translasi & regulasi

7/23/2019 Translasi & Regulasi

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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

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.

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

4). *omplementary base pairing

***+++,,,AAA,,,AAA***+++ RNA

,,,AAA***+++ RNA

***TTT,,,AAA DNA

hydrogenbonding

5. RNA stem loops

complementary

base pairinghelical!

A common RNA secondary structure

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

7A. ,ene numbers

4iruses

pro"aryotes

eu"aryotes

group appro3imategene number

55-%'2555

2555-%'2555

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

% gene

% mRNA

transcription

% polypeptide

translation

%. 63pression of single genes

63.%7 a single gene that encodes a protein

*. ,ene e3pression in pro"aryotes

% gene

transcription

degraded

% tRNA etc.RNA processing

63. '7 a single gene that encodes one

rRNA or tRNA

operont(o or more genes

transcribed together

a single RNA molecule that

represents more than one gene

polycistronic message

'. 63pression of operons

A B *DNA

transcription

polycistronic

12a. 0perons can encode se4eral

polypeptides or proteins.

% operonA B *

' or more polypeptides

translation

% polycistronic mRNA

transcription

% operon

processing

rRNArRNA

degraded ' or more rRNAs

b. 0perons can encode se4eral

rRNA molecules.

% polycistronic RNA

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.

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

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

17% gene (ith e3ons and introns

6 I I I6 6 6

transcription

% RNA representing e3ons and intronsprimary transcript!

primary transcript

% polypeptide

% mRNA

processing

b. /rimary transcripts

19c. /rocessing of primary transcripts

i. cappingii. splicing

iii. tailing

20i. *apping

Addition of a = cap

*apping usually occurs before

transcription is finished.TB

21*Hi l

*H&Typical = *A/

9-methylguanosine

= carbon

of RNA chain= to = lin"age

TB>no( the name methylguanosine cap2 = cap!2

but don=t memori;e structure.

22ii. plicing

The remo4al of introns.

primary transcriptsplicing

RNA (ithout intronsTB

Addition of a poly-A tail

iii. Tailing

A%A'...A8'55

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.

TRANSLATION

III /ro"aryotic translation

%. >ey components of translation

'. teps in translation&. The genetic code

270 i f " ti t l ti

2704er4ie( of pro"aryotic translation

/rotein synthesis from an mRNA template.

translated region

translation

protein of specific amino acid sequence

28%. >ey components of translation

A. mRNAB. tRNA

*. ribosomes and rRNA

translated region

series of codonsusually 8&55 codons!

start codon

A. mRNA

stop codon

Dalgarnosequence

RNA template for protein synthesis

30% hi D l

30%. hine-Dalgarno sequence

8A,,A,,2 ribosome binding sequence2

critical for ribosome binding

'. start codonsA+,2 ,+,2 or ++,

&. stop codons nonsense codons!

+AA2 +,A2 or +A,

31) T l t d i di !

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

AUGCAUUGUUCU...codons

protein f1et

- er ...

. *odons consist of & bases

% ' & )

33B tRNA

33B. tRNA

The adapter molecule for translation

%. /articular tRNAs carry

particular amino acids.

TBtRNA-f-1et

tRNA-His

34' /articular tRNAs recogni;e

AUGCAUUGUUCU...

codons

AA% AA'

'. /articular tRNAs recogni;e

particular codons.

amino acid AA!

This allo(s amino acids to be brought

together in a particular order. TB

35&. tRNA structure

All tRNAs are generally similarin structure.

a. %o structure

ssRNA 9&-@& nucleotides long

= &=+A*

36b 'o structure

36b. 'o structure

clo4er leaf

anticodon loop

TΨ* armD-arm

acceptor arm

e3tra arm

37c. &o structure

in4erted

38d Anticodon

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

39e. codon-anticodon interactions

AA+= &= mRNA

codon% ' &

anticodon

40) tRNA charging adding amino acid!

40). tRNA charging adding amino acid!

tRNAuncharged!

&=H'N-*H-*-0

aminoacyl-tRNAcharged!

tRNA charging uses the energy of AT/ TB

41Aminoacyl tRNA synthetases

41Aminoacyl-tRNA synthetases

amino acidAT/

aminoacyl-A1/

A1/ //i

aminoacyl-tRNA

A1/ < adenosine monophosphate //i < inorganic pyrophosphate

en;ymes that attach amino acids to tRNA

en;yme

42 tRNA facts

42. tRNA facts

tRNAs contain many modified bases.

/ro"aryotes ha4e about C5 differenttRNAs.

