Ch 7A ID Terms

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Ch 7A ID Terms
2015-03-10 23:48:41
Test Three
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  1. glucocorticoids
    • Released in the body during periods of starvation or intense exercise and signal the liver to increase the production of glucose from amino acids and other small molecules; the set of proteins whose production is induced includes enzymes such as tyrosine aminotransferase, which helps to convert tyrosine to glucose
    • When the hormone is no longer present, the production of these proteins drops to its normal level
    • Fat cells respond differently
  2. regulatory region of DNA
    Some are simple and act as switches thrown by a single signal; others are complex and resemble tiny microprocessors; found in all cells and can be: (1) short stretches of DNA of defined sequence or (2) gene regulatory proteins that recognize and bind to DNA
  3. gene regulatory proteins
    • aka: transcription factors
    • Turn specific sets of genes on or off and must recognize specific nucleotide sequences embedded within this structureEx: lambda repressor encoded by phage lambda
  4. lambda repressor
    Shuts off the viral genes that code for the protein components of new virus particles and enables the viral genome to remain a silent passenger in the bacterial chromosome, multiplying with the bacterium when conditions are favorable for bacterial growth
  5. lac repressor
    Turns off the production of the proteins responsible for lactose metabolism when lactose is absent from the medium
  6. helix-turn-helix motif
    • The first DNA-binding protein motif; made from two alpha helices connected by a short chain of amino acids that make the turn; held at a fixed angle
    • The C-terminal helix is the recognition helix because it fits into the major groove of DNA; its side chains are important for recognition fo DNA
  7. homeotic selector genes
    • Play a critical role in orchestrating fly development
    • Codes for a stretch of 60 amino acids called a homeodomain
  8. homeodomain
    Contains a helix-turn-helix that is always surrounded by the same structure; always presented to DNA in the same way
  9. Zinc fingers
    • Zinc-coordinated DNA-binding motifs; fall into two categories:
    • - simple structure in which the zinc holds an alpha helix and beta sheet together; found in clusters so that the alpha helix of each can contct the major groove of the DNA, forming a continuous stretch of alpha helices along the groove-> strong and specific DNA-protein interaction
    • - found in the large family of intracellular receptor proteins; forms a different type of structure in which two alpha helices are packed together with zinc atoms; usually form dimers that allow one of the two alpha helices of each subunit to interact with the major groove of the DNA
  10. Zinc fingers: two important features?
    both use zinc as a structural element and both use an alpha helix to recognize the major groove of the DNA
  11. P53
    • A critical tumor suppressor in humans that recognizes nucleotide pairs from both the major and minor grooves using loops
    • Fx: regulate cell growth and proliferation
  12. leucine zipper motif
    • The helices are held together by interacitons between hydrophobic amino acid side chains that extend from one side of the helix; they separate to form a Y-shaped structure, which allows their side chains to contact the major groove of DNA
    • Two alpha helical DNA-binding domains dimerize through their alpha-helical leucine zipper region to form an inverted Y-shaped structure 
  13. combinatorial control
    Heterodimerization is an example of this, in which combinations of different proteins, rather than individual proteins, control a cell process
  14. helix-loop-helix motif
    • DNA-binding motif that consists of a short alpha helix connected by a loop to a second, longer alpha helix
    • The flexibility of the loop allows one helix to fold back and pack against the other
    • Binds both to DNA and to the HLH motif of a second HLH protien
  15. helix-loop-helix motif: part two?
    • The second HLH protein can be the same (creating a homodimer) or different (creating a heterodimer)
    • Several of these lack the alpha-helical extension responsible for binding to DNA; these truncated proteins can form heterodimers with full-length HLH proteins, but the heterodimers are unable to bind DNA tightly because they form only half of the necessary contacts
  16. gel mobility shift assay
    • Allows trace amounts of a sequence-specific DNA-binding protein to be readily detected; in this assay, a short DNA fragment of specific length and sequence is radioactively labeled and mixed with a cell extract; the mixture is then loaded onto a polyacrylamide gel and subjected to electrophoresis
    • If the DNA fragment corresponds to a chromosomal region where several sequence-specific proteins bind, autoradiography will reveal a series of DNA bands, each retarded to a different extent and representing a distinct DNA-protein complex
    • The proteins responsible for each band on the gel can then be separated from one another by subsequent fractionations of the cell extract. Once a sequence-specific DNA protein has been purified, the gel-mobility shift assay can be used to study the strength and specificity of its ineteractions with different DNA sequences, the lifetime of DNA-protein complexes and other proteins critical to the functioning of the protien in the cell 
  17. DNA affinity chromatography
    • Can be used once the DNA sequence a gene regulatory protein recognizes is determined
    • Method: a double-stranded oligonucleotide of the correct is synthesized by chemical methods and linked to an insoluble porous matrix like agarose; the matrix with the oligonucleotide attached is used to construct a column that selectively binds proteins that recognize the particular DNA seqeucne
  18. DNA footprinting
    • Method of determining DNA sequences recognized by gene regulatory prtoeins
    • Requires a purified fragment of duplex DNA that contains within it a recognition site for the protein; DNA corresponding to the regulatory region for the gene that is controlled by the protien of interest should be used

