Chapter_15_Lecture_Presentation Canvas.pptx

Biological Science Seventh Edition Chapter 15 DNA and the Gene: Synthesis and Repair Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved 1 2 5 6 4 Group 3: Brown, 3 hlin, cL M aug Sarah Miller, Probst 8 7 9 12 10 13 11 16 14 15 17 18 © 2017 Pearson Education, Inc. Admin Will hav...

Biological Science Seventh Edition Chapter 15 DNA and the Gene: Synthesis and Repair Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved 1 2 5 6 4 Group 3: Brown, 3 hlin, cL M aug Sarah Miller, Probst 8 7 9 12 10 13 11 16 14 15 17 18 © 2017 Pearson Education, Inc. Admin Will have exams ready on Wednesday Chapter 15 Opening Roadmap Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved DNA is double-stranded: Each strand consists of deoxyribonucleotides: Deoxyribose sugar, phosphate group, and nitrogenous base Deoxyribonucleotides link together into polymer Phosphodiester linkage—covalent bond: Hydroxyl group on 3’ carbon of one deoxyribose joined by covalent bond to phosphate group attached to 5’ carbon of another deoxyribose Each strand of DNA has directionality (polarity): – One end has 3′ end exposed hydroxyl group on 3′ carbon of deoxyribose – Other end has exposed phosphate group on 5′ carbon – Molecule has distinctly different 3’ and 5’ Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved ends Figure 15.3 DNA Is a Polymer Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved 15.2 Testing Early Hypotheses about DNA Synthesis Existing strands of DNA could serve as a template for making a copy Three alternative hypotheses for DNA replication: 1. Semiconservative replication 2. Conservative replication 3. Dispersive replication Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved Pink = original DNA; blue = newly synthesized DNA © 2017 Pearson Education, Inc. 15.3 A Model for DNA Synthesis DNA polymerase: Enzyme that catalyzes DNA synthesis Several types of DNA polymerases Work only in one direction Can add deoxyribonucleotides only to 3′ end of a nucleic acid chain Therefore, DNA synthesis always proceeds in 5’ → 3’ direction Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved Two ways to remember “5 prime to 3 prime” 1. The 5’ phosphate is being added to the 3’ OH 2. The growth of the new strand as a whole seems to carry it away from the 5’ end © 2017 Pearson Education, Inc. dNTPs provide the energy input to polymerize DNA Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved Where Does Replication Start? Replication bubble forms when DNA is being synthesized: Forms at specific sequence—origin of replication: Bacteria have one and form one replication bubble Eukaryotic cells have many on each chromosome Each replication bubble has two replication forks: Because synthesis is bidirectional, replication bubbles grow in two directions Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved Figure 15.7 DNA Replication Forks Move in Two Directions from an Origin of Replication Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved Table 15.1: 7 Enzymes to know in DNA replication Helicase Separates the two strands of DNA (the double helix) Single-Strand Binding Holds separated single strands apart Topoisomeras e Relieves tension on DNA molecule ahead of fork (RNA) primase Synthesizes a short piece of RNA (the primer) DNA The main enzyme that adds polymerase III nucleotides © 2017 Pearson Education, Inc. DNA Polymerase I A repair enzyme that removes the RNA primer DNA ligase Repairs the sugar-phosphate backbone How is the Helix Opened and Stabilized? Several proteins are responsible for opening and stabilizing double helix: DNA helicase breaks hydrogen bonds between two DNA strands to separate them Single-strand DNA-binding proteins (SSBP s) attach to separated strands to prevent them from closing Unwinding DNA helix creates tension farther down helix: Topoisomerase cuts and rejoins DNA to relieve this tension Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved Opening the Helix © 2017 Pearson Education, Inc. How is the Leading Strand Synthesized? DNA polymerase has two parts: A sliding clamp that forms a ring around the DNA A part that grips the DNA strand Two important limitations on all DNA polymerases: DNA polymerase can synthesize only in 5’→ 3’ direction DNA polymerase cannot start synthesis from scratch on template strand DNA polymerase can only extend from 3’ end of existing strand 5’ to 3’ synthesis leads to opposite direction of synthesis on the two strands. Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved How is the Leading Strand Synthesized? The 3′ end is supplied by short strand of RNA called a primer: Primer is base paired to DNA template (Both DNA and RNA strands can serve as primers) Primers are made by enzyme called primase: Type of RNA polymerase Does not require free 3′ end to begin synthesis Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved How is the Leading Strand Synthesized? DNA polymerase adds dNTPs to primer’s 3′ end Since DNA strands are antiparallel, synthesis process differs for each strand: Strand that is synthesized toward replication fork is leading strand, or continuous strand It is synthesized continuously in the 5’ → 3’ direction Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved How is the Lagging Strand Synthesized? Lagging strand (discontinuous strand): Strand synthesized away from replication fork Occurs because DNA synthesis must proceed in 5’ → 3’ direction Discontinuous replication hypothesis: