A. Incorrect! A sugar residue is only part of a nucleotide. Go back and review the structure of nucleotides.

Transcription

1 Organic Chemistry - Problem Drill 24: ucleic Acids o. 1 of What are the components of a nucleotide? (A) A sugar residue (B) A sugar residue + a nitrogenous base (C) A sugar residue + a nitrogenous base + phosphate group(s) (D) A sugar residue + phosphate group(s) (E) A nitrogenous base + phosphate group(s) A sugar residue is only part of a nucleotide. Go back and review the structure of nucleotides. A sugar residue bonded to a nitrogenous base is called a nucleoside. Go back and review the structure of nucleotides. C. Correct! A nucleotide is composed of three parts: a sugar, a nitrogen base and at least one phosphate group. A sugar residue and phosphate groups are only part of a nucleotide. Go back and review the structure of nucleotides. A nitrogenous base and phosphate groups are only part of a nucleotide. Go back and review the structure of nucleotides. (1) Recall the structure of nucleotides. There are several components used to construct the nucleotides in chains of DA and RA. A sugar is bonded to a nitrogenous base first to form a nucleoside. The nucleoside is then phosphorylated one to three times to form various nucleotides. Once phosphorylated, the nucleotides are ready to place in a nucleic acid chain. Therefore, the correct answer is (C).

2 o. 2 of The sugar residue below will be found in which nucleic acid? O O O O (A) DA (B) t-ra (C) m-ra (D) r-ra (E) All RAs A. Correct! The sugar shown is 2 -deoxyribose and is the sugar found in DA only. t-ra contains 2 -ribose as a sugar where the 2 carbon has a hydroxyl group on it. Go back and review the structure of the different nucleic acids. m-ra contains 2 -ribose as a sugar where the 2 carbon has a hydroxyl group on it. Go back and review the structure of the different nucleic acids. r-ra contains 2 -ribose as a sugar where the 2 carbon has a hydroxyl group on it. Go back and review the structure of the different nucleic acids. All RAs contain 2 -ribose as a sugar where the 2 carbon has a hydroxyl group on it. Go back and review the structure of the different nucleic acids. (1) Recall the structure of the two nucleic acids DA and RA. The nucleotides used to construct DA and RA consist of a sugar, nitrogenous base and phosphorus groups. The sugar used will differ depending on which nucleic acid it will be used in. DA uses 2- deoxyribose and RA uses ribose. These sugars only differ by one hydroxyl group. In ribose, there is a hydroxyl group on carbon 2 of the ring. In 2-deoxyribose, this hydroxyl group has been replaced by a hydrogen. (2) Study the structure above and determine if it is ribose or deoxyribose. In the above structure, there are two hydrogens on carbon 2 of the ring instead of a hydrogen and a hydroxyl group. Thus, it must be 2-deoxyribose. Therefore, the correct answer is (A).

3 o. 3 of What is the name of the nitrogenous base below? 2 (A) Adenine (B) Thymine (C) Guanine (D) Cytosine (E) Uracil A. Correct! Adenine is a purine base found in both DA and RA. Thymine is a pyrimidine base not a purine base. Go back and review the structural difference between the two types of bases. Be able to identify all five bases by structure. While guanine is a purine base, this is not its structures. Go back and review the structural difference between the two types of bases. Be able to identify all five bases by structure. Cytosine is a pyrimidine base not a purine base. Go back and review the structural difference between the two types of bases. Be able to identify all five bases by structure. Uracil is a pyrimidine base not a purine base. Go back and review the structural difference between the two types of bases. Be able to identify all five bases by structure. (1) Recall the different types of nitrogenous bases used in nucleic acids. There are two types of nitrogenous bases used in nucleic acids: purines and pyrimidines. Purines are bicyclic compounds consisting of a five membered ring fused to a six membered ring. Both rings contain at least two nitrogen atoms. Pyrimidines are monocyclic compounds consisting of a six membered ring containing at least 2 nitrogens. There are two types of purines: adenine and guanine. There are three types of pyrimidines: thymine, uracil, and cytosine. (2) Look at the above structure and determine first whether it is a purine or pyrimidine. It is bicyclic so it must be one of the purines. (3) Determine whether the molecule is adenine or guanine. ere, it becomes important to have the ability to discern the differences between all the bases so that one can identify them on a test. The rings cyclic cores do not differ in adenine and guanine. The only differences in the two bases come from the groups attached to the bicyclic core. In adenine, there is an amino group attached to carbon 6. In guanine, there is a carbonyl at carbon 6 and an amino group attached to carbon 2. The compound above has an amino group at carbon 6 so it must be adenine. Therefore, the correct answer is (A).

