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There are many steps to produce a protein in a eukaryotic cell Each
There are many steps to produce a protein in a eukaryotic cell Each
Translation
Translation
Factors involved in initiation, elongation, & termination of protein
Factors involved in initiation, elongation, & termination of protein
Heterotrimeric G-proteins
Heterotrimeric G-proteins
Small GTP-binding proteins require helper proteins, to facilitate
Small GTP-binding proteins require helper proteins, to facilitate
A GTPase activating protein (GAP) causes a GTP-binding protein to
A GTPase activating protein (GAP) causes a GTP-binding protein to
Members of the family of small GTP-binding proteins have diverse
Members of the family of small GTP-binding proteins have diverse
Roles of some small GTP-binding proteins: IF-2, EF-Tu, EF-G, & RF-3:
Roles of some small GTP-binding proteins: IF-2, EF-Tu, EF-G, & RF-3:
Translation initiation
Translation initiation
Initiation of protein synthesis in E. coli requires participation of
Initiation of protein synthesis in E. coli requires participation of
As mRNA binds, IF-3 helps to correctly position the complex such that
As mRNA binds, IF-3 helps to correctly position the complex such that
Initiation
Initiation
Shine Delgarno Sites
Shine Delgarno Sites
initiation of translation in eukaryotes 1. charging of the tRNAs is
initiation of translation in eukaryotes 1. charging of the tRNAs is
There are many steps to produce a protein in a eukaryotic cell Each
There are many steps to produce a protein in a eukaryotic cell Each
Translation Initiation - Eukaryotes
Translation Initiation - Eukaryotes
Controlling Initiation
Controlling Initiation
The AUG start codon is recognized by methionyl-tRNAiMet
The AUG start codon is recognized by methionyl-tRNAiMet
Translation elongation
Translation elongation
Elongation cycle Ribosome structure and position of factors & tRNAs
Elongation cycle Ribosome structure and position of factors & tRNAs
Elongation requires participation of elongation factors EF-Tu (also
Elongation requires participation of elongation factors EF-Tu (also
EF-Tu-GTP binds and delivers an aminoacyl-tRNA to the A site on the
EF-Tu-GTP binds and delivers an aminoacyl-tRNA to the A site on the
As the aa-tRNA is delivered by EF-Tu to the A site on the ribosome,
As the aa-tRNA is delivered by EF-Tu to the A site on the ribosome,
A large conformational change in EF-Tu, when GTP
A large conformational change in EF-Tu, when GTP
EF-Ts functions as GEF to reactivate EF-Tu
EF-Ts functions as GEF to reactivate EF-Tu
Transpeptidation (peptide bond formation) involves acid/base catalysis
Transpeptidation (peptide bond formation) involves acid/base catalysis
The nascent polypeptide, one residue longer, is now linked to the tRNA
The nascent polypeptide, one residue longer, is now linked to the tRNA
Translocation of the ribosome relative to mRNA involves the
Translocation of the ribosome relative to mRNA involves the
EF-G-GTP binds in the vicinity of the A site
EF-G-GTP binds in the vicinity of the A site
Additionally, it has been postulated that translocation is spontaneous
Additionally, it has been postulated that translocation is spontaneous
Bacterial Elongation
Bacterial Elongation
Eukaryotic Elongation
Eukaryotic Elongation
Translation termination
Translation termination
Termination
Termination
RF-1 & RF-2 recognize & bind to STOP codons
RF-1 & RF-2 recognize & bind to STOP codons
termination, directed by the STOP codon
termination, directed by the STOP codon
Polyribosomes
Polyribosomes
The ribosome by SEM
The ribosome by SEM
There are many steps to produce a protein in a eukaryotic cell Each
There are many steps to produce a protein in a eukaryotic cell Each
Antibiotic Action
Antibiotic Action
Puromycin Mechanism
Puromycin Mechanism
Cap-dependent vs
Cap-dependent vs
43S particle recruitment strategies
43S particle recruitment strategies
There are many steps to produce a protein in a eukaryotic cell Each
There are many steps to produce a protein in a eukaryotic cell Each
There are many steps to produce a protein in a eukaryotic cell Each
There are many steps to produce a protein in a eukaryotic cell Each
There are many steps to produce a protein in a eukaryotic cell Each
There are many steps to produce a protein in a eukaryotic cell Each
There are many steps to produce a protein in a eukaryotic cell Each
There are many steps to produce a protein in a eukaryotic cell Each
There are many steps to produce a protein in a eukaryotic cell Each
There are many steps to produce a protein in a eukaryotic cell Each
There are many steps to produce a protein in a eukaryotic cell Each
There are many steps to produce a protein in a eukaryotic cell Each
There are many steps to produce a protein in a eukaryotic cell Each
There are many steps to produce a protein in a eukaryotic cell Each
There are many steps to produce a protein in a eukaryotic cell Each
There are many steps to produce a protein in a eukaryotic cell Each
There are many steps to produce a protein in a eukaryotic cell Each
There are many steps to produce a protein in a eukaryotic cell Each

