Combinatorial Control of Transcription

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Combinatorial Control of Transcription
TIC
A3 9-44
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Four major classes of transcription
factors Homeodomain (Helix-Turn-Helix)
proteins Hox, POU, LIM, Pax Basic Leucine Zipper
proteins (bZIP) Basic Helix-Loop-Helix proteins
(bHLH) Zinc Finger Proteins Standard Nuclear
Hormone Receptors (NHR)
Gilbert, Table 5.1, p. 114
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A3 9-13. Schematic diagram of how homeodomain
transcription factors bind to DNA, showing the
helix-turn-helix structure of the protein and the
interactions of helix 3 with bases in the major
groove of DNA.
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A3 9-18. Schematic of a leucine zipper (bZIP)
class transcription factor binding to DNA. These
proteins are named for the part of the protein
away from the DNA, through which it interacts
with other transcription factors at promoter
sites.
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A3 9-19. Leucine zipper (bZIP) transcription
factors can form heterodimers with different DNA
binding specificities than either homodimer -
another combinatorial phenomenon.
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A3 9-20. Helix-Loop-Helix family (bHLH)
transcription factors, also named for the
structure of their protein interaction domain,
are generally active as heterodimers.
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A3 9-21. Some bHLH proteins with no DNA binding
domain act as negative regulators for other bHLH
proteins, forming a heterodimer that cannot bind
DNA.
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A3 9-14. Transcription factors of the zinc
finger family, named for the structure of their
DNA binding domains, have a characteristic loop
containing histidine and cysteine residues that
can complex with a Zn ion, which is required for
their activity.
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A3 9-47. The last step in gene expression is
often activation of the protein, by binding to a
ligand or other protein or by enzymatic covalent
modification. Some proteins can be reversibly
activated or inactivated, for example by
phosphorylation or dephosphorylation. All the
kinds of examples diagrammed above are
encountered in developmental regulation of
protein activity.
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Combinatorial control
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(dont forget it)
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Combinatorial Control of Transcription
TIC
A3 9-44
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A3 9-2
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Which way is transcription going? Left to
right.
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G 5.27
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?
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1) Do all exons code for protein? a) Yes b)
No
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G7 5.28. Alternative splicing allows the rat to
synthesize seven different variants of
tropomyosin from the same gene in different types
of muscle cells.
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Alternative splicing of the Drosophila Dscam
gene 38,016 possible different proteins!
G 5.29
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A3 9-2
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Different 5 and 3 UTRs can result
in different rates of translation different
mRNA stabilities different localization of the
mRNA in the cell
G 5.28
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Casein mRNA stability control by prolactin
Pulse-chase experiment to cells in culture, add
very small amount of highly radioactive
nucleotide precursor for a few minutes, then add
an excess of non-radioactive (unlabeled)
precursor. Isolate mRNA at various times and
determine radioactivity.
G7 5.31
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(includes protein degradation via ubiquitin
ligase and proteasome)
A3 9-2
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?
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• 2) Two different cell types may contain
  different amounts of the same protein because
  they differ in
• rates of transcription initiation for the
• corresponding gene.
• b) alternative splicing of the corresponding
  transcript to give a different 3 UTR.
• c) alternative splicing of the corresponding
  transcript to give a different 5 UTR.
• d) (a) and (b)
• e) (a), (b), and (c)

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Differential regulation of alternative splicing,
translation rates, mRNA stability, protein
modification, and protein stability in different
cell types are more examples of . . . ?
G 5.28
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Combinatorial control
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??
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• 3. Which of the following statements about
  ligands and receptors is false?
• a) Components of the extracellular matrix can
  act as signaling ligands.
• b) In signaling by steroids, the receptor and
  the activated transcription factor are the same
  molecule.
• c) Juxtacrine signaling involves both
  membrane-bound ligands and membrane-bound
  receptors.
• d) Two different types of cells that carry the
  same receptor on their surfaces will generally
  respond in the same way to the ligand that the
  receptor recognizes.

