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DNA and RNA Review
1. What are nucleic acids? What is the historic origin of this name? DNA and RNA, the nucleic acids, are the molecules responsible for the hereditary information that commands the protein synthesis in living beings. The name “nucleic” derives from the fact that they were discovered (by the Swiss biochemist Friedrich Miescher, in 1869) within the cell nucleus. In that time it was not known that those substances contained the hereditary information. 2. Of what units are nucleic acids constituted? What are the chemical entities that compose that unit? Nucleic acids are formed by sequences of nucleotides. Nucleotides are constituted by one molecule of sugar (deoxyribose in DNA and ribose in RNA) bound to one molecule of phosphate and to one nitrogen-containing base (adenine, uracil, cytosine or guanine, in RNA, and adenine, thymine, cytosine and guanine, in DNA). Nucleic Acid Review - Image Diversity: nucleotide structure nitrogen-containing bases 3. What are pentoses? To what organic group do pentoses belong? Are nucleotides formed of only one type of pentose? Pentoses are carbohydrates made of five carbons. Deoxyribose is the pentose that constitutes DNA nucleotides and ribose is the pentose that is part of RNA nucleotides. 4. Into which two groups can the nitrogen-containing bases that form DNA and RNA be classified? What is the criterion used in that classification? The nitrogen-containing bases that form DNA and RNA are classified as pyrimidine and purine bases. By the analysis of the structural formulae of those nitrogen-containing bases it is possible to realize that three of them, cytosine, thymine and uracil, have only one nitrogenized carbon ring. The others, adenine and guanine, have two nitrogenized associated carbon rings. Nucleic Acid Review - Image Diversity: pyrimidine bases purine bases 5. Concerning the nitrogen-containing bases that participate in nucleotides, what is the difference between DNA and RNA? In DNA nucleotides can be formed of adenine (A), thymine (T), cytosine (C) or guanine (G). In RNA nucleotides can also contain adenine (A), cytosine (C) or guanine (G), however, instead of thymine (T) there is uracil (U). 6. Which are the nucleotides “portions” that bind in the formation of nucleic acids? What is meant by the 5’ and 3’ extremities of nucleic acids? The phosphate group of one nucleotide binds to the pentose of the other nucleotide and so on to make the polynucleotide chain. Each extremity of a DNA or RNA chain can be distinguished from the other extremity according to their terminal chemical entity. The phosphate-ended extremity is called 5’-extremity and the pentose-ended extremity is called 3’-extremity. So DNA or RNA chains can be run along the 5’-3’ way or along the 3’-5’ way. These ways are important in several biological functions of DNA and RNA since some reactions specifically occur following one way or the other way. 7. Bacteria are prokaryotic cells, i.e., they do not have a membrane-delimited nucleus. Eukaryotes have cells with a delimited nucleus. Where in these types of cells can DNA be found? In eukaryotic cells DNA is found within the cell nucleus. In prokaryotic cells DNA is found dispersed in the cytosol, the fluid space inside the cell. Other DNA molecules can also be found within mitochondria and chloroplasts, specialized organelles of eukaryotic cells. 8. Who were James Watson, Francis Crick and Maurice Wilkins? Watson (North American), Crick (British) and Wilkins (New Zealander) were the discoverers of the molecular structure of DNA, the double helix made of two polynucleotide chains paired by their nitrogen-containing bases. They won the Nobel prize in Medicine in 1962 for the discovery. Nucleic Acid Review - Image Diversity: Watson and Crick 9. According to the Watson-Crick model how many polynucleotide chains does a DNA molecule have? The DNA molecule is formed by two polynucleotide chains bound in antiparallel mode (5’-3’ to 3’-5’) and forming a helical structure. Nucleic Acid Review - Image Diversity: DNA double helix 10. What is the rule for the pairing of nitrogen-containing bases in the DNA molecule? And in the RNA? Is this last question appropriate? The rule for the pairing of nitrogen-containing bases of the polynucleotide chains that form the DNA molecule is pyrimidine base binds to purine base, under the condition that thymine (T) binds to adenine (A) and cytosine (C) binds to guanine (G). In RNA there is no binding between nitrogen-containing bases. That is because RNA is formed of only one polynucleotide chain; differently, DNA is formed of two chains. It is therefore not correct to question base pairing in RNA. Nucleic Acid Review - Image Diversity: DNA base pairing 11. What is the numeric relation between pyrimidine and purine bases in the DNA molecule? Is that relation valid in RNA molecules? The DNA molecule is made of two bound polynucleotide chains that form a helical structure (the double helix). The binding of the two chains is between their nitrogen-containing bases and it always obeys the following rules: adenine (A), a