Feedback D. Incorrect! No, although this is a correct characteristic of RNA, this is not the best response to the questions.

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1 Biochemistry - Problem Drill 23: RNA No. 1 of Which of the following statements best describes the structural highlights of RNA? (A) RNA can be single or double stranded. (B) G-C pairs have 3 hydrogen bonds. (C) A-U pairs have 2 hydrogen bonds. (D) Single-stranded, double-stranded, and loop RNA present different surfaces. (E) All of the above No, although this is a correct characteristic of RNA, this is not the best response to the questions. No, although this is a correct characteristic of RNA, this is not the best response to the questions. No, although this is a correct characteristic of RNA, this is not the best response to the questions. No, although this is a correct characteristic of RNA, this is not the best response to the questions. E. Correct! Yes, all of these statements are accurate with respect to the structure of RNA. Although each RNA molecule has only a single polynucleotide chain, it is not a smooth linear structure. It has extensive regions of complementary AU, or GC pairs. Therefore, the molecule folds on itself forming structures called hairpin loops. In the base paired region, the RNA molecule adopts a helical structure as in DNA. The correct answer is (E).

2 No. 2 of Which of the following is correct with respect to RNA structure? (A) RNA is a polymer having a ribose and nitrogen backbone. (B) RNA has four different bases: adenine, guanine, cytosine and thymine. (C) Adenine, guanine and cytosine are found in DNA uracil replaces adenine in RNA. (D) There are many modified bases and sugars in RNA. (E) Ψ pseudouridine the linkage between uracil and ribose is changed from a C P bond to a C N bond. No, RNA is a polymer having a ribose and phosphate backbone. B. Incorrect No, RNA has four different bases: adenine, guanine, cytosine and uracil. No, Adenine, guanine and cytosine are found in DNA uracil replaces thymine in RNA. D. Correct! Yes, there are many modified bases and sugars in RNA. No, Ψ pseudouridine the linkage between uracil and ribose is changed from a C N bond to a C C bond. RNA is a polymer having a ribose and phosphate backbone. RNA has four different bases: adenine, guanine, cytosine and uracil. Adenine, guanine and cytosine are found in DNA uracil replaces thymine in RNA. There are many modified bases and sugars in RNA. Ψ pseudouridine the linkage between uracil and ribose is changed from a C N bond to a C C bond. Inosine is a deaminated guanine base. Single stranded RNA has a right handed stacking pattern. The correct answer is (D).

3 No. 3 of Ribosome structure is very important to its function. Of the following statements which is correct with respect to the structure of ribosomes? (A) The ribosome is a nucleic acid. (B) In cells its function is to assemble DNA strands. (C) The active ribosome translates DNA into mrna. (D) The ribosome is a kind of enzyme and classified as a deoxyzyme. (E) The active site of the ribosome is made up of RNA. No, the ribosome is a protein. No, in cells its function is to assemble new proteins. No, the active ribosome translates mrna into protein. No, the ribosome is a kind of enzyme and classified as a ribozyme. E. Correct! Yes, the active site of the ribosome is made up of RNA. Messenger RNA (mrna) is translated into protein by the joint action of transfer RNA (trna) and the ribosome, The ribosome is composed of numerous proteins Translation is the whole process by which the base sequence of an mrna is used to order and to join the amino acids in a protein. The three types of RNA participate in this essential protein-synthesizing pathway in all cells; in fact, the development of the three distinct functions of RNA was probably the molecular key to the origin of life. The correct answer is (E).

4 No. 4 of The synthesis of RNA is similar to that of DNA synthesis with the following exception. (A) NTPs are used instead of dntps. (B) No primer is needed. (C) There is no proofreading function. (D) RNA and DNA synthesis is regulated directly by genes and their regulatory elements. (E) All of the above No, while this is a correct statement it is not the best response. No, while this is a correct statement it is not the best response. No, while this is a correct statement it is not the best response. No, while this is a correct statement it is not the best response. E. Correct! Yes, all of these statements are correct with respect the similarities of RNA and DNA replication. The process of DNA and RNA synthesis are similar with the following exceptions. NTPs instead of dntps (no deoxy-) are used. No primer is needed. No proofreading function. Adds Uracil (U) instead of thymine (T). RNA polymerase is involved. The correct answer is (E).

