AP Biology 2007-2008

Chapter 16DNA Replication

Slides with blue borders come from a slide show

by Kim Foglia (http://explorebiology.com)

STRUCTURE OF NUCLEIC ACIDS

Image by: Riedell

Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA)

Built from NUCLEOTIDE SUBUNITS

NITROGEN BASES CAN BE:

ADENINEGUANINECYTOSINETHYMINEURACIL

Arrow from: http://www.harrythecat.com/graphics/b/arrow48d.gif

DNA has no URACIL RNA has no THYMINE

PURINES (A & G) have 2 RINGS

PYRIMIDINES (T, C, & U) have 1 RING

http://student.ccbcmd.edu/courses/bio141/lecguide/unit6/genetics/DNA/DNA/fg4.htmlhttp://student.ccbcmd.edu/~gkaiser/biotutorials/dna/fg29.html

AP Biology

Directionality of DNA You need to

number the carbons! it matters!

OH

CH2

O

4

5

3 2

1

PO4

N base

ribose

nucleotide

This will beIMPORTANT!!

AP Biology

The DNA backbone Made of phosphates and

deoxyribose sugars

Phosphate on 5’ carbon

attaches to 3’ carbon of next nucleotide

OH

O

3

PO4

base

CH2

O

base

OPO

C

O–O

CH2

1

2

4

5

1

2

3

3

4

5

5

AP Biology

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 material.” Watson & Crick

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Anti-parallel strands Nucleotides in DNA

backbone are bonded from phosphate to sugar between 3 & 5 carbons DNA molecule has

“direction” complementary strand runs

in opposite direction

3

5

5

3

AP Biology

Bonding in DNA

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

3

5 3

5

covalentphosphodiester

bonds

hydrogenbonds

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Base pairing in DNA Purines

adenine (A) guanine (G)

Pyrimidines thymine (T) cytosine (C)

Pairing A : T

2 bonds C : G

3 bonds

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CHARGAFF’s RULES Erwin Chargaff analyzed DNA from different organisms and found A = T G = C

Now know its because:A always bonds with TG always bonds with C

A Purine always bonds to a Pyrimidine

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Chromosome

E. coli bacterium

Bases on the chromosome

Chromosome Structure in Prokaryotes

© Pearson Education Inc, publishing as Pearson Prentice Hall. All rights reserved

DNA molecule in bacteriasingle DOUBLE STRANDED circular loop

Approximately 5 million base pairs3,000 genes

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http://student.ccbcmd.edu/~gkaiser/biotutorials/dna/fg12.html

Starting place = ORIGIN OF REPLICATION

Bacteria have one

Bacterial replication

Eukaryotes-multiple origins

AP Biology http://bio.usuhs.mil/biochem4.html

HOW NUCLEOTIDES ARE ADDED

DNA REPLICATION FORK

DNA replication

Triphosphate addition

DNA replication 2

DNA replication/quiz

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Copying DNA Replication of DNA

base pairing allows each strand to serve as a template for a new strand

new strand is 1/2 parent template & 1/2 new DNA semi-conservative

copy process

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Replication: 1st step Unwind DNA

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

single-stranded binding proteins replication fork

helicase

DNA REPLICATION FORK

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DNAPolymerase III

Replication: 2nd step

Where’s theENERGY

for the bondingcome from?

Build daughter DNA strand add new

complementary bases DNA polymerase III

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energy

ATP

Energy of ReplicationWhere does energy for bonding usually come from?

ADPADPmodified nucleotide

We comewith our own

energy!

Youremember

ATP!

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ATP

Energy of ReplicationWhere does energy for bonding usually come from?

AMPmodified nucleotide

energy

We comewith our own

energy!

And weleave behind a

nucleotide!

Are thereother energynucleotides?

You bet!

DNA replication

AP Biology

Energy of Replication The nucleotides arrive as nucleoside triphosphates

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

DNA bases arrive with their own energy source for bonding

bonded by enzyme: DNA polymerase III

ATP GTP TTP CTP

See animation

AP Biology

Adding bases can only add

nucleotides to 3 end of a growing DNA strand need a “starter”

nucleotide to bond to

strand only grows 53

DNAPolymerase III

Replication

3

3

5

5need “primer” bases to add on to

AP Biology

DNAPolymerase III

energy

Replication

3

3

5

5

AP Biology

DNAPolymerase III

energy

Replication

3

3

5

5

AP Biology

Replication

3

3

5

5

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35

5

5

3

need “primer” bases to add on to3

energy

3 5

Can’t build3’ to 5’direction

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35

5

5

3

3

3 5

need “primer” bases to add on to

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35

5

5

3

need “primer” bases to add on to3

energy

3 5

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35

5

5

3

need “primer” bases to add on to3

energy

3 5

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35

5

5

3

3

3 5

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35

5

5

3

3

energy

3 5

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35

5

5

3

3

3 5

ligase

Joinsfragments

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Limits of DNA polymerase III can only build onto 3 end of

