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