Review Sheet for DNA Structure and Function

Review Sheet – DNA Structure and Function 14.2 – DNA Structure and Sequencing 1. What are the building blocks of DNA? Nucleotides 2. What are the components of a nucleotide? A nitrogenous base, deoxyribose (a 5- carbon sugar), and a phosphate group 3. What are the nitrogenous bases? Purines, ex. adenine and guanine. Pyrimidine, ex. cytosine and thymine 4. What sugar is in DNA and what sugar is in RNA? Deoxyribose in DNA and Ribose in RNA 5. What is the name of the bond that links one nucleotide to another in the formation of nucleic acids? Phosphodiester bonds 6. Describe the structure of a purine and a pyrimidine. Purines have a double ring structure with a six- membered ring fused to a five membered ring. Pyrimidines are smaller, and they have a single six membered ring structure. 7. How are the carbon atoms of the five-carbon sugar numbered? 1’, 2’, 3’, 4’, and 5’ one is read as prime 8. Describe the 5’-3’ phosphodiester bond. The Phosphate residue is attached to the hydroxyl group of the 5’ carbon of sugar of one nucleotide and the hydroxyl group of 3’ carbon of the sugar of the next nucleotide. 9. What was Pauling’s contribution to the determination of the structure of DNA? He discovered the secondary structure of proteins using x ray crystallography. 10. What tool was Rosalind Franklin using to understand the structure of DNA? X-ray defraction 11. Who were awarded the Nobel Prize for determining the structure of DNA? Watson & Crick & Wilkins 12. Why wasn’t Franklin included in this group? He passed away. 13. Describe DNA’s structure. It is a double helix with hydrogen bonds. 14. What are the complementary base pairs? How are they stabilized? Adenine and thymine are base pairs, as well as cytosine and guanine. They are stabilized by hydrogen bonds. 15. What does it mean when it’s said that the two strands are anti-parallel in nature? Antiparallel is a term applied to two molecules that are side by side but run in opposite directions. The two strands of DNA are antiparallel. The head of one strand is always laid against the tail of the other strand of DNA. 16. What makes up the backbone of the structure and what is stacked inside? The sugar and phosphate of the nucleotide. 17. How many base pairs are there per turn of the helix? 10 18. What pairings explain the uniform diameter of the molecule? Only the pairing between a purine and pyrimidine can explain the uniform diameter. 19. What role does the major and minor grooves serve? The (c) major and minor grooves are binding sites for DNA binding proteins during processes such as transcription (the copying of RNA from DNA) and replication. 20. Who developed the sequencing method used for the human genome sequencing project? Frederick Sagner and team in 1977 21. What is gel electrophoresis? A technique used to separate DNA fragments of different sizes. 22. What hominid was the closest ancestor of present-day humans? Neanderthals 23. When did they disappear from the fossil records? 30,000 years ago 24. What did their genome show that seems to contradict the view that all present-day humans can be traced to a small ancestral population in Africa? The neanderthal genome had 2 – 3 percent greater similarity to people living outside Africa than to people living in Africa. 25. What genes (governing what traits) seem to have undergone changes from those ancestors during the evolution of present-day humans? Cranial structure, metabolism, skin morphology and cognitive development have changed. DNA Packaging in Cells 26. Describe the typical prokaryotic chromosome and where it is located. Most prokaryotes contain a single, circular chromosome that is found in an area of the cytoplasm called the nucleoid. 27. How does DNA fit inside a small bacterial cell? The DNA is twisted by what is known as supercoiling. 28. Name a protein/enzyme that helps maintain the supercoiled structure? DNA gyrase 29. How do Eukaryotes fit their DNA inside the nucleus? DNA is wrapped around proteins known as histones to form structures called nucleosomes. 30. Describe a nucleosome. A basic unit of DNA packaging in eukaryotes, consisting of a segment of DNA wound in sequence around eight histone protein cores. 31. What are the heterochromatin and the euchromatin? The tightly packaged region is known as heterochromatin, and the less dense region is known as euchromatin. 14.3 – Basics of DNA Replication 1. What were the 3 models for DNA replication? Conservative, semi conservative and dispersive 2. Which model is correct? Semi-conservative 3. Describe how this model works? The two parental strands separate and each makes a copy of itself. After one round of replication, the two daughter molecules each comprises one old and one new strand. Note that after two rounds, two of the DNA molecules consist only of new material, while the other two contain one old and one new strand. 14.4 – DNA replication in Prokaryotes 1. Give a brief description of the DNA replication in E. coli. . E. coli has 4.6 million base pairs in a single circular chromosome and all of it gets replicated in approximately 42 minutes, starting from a single origin of replication and proceeding around the circle in both directions. 2. What is the role of DNA polymerase? It adds nucleotides one by one to the growing DNA chain that are complementary to the template strand. 3. Where is the energy that is used in the addition of nucleotides? Energy is obtained from the nucleotides that have three phosphates attached to them. 4. What are the roles of DNA pol I, DNA pol II, and DNA pol III? DNA pol III is the enzyme required for DNA synthesis. DNA pol I and DNA pol II are primarily used for repair. 5. Describe the origin of replication in E. coli. The replicon is comprised of the origin of replication and all of its control elements. The ORI is the place where DNA replication begins, enabling a plasmid to reproduce itself as it must to survive within cells. The replicons of plasmids are generally different from those used to replicate the host's chromosomal DNA, but they still rely on the host machinery to make additional copies. ORI sequences are generally high in Adenine and Thymine because A-T base pairs are held together with two hydrogen bonds not three as G-C pairs are. As a result, stretches of DNA that are rich in A-T pairs melt more readily at lower temperatures. 6. What enzyme unwinds the DNA and how does it do it? An enzyme called helicase unwinds the DNA by breaking the hydrogen bonds between the nitrogenous base pairs. 