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Translation mechanism
1.
INTRODUCTION The translation
of the mRNA codons into amino acid sequences leads to the synthesis of proteins A variety of cellular components play important roles in translation These include proteins, RNAs and small molecules In this chapter we will discuss the current state of knowledge regarding the molecular features of mRNA translation Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 1
2.
Proteins are
the active participants in cell structure and function Genes that encode polypeptides are termed structural genes These are transcribed into messenger RNA (mRNA) The main function of the genetic material is to encode the production of cellular proteins In the correct cell, at the proper time, and in suitable amounts Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 13.1 THE GENETIC BASIS FOR PROTEIN SYNTHESIS 2
3.
Copyright ©The McGraw-Hill
Companies, Inc. Permission required for reproduction or display First to propose (at the beginning of the 20th century) a relationship between genes and protein production Garrod studied patients who had defects in their ability to metabolize certain compounds Urine chemist He was particularly interested in alkaptonuria Patients bodies accumulate abnormal levels of homogentisic acid (alkapton) Disease characterized by Black urine and bluish black discoloration of cartilage and skin Archibald Garrod 3
4.
4
5.
Copyright ©The McGraw-Hill
Companies, Inc. Permission required for reproduction or display He proposed that alkaptonuria was due to a missing enzyme, namely homogentisic acid oxidase Garrod also knew that alkaptonuria follows an autosomal recessive pattern of inheritance He proposed that a relationship exists between the inheritance of the trait and the inheritance of a defective enzyme Archibald Garrod 5
6.
Metabolic pathway of
phenylalanine metabolism and related genetic diseases Figure 13.1 Dietary protein CH2 NH2 Phenylalanine Tyrosine Phenylalanine hydroxylase Tyrosine aminotransferase Hydroxyphenylpyruvate oxidase Homogentisic acid oxidase p-hydroxyphenylpyruvic acid Homogentisic acid Maleylacetoacetic acid Phenylketonuria Tyrosinosis Alkaptonuria COOHC CH2HO COOHC H H NH2 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 6
7.
Copyright ©The McGraw-Hill
Companies, Inc. Permission required for reproduction or display In the early 1940s, George Beadle and Edward Tatum were also interested in the relationship between genes, enzymes and traits Experiments supported Garrod’s idea that each gene codes for one enzyme Their genetic model was Neurospora crassa (a common bread mold) Their studies involved the analysis of simple nutritional requirements Beadle and Tatum’s Experiments 7
8.
Copyright ©The McGraw-Hill
Companies, Inc. Permission required for reproduction or display They analyzed more than 2,000 strains that had been irradiated to produce mutations They analyzed enzyme pathways for synthesis of vitamins and amino acids Figure 13.2 shows an example of their findings on the synthesis of the amino acid methionine Beadle and Tatum’s Experiments 8
9.
Figure 13.2 Every mutant
strain was blocked at one (and only one) particular step in the synthesis pathway, showing that each gene encoded one enzyme 1 3 4 1 3 1 3 1 3 1 2 3 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Neurospora growth WT WT WT WT WT 2 Minimal +O–acetylhomoserine +Cystathionine +Homocysteine +Methionine (a) Growth of strains on minimal and supplemented growth media (b) Simplified pathway for methionine biosynthesis Homoserine O–acetylhomoserine Cystathionine Homocysteine Methionine Enzyme 1 Enzyme 2 Enzyme 3 Enzyme 4 4 2 4 2 4 2 4 9
10.
Copyright ©The McGraw-Hill
Companies, Inc. Permission required for reproduction or display In the normal strains, methionine was synthesized by cellular enzymes In the mutant strains, a genetic defect in one gene prevented the synthesis of one protein required in one step of the pathway to produce that amino acid Beadle and Tatum’s conclusion: A single gene controlled the synthesis of a single enzyme This was referred to as the one gene–one enzyme hypothesis Beadle and Tatum’s Experiments 10
11.
