Chapter 5: DNA Replication, Repair, and Recombination Goals • Illustrate how structure of DNA affects its function • Describe enzymes involved in replication • Summarize their functions • Explain how DNA is repaired and why it needs to be repaired DNA Structure (A Review) • DNA consists of two strands – Each strand is a polymer of nucleotides – Strand has orientation due to nucleotide structure: 5’ and 3’ ends – The two strands are antiparallel DNA Function (A Review) • DNA function is information storage • Sequence of strand stores info – Genes are copied into RNA (transcription) – “Control elements” regulate protein interactions with DNA • DNA passed on to descendant cells – Accurate copying – Repair of any damage to avoid changes – Accurate subdivision Fig. 2.11 5’ end 3’ end Fig. 2.15 Functions Determine Form • Double strands of DNA allow “easy” replication – Rules for obligate pairing – Each strand acts as template for the other • Multiple proteins involved – Act in concert – Act as complexes – Recognize DNA by shape of bases Paired DNA Strands Replication Overview • Replication complex binds to replication “origin” • Double-stranded DNA is “melted” • Each strand is used as a template for DNA synthesis Mechanism of DNA Replication General Features of DNA Replication • • • • Semiconservative Complementary Base Pairing DNA Replication Fork is Assymetrical Replication occurs in 5’ 3’ Direction Semi-conservative Replication Alternative models of DNA replication (Fig 3.1): Semi-conservative Replication Equilibrium density gradient centrifugation (Box 3.1) DNA Replication 1955: Arthur Kornberg Worked with E. coli. Discovered the mechanisms of DNA synthesis. Four components are required: 1. dNTPs: dATP, dTTP, dGTP, dCTP (deoxyribonucleoside 5’-triphosphates) (sugar-base + 3 phosphates) 2. DNA template 3. DNA polymerase I (formerly the Kornberg enzyme) (DNA polymerase II & III discovered soon after) 4. Mg 2+ (optimizes DNA polymerase activity) 1959: Arthur Kornberg (Stanford University) & Severo Ochoa (NYU) DNA Replication DNA elongation (Fig. 3.4a): Tools of Replication • Enzymes are the tools of replication: • DNA Polymerase - Matches the correct nucleotides then joins adjacent nucleotides to each other • Primase - Provides an RNA primer to start polymerization • Ligase - Joins adjacent DNA strands together (fixes “nicks”) More Tools of Replication • Helicase - Unwinds the DNA and melts it • Single Strand Binding Proteins - Keep the DNA single stranded after it has been melted by helicase • Gyrase - A topisomerase that Relieves torsional strain in the DNA molecule • Telomerase - Finishes off the ends of DNA strands Initiation of replication, major elements: Segments of single-stranded DNA are called template strands. Gyrase (a type of topoisomerase) relaxes the supercoiled DNA. Initiator proteins and DNA helicase binds to the DNA at the replication fork and untwist the DNA using energy derived from ATP (adenosine triphosphate). (Hydrolysis of ATP causes a shape change in DNA helicase) DNA primase next binds to helicase producing a complex called a primosome (primase is required for synthesis), Primase synthesizes a short RNA primer of 10-12 nucleotides, to which DNA polymerase III adds nucleotides. Polymerase III adds nucleotides 5’ to 3’ on both strands beginning at the RNA primer. The RNA primer is later removed and replaced with DNA by polymerase I, and the gap is sealed with DNA ligase. Single-stranded DNA-binding (SSB) proteins (>200) stabilize the single-stranded template DNA during the process. Model of replication in E. coli (Fig. 3.5) In the Beginning… • Problems due to structure – DNA is double-stranded – Template must be single-stranded – Strands must be separated • Separation is difficult due to structure – Melting strands causes tension elsewhere – If unrelieved tension can snap DNA strand Topoisomerase (Gyrase) • • • • Relieves stress caused by melting DNA Cleaves DNA and spins around itself to unwind helix Type I cleaves one strand, type II cleaves both Reseals DNA strands after relaxation achieved DNA Replication DNA Helicase • Hydrolyze ATP when bound to ssDNA and opens up helix as it moves along DNA • Moves 1000 bp/sec • 2 helicases: one on leading and one on lagging strand • SSB proteins aid helicase by destabilizing unwound ss conformation Single Strand Binding Protein • Binds to DNA with no sequence preference • Binds tighter to single strand than double • Keeps separated strands from rejoining DNA Replication SSB proteins help DNA helicase destabilizing ssDNA Primase • Creates a primer for DNA polymerase • Template-dependent • An RNA polymerase • Active briefly