4 o. 4 of ow many hydrogen bonds can occur between the nitrogenous bases of guanine and cytosine? (A) 0 (B) 1 (C) 2 (D) 3 (E) 4 All of the sets of complimentary nitrogen bases can form some hydrogen bonds between their structures. Go back and review the complimentary nitrogen bases. All of the sets of complimentary nitrogen bases can form more than one hydrogen bond between their structures. Go back and review the complimentary nitrogen bases. Adenine and thymine can only form two hydrogen bonds between their structures. Go back and review the complimentary nitrogen bases. D. Correct! Guanine and cytosine can form three hydrogen bonds between them. Adenine and thymine can only form two. one of the sets of complementary nitrogen bases can form four hydrogen bonds between themselves. Go back and review the complimentary nitrogen bases. (1) Recall the structure of the nitrogenous bases and their complementarity. Adenine always pairs with thymine in DA or uracil in RA. Guanine always pairs with cytosine. The number of hydrogen bonds that can occur between each base pairing depends on the structure of the bases involved in the pairing. In the adenine-thymine (or uracil) pairing, only two hydrogen bonds can be formed: ydrogen bond O O Sugar Sugar In the guanine-cytosine pairing, three hydrogen bonds can be formed: O Sugar ydrogen bond O Sugar Therefore, the correct answer is (D).

5 o. 5 of Which statement below regarding the structure of DA is incorrect? (A) DA is a long polymer made up of nucleotides and has a backbone made of sugars and phosphate groups joined by phosphodiester bonds. (B) The nitrogenous bases found in DA include guanine and adenine, both purines, and thymine and cytosine, both pyrimidines. (C) A double helix structure is formed when two strands are joined together by hydrogen bonds. (D) The two strands of DA have direction with one end known as the 5 end, which is capped by a hydroxyl group, and the other end known as the 3 end, which is capped by a phosphate group. (E) The two strands in a double helix of DA are antiparallel meaning they run in opposite directions. The backbone of the strands of DA is comprised of sugars and phosphate groups joined by phosphodiester bonds. DA is essentially a long polymer of nucleotides that encodes genetic information.. Go back and review the structure of DA. DA is comprised of four nitrogenous bases: adenine, thymine, guanine, and cytosine. Adenine and guanine are purines and thymine and cytosine are pyrimidines.. Go back and review the structure of DA. The strands in a double helix of DA are held together by hydrogen bonds.. Go back and review the structure of DA. D. Correct! While the two strands of DA do have direction, the 5 end is capped with a phosphate group and the 3 end is capped with a hydroxyl group. DA strands in a double helix are antiparallel which means they run in opposite directions. The 5 end of one strand lines up with the 3 end of the other. Go back and review the structure of DA. (1) Recall what you learned about the structure of DA in this tutorial. DA is a long polymer made up of a backbone made of sugars and phosphate atoms joined by phosphodiester bonds. Each sugar has one of four nitrogenous bases attached to it: adenine, thymine, guanine, and cytosine. Adenine and guanine are purines which contain a bicyclic core while thymine and cytosine are pyrimidines which contain a monocyclic core. DA is double stranded and it has been determined that the bases in DA are complementary meaning the bases on one strand will pair up with those on the second strand. Adenine always pairs with thymine and guanine with cytosine. The two strands of DA are held together by hydrogen bonds between base pairs. The adenine-thymine base pairing can form two hydrogen bonds while the guanine-cytosine base pairing can form three hydrogen bonds per pairing. It has been determined that the two strands of DA form a helical structure with the two strands running in opposite directions (antiparallel). The 5 end of one strand pairs up with the 3 end of the other strand. All 5 ends of DA strands are capped by a phosphate group while all 3 ends of DA strands are capped by a hydroxyl group. (2) Read each statement carefully and determine which one is incorrect. Therefore, the correct answer is (D).

