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1Heredity -
-the transmission of characters to progeny.
DNA carries the information necessary for the transmission
of characters.The biological information is encoded
in the sequence of bases.TB
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2I. RNA ribonucleic acid!
A polymer of nucleosides heldtogether by phosphodiester bonds.
RNA plays a "ey role in decodingthe information in DNA.
RNA is usually single-stranded.
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3A. #unctions of the ma$or RNAs
%. messenger RNAs mRNA! containgenetic information to encode a protein
&. ribosomal RNAs rRNA! are structural and
catalytic component of ribosomes
'. transfer RNAs tRNA! act as adapters bet(een the mRNA nucleotide code and
amino acids during protein synthesis
phe
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4). *omplementary base pairing
***+++,,,AAA,,,AAA***+++ RNA
RNA
,,,AAA***+++ RNA
***TTT,,,AAA DNA
TB
hydrogenbonding
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5. RNA stem loops
complementary
base pairinghelical!
ssRNA
A common RNA secondary structure
TB
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6II. TRAN*RI/TI0N
1ost commonly2 gene e3pressionrefers to the decoding of genes
into proteins or RNAs.
% gene encodes % polypeptide2
% tRNA2 % rRNA2 or %other RNA TB
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7A. ,ene numbers
4iruses
pro"aryotes
eu"aryotes
group appro3imategene number
)-'55
55-%'2555
2555-%'2555
TB
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8Any gi4en species has a unique set
of genes that confers a unique set
of properties.
/roteins and RNAs determine all of thecharacteristics of organisms and cells.
63ample7 Escherichia coli has ))5 genes8%%9 encode RNAs tRNA2 rRNA!
8)':: encode proteins TB
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9
% gene
% mRNA
transcription
% polypeptide
translation
%. 63pression of single genes
63.%7 a single gene that encodes a protein
*. ,ene e3pression in pro"aryotes
TB
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10
% gene
transcription
% RNA
degraded
% tRNA etc.RNA processing
63. '7 a single gene that encodes one
rRNA or tRNA
TB
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11
operont(o or more genes
transcribed together
a single RNA molecule that
represents more than one gene
polycistronic message
'. 63pression of operons
TB
A B *DNA
transcription
polycistronic
mRNA
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12a. 0perons can encode se4eral
polypeptides or proteins.
TB
% operonA B *
' or more polypeptides
translation
AB
*
% polycistronic mRNA
transcription
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13
% operon
processing
rRNArRNA
degraded ' or more rRNAs
b. 0perons can encode se4eral
rRNA molecules.
% polycistronic RNA
TB
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14&. Important points
1ost pro"aryotes use operons.
0perons are used to coordinategene e3pression and often contain
genes of related function.
The details of organi;ation2processing and degradation are
different for different RNAs.
TB
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15
The e3pression of rRNA and
tRNA is similar in eu"aryotes
and pro"aryotes.
%. 63pression of eu"aryoticrRNA and tRNA genes
D. 6u"aryotic gene e3pression
TB
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16
gene6 I I I6 6 6
6 < e3on < coding sequences
I < intron < inter4ening2noncoding sequences
'. 6u"aryotic protein e3pression
a. Typical eu"aryotic genes ha4e e3ons and introns.
6u"aryotes do N0T ha4e operons TB
1
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17% gene (ith e3ons and introns
6 I I I6 6 6
transcription
% RNA representing e3ons and intronsprimary transcript!
TB
18
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18
primary transcript
% polypeptide
% mRNA
processing
TB
b. /rimary transcripts
19
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19c. /rocessing of primary transcripts
i. cappingii. splicing
iii. tailing
TB
20i i
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20i. *apping
Addition of a = cap
*A/
*apping usually occurs before
transcription is finished.TB
21*Hi l
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21
0*H'
H0
N
N N
N NH'
0
0H
*H&Typical = *A/
9-methylguanosine
//
/
= carbon
of RNA chain= to = lin"age
0
TB>no( the name methylguanosine cap2 = cap!2
but don=t memori;e structure.