Презентация на тему: «There are many steps to produce a protein in a eukaryotic cell Each step is a point of regulation to determine the efficiency of gene expression». Автор: MICHAEL ROSBASH. Файл: «There are many steps to produce a protein in a eukaryotic cell Each step is a point of regulation to determine the efficiency of gene expression.ppt». Размер zip-архива: 3515 КБ.

There are many steps to produce a protein in a eukaryotic cell Each step is a point of regulation to determine the efficiency of gene expression

содержание презентации «There are many steps to produce a protein in a eukaryotic cell Each step is a point of regulation to determine the efficiency of gene expression.ppt»
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1 There are many steps to produce a protein in a eukaryotic cell Each

There are many steps to produce a protein in a eukaryotic cell Each

step is a point of regulation to determine the efficiency of gene expression

2 Translation

Translation

Initiation Elongation Termination

3 Factors involved in initiation, elongation, & termination of protein

Factors involved in initiation, elongation, & termination of protein

synthesis. Many of these factors are GTP-binding proteins, & other proteins that control GDP/GTP exchange or GTPase activity of these GTP-binding proteins.

4 Heterotrimeric G-proteins

Heterotrimeric G-proteins

A GTP-binding protein has a different conformation depending on whether it has bound to it GTP or GDP. Usually GTP binding induces the active conformation. Hydrolysis of the bound GTP to GDP + Pi converts the protein to the inactive conformation. Reactivation occurs by release of bound GDP in exchange for GTP.

5 Small GTP-binding proteins require helper proteins, to facilitate

Small GTP-binding proteins require helper proteins, to facilitate

GDP/GTP exchange, or promote GTP hydrolysis.

A guanine nucleotide exchange factor (GEF) induces a conformational change that makes the nucleotide-binding site of a GTP-binding protein more accessible to the aqueous intracellular milieu, where [GTP] ? [GDP]. Thus a GEF causes a GTP-binding protein to release GDP & bind GTP (GDP/GTP exchange).

6 A GTPase activating protein (GAP) causes a GTP-binding protein to

A GTPase activating protein (GAP) causes a GTP-binding protein to

hydrolyze its bound GTP to GDP + Pi.

The active site for GTP hydrolysis is on the GTP-binding protein, although a GAP may contribute an essential active site residue. GEFs & GAPs may be separately regulated. Unique GEFs and GAPs interact with different GTP-binding proteins

7 Members of the family of small GTP-binding proteins have diverse

Members of the family of small GTP-binding proteins have diverse

functions. In some cases, the difference in conformation, with substitution of GDP for GTP allows a GTP-binding protein to serve as a "switch". In other cases the conformational change may serve a mechanical role or alter the ability of the protein to bind to membranes.

8 Roles of some small GTP-binding proteins: IF-2, EF-Tu, EF-G, & RF-3:

Roles of some small GTP-binding proteins: IF-2, EF-Tu, EF-G, & RF-3:

Protein synthesis initiation, elongation, & release factors. Ras: Growth factor signal cascades. Rab: Membrane vesicle targeting & fusion. ARF: Vesicle budding by formation of coatomer coats. Ran: Transport of proteins into & out of the nucleus. Rho: Regulation of the actin cytoskeleton.

9 Translation initiation

Translation initiation

Eukaryotes v. Prokaryotes

10 Initiation of protein synthesis in E. coli requires participation of

Initiation of protein synthesis in E. coli requires participation of

initiation factors IF-1, IF-2, & IF-3.

IF-3 binds to the 30S ribosomal subunit, freeing it from its complex with the 50S subunit. IF-1 assists binding of IF-3 to the 30S ribosomal subunit. IF-1 also occludes the A site of the small ribosomal subunit, helping insure that the initiation tRNAfMet will end up in the P site & that no other aa-tRNA can bind in the A site during initiation. IF-2 is a small GTP-binding protein. IF-2-GTP binds the initiator tRNAfMet & helps it to dock with the small ribosome subunit.

11 As mRNA binds, IF-3 helps to correctly position the complex such that

As mRNA binds, IF-3 helps to correctly position the complex such that

tRNAfMet interacts via base pairing with the mRNA initiation codon (AUG). A region of mRNA upstream of the initiation codon, the Shine-Dalgarno sequence, base pairs with the 3' end of the 16S rRNA, helping to position the 30S ribosomal subunit in relation to the initiation codon.