0.5 points
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4. Cellular oncogenes, in which dominant
gain-of-function mutations can cause tumor
formation, encode proteins whose normal function
is to a) inhibit cell division or prevent
apoptosis. b) promote cell division or prevent
apoptosis. c) inhibit cell division or initiate
apoptosis. d) promote cell division or initiate
apoptosis.
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5. The number of different signaling pathways
involved in embryonic development is a)
none b) between 5 and 10 c) 10 - 20 d) more
than 20
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The Gerhart Gallery of Signaling Pathways
Signaling pathways 1-4

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Signaling pathways 5-8


(out of date)
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Signaling pathways 9-12


or retinoid

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Signaling pathways 13-16


17. Cell death. See Gilbert
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Paracrine
Juxtacrine
Two modes of signaling
A3 15-1
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?
A3 15-14
Three classes of receptors
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Effects of growth factors on cells in the body
and,
in embryo, adopt new fates and/or behaviors
A3 15-8
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Most oncogenes and tumor suppressors are mutant
forms of genes that encode cell signaling
components.
Cellular oncogenes (the normal forms) are genes
that promote cell growth.
Tumor suppressor genes (the normal forms) are
genes that inhibit cell growth.
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Typical RTK pathway (ras pathway)
G 6.14
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Ras cycling between active and inactive forms
A3 15-50
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The MAP-kinase cascade
A3 15-54
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Typical RTK pathway (ras pathway)
G 6.14
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Receptor protein tyrosine phosphatase
pathways (RPTPs GG10) can act antagonistically
to RTK pathways.
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Wnt pathway
(No Wnt present)
G 6.24A
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Combinatorial Control of Transcription
TIC
A3 9-44
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Wnt pathway, constitutively on because of an
oncogenic mutation
G 6.24B
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TGF? Pathway
G 6.21
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Hedgehog pathway
G 6.25
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Cyclopic lamb from a ewe who ate Veratrum
californicum early in pregnancy
G 6.26
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Delta-Notch pathway
G 6.29
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Signaling pathways to remember
Details A. Wnt B. Receptor tyrosine kinase
(TK,ras) Others C. Hedgehog D.
Notch/Delta Which of the above involves
juxtacrine signaling? Which generally has growth
factors for ligands?
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Signaling pathways to remember Details A.
Wnt B. Receptor tyrosine kinase (TK,
ras) Others C. Hedgehog D. Notch/Delta E.
Nuclear hormone receptor
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Two types of cellular receptors
Most are of this type
e.g. NHRs
A3 15-16
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Programmed cell death pathway Malfunction of this
pathway can also cause tumors.
G 6.27
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How much of this should I be learning and
remembering?
How much do I have to know for the quizzes and
exams?
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The ECM can modulate paracrine signaling
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Components of extracellular matrix (ECM)
A3 19-57
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Integrins receptors for ECM components
A3 19-60
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How integrins connect the cyto-skeleton with ECM
components
G 6.34
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A3 19-29
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Biochemical signaling through integrins
G 6.37
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Cadherins are cell adhesion molecules (CAMs).
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Cadherins are largely responsible for cell
adhesion in cell sheets (epithelia)
A3 19-28
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Cadherins interact by homophilic binding
A3 19-26
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Interaction of cadherin with the cytoskeleton
through catenins
Remember b-catenin from the Wnt pathway? Wnt
signaling probably also can affect cadherin
functions and therefore cell adhesiveness, by
controlling availability of b-catenin.
A3 19-24
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Duplexed pathways
A3 15-16
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Multiplexed pathways
A3 15-69
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• 8. What can determine how a cell responds to a
  ligand?
• The receptors and downstream signaling proteins
  it has synthesized previously.
• The transcription factors, splicing factors, and
  other mRNA binding proteins it has synthesized
  previously.
• c) The presence of other signaling pathways in
  the cell and ligands in the cells vicinity.
• d) All of the above.
• e) All but one of (a), (b), and (c).

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How do these properties (which receptors are
displayed, etc.) relate to the determined or
committed state of the cell?
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Wnt pathway
G 6.24A
(Modified for group problem solving in lab).