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Lectures 30-32

by: Annie Notetaker

Lectures 30-32 BCM 475 - M001

Annie Notetaker
Biochemistry I
M. Braiman, R. Welch

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Protein Synthesis I, II, and III
Biochemistry I
M. Braiman, R. Welch
Class Notes
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This 12 page Class Notes was uploaded by Annie Notetaker on Sunday December 6, 2015. The Class Notes belongs to BCM 475 - M001 at Syracuse University taught by M. Braiman, R. Welch in Fall 2015. Since its upload, it has received 43 views. For similar materials see Biochemistry I in Biochemistry at Syracuse University.


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Date Created: 12/06/15
Lecture 1113 Protein Synthesis I p 887897 Translation Protein synthesis Location interface between SOS and 30S subunits of ribosomes cytoplasm Binding sites for an mRNA and 3 tRNA molecules are aligned RNA is solely responsible for catalyzing the growth of a polypeptidechain A single ribosome is sufficient for the synthesis of one polypeptide chain processivity Problems Associated with Protein Synthesis 1 Energetics Formation of peptide amide bond 9 endothermic and endergonic 20 k mol391 Specificity of amino acids The mRNA must be specific for the growing amino acid chain Solution aminoacyItRNAs AminoacyltRNA Activated amino acid Used to distribute specific amino acids to a growing protein chain because amino acids alone are incapable of recognizing an mRNA codon Composition carboxyl terminal of an amino acid joined Via an ester linkage to either the 2 or 3 OH group of the RNA s terminal ribose sugar AminoacyItRNA synthetase catalyzes the formation of aminoacyltRNAs from amino acids and tRNA molecules Organic Chemistry of Protein Synthesis 1 S 6 Figure 301 Growing amino acid chain with an ester linkage to tRNA molecule 1 at the carboxyl end Arrival of aminoacyltRNA 2 to growing chain Free amino group of incoming aminoacyltRNA 2 functions as a nucleophile and attacks the ester group at the carboxyl end Ester group with tRNA 1 is displaced Chain with one additional amino acid is formed with an ester linkage to tRNA 2 now at the carboxyl end of the growing chain Sequential addition of amino acids to the carboxyl terminus Accuracy of Protein Synthesis The probability p of forming a protein with no errors depends on n the number of amino acids and e the frequency of insertion of a wrong amino acidquot The limit to the error rate is the rate of attaching an incorrect amino acid to each tRNA moleculequot Yeast AlanyltRNA Amino acid alanine joined to a tRNA molecule Single chain of 76 ribonucleotides organized into a cloverleaf secondary structure Phosphorylated 5 terminus 3 OH amino acid attachment site Contains anticodon 5 IGC3 complementary to codon 5 GCC3 I in anticodon9 purine base inosine Insoine 9 modified nucleoside deaminated adenosine Note not all tRNAs contain an I in the anticodonquot Posttranscriptionally modified nucleosides present in the alanyltRNA sequence methylinosine m1 dihydrouridine UHz ribothymidine T pseudouridine 1p methylguanosine mG dimethylguanosine sz Universal Features of Transfer RNA Molecules 1 2 S gt1 All tRNA molecules are single chains containing 7393 ribonucleotides 25kd tRNA sequences contain many unusual bases 715 unusual bases per tRNA molecule Posttranscriptionally modified bases Eg methylated or dimethylated derivatives of A U C G Usually present in the loops of the cloverleaf secondary structure L shaped threedimensional structure CCA terminus with 5 and 3 ends is in one arm while the anticodon loop is present in the other arm of the L Helix stacking in tRNA Cloverleaf secondary structure Four regions of WatsonCrick base pairing The four regions stack to form two apparently continuous segments of double helixquot in the shape of an L Three of the four regions close into loops to form the following 1 TlJC loop ribothyminepseudouracilcytosine 2 DH U loop contains many dihydrouracil residues 3 Anticodon loop One region is called the extra arm a segment that contains a varying number of residues Phosphorylated 5 end 5 terminal residue 9 usually pG CCA overhang at 3 OH amino acid attachment site of acceptor stem Amino acids are