at beginning of strand synthesis DNA Replication DNA Primase • uses rNTPs to synthesize short primers on lagging Strand • Primers ~10 nucleotides long and spaced ~100-200 bp • DNA repair system removes RNA primer; replaces it w/DNA • DNA ligase joins Okazaki fragments Supercoiled DNA relaxed by gyrase & unwound by helicase + proteins: 5’ SSB Proteins Okazaki Fragments ATP 1 Polymerase III 2 3 Lagging strand Helicase + Initiator Proteins 3’ primase Polymerase III 5’ RNA Primer 3’ base pairs 5’ RNA primer replaced by polymerase I & gap is sealed by ligase 3’ Leading strand DNA Polymerase • Enzyme that synthesizes a DNA strand • Uses existing strand as template • Requires a free “3’ end” to add new nucleotides • Has several catalytic functions • Several forms exist Eukaryotic DNA Polymerases Enzyme Location Function • Pol (alpha) Nucleus DNA replication – includes RNA primase activity, starts DNA strand • Pol (gamma) Nucleus DNA replication – replaces Pol to extend DNA strand, proofreads • Pol (epsilon) Nucleus DNA replication – similar to Pol , shown to be required by yeast mutants • Pol (beta) • Pol (zeta) • Pol (gamma) Nucleus Nucleus Mitochondria DNA repair DNA repair DNA replication Maintenance of DNA Sequences DNA Polymerase as Self Correcting Enzyme • Correct nucleotide has greater affinity for moving polymerase than incorrect nucleotide • Exonucleolytic proofreading of DNA polymerase – DNA molecules w/ mismatched 3’ OH end are not effective templates; polymerase cannot extend when 3’ OH is not base paired – DNA polymerase has separate catalytic site that removes unpaired residues at terminus Maintenance of DNA Sequences High Fidelity DNA Replication • • Error rate= 1 mistake/109 nucleotides Afforded by complementary base pairing and proof-reading capability of DNA polymerase DNA Replication DNA Polymerase held to DNA by clamp regulatory protein • • • • Clamp protein releases DNA poly when runs into dsDN Forms ring around DNA helix Assembly of clamp around DNA requires ATP hydrolysis Remains on leading strand for long time; only on lagging strand for short time when it reaches 5’ end of proceeding Okazaki fragments DNA ligase seals the gaps between Okazaki fragments with a phosphodiester bond (Fig. 3.7) DNA Replication Okazaki Fragments • RNA that primed synthesis of 5’ end removed • Gap filled by DNA repair enzymes • Ligase links fragments together Extension - Okazaki Fragments 5’ 3’ Okazaki Fragment DNA Pol. 3’ 5’ RNA Primer DNA Polymerase has 5’ to 3’ exonuclease activity. When it sees an RNA/DNA hybrid, it chops out the RNA and some DNA in the 5’ to 3’ direction. 5’ 3’ DNA Pol. RNA and DNA Fragments 3’ 5’ RNA Primer DNA Polymerase falls off leaving a nick. 5’ 3’ Ligase Nick 3’ 5’ RNA Primer The nick is removed when DNA ligase joins (ligates) the DNA fragments. DNA Replication Initiation and Completion of DNA Replication in Chromosomes Bacteria ►Single Ori ►Initiation or replication highly regulated ►Once initiated replication forks move at ~400-500 bp/sec ►Replicate 4.6 x 106 bp in ~40 minutes DNA Replication Initiation and Completion of DNA Replication in Chromosomes DNA Replication Begins at Origins of Replication ►Positions at which DNA helix first opened ►In simple cells ori defined DNA sequence 100-200 bp ►Sequence attracts initiator proteins ►Typically rich in AT base pairs DNA Replication Initiation and Completion of DNA Replication in Chromosomes Eukaryotic Chromosomes Have Multiple Origins of Replication ►Relication forks travel at ~50 bp/sec ►Ea chromosome contains ~150 million base pairs ►Replication origins activate in clusters or replication units of 20-80 ori’s ►Individual ori’s spaced at intervals of 30,000-300,000 bp DNA Replication Initiation and Completion of DNA Replication in Chromosomes Mammalian DNA Sequences that Specify Initiation of Replication ►1000’s bp in length ►Can function when placed in regions where chromo not too condensed ►Human ORC required for replication initiation also bind Cdc6 and Mcm proteins ►Binding sites for ORC proteins less specific • Each eukaryotic chromosome is one linear DNA double helix • Average ~108 base pairs long • With a replication rate of 2 kb/minute, replicating one human chromosome would require ~35 days. • Solution ---> DNA replication initiates at many different sites simultaneously. Rates are cell specific! Fig. 3.17 What about the ends (or telomeres) of linear chromosomes? Big problem---If this gap is not filled, chromosomes would become shorter each round of replication! Solution: 1. Most eukaryotes have tandemly repeated sequences at the ends of their chromosomes. 