Structure of Nucleic Acids .om



The Building Blocks of Nucleic AcidsThis guide will focus on the "central dogma" of biochemistry and molecular biology. We will review the processes responsible for replicating the nucleic acid DNA, transcribing DNA into RNA, and translating an RNA sequence into a functional protein. Knowledge of these topics is critical before a more complex understanding of advanced molecular biology topics is possible. Just as importantly, knowledge of these topics is fundamental to understanding what inside our bodies allowed us to grow as humans and why our growth is different from that of other organisms.Figure 1: The Central Dogma of Biochemistry and Molecular BiologyDNA is the nucleic acid that is responsible for "programming" many or our traits. As the material that composes our genes, DNA has become one of the most fundamental molecules in molecular biology. In Molecular Genetics, we will address some fundamentally important questions. We will learn how DNA, our genetic material, is copied and passed on from generation to generation. We will also address the issue of how the genetic information encoded into a DNA sequence is used in organisms to express certain proteins, the major constituents of cells. In addressing these major questions, we will also see how these processes are not perfect and look at how organisms protect against mutations that could potentially kill cells.In this topic section, Structure of Nucleic Acids, we will begin our discussion at a more elementary level, investigating the structure of the nucleic acids DNA and RNA. As DNA and RNA are the major molecules of molecular biology, understanding their structure is critical to understanding the mechanisms of gene replication and protein synthesis. The structural elements of each of these molecules play key roles in their performance of the various processes of the central dogma. Structure of Nucleic AcidsNucleotides and Nucleic AcidsTermsProblemsBoth DNA and RNA are known as nucleic acids. They have been given this name for the simple reason that they are made up of structures called nucleotides. Those nucleotides, themselves comprising a number of components, bond together to form the double-helix first discovered by the scientists James Watson and Francis Crick in 1956. This discovery won the two scientists the Nobel Prize. For now, when we discuss nucleic acids you should assume we are discussing DNA rather than RNA, unless otherwise specified.NucleotidesA nucleotide consists of three things: A nitrogenous base, which can be either adenine, guanine, cytosine, or thymine (in the case of RNA, thymine is replaced by uracil).A five-carbon sugar, called deoxyribose because it is lacking an oxygen group on one of its carbons.One or more phosphate groups. The nitrogen bases are pyrimidine in structure and form a bond between their 1' nitrogen and the 1' -OH group of the deoxyribose. This type of bond is called a glycosidic bond. The phosphate group forms a bond with the deoxyribose sugar through an ester bond between one of its negatively charged oxygen groups and the 5' -OH of the sugar ().Figure 2.: A NucleotideNucleic AcidsNucleotides join together through phosphodiester linkages between the 5' and 3' carbon atoms to form nucleic acids. The 3' -OH of the sugar group forms a bond with one of the negatively charged oxygens of the phosphate group attached to the 5' carbon of another sugar. When many of these nucleotide subunits combine, the result is the large single-stranded polynucleotide or nucleic acid, DNA ()Figure 3. The Nucleic Acid DNAIf you look closely, you can see that the two sides of the nucleic acid strand shown above are different, resulting in polarity. At one end of the large molecule, the carbon group is unbound and at the other end, the -OH is unbound. These different ends are called the 5'- and 3'-ends, respectively.The Helical Structure of DNAshows a single strand of DNA. However, as stated earlier, DNA exists as a double-helix, meaning two strands of DNA bind together. Figure 4: Double-helical DNAAs seen above, one strand is oriented in the 5' to 3' direction while the complementary strand runs in the 3' to 5' direction. Because the two strands are oppositely oriented, they are said to be anti-parallel to each other. The two strands bond through their nitrogen bases (marked A, C, G, or T for adenine, cytosine, and guanine). Note that adenine only bonds with thymine, and cytosine only bonds with guanine. The nitrogen bases are held together by hydrogen bonds: adenine and thymine form two hydrogen bonds; cytosine and guanine form three hydrogen bonds. An important thing to remember about the structure of the DNA helix is that as a result of anti-parallel pairing, the nitrogen base groups face the inside of the helix while the sugar and phosphate groups face outward. The