DNA Replication

AP Biology


Watson and Crick

AP Biology

1953 article in Nature

Double helix structure of DNA

“It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic AP Biology material. ” Watson & Crick

Directionality of DNA §  You need to PO4


number the carbons! u 

it matters!

N base 5ʹ CH2

This will be IMPORTANT!!


3ʹ AP Biology



The DNA backbone §  Putting the DNA backbone together u 

refer to the 3ʹ and 5ʹ ends of the DNA §  the last trailing carbon Sounds trivial, but… this will be IMPORTANT!!

5ʹ PO4 5ʹ CH2 4ʹ

base O 1ʹ

C 3ʹ

O –O P O O 5ʹ CH 2

base O

1ʹ 2ʹ


AP Biology

Anti-parallel strands §  Nucleotides in DNA backbone are bonded from phosphate to sugar between 3ʹ & 5ʹ carbons

DNA molecule has “direction” u  complementary strand runs in opposite direction u 

AP Biology

Bonding in DNA 5ʹ

hydrogen bonds

covalent phosphodiester bonds

….strong or weak bonds? AP Biology How do the bonds fit the mechanism for copying DNA?

Base pairing in DNA §  Purines adenine (A) u  guanine (G) u 

§  Pyrimidines thymine (T) u  cytosine (C) u 

§  Pairing u 

A:T §  2 bonds

u  AP Biology

C:G §  3 bonds

Copying DNA §  Replication of DNA base pairing allows each strand to serve as a template for a new strand u  new strand is 1/2 parent template & 1/2 new DNA u 

AP Biology

DNA Replication

Let’s meet the team…

§  Large team of enzymes coordinates replication

AP Biology

Replication: 1st step §  Unwind DNA u 

helicase enzyme §  unwinds part of DNA helix §  stabilized by single-stranded binding proteins helicase

single-stranded binding proteins AP Biology

replication fork

Replication: 2nd step §  Build daughter DNA strand add new complementary bases u  DNA polymerase III u 

DNA Polymerase III AP Biology

But… Where’s the We’re missing ENERGY something! for the bonding! What?

Energy of Replication Where does energy for bonding usually come from? We come with our own energy!

You remember ATP! Are there there Are otherenergy ways other to get energy nucleotides? out You of betit? !


modified nucleotide

And we leave behind a nucleotide!

energy energy


Energy of Replication §  The nucleotides arrive as nucleosides u 

DNA bases with P–P–P §  P-P-P = energy for bonding

DNA bases arrive with their own energy source for bonding u  bonded by enzyme: DNA polymerase III u 

ATP AP Biology




Replication §  Adding bases u 

can only add nucleotides to 3ʹ end of a growing DNA strand §  need a “starter”

nucleotide to bond to u 

strand only grows 5ʹ→3ʹ

AP Biology

B.Y.O. ENERGY! The energy rules the process


DNA Polymerase III


DNA Polymerase III


DNA Polymerase III DNA Polymerase III


need “primer” bases to add on to

energy no energy to bond


energy energy

energy energy

ligase energy


AP Biology


Leading & Lagging strands Limits of DNA polymerase III u 

can only build onto 3ʹ end of an existing DNA strand Ok

ragm f i k a z a 3ʹ

ents 3ʹ


growing 3ʹ replication fork

Lagging strand

Leading strand 3ʹ

Lagging strand Okazaki fragments u  joined by ligase u 

AP Biology §  “spot

welder” enzyme



5ʹ 3ʹ

DNA polymerase III

Leading strand u 

continuous synthesis

Replication fork / Replication bubble 3ʹ

DNA polymerase III

leading strand 5ʹ

3ʹ 5ʹ

3ʹ 5ʹ

lagging strand

3ʹ 5ʹ

3ʹ 5ʹ lagging strand

5ʹ leading strand 3ʹ

growing replication fork 3ʹ

leading strand

lagging strand 5ʹ 5ʹ

AP Biology

growing replication fork 5ʹ

Starting DNA synthesis: RNA primers Limits of DNA polymerase III u 

can only build onto 3ʹ end of an existing DNA strand

3ʹ 3ʹ

5ʹ growing 3ʹ replication fork

DNA polymerase III

primase RNA 5ʹ

RNA primer built by primase u  serves as starter sequence DNA polymerase III AP for Biology u 

Replacing RNA primers with DNA DNA polymerase I u 

removes sections of RNA primer and replaces with DNA nucleotides

DNA polymerase I

5ʹ 3ʹ


growing 3ʹ replication fork RNA

5ʹ 3ʹ

But DNA polymerase I still can only build onto 3ʹ end of an existing DNA strand AP Biology

Chromosome erosion All DNA polymerases can only add to 3ʹ end of an existing DNA strand

Houston, we have a problem!

DNA polymerase I 5ʹ 3ʹ

5ʹ growing 3ʹ replication fork

DNA polymerase III RNA

Loss of bases at 5ʹ ends in every replication chromosomes get shorter with each replication AP Biologyto number of cell divisions? u  limit u 

5ʹ 3ʹ

Telomeres Repeating, non-coding sequences at the end of chromosomes = protective cap u 

limit to ~50 cell divisions

3ʹ 3ʹ

5ʹ growing 3ʹ replication fork


Telomerase TTAAGGG TTAAGGG TTAAGGG enzyme extends telomeres u  can add DNA bases at 5ʹ end u  different level of activity in different cells


AP Biology §  high

in stem cells & cancers -- Why?

5ʹ 3ʹ

Replication fork DNA polymerase I

5’ 3’

DNA polymerase III


lagging strand primase

Okazaki fragments




5’ 3’

3’ 5’ helicase

DNA polymerase III

leading strand direction of replication

AP Biology

SSB = single-stranded binding proteins

DNA polymerases §  DNA polymerase III 1000 bases/second! u  main DNA builder u 

Roger Kornberg 2006

§  DNA polymerase I 20 bases/second u  editing, repair & primer removal u 

DNA polymerase III enzyme

AP Biology

Arthur Kornberg 1959

Editing & proofreading DNA §  1000 bases/second = lots of typos!

§  DNA polymerase I u 

proofreads & corrects typos


repairs mismatched bases


removes abnormal bases §  repairs damage

throughout life u 

AP Biology

reduces error rate from 1 in 10,000 to 1 in 100 million bases

Fast & accurate! §  It takes E. coli