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TRANSCRIPTION

TRANSCRIPTION. A MESSENGER RNA ( m RNA) BE I NG MADE ON A DNA TEMPLATE WHICH D I RECT S THE SYNTHES I S OF SPEC I F I C PROTE I NS I N ASSOC I AT I ON W I TH R I BOSOMES. THE GENET I C CODE I S: 1. W R I TTEN I N L I NEAR FORM 2. RNA DER I VED FROM COMPLEMENTARY BASES I N DNA

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TRANSCRIPTION

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  1. TRANSCRIPTION

  2. A MESSENGERRNA (mRNA) BEING MADE ON A DNA TEMPLATE WHICH DIRECTS THE SYNTHESIS OF SPECIFIC PROTEINS IN ASSOCIATION WITH RIBOSOMES

  3. THE GENETIC CODE IS: 1. WRITTEN IN LINEAR FORM 2.RNA DERIVED FROM COMPLEMENTARYBASES IN DNA 3.IN mRNA, TRIPLET CODONSSPECIFY 1AMINO ACID 4. CODE CONTAINS “START” AND “STOP” SIGNALS 5. UNAMBIGUOUS- EACH TRIPLET SPECIFIES ONLY A SINGLE AMINO ACID

  4. THE GENETIC CODE IS: 6. DEGENERATE-A GIVEN AMINO ACID CAN BE SPECIFIED BY MORE THAN ONE TRIPLET CODON 7. COMMALESS-NO INTERNAL BREAKS USED IN THE CODE 8. NON-OVERLAPPING-ANY SINGLE RIBONUCLEOTIDE WITHIN THE mRNA IS PART OF ONLY ONE TRIPLET 9. NEARLY UNIVERSAL-WITH MINOR EXPECTIONS SINGLE CODING DICTIONARY IS USED BY ALL ORGANISMS

  5. GENETIC CODE ISDEGENERATE, MANY AMINOACIDS SPECIFIEDBYMORE THAN ONECODON ONLYTRYPTOPHANANDMETHIONINEARE ENCODEDBY ASINGLECODON THE GENETIC CODE SHOWS AN ORDER IN THAT CHEMICALLY SIMILAR AMINOACIDS OFTEN SHARE ONE OR TWOMIDDLE BASES IN THE TRIPLETSENCODING THEM

  6. INITIATOR CODON“AUG”IS THE ONLYCODON TO ENCODE FORMETHIONINE WHEN AUG APPEARS INTERNALLY IN mRNA, METHIONINE IS INSERTED INTOTHEPROTEIN IN BACTERIA THE INITIAL AMINO ACID INCORPORATED INTO ALL PROTEINS ISA MODIFIED FORM OF METHIONINE-N-formylmethionine (fmet) THREE CODONS (UAG, UAA, AND UGA)SERVEAS TERMINATION CODONSAND DONOTCODE FOR ANY AMINO ACID

  7. WOBBLEHYPOTHESIS PREDICTS THAT HYDROGEN BONDING BETWEEN THECODON AND ANTICODON AT THE THIRD POSITION IS SUBJECT TO MODIFIED BASE-PAIRING RULES

  8. tRNA(1st)mRNA(3rd) A U C G G C,U U A,G I A,U,G

  9. THE GENETIC CODE IS NEARLY UNIVERSAL MITOCHONDRIAL DNA REVEALED SOME EXCEPTIONS TO THE UNIVERSAL GENETIC CODE

  10. mRNA SERVES AS THE INTERMEDIATE MOLECULEBETWEEN DNA ANDPROTEINS mRNAIS SYNTHESIZED ON A DNATEMPLATE DURING TRANSCRIPTION

  11. TRANSCRIPTION

  12. RNA POLYMERASEDIRECTS THE SYNTHESIS OF RNAUSING A DNA TEMPLATE RNA POLYMERASEHAS SOME EXCEPTIONS; * THESUBSTRATENUCLEOTIDES CONTAIN THE RIBOSE RATHER THAN THE DEOXYRIBOSEFORM OF THE SUGAR * UNLIKE DNA POLYMERASE, NO PRIMER IS REQUIREDTO INITIATE SYNTHESIS

  13. RNA POLYMERASE RNA POLYMERASE FROM E. coliHAS BEEN EXTENSIVELYCHARACTERIZEDANDSHOWN TO CONSIST OF SUBUNITSDESIGNATEDα, β, β’, ω AND σ THECOMPLEX, ACTIVE FORM OF THE ENZYME, THE HOLOENZYME,CONTAINS THESUBUNITSα2, β, β’AND σ AND HASA MOLECULARWEIGHT OF ALMOST500,000Da OF THESE SUBUNITS, IT IS THE βandβ’, POLYPEPTIDES THATPROVIDE THECATALYTICMECHANISM ANDACTIVE SITE FORTRANSCRIPTION

