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Biochemistry Midterm II
N/A
32
Biochemistry
Undergraduate 3
03/02/2012

Additional Biochemistry Flashcards

 


 

Cards

Term
RNAP
Definition

DNA-DEPENDENT RNA POLYMERASE

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

Term
mRNA
Definition

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)

Term
rRNA
Definition

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

MAKES UP 85% OF TOTAL RNA

 

Term
tRNA
Definition
THE RNA THAT CARRIES AMINO ACIDS TO THE RIBOSOMES FOR TRANSLATION OF THE mRNA MESSAGE
Term
GENE
Definition

PORTION OF DNA MOLECULE THAT IS TRANSCRIBED

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

HASE 5'--> 3' DIRECTION

Term
RIFAMPICIIN
Definition

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

Term
ALPHA AMANATIN
Definition

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

Term
SIGMA 70
Definition

70 000

HOUSEKEEPING PROMOTER

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

Term
SIGMA 32
Definition

32 000

HEAT SHOCK PROMOTER

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

Term
UP-PROMOTER
Definition
MUTATIONS FOUND IN THESE REGIONS WILL INCREASE THE EFFICIENCY OF INITIATION IF THE MUTATION GIVES A SEQUENCE CLOSER TO CONSENSUS
Term
TATA BOX
Definition

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

FOUND AT -30

Term

TOPOISOMERASES

 

Definition
REMOVES THE NEGATIVE AND POSITIVE SUPERCOILS THAT ARE FORMED DURING TRANSCRIPTION
Term
PLASMIDS
Definition

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)

Term
DNAP
Definition

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

Term
REPLICON
Definition

THE ORIGIN PLUS GENES THAT ARE REPLICATED UNDER ITS CONTROL

(IN E.COLI)

Term
PROCESSIVITY
Definition

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

 

Term
DNAP I
Definition

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

Term
ERROR RATE
Definition

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

Term
KLENOW FRAGMENT
Definition

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

Term
DNA UNWINDING ELEMENT (DUE)
Definition

CONTAINS 3 NEARLY IDENTICAL 13 NUCLEOTIDE SEQUENCES

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

Term
HELICASE
Definition

EX DNAB

HELICASES ARE CLASSES OF PROTEINS THAT UNWIND DOUBLE STRANDED DNA

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

Term
SSB (SINGLE STRANDED BINDING PROTEINS)
Definition
AS THE DNAB HELICASES UNWIND THE DOUBLE HELIX, SSB PROTIENS BIND TO DNA AND STABILIZE THE SINGLE STRANDED DNA (PREVENTS RE-ANNEALING, PREVENTS FORMATION OF STEM LOOPS AND PROTECTS FROM NUCLEASES)
Term
DNA GYRASE (DNA TOPOISOMERASE II)
Definition
RELIEVES THE TOPOLOGICAL STRESS INDUCED AHEAD OF THE FORK BY THE UNWINDING REACTION
Term
PRIMOSOME
Definition

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

PRIMOSOME= DNAB HELICASE + PRIMASE (DNAG)

 

Term

NICK TRANSLATION

 

Definition

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)

Term
TUS (TERMINUS UTILIZATION SUBSTANCE)
Definition

BINDS TO THE TER SEQUENCES

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

 

Term
5' CAP
Definition

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

Term
3' POLY A TAIL
Definition

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

Term
CONSTITUTIVE GENES
Definition
HOUSEKEEPING GENES THAT ARE EXPRESSED CONTINUOUSLY (EX. GLYCOLYSIS ENZYMES)
Term
INDUCIBLE OR REPRESSIBLE GENES
Definition

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)

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