sugar and phosphate groups in the helix therefore make up the phosphate backbone of DNA. The backbone is highly negatively charged as a result of the phosphate groups.The Importance of the Hydrogen BondHydrogen bonding is essential to the three-dimensional structure of DNA. These bonds do not, however, contribute largely to the stability of the double helix. Hydrogen bonds are very weak interactions and the orientation of the bases must be just right for the interactions to take place. While the large number of hydrogen bonds present in a double helix of DNA leads to a cumulative effect of stability, it is the interactions gained through the stacking of the base pairs that leads to most of the helical stability.Hydrogen bonding is most important for the specificity of the helix. Since the hydrogen bonds rely on strict patterns of hydrogen bond donors and acceptors, and because these structures must be in just the right spots, hydrogen bonding allows for only complementary strands to come together: A- T, and C-G. This complementary nature allows DNA to carry the information that it does. Chargaff's RuleChargaff's rule states that the molar ratio of A to T and of G to C is almost always approximately equal in a DNA molecule. Chargaff's Rule is true as a result of the strict hydrogen bond forming rules in base pairing. For every G in a double-strand of DNA, there must be an accompanying complementary C, similarly, for each A, there is a complementary paired T.DNA is a Right-Handed HelixEach strand of DNA wraps around the other in a right-handed configuration. In other words, the helix spirals upwards to the right. One can test the handedness" of a helix using the right hand rule. If you extend your right hand with thumb pointing up and imagine you are grasping a DNA double helix, as you trace upwards around the helix with your fingers, your hand is moving up. In a left-handed helix, in order to have your hand move upwards with your thumb pointing up, you would need to use your left hand. DNA is always found in the right-handed configuration.The Major and Minor GroovesAs a result of the double helical nature of DNA, the molecule has two asymmetric grooves. One groove is smaller than the other. This asymmetry is a result of the geometrical configuration of the bonds between the phosphate, sugar, and base groups that forces the base groups to attach at 120 degree angles instead of 180 degrees. The larger groove is called the major groove while the smaller one is called the minor groove. Since the major and minor grooves expose the edges of the bases, the grooves can be used to tell the base sequence of a specific DNA molecule. The possibility for such recognition is critical, since proteins must be able to recognize specific DNA sequences on which to bind in order for the proper functions of the body and cell to be carried out. As you might expect, the major groove is more information rich than the minor groove. This fact makes the minor groove less ideal for protein binding.Characteristics of the DNA Double-HelixDNA will adopt two different forms of helices under different conditions--the B- and A-forms. These two forms differ in their helical twist, rise, pitch and number of base pairs per turn. The twist of a helix refers to the number of degrees of angular rotation needed to get from one base unit to another. In the B-form of helix, this is 36 degrees while in the A-form it is 33 degrees. Rise refers to the height change from one base pair to the next and is 3.4 angstroms in the B-form and 2.6 angstroms in the A-form. The pitch is the height change to get one full rotation (360 degrees) of the helix. This value is 34 angstroms in the B-form since there are ten base pairs per turn. In the A-form, this value is 28 angstroms since there are eleven base pairs per full turn.Of the two forms, the B-form is far more common, existing under most physiological conditions. The A-form is only adopted by DNA under conditions of low humidity. RNA, however, generally adopts the A-form in situations where the major and minor grooves are closer to the same size and the base pairs are a bit tilted with respect to the helical axis.Bases, Sugars, and PhosphatesProblemsProblemsNow that we've looked at the general structure of DNA, we should take a closer look at the structures that make up nucleotides.The Bases of DNAThe four nitrogen bases found in DNA are adenine, cytosine, guanine, and thymine. Each of these bases are often abbreviated a single letter: A (adenine), C (cytosine), G (guanine), T (thymine). The bases come in two categories: thymine and cytosine are pyrimidines, while adenine and guanine are purines (). Figure 5: DNA BasesThe pyrimidine structure is produced by a six-membered, two-nitrogen molecule; purine refers to a nine-membered, four-nitrogen molecule. As you can see, each constituent