    This method is based on nucleases or chemicals that randomly cleave DNA at every phosphodiester bond 
  19. chromatin immunoprecipitation
    • Provides a way of empirically determining sites on DNA that interact with proteins
    • Proteins are cross-lined to DNA in living cells, te cells are broken open, and the DNA is sheared into small fragments
    • Antibodies directed against a given GRP are used to purify DNA that became covalently cross-linked to that protein in the cell
    • If the DNA is hybridized to microarrays that contain the entire genome displayed as a series of discrete DNA framgents, the precise genomic location of each precipitated DNA fragment can be determined. In this way, all the sites occupied by the gene regulatory protein can be mapped on the cell’s genome
  20. operon
    Genes that are adjacent to one another on the chromosome of bacteria and are transcribed from a single promoter as one long mRNA molecule
  21. operator
    A shrot region of regulatory DNA of defined nucleotide sequence that is recognized by a repressor protein (in the case of tryptophan, a tryptophan repressor)
  22. Trp repressor
    A member of the helix-turn-helix family; when the repressor occupies the operator, it blocks access to the promoter by RNA polymerase, thereby preventing expression of the tryptophan-producing enzymes
  23. negative control
    When the active, DNA-binding form of the protein serves to turn the gene off, it is this; and the gene regulatory protiens that function in this way are called transcriptional repressors or gene repressor proteins
  24. positive control
    When the active, DNA-bidning form of a protein turns genes on, it is this; and the gene regulatory proteins are transcriptional activators or gene activator proteins
  25. transcriptional activators
    Must be bound to DNA to exert their effects; can increase the rate of transcription initiation up to 1000-fold; can operate as an on-off switch
  26. CAP
    Catabolite activator protein

    Activates genes that enable E. coli to use alterantive carbon sources when glucose is unavailable

    Falling levels of glucose cause an increase in cAMP, which binds to CAP, enabling it bind to its specific DNA sequence near target promoters and thereby turn on genes

    Expression on when cAMP is high; expression off when cAMP is low
  27. DNA loooping
    • A feature of regulation that allos two different proteins bound along a DNA double helix to contact one another readily. The DNA can be thought of as a tether, helping one DNA-bound protein interact with another even though thousands of nucleotide pairs may separate the binding sites for the two proteins.
    • An example is the lac operon: a single tetrameric molecule of the Lac repressor can bind two operators simultaneously, looping out the intervening NA; the ability to bind simultaneously to two operators strengths the overall interaction of the Lac repressor with DNA and leads to greater repression in the cell
  28. Gene
    Refers only to a segment of DNA that is transcribed into RNA
  29. Gene repressor proteins
    Used to regulator transcription in eucaryotes with many more possible mechanisms; do not directly compete with the RNA polymerase for access to the DNA; act through more than one mechanism at a given target gene
  30. regulatory region of the Eve gene
    • Very large; formed from simple regulatory modules, each containing multiple regulatory sequences and is responsible for specifying a particular stripe of Eve expression
    • Because the regulatory sequences in the Eve stripe 2 module are strung out along the DNA, many sets of gene regulatory proteins can be bound simultaneously at separate sites and influence the promoter of a gene; the promoter integrates the transcriptional cues provided by all four bound 
  31. Bicoid and Hunchback, Kruppel and Giant
    • Two gene regulatiory proteins that activate Eve transcription; Two regulatory proteins that repress Eve transcription
    • Concentations of tehse four proteins determine whether the protein complexes that form at stripe 2 module activate transcription of the Eve gene
    • Either of the two repressors can turn off the gene, whereas both Bicoid and Hunchback must bind for its maximal activation
  32. Barrier sequences
    Prevent the spread of heterochromatin into gees that need to be expressed; a type of DNA element