DNA Model Building and Replica3on

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Stephany Ethel Collins
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1 DNA Model Building and Replica3on

4 DNA Replication S phase

5 Origins of replication in E. coli and eukaryotes (a) Origin of replication in an E. coli cell Origin of replication Bacterial chromosome Doublestranded DNA molecule Only one origin of replication in prokaryotes. Two daughter DNA molecules Parental (template) strand Daughter (new) strand Replication bubble Replication fork (b) Origins of replication in a eukaryotic cell Wow! Hundreds or even thousands of Origin of origins of replication in eukaryotes. replication Eukaryotic chromosome Double-stranded DNA molecule Bubble Parental (template) strand Daughter (new) strand Replication fork Two daughter DNA molecules 0.5 µm 0.25 µm

6 The Trombone Model DNA replication resembles the slide of a trombone Leading strand template DNA pol III Parental DNA Leading strand Connecting protein DNA pol III Helicase Lagging strand template Lagging strand

7 DNA Replication Machine proteins involved in the initiation of DNA replication Primase Topoisomerase Replication fork RNA primer Helicase Single-strand binding proteins

8 At the end of each replica3on bubble is a replica(on fork, a Y- shaped region where new DNA strands are elonga3ng. Helicases are enzymes that untwist the double helix at the replica3on forks. Single- strand binding proteins bind to and stabilize single- stranded DNA. Topoisomerase corrects for overwinding ahead of replica3on forks by breaking, swiveling, and rejoining DNA strands. Prepara3on for replica3on of DNA; breaks the phosphate backbone of the DNA helix.

9 DNA Replication Machine proteins involved in the initiation of DNA replication Primase Topoisomerase Replication fork RNA primer Helicase Single-strand binding proteins

10 New strand Template strand Incorporation of a nucleotide into a DNA strand Sugar Phosphate A Base T A T C G C G G OH OH Nucleotide C A C DNA polymerase OH P P i Pyrophosphate 2 P i G T C A C

11 DNA polymerases cannot ini3ate synthesis of a polynucleo3de; they can only add nucleo3des to an exis3ng 3ʹ end. The ini3al nucleo3de strand is a short RNA primer. Topoisomerase Primase Replication fork RNA primer Helicase Single-strand binding proteins

12 An enzyme called primase can start an RNA chain from scratch and adds RNA nucleo3des one at a 3me using the parental DNA as a template. The primer is short (5 0 nucleo3des long), and the 3ʹ end serves as the star3ng point for the new DNA strand. Topoisomerase Primase Replication fork RNA primer Helicase Single-strand binding proteins

13 Synthesizing a New DNA Strand Enzymes called DNA polymerases catalyze the elonga3on of new DNA at a replica3on fork. Most DNA polymerases require a primer and a DNA template strand. The rate of elonga3on is about 500 nucleo3des per second in bacteria and 50 per second in human cells.

15 New strand Template strand Incorporation of a nucleotide into a DNA strand Sugar Phosphate A Base T A T C G C G G OH OH Nucleotide C A C DNA polymerase OH P P i Pyrophosphate 2 P i G T C A C

16 An#parallel Elonga#on The an(parallel structure of the double helix affects replica3on. DNA polymerases add nucleo3des only to the free 3ʹ end of the growing strand; therefore, a new DNA strand can elongate only in the 5ʹ to 3ʹ direc(on. Leading strand Origin of replication Lagging strand 5 3 Primer Lagging strand Overall directions of replication 3 5 Leading strand

Synthesis of the leading strand during DNA replication Leading strand Parental DNA Lagging strand DNA pol III starts to synthesize leading strand.

17 Synthesis of the leading strand during DNA replication Leading strand Parental DNA Lagging strand DNA pol III starts to synthesize leading strand. Origin of replication Primer Overall directions of replication Lagging strand Leading strand Origin of replication RNA primer Sliding clamp DNA pol III 2 Continuous elongation in the to direction

18 Leading strand Origin of replication Lagging strand 5 3 Primer Lagging strand Overall directions of replication 3 5 Leading strand

19 Synthesis of the leading strand during DNA replication DNA pol III starts to synthesize leading strand. Parental DNA Origin of replication RNA primer Sliding clamp DNA pol III 2 Continuous elongation in the to direction

20 Along one template strand of DNA, the DNA polymerase synthesizes a leading strand con3nuously, moving toward the replica3on fork. Leading strand Origin of replication Lagging strand 5 3 Primer Lagging strand Overall directions of replication 3 5 Leading strand

21 To elongate the other new strand, called the lagging strand, DNA polymerase must work in the direc3on away from the replica3on fork The lagging strand is synthesized as a series of segments called Okazaki fragments, which are joined together by DNA ligase.