43* Ribosomes and rRNA

43*. Ribosomes and rRNA

Ribosomesribonucleoprotein comple3es that

cataly;e protein synthesis.

rRNAsha4e structural and catalytic roles

44% /ro"aryotic 95s ribosome

44%. /ro"aryotic 95s ribosome

'&s rRNAs rRNA

&) proteins

%Cs RNA'% proteins

subunit

&5ssubunit

45' Ribosomal sites (here tRNAs bind

'. Ribosomal sites (here tRNAs bind

6 < e3it

// < peptidyl

A < aminoacyl

46&. %C rRNA

The &= end of the %Cs rRNA iscomplementary to the hine-

Dalgarno sequence ribosomebinding sequence of mRNAs!

47II teps in translation

/-sitef-met

hine-DalgarnoA,,A,,

on mRNA!

II. teps in translation

A. initiation &5s subunit

of ribosome

5s subunit

,T/ hydrolysis

&5s subunit TB

A,,A,,-----A+,

48% f t tRNA f l thi i tRNA!

48%. f-met tRNA formyl-methionine tRNA!

In Bacteria2 different met-tRNAs are used forelongation and initiation.

initiation2 formyl-methioninetRNAmetf

elongation2 methioninetRNAmetm

49' Initiation in different domains

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.

'. Initiation in different domains

B 6longation

/-site A-site

AA%. AA-tRNA binding

B. 6longation

51' peptide bond synthesis

peptidyl transferase!

'. peptide bond synthesis

52& translocation

52&. translocation

hydrolysis

53* Termination

*. Termination

AAAAAA

termination

stop codon

54D Additional notes on translation

/olysomes are mRNAs (ith

se4eral ribosomes attached

mRNAs can be translated by -%5

ribosomes simultaneously.

%. Ribosomes mo4e along the mRNA.

D. Additional notes on translation

55' In pro"aryotes only transcription

'. In pro"aryotes only2 transcription and translation are coupled.

Translation begins before

transcription ends.

mRNA TB

& / t i f ldi i t th ti f

&. /rotein folding into the acti4e form

can occur spontaneously or (ith the

help of a large protein comple3

called a molecular chaperone.

properly folded protein

improperly

folded proteinmolecular

chaperone

III Th i d

III. The genetic code

A. uni4ersal codeB. degenerate code

%. synonyms'. codon families

&. codon pairs

*. (obble base pairing

58III The genetic code

III. The genetic code

: codon families2 %) codon pairs2 & stop codons

Do not

memori;e!

59A The genetic code is almost

A. The genetic code is almost

uni4ersal.

1ost organisms use the same

genetic code.

60B The genetic code is degenerate

B. The genetic code is degenerate.

more than one codon can code for the same amino acid

+++ → phenylalanine

++* → phenylalanine

61% synonyms

%. 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

'. codon families

leucine

any nucleotide inthe &rd positions

63& codon pairs i idi i

&. codon pairs

++*phenylalanine

any pyrimidine in

the &rd position

glutamine

any purine in

the &rd position

64* Eobble base pairing

*. Eobble base pairing

codon mRNA!

anticodon tRNA!

+-, and ,-+ base pairs are allo(ed in

the &rd position of the codon.

Regulation of

Gene Expression

66Regulation of ,ene 63pression I7

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

Not all genes are turned one3pressed! all the time

In general2 they are turned on

only (hen needed.

I. Regulation of gene e3pression

68*ells can respond to en4ironmental

*ells can respond to en4ironmental

changes by regulating gene e3pression.

glucose

maltose

lactose

arginine

tryptophan

69Different genes are e3pressed (hen

cells gro( on different compounds.

maltoseglucose

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

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

B. ,ene e3pression

synthesis of a gene product

%. constituti4e

'. regulated

72% *onstituti4e gene e3pression

%. *onstituti4e gene e3pression

e.g. house"eeping genes li"e

primasessDNA binding proteins

e3pression of genes at about thesame le4el under all

en4ironmental conditions

73' Regulated gene e3pression

'. 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

a. gene induction

increase in gene e3pression

amount of

gene product

inducer

75e.g. genes that encode en;ymes for

en;ymes for

tryptophan

biosynthesismoleculescell!

tryptophan absent tryptophan present

e.g. genes that encode en;ymes for

tryptophan biosynthesis are

repressed by tryptophan.

76Important general principle

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

? regulation of RNA synthesis

? the most common method of

gene regulation in all cells

A. Regulatory proteins

B. Regulatory protein binding sites*. 6ffector molecules

78A. Regulatory proteins

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.