coupled to tRNAs to form aminoacyl tRNAs through L th linkages to either the 2 or the 3 hydroxyl group of the 3 adenosine residuequot of the CCA overhang of tRNAs The amino acid attachment site with the CCA overhang and the anticodon loop are always at opposite ends of the tRNA molecule The considerable distance between the amino acid attachment site and the anticodon loop ensures proper separation of the mRNA strand and the growing polypeptide chain AminoacyltRNA Used to distribute specific amino acids to a growing protein chain because amino acids alone are incapable of recognizing an mRNA codon Composition carboxyl terminal of an amino acid joined via an ester linkage to either the 2 or 3 OH group of the RNA s terminal ribose sugar AminoacyItRNA synthetase catalyzes the formation of aminoacyltRNAs from amino acids and tRNA molecules Codon Recognition The bases of a codon and the complementary bases of an anticodon interact via WatsonCrick interactions Total number of codons 64 43 61 codons code for amino acids 61 different tRNAs each with distinct anticodons could potentially exist However experiments reveal that only about 2530 tRNAs exist in most organisms suggesting that some tRNA molecules recognize more than one codon tRNA molecules can recognize more than one codon by allowing multiple codons corresponding to a particular amino acid to be read by a single tRNAquot Wobble hypothesis The third base of a codon can vary more freely than the first and second bases without affecting recognition by a tRNA Eg yeast alanyltRNA anticodon IGC recognizes the codons GCU GCC and GCA CodonAnticodon Interaction Codons that differ in either of their first two bases must be recognized by different tRNAsquot Eg although UUA and CUA both code for leucine they are recognized by different tRNA molecules because their first two bases differ The first base of an anticodon the 5 base determines whether a particular tRNA molecule reads one two or three kinds of codons C or A one codon U or G two codons or I three codons Inosine I can base pair with uridine adenosine and cytidine because inosine is less selective for instance guanine G is capable of base pairing with uridine adenosine and cytidine but a GC base pair is more favorable than a GU or a GA base pair because there are three hydrogen bonds in GC compared to two in both G U and GA inosine however forms two hydrogen bonds with uridine adenosine and cytidine enabling inosine to recognize all three bases equally Base pairing between the codon and anticodon is enforced by adenine 1493 one of three conserved bases in 16S rRNA Adenine 1493 forms two or three hydrogen bonds only with correctly formed base pairs of the codonanticodon duplex these interactions serve to check whether WatsonCrick base pairs are present in the first two positions of the duplex No such inspection device is present for the third position so more varied base pairs are toleratedquot AminoacyltRNA Synthetases Enzymes involved in establishing the genetic code Aka activating enzymes AminoacyltRNA synthetases activate amino acids for protein synthesis The error rate of mismatching an amino acid to tRNA is less than 10392 and attaining an error rate of less than 10394 can require proofreading activityquot There are a minimum of 20 aminoacyltRNA synthetases in an organism Eukaryotic mitochondria possess their own set of aminoacyltRNA synthetases Responsible for activating amino acids for protein synthesis Amino Acid Activation By Adenylation Step 1 Activation amino acid ATP aminoacylAMP PPi AminoacylAMP mixed anhydride an amino acid with its carboxyl group linked to the phosphoryl group of AMP The aminoacylAMP intermediate does not dissociate from the synthetasequot Step 2 Transfer aminoacylAMP tRNA aminoacyltRNA AMP Aminoacyl tRNA activated intermediate in protein synthesis amino acid ester of tRNA an amino acid with its carboxyl group linked to either the 2 or 3 OH group of the ribose unit at the 3 end of a tRNA molecule Overall reaction amino acid ATP tRNA aminoacyltRNA AMP PPi Catalyzed by aminoacyltRNA synthetase AG 9 close to O for this reaction AG 39 9 negative under cellular conditions The equivalent of two molecules ofA TP is consumed in the synthesis of each aminoacyltRNAquot AminoacyltRNA