Copyright ©The McGraw-Hill
Companies, Inc. Permission required for reproduction or display In later decades, this theory had to be modified 1. Enzymes are only one category of proteins 2. Some proteins are composed of two or more different polypeptides The term polypeptide denotes structure The term protein denotes function So it is more accurate to say a structural gene encodes a polypeptide In eukaryotes, alternative splicing means that a structural gene can encode many different polypeptides 3. Many genes have been identified that do not encode polypeptides For instance, functional RNA molecules (tRNA, rRNA, etc.) Beadle and Tatum’s Experiments 11
12.
Copyright ©The McGraw-Hill
Companies, Inc. Permission required for reproduction or display Translation involves an interpretation of one language into another In genetics, the nucleotide language of mRNA is translated into the amino acid language of proteins Translation relies on the genetic code Refer to Table 13.1 The genetic information is coded within mRNA in groups of three nucleotides known as codons The Genetic Code 12
13.
Triplet codons correspond to
a specific amino acid Multiple codons may encode the same amino acid. These are known as synonymous codons Three codons do not encode an amino acid. These are read as STOP signals for translation 13
14.
Copyright ©The McGraw-Hill
Companies, Inc. Permission required for reproduction or display Special codons: AUG (which specifies methionine) = start codon This defines the reading frame for all following codons AUG specifies additional methionines within the coding sequence UAA, UAG and UGA = termination, or stop, codons The code is degenerate More than one codon can specify the same amino acid For example: GGU, GGC, GGA and GGG all code for glycine In most instances, the third base is the variable base It is sometime referred to as the wobble base The code is nearly universal Only a few rare exceptions have been noted Refer to Table 13.3 14
15.
Figure 13.3 Figure
13.3 provides an overview of gene expression Note that the start codon sets the reading frame for all remaining codons 5′ Template strand Coding strand Transcription 3′ Translation DNA mRNA tRNAPolypeptide 5 untranslated′ − region 3 untranslated′ − region Start codon Codons Anticodons 3′ 3′ 5′ 5′ A C T G C C C A T G G G G C TC G A CA G GC G G G A A T A A C C G T C G A G G G G C A G C T C C C C G U C G A G G T T GC A C T G A C G G G T A C C C C G AG C T GT C CG C C C T T A T TA A CG T G 5′ 3′ A C U G C C C A U G G G G C UC G A CA G GC G G G A A U A AU U GC A C Met Gly LeuSer Asp Gly GluHis Leu Stop codon UAC CCC GAGUCG CUG CCC CUUGUG A AC Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 15
16.
Copyright ©The McGraw-Hill
Companies, Inc. Permission required for reproduction or display Polypeptide synthesis has a directionality that parallels the 5’ to 3’ orientation of mRNA During each cycle of elongation, a peptide bond is formed between the carboxyl group of the last amino acid in the polypeptide chain and the amino group in the amino acid being added The first amino acid has an exposed amino group Said to be N-terminal or amino terminal end The last amino acid has an exposed carboxyl group Said to be C-terminal or carboxy terminal end Refer to Figure 13.6 A Polypeptide Chain Has Directionality 16
17.
Figure 13.6 Copyright
©The McGraw-Hill Companies, Inc. Permission required for reproduction or display (a) Attachment of an amino acid to a peptide chain (b) Directionality in a polypeptide and mRNA H H H H H H3N+ H3N+ H3N+ H3N+ C C C CN C C C+ + N R1 R2O O O– O– R3 R4O C O H H H H H H Last peptide bond formed in the growing chain of amino acids H O– O– H2OC C C CN C CN C CN R1 R2O O R3 R4O O H HO H3C Amino terminal end Carboxyl terminal end Methionine Serine Peptide bonds Sequence in mRNA Valine CH2 CH3 CH3 CH2 CH2 OH CH S C C CN H O C CN C H O H Cysteine CH2 SH CN H O C Tyrosine CH2 OH H CN C H O H 5′ 3′A U G A G C GU U U A C U G C Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H 17
18.
