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GENERAL PROPERTIES OF THE GENETIC CODE
1. MULTIPLICITY: A DOUBLET CODE CAN ONLY SPECIFY 16 DIFFERENT AMINO ACDS WHILE ATRIPLET CODE CAN SPECIFY 64. NUCLEOTIDE TRIPLETS ARE THE MINIMUM THAT CAN RECOGNIZE20 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, UAAAND UGA WHICH ARE TERMINATION OR STOP CODONS.
3. NONOVERLAPPING: EXAMPLES OF NONOVERLAPPING AND OVERLAPPING TRIPLET CODESNONOVERLAPPING: 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 AMECHANISM TO ‘PHASE’ THE READING MECHANISM TO ONE OF THE 3 POSSIBLE READING FRAMESTHROUGH THE CHOICE OF A SPECIFIC INITIATION CODON (AUG).SEQUENCE SPECIFYING A SEGMENT OF A PROTEIN: UAUGUCCGUCA 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 ADAPTORMOLECULE (NOW KNOWN AS tRNA) THAT COULD MEDIATE BETWEEN THE SEQUENCE ENCODED INTHE 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 INTERACTIONWITH THE TEMPLATE (NOW KNOWN AS mRNA).
FRAMESHIFT MUTATIONS
FRAMESHIFT MUTATIONS STEM FROM THE ADDITION OR DELETION OF A BASE PAIR INDUCED BYTHE 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 INGROUPS OF THREE NUCLEOTIDES FROM A FIXED STARTING POINT
THE RESTORATION OF THE PROPER READING FRAME AFTER A SHORT SEQUENCE ALTERATIONOFTEN 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 DEGENERATETRIPLET CODE WHICH MUST BE INITIATED IN THE CORRECT READING FRAME ON THE mRNA
REPEATING DINUCLEOTIDE SPECIFIES A REPEATING DIPEPTIDEREPEATING TRIPLETS SPECIFY THREE DIFFERENT HOMOPOLYPEPTIDESREPEATING TETRANUCLEOTIDE SPECIFIES REPEATING TETRAPEPTIDE
CODING PROPERTIES OF SYNTHETIC mRNAs
WEAVER: FIG. 18.4
BINDING OF LYSYL-tRNA TO RIBOSOMES IN RESPONSE TO VARIOUS CODONS
WEAVER: FIG. 18.5
CODONS RELATED TO THE AMBER CODON BY A SINGLE BASE CHANGEPERMITTED WEIGERT AND GAREN TO DEDUCE THE AMBER CODON SEQUENCE
WEAVER: FIG. 18.33
VOET & VOET: TABLE 30.2
WOBBLE BASE PAIRS
WEAVER: FIG. 18.7
NORMAL AND WOBBLE BASE PAIRING BETWEENmRNA CODONS AND tRNA ANTICODONS
WEAVER: FIG. 18.8
MORE ‘WOBBLE’ BASE PAIRS
CRICK’S RULE:Anticodon Codonfirst letter third letterG U,CC GU A,GI U,C,A
PRESENT RULE:Anticodon Codonfirst letter third letterG U,CC Gk2C AA U,C,(A),GU U,(C),A,GU* A,(G)xo5U U,A,GI U,C,A
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 GlutamineMycoplasma UGA Stop Tryptophan
WEAVER: TABLE 18.1
EXPERIMENTAL STRATEGY FOR DETERMINING THE DIRECTION OF TRANSLATION
WEAVER: FIG. 18.1
Isolatecompletedchains
DETERMINATION OF THE DIRECTION OF TRANSLATION
WEAVER: FIG. 18.2
SECONDARY STRUCTURE OF tRNAPhe
IN TYPICAL CLOVERLEAF PATTERNTERTIARY STRUCTURE OF tRNAPhe
DETERMINED BY X-RAY CRYSTALLOGRAPHY
VOET & VOET: FIG. 30.14
SOME OF THE MODIFIED BASES THAT OCCUR IN tRNA
WEAVER: FIG. 19.30
SCHEME SHOWING HOW THE SECONDARY STRUCTURE OF tRNA ACHIEVESITS THREE-DIMENSIONAL CONFORMATION
THE VARIOUS PARTS OF THE MOLECULE ARE COLOR CODED TO SHOW THE PATTERN OF FOLDING
WEAVER: FIG. 19.31
THE TERTIARY INTERACTIONS THAT STABILIZE THE 3D STRUCTURE OF tRNAVOET & VOET: FIG. 30.15
SECONDARY STRUCTURE OF tRNAPhe
IN TYPICAL CLOVERLEAF PATTERNTERTIARY STRUCTURE OF tRNAPhe
DETERMINED BY X-RAY CRYSTALLOGRAPHY
VOET & VOET: FIG. 30.14
tRNA IDENTITY
THE ‘IDENTITY’ OF A tRNA MOLECULE IS DEFINED BY THE SET OF STRUCTURALFEATURES AT THE PRIMARY, SECONDARY AND TERTIARY LEVELS THAT IS
REQUIRED FOR RECOGNITION BY A LIGAND, AS WELL AS THE ANTIDETERMINANTSTHAT PREVENT INTERACTION WITH THE INCORRECT PARTNER.
THE NOTION OF tRNA IDENTITY WAS ORIGINALLY APPLIED TOtRNA:RS INTERACTIONS BUT IS USEFUL IN DESCRIBING ANY INTERACTION
WITH ANOTHER MACROMOLECULE IN WHICH tRNA PARTICIPATES
tRNA IDENTITY
MAIN FEATURES RECOGNIZED BYAMINOACYL-tRNA SYNTHETASES
tRNAAla: Acceptor Stem
tRNAAsp: Antocodon D Stem
tRNAGln: Acceptor Stem, Anticodon
tRNASer: Acceptor Stem, Variable Loop
VOET & VOET: FIG. 30.17
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
EDITING FUNCTION OF ILE-tRNA SYNTHETASETHE 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
TWO VIEWS OF THE THREE-DIMENSIONAL STRUCTURE OFGLUMTAMINYL-tRNA SYNTHETASE COMPLEXED WITH tRNA AND ATP
WEAVER: FIG. 19.36
CRYSTALLOGRAPHIC STRUCTURE OFGlnRS-tRNAGln, A CLASS I COMPLEX
CRYSTALLOGRAPHIC STRUCTURE OFAspRS-tRNAAsp, A CLASS II COMPLEX
WEAVER: FIG. 19.37
EF-Tu•AMINOACYL-tRNA COMPLEX EF-G
WEAVER: FIG. 18.29
THE RIBOSOME RESPONDS TO THE IDENTITY OF THE CODONOF AMINOACYL-tRNA, NOT THE AMINO ACID
WEAVER: FIG. 19.34