DNA-DEPENDENT RNA POLYMERASE

COPIES ONE OF THE STRANDS BY MATCHING THE DNA BASES WITH RNA BASES THRU COMPLEMENTARY BASE PAIRING

RNA THAT IS MADE TO DIRECT PROTEIN SYNTHESIS

MAKES UP A VERY SMALL PROPORTION

1-3%

HAS A VERY SHORT HALF-LIFE (2 OR 3 MINS IN PROKARYOTES AND 10 HRS IN EUKARYOTES)

THE RNA THAT MAKES UP THE RIBOSOMES IN BOTH PROKARYOTIC AND EUKARYOTIC

MAKES UP 85% OF TOTAL RNA

PORTION OF DNA MOLECULE THAT IS TRANSCRIBED

BEGINS AT THE POINT WHERE TRANSCRIPTION BEGINS (+1 NUCLEOTIDE)

HASE 5'--> 3' DIRECTION

ANTIBIOTIC

DETERMINED THAT RNAP CATALYZES THE SYNTHESIS OF ALL 3 TYPES OF RNA

IT INHIBITS SYNTHESIS OF ALL 3 TYPES OF RNA BOTH IN VIVO AND IN VITRO

A MUTANT WAS FOUND WHICH WAS RESISTANT TO RIFAMPICIN- MUTATION WAS IN GENE FOR RNAP

AND THIS MUTANT COULD SYNTHESIZE ALL TYPES OF RNA IN PRESENCE OF RIFAMPICIN THEREFORE RNAP MUST BE THE ENZYME THAT CATALYZES ALL 3

A TOXIN IN AMANITA MUSHROOM

HELPED SHOWED THAT THERE WERE 3 RNA POLYMERASES IN EUKARYOTES

BINDS TIGHTLY TO RNAP II THUS BLOCKING THE SYNTHESIS OF mRNA (BLOCKS ELOGNATION PHASE)

THE OTHER RNAP'S ARE NOT INHIBITED

70 000

HOUSEKEEPING PROMOTER

USED FOR SYNTHESIS OF RNA WHICH CODES FOR PROTEINS NEEDED IN THE DAY TO DAY RUNNING OF THE CELL

32 000

HEAT SHOCK PROMOTER

IT IS ONLY TURNED ON WHEN E. COLI NEEDS TO RECOVER FROM STRESS INDUCED BY INCREASED TEMPERATURE

THE MAJOR ASSEMBLY POINT FOR THE PROTEINS OF THE PRE-INITIATION COMPLEXES IN POL II

FOUND AT -30

TOPOISOMERASES

HAVE THEIR OWN ORiR AND REPLICATE INDEPENDENTLY

CAN BE MANY COPIES IN EACH CELL

SOME CONFER RESISTANCE TO ANTIBIOTICS (LACTAMASE) OR CONFER DEFENSE AGAINST OTHER BACTERIA(BACTERIOCINS)

SOME ARE CALLED EPISOMES (UNDER INTEGRATION INTO THE HOST CHROMOSOME AND THEN REPLICATE IN SYNCHRONY WITH THE HOST)

SYNTHESIS OF A NEW DNA CHAIN USING A TEMPLATE OF DNA

USES COMPLEMENTARITY

REQUIRES (TEMPLATE, PRIMER, dNTP'S)

5' --> 3' DIRECTION (MAKES A PHOSPHODIESTER BOND)

NEW CHAIN IN THE ANTI-PARALLEL DIRECTION

ADDS dNTP'S TO AN EXISTING CHAIN WITH A FREE 3' OH GROUP

THE ORIGIN PLUS GENES THAT ARE REPLICATED UNDER ITS CONTROL

(IN E.COLI)

THE AVERGAE NUMBER OF NUCLEOTIDES ADDED BEFORE A POLYMERASE DISSOCIATES

(EX. THE ABILITY OF A POLYMERASE TO REMAIN ATTACHED TO A GIVEN TEPLATE AND REPLICATE IT RIGHT TO THE END)

DNAP III HAS VERY HIGH PROCESSIVITY DUE TO THE BETA SUBUNITS

HAS PROF-READING FUNCTION

WORKS BY...

