ch 23

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doncheto
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251601
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ch 23
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2013-12-08 15:05:33
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gene
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  1. What does selective gene expression accomplish for the cell?
    •Be metabolically thrifty

    •Fulfill specialized roles
  2. What does "constitutively active" mean?
    • always active
    • •Regulated or made upon demand
  3. How do catabolic and anabolic enzymes differ in their function?
    –Catabolic enzymes degrade specific substrates; they are induced by substrates

    • •Induction means turn on
    • expression/synthesis of the enzymes

    –Anabolic enzymes synthesize products; they are repressed by end-products

    • •Repression means turn off or
    • reduce expression/synthesis of the enzymes

    –Repression ≠ inhibition
  4. How is their expression or synthesis regulated
    differently?
    –Catabolic enzymes degrade specific substrates; they are induced by substrates

    • •Induction means turn on
    • expression/synthesis of the enzymes

    –Anabolic enzymes synthesize products; they are repressed by end-products

    • •Repression means turn off or
    • reduce expression/synthesis of the enzymes

    –Repression ≠ inhibition
  5. What is an operon?
    • –Operon: a set of genes that is transcribed into a single mRNA from a
    • single promoter (polycistronic); the individual genes within an
    • operon are usually functionally related
  6. What is an operator?
    –Within promoter is operator (short DNA sequence)
  7. What proteins bind to operators?
    –Gene regulatory proteins

    • •Binds to operator (regulatory
    • site)

    • •May be activators (bind and help position RNA polymerase) or repressors (block promoters)
    • •Are allosteric and bind to effectors (small organic  molecules 
    • such as the substrate or end-product)

    •Are constitutively expressed
  8. What does "allosteric" mean?
    • •Are allosteric and bind to effectors (small organic  molecules 
    • such as the substrate or end-product)

    •Are constitutively expressed
  9. What are inducers and corepressors?
    inducers turn on expression/synthesis of the enzymes

    • corepressors encodes a repressor
    • protein that is active when bound to a specific proteins.
  10. Does the trp operon encode for catabolic or anabolic enzyme for tryptophan metabolism?
    Catabolic
  11. How do tryptophan and trp
    repressor exert control over the trp operon?
    •Trp operon

    • –Encodes for enzymes for
    • tryptophan biosynthesis

    • –Low trp: repressor does not bind trp nor
    • operator; operon ON

    • –High trp: repressor binds trp and
    • operator; operon OFF
  12. Why is the action of Trp
    repressor a useful property?
    • no
    • overproduction
  13. •What would happen to the regulation of the Trp operon in
    cells that expresss a
    mutant form of Trp repressor that (1) cannot bind to DNA or (2)
    binds to DNA even if no trp is bound to it?
  14. 1. overproduction
    2. will not make tryptophan
  15. •What would happen in scenarios (1) and (2) if
    the cells, in addition, produced normal Trp repressor protein from a second, normal
    gene?
    • 1. it will help
    • 2. it will not stop from binding
  16. •If the Trp operon is instead regulated by a Trp
    activator, would you expect the binding of trp to increase or decrease its affinity for its
    regulatory sequences? Why?
    • .
    • it shoud decrease it affinity because it is the opposite of repressor

    • ---
    • leader sequence if the celll does bind it wil make the whole trancript go
    • through includes start codon, decides how many enzymes should be made, another
    • way to regulate- more specific, 1st region needs tryptophan to sence how much
    • tryptophan is around.

    • Region
    • 3 and 4 can base pair and thats a signal to stop

    • If
    • 2 and 3 form base pairs, it is not a termination

    • Since
    • transcription and translation is couples in bacteria, it could make the first the
    • peptide and stop if it senses that there is tryptophan.

    • Another
    • scenario is when the tryptophan lv is low it will make a hairpin on region 2
    • and 3 that will countiue translation.

