Micro Final!

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  1. Plasmids
    • Moves things around so they can survive better
    • 4 Factors of Plasmids:
    • Fertility
    • Resistance
    • Bacteriocin
    • Virulence
  2. Bacteriocin Plasmid Factors
    • Significant in competition cuz gram - will over grow the gram + and it can potentially destroy the cell.
    • Ex. E.Coli will suppress the gram + bacteria cuz it's gram - and will allow gram - to dominate
  3. Fertility Plasmid Factors
    • Bacterial Sex Concept
    • F+ plasmid the male has f+ plasmid and can tranfer it to the recipient which is f- and during ocnjugation the f- can be converted to f+ simply through transfer
  4. Resistant Plasmid Factors
    Problem cuz bacteria is mobalized and have own sequences that guarantee the passage. ~ get info from phone
  5. Virulence Plasmid Factors
    They can inc/greater change of infection
  6. Viral Oncogenesis Theory
    • Virus infections can lead to cancer
    • The protective mechanism is DNA Methylation
    • To prevent cervical cancer associated with HPV
  7. Which group of organisms cause the most infections in humans?
  8. T/F: E.Coli is the workforce of the microbial world
  9. Topoisomeraze
    • Also called DNA Gyrase
    • 1st Step: Uncoils DNA
  10. Helicase
    2nd Part: Separates the DNA strands apart
  11. Direction of Synthesis
    Regardless if RNA or DNA it must always be 5' to 3'
  12. Telomerase
    • Keeps the cell viable because it adds nucleotides back into the DNA that was cut and preserves genetic stability. 
    • Unique to eukaryotes. Also called the fountain of youth.
    • Not present in all cells.
  13. Gardicil Survirus
    HPA vaccine and prevents cervical cancer especially in females.
  14. RNA Primers in leading and lagging strands
    • Leading = 1 RNA Primer
    • Lagging = several RNA primers
  15. How to express genes
    DNA Replication -> (Transciption) RNA -> (translation) Proteins
  16. Bidirectional
    • Replication occurring in both directions.
    • Ex. E. Coli divides once every 20min instead of 1 hr cuz you replicate from both sides
  17. Replication Forks
    Replication forks are determined by how many chromosomes an organism has.
  18. Cytopathogenic Effects (CPE)
    Effects associated with viruses infection humans and other animals.
  19. T/F The vast majority of microorganisms have not been cultured in the lab
    True cuz we don't know what we the bacteria need in order to grow
  20. T/F  Genotype determines Phenotype
  21. Structure of DNA and RNA
    • Primary Structure = how amino acids are
    • 2nd - how they are arranged
    • 3rd - How they are linked other
    • 4. How they are put together
  22. Junk DNA
    99 or 98.5 is junk DNA
  23. Expressed Genes
    Only 1% of genes are expressed in out bodies
  24. Introns
    None coding region, , there is no gene product
  25. Exons
    Coding regions so when ywe make RNA you want to take out the introns because they don't code for anything.
  26. Antisense RNA
    Not the one used for RNA to code poteins
  27. Barr BOdy
    Found in females only
  28. Sense RNA
    Sequences that is used to make proteins
  29. Interference DNA
    Silence. block genes
  30. RNAi
    Works by introducing double stranded RNA into the cells and the genes silencing involves the RISC
  31. Bacria DNA is similar to dna replictaion
  32. How does the mRNA know how to bring the amino acids to the cell.
    They use anticodon because it recognizes the codon and tell the cell to make the protein with these amino acides
  33. Chloraphenicol
    Causes a potentiall fatal aplastic anemia
  34. Tetracycline
    Causes mottling of teeth
  35. Anticodons
    • Must be complimentary to the codon,
    • Anticodon is on the tRNA and codon is on the m RNA
  36. Specificity of antibiotic action used to treat microbes
    Structural and physiological differences between target microbes and the human body for example ribosome size, enzyme affinity for antibiotics, metabolic inhibition of precursors, and the presence of PG in bacterial cell wall
  37. Advantages of Degenerate code
    • Variety of codons lessens of nullifies the effect of mutations
    • Introduces viability
    • Provides flexibility
    • Contributes to genetic stability
    • Favors survival or organisms by providing constancy of genetic information
  38. Rybozymes
    Auto catalytic because the RNA, tRNA, mRNA to convert between each other.