2. Telomerase (contains protein and RNA complementary to the telomere repeat) binds to the terminal telomere repeat and catalyzes the addition of of new repeats. 3. Compensates by lengthening the chromosome. 4. Absence or mutation of telomerase activity can result in chromosome shortening and limited cell division. The Eukaryotic Problem of Telomere Replication RNA primer near end of the chromosome on lagging strand can’t be replaced with DNA since DNA polymerase must add to a primer sequence. Different types of Nucleotide Polymerases 1) DNA polymerase Uses a DNA template to synthesize a DNA strand 2) RNA polymerase Uses a DNA template to synthesize an RNA strand (= transcription) 3) Reverse transcriptase Uses an RNA template to synthesize a DNA strand Found in many viruses Telomerase is a specialized reverse transcriptase Telomerase Two components of the human telomerase: – the human RNA subunit(hTR) 5’-CUAACCCUAAC-3’ –The human telomerase reverse transcriptase(hTERT) • Function: Telomerase – Specialized reverse transcriptase – Prevents “shortening ends problem” problem by adding telomeres to the end – Copies only a small segment of RNA that it carries by itself – Requires a 3’ end as a primer – Synthesis proceeds in 5’ – 3’ direction – Synthesizes one repeat then repositions itself – When active provides cell immortality Telomerase is composed of both RNA and protein What are telomeres? • Telomeres are… – Repetitive DNA sequences at the ends of all human chromosomes – They contain thousands of repeats of the sixnucleotide sequence, TTAGGG – In humans there are 46 chromosomes and thus 92 telomeres (one at each end) Telomeres Repeated G rich sequence on one strand in humans: (TTAGGG)n Repeats can be several thousand basepairs long. In humans, telomeric repeats average 5-15 kilobases Telomere specific proteins, eg. TRF1 & TRF2 bind to the repeat sequence and protect the ends Without these proteins, telomeres are acted upon by DNA repair pathways leading to chromosomal fusions What do telomeres do? • They protect the chromosomes. • They separate one chromosome from another in the DNA sequence • Without telomeres, the ends of the chromosomes would be "repaired", leading to chromosome fusion and massive genomic instability. Telomere function, cont’. • Telomeres are also thought to be the "clock" that regulates how many times an individual cell can divide. Telomeric sequences shorten each time the DNA replicates. Telomerase 1. Telomerase binds to the telomer and the internal RNA component aligns with the existing telomer repeats. 2. Telomerase synthesizes new repeats using its own RNA component as a template 3. Telomerase repositions itself on the chromosome and the RNA template hybridizes with the DNA once more. and Primase Structure of Telomeres • Elongated strand of telomere repeats are rich in guanine nucleotides • 5’-TTTTGGGGTTTTGGGGTTTTGGGG-3’ • They have the capacity to hydrogen bond to one another in the form of G-quartets. • These create three-dimensional structures. How Does Telomerase Work? • Telomerase works by adding back telomeric DNA to the ends of chromosomes, thus compensating for the loss of telomeres that normally occurs as cells divide. • Most normal cells do not have this enzyme and thus they lose telomeres with each division. How Does Telomerase Work? • In humans, telomerase is active in germ cells, in vitro immortalized cells, the vast majority of cancer cells and, possibly, in some stem cells. How Does Telomerase Work? • Research also shows that the counter that controls the wasting away of the telomere can be "turned on" and "turned off". The control button appears to be an enzyme called telomerase which can rejuvenate the telomere and allow the cell to divide endlessly. Most cells of the body contain telomerase but it is in the "off" position so that the cell is mortal and eventually dies. How Does Telomerase Work? • Some cells are immortal because their telomerase is switched on • Examples of immortal cells: blood cells and cancer cells • Cancer cells do not age because they produce telomerase, which keeps the telomere intact. Telomerase and Cancer • There is experimental evidence from hundreds of independent laboratories that telomerase activity is present in almost all human tumors but not in tissues adjacent to the tumors. Telomerase and Cancer • Thus, clinical telomerase research is currently focused on the development of methods for the accurate diagnosis of cancer and on novel anti-telomerase cancer therapeutics Experimentation • Many experiments have shown that there is a direct relationship between telomeres and aging, and that telomerase has the ability to prolong life and cell division.