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96 Cards in this Set
- Front
- Back
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PCR
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used to amplify DNA sequence
you can use to focus in on a small segment of DNA and copy it billions |
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ELISAs
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use antibody technology to diagnose infectious disease
Detect antigens |
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Indirect ELISA’s
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detect antibodies in a patients sample rather than an antigen such as drugs. For example, to screen blood for antibodies to HIV.
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Agglutination
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(clumping) can be used to quantify (titer) antibody, neutralize, or test for viruses
-detect antibodies against relatively large cellular antigens, i.e. on red blood cells, bacteria, and fungi. |
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PHOTOTROPHS (Gram-negative)
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Anoxygenic-
Chlorobi (green sulfur)- donate H2S Chloroflexi (green nonsulfur)- donate organic compounds Purple sulfur bacteria- alphaproteobacteria Oxygenic- cyanobacteria |
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Cyanobacteria
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carry out nitrogen fixation in addition to oxygenic photosynthesis
oxygenic and anoxygenic |
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Alphaproteobacteria
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Purple nonsulfur phototrophs
Rickettsial Azospirillum- Nitrogen fixing Rhizobium- Nitrogen fixing |
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Gammaproteobacteria
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Purple sulfur bacteria
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PROTEOBACTERIA
(Classes) |
Alpha
Beta Gamma Delta Epsilon |
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Rickettsial
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obligate intracellular parasites
cause typhus and spotted fevers They'ren transmitted to humans by bites of humans and ticks. They enter the host by inducing phagocytosis. The infections damage the permeability of blood capillaries which results in a characteristic spotted rash. |
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Betaproteobacteria
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Bordatello- causes whooping cough
Neisseria- causes gonorrhea and meningitis |
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Gammaproteobacteria
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Pseudomonads
Vibrios Enterics Purple sulfur bacteria- anoxygenic |
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Nosocomial Infections cause
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P. aeruginosa biofilm
Pyocynanin- blue/green pus |
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Enterobacteriaceae
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(Gram negative proteobacteria)
Gammaproteobacteria -have a number of virulence factors -They are facultative anaerobic, gram negative, straight rods, with fimbriae that help to adhere to surfaces or mucous membranes. -They can be antibiotic resistant because they have specialized sex pill that aid in exchange of genetic information between cells |
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Deltaproteobacteria
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Bdellovibrio
Desulfovibrionales- reduce SO42- into H2S gas |
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Epsilonproteobacteria
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Helicobacter genus- most common cause of peptic ulcers.
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GRAM-NEGATIVE NON-PROTEOBACTERIA
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Chlamydias
Spirochaetes Bacteroidetes- human intestinal tract and mammal oral cavity, degrade cellulose in soil |
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Chlamydias
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are obligate intracellular parasites with no peptidoglycan
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Spirochaetes
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distinguished by their mode of locomotion (axial filaments)
i.e. Borrelia burgdorferi (Lyme disease) Treponema pallidum (syphillis) Leptospira- spread to humans by water contaminated with Leptospira |
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Gut microbiota
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primarily consist of Bacteroides speciesIntestinal ---- Bacteroides from lean humans can confer protection against fat gain in experimental mice.
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GRAM POSITIVE BACTERIA
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Firmicutes (Low G+C)
Actinobacteria (High G+C) |
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Firmicutes
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Clostridium species- have endospores
Mycoplasmatales (pneumoniae)- no cell wall Bacillus species - have endospores Staphylococcus- survive in high osmotic pressure and low moisture (i.e. nasal secretions) Streptococcus species- cause more illnesses than any other bacteria |
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Bacillus species
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species are endospore-forming & soil born
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Clostridium species
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are terminal endspore-forming, toxin producing anaerobes
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Mycoplasmatales (pneumoniae)
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are small, wall-less and pleiomorphic
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Staphylococcus and Streptococcus species produce many toxins
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Staph causes impetigo
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Actinobacteria
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Mycobacterium
Streptomyces |
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Mycobacterium
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characterized by the presence of mycolic acids in their cell walls
causes: M. tuberculosis and M. leprae . |
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Streptomyces
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are strict aerobes and produce many commercial antibiotics
- Coils of conidiospores supported by filaments of the streptomycete. |
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Nitrogen cycle bacteria
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Azospirillum,
Rhizobium Nitrobacter Nitrosomonas |
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Nitrogen fixation
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nitrogen gas (N2) is converted to ammonia (NH3).