    • This
    • happend in mRNA
  17. What enzymes do LacZ and LacY encode? What are the functions of those
    enzymes?
    • LacZ- β Galactosidase - Hydrolyzes (breaks down) Galactose
    • LacY- Galactoside permease - Transports lactose into the cell
  18. How do lactose, lac
    repressor, glucose, cAMP, and CRP/CAP exert control over the lac operon? Make
    sure you know and can explain the mechanism.
    • –Lactose present: repressor binds
    • lactose but not DNA; operon can be ON

    lac repressor: Blocks the operator when lactose is bound to it.

    glucose: –Low glucose: cAMP level is high, CAP/CRP binds cAMP and DNA, operon can be ON
  19. How do different cell types in a multicellular organism take on
    distinct characteristics?
    • •When
    • cells specialize and make different RNA and proteins, they become
    • differentiated and have differential gene expression.
  20. What is meant by "housekeeping" genes?
    • •Differentiated
    • cells express the common housekeeping genes (such as those for ribosomal
    • proteins and metabolic enzymes) plus specialized genes.
  21. On which five main levels can eukaryotic gene expression be controlled?
    Know the various methods discussed for regulating gene expression. Know which
    methods belong under which level.


  22. What do developing oocytes in Xenopus
    use to increase production of ribosomes that occurs during oogenesis?
    • Many
    • nucleoi are formed by the
    • 4000-fold replication of rRNA genes in an
    • amphibian oocyte. These genes are
    • amplified to produce enough ribosomes to sustain early
    • embryonic development
  23. Know the structure of an antibody: heavy and light chains, constant and
    variable regions.
  24. How can each lymphocyte produce one unique type of
    antibody that is different from that produced by a separate lymphocyte when all
    lymphocytes arise from precursor cells that have the same genome?
    • DNA rearrangement occurs during
    • lymphocyte development so each lymphocyte gets one unique combination of the
    • millions possible.

    • The V, D, and J
    • segments shown together code for variable regions/domains of the antibody heavy
    • chains.
  25. What are V, D, and J segments? Together do they code for constant or
    variable regions of antibodies?
    • The
    • V, D, and J segments shown together code for variable regions/domains of the
    • antibody heavy chains
  26. What typically happens to its transcriptional activity when the
    promoter of a gene is methylated?
    • •DNA
    • methylation is associated with
    • reduced gene activity

    • •Addition
    • of methyl groups to selected cytosine bases

    • •Methylation of promoter regions
    • tends to inactivate transcription by

    • –Blocking
    • access of proteins required for transcription activation or

    • –Serving
    • as binding sites for proteins that condense chromatin
  27. What do epigenetic changes mean?
    • •DNA
    • methylation can create epigenetic changes, stable alterations in
    • gene expression, transmitted from one cellular generation to the next, with no
    • change in DNA sequence.
  28. What is X-inactivation?
    • •X-inactivation: one X chromosome in
    • the female is extensively methylated and the chromatin
    • fibers are tightly condensed into heterochromatin (called a Barr body under a
    • microscope, appear as a dark spot)

    • –Once
    • a certain X is inactivated in a cell, all the daughter cells produced by the
    • original cell have the same X inactivated
  29. What is a Barr body?
    • one
    • X chromosome in the female is extensively methylated
    • and the chromatin fibers are tightly condensed into heterochromatin (called a
    • Barr body under a microscope, appear as a dark spot
  30. What does genomic imprinting mean? What accounts for
    the difference in gene expression when the genes are inherited from father vs.
    mother?
    • •DNA
    • methylation is also involved in genomic imprinting which causes certain genes to be expressed differently
    • depending on the parent from which they are inherited

    • •The
    • difference in expression results from differing methylation patterns.

    • •Some
    • genes are maternally imprinted (methylated)
    • so only the paternal copy is active; and vice versa for paternally imprinted
    • genes
  31. What do chromosome puffs from Drosophila
    polytene chromosomes suggest about the compaction of DNA? Are genes in these
    regions more or less actively transcribed?
    • Puffs are regions in which transcriptionally active chromatid has become less
    • condensed.
  32. What effect does histone acetylation typically have on
    transcription?
    • •Histone modification
    • (addition of methyl, acetyl, or phosphate groups) can alter genome activity