Figure 13.7 Copyright
©The McGraw-Hill Companies, Inc. Permission required for reproduction or display There are 20 amino acids that may be found in polypeptides Each contains a different side chain, or R group Each R group has its own particular chemical properties Nonpolar amino acids are hydrophobic They are often buried within the interior of a folded protein H H Glycine (Gly) G (a) Nonpolar, aliphatic amino acids H3N C COO– CH3 CH3 CH H Alanine (Ala) A H3N COO– CH3 CH3 CH CH2 H Valine (Val) V H3N C COO– + CH2CH2 CH2 H Proline (Pro) P H2N C COO– + CH2 CH3 CH3 CH H Leucine (Leu) L Methionine (Met) M H3N C COO– + Cysteine (Cys) C + CH2 SH H H3N C COO– CH2 CH2 CH3 S H H3N C COO– + H Isoleucine (Ile) I H3N C COO– + (b) Aromatic amino acids Phenylalanine (Phe) F Tyrosine (Tyr) Y H H3N C COO– + CH2 H H3N C COO– + CH2 OH Tryptophan (Trp) W H H3N C COO– + CH2 N H Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. + CH3 C + 18
19.
Figure 13.7 Copyright
©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Polar and charged amino acids are hydrophilic They are more likely to be on the surface of a protein (c) Polar, neutral amino acids Serine (Ser) S Threonine (Thr) T H H3N C COO– + CH2 OH H HCOH H3N C CH3 COO– + H Glutamine (Gln) Q H3N C COO– + CH2 C O NH2 H Asparagine (Asn) N H3N C COO– + CH2 CH2 C O NH2 H Glutamic acid (Glu) E H3N C COO– + CH2 C O O– H Aspartic acid (Asp) D H3N C COO– + CH2 CH2 C O O– (d) Polar, acidic amino acids (e) Polar, basic amino acids Histidine (His) H H H3N C COO– + + + + CH2 NH HN Lysine (Lys) K H H3N C COO– + CH2 CH2 CH2 CH2 NH3 Arginine (Arg) R H H3N C COO– + CH2 CH2 CH2 C NH NH2 NH2 (f) Nonstandard amino acids Selenocysteine (Sec) H H3N C COO– + CH2 SeH N CH3 Pyrrolysine (Pyl) H H3N C COO– + CH2 CH2 CH2 CH2 NH C O Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 19
20.
Copyright ©The McGraw-Hill
Companies, Inc. Permission required for reproduction or display There are four levels of structure in proteins 1. Primary 2. Secondary 3. Tertiary 4. Quaternary A protein’s primary structure is its amino acid sequence Refer to Figure 13.8 Levels of Structure in Proteins 20
21.
Lys NH3 + 1 10 20 30 40 50 60 70 80 90 100 110 120 129 Val Phe Gly Arg
Cys Glu Leu Ala Ala Ala Met Lys Arg His GlyLeuAspAsnTyrArgGlyTyr Ser Thr Asp Tyr Gly Leu Asn SerGluPheLysAlaAlaCysValTrp Asn Leu Gly Phe Asn ThrGin Ala ThrAsnArgAsn Thr Asp Gly Ser lle Gln lle Asn Ser Arg Trp Trp Cys Asn Asp Gly ArgThrProGlySerArgAsnLeu Cys Asn lle Pro Cys Ser Ala Leu Leu Ser Ser Asp lle Thr Arg Asn Arg Cys Lys Gly Thr Asp AlaTrp ValAla Asn Met Gly Asp Gly Asp Ser Val lle Lys Lys Ala Cys Asn Val Ser Ala Val GlnAlaTrplleArgGlyCys Arg Leu Trp COO– Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Figure 13.8 The amino acid sequence of the enzyme lysozyme 129 amino acids long Within the cell, the protein will not be found in this linear state Rather, it will adopt a compact 3-D structure Indeed, this folding can begin during translation The progression from the primary structure to the 3-D structure is dictated by the amino acid sequence within the polypeptide Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 21
22.