  39. F. Methaionine was found in the archeaic bacteria because they have the same format of DNA codon.
  40. Epigenetics
    Dietary intake using the agouti mouse you can divide the group into two sections
  41. Mutation
    A simple change in base associated/leads to with associated/leads to with an alternat or deficient function
  42. Silent Mutations
    Same amino acid that is produced and because of the same amino acid it tells you what is produced
  43. Detection of Mutations
    If the chemical is a mutagen than it raises the posisblity that it's a cacinogen
  44. Methods to Detect Mutagens
    • Ames mutagenecity test
    • Chromosomal dysjunction
    • Mouse micronucleus
    • CHO
  45. Negative and Positive Controls
    • They provide comparison, the truly negative will not have an effect and the positive will indicate a mutation event
    • Done with chemicals
  46. Activation by rat liver microsomal extract
    The liver processing can convert the pre carcinogen to a carcinogen and pre mutagen to a mutagen or carcinogen
  47. Dose Dependent response
    As you increase concentration you also increase the mutation rate of the test chemical
  48. Ames test for ID of mutagens
    • Uses histidine auxotroph of salmonella tyhimurium
    • If it's a auxotroph it requires histidine for growth
    • Looking for conversion from a histadine negative to a histadine positive where it will make it's own histidine
    • If it grows in the medium that lacks histidine that means that it makes its own and its a mutation
  49. Cancer Growth Regulation
    • Has high telomerase activity
    • If you look at the cancer cell, it keeps on dividing because it loses contact inhibition and divides in ongoing fashion. It is also a transformed cell, which means that the control mechanisms of the cell are no longer operative and that is what cancers divide
  50. Oncogen Hypothesis
    • Basically says that cancer is the result of a stimulation of turn on of genes that lead to abnormal cell growth. Has 3 possibilities
    • Loss of overproduction control. 
    • Cancer = loss of control with association of an oncogene
    • Oncogene = a gene when turned on causes cancer, copied, transcribed, or activated leads to cancer
  51. Colorectum Cancer Module
    Loss of tumor suppressor gene which is triggered by radiation or diet
  52. Viral Oncogenesis Theory
    • Herpes has an abnormal growth of cells that gives lesions.
    • HPV - 2nd leading cause of death in females by cervical cancer
  53. Pap Smear
    • Looks for cancer cells by hyperplasia which means abnormal cell growth
    • The vaccines are cirvirix and guardacil and protect against the 4 main types of HPV
  54. T/F Exposure to antibiotics in bacteria is not a prereq to develop resistance.
    True it can be made intrinsically
  55. Transduction
    • Acquisition of characteristics associated of introduction of genetic elements by bacterial virus.
    • Ex. Transfer of genetic elements into org. where the transfer is being mediated or effected by the bacterial virus
  56. Transformation
    • Uptake of naked DNA, not associated with plasmid or vector and not a result of conjugation with sex pilus.
    • Ex. If dead cell has capsule and living doesn't the living can take that capsule
  57. Competence of cells can be achieved by the following. (Cells that take up DNA are competent)
    • Treatment with calcium chloride
    • Electroporation
    • Treatment with detergents and lysozome
    • Blasting microscopic pellets covered with DNA into bacterial cell
    • Increase pressure in a French press
  58. Electroporation
    Blasting the cells in an electrical field that produces holes in the wall to allow DNA to come in
  59. 2 Types of transductions
    • It depends on what part of the genome is transferred when the phage moves through the cell. The shuttle bacteria could also transfer resistances
    • Specialized transduction
    • Generalized transduction
  60. Specialized Transduction
    If the transfer involves elements that are near insertion point
  61. Generalized Transduction
    If it occurs in any part of the host genome
  62. Polymerase Chain Reaction (PCR)
    • Devised by Kerry Mullis
    • Most dominant procedure in the last century
    • It is an amplification procedure
    • Takes DNA/RNA and makes multiple copies within hours
    • Ex. Bill Clinton
  63. T/F Bill Clinton would not have been subject for impeachment if it had not been for PCR
  64. What PCR can do
  65. Can detect viral load and monitor HIV infection and response to therapy to make sure the medication is working or not. 
    Can take specimen of genetic material from just one cell and use it as a basis for phorensic information
  66. Routine Diseases Detection using PCR
    • HIV
    • Hep B and C
    • HPV
    • Clamydia
    • Nisseria Ghonorriah
    • Cytomegalovirus
    • Mycobacterium Tuberculosis
  67. How PCR monitors diseases
    What it does is it has quantitative analysis and real time PCR can determine the ID and # of infection by using algorithms
  68. Cytomegalovirus
    Huge problem in HIV/AIDS patient because it causes blindness
  69. PCR Applications
    • USed a heat stable DNA polymerase from thermos aquaticus which is a hyperthermophile.