Synthetases and Amino Acid Specificity Each aminoacyltRNA synthetase has high specificity for a particular amino acid A synthetase will incorporate the incorrect amino acid only once in 104 or 105 catalytic reactionsquot How do aminoacyltRNA synthetases selectively incorporate the correct amino acid onto a tRNA molecule Consider the amino acids threonine valine and serine The similarities that exist between the three amino acids create a challenge for threonyltRNA synthetases enzymes responsible for catalyzing the activation and coupling of threonine to threonyltRNA The structure of the active site of threonyltRNA synthetase plays a role in solving this problem The amino acidbinding site of threonyltRNA synthetase contains a zinc ion Threonine coordinates to the zinc ion through its amino group and its sidechain hydroxyl group The sidechain OH group is further recognized by an aspartate residue that hydrogen bonds to itquot The lack of a hydroxyl group and the presence instead of an extra methyl group in valine prevents this similar amino acid from coordinating with the active site of threonyltRNA synthetase Valine therefore is not transferred to threonyltRNA Serine however does possess a hydroxyl group capable of binding to the zinc ion and subsequently causing translation errors Proofreading By AminoacyltRNA Synthetases Most aminoacyltRNA synthetases possess two different catalytic sites 1 Activation sites Site at which amino acids are activated by aminoacyltRNA synthetases 2 Editing sites Responsible for reducing errors in protein synthesis ThreonyltRNA synthetase contains an additional functional site the editing site that hydrolyzes SertRNAThr but not ThrtRNAThFquot hence preventing the incorporation of serine into threonyltRNA Activation and editing sites work together as complementary pairs to ensure the fidelity of protein synthesis The activation site will typically have an error rate that is too high eg 102 but editing improves the overall error rate down to the biologically required level of 10394quot Activation vs editing sites Activation sites accept amino acids smaller than the correct amino acid reject amino acids larger than the correct amino acid accept amino acids with a particular functional group eg the coupling of OH containing threonine and serine to threonyltRNA Editing sites 9 hydrolyze incorrect amino acids smaller than the correct amino acid Editing of aminoacyltRNA The aminoacylated CCA acceptor stem is exible and can therefore swing out of the activation site and into the editing sitequot enabling editing without dissociation from the synthetasequot Transfer RNA Recognition by Synthetases Synthetases recognize many different features of tRNA molecules Some synthetases recognize the anticodon loops of tRNA molecules Classes of AminoacyltRNA Synthetases Class I In a tRNAsynthetase complex the CCA arm is in the hairpin conformation Acylate the 2 hydroxyl group of the terminal adenosine of tRNAquot Mostly monomeric Class II In a tRNAsynthetase complex the CCA arm is in the helical conformation Acylate the 3 hydroxyl groupquot Mostly dimeric Class I and class II synthetases recognize different faces of the tRNA moleculequot and bind ATP in different conformationsquot Figure 303 Lecture 1118 Protein Synthesis II p 897907 Prokaryotic Ribosome Site of translation Sedimentation coefficient of an E coli ribosome9 7OS Components large subunit SOS and small subunit 308 308 subunit 9 21 different proteins 8182 1 168 RNA molecule SOS subunit 9 34 different proteins LlL34 238 RNA molecule SS RNA molecule The SOS and 308 subunits do not join to form a complete ribosome without an mRNA and an initiator tRNA bound to the 308 subunit The 708 ribosome does not exist except during active protein translation with mRNA boundquot Ribosomal RNA rRNA The three ribosomal RNA molecules SS 16S and 23S play a significant role in the function and structure of ribosomes Figure 3015 displays the secondary and tertiary structure of 16S ribosomal RNA Distinct domains are displayed in both the secondary and tertiary structure The structures of the domains are similar to those of the 23S rRNA molecule rRNA can fold in the absence of protein into its stable threedimensional structurequot rRNA molecules play a