22
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22ii. plicing
The remo4al of introns.
primary transcriptsplicing
RNA (ithout intronsTB
23
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23
Addition of a poly-A tail
iii. Tailing
A%A'...A8'55
TB
24
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24&. Notes on eu"aryotic RNA processing
/rocessing occurs in the nucleus
The e3act order of capping2 tailingand splicing 4aries for different genes.
/oly-A tails are added by poly-A
polymerase2 N0T during transcription.
TB
25
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25
TRANSLATION
26
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26
III /ro"aryotic translation
%. >ey components of translation
'. teps in translation&. The genetic code
270 i f " ti t l ti
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2704er4ie( of pro"aryotic translation
/rotein synthesis from an mRNA template.
mRNA
translated region
translation
protein of specific amino acid sequence
TB
phe
28
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28%. >ey components of translation
A. mRNAB. tRNA
*. ribosomes and rRNA
29
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29
translated region
series of codonsusually 8&55 codons!
mRNA
start codon
A. mRNA
stop codon
hine-
Dalgarnosequence
TB
RNA template for protein synthesis
30% hi D l
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30%. hine-Dalgarno sequence
8A,,A,,2 ribosome binding sequence2
critical for ribosome binding
'. start codonsA+,2 ,+,2 or ++,
TB
&. stop codons nonsense codons!
+AA2 +,A2 or +A,
31) T l t d i di !
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31). Translated region coding sequence!
? eries of codons that determines
the amino acid sequence of the
encoded protein.
? *oding sequences ha4e an a4erage
of about &55 codons.
? 63cept for the stop codon2 each
codon specifies a particular amino
acid. TB
32 *odon con i t of & ba e
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32
AUGCAUUGUUCU...codons
protein f1et
% '
- His
&
- *ys
)
- er ...
. *odons consist of & bases
TB
% ' & )
start
codon
33B tRNA
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33B. tRNA
The adapter molecule for translation
%. /articular tRNAs carry
particular amino acids.
TBtRNA-f-1et
f-1et
tRNA-His
His
His
34' /articular tRNAs recogni;e
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34
AUGCAUUGUUCU...
codons
AA% AA'
tRNAs
'. /articular tRNAs recogni;e
particular codons.
amino acid AA!
This allo(s amino acids to be brought
together in a particular order. TB
35
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35&. tRNA structure
All tRNAs are generally similarin structure.
TB
a. %o structure
ssRNA 9&-@& nucleotides long
= &=+A*
36b 'o structure
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36b. 'o structure
clo4er leaf
anticodon loop
TΨ* armD-arm
acceptor arm
e3tra arm
TB
37
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37c. &o structure
in4erted
TB
38d Anticodon
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38d. AnticodonA & base sequence in tRNA
complementary to a specific codon.
anticodon
Base pairing bet(een an anticodon and a codon
allo(s a tRNA to recogni;e a specific codon. TB
39d ti d i t ti
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39e. codon-anticodon interactions
AA+= &= mRNA
codon% ' &
++A
anticodon
%'&
=&=
tRNA
TB
40) tRNA charging adding amino acid!
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40). tRNA charging adding amino acid!
&=
tRNAuncharged!
&=H'N-*H-*-0
R
0
aminoacyl-tRNAcharged!
tRNA charging uses the energy of AT/ TB
41Aminoacyl tRNA synthetases
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41Aminoacyl-tRNA synthetases
amino acidAT/
tRNA
aminoacyl-A1/
A1/ //i
aminoacyl-tRNA
A1/ < adenosine monophosphate //i < inorganic pyrophosphate
en;ymes that attach amino acids to tRNA
TB
en;yme
42 tRNA facts
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42. tRNA facts
tRNAs contain many modified bases.
/ro"aryotes ha4e about C5 differenttRNAs.