purine base, binds with thymine (T), a pyrimidine base, and guanine (G), a purine base, binds to cytosine (C), a pyrimidine base. Therefore in one molecule of DNA there will be the same number of adenine (A) and thymine (T) and same number of cytosine (C) and guanine (G). The quantities of purine and of pyrimidine bases then will also be the same in a 50% proportion for each type. The relation A = T and C = G, or A/T = C/G = 1, is called Chargaff’s relation and the pairing rules described above are known as Chargaff’s rules. In RNA there are not two nucleotide chains. RNA is a simple chain molecule and there is no necessary proportionality of nitrogen-containing bases to form it. 12. Which type of chemical bond maintains the pairing of each chain in the DNA molecule? To form the DNA molecule, purine bases bind to pyrimidine bases by intermolecular bonds called hydrogen bonds. Hydrogen bonds occur when there is hydrogen near one of these electronegative elements: fluorine, oxygen or nitrogen. In such conditions hydrogen looks like having lost electrons for those elements and a very strong polarization is created. The highly positive hydrogen attracts pairs of electrons of other molecules making a hydrogen bond. 13. What is the completing sequence of nitrogen-containing bases for a AGCCGTTAAC fragment of a DNA chain? TCGGCAATTG. 14. What is the name of the DNA duplication process? What is the main enzyme that participates in it? The process of copying, or duplication, of the DNA molecule is called replication. The enzyme that participates in the formation of a new DNA chain is the DNA polymerase. There are also other important enzymes in the replication process, the helicase, the gyrase and the ligase. Nucleic Acid Review - Image Diversity: DNA replication 15. Why is it not correct to assert that DNA self-replicates? DNA is not completely autonomous in its duplication process because the replication does not occur without enzymatic activity. So it is not entirely correct to assert that DNA self-replicates. 16. How do the two complementary nucleotide chains of the DNA facilitate the replication process of the molecule? The fact that the DNA molecule is made of two polynucleotide chains whose nitrogen-containing bases form hydrogen bonds facilitates the duplication of the molecule. During the DNA replication, the binding of the two chains is broken and each of them serves as a template for the formation of a new nucleotide sequence along it, with the help of the enzyme DNA polymerase and obeying the pairing rule A-T, C-G. At the end of the process two double helix of DNA are produced, each made of an original template chain and of a new synthesized polynucleotide chain. 17. What are the chemical bonds of the DNA molecule that are broken for the replication process to occur? During the DNA replication process, hydrogen bonds between nitrogen-containing bases of the polynucleotide chains are broken. 18. As a result of DNA replication two DNA molecules come into existence. Why is it not correct to assert that two “new” DNA molecules are created? What is the name given to the process concerning that fact? During replication each chain of the DNA molecule acts by pairing new nucleotides and after the process two newly formed chains made with the union of these nucleotides appear. Then two DNA molecules are created, each with one chain from the original molecule and one new chain formed by new nucleotides. Thus it is not entirely correct to assert that the replication produces two new molecules of DNA. It is better to affirm that two new half-molecules are created. For this phenomenon DNA replication is called semiconservative replication. 19. Does DNA replication occur in cell division? Yes. DNA replication occurs in mitosis as well in meiosis. 20. One characteristic of the DNA molecule is its replication capability. What are the consequences of failures during DNA replication? Ideally a DNA molecule should replicate in a perfect way. Sometimes however failures in the duplication occur, with alteration (deletion, addition or substitution) of one or more nucleotides in the molecule. Those mistakes, or mutations, therefore make changes in the protein synthesis process too. For example, the production of an important protein for cells or tissues may be suppressed, new utile or inutile proteins can be created, etc. The mistake in the DNA duplication and the resulting production of altered genetic material are some of the main creative forces for the biological evolution and the diversity of species. 21. Mistakes may happen during every copying process. The same is true for DNA replication. Are there correction systems in cells that try to fix those mistakes? Under which situation are the mistakes carried only by the individual owner of the cell within which the mistake has occurred and in which situation are they transmitted to other individuals? The cell is equipped with an enzymatic system that tries to fix mistakes of the DNA replication process. This system however is not completely efficient. DNA replication mistakes are kept in the original individual where the failure occurred when the phenomenon affects somatic cells. If a replication mistake occurs in the formation of a germline cell (e.g., in gametes) the DNA alteration may be transmitted to the offspring of the individual. 