Azospirillum and Rhizobium assist with the process of nitrogen fixation important because ammonium ions (NH4+) can be used towards amino acid synthesis in plants and other bacteria. |
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nitrification
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NH3 is converted to nitrites (NO2-) and nitrates (NO3-).
important in returning nitrogen to the atmosphere as nitrogen gas, or its assimilation into plant biomass. Nitrobacter and Nitrosomonas assist with the process of nitrification |
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Neisseria gonorrhea
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have paired arrangements and the fimbriae enable the organism to attach to mucous membrane.
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Vibrio
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human pathogen. rods that often slightly curved. causes cholera which causes watery diarrhea. inhabits coastal salt waters.
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Proteus
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found in human intestinal bacterial; occasional pathogens
has an appearance of a series of concentric rings. can cause infections in urinary tracts and wounds |
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Escherichia
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not usually pathogenic. Can cause urinary tract infections and travelers diarrhea.
found in intestines |
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Yersinia
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Causes plague
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Bdellovibrio
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attacks other gram negative bacteria.
It attaches to tightly and after penetrating the outer layer of the gram negative bacteria, it reproduces in the periplasm. The host cell then lyses, releasing the Bdellovibrio cell |
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Sulfur cycle bacteria
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(Desulfovibrio)
this element is cycled between many oxidized and reduced states. Desulfovibrio participate in this cycle by reducing SO42- to H2S through anaerobic respiration. |
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Streptomyces
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characteristic earthy odor, forms fungus-like filamentous structures, and produces over two thirds of the clinically useful antibiotics, such as erythromycin and neomycin.
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Primers
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de in a laboratory. In a PCR experiment, two primers are designed to match to the segment of DNA you want to copy. Through complementary base pairing, one primer attaches to the top strand at one end of your segment of interest, and the other primer attaches to the bottom strand at the other end. In most cases, 2 primers that are 20 or so nucleotides long will target just one place in the entire genome.Primers are also necessary because DNA polymerase can't attach at just any old place and start copying away. It can only add onto an existing piece of DNA.
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Target sequence
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The DNA sequence that you want to copy. A specific part of the genome.
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DNA polymerase
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a naturally-occurring complex of proteins whose function is to copy a cell's DNA before it divides in two. When a DNA polymerase molecule bumps into a primer that's base-paired with a longer piece of DNA, it attaches itself near the end of the primer and starts adding nucleotides. (In nature, these primers are made by an enzyme called primase).
The DNA polymerase in our bodies breaks down at temperatures well below 95 °C (203 °F) ; the temperature necessary to separate two complementary strands of DNA in a test tube.
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Thermus
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The DNA polymerase that's most often used in PCR comes from a strain of bacteria called Thermus aquaticus that live in the hot springs of Yellowstone National Park. It can survive near boiling temperatures and works quite well at 72 °C (162 °F).
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Nucleotides—
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building blocks that DNA molecules are made of. You add a mixture of four types of nucleotides to your PCR reaction -- A's, C's, G's and T's. DNA polymerase grabs nucleotides that are floating in the liquid around it and attaches them to the end of a primer.
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Why does a PCR include a DNA polymerase that is isolated from the bacterium Thermus acquaticus?
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The temperature that is necessary to separate two complementary strands of DNA in a test tube is 95*C and Thermus acquaticus can survive near boiling temperatures and works well at 72*C.
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RT-PCR, COME BACK
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It's one of many variations of polymerase chain reaction (PCR). It's used to detect RNA expression levels. RT-PCR is used to clone expressed genes by reverse transcribing the RNA of interest into its DNA complement through the use of reverse transcriptase.
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Cyclic process of a PCR
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Extract DNA, place in a PCR tube, and add Primer 1, Primer 2, nucleotides, and DNA Polymerase to the PCR tube. Place PCR tube in the DNA Thermal Cycler. Once inside the DNA Thermal Cycler the tube heats up to 95*C and separates the double helix into two single-strained DNA molecules. Then it cools to 50*C. Then it changes to 72*C which activates DNA polymerase.
Same process happens in cycle 2 At the end of cycle 4 yo have eight fragments that contain only your target sequence. By cycle 5, you have 22 fragments that contain only your target sequence. By cycle 30, you have over a billion fragments that contain only your target sequence which is a solution of nearly pure target sequence. |
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Indirect (passive) Agglutination-
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antibodies react with the soluble antigen adhering to the particles. Antigens are absorbed onto particles such as bentonite clay or, most often minute latex spheres. These tests are known as latex agglutination tests.
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Hemagglutination
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agglutination reactions that involve the clumping of red blood cells; used in blood typing and in the diagnosis of infectious mononucleosis.
