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!"#$%&'"()*+ --./0
1234 5&"6&'4667 8%9
"234:%&"6&'466;?! -@.
AB$& %#
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!4$)&*"42 )*46($*"HI#6
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!"#$%&"'(!')$ #$+
!,- "-./0#!')$ )1
.-$- -2("-%%')$
"#$ %&'% $( &')( '** %&+, -,(.-*
+/.#01'2#/3 +% $#-*4 5( /+6( %# 4#
,#1(%&+/7 $+%& +%8
90#1 %&( J6"K
8*#L*4''&*( >46
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T??TUM10V WJT?M1AU
5#= 4*& )%& L&6&( #X H*#34*+#)&( Y46E&
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022 S&22( S#6)4"6 M%*&& >4\#* S24((&( #X NU0 ]
'NU07 *NU07 46E )NU0
022 )%*&& X#*'( H4*I$"H4)& "6 H*#)&"6(+6)%&("(:
022 NU0( 4*& (+6)%&("^&E X*#' 9U0 )&'H24)&(P+ +$#3456574578 "$# 69:;?5?@
M%"( H*#$&(( "( $422&E 8=>7?A=B6C97@
A62+ 'NU0(E"*&$) )%& (+6)%&("( #X H*#)&"6(: *NU07 46E )NU0 4*& *&_
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Transcription
DNA-directed synthesis of RNA
All human RNAs are transcribed from DNA
templates
TYPE of RNA FUNCTION
Ribosomal RNA (rRNA) Components of ribosome
Transfer RNA (tRNA) Delivery of amino acidsMessenger RNA (mRNA) Template for protein synthesis
Short nuclear RNAs (snRNAs) Components of spliceosome
Short interfering RNAs (siRNAs) or
micro RNAs (miRNAs)
Regulation of gene expression
Short nucleolar RNAs (snoRNAs) Methylation of rRNAs
Not necessarily true for viruses (ex. HIV, HepB) --> some viruses have RNA genes/used as templates
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A62+ -` #X L&6&( "6 4 )+H"$42 $&22 4*&
4\#* S24((&( #X NU0 ]
'NU07 *NU07 46E )NU0
Only need certain things at certain times --> tightly regulated
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5Ab 0NT cTUT? MN0U?SN1!T9 1U
8NAd0NeAMT?[
NU0 $%4"6 L*#=( @fG-f E
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5Ab 0NT cTUT? MN0U?SN1!T9 1U
8NAd0NeAMT?[
16 H*#34*+#)&(7 a"*)
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M*46($*"HI#6
M*46($*"HI#6 $46 P& E"a"E&E "6)# X#
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S#6a&6I#6( J(&E "6 TKH*&(("6L )%& ?&_
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S#6a&6I#6( J(&E "6 TKH*&(("6L )%& ?&_74@
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S#6a&6I#6( J(&E "6 TKH*&(("6L )%& ?&_74@Sequence of RNA transcript is parallel to non-template
strand
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S#6a&6I#6( J(&E "6 TKH*&(("6L )%& ?&_ parallel to AUG in RNA transcript
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S#6a&6I#6( J(&E "6 TKH*&(("6L )%& ?&_
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M*46($*"HI#6
M*46($*"HI#6 $46 P& E"a"E&E "6)# X#
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5#= E#&( )%& H#2+'&*4(& 36#= =%&*& )#
()4*)[[[ ?H&$"42 (
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F: !"6E"6L #X 8#2+'&*4(& )# M&'H24)&
9U0 8#2+'&*4(& P"6E( 6#6G(H&$"g$422+ )# 9U0 =")% 2#=
4B6")+ 46E '"L*4)&( 42#6L ")7 2##3"6L X#* H*#'#)&*:
?"L'4 (
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8*#H&*I&( #X 8*#34*+#I$ 8*#'#)&*(
8*#'#)&*( *&$#L6"^&E P+ )%& i X4$)#* )+H"$422+ $#6("()
#X 4 hl PH *&L"#6 #6 )%& @fG("E& #X )%& )*46($*"HI#6()4*) (")&:
b")%"6 )%& H*#'#)&* 4*& )=# A97?57?N? ?5ON57A55:5
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S#6(&6(
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Bacterial RNA Polymerase (RNAP)
Synthesizes all RNA except primers for replication
Positively-charged
cleft binds DNA
Mg2+in active site
!"
Thermus thermophilusRNAP
Core enzyme: !2""'#
(alpha2, sigma, sigma, omega)
DNA non-template
9U0
)&'H24)&
RNA
------------- -------------
beta beta'
4 diff proteins to form 1
polymerase
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?"L'4 X4$)#*(
O,6&(0+6&+' 6#*+C n ("L'4 X4$)#*(
:'6+**-, ,-52*+,C /l ("L'4 X4$)#*(
!J(
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RNAP core enzyme
!factor recognizes promoters
RNAP holoenzyme
$is extended and interacts with -35 and -10
regions Rainbow coloured coils stretching across entire DNA section along enzyme
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M*46($*"HI#6
M*46($*"HI#6 $46 P& E"a"E&E "6)# X#
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16"I4I#6 #X 8#2+'&*"^4I#6
NU0 H#2+'&*4(& %4( )=# P"6E"6L (")&( X#* UM8(:
M%& B7BC>C97 ?B85 H*&X&*( )# P"6E 0M8 46E cM8 Y'#()
NU0( P&L"6 =")% 4 H
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S%4"6 T2#6L4I#6
M%& 6#0( C#*;1(0',( Y=")%#
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8*#34*+#I$ 16"I4I#6 46E T2#6L4I#6
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8*#34*+#I$ 16"I4I#6 46E T2#6L4I#6
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9U0 D##)H*"6I6LC 1E&6IX+"6L )%& U
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9U0 D##)H*"6I6L
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?
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M*46($*"HI#6
M*46($*"HI#6 $46 P& E"a"E&E "6)# X#
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S%4"6 M&*'"64I#6
M=# )+H&( #X )*46($*"HI#6 )&*'"64I#6'&$%46"('( #H&*4)& "6 P4$)&*"4C A6& E&H&6E(#6 "U9 85=C97 T>A89=
N%# "( 46 0M8GE&H&6E&6) %&2"$4(&:
1) '#a&( 42#6L NU0 )*46($*"H)7 g6E( )%&)*46($*"HI#6 P
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M*46($*"HI#6 M&*'"64I#6 P+ *%# D4$)#*
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DJ Koslover et al.(2012) J Mol Biol423:664-76
Model of Rho-mediated termination
Rho recognizes rut site, then
closes around RNA and
advances toward RNAP
Rho causes allosteric changein RNAP that releases
template
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16)*"6("$ M&*'"64I#6
M%& (&$#6E )&*'"64I#6 '&$%46"(' "( )&*'&E B78=B7?BA85=C97@
5&*&7 )&*'"64I#6 "( E&)&*'"6&E P+ (H&$"g$ (&_
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M%& M&*'"64I#6 ?")& X#*
O8 6#*+%0CAH&*#6
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Operons
Operon (in bacteria): two or more genestranscribed together as one RNA molecule
The mRNA is polycistronic
Genes in an operon usually have related
functions
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Overview of bacterial transcription
$dissociates
Fig 12-3 from Watson et al., Molecular
Biology of the Gene, 6thed.
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Summary of bacterial transcription
Transcription of genes is carried out by RNApolymerase (RNAP), a multisubunit complex
Bacterial RNAP recognizes promoters with a
defined consensus sequence via the $subunit
DNA strands are separated and RNA synthesis
occurs, possibly after abortive initiation
Termination is mediated by a termination hairpin
structure or by Rho factor