TB
43* Ribosomes and rRNA
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43*. Ribosomes and rRNA
Ribosomesribonucleoprotein comple3es that
cataly;e protein synthesis.
rRNAsha4e structural and catalytic roles
TB
44% /ro"aryotic 95s ribosome
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44%. /ro"aryotic 95s ribosome
'&s rRNAs rRNA
&) proteins
%Cs RNA'% proteins
5s
subunit
&5ssubunit
TB
45' Ribosomal sites (here tRNAs bind
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45
A
'. Ribosomal sites (here tRNAs bind
6 < e3it
// < peptidyl
A < aminoacyl
6
TB
46
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46&. %C rRNA
The &= end of the %Cs rRNA iscomplementary to the hine-
Dalgarno sequence ribosomebinding sequence of mRNAs!
47II teps in translation
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47
A+,
/-sitef-met
hine-DalgarnoA,,A,,
on mRNA!
II. teps in translation
mRNA
A. initiation &5s subunit
of ribosome
5s subunit
,T/ hydrolysis
f-met
&5s subunit TB
A,,A,,-----A+,
48% f t tRNA f l thi i tRNA!
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48%. f-met tRNA formyl-methionine tRNA!
In Bacteria2 different met-tRNAs are used forelongation and initiation.
initiation2 formyl-methioninetRNAmetf
elongation2 methioninetRNAmetm
TB
49' Initiation in different domains
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49
In 6u"arya2 the ribosome recogni;esthe 9-methylguanosine cap at the end of
mRNA and initiates at the first A+,.
In 6u"arya and Archaea2 initiation begins (ith methionine rather than f-met.
In Bacteria2 the formyl group of the initiatorformylmethionine f-met! is later remo4ed.
TB
'. Initiation in different domains
50
B 6longation
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50
AA
/-site A-site
AA%. AA-tRNA binding
AA AA
mRNA
B. 6longation
TB
51' peptide bond synthesis
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51
AA AA
AA
AA
peptidyl transferase!
'. peptide bond synthesis
TB
52& translocation
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52&. translocation
AA
AA
,T/
hydrolysis
TB
AA
AA
53* Termination
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AA AA
*. Termination
AAAAAA
+AA
AAAA
AAAAAA
termination
stop codon
TB
54D Additional notes on translation
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/olysomes are mRNAs (ith
se4eral ribosomes attached
mRNA
mRNAs can be translated by -%5
ribosomes simultaneously.
%. Ribosomes mo4e along the mRNA.
D. Additional notes on translation
TB
55' In pro"aryotes only transcription
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'. In pro"aryotes only2 transcription and translation are coupled.
Translation begins before
transcription ends.
DNA
mRNA TB
56
& / t i f ldi i t th ti f
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&. /rotein folding into the acti4e form
can occur spontaneously or (ith the
help of a large protein comple3
called a molecular chaperone.
AT/
AD/
properly folded protein
improperly
folded proteinmolecular
chaperone
57
III Th i d
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III. The genetic code
A. uni4ersal codeB. degenerate code
%. synonyms'. codon families
&. codon pairs
*. (obble base pairing
58III The genetic code
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III. The genetic code
: codon families2 %) codon pairs2 & stop codons
Do not
memori;e!
59A The genetic code is almost
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A. The genetic code is almost
uni4ersal.
1ost organisms use the same
genetic code.
TB
60B The genetic code is degenerate
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B. The genetic code is degenerate.
more than one codon can code for the same amino acid
TB
+++ → phenylalanine
++* → phenylalanine
61% synonyms
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%. synonyms
codons that code for the same
amino acid
Not all synonyms are used (ith equalfrequency. This is called codon
usage bias.
+++ → phenylalanine
++* → phenylalanine
62' codon families
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'. codon families
*++
*+*
*+A
*+,
leucine
any nucleotide inthe &rd positions
TB
63& codon pairs i idi i
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&. codon pairs
+++
++*phenylalanine
any pyrimidine in
the &rd position
*AA
*A,
glutamine
any purine in
the &rd position
TB
64* Eobble base pairing
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*. Eobble base pairing
+++
AA,
codon mRNA!
anticodon tRNA!
=
&=
&=
=
+-, and ,-+ base pairs are allo(ed in
the &rd position of the codon.
