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Translation, Genetic Code,

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  • Voet, 2nd ed., Table 30-2
  • ASM tRNA Book
  • Voet, 2nd ed.,Fig. 30-14
  • Voet, 2nd ed.,Fig. 30-15
  • Voet, 2nd ed.,Fig. 30-17
  • Voet, 2nd ed.,Fig. 30-20
  • Voet, 2nd ed.,Fig. 30-22
  • Transcript

    • 1. GENERAL PROPERTIES OF THE GENETIC CODE 1. MULTIPLICITY: A DOUBLET CODE CAN ONLY SPECIFY 16 DIFFERENT AMINO ACDS WHILE A TRIPLET CODE CAN SPECIFY 64. NUCLEOTIDE TRIPLETS ARE THE MINIMUM THAT CAN RECOGNIZE 20 AMINO ACIDS, BUT WHY 64 TRIPLETS FOR 20 AMINO ACIDS, WHY SUCH OVERSPECIFICATION? 2. DEGENERACY: MOST AMINO ACIDS ARE SPECIFIED BY MORE THAN ONE TRIPLET OR CODON; ALMOST ALL TRIPLETS ARE USED TO SPECIFY AMINO ACIDS WITH THE EXCEPTION OF UAG, UAA AND UGA WHICH ARE TERMINATION OR STOP CODONS. 3. NONOVERLAPPING: EXAMPLES OF NONOVERLAPPING AND OVERLAPPING TRIPLET CODES NONOVERLAPPING: UAUGUCCGU IS READ AS UAU.GUC.CGU AND ENCODES Tyr-Leu-Arg... PARTIALLY OVERLAPPING: UAUGUCCGU IS READ AS UAU.UGU.UCC.CGU AND ENCODES Tyr-Cys-Ser… OVERLAPPING: UAUGUCCGU IS READ AS UAU.AUG.UGU.GUC AND ENCODES Tyr-Met-Cys… OVERLAPPING THEREFORE HAS MAJOR IMPLICATIONS FOR THE SEQUENCE OF THE ENCODED PROTEIN 4. READING FRAME: IF JUST ABOUT ALL CODONS SPECIFY AMINO ACIDS, THEN THERE MUST BE A MECHANISM TO ‘PHASE’ THE READING MECHANISM TO ONE OF THE 3 POSSIBLE READING FRAMES THROUGH THE CHOICE OF A SPECIFIC INITIATION CODON (AUG). SEQUENCE SPECIFYING A SEGMENT OF A PROTEIN: U AUG UCCGUCA IN FRAME -1 , SEQUENCE IS READ AS: Tyr-Val-Arg… IN FRAME 0, SEQUENCE IS READ AS Met -Ser-Ala… IN FRAME +1 , SEQUENCE IS READ AS: Cys-Pro-Ser 5. ADAPTOR: IN 1956, FRANCIS CRICK POINTED OUT THAT THERE WAS LIKELY TO BE AN ADAPTOR MOLECULE (NOW KNOWN AS tRNA) THAT COULD MEDIATE BETWEEN THE SEQUENCE ENCODED IN THE GENE AND AMINO ACIDS; CRICK POSTULATED THAT THIS WAS PROBABLY A SMALL RNA THAT CAN LINK TO AN AMINO ACID AND GUIDE IT TO A SPECIFIC CODON VIA COMPLEMENTARY INTERACTION WITH THE TEMPLATE (NOW KNOWN AS mRNA).
    • 2. FRAMESHIFT MUTATIONS FRAMESHIFT MUTATIONS STEM FROM THE ADDITION OR DELETION OF A BASE PAIR INDUCED BY THE INTERCALATION OR STACKING OF ACRIDINE DYES WITHIN THE REPLICATING DNA MOLECULE WILD-TYPE: AUG GUC CGU AAA…  Met-Val-Ala-Lys…… - 1: AUG GCC GUA AAU…  Met-Ala-Val-Asn…… +1: AUG GUC CAG UAA…  Met-Val-Gln-STOP -3 : AUG GCG AAA…  Met-Ala-Lys………… ±1: AUG GCC AGU AAA…  Met-Ala-Ser-Lys…...  ANALYSIS OF THE RELEVANT MUTANTS STRONGLY IMPLIED THAT GENETIC CODE IS READ IN GROUPS OF THREE NUCLEOTIDES FROM A FIXED STARTING POINT THE RESTORATION OF THE PROPER READING FRAME AFTER A SHORT SEQUENCE ALTERATION OFTEN RESULTS IN AN ACTIVE PROTEIN, WHEREAS LONG OUT-OF-FRAME SEQUENCES OFTEN LEAD TO A STOP CODON THESE EXPERIMENTS HELPED TO ESTABLISH THAT THE GENETIC CODE IS A DEGENERATE TRIPLET CODE WHICH MUST BE INITIATED IN THE CORRECT READING FRAME ON THE mRNA
    • 3. WEAVER: FIG. 18.4 REPEATING DINUCLEOTIDE SPECIFIES A REPEATING DIPEPTIDE REPEATING TRIPLETS SPECIFY THREE DIFFERENT HOMOPOLYPEPTIDES REPEATING TETRANUCLEOTIDE SPECIFIES REPEATING TETRAPEPTIDE CODING PROPERTIES OF SYNTHETIC mRNAs
    • 4. WEAVER: FIG. 18.5 BINDING OF LYSYL-tRNA TO RIBOSOMES IN RESPONSE TO VARIOUS CODONS
    • 5. CODONS RELATED TO THE AMBER CODON BY A SINGLE BASE CHANGE PERMITTED WEIGERT AND GAREN TO DEDUCE THE AMBER CODON SEQUENCE WEAVER: FIG. 18.33
    • 6. VOET & VOET: TABLE 30.2