The large ribosomal subunit then joins the complex. GTP on IF-2 is hydrolyzed, leading to dissociation of IF-2-GDP and dissociation of IF-1. A domain of the large ribosomal subunit serves as GAP (GTPase activating protein) for IF-2.

Once the two ribosomal subunits come together, the mRNA is threaded through a curved channel that wraps around the "neck" region of the small subunit.

12 Initiation

Initiation

13 Shine Delgarno Sites

Shine Delgarno Sites

14 initiation of translation in eukaryotes 1. charging of the tRNAs is

initiation of translation in eukaryotes 1. charging of the tRNAs is

the same 2. Association of the translation machinery - terminology difference initiation factors called eIFs rather than IFs - charged tRNA is delivered by eIF2-GTP (which is hydrolized to GDP to provide energy) - eukaryotic mRNA is capped, this is recognized by an additional protein eIF-4E 3. identification of initiator codon - ribosome tRNA complex scans for first AUG and stops there - directed by the eIF-4E on the CAP site rather than the Shine-Delgarno site 4. completion of initiation- same

15 There are many steps to produce a protein in a eukaryotic cell Each
16 Translation Initiation - Eukaryotes

Translation Initiation - Eukaryotes

17 Controlling Initiation

Controlling Initiation

Eukaryotic mRNA has cap on 5’ end Bacteria have no “5’ end marker” Translation is coupled to transcription Ribosomes bind to RNA as it is made Where to start reading mRNA? Shine Delgarno sequence in bacteria, Kozak sequence in eukaryotes Adjacent to the first codon

18 The AUG start codon is recognized by methionyl-tRNAiMet

The AUG start codon is recognized by methionyl-tRNAiMet

19 Translation elongation

Translation elongation

20 Elongation cycle Ribosome structure and position of factors & tRNAs

Elongation cycle Ribosome structure and position of factors & tRNAs

based on cryo-EM with 3D image reconstruction.

Colors: large ribosome subunit, cyan; small subunit, pale yellow; EF-Tu, red; EF-G, blue. tRNAs, gray, magenta, green, yellow, brown.

21 Elongation requires participation of elongation factors EF-Tu (also

Elongation requires participation of elongation factors EF-Tu (also

called EF-1A) EF-Ts (EF-1B) EF-G (EF-2) EF-Tu & EF-G are small GTP-binding proteins. The sequence of events follows.

22 EF-Tu-GTP binds and delivers an aminoacyl-tRNA to the A site on the

EF-Tu-GTP binds and delivers an aminoacyl-tRNA to the A site on the

ribosome. The loaded tRNA must have the correct anticodon to base pair with the mRNA codon positioned at the A site. tRNA binding causes a conformational change in the small ribosomal subunit that causes universally conserved bases of 16S rRNA to interact closely with the minor groove of the first two base pairs of the codon/anticodon complex, helping insure that only the correct tRNA binds. Proofreading in part involves release of the aa-tRNA prior to peptide bond formation if a particular ribosomal conformation is not stabilized by this interaction.

23 As the aa-tRNA is delivered by EF-Tu to the A site on the ribosome,

As the aa-tRNA is delivered by EF-Tu to the A site on the ribosome,

GTP on EF-Tu is hydrolyzed to GDP + Pi. A domain of the ribosome serves as GAP for EF-Tu. This function depends on codon-anticodon recognition correctly positioning the aa-tRNA in relation to the large ribosomal subunit.

EF-Tu colored red

24 A large conformational change in EF-Tu, when GTP

A large conformational change in EF-Tu, when GTP

GDP + Pi, promotes dissociation of EF-Tu. Release of EF-Tu leads to repositioning of the aa-tRNA to promote peptide bond formation.

EF-Tu colored red

25 EF-Ts functions as GEF to reactivate EF-Tu

EF-Ts functions as GEF to reactivate EF-Tu

EF-Ts induces EF-Tu to release bound GDP & bind GTP. EF-Ts dissociates from EF-Tu when EF-Tu changes its conformation, upon binding GTP.

26 Transpeptidation (peptide bond formation) involves acid/base catalysis

Transpeptidation (peptide bond formation) involves acid/base catalysis

by a universally conserved adenosine of the 23S rRNA of the large ribosomal subunit. No protein is found adjacent to the active site adenosine. (Recall Chime exercise on the large ribosomal subunit.) The 23S rRNA may be considered a "ribozyme.“ The amino N of the amino acid linked to the 2' or 3' OH of the terminal adenosine of tRNA in the A site reacts with the carbonyl C of the amino acid (with attached nascent polypeptide) linked to the tRNA in the P site.

