Biol 107

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mct
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147964
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Biol 107
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2012-04-21 12:57:37
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Part Three
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Cell reproduction & Genomics
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  1. Genome
    The genetic material of an organism or virus; the complete complement of an organism's or virus's genes along with its noncoding nucleic acid sequences
  2. Chromatin
    The complex of DNA and proteins that makes up eukaryotic chromosomes. When the cell is not dividing, chromatin exists in its dispersed form, as a mass of very long, thin fibers that are not visible with a light microscope.
  3. Chromosomes
    • A cellular structure carrying genetic material, found in the nucleu of eukaryotic cells. Each chromosomes consists of one very long DNA molecule and associated proteins. (A bacterial chromosome usually consists of a single circular DNA molecule and associated proteins. It is found in the nucleoid region, which is not membrane bounded.)
    • Condensed chromatin
  4. Chromatids
    Paired chromosomes (sisters)
  5. Centromere
    In a duplicated chromose, the region on each sister chromatid where they are most closely attached to each other by proteins that bind to specific DNA sequences; this close attachment causes a constriction in the condensed chromosome. (An uncondensed, unduplicated chromosome has a single centromere, identified by its DNA sequence.)
  6. Cytokinesis
    The division of the cytoplasm to form two seperate daughter cells immediately after mitosis, meiosis I, or meiosis II.
  7. MTOC
    Microtubule Organizing Center
  8. Prophase
    The first stage of mitosis, in which the chromatin condenses into discrete chromosomes visible with a light microscope, the mitotic spindle begins to form, and the nucleolus disappears but the nucleus remains intact.
  9. G2 phase
    The second gap, or growth phase, of the cell cycle, consisting of the portion of interphase after DNA synthesis occurs.
  10. Prometaphase
    The second stage of mitosis, in which the nuclear envelope fragments and the spindle microtubules attach to the kinetochores of the chromosomes.
  11. Metaphase
    The third stage of mitosis, in which the spindle is complete and the chromosomes, attached to microtubules at their kinetochores, are all aligned at the metaphase plate.
  12. Anaphase
    The fourth stage of mitosis, in which the chromatids of each chromosome have separated and the daughter chromosomes are moving to the poles of the cell.
  13. Telophase
    The fifth and final phase of mitosis, in which daughter nuclei are forming and cytokinesis has typically begun.
  14. Anchorage dependence
    The requirement that a cell must be attached to a substratum in order to initiate cell division. (Example, not blood cells) Non-circulating cells need to be attached to a solid surface before they divide.
  15. Density-dependent inhibition
    The phenomenon observed in normal animal cells that causes them to stop dividing when they come into contact with one another
  16. Transformed cells
    Mutation of genes, defects are passed on: may make own growth factors or have a defect in a checkpoint. Many are killed by the immune system. The loss of either anchorage dependence or density-dependent inhibition which prevent uncontroleed cell growth
  17. Benign tumore
    Localized, slow growth - easily treated, lost density dependence and may have lost G1 chechpoint
  18. Malignant tumour
    Invasive, may change form & chromosomes. Cancer! Lost density dependence and may have lost G1 checkpoint
  19. Metastatic
    Breakaway cells get into circulation and other tissues. Lost anchorage-dependence inhibition
  20. PDGF
    Platelet derived growth factor - stimulates fibroblast division at wound sites
  21. Histone
    A small protein with a high proportion of positively charged amino acids that binds to the negatively charged DNA and plays a key role in chromatin structure
  22. Nucleosomes
    The basic, beadlike unit of DNA packing in eukaryotes, consisting of a segment of DNA wound around a protein core composed of two copies of each of four types of histone (eight histones).
  23. Octamer
    An 8 sub-unit protein complex (the nucleosome core)
  24. H1
    The negatively charged DNA wraps twice around the positively charged complex of 8 histone proteins. The wrapped DNA is held in place by a ninth histone called H1. This locks the DNA in place. It also allows the 10nM fibre to further coil into 30 nm fibres
  25. 30nm fibres
    The H1 histone allows the 10nm fibre to further coil into 30nm fibres. This is level two packaging.