22. Where can RNA be found within cells? In the eukaryote cell nucleus RNA can be found dispersed in the nuclear fluid, along with DNA, and as the main constituent of the nucleolus. In cytosol (in eukaryotes or in bacteria) RNA molecules can be found free, as structural constituent of ribosomes (organelles specialized in protein synthesis) or even associated to them in the process of making proteins. Mitochondria and chloroplasts also have their own DNA and RNA. 23. Does RNA molecule have two polynucleotide chains like DNA? Only DNA has two polynucleotide chains. RNA is formed by just one polynucleotide chain. Nucleic Acid Review - Image Diversity: RNA molecule 24. What is the production of RNA called and what is the enzyme that catalyzes the process? The making of RNA from information contained in DNA is called transcription. The enzyme that catalyzes the process is the RNA polymerase. Nucleic Acid Review - Image Diversity: RNA transcription 25. What are similarities and differences between the transcription process and the replication processes? A DNA polynucleotide chain serves as a template in replication (DNA duplication) as well as in transcription (RNA formation). In both processes the pairing of the two polynucleotide chains of the original DNA molecule is broken by the breaking of hydrogen bonds for the chains to be exposed as templates. The reaction is catalyzed by specific enzymes in transcription and in replication. In replication the enzyme DNA polymerase catalyzes the formation of a new polynucleotide chain using free nucleotides in solution and putting them in the new chain according to the DNA template exposed and to the rule A-T, C-G. In transcription the enzyme RNA polymerase makes a new polynucletide chain according to the DNA template exposed obeying, however, the rule A-U, C-G. In replication the original template DNA chain is kept bound by hydrogen bonds to the newly formed DNA chain and a new DNA molecule is then created. In transcription the association between the template DNA chain and the newly formed RNA is undone and RNA constituted of only one polynucleotide chain is liberated. 26. What are the three main types of RNA? What is meant by heterogeneous RNA? Messenger RNA, or mRNA, transfer RNA, or tRNA, and ribosomal RNA, or rRNA, are the three main types of RNA. The newly formed RNA molecule, a precursor of mRNA, is called heterogeneous RNA (hnRNA). The heterogenous RNA bears portions called introns and portions called exons. The hnRNA is processed in many chemical steps, introns are removed and mRNA is created formed only of exons, the biologically active nucleotide sequences. 27. Concerning their biological function what is the difference between DNA and RNA? DNA is the source of information for RNA production (transcription) and thus for protein synthesis. DNA is still the basis of heredity due to its replication capability. The messenger RNA is the template for protein synthesis (translation). In this process tRNA and rRNA also participate since the first carries amino acids for the polypeptide chain formation and the second is a structural constituent of ribosomes (the organelles where proteins are made). 28. Is there any situation in which DNA is made based on a RNA template? What is the enzyme involved? The process in which DNA is synthesized having as template a RNA chain is called reverse transcription. In cells infected by retroviruses (RNA viruses, like the AIDS or SARS viruses) reverse transcription occurs and DNA is made from information contained in the viral RNA. Viral RNA within the host cell produces DNA with the help of an enzyme called reverse transcriptase. Based on that DNA the host cell then makes viral proteins, new viruses are assembled and viral replication occurs. Nucleic Acid Review - Image Diversity: reverse transcription 29. Do the phosphate and the pentose groups give homogeneity or heterogeneity to the nucleic acid chains? What about the nitrogen-containing groups? Supported by that, which of those groups is expected to directly participate in the highly diverse and heterogeneous genetic coding, i.e., which of those groups is the basis of the information for protein production? The phosphate and the pentose groups are the same in every nucleotide that forms the nucleic acid and so they give homogeneity to the molecule. The nitrogen-containing bases however can vary among adenine, thymine, cytosine, guanine (in DNA) and uracil (in RNA). These variations provide the heterogeneity of the nucleic acid molecule. Homogeneous portions of a molecule seldom would store any information, by the same reason that a sequence of the same letter of the alphabet cannot make many words with different meanings. The nitrogen-containing bases, on the other hand, because they are different (four different types for RNA or DNA), can make different sequences and combinations that allow the diversity of the genetic code. |