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Direct fluorescent antibody test
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used to identify microorganisms in in a clinical specimen
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Indirect fluorescent antibody test
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used to detect the presence of a specific antibody in a serum following exposure to a microorganism.
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innate immunity
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defenses that are present at birth, i.e. intact skin, normal microbiota, and antimicrobial substances. It's called nonspecific immunity because, unlike adaptive immunity, innate invokes defenses against any pathogen not specific ones, regardless of species.
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adaptive immunity
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defenses against a specific pathogen. Its based on a specific response to a specific microbe once a microbe has breached the innate immunity defenses. It adapts or adjusts to handle a particular microbe
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Toll like receptors
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the responses of the innate system are activated by proteins receptors in the plasma membranes of defensive cells. They attach to PAMPS
TLR's help the microbes adhere to the phagocyte. |
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pathogen-associated molecular patterns (PAMPs).
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PAMP's are found in the peptidoglycan of the cell wall.
various components components commonly found on pathogens EX: lipopolysaccharide of the outer membrane of gram negative bacteria, flagellin in the flagella of motile bacteria, the peptidoglycan in the cell wall of gram positive bacteria. |
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First line of defense
Innate defence |
intact skin, mucous membranes and their secretions, and normal microbiota.
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Second line of defense
Innate defense |
Phagocytes, such as neutrophils, eosinophils, dendritic cells, and macrophages. Inflammation, fever, and antimicrobial substances.
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Third line of defense
Adaptive defense |
Specialized lymphocytes: T cells and B cells. Antibodies
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leukocytes
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white blood cells
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lymphocytes
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specialized leukocytes involved in specific immune responses.
3 types: natural killer cells, T cells, and B cells |
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Natural killer cells
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kill a wide variety of infected body cells and certain tumor cells. NK cells attack any body cells that display abnormal or unusual plasma membrane proteins.
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T and B cells
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are not phagocytic but play a key role in adaptive immunity. They occur in the lymphoid tissues of the lymphatic system and also circulate in the blood.
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process of phagocytosis
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1. Chemotaxis and adherence of phagocyte to microbe
2. Ingestion of microbe by phagocyte 3. Formation of phagosome (phagocytic vesicle) 4. Fusion of phagosome with a lysosome to form a phagolysosome 5. Digestion of ingested microbes by enzymes in the phagolysosome 6. Formation of the residual body containing indigestible material 7. Discharge of waste materials |
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Process of inflamation
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1. Tissue is damaged and chemicals such as histamines, kinins, prostaglandins, leukotrienes, and cytokines are released by damaged cells.
2. Blood clots form. 3. abscess starts to form. 4. Margination- phagocytes stick to endothelium 5. Diapedesis- phagocytes squeeze between endothelial cells 6. phagocytosis of invading bacteria occurs |
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Fever
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A fever is a systematic response to an invasion of pathogens. Cytokines are released when phagocytes ingest gram-negative bacteria; this causes the hypothalamus to release prostaglandins that reset the hypothalamic thermostat causing a fever. Body temperature begins to climb but the skin stays cold and this causes a chill. Once the skin becomes warm and the person starts to sweat the body temperature begins to lower and this is called the crisis of the fever.
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Complement system and its process
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Compliment system is another way the body fights infection and destroys pathogens. This component of innate immunity complements other immune systems.
1. inactivated C3 splits into activated C3a and C3b 2. C3b binds to microbe, resulting in opsonization 3. C3b also splits C5 into C5a and C5b 4. C5b, C6, C7 and C8 bind together sequentially and insert into the microbial plasma membrane, where they function as a receptor to attract a C9 fragments; additional C9 fragments are added to form a channel. Together, C5b through C8 and the multiple C9 fragments form the membrane attack the complex, resulting in cytolysis. 5. C3a and C5a cause mast cells to release histamine, resulting in inflammation; C5 also attracts phagocytes. |
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Humoral immunity
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associated with B lymphocytes that recognize antigens and make specific
antibodies against them. |
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Cellular immunity
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associated with T lymphocytes that recognize antigens by means of specific receptors on their surface.
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antigen
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any substance that causes the host immune system to produce antibodies against it.
EX: Capsules, cell walls, flagella, fimbriae, and toxins of bacteria; coats of viruses, surface of other types of microbes. |
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epitope or antigenic determinants.
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The specific region of an antigen that antibodies recognize
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why are antibodies specific for one type of epitope
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Antibodies are made in response to an antigen and can recognize and bind to that antigen. Each antibody has at least two identical sites that bind to epitopes called antigen binding sites.