22 Leading strand Lagging strand Overview Origin of replication Lagging strand Synthesis of the lagging strand Template strand 3 2 Overall directions of replication Primase makes RNA primer. RNA primer for fragment DNA pol III detaches. 2 Okazaki fragment Origin of replication DNA pol III makes Okazaki fragment. Leading strand RNA primer for fragment 2 Okazaki fragment DNA pol III makes Okazaki fragment 2. DNA pol I replaces RNA with DNA. DNA ligase forms bonds between DNA fragments. Overall direction of replication

23 Figure 6.6a Leading strand Synthesis of the lagging strand Overview Lagging Origin of replication strand Lagging strand 2 Overall directions of replication Leading strand

24 Figure 6.6b- Template strand Primase makes RNA primer. Synthesis of the lagging strand (Step ) Origin of replication

25 Figure 6.6b-2 Template strand Primase makes RNA primer. RNA primer for fragment 2 Synthesis of the lagging strand (Step 2) Origin of replication DNA pol III makes Okazaki fragment.

26 Template strand Primase makes RNA primer. RNA primer for fragment 2 Synthesis of the lagging strand (Step 3) Origin of replication DNA pol III makes Okazaki fragment. 3 DNA pol III detaches. Okazaki fragment

RNA primer for fragment 2 Okazaki fragment 2 2 4 Synthesis of

27 RNA primer for fragment 2 Okazaki fragment Synthesis of the lagging strand (Step 4) DNA pol III makes Okazaki fragment 2.

RNA primer for fragment 2 Okazaki fragment 2 2 4 Synthesis of the lagging strand

28 RNA primer for fragment 2 Okazaki fragment Synthesis of the lagging strand (Step 5) DNA pol III makes Okazaki fragment DNA pol I replaces RNA with DNA.

RNA primer for fragment 2 Okazaki fragment 2 2 4 Synthesis of the lagging strand (Step 6) DNA pol III makes Okazaki

29 RNA primer for fragment 2 Okazaki fragment Synthesis of the lagging strand (Step 6) DNA pol III makes Okazaki fragment DNA pol I replaces RNA with DNA. 2 6 DNA ligase forms bonds between DNA fragments. Overall direction of replication

30 The Trombone Model DNA replication resembles the slide of a trombone Leading strand template DNA pol III Parental DNA Leading strand Connecting protein DNA pol III Helicase Lagging strand template Lagging strand

31 Proofreading and Repairing DNA: DNA polymerases proofread newly made DNA, replacing any incorrect nucleo3des. In mismatch repair of DNA, repair enzymes correct errors in base pairing. DNA can be damaged by exposure to harmful chemical or physical agents such as cigareue smoke and X- rays; it can also undergo spontaneous changes. In nucleo(de excision repair, a nuclease cuts out and replaces damaged stretches of DNA.

32 Nuclease Nucleotide excision repair of DNA damage DNA polymerase DNA ligase

complete the 5ʹ ends, so repeated rounds of replica3on produce shorter DNA molecules with

33 Replica(ng the Ends of DNA Molecules Limita3ons of DNA polymerase create problems for the linear DNA of eukaryo3c chromosomes The usual replica3on machinery provides no way to complete the 5ʹ ends, so repeated rounds of replica3on produce shorter DNA molecules with uneven ends This is not a problem for prokaryotes, most of which have circular chromosomes.

34 Eukaryo3c chromosomal DNA molecules have special nucleo3de sequences at their ends called telomeres. Telomeres do not prevent the shortening of DNA molecules, but they do postpone the erosion of genes near the ends of DNA molecules. It has been proposed that the shortening of telomeres is connected to aging.

35 If chromosomes of germ cells became shorter in every cell cycle, essen3al genes would eventually be missing from the gametes they produce. An enzyme called telomerase catalyzes the lengthening of telomeres in germ cells.

36 The shortening of telomeres might protect cells from cancerous growth by limi3ng the number of cell divisions. There is evidence of telomerase ac(vity in cancer cells, which may allow cancer cells to persist.

The enzyme telomerase may help unlock secrets of aging and cancer "Telomerase is crucial for telomere maintenance and genome integrity," explains Julian Chen, professor of chemistry and

37 The enzyme telomerase may help unlock secrets of aging and cancer "Telomerase is crucial for telomere maintenance and genome integrity," explains Julian Chen, professor of chemistry and biochemistry at ASU and one of the project's senior authors. "Mutations that disrupt telomerase function have been linked to numerous human diseases that arise from telomerase gene activity.

38 So, grab a DNA Replication Machine Kit and start duplicating!

Fig. 16-7a. 5 end Hydrogen bond 3 end. 1 nm. 3.4 nm nm

Fig. 16-7a. 5 end Hydrogen bond 3 end. 1 nm. 3.4 nm nm Fig. 16-7a end Hydrogen bond end 1 nm 3.4 nm 0.34 nm (a) Key features of DNA structure end (b) Partial chemical structure end Fig. 16-8 Adenine (A) Thymine (T) Guanine (G) Cytosine (C) Concept 16.2: Many