5 No. 5 of The initiation phase of RNA synthesis is characterized by a number of steps. Which of the following is not characteristic of RNA synthesis initiation? (A) RNA polymerase combines with a sigma factor (a polypeptide) to create RNA polymerase holoenzyme. (B) The RNA polymerase recognizes the promoter and initiates transcription. (C) The sigma factor required for efficient binding and transcription. (D) The same sigma factor recognizes a diversity of promoter sequences. (E) RNA polymerase holoenzyme binds promoters and untwists DNA. No, this is characteristic of the initiation phase of RNA synthesis. No, this is characteristic of the initiation phase of RNA synthesis. No, this is characteristic of the initiation phase of RNA synthesis. D. Correct! Yes, different sigma factors recognize different promoter sequences. No, this is characteristic of the initiation phase of RNA synthesis. The initiation phase RNA synthesis is characterized by: RNA polymerase combines with sigma factor (a polypeptide) to create RNA polymerase holoenzyme Recognizes promoters and initiates transcription. Sigma factor required for efficient binding and transcription. Different sigma factors recognize different promoter sequences. RNA polymerase holoenzyme binds promoters and untwists DNA Binds loosely to the -35 promoter (DNA is double stranded) Binds tightly to the -10 promoter and untwists Different types and levels of sigma factors influence the level and dynamics of gene expression (how much and efficiency). The correct answer is (D).

6 No. 6 of The elongation process of RNA synthesis is characterized by a discrete set of events. Which of the following statements is not characteristic of RNA synthesis elongation process? (A) Following the synthesis of about 100 RNA base pairs the sigma factor is released and recycled for other reactions. (B) RNA polymerase completes the transcription at bp/second. (C) DNA untwists rapidly, and re-anneals behind the enzyme. (D) Part of the new RNA strand is hybrid DNA-RNA, but most RNA is displaced as the helix reforms. (E) RNA synthesis involves separation of the DNA strands and synthesis of an RNA molecule in the 5' to 3' direction by RNA polymerase, using one of the DNA strands as a template. A. Correct! No, following the initiation of RNA synthesis of about 8-10 RNA base pairs the sigma factor is released and recycled for other reactions. No, this is characteristic of the elongation phase of RNA synthesis. No, this is characteristic of the elongation phase of RNA synthesis. No, this is characteristic of the elongation phase of RNA synthesis. No, this is characteristic of the elongation phase of RNA synthesis. Following the initiation of RNA synthesis of about 8-10 RNA base pairs the sigma factor is released and recycled for other reactions. The correct answer is (A).

7 No. 7 of RNA synthesis is essentially a chemical reaction that is mediated by enzymes. Which of the following statements does not accurately reflect the chemistry of RNA synthesis? (A) The fundamental reaction of RNA synthesis is the formation of a phosphodiester bond. (B) The 3 -hydroxyl group of the last nucleotide in the chain electrophilically attacks the α-phosphate group of the incoming nucleoside triphosphate with the concomitant release of a pyrophosphate. (C) This reaction is thermodynamically favorable, and the subsequent degradation of the pyrophosphate to orthophosphate locks the reaction in the direction of RNA synthesis. (D) The chemistry of RNA synthesis is identical for all forms of RNA, including messenger RNA, transfer RNA, and ribosomal RNA. (E) The basic steps just outlined also apply to all forms. Their synthetic processes differ mainly in regulation, posttranscriptional processing, and the specific polymerase that participates. No, this statement is correct with respect to the chemistry of RNA synthesis. B. Correct! Yes, the attack is a nucleophilic attack not an electrophilic attack. No, this statement is correct with respect to the chemistry of RNA synthesis. No, this statement is correct with respect to the chemistry of RNA synthesis. No, this statement is correct with respect to the chemistry of RNA synthesis. The fundamental reaction of RNA synthesis is the formation of a phosphodiester bond. The 3 -hydroxyl group of the last nucleotide in the chain nucleophilically attacks the α-phosphate group of the incoming nucleoside triphosphate with the concomitant release of a pyrophosphate. This reaction is thermodynamically favorable, and the subsequent degradation of the pyrophosphate to orthophosphate locks the reaction in the direction of RNA synthesis. The chemistry of RNA synthesis is identical for all forms of RNA, including messenger RNA, transfer RNA, and ribosomal RNA. The basic steps just outlined also apply to all forms. Their synthetic processes differ mainly in regulation, posttranscriptional processing, and the specific polymerase that participates. The correct answer is (B).