greater role in protein synthesis than do ribosomal proteins Transfer RNABinding Sites Three tRNAbinding sites are present in ribosomes 1 A aminoacyl site 2 P peptidyl site 3 E exit site At a given point in time tRNA molecules can bind to a maximum of two adjacent tRNAbinding sites A minimum of one P site is always occupied in the holoribosomequot The mRNA fragment being translated is basepaired with tRNA molecules in sites A and P because only A and P sites are close enough to the mRNA to have codon anticodon hydrogen bondingquot An Active Ribosome In an active ribosome the mRNA strand being translated is bound to the 308 subunit and all tRNA molecules are in contact with both the 308 and SOS subunit Channels present in 308 and SOS subunits In 308 9 doubleended channel for mRNA strand being translated In SOS 9 oneended exit channel polypeptide channel extending from the P site through which the newly synthesized polypeptide chain passes Initiation of Protein Synthesis in Prokaryotes Initiation of peptide synthesis formation of ternary complex between P site of 30S ribosome subunit initiator tRNA and mRNAquot Determinants of starting point of protein synthesis 1 The alignment of an mRNA start codon with the anticodon of an initiator tRNA Start codon AUG or GUG or UUG AUG 9 methionine most common GUG 9 valine less frequent UUG 9 leucine rare ShineDalgarno sequence Purinerich sequence The 3 end of this rRNA component of the 30S subunit contains a sequence of several bases that is complementary to the purinerich region in the initiator sites of mRNAquot Bacterial Protein Synthesis Bacterial protein synthesis is initiated with the incorporation of a modified methionine known as Nformylmethionine fMet fMet is transported to the ribosome by a special tRNA molecule the initiator tRNA tRNAf tRNAf tRNAf is different from other tRNA molecules tRNAm that transfer methionine to locations other than the first site of protein synthesis The subscript f in tRNAfD indicates that methionine attached to the initiator tRNA can be formylated whereas it cannot be formylated when attached to tRNAmquot Anticodon of tRNAf and tRNAm 9CAU Formation of fMettRNAf 1 tRNAf methionine 9 Met tRNAf The aminoacyltRNA synthetase that attaches methionine to tRNAf and tRNAm is identical Transfer of formyl group to Met tRNAf The formyl group is obtained from N10formyltetrahydrofolate Transformylase catalyzes this reaction Transformylase is specific for just the initiator MettRNAquot Translation Initiation in Prokaryotes 1 rlgt 990N935 Complex formed from a 30S ribosomal subunit and two protein initiation factors IF1 and IF3 Initiation factors bind and prevent the 30S subunit from joining to the SOS subunit without mRNA and fMettRNAf IF1 binds near the A site and directs the fMettRNAfto the P sitequot IFZ a Gprotein binds GTP IFZGTP associates with fMettRNAf IFZGTPinitiatortRNA complex binds with mRNA and the 30S subunit to form the 305 initiation complexquot 3OS initiation complex undergoes structural changes IF1 and IF3 leave the 30S ribosomal subunit IFZ stimulates the association of the SOS subunit to the complexquot IFZGTP dissociates upon hydrolysis 7OS initiation complex is assembled and the ribosome is now ready for protein synthesis Mechanism of Protein Synthesis Delivery of aminoacyltRNA to the ribosome 1 fMettRNAf binds to the P site the A site is empty 2 AminoacyltRNA associates with elongation factor T u EFTu in its GTP form EFTu 9 Gprotein GTP essential for function quotEF Tu does not interact with fMet tRNAf but MettRNAm does 3 AminoacyltRNA with the assistane of EFTu is transported from the synthetase to the ribosomal A site 4 When the EFTuaminoacyltRNA complex and the ribosome are properly paired EFTu is hydrolyzed into its GDP form EFTu ensures accurate protein synthesis by releasing only the proper aminoacyltRNA molecule into the ribosome S Upon GTP hydrolysis the aminoacyltRNA is released into the ribosome 6 Elongation factor Ts resets EFTU back into its GTP form by inducing the dissociation of GDPquot 7 GTP binds to EFTu 8 EFTs is released Peptidebond synthesis Spontaneous exergonic reaction Catalyzed by the peptidyl transferase center a site on the 23S rRNA of the SOS subunitquot 1 The ribosome brings the aminoacyltRNA