Copyright ©The McGraw-Hill
Companies, Inc. Permission required for reproduction or display The primary structure of a protein folds to form regular, repeating shapes known as secondary structures There are two types of secondary structures α helix β sheet Certain amino acids are good candidates for each structure These secondary structures are stabilized by the formation of hydrogen bonds between atoms located in the polypeptide backbone Refer to Figure 13.9 Levels of Structures in Proteins 22
23.
Copyright ©The McGraw-Hill
Companies, Inc. Permission required for reproduction or display The short regions of secondary structure in a protein fold into a three-dimensional tertiary structure Refer to Figure 13.9 This is the final conformation of proteins that are composed of a single polypeptide Structure determined by hydrophobic and ionic interactions as well as hydrogen bonds and Van der Waals interactions Proteins made up of two or more polypeptides have a quaternary structure This is formed when the various polypeptides associate with one another to make a functional protein Refer to Figure 13.9 Levels of Structures in Proteins 23
24.
Figure 13.9 Copyright
©The McGraw-Hill Companies, Inc. Permission required for reproduction or display α helix β sheet Primary structure Secondary structure Quaternary structure Tertiary structure Protein subunit Ala C O C C C C O O Val Phe Glu Tyr Leu Iso Ala H N NH3 + NH3 + COO– COO– NH3 + COO– H N C C C C O O HH NN H N C C C C C C O O C O H H N NN Depending on the amino acid sequence, some regions may fold into an helix orα sheet.β Two or more polypeptides may associate with each other. Regions of secondary structure and irregularly shaped regions fold into a three-dimensional conformation. C C C C O H H N N N C C C C C C O O H H N C C C O N C C C O NC O HC C C O O H H NC HC C O H N O C C HC C O H C C O H C C O H (a) (b) (c) (d) H C O O C H H H O C Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 24
25.
Copyright ©The McGraw-Hill
Companies, Inc. Permission required for reproduction or display To a great extent, the characteristics of a cell depend on the types of proteins its makes Proteins can perform a variety of functions Refer to Table 13.5 A key category of proteins are enzymes Accelerate chemical reactions within a cell Can be divided into two main categories Anabolic enzymes Synthesize molecules and macromolecules Catabolic enzymes Break down large molecules into small ones Important in generating cellular energy Functions of Proteins 13-38 25
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13-39 26
27.
In the
1950s, Francis Crick and Mahon Hoagland proposed the adaptor hypothesis tRNAs play a direct role in the recognition of codons in the mRNA In particular, the hypothesis proposed that tRNA has two functions 1. Recognizing a 3-base codon in mRNA 2. Carrying an amino acid that is specific for that codon Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 13.2 STRUCTURE AND FUNCTION OF tRNA 27
28.
Copyright ©The McGraw-Hill
Companies, Inc. Permission required for reproduction or display During mRNA-tRNA recognition, the anticodon in tRNA binds to a complementary codon in mRNA Recognition Between tRNA and mRNA Figure 13.10 tRNAs are named according to the amino acid they bear The anticodon is anti-parallel to the codon Phenylalanine tRNAPhe tRNAPro Phenylalanine anticodon Phenylalanine codon Proline codon A G Proline Proline anticodon U C 3 mRNA′5′ Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. G CA G U C C G 28
29.
Copyright ©The McGraw-Hill
Companies, Inc. Permission required for reproduction or display The secondary structure of tRNAs exhibits a cloverleaf pattern It contains Three stem-loop structures A few variable sites An acceptor stem with a 3’ single strand region The actual three-dimensional or tertiary structure involves additional folding In addition to the normal A, U, G and C nucleotides, tRNAs commonly contain modified nucleotides More than 80 of these can occur tRNAs Share Common Structural Features 29
30.
Anticodon U G G C G A A UH2 UH2 UH2 30 10 19 40 60 70 Acceptor stem 50 U I
C mI P G PO4 OH U U A G C P T m2G A C C 3′ 5′ A C C NH3 + C R C O H O Covalent bond between tRNA and an amino acid U Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Stem–loop Structure of tRNAFigure 13.12 Found in all tRNAs Not found in all tRNAs Other variable sites are shown in blue as well The modified bases are: I = inosine mI = methylinosine T = ribothymidine UH2 = dihydrouridine m2G = dimethylguanosine ψ = pseudouridine 30
31.