    • •Acetylated histones are associated with
    • gene activation by loosening chromatin packing and thereby facilitating access
    • of transcription factors
  33. What is HAT and what is its function?
    Histone acetyl transferase-acetylate nucleosomes and activating them.
  34. What are chromatin remodeling complexes?
    • Chromatin remodeling
    • complexes alter nucleosome structure.
    • Loosen histones for gene expressions and DNA replication.
  35. Which two experimental techniques can be used to show that different
    genes are expressed by different tissue types? Which of these techniques allows
    for the screening of thousands of genes simultaneously?
    • differential
    • transcription by
    • nuclear run-on transcription assays

    • DNA microarrays allow
    • the expression of thousands of genes to be monitored simultaneously.
  36. What are control elements, enhancers/silencers, activators/repressors,
    and coactivators in eukaryotes?
    • –Control elements
    • (sequences outside of core promoter bound by gene regulatory proteins)

    • •Can be proximal
    • (within about 100-200bps of it) or distal
    • (located at distances up to several hundred thousand base pairs upstream or
    • downstream from the core promoter)

    • •Also called enhancers
    • or silencers

    • Bound by gene
    • regulatory proteins called activators
    • or repressors (these are the regulatory transcription factors)

    • Coactivators mediate interaction
    • between activators and the trxn preinitiation complex. They
    • include

    - Histone acetyltransferases

    - Chromatin remodeling complexes

    • - Mediators that bridge together the activator proteins associated
    • with enhancers and RNA polymerase and general transcription factor at the core
    • promoter (DNA forms a loop)
  37. What proteins bind to the core promoter? Which ones bind to the control
    elements?
    • 1. Mediators
    • 2. Regulatory transcription factors.Bound
    • by gene regulatory proteins called activators
    • or repressors
  38. What conclusions can be made from the experiment
    described in Fig. 23-21?
    • Core promoter is
    • necessary for transcription.



    • Enhancer increases
    • transcription efficiency and has an effect upstream or downstream, proximal or
    • distal, and when inverted in orientation.
  39. What are three types of coactivators? What function does each serve?
    Histone acetyltransferases

    - Chromatin remodeling complexes

    - Mediators
  40. How can proteins that bind to enhancers located at a great distance away interact with the RNA polymerase and general transcription
    factors at the core promoter?
  41. What is the combinatorial model of gene regulation?
    • Combinatorial model
    • for gene regulation: different cell types have different sets of regulatory
    • transcription factors that interact with different control elements.
  42. On which region of the DNA double helix do most gene regulatory
    proteins (activators and repressors) bind? What types of bonds stabilize the
    binding?
    • •Most cases: bind to major groove
    • •Form H bonds, ionic bonds, hydrophobic interactions with
    • edges of the bases
  43. What are the common DNA binding motifs found in gene regulatory
    proteins?
    •Most have one of the following DNA binding motifs:

    –Helix-loop-helix

    –Helix-turn-helix

    –Zinc finger (Zn2+ holds an a helix and a b sheet together)

    –Leucine zipper (dimer of two a helices)

    Homeodomain (3 linked a helices
  44. What are response elements? How are they used by eukaryotes? Know the
    two examples given in class.
    • •Prokaryotes
    • have operons, eukaryotes don’t.
    • How do eukaryotes activate a group of related genes at the same time?

    • –Some use response elements to turn trxn on or off in
    • response to a particular environmental or developmental signal (e.g. hormones).

    • All the genes
    • activated by a particular steroid hormone are associated with the same type of
    • response element allowing them to be regulated together.
  45. What are homeotic genes? In which organism were they
    first discovered?
    • Homeotic genes code for
    • transcription factors that activate or inhibit the transcription of
    • developmentally important genes by binding to specific DNA sequences.
    • Homeobox encodes a homeodomain, the DNA-binding domain
    • Found in Drosophila
  46. What is a homeobox or homeodomain?
    • Part of the DNA that contains the homeotic genes.Homeobox encodes a homeodomain, the DNA-binding
    • domain
  47. What can happen when homeotic genes are mutated?
    The phenotype changes and the developmental process.
  48. What are hox genes? Are they found in humans? What is interesting about
    their pattern of expression in the body?
    • Hox genes (examples of homeotic  genes) are highly conserved in animals.
    • In flies and
    • vertebrates the 3¢ to 5¢ location of these genes corresponds to the anterior to
    • posterior position along the body axis 
    • They are found in human.

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