in the A site and the initiator tRNA in the P site close together 2 The peptidyl transferase center enables the formation of an NH2 group on the aminoacyltRNA in the Asite 3 The amino group of the aminoacyltRNA in the A site attacks the ester linkage between the initiator tRNA and the formylmethionine molecule in the P sitequot 4 A tetrahedral intermediate is formed The peptidyl transferase center stabilizes this intermediate 5 The tetrahedral intermediate collapses 6 The peptide bond is formed 7 The deacylated tRNA is released GTPdriven translocation II The peptide chain remains in the P site on the 503 subunit throughout translocation 1 Elongation factor G EFG in the GTP form binds to the ribosome near the A site interacting with the 23S rRNA of the SOS subunitquot 2 GTP is hydrolyzed to GDP and Pi upon the binding of EFG to the ribosome EFG undergoes a conformational change upon GTP hydrolysis 4 PeptidyltRNA moves from the A site to the P site mRNA moves by three nucleotides one codon Deacylated tRNA moves from the P site to the E site 5 Once translocation is completed the empty tRNA which has lost contact with mRNA will spontaneously dissociate as will EFGquot 9 The energy required so far 2 highenergy bonds used up for each aminoacyl tRNA formed 1 for each EFTu 1 for each EFG 4 total 120 kImolquot Termination of protein synthesis Protein synthesis termination begins with the recognition of a stop codon by release factors RFS RF1 9 recognizes UAA or UAG RF2 9 recognizes UAA or UGA RF1 resembles an aminoacyltRNA Release factors assist in the attack by a water molecule hydrolysis on the ester linkage between the tRNA and the polypeptide chainquot for the release of the synthesized protein from the tRNA Prokaryotic Gene Expression In prokaryotes the amount of time as well as distance between translation and transcription is relatively short mRNA can be transcribed while still being synthesized and many ribosomes can be translating an mRNA molecule simultaneouslyquot This results in the formation of a polysome or a group of ribosomes bound to an mRNA moleculequot This can cause topological problems especially when expressing membrane proteinsquot Lecture 1120 Protein Synthesis III p 907915 Eukaryotic Proteins Synthesis vs Prokaryotic Protein Synthesis Di ferences observed primarily in translation initiation Similarities and differences 1 Ribosomes Eukaryotic ribosomes 9 80S ribosome 60S and 40S subunits 4200 kd Prokaryotic ribosomes 9 70S ribosome 50S and 30S subunits 2700 kd Initiator tRNA Eukaryotic initiating amino acid 9 methionine Prokaryotic initiating amino acid 9 Nformylmethionine Both eukaryotes and prokaryotes require a special tRNA molecule for initiation MettRNAi or MettRNAf Initiation Eukaryotic initiating codon 9 always AUG Eukaryotes in contrast with prokaryotes do not have a specific purinerich sequence ShineDalgarno sequence on the 5 side to distinguish initiator AUGs from internal onesquot Eukaryotes usually only have one start site no purinerich sequences whereas prokaryotes have multiple start sites ShineDalgarno sequences that enable the synthesis of more than one protein Eukaryotic translation initiation 1 AUG codon closest to the 5 end of the mRNA is designated the start codon 2 40S ribosome with bound MettRNAibinds to 5 cap of eukaryotic mRNA 3 The 40S ribosome MettRNAi complex travels along the mRNA strand in the 3 direction movement powered by ATP hydrolysis to the first AUG codon 4 Base pairing occurs between the AUG codon on the mRNA strand and specific anticodon on MettRNAi 5 The 60S subunit is added 6 The 808 initiation complex is formed Eukaryotic translation initiation requires more initiation factors than in prokaryotic initiation Eukaryotic initiation factors eIF eIF4E 9 binds to 7methylguanosine cap eIFZ 9 responsible for delivering MettRNAi to the ribosome The 5 end of mRNA is readily available to ribosomes immediately after transcription in prokaryotes In contrast in eukaryotes premRNA must be processed and transported to the cytoplasm before translation is initiatedquot Messenger RNA structure Eukaryotic mRNA is circular because the 5 cap and polyA tail are brought close together via various protein interactions Protein interactions that circularize eukaryotic mRNA 