Copyright ©The McGraw-Hill
Companies, Inc. Permission required for reproduction or display The enzymes that attach amino acids to tRNAs are known as aminoacyl-tRNA synthetases There are 20 types One for each amino acid Aminoacyl-tRNA synthetases catalyze a two-step reaction involving three different molecules Amino acid, tRNA and ATP Refer to Figure 13.13 Charging of tRNAs 31
32.
Copyright ©The McGraw-Hill
Companies, Inc. Permission required for reproduction or display The aminoacyl-tRNA synthetases are responsible for the “second genetic code” The selection of the correct amino acid must be highly accurate or the polypeptides may be nonfunctional Error rate is less than one in every 100,000 Sequences throughout the tRNA including but not limited to the anticodon are used as recognition sites Modified bases may affect translation rates recognition by aminoacyl-tRNA synthetases Codon-anticodon recognition Charging of tRNAs 32
33.
Figure 13.13 The amino
acid is attached to the 3’ end of the tRNA by an ester bond P P P P P Pyrophosphate Specific amino acid Aminoacyl-tRNA synthetase A P A P A 3′ 3′ 5′ 3′ 5′ 5′ AMP ATP An amino acid and ATP bind to the enzyme. AMP is covalently bound to the amino acid, and pyrophosphate is released. The correct tRNA binds to the enzyme. The amino acid becomes covalently attached to the 3 end of the tRNA. AMP is′ released. The “charged” tRNA is released. tRNA Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 33
34.
Copyright ©The McGraw-Hill
Companies, Inc. Permission required for reproduction or display As mentioned earlier, the genetic code is degenerate With the exception of serine, arginine and leucine, this degeneracy always occurs at the codon’s third position To explain this pattern of degeneracy, Francis Crick proposed in 1966 the wobble hypothesis In the codon-anticodon recognition process, the first two positions pair strictly according to the A – U /G – C rule However, the third position can actually “wobble” or move a bit Thus tolerating certain types of mismatches tRNAs and the Wobble Rule 34
35.
U 3′ 5′ 5′ Wobble position Nucleotide of of tRNA
anticodon Third nucleotide of mRNA codon G C A U I xm5 s2 U xm5 Um C, U G U, C, G, (A) A, U, G, (C) U, C, A A, (G) U, A, G A a) Location of wobble position (b) Revised wobble rules Phenylalanine Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 3′ Um xm5 U xo5 U k2 C A A G U U Wobble position and base pairing rulesFigure 13.14 tRNAs that can recognize the same codon are termed isoacceptor tRNAs Recognized very poorly by the tRNA 5-methyl-2-thiouridine inosine 5-methyl-2’-O-methyluridine 5-methyluridine lysidine 2’-O-methyluridine 5-hydroxyuridine Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 35 You don’t need to memorize these rules
36.
Translation occurs
on the surface of a large macromolecular complex termed the ribosome Bacterial cells have one type of ribosome Found in their cytoplasm Eukaryotic cells have two types of ribosomes One type is found in the cytoplasm The other is found in organelles Mitochondria ; Chloroplasts Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 13.3 RIBOSOME STRUCTURE AND ASSEMBLY 36
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Unless otherwise
noted the term eukaryotic ribosome refers to the ribosomes in the cytosol A ribosome is composed of structures called the large and small subunits Each subunit is formed from the assembly of Proteins rRNA Table 13.6 presents the composition of bacterial and eukaryotic ribosomes Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 13.3 RIBOSOME STRUCTURE AND ASSEMBLY 37
38.
Copyright ©The McGraw-Hill
Companies, Inc. Permission required for reproduction or display 38
39.
Copyright ©The McGraw-Hill
Companies, Inc. Permission required for reproduction or display During bacterial translation, the mRNA lies on the surface of the 30S subunit As a polypeptide is being synthesized, it exits through a channel within the 50S subunit Ribosomes contain three discrete sites Peptidyl site (P site) Aminoacyl site (A site) Exit site (E site) Ribosomal structure is shown in Figure 13.15 Functional Sites of Ribosomes 39
40.