  26. Looped domains
    Level 3 packaging. Loops on a scaffold
  27. Level 4
    Super coil within chromosomes (chromatid).
  28. Euchromatin
    The less condensed form of eukaryotic chromatin that is available for transcription, consists of Level 1 and 2 packaging.
  29. Heterochromatin
    Eukaryotic chromatin that remains highly compacted during interphase and is generally not transcribed. More condensed, 30nm fibres looped onto the nuclear lamina and a protein scoaffold called the nuclear matrix
  30. Nuclear lamina
    A netlike array of protein filaments that lines the inner surface of the nuclear envelope and helps maintain the shape of the nucleus.
  31. G0 phase
    A non dividing state occupied by cells that have left the cell cycle, sometimes reversibly
  32. G1 phase
    The first gap, or growth pahse, of the cell cycle, consisting of the portion of interphase before DNA synthesis begins
  33. Nuclear matrix
    A protein 'web' that extends through the nucleoplasm and also helps maintain the shape of the nucleus and binds and organizes the 30nm fibres as heterochromatin
  34. Acetylation
    Acetylation of histone tails promotes loose chromatin structure that permits transcription of euchromatin. DNA accessible
  35. Methylation
    Mythlation of histone tails effectively 'locks' up the DNA so it can't be transcribed. 30 nm fiber inaccessible
  36. Deoxyribose
    The sugar component of DNA nucleotides, having one fewer hydroxyl group than ribose, the sugar component of RNA nucleotides
  37. Nitogrenous bases
    • Adenine A
    • Guanine G
    • Cytosine C
    • Uracil U
    • Thymine T
  38. Nucleotides
    • The building block of a nucleic acid, consisting of a five-carbon sugar covalently bonded to a nitrogenous base and one or more phosphate groups.
    • Adenosine-monophosphate (AMP)
    • Guanosine-monophosphate (GMP)
    • Cytidine-monophosphate (CMP)
    • Uridine-monophosphate (UMP)
    • Deoxythymidine-monophosphate (dTMP)
  39. Bacterial Transformation
    Bacteria can take up and incorporate genetic material from dead bacteria and use it to make a pathogenic capsule coat.
  40. Bacteria
    One of two prokaryotic domains, the other being Archaea
  41. Fred Griffith
    1928 accidently discovers that bacteria can take up and incorporate genetic material from dead bacteria and use it to make a pathogenic capsule coat.
  42. Avery, McLeod & McCarthy
    follow up on Griffiths work and isolate or enzymatically destroy each of the classes of macrmolecules and test in bacterial transformation experiments. Only intact nucleic acid transforms the bacteria.
  43. Hershey and Chase
    In 1952 made either DNA or protein radioactive. Tracked to see which compound passed on to new viruses/phage
  44. Chargaff's rule
    Porportionally # of A = # of T & # of G = # of C

    Knew that there were nucleotide polymers with defferent nitrogenous bases, determined that different organisms had different ratio's of each base: Adenine, Thymine, Guanine & Cytosine - therefore some diversity
  45. Linus Pauling
    California, predicted a triple helix (wrong)
  46. Maurice Wilkins & Rosalind Franklin
    London, created the data but didn't fully resolve the structure
  47. James Watson and Francis Crick
    Collaborated and made a model to fit the x-ray diffraction data, a probable helix, consistently 2 nm in diameter. Eventually put together that nitrogenous bases face each other, and figured out that they are held together by hydrogen bonds. Only A with T and G with C. This had consistent width and met Chargaff's rule
  48. Potential diversity
    Ability within the structure to have random order within a DNA helix
  49. Strand Complementarity
    In DNA, the two strands that complement each other always go together.
  50. Anit-parallel
    Referring to the arrangement of the sugar-phosphate backbones in a DNA double helix (they run in opposite 5` to 3` directions).
  51. Double Helix
    has two strands that complement each other, therefore you can use one strand to reproduce or replicate the other as T always pairs with A & G always pairs with C
  52. Polymerase
    Adds nucleotides to the chain in the 5` to 3` direction.