5 capeIF4E 9eIF 4G 9 polyA tail binding proteins PABPI and PABPI The circular structure of eukaryotic mRNA facilitates repeated translations of the same protein by a ribosome by bridging the site where it falls off when terminating one protein molecule closer to the site where it needs to initiate the next onequot Antibiotic Inhibitors of Protein Synthesis Table 304 Different ribosomes present in eukaryotes and prokaryotes facilitate the development of antibiotics against certain bacteria prokaryotic microorganisms Streptomycin an antibiotic inhibits the initiation of prokaryotic protein synthesis by preventing the binding of fMettRNA to the small prokaryotic ribosomal subunit Puromycin Antibiotic Inhibits both eukaryotic and prokaryotic protein synthesis by acting as an analog of the 3 amino terminus of an aminoacyltRNA molecule Possesses a free alphaamino group As the amino group in an aminoacyltRNA molecule would form a peptide bond with the carboxyl group of the growing peptide so too could the free alphaamino group of puromycin form a peptide linkage with the growing peptide chain Puromycin can therefore act as an aminoacyltRNA and transfer a methyltyrosine to the carboxyl terminus of the growing peptide chain The transferred amino acid methyltyrosine however lacks both an aminoacyl ester linkage an amide linkage is substituted and a full tRNA chain to occupy the A or P sitesquot The growing chain with the puromycin residue is terminated early Polymerization Types in Biology Figure 3014 in lecture slide two contrasting types of polymerization in Biologyquot TypeI Protein synthesis Activating group X is cleaved from existing polymerquot Activated monomer retains X group Growing peptide chain receives tRNA with ester linkage Type 11 RNA and DNA polymerization Activating group X pyrophospate is cleaved from the monomer nucleoside triphospate which is being addedquot Ribosomes The region in the endoplasmic reticulum ER that binds ribosomes is known as the rough ER RER Protein synthesis takes place in the RER While prokaryotic cells can direct newly synthesized protein to remain in the cytoplasm or to the plasma membrane the outer membrane the space between the plasma and outer membrane or the extracellular medium eukaryotic cells can direct newly formed protein to internal sites such as lysosomes mitochondria chloroplasts and the nucleusquot Eukaryotes in contrast to prokaryotes possess different types of intracellular membranes The SRP Targeting Cycle in Eukaryotes 1 2 S gt1 8 9 Protein synthesis occurs on free ribosomes in the cytoplasm The signal sequence exits the free ribosome Signal sequence a sequence of 9 to 12 hydrophobic amino acid residues that identifies the nascent peptide as one that must cross the ER membranequot The signalrecognition particle SRP binds to the signal sequence SRP ribonucleoprotein 7S RNA 6 other proteins including the SRP54 protein SRP549 GTPase Protein synthesis stops SRP binds to the SRP Receptor SR embedded in the ER membrane SR SRa SR3 SRa 9 GTPase The SRP and the SRP receptor simultaneously hydrolyze bound GTPsquot SRP disassociates from the signal sequence and protein synthesis resumes in the ER lumen Signal peptidase removes the signal sequence Protein is continuously synthesized ProteinSorting Pathways 1 2 3 7 Newly synthesized protein in ER lumen are collected into membrane budsquot The membrane buds containing protein pinch off from the ER and form transport vesicles The transport vesicles arrive at the Golgi complex The transport vesicles fuse with the Golgi complex and transfer the protein to the interior of the Golgi complex The newly synthesized protein undergoes posttranslational modifications in the Golgi Eg glycosylation The modified protein leaves the Golgi complex in secretory granules that pinch off from the Golgi complex The secretory granules fuse with the plasma membrane or lysosomes for degradation Throughout this process the topology of the newly synthesize protein is maintained Note Quotations indicate text obtained directly from textbook or lecture slides References Berg Jeremy John Tymoczko and Lubert Stryer Biochemistry 7th ed WH Freeman 2012 1 246 Print BCM 475 Braiman lecture notes


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