WHEN THE ENZYME FINDS A MISPAIR, IT RETREATS, THE 3' EXONUCLEASE REMOVES THE LAST BASE AND THE POLYMERASE THEN TRIES AGAIN TO GET A CORRECT ONE

THE BASE SELECTION (POLYMERIZATION) FUNCTION OF THIS ENZYME HAS A VERY LOW ERROR RATE, ABOUT 10-4

THE 3' --> 5' EXONUCLEASE HAS AN ERROR RATE OF 10-3

ALTOGETHER THE DNAP LEAVES A 1 NET ERROR FOR EVERY 107 BASES

PROTEOLYSIS OF DNAP I SPLITS IT INTO TWO FRAGMENTS

1. LARGE FRAGMENT= KLENOW FRAGMENT

-CONTAINS THE POLYMERASE AND THE 3' EXONUCLEASE ACTIVITY

2. SMALL FRAGMENT- 5' --> 3' EXONUCLEASE

CONTAINS 3 NEARLY IDENTICAL 13 NUCLEOTIDE SEQUENCES

ALL STARTING WITH GATC AND RICH IN A=T BASE PAIRS

EX DNAB

HELICASES ARE CLASSES OF PROTEINS THAT UNWIND DOUBLE STRANDED DNA

HELICASES ARE ATP DEPENDENT BECAUSE OF THE STABILITY OF THE DOUBLE HELIX

AFTER RECOGNITION OF THE ORIGIN AND OPENING OF THE HELIX, PRIMER SYNTHESIS IS MEDIATED BY A PROTEIN ASSEMBLY

PRIMOSOME= DNAB HELICASE + PRIMASE (DNAG)

NICK TRANSLATION

THE 5' EXONUCLEASE REMOVES THE RNA PRIMER, ONE BASE AT A TIME

WHIEL THE POLYMERASE FILLS IN THE CORREST DNA BASES

BECAUSE IT BEGINS AT A NICK, AND A NICK REMAINS WHERE DNAP I EVENTUALLY DISSOCIATES (LATE SEALED BY LIGASE)

BINDS TO THE TER SEQUENCES

THE TUS-TER COMPLEX ARRESTS A REPLICATION FORK (ESSENTIALLY BLOCKS THE DNAP COMPLX AS IT COMES AROUND)

A RESIDUE OF 7-METHYL GUANOSINE IS LINKED TO THE 5'-TERMINAL RESIDUE OF THE mRNA THROUGH AN UNUSUAL 5' TO 5' TRIPOSPHATE LINKAGE

NEXT TWO BASES ARE METHYLATED VIA SAM PATHWAY

THE FUNCTION OF THE 5' CAP IS

1. PROTECT THE mRNA FROM RIBONUCLEASES

2. PARTICIPATES IN BINDING OF mRNA TO RIBOSOME TO INITIATE TRANSLATION

POL II SYNTHESIZES RNA BEYOND THE SEGMENT OF THE TRANSCRIPT CONTAINING THE CLEAVAGE SIGNAL SEQUENCES, INCLDING THE HIGHLY CONSERVED UPSTREAM SEQUENCE (5') AAUAAA

RNA IS CLEAVED BY THE ENDONUCLEASE AT A POINT 10 TO 30 NUCLEOTIDES 3' TO (DOWNSTREAM OF) THE SEQUENCE AAUAAA

POLYADENYLATE POLYMERASE SYNTHESIZES A POLY A TAIL 80 TO 250 NUCLEOTIDES LONG, BEGINNING AT THE CLEAVAGE SITE

ENCODE GENE PRODUCTS WHOSE CELLULAR LEVELS RISE AND FALL IN RESPONSE TO MOLECULER SIGNALS (EX. REGULATED GENE EXPRESSION)

ARE GENES TAHT CODE FOR INDUCIBLE OR REPRESSIBLE ENZYMES/GENE PRODUCTS (EX. ENZYMES TO USE LACTOSE)