DNA Organization in Eukaryotes and Prokaryotes (6.5) PDF

DNA Organization in Eukaryotes 6.5 and Prokaryotes If you unravelled all the chromosomes in a single human cell, isolated the DNA, and then joined all the double helices end...

DNA Organization in Eukaryotes 6.5 and Prokaryotes If you unravelled all the chromosomes in a single human cell, isolated the DNA, and then joined all the double helices end to end, the molecule you produced would be about 1.8 m long. This entire length of DNA must fit into a cell nucleus that is only 10 µm across. What strategies has life evolved to make it fit? The Packing of Eukaryotic DNA Imagine that you are trying to store a garden hose. The hose takes up much less space if you coil it neatly around a spool. This is exactly what happens in eukaryotic cells. DNA is wound around special proteins, called histones, that act like spools (Figure 1). solenoid DNA double helix (30 nm across) (2.0 nm across) nucleosome chromosome histones in metaphase Figure 1 To fit inside the nucleus, DNA strands wrap around clusters of eight histone proteins to form a nucleosome. Further packing reduces the volume of six nucleosomes to just 30 nm. A length of about 147 nucleotides is wrapped around each group of histones. Histones are positively charged proteins, and the negatively charged DNA strands are attracted to them. This attraction causes the DNA strands to wrap tightly around a cluster of eight histones, greatly reducing the amount of space that the DNA occu- pies. Each unit, consisting of eight histone proteins and the wrapped DNA, is called a nucleosome (Figure 1). Stretches of DNA, called linkers, connect one nucleosome to nucleosome a unit of DNA storage, the next. At this level of organization, the strands of chromatin appear like a string consisting of eight histones with DNA of beads. strands wrapped around them; the The volume of the DNA has now been reduced by a factor of seven. Further DNA around each nucleosome is about packing of the DNA is accomplished by coiling strings of nucleosomes into cylin- 147 nucleotides in length drical fibres with a diameter of 30 nm (3.0 × 10–10 m). These are commonly known as 30 nm chromatin fibres, but they are also called solenoids. Each coil of a solenoid solenoid a group of six nucleosomes contains six nucleosomes (Figure 1). Most of the DNA in the nucleus during the interphase stage is in the form of loosely packed nucleosomes or solenoids. If the DNA contains active genes, the nucleosomes must be altered to allow the proteins and enzymes that are needed for gene expression to access the coding sequences of the bases. Histone molecules may even assist in the regulation of this process. If the DNA contains inactive genes or non-coding sections of genes, the solenoids function as compact storage units that protect the DNA from potential damage. When a cell enters the reproductive stage of its life cycle, the solenoids can be further supercoiled to form the typical X-shaped chromosomes that are visible during the metaphase stage of mitosis. NEL 6.5 DNA Organization in Eukaryotes and Prokaryotes   291 7923_Bio_Ch06_pp264-302.indd 291 3/27/12 5:21 PM  Mini Investigation Packing Mini DNA Investigation skills Skills: Performing, Observing, Analyzing handbook A2.1 Cells have evolved mechanisms for storing large amounts of DNA C. How does this activity differ from the packing of DNA into in small spaces. In this investigation, you will attempt to mimic a nucleus? T/I the storage process using a piece of thread (representing the D. What advantage might there be in having DNA packed as DNA) and a pill capsule (representing a human cell nucleus). chromatin rather than free-floating? T/I Equipment and Materials: empty gelatin capsule (gel cap); E. The gel capsule is approximately 1000 times the size of an 2 m piece of thread actual human cell nucleus. The thread is the same length 1. Using any strategy, try to fit the 2 m piece of thread into as the real DNA in a single human cell. Real DNA, however, the gel capsule. is only about 2.5 nm wide, while the thread you used is A. Were you successful in fitting all the thread into the perhaps 500 000 nm across. How would your results have capsule? Why or why not? T/I changed if the thread had been the true thickness? T/I B. How does this activity mimic the packing of DNA into a cell nucleus? T/I origin Prokaryotic DNA Organization DNA The organization of DNA in both eubacteria and archaea is simpler and has other double helix replication forks features that set it apart from eukaryotic DNA. In this section, however, the discussion will be limited to DNA organization in eubacteria. The bacterial DNA consists almost entirely of one chromosome that is commonly circular (Figure 2). Linear chromo- somes do occur in some forms of bacteria, but they are rare. Unbound by a nuclear membrane, the DNA is less tightly bound and more easily accessed by the enzymes and other molecules involved in replication than eukaryotic DNA is. In addition to the primary circular DNA, smaller circular pieces of DNA float throughout the cell. In a process called conjugation, these smaller circular pieces of DNA, called plasmids, are able to exit one cell and enter another. When two bacteria are close together, a plasmid in one bacterium can pass into the other. The recipient bacterium incorporates the new plasmid into its genome (Figure 3). This feature allows natural variation of bacteria and is very useful for genetic engineering research, since it allows scientists to insert plasmids with desired genes into host bacteria. (You will learn about genetic engineering in Chapter 8). Despite the simplicity of their genomes, prokaryotes face the same problem as eukaryotes when packing their DNA into a small cell. Whereas eukaryotes have addi- Figure 2 Prokaryotic DNA is one long tional proteins that package their DNA, prokaryotes use a coiling technique. Imagine chromosome that may be circular. (or try) twisting an elastic band so that it forms tiny coils along its length. Then keep bacterial chromosome 5 3 plasmid 1 A donor bacterial cell 2 One strand of the plasmid breaks 3 DNA replication of the plasmid 4 When complete, replication has joins with a recipient cell. and begins to move through the bridge is continuous in the donor and produced a copy of the plasmid in from donor to recipient. discontinuous in the recipient. both the donor and recipient cells. Figure 3 Neighbouring bacteria can replicate plasmids, donating the replicated plasmid to the other bacterium. 