27 The nascent polypeptide, one residue longer, is now linked to the tRNA

The nascent polypeptide, one residue longer, is now linked to the tRNA

in the A site. However, peptide bond formation is associated with rotation of the acceptor stem of the A site tRNA, so that the nascent polypeptide is positioned to feed via the P site into

the tunnel in the large subunit. The unloaded tRNA in the P site will shift to an exit (E) site during translocation.

28 Translocation of the ribosome relative to mRNA involves the

Translocation of the ribosome relative to mRNA involves the

GTP-binding protein EF-G. The size & shape of EF-G are comparable to that of the complex of EF-Tu with an aa-tRNA.

tRNA grey, EF-Tu red, EF-G blue

29 EF-G-GTP binds in the vicinity of the A site

EF-G-GTP binds in the vicinity of the A site

EF-G-GTP binding may push the tRNA with attached nascent polypeptide from the A site to the P site. Unloaded tRNA that was in the P site shifts to an exit site. Since tRNAs are linked to mRNA by codon-anticodon base pairing, the mRNA would move relative to the ribosome.

30 Additionally, it has been postulated that translocation is spontaneous

Additionally, it has been postulated that translocation is spontaneous

after peptide bond formation because: the deacylated tRNA in the P site has a higher affinity for the E site, & the peptidyl-tRNA in the A site has a higher affinity for the P site. Interaction with the ribosome, which acts as GAP (GTPase activating protein) for EF-G, causes EF-G to hydrolyze its bound GTP to GDP + Pi. EF-G-GDP then dissociates from the ribosome. A domain of EF-G functions as its own GEF (guanine nucleotide exchange factor) to regenerate EF-G-GTP.

31 Bacterial Elongation

Bacterial Elongation

Elongation factor Tu uses GTP hydrolysis to help bring tRNA to A site Elongation factor Ts helps restore fresh GTP to EF-Tu Elongation factor G uses GTP hydrolysis to help move tRNA from A to P site

32 Eukaryotic Elongation

Eukaryotic Elongation

One factor (eEF-1) does job of EF-Tu and EF-Ts eEF-2 does job of EF-G As with bacteria, the elongation factors work within the ribosome

33 Translation termination

Translation termination

Eukaryotes v. Prokaryotes

34 Termination

Termination

Three codons lack complementary tRNAs Recognized by “release factors” Three proteins in bacteria Two can bind to “stop codon” Third helps with interaction, uses GTP Eukaryotes have one release factor Induce the breakage of tRNA-amino acid bond of tRNA in P site

35 RF-1 & RF-2 recognize & bind to STOP codons

RF-1 & RF-2 recognize & bind to STOP codons

One or the other binds when a stop codon is reached. RF-3-GTP facilitates binding of RF-1 or RF-2 to the ribosome. Once release factors occupy the A site, Peptidyl Transferase catalyzes transfer of the peptidyl group to water (hydrolysis). The uncharged tRNA is released. Hydrolysis of GTP on RF-3 causes a conformational change that results in dissociation of the release factors. The ribosome dissociates from mRNA. IF-3, assisted by IF-1, promotes dissociation of the two ribosomal subunits for another round of initiation.

36 termination, directed by the STOP codon

termination, directed by the STOP codon

peptide chain-

A

3’

5’

Release factor

peptide chain-

A

peptide chain-

3’

5’

A: (aminoacyl) site P: (peptidyl) site E: (exit) site

UUU

AUG

GCC

UAA

EF-G-GDP

EF-G-GTP

37 Polyribosomes

Polyribosomes

these structures are formed by the presence of several ribosomes working sequentially on a single mRNA

38 The ribosome by SEM

The ribosome by SEM

Functional concept of the ribosome

39 There are many steps to produce a protein in a eukaryotic cell Each
40 Antibiotic Action

Antibiotic Action

41 Puromycin Mechanism

Puromycin Mechanism

42 Cap-dependent vs

Cap-dependent vs

cap-independent translation initiation

Cap-Dependent

Cap-Independent

43 43S particle recruitment strategies

43S particle recruitment strategies

44 There are many steps to produce a protein in a eukaryotic cell Each
45 There are many steps to produce a protein in a eukaryotic cell Each
46 There are many steps to produce a protein in a eukaryotic cell Each
47 There are many steps to produce a protein in a eukaryotic cell Each
48 There are many steps to produce a protein in a eukaryotic cell Each
49 There are many steps to produce a protein in a eukaryotic cell Each
50 There are many steps to produce a protein in a eukaryotic cell Each
51 There are many steps to produce a protein in a eukaryotic cell Each
52 There are many steps to produce a protein in a eukaryotic cell Each
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