    • Can use it to establish ID
    • Read the application on notes.
  70. Transposons
    • Segments of DNA that move from one location to another in the same or different molecules.
    • Also called jumping genes and was discovered by Barbara Mcclintock
  71. Recombinant DNA
    Using DNA from different sources of individuals to make them combine to get a new product.
  72. Synthesizing antisense nucleic acid molecules
    Antisense - not normally transcribed to make RNA so if you get a product that will interfere you can rest on voice
  73. Restriction Enzymes
    • The most important in recombinant DNA
    • They chop up DNA based on recognition of specific sequences
  74. Restriction Endonucleases
    Are DNA scissors they chop up DNA dependent on their sequences and then you do electrophoresis and separate them you will be able to tell 2 different individuals
  75. Restriction Fragment Length Polymorphism (RFLP)
    Means that the same restriction in the nucleus will cut up the DNA based on recognition of characteristic sequences and they differ in different individuals
  76. Know the difference between blunt and sticky ends when cutting
  77. Why do you start with mRNA and not DNA
    • Cuz RNA doesn't have entrons.
    • So if you want to make the proein you start with RNA because it will give you the actual sequence to make that protein
  78. Gene Libraries
    A collection of bacterial or phage clones
  79. You have a mix that consists of DNA from an organism and you then have tag polymerase and nucleotides.
    1. After the PCR what is the product? What are you amplifying?
    2. Why would you not have tag DNA in the mix?
    • 1. You are amplifying the DNA that comes from the individual or the organism
    • 2. Because you use the enzyme not the DNA of thermous aquatics cuz in PCR if you have a contaminatio then you will amplify that as well and you don't want to do that
  80. Gel Electrophoresis
    Separates molecules based on electrical charge, size and shape. Cuz the larger they are the slower it will move and the shorter the distance it will cover
  81. Southern Blot
    • Used to detect DNA
    • Allows you to ID the genes of intereest becasue you transferred it.
  82. Northern Blot
    Used to detect RNA
  83. Microarray
    • A combination of different genes of that organism and is used for detecting appropriate genes.
    • Org. can be ID by microarray in the future but the genomes of the organism must all be known
  84. A bacteria that is able to take up features of DNA is called competent. Can you induce a bacteria to take up DNA?
    Yes, like using the French Press, shoot particles that are coded with DNA into the materia. Can use a detergent that breaks up the wall and that will take over the DNA
  85. Genetic Mapping
    You want to tell where the genes are
  86. Burkitt Lymphoma
    Associated with the virus that causes monouceliosis
  87. How does the Ebstine Biovirus constitute the cause of Birkitts Lymphoma?
    They must turn on the genes in order to turn on the cancer gene to make the lymphoma
  88. Fluorescent in Situ Hybridization (FISH)
    • If you know the sequence for the particular protein you can look into the RNA and mRNA and you can design the probe to bind to those appropriate sequences in order to tell where a particular gene is on a chromosome
    • Most diagnosis are made post mortom and the sputum and feces and if the Candida Albicans were found in 2 places then you can tell that, that is the reason why they dided
  89. Evidence for viral oncogenesis
    Presence of viral genomes in humans, viral infections associated with cancers, herpes, HIV/AIDS etc
  90. Western Blot
    This is a direct test you're looking for the proteins present in HIV in order to diagnose it
  91. Protein Synthesis
    • Part of the pharmaceutical and therapeutic applications.
    • Creation of synthetic peptides for cloning
  92. Vaccines
    • Part of the pharmaceutical and therapeutic applications
    • Injecting humans with plasmid carrying gene from pathogen
  93. Genetic Screening
    • Part of the pharmaceutical and therapeutic applications
    • DNA microarrays used to screen individuals for inherited disease cause by mutations. Can also ID pathogens DNA in blood or tissues
  94. DNA Fingerprinting
    • Part of the pharmaceutical and therapeutic applications
    • ID individuals or org. by their unique DNA sequence
  95. Gene Therapy
    • Part of the pharmaceutical and therapeutic applications
    • Missing or defective genes replaced with normal copies
  96. Medical Diagnosis
    • Part of the pharmaceutical and therapeutic applications
    • Patient specimens can be examined for presence of gene sequences unique to certain pathogens
  97. Xenotransplants
    • Part of the pharmaceutical and therapeutic applications
    • Animal cells, tissues, or organs introduced into human body
  98. Production of transgenic organisms
    • Part of Agricultural Applications
    • recombinant plants and animals altered by addition of genes from other organisms
  99. Phytophthora
    Important because it is a fungus that lead to the migration that spawned America since the potatoes were getting destroyed by this fungus
  100. Gene for B-Carotene
    Vitamin A i potatoes and yams and this is a big problem in agriculture
  101. Ethical Issues
    • Routine Screenings?
