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AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA)...

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AP Biology 2007-2008 DNA Replication
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Page 1: AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA) Built from NUCLEOTIDE SUBUNITS NITROGEN BASES.

AP Biology 2007-2008

DNA Replication

Page 2: AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA) Built from NUCLEOTIDE SUBUNITS NITROGEN BASES.

STRUCTURE OF NUCLEIC ACIDS

Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA)

Built from NUCLEOTIDE SUBUNITS

NITROGEN BASES CAN BE:

ADENINEGUANINECYTOSINETHYMINEURACIL

Page 3: AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA) Built from NUCLEOTIDE SUBUNITS NITROGEN BASES.

DNA has no URACIL RNA has no THYMINE

PURINES (A & G) have 2 RINGS

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

Page 4: AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA) Built from NUCLEOTIDE SUBUNITS NITROGEN BASES.

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

Page 5: AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA) Built from NUCLEOTIDE SUBUNITS NITROGEN BASES.

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

Page 6: AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA) Built from NUCLEOTIDE SUBUNITS NITROGEN BASES.

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

Page 7: AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA) Built from NUCLEOTIDE SUBUNITS NITROGEN BASES.

AP Biology

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

Page 8: AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA) Built from NUCLEOTIDE SUBUNITS NITROGEN BASES.

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

Page 9: AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA) Built from NUCLEOTIDE SUBUNITS NITROGEN BASES.

AP Biology

Base pairing in DNA Purines

adenine (A) guanine (G)

Pyrimidines thymine (T) cytosine (C)

Pairing A : T

2 bonds C : G

3 bonds

Page 10: AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA) Built from NUCLEOTIDE SUBUNITS NITROGEN BASES.

AP Biology

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

Page 11: AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA) Built from NUCLEOTIDE SUBUNITS NITROGEN BASES.

AP Biology

Semi-

Conservative

Conservative

Dispersive

Page 12: AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA) Built from NUCLEOTIDE SUBUNITS NITROGEN BASES.

AP Biology

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

Page 13: AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA) Built from NUCLEOTIDE SUBUNITS NITROGEN BASES.

AP Biology

Starting place = ORIGIN OF REPLICATION

Bacteria have one

Bacterial replication

Eukaryotes-multiple origins

Page 15: AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA) Built from NUCLEOTIDE SUBUNITS NITROGEN BASES.

AP Biology

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

Page 16: AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA) Built from NUCLEOTIDE SUBUNITS NITROGEN BASES.

AP Biology

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

Page 17: AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA) Built from NUCLEOTIDE SUBUNITS NITROGEN BASES.

AP Biology

DNAPolymerase III

Replication: 2nd step

Where’s theENERGY

for the bondingcome from?

Build daughter DNA strand add new

complementary bases DNA polymerase III

Page 18: AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA) Built from NUCLEOTIDE SUBUNITS NITROGEN BASES.

AP Biology

energy

ATP

Energy of ReplicationWhere does energy for bonding usually come from?

ADPADPmodified nucleotide

We comewith our own

energy!

Page 19: AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA) Built from NUCLEOTIDE SUBUNITS NITROGEN BASES.

AP Biology

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

Page 20: AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA) Built from NUCLEOTIDE SUBUNITS NITROGEN BASES.

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

Page 21: AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA) Built from NUCLEOTIDE SUBUNITS NITROGEN BASES.

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

Page 22: AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA) Built from NUCLEOTIDE SUBUNITS NITROGEN BASES.

AP Biology

DNAPolymerase III

energy

Replication

3

3

5

5

Page 23: AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA) Built from NUCLEOTIDE SUBUNITS NITROGEN BASES.

AP Biology

DNAPolymerase III

energy

Replication

3

3

5

5

Page 24: AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA) Built from NUCLEOTIDE SUBUNITS NITROGEN BASES.

AP Biology

Replication

3

3

5

5

Page 25: AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA) Built from NUCLEOTIDE SUBUNITS NITROGEN BASES.

AP Biology

35

5

5

3

need “primer” bases to add on to3

energy

3 5

Can’t build3’ to 5’direction

Page 26: AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA) Built from NUCLEOTIDE SUBUNITS NITROGEN BASES.

AP Biology

35

5

5

3

3

3 5

need “primer” bases to add on to

Page 27: AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA) Built from NUCLEOTIDE SUBUNITS NITROGEN BASES.

AP Biology

35

5

5

3

need “primer” bases to add on to3

energy

3 5

Page 28: AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA) Built from NUCLEOTIDE SUBUNITS NITROGEN BASES.

AP Biology

35

5

5

3

need “primer” bases to add on to3

energy

3 5

Page 29: AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA) Built from NUCLEOTIDE SUBUNITS NITROGEN BASES.

AP Biology

35

5

5

3

3

3 5

Page 30: AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA) Built from NUCLEOTIDE SUBUNITS NITROGEN BASES.

AP Biology

35

5

5

3

3

energy

3 5

Page 31: AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA) Built from NUCLEOTIDE SUBUNITS NITROGEN BASES.

AP Biology

35

5

5

3

3

3 5

ligase

Joinsfragments

Page 32: AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA) Built from NUCLEOTIDE SUBUNITS NITROGEN BASES.

AP Biology

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

Page 33: AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA) Built from NUCLEOTIDE SUBUNITS NITROGEN BASES.

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

Page 34: AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA) Built from NUCLEOTIDE SUBUNITS NITROGEN BASES.

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

Page 35: AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA) Built from NUCLEOTIDE SUBUNITS NITROGEN BASES.

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

Page 36: AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA) Built from NUCLEOTIDE SUBUNITS NITROGEN BASES.

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

Page 37: AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA) Built from NUCLEOTIDE SUBUNITS NITROGEN BASES.

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

Page 38: AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA) Built from NUCLEOTIDE SUBUNITS NITROGEN BASES.

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

ANIMATION

Page 39: AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA) Built from NUCLEOTIDE SUBUNITS NITROGEN BASES.

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

Page 40: AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA) Built from NUCLEOTIDE SUBUNITS NITROGEN BASES.

AP Biology

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

Page 41: AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA) Built from NUCLEOTIDE SUBUNITS NITROGEN BASES.

AP Biology

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

Page 42: AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA) Built from NUCLEOTIDE SUBUNITS NITROGEN BASES.

AP Biology

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

Page 43: AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA) Built from NUCLEOTIDE SUBUNITS NITROGEN 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

Page 44: AP Biology 2007-2008 DNA Replication STRUCTURE OF NUCLEIC ACIDS Sugar can be DEOXYRIBOSE (DNA) RIBOSE (RNA) Built from NUCLEOTIDE SUBUNITS NITROGEN BASES.

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


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