of the ring making up the base is numbered to help with specificity of identification.Base Pairing in DNAThe nitrogen bases form the double-strand of DNA through weak hydrogen bonds. The nitrogen bases, however, have specific shapes and hydrogen bond properties so that guanine and cytosine only bond with each other, while adenine and thymine also bond exclusively. This pairing off of the nitrogen bases is called complementarity. In order for hydrogen bonding to occur at all, a hydrogen bond donor must have a complementary hydrogen bond acceptor in the base across from it. Common hydrogen bond donors include primary and secondary amine groups or hydroxyl groups. Common acceptor groups are carbonyls and tertiary amines ().Figure 6: Common Hydrogen Bond Donors and AcceptorsThere are three hydrogen bonds in a G:C base pair. One hydrogen bond forms between the 6' hydrogen bond accepting carbonyl of the guanine and the 4' hydrogen bond accepting primary amine of the cytosine. The second between the 1' secondary amine on guanine and the 3' tertiary amine on cytosine. And the third between the 2' primary amine on guanine and the 2' carbonyl on cytosine ().Figure 7: Guanine : Cytosine Base PairBetween an A:T base pair, there are only two hydrogen bonds. One is found between the 6' primary amine of adenine and the 4' carbonyl of thymine. The other between the 1' tertiary amine of adenine and the 2' secondary amine of thymine ().Figure 8: Adenine : Thymine Base PairThe Deoxyribose SugarThe deoxyribose sugar in DNA is a pentose, a five-carbon sugar. Four carbons and an oxygen make up the five-membered ring; the other carbon branches off the ring. Similar to the numbering of the purine and pyrimidine rings (seen in ), the carbon constituents of the sugar ring are numbered 1'-4' (pronounced "one-prime carbon"), starting with the carbon to the right of the oxygen going clockwise (). The fifth carbon (5') branches from the 4' carbon.Figure 9: Deoxyribose SugarIt is from this numbering system of the sugar group that DNA gets its polarity. The linkages between nucleotides occur between the 5' and 3' positions on the sugar group. One end has a free 5' end and the other has a free 3' end.Attached to the remaining free carbons at the 1', 3' and 5' positions is an oxygen-containing hydroxyl group (-OH). The DNA sugar is called a deoxyribose because it is lacking a hydroxyl group at the 2' position. Instead there is just a hydrogen (see ).PhosphatesA phosphate group consists of a central phosphorous surrounded by four oxygens. Figure 10: Phosphate GroupThe phosphorous is single-bonded to three of the oxygens and double-bonded to the fourth. Due to the nature of the chemical bonds, there is a negative charge on each oxygen that has only one bond coming off of it. This negative charge accounts for the overall negative charge on the phosphate backbone of a DNA molecule.RNAProblemsProblemsDifferences Between DNA and RNAStructurally, DNA and RNA are nearly identical. As mentioned earlier, however, there are three fundamental differences that account for the very different functions of the two molecules. RNA is a single-stranded nucleic acid.RNA has a ribose sugar instead of a deoxyribose sugar like DNA.RNA nucleotides have a uracil base instead of thymine.Other than these differences, DNA and RNA are the same. Their phosphates, sugars, and bases show the same bonding patterns to form nucleotides and their nucleotides bind to form nucleic acids in the same way.The Uracil BaseThe uracil base replaces thymine in RNA. Thymine and uracil are structurally very similar. Uracil has fundamentally the same structure as thymine, with the deletion of a methyl group at the 5' position. Uracil will base pair with adenine in the same way as thymine pairs with adenine ().Figure 11. Adenine:Uracil Base PairThe Ribose SugarThe ribose sugar is structurally identical to the deoxyribose sugar, with the addition of a hydroxyl group at the 2' position ().Figure 12: Ribose SugarThe Three-Dimensional Structure of RNAUnlike DNA, RNA cannot adopt the B-form helix because the additional 2' hydroxyl interferes with the arrangement of the sugars in the phosphate backbone. Although RNA does not adopt the highly ordered B-form of helix, it can be found in the A-form and does base pair to form complex secondary and tertiary structures. The primary structure of a nucleic acid refers to its sequence of base pairs. In RNA, the secondary structures are the two- dimensional base-pair foldings in which local sequences have regions of self- complementarity, giving rise to base pairs and turns. Common secondary structural motifs include hairpins, bulges, and loops.Figure 13: Common Secondary Structures of RNAThe main difference between the three-dimensional structures of DNA and RNA is that in RNA the three-dimensional structure is