Chapter 25 Homework Assignment

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1 Chapter 25 Homework Assignment The following problems will be due once we finish the chapter: 4, 5, 8, 9, 11 Minimal Coverage of Section 25.3 Chapter 25 1 Chapter 25 DNA Metabolism DNA Polymerase III 1

2 We Need Nucleic Acids! RNA rrna DNA RNA mrna Protein Protein Trait Pol trna DNA contains genes, the information needed to synthesize functional proteins and RNAs DNA also contains segments that play a role in regulation of gene expression (promoters, operators, etc.) Messenger RNAs (mrnas) are transcribed from DNA by RNA polymerases and carry genetic information from a gene to the ribosome complex Ribosomal RNAs (rrnas) are components of the ribosomes and play a role in protein synthesis in conjunction with the template mrna and the AA carrying trna Transfer RNAs (trnas) carry the AAs designated by the codons of the mrna and bind to the Ribosome to help form the growing polypepide chain Chapter 25 3 Nucleotides and Nucleic Acids Nucleotides are the building blocks of nucleic acids A nitrogenous base A phosphate p group (pyrimidines or purine) A pentose sugar Nucleotides have three characteristic components Chapter

3 Structure of a Nucleotide Major Bases in Nucleic Acids The bases are abbreviated by their first letters (A, G, C, T, U). The purines (A, G) occur in both RNA and DNA The pyrimidine C occurs in both RNA and DNA, but T occurs only in DNA, and U occurs only in RNA Chapter 25 5 Nucleic Acid Structure DNA DNA consists of two helical chains wound around the same axis in a right-handed h d fashion aligned in an antiparallel fashion. There are 10.5 base pairs, or 36 Å, per turn of the helix. Alternating deoxyribose and phosphate groups on the backbone form the outside of the helix. The planar purine and pyrimidine bases of both strands are stacked inside the helix. Chapter

4 Nucleic Acid Structure DNA Strands The opposing strands of DNA are not identical, but are complementary. This means: they are positioned to align complementary base pairs: C with G, and A with T, but the strands run antiparallel to each other You can thus predict the sequence of one strand given the sequence of its complementary strand. Note that sequence conventionally is written from the 5' to 3' end Such a structure is useful for information storage and transfer! Chapter 25 7 Nucleic Acid Structure Stabilization of Double Helix Weak forces stabilize the double helix: (1) Hydrophobic Effects: Burying purine and pyrimidine rings in the interior of the helix excludes them from water (2) Stacking interactions: Stacked base pairs form van der Waals contacts (3) Hydrogen Bonds: H-bonding between the base pairs (not on the backbone!) (4) Charge-charge interactions: Electrostated repulsion of negatively charged phosphate groups is decreased by cations (e.g. Mg 2+ ) and cationic proteins Chapter

5 Nucleic Acid Structure Interstrand H-bonding Between DNA Bases Watson-Crick base pairing Chapter 25 9 Nucleic Acid Structure DNA Structure Summary Chapter

6 DNA Metabolism The BIG Picture DNA is the molecular vehicle used for the stable storage of genetic information Stable does not mean static however! DNA metabolism encompasses: Processes that yield faithful copies of DNA molecules (aka. Replication) Processes that affect the inherent structure of the information (aka. Repair and Recombination) ) What do you think is the most important requirement for any copy of DNA? Chapter DNA Metabolism Gene Naming An Aside Most of what we now know about the replication process was gleaned by observation of bacterial systems (WHY?) In this chapter, you will see the names of numerous genes and their products Bacterial genes are usually names using three lower case, italicized letters that often reflect the gene s apparent function. If more than one gene affects the same process the letters A, B, C, etc. are added dnaa: Gene product that affects DNA replication recb: Gene product that affects recombination Bacterial proteins often retain the name of their genes, except you capitalize the first letter and lose the italics Chapter

7 DNA Metabolism Chapter 25 Chapter 26 Chapter 27 Chapter DNA Replication Replication Follows a Set of Fundamental Rules DNA replication follows a set of fundamental rules that were determined based on early research with bacterial DNA processes: (1) Replication is semi-conservative (2) Replication begins at an origin and usually proceeds bidirectionally (3) DNA synthesis proceeds in a 5 3 direction and is semi-discontinuous Chapter