292   Chapter 6 DNA: Hereditary Molecules of Life NEL 7923_Bio_Ch06_pp264-302.indd 292 3/27/12 5:21 PM  twisting the elastic band until the coils bunch on top of each other and form a tight ball. This formation happens with a bacterial genome and is called supercoiling. Whether supercoiling the continuous twisting of DNA is packed using a complex arrangement (as in eukaryotes) or a supercoil (as in prokaryotic DNA that reduces the volume prokaryotes), nature has evolved different strategies to fit so much information into of the DNA such a small space. Telomeres: A Key Difference The structure of eukaryotic DNA presents another problem: DNA loss during replica- tion. As you learned in Section 6.4, DNA polymerase produces small pieces of DNA (the Okazaki fragments) in the 59 to 39 direction of the lagging strand. The 59 end of each Okazaki fragment is initially attached to an RNA primer (Figure 4(a)). The last Okazaki fragment on the lagging strand begins at the last RNA primer position, which is located close to, but not at, the end of the strand. Normally, the DNA being assembled as part of each following Okazaki fragment meets up with an RNA primer. DNA poly- merase attaches to the end of the DNA fragment and then removes and replaces the RNA primer. However, this does not happen to the primer on the final Okazaki frag- ment, since no DNA is adjacent to the 59 end. Instead, the RNA primer is removed but not replaced. Thus, no DNA is assembled on the lagging strand beyond the position of the last primer. Since the last sequence at the end of the parent strand is not copied, the final DNA is shorter by the amount of this uncopied segment (Figure 4(b)). replication origin end of chromosome 3 parent strand 1 5 5 RNA primer 3 5 replicating DNA 3 leading strand lagging strand 3 DNA 5 3 RNA primer 5 3 replicating DNA 5 3 RNA primer 5 5 parent strand 2 3 (a) during replication DNA polymerase adds only to 3 ends of primer or DNA 3 parent strand 1 5 5 final leading strand of DNA 3 RNA primer removed but not replaced with DNA nucleotides 3 final lagging strand of DNA 5 5 parent strand 2 3 (b) replication complete Figure 4 (a) During replication, the last RNA primer on the lagging strand is positioned close to, but not at, the end of the chromosome. DNA polymerase is unable to synthesize the matching DNA at the end of the parent strand. (b) The last primer on the lagging strand is the only primer removed but not replaced by DNA polymerase. After replication is complete, this new chromosome loses DNA from one end. Note that the new chromosome that includes the other template strand loses DNA from the opposite end (not shown). The loss of DNA during every cycle of replication causes chromosomes to continu- ally shorten and can lead to the loss or damage of important genes. To prevent the loss of essential coding regions of DNA, zones of repetitive, non-coding sequences are telomere a repeating sequence of DNA found at the ends of eukaryotic chromosomes. These sequences are called telomeres. at the end of a chromosome that protects Every time that DNA replicates, part of its telomeres are lost, but the coding regions coding regions from being lost during of DNA remain complete. Telomeres will be discussed in more detail in Section 6.6. replication NEL 6.5 DNA Organization in Eukaryotes and Prokaryotes   293 7923_Bio_Ch06_pp264-302.indd 293 3/27/12 5:21 PM  6.5 Review Summary Cells store their genetic information in the form of chromosomes and plasmids. Eukaryotic chromosomes consist of DNA bound to histones. Together, the DNA and histones form nucleosomes, which are further wound and bundled into solenoids. Bacterial DNA is circular, lacks histones, and undergoes supercoiling to reduce its volume. Plasmids are small circular pieces of bacterial DNA. During conjugation, plasmids move from one bacterium to another. Telomeres are repeating sequences of DNA that are found on the ends of chromosomes. They prevent the loss of the coding regions of DNA during replication. Questions 1. Place the following structures in order of size, 6. Histones play an important role in the activation from smallest to largest: solenoid, nucleosome, of genes. Do online research to learn how the chromosome, histone. T/I methylation of histone proteins is used to turn 2. The nucleus of a certain cell measures 10 µm across, genes on and off. T/I and a solenoid in the cell measures 30 nm across. (a) What is methylation? How many solenoid structures could fit, side by (b) How is this related to what are called the “tails” side, in this nucleus? T/I of histone proteins? 3. What enables DNA to wrap so tightly around a 7. Histones help to protect DNA but are themselves histone complex that it can conserve so much proteins that are coded for by DNA. They can be space? K/U defective if the corresponding DNA has a harmful 4. Use a t-chart or table to compare and contrast the mutation. Go online to find out what diseases are DNA-packing strategies of bacteria and eukaryotes. associated with defects in histone proteins. Would List as many similarities and differences as you can. you expect such diseases to be serious? Why or K/U C why not? T/I 5. Develop a hypothesis to explain why DNA 8. Explain the benefits of having large non-coding replication in bacteria occurs in only one location, regions at the ends of eukaryotic chromosomes. whereas in eukaryotes it occurs in many locations K/U T/I simultaneously. K/U T/I 9. Predict the impact of losing DNA in the telomere region throughout the organism’s life. K/U T/I WEB LINK 294   Chapter 6 DNA: Hereditary Molecules of Life NEL 7923_Bio_Ch06_pp264-302.indd 294 3/27/12 5:21 PM