8 No. 8 of The RNA polymerase is a critical component in the replication of RNA and facilitates the chemistry of bond formation. Which of the following statements is incorrect with respect to the function of RNA polymerase and its involvement with RNA synthesis? (A) RNA polymerase slides along the DNA, forming an open complex as it moves. (B) The DNA strand known as the template strand is used to make a complementary copy of RNA as an RNA-DNA hybrid. (C) The RNA is synthesized in a 5 to 3 direction using ribonucleoside triphosphates as precursors. Pyrophosphate is released. (D) The complementary rule is the same as the AT/GC rule. (E) The DNA strand known as the template strand is used to make a complimentary copy of RNA as an RNA-DNA hybrid. No, this is a correct statement with respect to RNA polymerase and synthesis. No, this is a correct statement with respect to RNA polymerase and synthesis. No, this is a correct statement with respect to RNA polymerase and synthesis. D. Correct! The complementary rule is the same as the AT/GC rule except that U is substituted for T in the RNA. RNA polymerase slides along the DNA, creating an open complex as it moves. No, this is a correct statement with respect to RNA polymerase and synthesis. RNA polymerase slides along the DNA, forming an open complex as it moves. The DNA strand known as the template strand is used to make a complementary copy of RNA as an RNA-DNA hybrid. The RNA is synthesized in a 5 to 3 direction using ribonucleoside triphosphates as precursors. Pyrophosphate is released. The complementary rule is the same as the AT/GC rule except that U is substituted for T in the RNA. RNA polymerase slides along the DNA, creating an open complex as it moves. The DNA strand known as the template strand is used to make a complementary copy of RNA as an RNA-DNA hybrid. The RNA is synthesized in a 5 to 3 direction using ribonucleoside triphosphates as precursors. Pyrophosphate is released. The complementary rule is the same as the AT/GC rule except that U is substituted for T in the RNA. The correct answer is (D).

9 No. 9 of Immediately following synthesis of mrna it must be processed. Which of the following statements is incorrect with respect to the processing of mrna? (A) 5 cap occurs while the RNA molecule is being transcribed after about 30 nucleotides have been added. (B) Cleavage of the 3 end is followed by adding polyadenosine (poly-a) tail. (C) RNA splicing occurs: exons are removed from the pre-mrna leaving exons connected. (D) RNA splicing is catalyzed by a large protein complex called the spliceosome. (E) All of the statements are correct. No, while this answer is correct it is not the best answer. No, while this answer is correct it is not the best answer. No, while this answer is correct it is not the best answer. No, while this answer is correct it is not the best answer. E. Correct! Yes, all of the answers are correct, so this is the best answer choice. 5 cap occurs while the RNA molecule is being transcribed after about 30 nucleotides have been added. Cleavage of the 3 end is followed by adding polyadenosine (poly-a) tail. RNA splicing occurs: exons are removed from the pre-mrna leaving exons connected. RNA splicing is catalyzed by a large protein complex called the spliceosome. In eukaryotes during post transcriptional modification mrna is converted into mature mrna. The correct answer is (E).

10 No. 10 of There are a number of polymerases involved in RNA synthesis. The following characteristics are associated with which of these polymerase molecules? 1. Transcribes DNA to synthesize rrna. 2. It is made up of 12 protein subunits. 3. It carries out about 80% of all the transcription in a cell. (A) RNA polymerase I (B) RNA polymerase II (C) RNA polymerase III (D) RNA polymerase IV (E) None of the above A. Correct! Yes, RNA polymerase I consists of 12 protein subunits, carries out about 80% of the transcription in a cell and transcribes DNA to synthesize rrna. No, these characteristics are not that of RNA II. No, these characteristics are not that of RNA III. No, there is no such thing as RNA polymerase IV. No, one of the listed polymerases is accurately described. RNA polymerase I: transcribes DNA to synthesize rrna. It is made up of 12 protein subunits. It carries out about 80% of all the transcription in a cell. RNA polymerase II: also called RNAP II catalyzes the transcription of DNA to synthesize precursors of mrna and most snrnas. Requires many transcription factors for it to bind to its promoter. RNA polymerase III: transcribes DNA to synthesize ribosomal 5S rrna, trna and other small RNAs. RNA pol III transcribes housekeeping genes that are required in virtually all cell types. Regulation of Pol II is tied to regulation The correct answer is (A).