8 DNA Replication Replication is Semi-conservative Similar to what we see in PCR, each strand of the duplex DNA serves as a template for the synthesis of a new DNA strand The use of these old DNA strands as templates produces two new DNA strands that are duplexed with their template. This process yields four DNA strands in two old/new duplexes This is semi-conservative replication What do you think conservative replication would be? Chapter DNA Replication Replication is Semi-conservative This hypothesis (proposed by our good friends Watson and Crick) was verified by Meselson and Stahl in their CsCl gradient experiment. Chapter

9 DNA Replication So how does Replication start and/or run? Once semi-conservatism was confirmed several other questions came up: Are the parent DNA strands completely unwound before replication? Does replication begin at random points or a unique site? Once initiated, does replication move in uni- or bidirectional directions? Chapter DNA Replication Replication begins at an Origin To be used as a template, the double helix must first be opened up and the two strands separated a ed to expose unpaired bases. The positions at which the DNA helix is first opened are called replication origins In simple cells like those of bacteria or yeast, origins are specified by DNA sequences several hundred nucleotide pairs in length. This DNA contains short sequences that t attract initiator proteins, as well as stretches of DNA that are especially easy to open. What bases do you think are present at the origin? Chapter

10 DNA Replication Now the strands are open, what next? The opening of the duplex puts a bubble of single stranded DNA with two replication forks ready for strand synthesis John Carins demonstrated experimentally that synthesis of the new DNA strands is simultaneous and bidirectional Chapter DNA Replication DNA Synthesis Proceeds 5 3 A new strand of DNA is always synthesized 5 to 3 with the new dntp being added to the 3 OH group The leading strand is the template that is read from its 3 end to its 5 end. The lagging strand is read 5 to 3. What does that mean for the synthesized strand? Uh oh. Reiki Okazaki determined that the lagging strand is in fact synthesized discontinuously in pieces called Okazaki fragments. These fragments are connected later by another enzyme. Chapter

11 Who does all the work? Enzymes of course! Nucleases: DNA Replication Catalyze the hydrolysis of DNA (DNases) or RNA (RNases) Either externally (exonucleases) or at internal sites (endonucleases) Polymerases: Catalyze the formation of a phosphodiester bond between the 5 phosphate and the 3 - OH (dnmp) n + dntp (dnmp) n+1 + PP i Requires a primer, a short strand of DNA (or RNA) that t has a free 3 OH group for elongation All the other players: Helicases, Ligases, Topoisomerases, DNA binding proteins, and many more! Chapter DNA Replication DNA Polymerase Prokaryotes and Eukaryotes actually possess several distinct DNA Polymerases They all catalyze the same fundamental reaction, a phosphoryl group transfer. There are two requirements for DNA polymerization: All DNA Polymerases require a template. All DNA Polymerases require a primer with a free 3 OH group for polymerization. Most primers are RNA that is synthesized by specialized enzymes (e.g. g DNA Primase) The average number of nucleotides added before a DNA polymerase dissociates from a growing strand defines its processivity DNA Polymerases vary greatly in this value. Chapter

12 DNA Replication DNA Polymerase The general DNA Polymerase reaction is a nucleophilic attack of the 3 OH group (the nucleophile) on the α phosphate group of an incoming deoxynucleoside Hydrolysis of PP i will give us another 19 kj/mol of energy to push the reaction Chapter DNA Replication DNA Polymerase Replication is VERY accurate. Good thing! The pairing of bases depends on more than the hydrogen bonding patterns between the bases. In addition, the active site of DNA polymerase accommodates only base pairs with aligned geometries. An incorrect dntp may be able to hydrogen bond with another base, but it generally will not fit in the enzyme active site! Chapter

13 DNA Replication DNA Polymerase Fit in the active site cannot account wholly for the high fidelity of replication An incorrect base is still incorporated for every 10 4 to 10 5 bases added. Almost all DNA polymerases have an intrinsic, separate 3 5 exonuclease activity that double-checks each dntp after it is added. This activity, known as proofreading, is not simply the reverse of the polymerization reaction. Taken with the base selection, DNA Polymerase leaves behind one net error for every 10 6 to 10 8 bases added. Chapter DNA Polymerase III DNA Replication DNA Polymerase Chapter

