Upcoming Biochemistry Faculty Search Seminars

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Upcoming Biochemistry Faculty Search Seminars

• Amy Springer R April 17 315 pm SL 140

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Transcription
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Initiation
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MVA Fig. 26A. DNA footprinting (Nuclease
protection assay)
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DNA Footprinting
http//users.rcn.com/jkimball.ma.ultranet/BiologyP
ages/F/ Footprinting.html
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Figure 31-10 The sense (nontemplate) strand
sequences of selected E. coli promoters.
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Figure 31-12a The sequence of a fork-junction
promoter DNA fragment. Numbers are relative to
the transcription start site, 1.
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MVA Fig. 26.6
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Figure 31-15 RNA chain elongation by RNA
polymerase.
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Figure 31-16 An electron micrograph of three
contiguous ribosomal genes from oocytes of the
salamander Pleurodeles waltl undergoing
transcription.
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MVA Fig. 26.8
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RNA Backtracking
MVA Fig. 26.10
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MVA Fig. 26.15
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MVA Fig. 26.16
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Figure 31-18 A hypothetical strong (efficient) E.
coli terminator.
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Regulation Possiblilites
Regulate transcription Regulate
translation Regulate activity
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The lac operon

• E-coli uses three enzymes to take up and
  metabolize lactose.
• The genes that code for these three enzymes are
  clustered on a single operon the lac Operon.

Whats lactose??
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Figure 31-2 Genetic map of the E. coli lac operon.
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The lac repressor gene

• Prior to these three genes is an operator region
  that is responsible for turning these genes on
  and off.
• When there is not lactose, the gene for the lac
  repressor switches off the operon by binding to
  the operator region.
• A bacteriums prime source of food is glucose.
• So if glucose and lactose are around, the
  bacterium wants to turn off lactose metabolism in
  favor of glucose metabolism.

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Isopropyl thio -? -D- galactoside
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Figure 31-25 The base sequence of the lac
operator.
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• Lac repressor binding to DNA animation
• http//molvis.sdsc.edu/atlas/morphs/lacrep/index.h
  tm

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Figure 31-26 The nucleotide sequence of the E.
coli lac promoteroperator region.
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Figure 31-27 The kinetics of lac operon mRNA
synthesis following its induction with IPTG, and
of its degradation after glucose addition.
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Figure 31-36 X-Ray structure of the lac repressor
subunit.
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Figure 31-37a X-ray structure of the lac
repressor-DNA complex.
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Induction.

• Allolactose is an isomer formed from lactose that
  derepresses the operon by inactivating the
  repressor,
• Thus turning on the enzymes for lactose
  metabolism.

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The lac operon in action.

• When lactose is present, it acts as an inducer of
  the operon (turns it on).
• It enters the cell and binds to the Lac
  repressor, causing a shape change that so the
  repressor falls off.
• Now the RNA polymerase is free to move along the
  DNA and RNA can be made from the three genes.
• Lactose can now be metabolized (broken down).

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When the inducer (lactose) is removed

• The repressor returns to its original shape and
  binds to the DNA, so that RNA polymerase can no
  longer get past the promoter. No RNA and no
  protein is made.
• Note that RNA polymerase can still bind to the
  promoter though it is unable to move past it.
  That means that when the cell is ready to use the
  operon, RNA polymerase is already there and
  waiting to begin transcription.

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Lac movie
Lac and trp
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Lac repressor induces major conformational
changes in DNA
http//molvis.sdsc.edu/atlas/morphs/lacrep/lacrep_
anim_large.gif
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Catabolite repression happens when glucose (a
catabolite) levels are high.

• Then cyclic AMP is inhibited from forming.
• When glucose levels drop, more cAMP forms.
• cAMP binds to a protein called CAP (catabolite
  activator protein), which is then activated to
  bind to the CAP binding site.
• This activates transcription, perhaps by
  increasing the affinity of the site for RNA
  polymerase.
• This phenomenon is called catabolite repression,

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Suggested readings on regulation/dna bp Voet
pp 1237-1253 Problems 2, 4 Heres a quiz on the
lac operon http//www.bio.davidson.edu/courses/
movies.html
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Figure 31-28a X-Ray structures of CAPcAMP
complexes. (a) CAPcAMP in complex with a
palindromic 30-bp duplex DNA.
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Figure 31-39 A genetic map of the E. coli trp
operon indicating the enzymes it specifies and
the reactions they catalyze.
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Figure 31-40 The base sequence of the trp
operator. The nearly palindromic sequence is
boxed and its 10 region is overscored.
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Figure 31-41 The alternative secondary structures
of trpL mRNA.
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Figure 31-42a Attenuation in the trp operon. (a)
When tryptophanyltRNATrp is abundant, the
ribosome translates trpL mRNA.
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Figure 31-42b Attenuation in the trp operon. (b)
When tryptophanyltRNATrp is scarce, the ribosome
stalls on the tandem Trp codons of segment 1.
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Table 31-3 Amino Acid Sequences of Some Leader
Peptides in Operons Subject to Attentuation.
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Figure 31-43 The structure of the 5 cap of
eukaryotic mRNAs.
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Figure 31-46 An electron micrograph and its
interpretive drawing of a hybrid between the
antisense strand of the chicken ovalbumin gene
and its corresponding mRNA.
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Figure 31-47 The sequence of steps in the
production of mature eukaryotic mRNA as shown for
the chicken ovalbumin gene.
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Figure 31-48 The consensus sequence at the
exonintron junctions of vertebrate pre-mRNAs.
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Figure 31-49 The sequence of transesterification
reactions that splice together the exons of
eukaryotic pre-mRNAs.
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Table 31-4 Types of Introns.
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