7. Describe the replications forks. Very active Y shaped structure where DNA replication takes place. 2 strands of DNA are exposed when the double helix is opened. 8. What is the role of the binding proteins? To coat the single strands of DNA near the replication fork to prevent the single stranded DNA from unwinding. 9. What is the direction in which a new DNA strand can be extended. DNA polymerase is able to add nucleotides only in the 5' to 3' direction (a new DNA strand can be only extended in this direction). 10. If a free 3’-OH group is needed to add a nucleotide, then how does it add the first nucleotide? The problem is solved with the help of a primer that provides the free 3'-OH end. Another enzyme, RNA primase, synthesizes an RNA primer that is about five to ten nucleotides long and complementary to the DNA. 11. Describe the primer and what enzyme makes it. Primase is an enzyme. DNA primase is a type of polymerase that creates an RNA primer, which helps in the process of DNA replication. 12. The nucleotides being added to the growing daughter strand must be on the 3’ end of the template strand. 13. What is the role of topoisomerase? Topoisomerase binds at the region ahead of the replication fork to prevent supercoiling. 14. What are Okazaki fragments? Short sequences of DNA nucleotides which are synthesized discontinuously and later linked together by the enzyme DNA ligase to create the lagging strand during DNA replication. 15. What is the role of ligase? DNA ligase is an enzyme that repairs irregularities or breaks in the backbone of doublestranded DNA molecules. It has three general functions: It seals repairs in the DNA, it seals recombination fragments, and it connects Okazaki fragments. 16. How quickly does the replication fork move? 500-1000 nucleotide pairs per second in bacteria, and 50-100 nucleotide pairs per second in eukaryotic cells, so 10-fold slower. 17. What does it mean when we say the DNA double helix is anti-parallel? DNA is linked in a 5' to 3' direction, meaning that the bases must run from 5' to 3', making the two strands anti-parallel. 18. What does that mean for the new daughter strands? [remember, semi-conservative replication means the double s Each new daughter strand is complementary to its respective parental strand. Because the two parental strands are antiparallel, the two new strands cannot be synthesized in the same way. 19. How many primers are needed for the leading strand and how many are needed for the lagging strand? On the leading strand, only one initial primer is needed because, after the initial priming, the growing DNA strand serves as the primer for continuous addition. On the lagging strand, every Okazaki fragment needs its own primer. The RNA chain composing the primer is then extended as a DNA chain by DNA pol 3. 20. What is the role of the sliding clamp? Helps to hold the DNA polymerase in place when nucleotides are being added. 21. Look at the summary of the process of DNA replication. 14.5 – DNA Replication in Eukaryotes 1. The human genome has how many base pairs per haploid set of chromosomes? 3 billion base pairs 2. What is the rate of replication in eukaryotes and humans can have up to how many origins of replication? The rate of replication is approximately 100 nucleotides per second. 100,000 origins of replication can be found in a single human cell. 3. How many DNA polymerases are there in eukaryotes? 14 4. What is the role of helicase? DNA helicase uses the energy from ATP hydrolysis and opens up the DNA helix. 5. The leading strand is synthesized by what enzyme and the lagging strand by what enzyme? While the leading strand is continuously synthesized by the enzyme pol δ, the lagging strand is synthesized by pol ε. 6. Describe what happens at the end of a linear chromosome due to there being no place for a primer to be made for the DNA fragment of be copied of the end of the chromosome. These ends remain unpaired, and over time these ends may get progressively shorter as cells continue to divide. 7. What are telomeres and what is there role during division? The ends of the linear chromosomes which have repetitive sequences, or codes for genes. 8. What is the 6 base pair sequence in human telomeres? TTAGGG 9. Describe the telomerase enzyme and its role in the replication process. The telomerase enzyme contains a catalytic part and a built-in RNA template. It attaches to the end of the chromosome, and complementary bases to the RNA template are added on the 3' end of the DNA strand. 10. In which cells are telomerase active and not active? Active in germ cells and adult stem cells. It is not active in adult somatic cells. 11. How is telomere shortening associated with aging? Cells that undergo cell division continue to have their telomeres shortened because most somatic cells do not make telomerase. This essentially means that telomere shortening is associated with aging 12. What is the role of telomerase in cancer cells? It reduces DNA damage. 1.6 – DNA Repair 1. How are most mistakes during DNA replication corrected? Mismatch repair enzymes recognize mis-incorporated bases, remove them from DNA, and replace them with the correct bases. In nucleotide excision repair, enzymes remove incorrect bases with a few surrounding bases, which are replaced with the correct bases with the help of a DNA polymerase and the template DNA. 2. If a mistake is found, what happens? If an incorrect base has been added, the enzyme makes a cut at the phosphodiester bond and releases the wrong nucleotide. 3. What is mismatch repair? Mis-incorporated bases 4. What is nucleotide excision repair? It is a type of DNA repair mechanism in which the wrong base, along with a few nucleotides upstream or downstream, are removed. AKA proofreading 5. What are silent mutations, point mutations, substitution mutations, insertion mutations, deletion mutations, and translocation mutations? Mutations may have a wide range of effects. Some mutations are not expressed; these are known as silent mutations. Point mutations are those mutations that affect a single base pair. The most common nucleotide mutations are substitutions, in which one base is replaced by another. 6. What is the result of a mutation occurring in germ cells (the cells that form the gametes, sperm and eggs)? Germ cells are cells that give rise to the gametes, so a mutation in germ cell will be seen in a sperm cell or egg cell but not in a skin cell, for example.