14 DNA Replication So, let s replicate! What needs to be done? (1) Locate the Origin of replication (2) Unwind the DNA (and continue to unwind it as we move along the template!) (3) We should also probably stabilize the ssdna structure (4) Prime the DNA for the polymerase (remember PCR?) (5) Replicate the DNA (6) Replace the primer (if it was RNA!) (7) Fix the nicks (8) Find the terminus sequence and stop (9) CHECK OUR WORK! Initiation Elongation Termination Chapter DNA Replication DNA Replicase System Replication in E. coli requires 20 or more different enzymes and proteins, each performing a specific task. Taken together, the entire complex is called the DNA Replicase System or the DNA Replisome Components include: Helicases moves along the DNA template and separates the strands using chemical energy (ATP) Topoisomerases relieves topological stress induced by strand separation. DNA-Binding proteins stabilize the separated DNA strands Primases synthesize the RNA primers on the template DNA ligases seal nicks in the phosphodiester backbone Chapter

15 DNA Replication Initiation Chapter DNA Replication Elongation Chapter

16 DNA Replication Elongation The replisome promotes rapid DNA synthesis, adding ~ 1000 nucleotides per second to each strand. Once the Okazaki fragment has be completed, its RNA primer is removed and replaced with DNA by DNA Pol I The remaining nick is sealed by DNA Ligase Chapter DNA Replication DNA Ligase Chapter

17 DNA Replication Termination Eventally, replication forks will meet at a terminus region containing multiple copies of a 20 bp sequence called Ter The Ter sequence is a binding site for the Tus protein (terminus utilization substance) and a Tus-Ter complex is formed. When a replication fork runs into a Tus-Ter complex, it stops. Replication halts when the second fork runs into the stopped fork Chapter DNA Replication Termination Eventually, replication forks will meet at a terminus region containing multiple copies of a 20 bp sequence called Ter The Ter sequence is a binding site for the Tus protein (terminus utilization substance) and a Tus-Ter complex is formed. When a replication fork runs into a Tus-Ter complex, it stops. Replication halts when the second fork runs into the stopped fork Chapter

18 DNA Repair Mutations Unrepaired DNA damage (a lesion) can result in a change in the base sequence of the DNA. If replicated, this change can be passed onto daughter cells and become permanent, a mutation. The mutation can involve base substitutions or the addition/ deletion of one or more base pairs. If the mutation takes place in nonessential DNA or has a negligible effect on gene function, it is termed a silent mutation. A typical mammalian genome accumulates 1000s of lesions in 24 hours Our repair systems manage to keep mutations at around 1 in 1000 lesions. Chapter DNA Repair Repair Systems Chapter

19 DNA Repair Mismatch Repair Mismatches are corrected to reflect the information of the original (template) strand. The repair system must be able to discriminate between the new strand and the template. In E. coli, the cell uses methylation of the template strand to tag it as the original strand. This tagging is catalyzed by Dam methylase Dam methylase methylates DNA at the N 6 position of adenines within (5 )GATC sequences. The tagging mechanism of other bacteria and eukaryotes is still unknown! Chapter DNA Repair Mismatch Repair Chapter

20 DNA Repair Base-Excision Repair The DNA Glycosylases recognize common DNA lesions, such as products of cytosine and adenine deamination, and remove the effected base by cleaving the N-glycosyl bond (CHP 8) This cleavage leaves an apurinic or apyrimidinic site in the DNA (aka. The AP site or abasic site) Now, we need to repair the DNA. This is not merely attaching an undamaged base: AP endonuclease cuts the backbone near the AP site, marking the lesion. DNA Polymerse I removes a segment of DNA at the AP site then synthesizes a new strand from the free 3 OH. DNA Ligase then seals the remaining nick. Chapter DNA Repair Nucleotide-Excision Repair DNA lesions can also cause large distortions of the helical structure of the dsdna (Cyclobutane pyrimidine dimers for example) These distortions are generally repaired by removing whole sections of DNA and replacing it with newly synthesized DNA (aka. Nucleotide - excision repair) Exinuclease because it can cleave at two sites within the same strand Chapter