    • 7. WEAVER: FIG. 18.7 WOBBLE BASE PAIRS
    • 8. WEAVER: FIG. 18.8 NORMAL AND WOBBLE BASE PAIRING BETWEEN mRNA CODONS AND tRNA ANTICODONS
    • 9. MORE ‘WOBBLE’ BASE PAIRS CRICK’S RULE: Anticodon Codon first letter third letter G U,C C G U A,G I U,C,A PRESENT RULE: Anticodon Codon first letter third letter G U,C C G k 2 C A A U,C,(A),G U U,(C),A,G U* A,(G) xo 5 U U,A,G I U,C,A
    • 10. WEAVER: TABLE 18.1 DEVIATIONS FROM THE ‘UNIVERSAL’ GENETIC CODE SOURCE CODON USUAL MEANING NEW MEANING Fruit fly mitochondria UGA Stop Tryptophan AGA,AGG Arginine Serine AUA Isoleucine Methionine Mammalian mitochondria AGA,AGG Arginine Stop AUA Isoleucine Methionine UGA Stop Tryptophan Yeast mitochondria CUN Leucine Threonine AUA Isoleucine Methionine UGA Stop Tryptophan Plant mitochondria UGA Stop Tryptophan CGG Arginine Tryptophan Protozoa cytoplasm UAA,UAG Stop Glutamine Mycoplasma UGA Stop Tryptophan
    • 11. EXPERIMENTAL STRATEGY FOR DETERMINING THE DIRECTION OF TRANSLATION WEAVER: FIG. 18.1 Isolate completed chains
    • 12. WEAVER: FIG. 18.2 DETERMINATION OF THE DIRECTION OF TRANSLATION
    • 13. VOET & VOET: FIG. 30.14 SECONDARY STRUCTURE OF tRNA Phe IN TYPICAL CLOVERLEAF PATTERN TERTIARY STRUCTURE OF tRNA Phe DETERMINED BY X-RAY CRYSTALLOGRAPHY
    • 14. WEAVER: FIG. 19.30 SOME OF THE MODIFIED BASES THAT OCCUR IN tRNA
    • 15. WEAVER: FIG. 19.31 SCHEME SHOWING HOW THE SECONDARY STRUCTURE OF tRNA ACHIEVES ITS THREE-DIMENSIONAL CONFORMATION THE VARIOUS PARTS OF THE MOLECULE ARE COLOR CODED TO SHOW THE PATTERN OF FOLDING
    • 16. VOET & VOET: FIG. 30.15 THE TERTIARY INTERACTIONS THAT STABILIZE THE 3D STRUCTURE OF tRNA
    • 17. VOET & VOET: FIG. 30.14 SECONDARY STRUCTURE OF tRNA Phe IN TYPICAL CLOVERLEAF PATTERN TERTIARY STRUCTURE OF tRNA Phe DETERMINED BY X-RAY CRYSTALLOGRAPHY
    • 18. tRNA IDENTITY THE ‘IDENTITY’ OF A tRNA MOLECULE IS DEFINED BY THE SET OF STRUCTURAL FEATURES AT THE PRIMARY, SECONDARY AND TERTIARY LEVELS THAT IS REQUIRED FOR RECOGNITION BY A LIGAND, AS WELL AS THE ANTIDETERMINANTS THAT PREVENT INTERACTION WITH THE INCORRECT PARTNER. THE NOTION OF tRNA IDENTITY WAS ORIGINALLY APPLIED TO tRNA:RS INTERACTIONS BUT IS USEFUL IN DESCRIBING ANY INTERACTION WITH ANOTHER MACROMOLECULE IN WHICH tRNA PARTICIPATES
    • 19. VOET & VOET: FIG. 30.17 tRNA IDENTITY MAIN FEATURES RECOGNIZED BY AMINOACYL-tRNA SYNTHETASES tRNA Ala : Acceptor Stem tRNA Asp : Antocodon D Stem tRNA Gln : Acceptor Stem, Anticodon tRNA Ser : Acceptor Stem, Variable Loop
    • 20. ANINOACYLATION ENTAILS TWO CONSECUTIVE REACTIONS: (1) RS CATALYZES FORMATION OF 5’-AMINOACYL AMP (2) RS TRANSFERS AMINOACYL MOIETY FROM AMP TO 2’ (CLASS I) OR 3’ (CLASS 2) HYDROXYL OF 3’-TERMINAL ADENOSINE OF tRNA TO FORM AMINOACYL-tRNA
    • 21. EDITING FUNCTION OF ILE-tRNA SYNTHETASE THE SYNTHETASE CAN ACTIVATE A NUMBER OF SIMILAR AMINO ACIDS BUT CANNOT ATTACH THE MIS-ACTIVATED AMINO ACID TO THE CORRESPONDING tRNA WEAVER: FIG. 19.38
    • 22. WEAVER: FIG. 19.36 TWO VIEWS OF THE THREE-DIMENSIONAL STRUCTURE OF GLUMTAMINYL-tRNA SYNTHETASE COMPLEXED WITH tRNA AND ATP
    • 23. WEAVER: FIG. 19.37 CRYSTALLOGRAPHIC STRUCTURE OF GlnRS-tRNA Gln , A CLASS I COMPLEX CRYSTALLOGRAPHIC STRUCTURE OF AspRS-tRNA Asp , A CLASS II COMPLEX
    • 24. WEAVER: FIG. 18.29 EF-Tu•AMINOACYL-tRNA COMPLEX EF-G
    • 25. WEAVER: FIG. 19.34 THE RIBOSOME RESPONDS TO THE IDENTITY OF THE CODON OF AMINOACYL-tRNA, NOT THE AMINO ACID

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