  14. RNA POLYMERASE THE σ (sigma) FACTOR PLAYS AREGULATORY FUNCTION INTHE INITIATIONOFRNA TRANSCRIPTION EUKARYOTES DISPLAY THREE DISTINCT FORMS OFRNAPOLYMERASE, EACH CONSISTING OFGREATER NUMBER OF POLYPEPTIDE SUBUNITSTHAN INBACTERIA

  15. PROMOTERS, TEMPLATE BINDING AND SIGMA SUBUNIT THE RNA POLYMERASE SIGMA (σ) SUBUNIT RECOGNIZES SPECIFICDNA SEQUENCES CALLED PROMOTERS THESESEQUENCES ARE LOCATED INTHE 5’ REGION, UPSTREAMFROM THE POINT OF INITIAL TRANSCRIPTION OF A GENE

  16. WHEN THE ENZYME ENCOUNTERS APROMOTER REGION AND BINDS THERE TOABOUT 60NUCLEOTIDE PAIRS ALONG THEHELIX, 40 OFWHICHARE UPSTREAM FROMTHEPOINT OF INITIALTRANSCRIPTION ONCE THIS OCCURS, THE HELIX IS DENATURED ORUNWOUND,LOCALLY, MAKING THETEMPLATE STRAND OF THE DNAACCESSIBLETO THE ACTION OF THE ENZYME THE POINT ATWHICH TRANSCRIPTIONACTUALLY BEGINS ISCALLED THETRANSCRIPTIONSTART SITE

  17. TWO CONSENSUSSEQUENCES HAVE BEENFOUND IN BACTERIALPROMOTERS: 1.-TATAAT- WHICH IS LOCATED 10NUCLEOTIDESUPSTREAM FROM THE SİTE OF INITIALTRANSCRIPTION (THE -10REGION OR PRIBNOW BOX) 2. -TTGACA- IS LOCATED 35 NUCLEOTIDESUPSTREAM (THE -35 REGION) MUTATIONS IN EITHERREGION DIMINISH TRANSCRIPTION

  18. CONSENSUS SEQUENCESARE SIMILAR (HOMOLOGOUS) INDIFFERENT GENES OF THESAME ORGANISM OR INONE OR MORE GENES OF RELATEDORGANISMS THEIRCONSERVATION DURING EVOLUTION ATTESTSTO THE CRITICAL NATURE OF THEIR ROLE INBIOLOGICAL PROCESSES

  19. SEQUENCES WHICH ARE LOCATED IN THE REGIONS ADJACENT TO THE GENE ITSELF ARE NAMED ASCIS-ACTING ELEMENTS IN MOLECULARGENETICS, CIS-ELEMENTSARE ADJACENT PARTS OF THESAME DNAMOLECULE IN CONTRAST, TRANS-ACTING FACTORSARE MOLECULESTHAT BIND TO THESE DNA ELEMENTS

  20. IN MOST EUKARYOTIC GENES STUDIED, A CONSENSUS SEQUENCE COMPARABLE TO THAT IN THE -10REGION HAS BEEN RECOGNIZED IT IS RICH IN ADENINEANDITHYMINERESIDUES, IT IS CALLED THE TATABOX

  21. THE DEGREE OF RNA POLYMERASEBINDING TODIFFERENT PROMOTERS VARIESGREATLY, CAUSINGVARIABLE GENEEXPRESSION INBACTERIA, BOTH STRONG PROMOTERS ANDWEAK PROMOTERSHAVE BEEN DISCOVERED Ex:VARIATION IN TIME OF INITIATION FROM ONCE EVERY 1 TO 2 SECONDS TO ONCE EVERY 10 TO 20 MINUTES

  22. PROMOTER EFFICIENCY IS ASSOCIATED WITH THE σ (sigma) SUBUNIT OF RNA POLYMERASE THE MAJOR FORM WHICH PROMOTERS OF MOST BACTERIAL GENES RECOGNIZE IS THE σ70(MW 70 kDa) SEVERAL ALTERNATIVE FORMS OF RNAPOLYMERASE IN E. coli HAVEUNIQUEσ SUBUNITSASSOCIATED WITH THEM (ex: σ34, σ54, σSAND σE) EACH FORM RECOGNIZES DIFFERENT PROMOTER SEQUENCES, WHICH IN TURNPROVIDES SPECIFICITY TO THE INITIATION OFTRANSCRIPTION

