. Often they destroy the cancerous cell, ending the threat. However, if they do not, the presence of the innate immune cell can lead to inflammation. More and more research is showing that inflammation is the switch that takes a precancerous cell and turns it into a full-fledged cancer cell. Thus, innate immune cells that attack a cancer cell but fail to kill it may just make it stronger.
What determines the family in which a virus is categorized?
The main factors determining the family of a virus is whether its genome is DNA or RNA and whether it has a membrane envelope. Whether the nucleic acid is single- or double-stranded and the method of incorporation of the virus are also considered
Why are the proteins called p53 and Ras studied so much these days?
The protein called p53 is a tumor suppressor. Mutations of p53 have been found in more than half of all human cancers. Ras is involved in cell division, and mutations in this protein are involved in 30% of human tumors.
How does p53 suppress tumors?
The role of p53 is to slow down cell division and to promote cell death (apoptosis) under certain circumstances, including when DNA is damaged or when cells are infected by viruses. p53 is a traffic cop at G1 → S. If it sees damage it upregulates repair enzymes. If repair not possible it upregulates BAX. BAX disrupts Bcl2. Bcl2 normally stabalizes mitchondrial membrane. With disruption, cytochrome c leaks. Caspases are activated, activating apoptosis.
What types of viruses are used for gene therapy, and how are they manipulated to make them useful?
The two most common are the Maloney murine leukemia virus (MMLV) and adenovirus. Both must be manipulated so that the critical genes for replication are removed and replaced with an expression cassette containing the therapeutic gene.
How does a virus infect a cell?
The virus attaches to a specific protein on the host cell's membrane and injects its nucleic acid inside the cell.
How does HIV gain entry into the cells it attacks?
The virus binds to the CD4 receptor on the helper T cell via a viral protein - gp120.
All retroviruses have 3 genes in common:
There is a gene for proteins of the nucleocapsid, often called coat proteins (CP) Reverse transcriptase (RT) Envelope proteins (EP)
Is there a correlation between the speed of a viral infection and its potential mortality rate? Explain.
There is no correlation. Some viruses, such as Ebola virus, are fast acting and very lethal; others, such as HIV, are slow and just as lethal. The influenza virus is fast-acting, but it is rarely lethal these days.
Two main aspects of immunity
Those that operate on a *cellular* level and *molecular* level
T cells mature in ___
Thymus
Two main types of DNA mutations associated with cancer
Tumor suppressor, Oncogene
Factors that make HIV so persistent
Type of cell it targets slow acting hard for immune system to find
Steps of lysogenic pathway
Viral DNA inserts into host DNA without lysing cell (membrane still intact)
Structure of viruses
Virion - complete virus particle, nucleic acid present at center, any form of RNA or DNA (ss or ds); Capsid - protein coat of virus Nucleocapsid - combination of nucleic acid and capsid
What is virotherapy?
Virotherapy is the process of using a virus to attempt to treat cancer. There are two strategies for virotherapy. 1. One is to use the virus to attack and kill cancer cells directly. In this case, the virus has a protein on its surface that is specific for a cancer cell. Once inside, it kills the cancer cell. 2. The second is to have the virus ferry a gene into the cancer cell that makes the cell more susceptible to a chemotherapeutic agent.
Some viruses can undergo lysis or lysogeny even in the same host. What might be a reason for this? Under what conditions might the virus favor the one strategy over the other?
Viruses can often switch from one pathway to another, based on the condition of the host cells. If the host is healthy, there is sufficient material to allow the virus to replicate and to produce new virions. If the host cell is starved or unhealthy, there may be insufficient energy and material to do so. In this case, lysogeny allows the DNA to incorporate in the host cell, where it can wait until the cell's health improves.
How are viruses related to cancer?
Viruses have been implicated in many cancers. Retroviruses are particularly dangerous because they insert their DNA into the host's DNA. When this happens in a tumor-suppressor gene, the tumor suppressor is inactivated, causing cancer. Also, the homology between proto-oncogenes and oncogenes makes it likely that the infection cycle of viruses may be responsible for some proto-oncogenes becoming oncogenic.
Describe how the cells of the acquired-immunity system develop so that they do not recognize self-antigens but do recognize foreign antigens.
When T cells and B cells are developing, they are, in a sense, "trained." If they contain receptors that recognize self-antigens, they are eliminated when they are still young. If they don't ever see any antigens they recognize, then they die by neglect. This leaves a set of precursors to T cells and B cells with receptors that recognize foreign antigens but not self-antigens.
What are the potential hazards of gene therapy?
When retroviruses, such as MMLV, are used, there is the danger that the therapeutic gene will incorporate in a place that will disrupt another gene. In more cases than would be predicted by random chance, this seems to occur in a place that disrupts a tumor-suppressor gene, causing cancer. There is also the danger that the patient will have a strong reaction to the virus used to introduce the therapeutic gene. In at least one case, this has had fatal consequences.
What are the main structural components of immunoglobulins?
Y-shaped glycoproteins 2 identical heavy chains and 2 identical light chains held together by disulfide bonds
General function of immune system
ability to distinguish self from non-self ability to detect abnormal growth (cancer)
Monoclonal antibodies are used to assay for substances that __
act as antigens - like HIV
general steps of transductional targeting
antibodies attached to virus so binds specifically to cancer cells virus goes thru lytic cycle and destroys cancer cell