single-stranded. The base- pairing that occurs in RNA is all through regions of self-complementarity. This three-dimensional arrangement is called the tertiary structure of RNA and it can be very complex.TermsIntroductionNucleotides and Nucleic AcidsAnti-parallel - Refers to the orientations of the two single strands that compose a double-stranded DNA helix. Strands are oriented such that one strand's 5' end is directly across from the other strand's 3' end. Complementary - Term used to refer to the natural pairing of the nitrogen bases within DNA and RNA. In DNA, cytosine pairs with guanine and adenine with thymine. In RNA, the thymine is replaced with uracil, which pairs with adenine. Each member of these pairs are said to be a "complements" of the other. Deoxyribose - A five-membered sugar ring that lacks a hydroxyl group at one position, and is the sugar group for DNA. Double-stranded helix - A common structural motif of DNA. Two linear strands of single-stranded DNA fold into a helical shape stabilized internally by hydrogen bonds between complementary base pairs. Ester bond - In DNA, refers to the oxygen-carbon linkage between the triphosphate group and the 5' carbon of the ribose sugar group in a single DNA or RNA nucleotide. Glycosidic Bond - In DNA, refers to the nitrogen-carbon linkage between the 9' nitrogen of purine bases or 1' nitrogen of pyrimidine bases and the 1' carbon of the sugar group. Helical Twist - The angular rotation needed to get from one nucleotide to another in helical structures. Hydrogen Bonding - Weak, noncovalent linkages between a donor and an acceptor which, when lined up next to each other, have favorable electrostatic interactions. Provide small amount of stability to DNA and RNA helices. Provide specificity of the interactions between polynucleotide strands. Hydrogen Bond Acceptor - A group with at least one free lone pair of electrons. In DNA and RNA, common acceptor groups include: carbonyls, hydroxyls, and tertiary amines. Hydrogen Bond Donor - A group with a free hydrogen group. In DNA and RNA, common donors include secondary amines and hydroxyl groups. Major groove - In a helix, refers to the larger of the unequal grooves that are formed as a result of the double-helical structure of DNA. As a result of the patterns of hydrogen bonding between complementary bases of DNA, the sugar groups stick out at 120 degree angles from each other instead of 180. The major groove is generated by the larger angular distance between sugars. Minor groove - In a helix, refers to the smaller of the unequal grooves that are formed as a result of the double-helical structure of DNA. As a result of the patterns of hydrogen bonding between complementary bases of DNA, the sugar groups stick out at 120 degree angles from each other instead of 180. The minor groove is generated by the smaller angular distance between sugars. Nitrogen Base - One of three components of a nucleotide, nitrogen bases come in two general types: purines and pyrimidines. Of the four nitrogen bases, adenine and guanine are purines, while cytosine and thymine are pyrimidines. Through hydrogen bonding, base pairs link in a complementary nature: adenine with thymine and guanine with cytosine, forming the double-stranded helix of DNA. In RNA, thymine is replaced by uracil. Nucleic Acid - A chain of nucleotides joined together by phosphodiester bonds. Both DNA and RNA are nucleic acids. Nucleotide - A five-membered sugar group with a purine or pyrimidine nitrogen base group attached to its 1' carbon via a glycosidic bond and one or more phosphate groups attached to its 5' carbon via an ester bond. Phosphate Backbone - Refers to the structural organization of the DNA double-helix in which the pyrimidine and purine basic groups face the interior while the phosphate groups line the exterior of the helix. The phosphate backbone carries a negative charge. Phosphate Group - One of three components of a nucleotide, comprised of a central phosphorous surrounded by four oxygens. The phosphate links to the sugar group, carries a negative charge because of the chemical interaction between phosphorous and oxygen, and forms the exterior of the phosphate backbone. Phosphodiester linkage - In a polynucleotide, refers to the bond between the 3' hydroxyl of a sugar group in a nucleotide and a phosphate group attached to the 5' carbon of another sugar group. Pitch - In a helix, refers to the vertical distance traveled in one full turn (360 degrees of twist). Primary Structure - In DNA and RNA, refers to the linear sequence of base pairs or amino acids in a polynucleotide chain. Purine - One of two categories of nitrogen base ring compounds found in DNA and RNA. A purine is a nine-membered double ring composed of one five-membered joined to a six membered ring containing four nitrogens. See pyrimidine. Pyrimidine - One of