Copyright ©The McGraw-Hill
Companies, Inc. Permission required for reproduction or display Figure 13.15 (c) Model for ribosome structure Polypeptide 30S 50S 3′5′ tRNA mRNA E P A Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 40
41.
Translation can
be viewed as occurring in three stages Initiation Elongation Termination Refer to 13.16 for an overview of translation Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 13.4 STAGES OF TRANSLATION 41
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mRNA UAC Anticodon Initiator tRNA – tRNA with
first amino acid AUG Start codon AUG Start codon UAG Stop codon UAG Stop codon Completed polypeptide Termination Elongation (This step occurs many times.) Recycling of translational components Release factor Small Large Ribosomal subunits EE A E AP aa1 aa2 aa3 aa4 aa5 aa1 aa1 3′3′ 5′5′ 3′5′ 3′ 5′ Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. P P A Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Figure 13.16 Initiator tRNA Initiation 42
43.
Copyright ©The McGraw-Hill
Companies, Inc. Permission required for reproduction or display The mRNA, initiator tRNA, and ribosomal subunits associate to form an initiation complex This process requires three Initiation Factors The initiator tRNA recognizes the start codon in mRNA In bacteria, this tRNA is designated tRNAfmet It carries a methionine that has been covalently modified to N-formylmethionine The start codon is AUG, but in some cases GUG or UUG In all three cases, the first amino acid is N-formylmethionine The Translation Initiation Stage 43
44.
Shine-Dalgarno sequence mRNA 5′ 3′A U
C U A G U A A G U U C A GG G U CG A GU C A C G C A GU G GG U A 3′ Start codon A U U C C C A C A G C 16S rRNAU Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display The binding of mRNA to the 30S subunit is facilitated by a ribosomal-binding site or Shine-Dalgarno sequence This is complementary to a sequence in the 16S rRNA Figure 13.17 outlines the steps that occur during translational initiation in bacteria Figure 13.18 Hydrogen bonding Component of the 30S subunit 44
45.
Figure 13.17 Copyright
©The McGraw-Hill Companies, Inc. Permission required for reproduction or display IF2, which uses GTP, promotes the binding of the initiator tRNA to the start codon in the P site. Portion of 16S rRNA The mRNA binds to the 30S subunit. The Shine-Dalgarno sequence is complementary to a portion of the 16S rRNA. IF1 and IF3 bind to the 30S subunit. 3′ 5′ 30S subunit Shine- Dalgarno sequence (actually 9 nucleotides long) Start codon IF3 IF1 IF1IF3 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 45
46.
Figure 13.17 70S initiation complex This
marks the end of the initiation stage Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display IF1 and IF3 are released. IF2 hydrolyzes its GTP and is released. The 50S subunit associates. tRNAfMet IF2 GTP E AP 3′ 5′ 3′ 5′ 70S initiation complex IF1IF3 Initiator tRNA tRNAfMet 46
47.
Copyright ©The McGraw-Hill
Companies, Inc. Permission required for reproduction or display In eukaryotes, the assembly of the initiation complex is similar to that in bacteria However, additional factors are required Note that eukaryotic Initiation Factors are denoted eIF Refer to Table 13.7 The initiator tRNA is designated tRNAmet It carries a methionine rather than a formylmethionine The Translation Initiation Stage 47
48.
Copyright ©The McGraw-Hill
Companies, Inc. Permission required for reproduction or display The start codon for eukaryotic translation is AUG Ribosome scans from the 5’ end of mRNA until it finds the AUG start codon (not all AUGs can act as a start) The consensus sequence for optimal start codon recognition is show here Start codon G C C (A/G) C C A U G G -6 -5 -4 -3 -2 -1 +1 +2 +3 +4 Most important positions for codon selection These rules are called Kozak’s rules After Marilyn Kozak who first proposed them With that in mind, the start codon for eukaryotic translation is usually the first AUG after the 5’ Cap! 48
49.