  53. Origins of replication
    Site where the replication of a DNA molecule beings, consisting of a specific sequence of nucleotides
  54. Helicases
    An enzyme that untwists the double helix of DNA at replication forks, seperating the two strands and making them available as template strands
  55. DNA polymerase
    An enzyme that catalyzed the elongation of new DNA (for example, at a replication fork) by the addition of nucleotides to the 3` end of an existing chain. There are several different DNA polymerases; DNA polmerase III and DNA polymerase I play major roles in DNA replication of E. coli
  56. Single strand binding protiens
    A protein that binds to the unpaired DNA strand during DNA replication, stabilizing them and holding them apart while they serve as templates for the synthesis of complementary strands of DNA
  57. Primase
    An enzyme that joins RNA nucleotides to make a primer during DNA replication, using the parental DNA strand as a template
  58. Topoisomerase
    A protein that breaks, swivels, and rejoins DNA strands. During DNA replication, topoisomerase helps to relieve strain in the double helix ahead of the replication fork
  59. Okazaki Fragments
    A short segment of DNA synthesized away from the replication fork on a templacte strand durin DNA replication. Many such segments are joined together to make up the lagging strand of newly synthesized DNA.
  60. Pol I
    A distinct DNA Polymerase replaces the RNA primer with DNA and then Ligase joins the Okazaki fragments together
  61. Ligase
    Ligates/joins the all- DNA Okazaki fragments
  62. Gyrase
    Has similar function to topoisomerase in preventing DNA 'knots'
  63. Frederick Sanger
    In 1953, he showed that core the core element of a protein is a sequence of amino acids, therefor DNA sequence is the blueprint for amino acid sequence.
  64. genes
    Contain both instructional information and design information
  65. Transcription
    The synthesis of RNA using a DNA template
  66. Translation
    The synthesis of a polypeptide using the genetic information encoded in an mRNA molecule. There is a change of "language" from nucleotides to amino acids.
  67. Codon
    A three-nucleotide sequence of DNA or mRNA that specifies a particular amino acid or termination signal; the basic unit of the genetic code.
  68. AUG
    Methionine, start codon
  69. UAA
    UAG
    UGA
    Stop codons
  70. Silent mutation
    No change to AA encoded
  71. Mis-sense
    Codon change causes AA change
  72. Non-sense
    Codon changes to stop codon
  73. Frame shift
    Can occur when a nucleotide is deleted or added, as the sequence is read in 3 reading frames
  74. Inter-genic DNA
    In eukaryotes the genes are seperated from one another with these non-coding DNA
  75. Pre-RNA
    The step that eukaryotes take before RNA, prokaryotes skip this step.
  76. Eukaryotic Transcription Initiation
    Sequence 'motifs' in the promoter are recognized by transcription factors
  77. Promoter
    A specific nucleotide sequence in the DNA of a gene that bonds RNA polymerase, positioning it to start transcribing RNA at the appropriate place.
  78. Transcription factors (TFs)
    A regulatory protien that binds to DNA and affects transcription of specific genes
  79. Transcription initiation start point
    TFs bind both DNA and the RNA polymerase and direct the latter to this
  80. Transcription Initiation Complex
    The complete assembly of transcription factors and RNA polymerase bound to a promoter
  81. TATA box
    A DNA sequence in eukaryotic promoters crucial in forming the transcription initiation complex.
  82. Coding strand
    The RNA Transcript has same sequence as the coding strand
  83. Template strand
    The DNA strand that provides the pattern, or template, for ordering, by complementary base pairing, the sequence of nucleotides in an RNA transcript (with uracil substituted for thymine)
  84. Elongation
    The transcription continues and the RNA strand gets longer
  85. Termination
    When the transcription is complete, the transcription is ended.
  86. Termination Sequence
    AAUAAA tells the Polymerase to stop transcribing
  87. Poly (A) tail
    A sequence of 50-250 adenine nucleotides added onto the 3` end of a pre-mRNA molecule
  88. Non-templated addition
    The Poly A tails are not on the template strand
  89. AAUAAA
    frequently referred to as the Poly (A) signal
  90. Introns
    A noncoding, intervening sequence within a primary transcript during RNA processing; also refers to the region of DNA from which this sequence was transcribed. Introns space out the exons
  91. Exons
    A sequence within a primary transcript that remains in the RNA after RNA processing; also refers to the region of DNA from which this sequence was transcribed. These are spaced out by non-coding introns
  92. Spliceosome
    A large complex made up of proteins and RNA molecules that splices RNA by interacting with the ends of an RNA intron, releasing the intron and joinging two adjacent exons.