TB
65
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Regulation of
Gene Expression
66Regulation of ,ene 63pression I7
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Regulation of ,ene 63pression I7
I. Regulation of gene e3pression
II. Transcriptional regulationIII. 63amples of gene repression
IF. 63ample of gene induction
67I Regulation of gene e3pression
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Not all genes are turned one3pressed! all the time
In general2 they are turned on
only (hen needed.
I. Regulation of gene e3pression
TB
68*ells can respond to en4ironmental
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*ells can respond to en4ironmental
changes by regulating gene e3pression.
glucose
maltose
lactose
arginine
tryptophan
69Different genes are e3pressed (hen
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g p
cells gro( on different compounds.
maltoseglucose
T*A
lactose
/ 0 lacZ lacY lacA
lac permease transport protein!β-galactosidase
e.g. ,ro(th on
lactose requires
e3pression of atleast three
additional genes.
galactose-β-%2)-glucose!
70A Ehy regulate gene e3pressionG
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A. Ehy regulate gene e3pressionG
Regulation allo(s cells to respondto en4ironmental conditions by
synthesi;ing selected gene productsonly (hen they are needed.
71B ,ene e3pression
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B. ,ene e3pression
synthesis of a gene product
%. constituti4e
'. regulated
72% *onstituti4e gene e3pression
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%. *onstituti4e gene e3pression
e.g. house"eeping genes li"e
primasessDNA binding proteins
e3pression of genes at about thesame le4el under all
en4ironmental conditions
TB
73' Regulated gene e3pression
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'. Regulated gene e3pression
*ontrol of the rate of proteinor RNA synthesis as an adapti4e
response to stimuli.
induction7 increase in gene e3pression
repression7 decrease in gene e3pression
74a gene induction
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a. gene induction
increase in gene e3pression
amount of
gene product
time
inducer
TB
75e.g. genes that encode en;ymes for
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en;ymes for
tryptophan
biosynthesismoleculescell!
time
tryptophan absent tryptophan present
e.g. genes that encode en;ymes for
tryptophan biosynthesis are
repressed by tryptophan.
76Important general principle
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Important general principle
? catabolic substrates e.g. maltose andlactose! induce the genes required for
their catabolism
? biosynthetic molecules e.g. amino acids
and purines! repress the genes required
for the biosynthesis
77II. Transcriptional regulation
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p g
? regulation of RNA synthesis
? the most common method of
gene regulation in all cells
A. Regulatory proteins
B. Regulatory protein binding sites*. 6ffector molecules
TB
78A. Regulatory proteins
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A. Regulatory proteins
? *ells ha4e many different regulatory
proteins.? pecific regulatory proteins control the
transcription of specific groups of genes.
? Transcriptional regulation is
mediated by regulatory proteins.
TB
? 63amples of regulatory proteins are
repressor proteins and acti4ator proteins.
79% Repressor proteins
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DNA
RNA polymerase/
/romoter
Repressor protein dimer!
Repressor proteins decrease transcription
(hen bound to DNA by interfering (ith the
acti4ity or binding of RNA polymerase
%. Repressor proteins
TB
80'. Acti4ator proteins
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RNA polymerase
'. Acti4ator proteins
DNA
P
(ea" promoter
Acti4ator protein
Acti4ator proteins increase transcription (hen
bound to DNA by helping RNA polymerase bind
to (ea" promoters TB
81B Regulatory protein binding sites
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B. Regulatory protein binding sites
Regulatory proteins bind to specificDNA sequences.
A particular regulatory protein (illonly control the e3pression of
genes ha4ing appropriate bindingsites.
TB
82%. 0perator sites
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p
Imperfect palindrome
GTG TAAACGATTCCAC
CACATTTGC TAAGGTG
binding sites for repressor proteins
+sually found near promoters
lac
repressorbinding site
TB
83'. Acti4ator binding sites
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g
GTGAG T TAGCTCAC
CACTCAA TCGAGTG
Imperfect palindrome
Binding sites for acti4ator proteins
+sually found near promoters
crp
bindingsite
TB
84*. 6ffector molecules
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mall molecules from the
en4ironment or made inside cells!
that signal specific changes
in gene e3pression.