  23. INITIATION, ELONGATION AND TERMINATION OF RNA SYNTHESIS RNA POLYMERASE CATALYZES INITIATION, THE INSERTIONOF THEFIRST5-RIBONUCLEOSIDE TRIPHOSPHATE,WHICH ISCOMPLEMENTARY TO THEFIRST NUCLEOTIDEATTHE STARTSITE OF THE DNA TEMPLATE STRAND SUBSEQUENTRIBONUCLEOTIDECOMPLEMENTS ARE INSERTED ANDLINKED TOGETHER BY PHOSPHODIESTERBONDS AS RNA POLYMERIZATIONPROCEEDS (5 TO 3 DIRECTION)

  24. ONCE INITIATION HAS BEEN COMPLETED WITH THE SYNTHESIS OF THE FIRST 8–9 NUCLEOTIDES, SIGMA (σ) DISSOCIATES AND ELONGATION PROCEEDS WITH THE CORE ENZYME

  25. THE ENZYME TRAVERSES THE ENTIRE GENE UNTIL IT ENCOUNTERSA SPECIFICNUCLEOTIDE SEQUENCE THATACTS AS ATERMINATIONSIGNAL (40bp LONG) THE UNIQUE SEQUENCE OF NUCLEOTIDES IN THIS TERMINATION REGIONCAUSES THE NEWLY FORMEDTRANSCRIPT TO FOLD BACK ON ITSELF, FORMINGA HAIRPIN SECONDARY STRUCTURE, HELDTOGETHER BYHYDROGEN BONDS IN SOME CASES, TERMINATION DEPENDS ON THE RHO ()TERMINATION FACTOR

  26. THE SYNTHESIZED RNA MOLECULE ISPRECISELY COMPLEMENTARYTO THE DNASEQUENCE OF THE TEMPLATE STRAND OF THEGENE WHEREVERAN A, T, C, OR G RESIDUE WAS ENCOUNTERED THERE, A CORRESPONDING U, A, G, OR C RESIDUE, RESPECTIVELY, WAS INCORPORATED INTO THE RNA MOLECULE

  27. GENES IN BACTERIAARE SOMETIMES CALLED CISTRONS, THE mRNA IS CALLED A POLYCISTRONIC mRNA THE PRODUCTS OF GENES TRANSCRIBED IN THIS FASHION ARE USUALLYNEEDED BY THE CELL AT THE SAME TIME IN EUKARYOTES, MONOCISTRONIC mRNAsARE THE RULE

  28. TRANSCRIPTION IN EUKARYOTES DIFFERS FROM PROKARYOTIC TRANSCRIPTION IN SEVERAL WAYS OCCURS IN NUCLEUS AND IS NOT COUPLED TO TRANSLATION REQUIRES CHROMATIN REMODELING IN ADDITION TO PROMOTERS, ENHANCERS ALSO INFLUENCETRANSCRIPTION REGULATION EUKARYOTIC mRNAs REQUIRE PROCESSING TO PRODUCEMATURE mRNAs

  29. EUKARYOTES POSSESS THREE FORMS OF RNA POLYMERASE EACH OF WHICH TRANSCRIBES DIFFERENT TYPES OF GENES

  30. RNA POLYMERASE II (RNP II)IS THE ENYZME RESPONSIBLE FOR THE PRODUCTION OF ALL mRNAs IN EUKARYOTES THE ACTIVITY OF RNP II IS DEPENDENT UPON BOTH CIS-ACTING ELEMENTS IN THE GENE ITSELF AND A NUMBER OF TRANS ACTING TRANSCRIPTION FACTORS THAT BIND TO THESE DNA ELEMENTS

  31. AT LEAST THREE CIS-ACTING DNA ELEMENTS REGULATE THE INITIATION OF TRANSCRIPTION BYRNP II THE FIRST OF THESESEQUENCES, CALLEDA CORE-PROMOTER ELEMENTDETERMINESWHERE RNP II BINDS TO THE DNA AND WHERE ITBEGINS COPYING THEDNA INTO RNA THE OTHER TWO TYPES OF REGULATORY DNA SEQUENCES: PROMOTERAND ENHANCERELEMENTS THEY INFLUENCETHE EFFICIENCY OR THERATE OF TRANSCRIPTIONBY RNP II AS THEPROCESS PROCEEDS FROM THE COREPROMOTER ELEMENT

  32. IN MOST OF THE GENES THE CIS-ACTING CORE-PROMOTERELEMENT IS THE GOLDBERG–HOGNESSOR TATA BOX PRESENT IN ALMOSTALL EUKARYOTICGENES LOCATED ABOUT 35 NUCLEOTIDE PAIRS UPSTREAM (-35) FROMTHE START POINT OFTRANSCRIPTION THE TATA BOXES SHARE ACONSENSUS SEQUENCE -TATAAAA-