    • Who should pay?
    • genetic privacy rights?
    • Profits from genetically altered organisms?
    • Required genetic screening?
    • Forced correction of genetic abnormalities?
  102. Karyotype
    • Used to show differences in genetic makeup (genotype), which determines the features that person has (phenotype).
    • Typically shown in metaphase and the chromosomes are fixed and can be arranged by different sizes
  103. Klinefelter's Syndrome
    • Has 3 sex chromosomes XXY instead of 2.
    • Are males with some development of breast tissue, little body hair present, and usually tall with or without mental retardation
  104. Turner's Syndrome
    • Has 1 sex chromosome either X_ or X0.
    • The Y chromosome is missing.
    • Female with underdeveloped ovaries, short statue, bull neck, and broad chest. They are sterila nd lack secondary sexual characteristics.
  105. Down's Syndrome
    • Has 3 copies of chromosome #21 rather than 2.
    • Characterized by differing degrees of mental retardation, skin fold over eye, short stature, and short hands with deep crease.
    • Also known as mongolism
  106. Epigenetics
    The expression of individuals is not solely determined by the genes but also the diet and the environment. Tested with the Agouti gene in mice
  107. T/F DNA is life the rest is just stuff
  108. DNA is life the rest is just stuff. What is the evidence to support this concept?
    • Genotype determines phenotype
    • Evidence is mutation, turner, downs, gene replacement therapy etc.
  109. About 98.5% of DNA represents?
    • Junk. Called junk because we don't know what it does, and the functions are unknown.
    • So the rest 1.5% is the important one
  110. T/F Every dingle antibiotic within  6 months of introduction known to date, resistance has been documented
  111. T/F Prior exposure to antibiotics is not a pre req. for resistance to development
  112. Selective Toxicity
    • Targets the organism instead of the human. The basis for the targeting is bacteria and microbes that are different from the cells in your body.
    • Differences include anatomical, metabolic, and genetic.
  113. Peptidoglycan Susceptibility
    The bacteria which is acted on by beta lactams and it is also part of the bacterial cell wall so you can tell if it's gram negative or gram positive because the gram negative are less susceptible to antibiotics because they have less PG and the opposite is for gram positive
  114. Sulfometaxeso
    This is the first line of therapy for the UTI
  115. Floroquindolones (FQ) and how the FQ inhibit bacterial synthesis
    • DNA gyrase and bacteria is specifically inhibited by FQ because they have a greater affinity for the bacterial DNA gyrase.
    • Because of the differnt affinity there are side effects that are present like: photosensitivity, joint pain, and tendon rupture.
  116. FQ inhibiting effects
    When inhibiting bacteria you are also inhibiting mitochondrial replication in the human body that is why you get tendon rupture and if you treat a kid that means i can damage their growth and stuff like that
  117. Which eukaryotic organisms infect humans and cause disease.
    Fungus, hemiths, protozoa.
  118. Why are there fewer drugs to treat eukaryotic infections?
    Because you have the same cells so toxicity becomes a huge problem when dealing with eukaryotic organisms just like yourself.
  119. Whey are there even fewer drugs that treat viruses?
    Because they need a host cell in order to produce a virus so in order to get rid of a virus you have to get rid of the host cell. That is why its is hard
  120. L Forms are associated with subacute endocarditis
    The treatment is a combination of beta lactamines so you can prevent cell wall formation as well as remove the cell wall, and if the L forms are present you also have to inhibit the protein synthesis
  121. Best treatment for L Forms
    Best treated with beta lactum like penicillin which attacks the protein synthesis and an aminoglycoside which inhibits cell wall formation. So it is a combination therapy treatment since it is not likely to develop resistances to both antibiotics at the same time
  122. What is cloromphinical do/act?
    Why does this cause potentially fatal aplastic anemia?
    • It inhibits protein synthesis in bacteria specifically and also in mitochondria.
    • If you inhibit mitochondrial replication you get decreased cellular function because hematopoesis is suppressed
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Micro Final!
2015-06-07 05:26:15
Micro Final

Micro Final!
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