TB
85%. *lasses of effectors
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e.g. catabolic substrates7
sugars2 amino acids2 fatty acids
a. inducerssmall molecules that mediate
gene induction
lactose
maltose
TB
86b. corepressors
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e.g. biosynthetic products7amino acids2 purines2 pyrimidines2
fatty acids etc.
p
small molecules that mediate
gene repression
tryptophanarginine
TB
87'. Ho( effectors (or"
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conformational change
change in &-D structure!
regulatory protein effector
6ffectors change the DNA binding affinity
of regulatory proteins for their binding sites.
TB
88A. ome effectors increase
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DNA
conformational change
change in &-D structure!
regulatory protein
effector
A. ome effectors increase
DNA binding affinity
TB
89B. ome effectors decrease
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DNA
regulatory protein
conformational change
change in &-D structure!
o e e ecto s dec ease
DNA binding affinity
effectorTB
90ince most regulatory proteins influence
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g y p
transcription (hen bound to DNA2
the binding of effectors to regulatoryproteins changes gene e3pression.
TB
effector
regulatory
protein
91III. 63amples of gene repression
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TB
A. Regulation of the trp operonB. Regulation of the arg operon
92A. The trp operon is a group of genes used forbi th i f th i id t t h T !
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The trp operon
polycistronic mRNA
6 D * B A
#i4e en;ymes for tryptophan biosynthesis
trp genespromoter
TB
biosynthesis of the amino acid tryptophan Trp!.
93%. Ehen Trp is N0T a4ailable in the
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'. Ehen Trp is a4ailable2 E. coli
ta"es up Trp from the en4ironment
and represses the trp operon.
%. Ehen Trp is N0T a4ailable in the
en4ironment2 e3pression of the trp
operon allo(s Escherchia coli to
ma"e Trp needed for protein
synthesis.
TB
94trp promoter
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operatorinacti4e
repressor
genes onTB
RNA polymerase
tryptophan
acti4erepressor
genes off
95Note7 Repression of the trp operon by
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tryptophan in4ol4es a repressor protein.
? Ehen tryptophan binds to the repressor
protein2 the repressor protein binds to DNA.
? Transcription is bloc"ed.
Result7 F6R lo( amounts of tryptophanare synthesi;ed (hen the cell can get
tryptophan from the en4ironment
96B. Regulation of the arg operon
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/
for arginine biosynthesis
operator arg biosynthetic genes
argC argB argH
If arginine is present in large amounts
? arg biosynthetic en;ymes N0T needed
? RNA polymerase can=t bind to promoter
? arg binds repressor ? arg-repressor binds DNA
∴ transcription rate decreases
97
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/
operator arg biosynthetic genes
argC argB argH
If arg is absent2 the cell needs to ma"e arg
? repressor doesn=t bind DNA ? RNA polymerase can bind ? transcription of arg genes occurs
98IF. 63ample of gene induction7
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Regulation of the lac operon
A. The lac operon is a group of genes
used for catabolism of the sugar lactose.
J A
lac genespromoter
operator
TB
99
? Ehen lactose is una4ailable the
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? Ehen lactose is a4ailable2 E. coli
induces e3pression of lac operon.
? Ehen lactose is una4ailable2 the
catabolic en;ymes are N0Tneeded.
The lac operon ise3pressed at only 4ery lo( le4els.
TB
100B. actose una4ailable
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In the AB6N*6 of lactose2
the lac repressor protein binds DNA.
J A
lac promoter
genes
off
Note7 the role of crpcA1/ in control of the
lac operon is not considered here TB
101*. actose a4ailable
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J A
lac promoter
geneson
RNA polymerase
lactose allolactoserepressor does not
bind DNA TB
102Important points
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Repressor proteins can mediate
gene repression e.g. trp operon!
or gene induction lac operon!.
Acti4ator proteins can mediate bothgene induction and gene repression.