Copyright ©The McGraw-Hill
Companies, Inc. Permission required for reproduction or display Translational initiation in eukaryotes can be summarized as such: An initiation factor protein complex (eIF4) binds to the 5’ cap in mRNA These are joined by a complex consisting of the 40S subunit, tRNAmet , and other initiation factors The entire assembly moves along the mRNA scanning for the right start codon Once it finds this AUG, the 40S subunit binds to it The 60S subunit joins This forms the 80S initiation complex 49
50.
Copyright ©The McGraw-Hill
Companies, Inc. Permission required for reproduction or display During this stage, amino acids are added to the polypeptide chain, one at a time The addition of each amino acid occurs via a series of steps outlined in Figure 13.19 This process, though complex, can occur at a remarkable rate In bacteria 15-20 amino acids per second In eukaryotes 2-6 amino acids per second The Translation Elongation Stage 50
51.
Figure 13.19 The 23S
rRNA (a component of the large subunit) is the actual peptidyl transferase Thus, the ribosome is a ribozyme! Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 3′ P site Codon 3 Codon 4 mRNA E site A site aa1 aa2 aa3 Ribosome aa1 aa2 aa3 E AP aa4 A charged tRNA binds to the A site. EF-Tu facilitates tRNA binding and hydrolyzes GTP. Peptidyltransferase, which is a component of the 50S subunit, catalyzes peptide bond formation between the polypeptide and the amino acid in the A site.The polypeptide is transferred to the A site. 5′ 5′ 3′ 51
52.
Figure 13.19 tRNAs at
the P and A sites move into the E and P sites, respectively Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Codon 4 Codon 5 Codon 3 3′5′ aa1 aa2 aa3 aa4 aa1aa2 aa3 E A A Codon 4 Codon 5 Codon 3 3′ 5′ aa1 aa2aa3 aa4 E A P P aa4 This process is repeated, again and again, until a stop codon is reached. An uncharged tRNA is released from the E site. The ribosome translocates 1 codon to the right. This translocation is promoted by EF-G, which hydrolyzes GTP. 5′ 3′ E P Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 52
53.
Copyright ©The McGraw-Hill
Companies, Inc. Permission required for reproduction or display The final stage occurs when a stop codon is reached in the mRNA In most species there are three stop or nonsense codons UAG UAA UGA These codons are not recognized by tRNAs, but by proteins called release factors Indeed, the 3-D structure of release factors mimics that of tRNAs The Translation Termination Stage 53
54.
Copyright ©The McGraw-Hill
Companies, Inc. Permission required for reproduction or display Bacteria have three release factors RF1, which recognizes UAA and UAG RF2, which recognizes UAA and UGA RF3, which does not recognize any of the three codons It binds GTP and helps facilitate the termination process Eukaryotes only have one release factor eRF, which recognizes all three stop codons The Translation Termination Stage 54
55.
Figure 13.20 3′ 5′ Stop codon in
A site tRNA in P site carries completed polypeptide E A 3′ 5′ E A mRNA A release factor (RF) binds to the A site. The polypeptide is cleaved from the tRNA in the P site. The tRNA is then released. The ribosomal subunits, mRNA, and release factor dissociate. Release factor 3′ + 3′ 5′ 5′ 50S subunit 30S subunit mRNA Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. P P 55
56.
56
57.
Copyright ©The McGraw-Hill
Companies, Inc. Permission required for reproduction or display Bacteria lack a nucleus Therefore, both transcription and translation occur in the cytoplasm As soon an mRNA strand is long enough, a ribosome will attach to its 5’ end So translation begins before transcription ends This phenomenon is termed coupling Refer to Figure 13.21 Bacterial Translation Can Begin Before Transcription Is Completed 57
58.
Copyright ©The McGraw-Hill
Companies, Inc. Permission required for reproduction or display Figure 13.21 Coupling between transcription and translation in bacteria 58
59.
Copyright ©The McGraw-Hill
Companies, Inc. Permission required for reproduction or display 59
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