? 63amples of regulatory proteins are

repressor proteins and acti4ator proteins.

79% Repressor proteins

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

80'. Acti4ator proteins

RNA polymerase

'. Acti4ator proteins

(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

B. Regulatory protein binding sites

Regulatory proteins bind to specificDNA sequences.

A particular regulatory protein (illonly control the e3pression of

genes ha4ing appropriate bindingsites.

82%. 0perator sites

Imperfect palindrome

GTG TAAACGATTCCAC

CACATTTGC TAAGGTG

binding sites for repressor proteins

+sually found near promoters

repressorbinding site

83'. Acti4ator binding sites

GTGAG T TAGCTCAC

CACTCAA TCGAGTG

Imperfect palindrome

Binding sites for acti4ator proteins

+sually found near promoters

bindingsite

84*. 6ffector molecules

mall molecules from the

en4ironment or made inside cells!

that signal specific changes

in gene e3pression.

85%. *lasses of effectors

e.g. catabolic substrates7

sugars2 amino acids2 fatty acids

a. inducerssmall molecules that mediate

gene induction

lactose

maltose

86b. corepressors

e.g. biosynthetic products7amino acids2 purines2 pyrimidines2

fatty acids etc.

small molecules that mediate

gene repression

tryptophanarginine

87'. Ho( effectors (or"

conformational change

change in &-D structure!

regulatory protein effector

6ffectors change the DNA binding affinity

of regulatory proteins for their binding sites.

88A. ome effectors increase

regulatory protein

effector

A. ome effectors increase

DNA binding affinity

89B. ome effectors decrease

regulatory protein

o e e ecto s dec ease

DNA binding affinity

effectorTB

90ince most regulatory proteins influence

transcription (hen bound to DNA2

the binding of effectors to regulatoryproteins changes gene e3pression.

effector

regulatory

protein

91III. 63amples of gene repression

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 !

The trp operon

polycistronic mRNA

6 D * B A

#i4e en;ymes for tryptophan biosynthesis

trp genespromoter

biosynthesis of the amino acid tryptophan Trp!.

93%. Ehen Trp is N0T a4ailable in the

'. 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.

94trp promoter

operatorinacti4e

repressor

genes onTB

RNA polymerase

tryptophan

acti4erepressor

genes off

95Note7 Repression of the trp operon by

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

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

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

Regulation of the lac operon

A. The lac operon is a group of genes

used for catabolism of the sugar lactose.

lac genespromoter

operator

? Ehen lactose is una4ailable the

? 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.

100B. actose una4ailable

In the AB6N*6 of lactose2

the lac repressor protein binds DNA.

lac promoter

Note7 the role of crpcA1/ in control of the

lac operon is not considered here TB

101*. actose a4ailable

lac promoter

geneson

RNA polymerase

lactose allolactoserepressor does not

bind DNA TB

102Important points

Repressor proteins can mediate

gene repression e.g. trp operon!

or gene induction lac operon!.

Acti4ator proteins can mediate bothgene induction and gene repression.

103ome repressor proteins mediate gene induction.6 l th l

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/

63ample7 the lac repressor

actose ! induces the e3pression of lac genesome repressor proteins mediate gene induction.

/ 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

105D. The catabolite acti4ator protein

%. 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.

cA1/*A/

comple3

binds DNATB

106NH'

cyclic A1/ cA1/!

cyclic adenosine monophosphate

memori;e!

Role of *A/ crp! in the lac operon

/ 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

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

coli to use glucose in preference to other

carbon sources. maltoseglucose

binding site

lac permease transport protein!

lactose

β -galactosidase

actose

utili;ationrequires

additional

proteins.galactose-β-%2)-glucose!

110'. >ey components of catabolite

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

111&. *A/cA1/ binds to DNA and

*A/ or crp!

bacterial

chromosome

*A/ or crp!binding sites

cA1/*A/

comple3

regulates transcription.

112). Ho( does catabolite repression (or"Ga ,enes needed for the catabolism of

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

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

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/

III. T(o-component regulatory systems

III. T(o component regulatory systems

Transcriptional regulatory systemscomposed of a sensor "inase and

response regulator.

116A. ensor "inase

Integral membrane proteins that

sense en4ironmental conditions andphosphorylate proteins

B. Response regulator

*ytoplasmic transcriptional regulatoryproteins controlled by sensor "inases

through phosphorylation TB

sensoreffector

cytoplasmimembrane

"inase

responseregulator

//dephosphorylation

phosphorylation

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