Primase synthesizes new RNA primers on lagging strand as replication fork opens DNA polymerase synthesizes short fragments of DNA along lagging strand Fragments are then linked into continuous strand Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved Leading strand synthesized 5′ → 3′ DNA unwinds Time 1 Lagging strand synthesized 5′→ 3′ Time 2 Region of singlestranded DNA © 2017 Pearson Education, Inc. Lagging strand- Okazaki Fragments The lagging strand is synthesized as short discontinuous fragments called Okazaki fragments DNA polymerase I removes the RNA primers and replaces them with DNA – distinct enzyme from DNA poly III The enzyme DNA ligase joins the Okazaki fragments The lagging strand is thus made intact, but with a delay relative to the leading strand © 2017 Pearson Education, Inc. Animation of DNA leading and lagging strands https://youtu.be/2Svz8h9J1RA Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved In fact, both strands are copied coordinately by a large grouping called a “replisome.” Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved 15.4 Replicating DNA: Ends of Linear Chromosomes Telomeres—region at end of eukaryotic chromosome Replication of telomeres can be problematic: Leading strand is synthesized all the way to the end: Produces double-stranded copy For the lagging strand, primase adds a R NA primer close to end of chromosome: Final Okazaki fragment is made and primer is removed DNA polymerase cannot add to end with no primer Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved The End Replication Problem Single-stranded DNA is left at end of the lagging strand Single-stranded DNA is eventually degraded: This would shorten chromosome by 50 to 100 nucleotides each time replication occurs Over time, linear chromosomes would vanish The solution: telomeres (which do not contain genes): Consist of short, repeating stretches of bases Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved Telomerase Solves the End Replication Problem Enzyme telomerase replicates telomeres, using an RNA template that it carries: 1. The 3′ end of the lagging strand forms a singlestranded “overhang” 2. Telomerase binds to overhang and uses RNA that it carries as template for DNA synthesis 3. Telomerase continues to move down new strand, adding more short DNA sequences to the end of the parent strand 4. Once overhang is long enough, normal DNA synthesis can occur Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved Figure 15.13 Telomerase Prevents Shortening of Telomeres during Replication Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved Effect of Telomere Length on Cell Division Telomerase is primarily found in gametes and stem cells- and in cancer cells!! Somatic cells normally lack telomerase: Chromosomes progressively shorten as individual ages It’s proposed that the number of cell divisions is limited by the initial length of cell’s telomeres: Once chromosome are shortened to threshold length, further divisions are shut down For cells grown in vitro, telomere length goes down with the number of cell divisions Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved Effect of Telomere Length on Cell Division Adding telomerase to cells in culture allows them to continue dividing longer Most cancer cells have active telomerase: May allow unlimited division of cancer cells Could inhibiting telomerase slow or stop cancer? Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved Stop here Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved Correcting Mistakes in DNA Synthesis DNA replication is very accurate DNA polymerase matches bases with high accuracy: Correct bases are the most energetically favorable Correct base pairs have a distinct shape Inserts an incorrect base about once every 100,000 bases DNA polymerase can proofread on the spot Other repair enzymes remove defective or damaged bases and replace them with the correct one Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved DNA Polymerase Proofreads DNA polymerase can proofread its work: Mismatched bases have distinct shape DNA polymerase will add nucleotide only if previous base pair is correct Exonuclease active site: Mismatched deoxyribonucleotide moves this region of the protein Site catalyzes removal of incorrect deoxyribonucleotide Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved Figure 15.14 DNA Polymerase Can Proofread Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved Mismatch Repair DNA polymerase sometimes leaves a mismatched pair behind despite proofreading Mismatch repair occurs when mismatched bases are corrected after DNA synthesis is complete Mismatch repair enzymes: Recognize mismatched pair Remove section of newly synthesized strand that contains incorrect base Fills in correct bases Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved Mismatch repair- happens soon after synthesis A bulge from poor base-pairing  The organism needs to know which strand is the old strand and which was just copied! From Khan academy (link in Canvas) Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved Other repair mechanisms DNA bases could be chemically damaged The DNA strand can get broken (either one strand or both strands) There are a handful of repair systems that are activated when DNA damage is detected outside of DNA replication. Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved Not on test- escalating cell response to DNA damage Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved