DNA polymerase

-polymerizes deoxyribonucleotides into DNA

-can only work in one direction

-can add deoxyribonucleotides to only the 3' end of the growing DNA chain 

Deoxyribonucleoside triphosphates

(dNTPs)

-have high PE

make the formation of phosphodiester bonds in a growing DNA strand exergonic

Origin of replication

bacterial chroms have single location

eukaryotes have multiple sites along each chrom where DNA sythesis occurs

bidirection

occurs in both direction at the same time

(sythesis)

Replication bubble

grows as DNA replication proceeds

-once opens a different suit of enzymes takes over and initiates the rxn

replication fork

-corner of each replication bubble

-Y shaped region where the parent DNA double helix is split into 2 single strands (which are then copied)

Helicase

breaks down the H bonds btwn deoxyribonucleotides

"unzips" the DNA (unzipping occurs at the replciation fork)

Single Strand DNA binding proteins

(SSBPS)

-attach to the separated strands and prevent them from snapping back into a double helix 

-make both strands available for copying

-stabilizes single stranded DNA

Topoisomerase

 -release tension so doesnt wind back up

-cuts the DNA allows it to unwind and rejoins it ahead of the advancing replication fork

-breaks and rejoins the DNA double helix to relieve twisting forces cause by opeing of helix

-DNA poly requires a primer bc it porivdes a 3' hydroxyl that can combine w/an incoming dNTP to form phosophodiester bond

look at the pictures

primer

contsists of a few tecleotides bonded to the template strand

DNA requires it; primase and other RNA pol do not

primase

enzyme that has to synthesize a short stretch of RNA that acts as a primer for DNA polymerase

leading/continuous strand

enzyme product

leads into the replication fork and is synthesized continuously

lagging(discontinuous) strand

-strand that is ynthesized in the opp direction of replication fork

-synthesis starts when primase synthesizes a short stretch of RNA that acts as a primer; DNA poly II then adds bases to the 3' end of the primer

Discontinuous replication hypothesis

-once primas synthesizes an RNA primer on the laggin strand DNA polymerase might synthesize short fragments of DNA along the lagging strand

-these fragments would later be linked together to form a continuous whole

okazaki fragments

 short segment of DNA produced during replication of the 5' to 3' template strand

-many make up the lagging strand in newly synthesized DNA

-synthesized independently and joined togehter later

DNA ligase

enzyme that catalyzes the formation of phosphodiester bond btwn adjacent fragments

primase

catalyzes the synthesis of the RNA primer

sliding clamp

holds the DNA poly in place during strand extension

DNA poly III (Leading strand synthesis)

extends the leading strand

Primase (lagging strand  synthesis)

catalyzes the syntheiss of the RNA primer on an Okazaki fragment

DNA Poly III (lagging strand  synthesis)

extends the Okazaki frament

DNA poly I (lagging strand  synthesis)

removes the RNA primer and replaces it with DNA

DNA ligase (lagging strand  synthesis)

catalyzes the joining of akazaki fragments into a continuous strand

Telomere

region at the end of linear chromosome

4 main problems with copying the ends of linear chromosomes

(1) DNA unwiding completed (helicase unwinds end of DNA helix @ end of chrom)

(2) Leading Strand Completed (DNA poly completes the leading strand; primase synthesizes RNA primer near end of lagging strand)

(3) Lagging Strand Completed (DNA poly synthesizes the last okazaki fragment in the lagging strand

(4) Lagging Strand Too Short (no  DNA synthesis occurs after primer is removed)

2 ways eukaryotes maintain integrity of their linear chromosomes?

(1) telomeres do not contain genes that code for products needed in the cell

(2) telomerase is involved in replicating telomeres

Telomerase

catalyzes the synthesis of DNA from RNA template

4 Steps of Telomere Replication

(1) End is unreplication

(2) Telomerase extends unreplicated end

(3) Telomerase extends unreplicated end (again)

(4) Laggin strand is completed

End is unreplicated (telomere replication)

when the RNA primer is removed from the 5' end of the lagging strand a strand of parent DNA remains unreplicated

Telomerase extends unreplicated end

(telomere replication)

-telomerase binds to the "overhauling" section of single stranded DNA

-telomerase adds deoxyribonucleotids to the end of the parent DNA, extending it

Telomerase extends unreplicated ends (again)

(telomere replication)

-telomerase moves down stran and adds additional repeats

Lagging strand is completed

(telomere replication)

primase, DNA poly, and ligase then synthesize the laggin strand in the 5'-->3' direction which prevents the chromosome from shortening

Mismathc repair

-if DNA poly II (profread/corrects) leaves a mismathed pair behind int he newly sythesized strand

-->battery of enzymes spring into action to correct it

4 Steps of Nucleotide Excision Repair

(1) Error Detection-an enzyme detects an irregularity in DNA and cuts the damage strand

(2) Nucleotide excision-an enzyme excises a stretch of nucleotides that includes the damage

(3) Nucleotide replacement- DNA poly fills in the gap in the 5'-->3' direction

(4) Nucleotid linkage- DNA ligase links the new and old nucleotides

5 steops of synthesis of Lagging Strand

(1) primer added- primase synthesizes RNA primer

(2) 1st Fragment synthesiszed-DNA poly III works in 5' 3' direction synthesizing first okazaki fragment of the lagging strand

(3) 2nd Fragment synthesized - primase and DNA poly II synthesize other Okazaki fragments

(4) Primer Replaced-DNA poly I removes ribonucleotides of primer, replaces them w/ deoxyribonucelotides in the 5' 3' direction

(5) Gap Closed - DNa ligase closes gap in sugar phosphate backbone