6 o. 6 of What is the complementary base sequence for 5 ATCGGTGTCC 3? (A) 5 TAGCCACAGG 3 (B) 5 CGTAGGCACC 3 (C) 3 TAGCCACAGG 5 (D) 3 CGTAGGCACC 5 (E) 5 TAGCCTGTGG 3 If the given sequence runs from 5 to 3, what direction does the complementary strand have to run? Go back and study base pairing and directionality of DA strands. If the given sequence runs from 5 to 3, what direction does the complementary strand have to run? Also, recall that A pairs with T and C pairs with G. Are the bases in this sequence paired correctly? Go back and study base pairing and directionality of DA strands. C. Correct! The given sequence runs 5 to 3 so the complementary strand must run 3 to 5. Also, the bases are correctly paired in this answer. Recall that A pairs with T and C pairs with G. Are the bases in this sequence paired correctly? Go back and study base pairing and directionality of DA strands. If the given sequence runs from 5 to 3, what direction does the complementary strand have to run? Also, recall that A pairs with T and C pairs with G. Are the bases in this sequence paired correctly? Go back and study base pairing and directionality of DA strands. (1) Recall the directionality of the two strands of DA. DA is composed of two complementary strands of nucleotides. The two strands are antiparallel which means the 5 end of one strand pairs up with the 3 end of the other strand. This fact means that the correct answer will be written in the 3 to 5 direction. Knowing this allows us to eliminate three of the five possible choices. (2) Recall how the nitrogenous bases pair up in DA. Adenine (A) pairs with thymine (T). Guanine (G) pairs with cytosine (C). (3) Write out the correct complementary base sequence for the one given: 5 ATCGGTGTCC 3 3 TAGCCACAGG 5 Therefore, the correct answer is (C).

7 o. 7 of Which nucleotide does not appear in RA? (A) AMP (B) CMP (C) GMP (D) UMP (E) TMP AMP is found in both DA and RA. Go back and review the structure of RA. CMP is found in both DA and RA. Go back and review the structure of RA. GMP is found in both DA and RA. Go back and review the structure of RA. UMP is found only in RA. It replaces one of the other nucleotides. Go back and review the structure of RA. E. Correct! TMP is replaced with UMP in RA. (1) Recall the nucleotides used in nucleic acids. AMP = adenosine 5 -monophosphate CMP = cytidine 5 -monophosphate GMP = guanosine 5 -monophosphate UMP = uridine 5 -monophosphate TMP = thymidine 5 -monophosphate We have seen that DA uses AMP, GMP, CMP, and TMP. But RA substitutes uracil for thymine so it uses UMP instead. Therefore, the correct answer is (E).