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Agglutination
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Causes antigens/microbes to clump together so that they’re easier to ingest by phagocytes
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Opsonization
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Coating antigen with antibody enhances phagocytes
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Neutralization
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antibodies inactivate microbes by blocking their attachment to host cells and neutralize toxins in a similar manner.
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Activation of complement
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Causes inflammation and cell lysis which then attracts phagocytes and other defensive immune system cells in that area.
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Antibody-dependent cell-mediated cytotoxicity
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Antibodies attach to target cells and cause destruction by macrophages, eosinophils, and NK cells. Destruction of of the target cell is by immune system cells that remain external to the target cell.
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major histocompatibility complexes (MHCs)
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A collection of genes that encode molecules of genetically diverse glycoproteins (part carbohydrate, part protein) that are found on the plasma membranes of mammalian nucleated cells.
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MHC I
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nearly every nucleated cell of the body
endogenous CD 8+/ killer |
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MHC II
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only on antigen-presenting cells and B cell lymphocytes
exogenous CD 4+/ helper |
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Dendritic cells
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If T cells are to recognize specific antigens, the antigens must first be processed and presented on MHCs to the T cell by cells called Dendritic cells
3 types are: Dendritic, macrophage, and activated macrophage cells. , |
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events that lead to T helper cell activation
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TCR recognizes an antigen that has been processed and is presented as fragments held in a complex with proteins of MHC class II on the surface of APC. This is the initial signal of activation; a second signal, requires a costimulatory cytokine, such as IL- 2 and others, which is present on the APC.
Th1 activates mostly those cells related to important elements of cellular immunity, such as delayed-type hypersensitivity. Th2 produce cytokines that are associated primarily with the production of antibodies, especially with IgE, that are important in all allergic reactions. |
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how B cells are activated to become plasma cells and produce antibodies, or differentiate into memory B cells.
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B cells bind to antigens to form an antibody-antigen complex which tags foreign cells and molecules for destruction by phagocytes and complement.
Antibody-dependent cell mediated cytotoxicity and neutralization are both invalid. In neutralization, IgG antibodies inactivate microbes by blocking their attachment to host cells, and they neutralize toxins in a similar matter. Antibody-dependent cell mediated cytotoxicity resembles opsonization in that the target organism becomes coated with antibodies, however, destruction of the target cell is by immune system cells that remain external to the target cell. IgG or IgM may trigger activation of the complement system, i.e. inflammation. |
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Relationship between genotype and phenotype
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Phenotype is a manifestation of the genotype.
Genetic information in DNA is transcribed into mRNA and then translated into protein. |
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primary antibody response.
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Primary antibody response- After the initial contact with the antigen, the exposed persons serum contains no detectible antibodies for 4 to 7 days. Then there is a slow rise in antibody titer: first, IgM class antibodies are produced, followed by IgG peaking n about 10 to 17 day, after which antibody titer gradually declines.
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secondary antibody response.
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Secondary antibody response- this response is more rapid, reaching a peak in only 2 to 7 days, lasts many days, and is considerably greater in magnitude. Activated B cells do not become antibody producing plasma cells but persist as long lived but nonproliferation memory cells. Years or even decades later, if these cells are stimulated by the same antigen, they very rapidly differentiate into antibody yproducing plasma membrane.
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Immunity
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acquired actively or passively when a person is exposed and responds to foreign molecules or microbes. Immunity is acquired passively whe
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Naturally acquired active immunity:
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develops when a person becomes ill and hen recovers; i.e. measles. Once acquired, immunity is lifelong.
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Naturally acquired passive immunity:
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natural transfer of antibodies from other to her infant; i.e. if the mother is immune to rubella or polio the newborn will be temporarily immune to these diseases.
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Artificially acquired active immunity:
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injection of antigens into the body, result of vaccination; i.e. chickenpox vaccine.
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Artificially acquired passive immunity:
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injection of antibodies into the body
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Silent
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3rd position in the mRNA codonno change in the product encoded by the gene.
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Missense
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base substitution results in an amino acid sub in the synthesized protein
at the ned of a DNA strand change from glutamic acid to valine in the protein. Effect of this change is that the shape of the hemoglobin molecule changes under conditions of low oxygen. |
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Nonsense
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In the middle of an mRNA molecule
some can effectively prevent the synthesis of a complete functional protein; only a fragment synthesizes. |
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Point mutations
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most common type of mutation. a single base at one point in the DNA sequence is replaced with a different base. When the DNA replicates, the result is a substituted base pair.
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Frameshift mutations
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when one or a few nucleotide pairs are deleted or inserted in the DNA
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