  93. snRNP
    Make up the spiceosome, they are small nuclear ribonucleo-proteins
  94. snRNA
    Small nuclear RNA approx 150 nt in length (between 100-200 nt)
  95. UTR
    Untranslated regions, these are flanking RNA sequences for the coding segment that provide a bit of flexibility (slack at both ends) and can regulate translation rates.
  96. Promoter
    Defines transcription start site for RNA Poylmerase (Pol)
  97. Enhancer
    Regulates the role of the promoter - transcription factors bound to the enhancer can either block or speed up the loading of RNA Pol at the promoter. They can be upstream of downstream of the gene, or in introns
  98. Sigma Factor
    In bacteria, instead of transcription factors, the sigma factors bind first to the RNA Polymerase and this complex binds to the promoter sequence
  99. Polyeistronic
    In bacteria, one mRNA can encode multiple different polypeptides (this is unique to bacteria).
  100. Consensus motif
    An optimal sequence motif for binding
  101. Operon
    A unit of genetic function found in bacteria and phages, consisting of a promoter, an operator, and a coordinately regulated cluster of genes whose products function in a common pathway.
  102. Operator
    A key element of an operon, which is a DNA nucleotide motif that controls whether RNA Pol can pass by
  103. Repressor
    A protein that inhibits gene transcription. In prokaryotes, repressors bind to the DNA in or near the promoter. In eukaryotes, repressors may bind to control elements within enhancers, to activators, to activators, or to other proteins in a way that blocks activators from binding to DNA
  104. Post-translational modifications
    Polypeptides are often modified in preparation for their final function
  105. Obligates
    Pathogens that are obligated to have a host to reproduce
  106. Facultative
    Pathogens that do not require a host.
  107. Viruses
    • Not living things, they lack: ability to take up energy & make use of it, ability to transport themselves, ability to reproduce themselves, and lack any metabolic abilities or function.
    • They are just genetic material and usually a protective casing.
  108. Capsid
    The protein shell that encloses a viral genome. It may be rod-shaped, polyhedral, or more complex in shape.
  109. Virion
    An infectious virus particle
  110. Reverse Transcriptase
    An enzyme encoded by certain viruses (retroviruses) that uses RNA as a template for DNA synthesis.
  111. Provirus
    A viral genome that is permanently inserted into a host genome
  112. Apoptosis
    A type of programmed cell death, which is brought about by activation of enzymes that break down many chemical components in the cell. If the virus can disturb this, there is a potential for cancer.
  113. Provirus
    A viral genome that is permanently inserted into a host genome.
  114. Lytic
    A type of phage replicative cycle resulting in the release of new phages by lysis (and death) of the host cell.
  115. Lysogenic
    A type of phage replicative cycle in which the viral genome becomes incorporated into the bacterial host chromosome as a prophage, is replicated along with the chromosome, and does not kill the host.
  116. Transduction
    A proces in which phages (viruses) carry bacterial DNA from one bacterial cell to another. When these two cells are members of different species, transduction results in horizontal gene transfer.
  117. Four mechanisms that bacteria use to become antibiotic resistant
    • Pump the antibiotics out the cells via efflux pumps
    • Develop enzymes that degrade the antibiotic
    • Develop enzymes that alter the antibiotic to inactivate it
    • Alter the chemistry of the antibiotics target, so that antibiotic can't bind to it's target
  118. Virulence factors
    • Allow the pathogen to:
    • Invade the host or a specific site in the host
    • Enter or leave a host cell (intracellular pathogens)
    • Evade the host immune response (e.g. bacterial capsule)
    • Obtain nutrients from the host (catabolize the host)
  119. Prions
    An infectious agent that is a misfolded version of a normal cellular protein. Prions appear to increase in number by converting correctly folded versions of the protein to more prions

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