TB
103ome repressor proteins mediate gene induction.6 l th l
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actose a sugar! can be an energy source.If lactose is absent2
? en;ymes for using lactose are not needed
? lac repressor binds to the lac operator ? the lac genes are not e3pressed
/ 0 lacZ lacY lacA*A/
site
63ample7 the lac repressor
104
actose ! induces the e3pression of lac genesome repressor proteins mediate gene induction.
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/ 0 lacZ lacY lacA
actose ! induces the e3pression of lac genes.
If lactose is present2? en;ymes for using lactose are needed
? allo!lactose binds to the lac repressor and
causes a conformational change? repressor-lac does N0T bind to DNA
? e3pression of lac genes is possible
*A/
site
K
105D. The catabolite acti4ator protein
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%. In the lac operon2 the acti4ator
protein is called the catabolite
acti4ator protein *A/! or the
cyclic A1/ receptor protein crp!.
'. Ehen cyclic A1/ cA1/! is
present2 the cA1/*A/ crp!comple3 binds DNA and
acti4ates transcription.
*A/
crp!
cA1/
cA1/*A/
comple3
binds DNATB
106NH'
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0
N
N N
N*H'
0H
H0/<0
0
cyclic A1/ cA1/!
cyclic adenosine monophosphate
Don=t
memori;e!
TB
107
Role of *A/ crp! in the lac operon
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/ 0 lacZ lacY lacA c r p
/ 0 lacZ lacY lacAcrp
binding site
Eithout acti4ator protein2 RNA polymerase
binds (ea"ly and the transcription rate is lo(.
Eith acti4ator protein crp!2 RNA polymerase
binds (ell and the transcription rate is higher.
108&. 1AN operons that encode catabolic
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p
en;ymes ha4e the same crp binding
site ! and are controlled by the
same regulatory protein *A/ or crp!.
bacterial chromosome
crp binding site
109%. *atabolite repression enables Escherichia
li t l i f t th
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coli to use glucose in preference to other
carbon sources. maltoseglucose
T*A
/ 0 lacZ lacY lacAcrp
binding site
lac permease transport protein!
lactose
β -galactosidase
actose
utili;ationrequires
additional
proteins.galactose-β-%2)-glucose!
110'. >ey components of catabolite
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a. cA1/ cyclic A1/!an effector molecule that increases
the DNA binding affinity of
the catabolite acti4ator protein
b. *A/ or crp!
*atabolite acti4ator protein2 a
transcriptional regulatory proteinL
also called crp cA1/ receptor protein!
repression
TB
111&. *A/cA1/ binds to DNA and
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*A/ or crp!
bacterial
chromosome
*A/ or crp!binding sites
cA1/
cA1/*A/
comple3
regulates transcription.
TB
112). Ho( does catabolite repression (or"Ga ,enes needed for the catabolism of
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c. Eithout cA1/*A/2 genes required to
cataboli;e nonglucose energy sources
are transcribed at 4ery lo( rates.
a. ,enes needed for the catabolism of
many carbon and energy sourcesrequire cA1/*A/ for e3pression.
Mb. ,lucose decreases cellular cA1/ le4els.
d. Therefore2 glucose is preferentially used
as a carbon and energy source
113*. ,lobal regulation is often used
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together (ith other more specific
regulatory systems.
63ample7 the lactose operonrequires both lactose and
cA1/*A/ for induction.
114Both lactose and cA1/*A/ are needed
f hi h i d i f l
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/ 0 lacZ lacY lacAcrp
binding site
for high induction of lac operon.
/ 0 lacZ lacY lacA c r p glucose absent2
lactose present
glucose present2lactose absent
lac repressor binds DNA in absence of lactose
glucose decreases cA1/
115
III. T(o-component regulatory systems
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III. T(o component regulatory systems
Transcriptional regulatory systemscomposed of a sensor "inase and
response regulator.
TB
116A. ensor "inase
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Integral membrane proteins that
sense en4ironmental conditions andphosphorylate proteins
B. Response regulator
*ytoplasmic transcriptional regulatoryproteins controlled by sensor "inases
through phosphorylation TB
117
sensoreffector
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cytoplasmimembrane
"inase
/
responseregulator
//dephosphorylation
phosphorylation