two categories of nitrogen base ring compounds found in DNA and RNA. A six-membered ring containing two nitrogens. See purine. Ribose - The sugar group of RNA, a five-membered sugar ring containing one oxygen and four carbons with one additional carbon attached to the 4' carbon in the ring and hydroxyl groups attached to the 1', 2', 3', and 5' carbons. See deoxyribose. Right Hand Rule - A trick used to quickly determine the "handedness" or orientation of a helix. In a right-handed helix, if one extends his or her right hand and traces with fingers along the backbone of the helix, the hand and thumb move upwards. Rise - In a helix, the vertical distance traveled when moving from one base pair to the adjacent base pair. Secondary Structure - In DNA and RNA, the local folding patterns of a polynucleotide based on complementary base-pairing. Common motifs include alpha helices and bet-pleated sheets. Sugar Group - One of three components of a nucleotide, a five-ringed carbon sugar, either ribose or deoxyribose in form. The sugar group bonds to the nitrogen base and to the phosphate group. Tertiary Structure - In DNA and RNA, the complex three-dimensional form of a polynucleotide. GUIDE PROBLEMSNucleotides and Nucleic AcidsBases, Sugars, and PhosphatesProblem 1: Name the four DNA bases. Which two are purines? pyrimidines?The four bases are adenine, cytosine, guanine, and thymine. Purine bases are adenine and guanine. Pyrimidine bases are cytosine and thymine. Problem 2: Which position on purine bases binds to the ribose? On pyrimidines?Purine bases bind from their 9' nitrogen to the ribose group. Pyrimidine bases bind from their 1' nitrogen. Problem 3: Why is the DNA sugar group called a "deoxyribose"? What group is the DNA ribose group missing and at what position?The DNA sugar group is called a deoxyribose, instead of a ribose, because it lacks an -OH group at its 2' position. Problem 4: What force holds complementary base pairs together?Hydrogen bonds between hydrogen bond donors and acceptors on each base. Problem 5: Problem 6:Identify the three major groups in the figure.SolutionProblem 7: What three structures compose a nucleotide?A nucleotide is composed of a five-carbon sugar, nitrogen base, and one or more phosphate groups. Problem 8: What is the name of the type of bond that occurs between a phosphate and ribose group? Between a ribose and nitrogen base group?An ester bond forms between a phosphate group and a ribose group. A glycosidic bond forms between a ribose group and a nitrogen base group. Problem 9: Name the bond that forms between nucleotide groups.A phosphodiester bond forms between nucleotides to form nucleic acids. Problem 10: Explain the significance of hydrogen bonds in DNA helices.While hydrogen bonds do contribute a small amount to the stability of helices, their main contribution is to the specificity of a helix. Hydrogen bonds dictate the complementary base pairing that aligns anti-parallel nucleic acids strands in a DNA helix. Problem 11: What does Chargaff's rule say?Chargaff's rule states that the molar ratios of A to T and G to C bases are approximately equal in a DNA helix. This is a result of complementary base pairing between single strands of DNA in a helix. Each A pairs with a T and each G pairs with a C, making their molar ratios equal.Problem 12: What is the name of the sugar group in RNA? How is this different from the sugar group in DNA?The RNA sugar group is a ribose group. DNA contains a 2' deoxyribose group. They are different in that the DNA sugar lacks a 2' –OH group that is present in the RNA sugar. Problem 13: RNA does not contain the base group thymine. What base is found in its place? What is the structural difference between this base and thymine?RNA contains the base uracil. Structurally, uracil is identical to thymine except that it lacks a methyl group attached to its 5' carbon. Problem 14: What is the main three-dimensional structural difference between DNA and RNA?While DNA is found in a double-stranded helix, RNA is found in single strands. Although it is not found in double-strands, it still adopts complex three-dimensional helical structures. Problem 15: What prevents RNA from adopting the B helical form?RNA contains an additional –OH attached to its 3' carbon. This additional group prevents the B helical form because it is too large. As a result, RNA adopts the A helical form. Problem 16: Why does Chargaff's rule not apply to RNA?RNA is found as a single stranded molecule. Chargaff's rule states that DNA helices contain equal molar ratios of A to T and G to C. This is because DNA is found as a double stranded helix in which A and T and G and C bases pair complementarily. RNA only forms local helices meaning that it doesn't necessarily contain equal ratios. ................
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