  33. TATA BOX THESEQUENCE AND FUNCTION ARE ANALOGOUSTO THATFOUND IN THE -10PROMOTER REGION OF PROKARYOTICGENES BECAUSE THIS REGION IS COMMON TO MOST EUKARYOTICGENES, THE TATABOX IS THOUGHT TO BE NONSPECIFIC ANDTO BE RESPONSIBLE ONLY FOR FIXINGTHE SITE OFTRANSCRIPTION INITIATION BY FACILITATING DENATURATIONOFTHE HELIX (A=T BASEPAIRS ARELESS STABLE THAN G≡CPAIRS)

  34. ANOTHER CIS-ACTING DNA SEQUENCE IS THE CAATBOX THIS CONSENSUS SEQUENCE “GGCCAATCT”IS LOCATED UPSTREAM(IN THE 5 REGION) OFTHE GENEATABOUT 80 NUCLEOTIDES FROM THE START OFTRANSCRIPTION (-80) OTHERUPSTREAM REGULATORY REGIONSHAVE BEENFOUNDAND MOST GENES CONTAIN ONE OR MOREOFTHEMTHEY INFLUENCE THE EFFICIENCY OF THEPROMOTER, ALONGWITH THETATA BOX AND CAAT BOX

  35. DNA REGIONS CALLED ENHANCERS REPRESENT ANOTHER CIS-ACTING ELEMENT ALTHOUGH THEIR LOCATIONS CAN VARY, ENHANCERS ARE OFTEN FOUNDFURTHER UPSTREAM THAN THE REGIONS ALREADY MENTIONED, OR EVENDOWNSTREAM OR WITHIN THE GENE

  36. TRANS-ACTING FACTORS ARE OTHER TYPE OF REGULATORY SEQUENCES THATFACILITATE RNPII BINDING (THE INITIATION OFTRANSCRIPTION) THESE AREPROTEINS REFERRED TO ASTRANSCRIPTIONFACTORS THERE ARE TWO BROAD CATEGORIES OF TRANSCRIPTIONFACTORS: • THE GENERAL TRANSCRIPTION FACTORS THAT ARE ABSOLUTELY REQUIREDFOR ALL RNP II–MEDIATED TRANSCRIPTION • THE SPECIFIC TRANSCRIPTION FACTORS THAT INFLUENCE THE EFFICIENCY AND THE RATE OF RNPII MEDIATED TRANSCRIPTION

  37. THE GENERAL TRANSCRIPTION FACTORSARE ESSENTIAL BECAUSE RNA POLYMERASE II CANNOT BIND DIRECTLY TO EUKARYOTIC PROMOTERSITES AND INITIATE TRANSCRIPTION WITHOUT THEIR PRESENCE THE GENERALTRANSCRIPTION FACTORS INVOLVED WITH HUMAN RNPII ARE WELLCHARACTERIZED AND NAMED ASTFIIA,TFIIB, AND SOON…. ONE OFTHESE, TFIID,BINDS DIRECTLY TO THE TATA-BOX SEQUENCE TFIID CONSISTSOF ABOUT 10 POLYPEPTİDE SUBUNITS, ONE OF WHICH ISSOMETIMESCALLED THE TATA-BINDING PROTEIN (TBP) ONCE INITIAL BINDING TODNA OCCURS, AT LEAST SEVEN OTHER GENERALTRANSCRIPTION FACTORS BINDSEQUENTIALLY TO TFIID, FORMING ANEXTENSIVEPRE-INITIATION COMPLEX,WHICH IS THEN BOUND BY RNAPOLYMERASE II

  38. KORNBERG, FOUND OUT THAT RNA POLYMERASEII IN YEAST CONTAINS TWO LARGE SUBUNITS AND TEN SMALLER ONES, FORMING A HUGE THREEDIMENSIONAL COMPLEX WITH A MOLECULAR WEIGHT OF ABOUT 500 kDa.

  39. IN BACTERIA, THE RELATIONSHIP BETWEEN DNA AND mRNAAPPEARS TO BE QUITEDIRECT THE DNA BASESEQUENCE IS TRANSCRIBED INTO AN mRNASEQUENCEWHICH IS THEN IMMEDIATELY TRANSLATED INTO AN AMINO ACID SEQUENCE ACCORDING TO THE GENETIC CODE IN EUKARYOTES, BYCONTRAST, THERNA MUST UNDERGOSIGNIFICANTPROCESSING BEFORE BEINGTRANSPORTEDTO THECYTOPLASM AS mRNA TOPARTICIPATE INTRANSLATION

  40. HETEROGENEOUS NUCLEAR RNA (hnRNA) IS POSTTRANSCRIPTIONALY PROCESSED BY THE ADDITION OF A 5' 7-METHYLGUANOSINE CAP AND A POLY-A TAIL INTRONS ARE REMOVED BY SPLICING EXONS SPLICED TOGETHER

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