21 Some damage can be repaired in place. Once such process is catalyzed by the DNA Photolyases These enzymes can utilize energy derived from absorbed light to reverse damage produced from UV light (Pyrimidine dimers!) The chromophore of these enzymes is FADH - and a folate Placental animals (including humans) do not have this class of enzymes. DNA Repair Direct Repair Chapter DNA Repair Direct Repair Enzymes are also available to repair methylated bases. The AlkB protein is an α-kg-fe 2+ - dependent dioxygenase Chapter

22 DNA Repair Recombinational DNA Repair A potentially dangerous type of DNA damage occurs when both strands of the double helix are broken, leaving no intact template strand for repair. If these lesions were left unrepaired, they would quickly lead to the breakdown of chromosomes into smaller fragments The end-joining mechanism, which can be viewed as an emergency solution to the repair of double-strand breaks, is a common outcome in mammalian cells. WHY is this OK??!! The second mechanism transfers nucleotide sequence information from the intact DNA double helix of the homologous chromosome to the site of the double-strand break in the broken helix. A DNA replication process uses the undamaged chromosome as the template for transferring genetic information to the broken chromosome, repairing it with no change in the DNA sequence Chapter 25 Figure 5-53 Alberts et al. Molecular Biology of the Cell 4 th Ed. 43 DNA Recombination The rearrangement of genetic information within and among DNA molecules can collectively be termed genetic recombination These events can fall into three categories: Homologous Genetic Recombination the exchange of genetic information between any two DNA molecules (or segments) that share an extended region of nearly identical sequence. Site-Specific Recombination exchanges occur only at a particular DNA sequence. DNA Transposition usually involves a short segment of DNA with the capacity to move from one location in a chromosome to another. The function of these systems include: DNA Repair; DNA Replication; Regulation of Gene Expression; Chromosome segregation; Maintenance of genetic diversity; and programmed genetic rearrangements during embryonic development. Chapter

23 DNA Recombination Homologous Genetic Recombination The homologous genetic recombination reaction is essential for every proliferating cell because accidents occur in nearly every round of replication that interrupt the replication fork. Recombination occurs with the highest frequency during meiosis Recombination occurs due to the need to keep the two pairs of sister chromatids in close contact for even distribution among the resulting haploid gametes Chapter Figure 5-55 Alberts et al. Molecular Biology of the Cell 4 th Ed. DNA Recombination Site-Specific Recombination Site-specific recombination is limited to specific sequences and is catalyzed by a system including enzymes and a unique recognition site A DNA Recombinase recognizes a recombination site (20 to 200 bp sequence) Chapter

24 DNA Recombination Transposons Recombination also allows for the movement of transposable elements (aka. Transposons) These segments of DNA are found in all cells and can jump from one place on a chromosome to another on the same or a different chromosome. The new location is determined randomly, requiring tight regulation as insertion of an element into a vital gene could result in cell death. Movement is catalyzed by a Transposase that recognizes the terminal repeats at the end of a transposon. Once inserted into the new site, the overhangs are paired by DNA Polymerase and sealed by DNA Ligase. This gives a short direct repeat of the sequence on either side of the insert Chapter 25 Figure 5-70 Alberts et al. Molecular Biology of the Cell 4 th Ed. 47 DNA Recombination Transposons - Immunoglobulins Transposition is an excellent way to introduce diversity into a specific gene area as long as it is regulated. One example of programmed transposition is the generation of complete immunoglobulin genes from separate gene segments within the genome. Like going to the itunes (your genome) and putting together your own playlist (the final Ig) by selecting individual songs (the transposable gene segments). Let s us make millions of Igs without maintaining millions of separate genes. Cool! Chapter

25 DNA Recombination Transposons - Retroviruses Outside the cell, a retrovirus (like HIV) exists as a singlestranded RNA genome packed into a protein capsid along with a virus-encoded reverse transcriptase enzyme. Specific DNA sequences near the two ends of the doublestranded DNA product produced by reverse transcriptase are then held together by a virus-encoded integrase enzyme. This integrase creates activated 3 -OH viral DNA ends that can directly attack a target DNA molecule through a mechanism very similar to that used by the cut-and-paste transposons. Figures 5-73 and 5-75 Alberts et al. Molecular Biology of the Cell 4 th Ed. Chapter

4. DNA replication Pages: 979-984 Difficulty: 2 Ans: C Which one of the following statements about enzymes that interact with DNA is true?

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