8 o. 8 of Which statement about RA structure is incorrect? (A) RA is a linear polymer made up of nucleotide monomers linked by phosphodiester bonds. (B) RA is single stranded and therefore does not form a double helix. (C) The secondary structure of RA molecules typically consists of stem and loop domains. (D) There are three kinds of RA: transfer RA (t-ra), messenger RA (m-ra), and ribosomal RA (r-ra). All three RAs are involved in the process of protein synthesis. (E) Loop regions in RA structure arise from base pairing between complementary stretches of bases within the same strand. The nucleotide monomers of ATP, CTP, GTP, and UTP combine to form a linear polymer of RA and these monomers are linked by phosphodiester bonds. Go back and study the structure of RA to help determine the correct answer. RA is single stranded and will not form a double-stranded double helix like DA does. Go back and study the structure of RA to help determine the correct answer. Stems and loops comprise the secondary structure of RA. Go back and study the structure of RA to help determine the correct answer. The three types of RA, m-ra, t-ra and r-ra, are involved in protein synthesis. Go back and study the structure of RA to help determine the correct answer. E. Correct! Loop regions in RA molecules occur where a lack of complementary bases prevents base pairing. Double helical regions arise from base pairing between complementary stretches of bases within the same strand. (1) Recall the information regarding RA structure that was covered in this tutorial. RA and DA do share some similarities but they also have several differences. RA is a linear polymer made up of nucleotide monomers linked by phosphodiester bonds. Unlike DA, adenine, guanine, cytosine and uracil are the four nitrogenous bases used in RA; thymine is not used at all. Another difference between RA and DA is that RA does not form a double helix because it is single stranded. The secondary structure of RA includes areas called loops and stem domains. Loop regions occur where the lack of complementary bases prevent base pairing. Stem regions are double helical regions that arise from base pairing between complementary stretches of bases within the same strand. There are three types of RA: messenger RA (m-ra), transfer RA (t-ra), and ribosomal RA (r- RA). All three types have some sort of function in protein synthesis. t-ra transfer a specific amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis. m-ra carries information from DA to the ribosome. r-ra binds m-ra during protein synthesis. (2) Read each statement carefully and determine which one contains inaccurate information. Therefore, the correct answer is (E).

9 o. 9 of Which statement best completes this sentence: Transfer RA (t-ra): (A) Transfers a specific amino acid to a growing peptide chain at the ribosome during protein synthesis. (B) as an anticodon region used for codon recognition that binds to specific sequences of mra. (C) Binds to mra by hydrogen bonding. (D) as a CCA tail sequence at the 3 end that is required for recognition of tra by enzymes used in protein translation. (E) All of the above. t-ra is used for transferring amino acids during protein synthesis at the ribosome, however, is this choice the only one that best completes the sentence? t-ra strands have an anticodon region that binds to specific sequences of mra, however, is this choice the only one that best completes the sentence? t-ra does bind to mra by hydrogen bonding, however, is this choice the only one that best completes the sentence? t-ra does have a CCA 3 tail sequence that is used by enzymes to recognize the molecule during translation, however, is this choice the only one that best completes the sentence? E. Correct! All statements correctly describe t-ra s structure and uses. (1) Recall what you learned about transfer RA in the tutorial. t-ra is one of the three types of RA found in the body. It consists of a small RA chain of about nucleotides. It has many interesting structural features including an anticodon region for codon recognition that binds to specific sequences of mra using hydrogen bonding to determine what amino acid should be placed in the amino acid sequence of the growing peptide. It then transfers that specific amino acid to the growing peptide chain at the ribosome during protein synthesis using a CCA tail sequence at the 3 end of the strand. The CCA tail also aids in enzymes recognizing the t-ra during protein translation. (2) Read each statement carefully and determine which best completes the sentence. All answers given are correct and could be used to complete the sentence. Therefore, the correct answer is (E).

10 o. 10 of Which below is the process of producing RA from DA? (A) Replication (B) Transcription (C) Splicing (D) Translation (E) Condensation Replication is the process of making copies of DA from DA during cell division. Go back and review the process of going from DA to a complete protein. B. Correct! Transcription is the process of producing RA molecules from DA. Splicing is the process used to remove non-coding regions of DA. Go back and review the process of going from DA to a complete protein. Translation is the process of producing proteins from RA. Go back and review the process of going from DA to a complete protein. Condensation is the type of reaction that occurs during the process of nucleotide formation. Go back and review the process of going from DA to a complete protein. (1) Recall all the processes used to turn the genetic information coded in DA into proteins. Replication is a process where copies of DA are made from the DA found in the nucleus of the cell during cell division. Transcription is the process of producing RA from DA. Splicing is a process to remove non-coding regions from the copies of DA prior to RA synthesis. Translation is the process of producing proteins from RA. (2) Determine which process is used to make RA from DA. Transcription is used to make RA from DA. Therefore, the correct answer is (B).