an existing DNA strand

Leading & Lagging strands

5

5

5

5

3

3

3

53

53 3

Leading strand

Lagging strand

Okazaki fragments

ligase

Okazaki

Leading strand continuous synthesis

Lagging strand Okazaki fragments joined by ligase

“spot welder” enzyme

DNA polymerase III

3

5

growing replication fork

AP Biology

DNA polymerase III

Replication fork / Replication bubble

5

3 5

3

leading strand

lagging strand

leading strand

lagging strandleading strand

5

3

3

5

5

3

5

3

5

3 5

3

growing replication fork

growing replication fork

5

5

5

5

53

3

5

5lagging strand

5 3

AP Biology

DNA polymerase III

RNA primer built by primase serves as starter sequence

for DNA polymerase III

Limits of DNA polymerase III can only build onto 3 end of

an existing DNA strand

Starting DNA synthesis: RNA primers

5

5

5

3

3

3

5

3 53 5 3

growing replication fork

primase

RNA

AP Biology

DNA polymerase I removes sections of RNA

primer and replaces with DNA nucleotides

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

Replacing RNA primers with DNA

5

5

5

5

3

3

3

3

growing replication fork

DNA polymerase I

RNA

ligase

AP Biology

Loss of bases at 5 ends in every replication chromosomes get shorter with each replication limit to number of cell divisions?

DNA polymerase III

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

Chromosome erosion

5

5

5

5

3

3

3

3

growing replication fork

DNA polymerase I

RNA

Houston, we have a problem!

TELOMERES & TELOMERASE

Image from: AP BIOLOGY by Campbell and Reese 7th edition

Primer removed butcan’t be replaced withDNA because no3’ end available forDNA POLYMERASE

Each replicationshortensDNA strand

TELOMERES-repetitive sequences added to ends of genes to protect information in code

TELOMERASE can add to telomere segments in cells that must divide frequently

Shortening of telomeres may play a role in aging

Cells with increased telomerase activity which allows them to keep dividing

EX: Cells that give rise to sperm & eggs, stem cells, cancer cells

http://stemcells.nih.gov/info/scireport/appendixC.asp

ANIMATION

AP Biology

Replication fork

3’

5’

3’

5’

5’

3’

3’ 5’

helicase

direction of replication

SSB = single-stranded binding proteins

primase

DNA polymerase III

DNA polymerase III

DNA polymerase I

ligase

Okazaki fragments

leading strand

lagging strand

SSB

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DNA polymerases DNA polymerase III

1000 bases/second! main DNA builder

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

DNA polymerase III enzyme

Arthur Kornberg1959

Thomas Kornberg

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Fast & accurate! It takes E. coli <1 hour to copy

5 million base pairs in its single chromosome divide to form 2 identical daughter cells

Human cell copies its 6 billion bases & divide into daughter cells in only few hours remarkably accurate only ~1 error per 100 million bases ~30 errors per cell cycle

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Editing & proofreading DNA 1000 bases/second =

lots of typos!

DNA polymerase I proofreads & corrects

typos repairs mismatched bases removes abnormal bases

repairs damage throughout life

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

PROOFREADING & REPAIR

Errors can come from: “proofreading mistakes” that are not caught Environmental damage from CARCINOGENS

(Ex: X-rays, UV light, cigarette smoke, etc)

EX: Thymine dimers

http://www.mun.ca/biology/scarr/Thymine-Thymine_Dimers.html

http://www.personal.psu.edu/staff/d/r/drs18/bisciImages/index.html

AP Biology

Semi-

Conservative

Conservative

Dispersive

NUCLEOTIDE EXCISION REPAIR Cells continually monitor DNA and make repairs

NUCLEASES-DNA cutting enzyme removes errors

DNA POLYMERASE AND LIGASE can fill in gap and repair using other strand

Xeroderma pigmentosum- genetic disorder mutation in DNA enzymes that repair UV damage in skin cells can’t go out in sunlight increased skin cancers/cataracts

http://www.maximilien.asso.fr/images/maxcasque.jpg

http://www.nature.com/jid/journal/v128/n3/images/jid200825i2.jpg