Learn key concepts related to DNA and RNA for the DAT, plus practice questions and answers

DNA and RNA for the DAT green banner — Everything you need to know about DNa and rna for the dat

Part 1: Introduction to DNA and RNA

DNA contains the genetic information that makes up our chromosomes. It can replicate to synthesize more DNA strands, and it can be transcripted into RNA. RNA can subsequently be translated into amino acids, which form proteins that are essential for functioning. While these concepts can be confusing at first, they are high-yield on the DAT. Study this guide closely, paying attention to any bolded terms.

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Part 2: Structure of DNA

Let's examine the structure of DNA. DNA adopts a double helix configuration, which is its distinctive feature. Within the double helix, two DNA strands coil around each other to form a helical pattern resembling a twisted ladder. The DNA molecule comprises two essential components: nucleotides and the sugar-phosphate backbone. These nucleotides, including adenosine monophosphate (adenine), guanosine monophosphate (guanine), cytidine monophosphate (cytosine), and deoxythymidine monophosphate (thymine), pair up to form the rungs of the ladder. Each nucleotide possesses a distinct structure, as detailed below.

FIGURE 1: NUCLEOTIDE BASES IN DNA — **FIGURE 1:** NUCLEOTIDE BASES IN DNA

What is the commonality among these four nucleotides? They all share a highly similar structure. Each nucleotide comprises a phosphate group (PO4-), a nitrogenous base, and a pentose sugar that serves as a linkage between the other two components. In contrast, nucleosides are molecules composed solely of a nitrogenous base and a pentose sugar.

a) Nitrogenous bases

Nucleotides are the building blocks of DNA. They can be categorized into two main classes: purines and pyrimidines. While both purines and pyrimidines share the characteristic of being aromatic nitrogenous bases, they differ significantly in their size and ring structure. Purines consist of two fused rings, making them larger than pyrimidines, which contain only a single ring.

Examining the structure of nitrogenous bases further reveals that adenine and guanine are classified as purine nucleotides, while cytosine and thymine are categorized as pyrimidine nucleotides. However, it is crucial to note that adenine and guanine exhibit differences in organic structure, such as variations in the number and location of attached carbonyl (C=O) bonds. These differences mirror the distinctions found in cytosine and thymine.

Each nucleotide adheres to strict rules governing its interactions with other nucleotides. In DNA, purine bases selectively bond with pyrimidine bases, and vice versa, rather than forming bonds with other purines. Specifically, guanine binds with cytosine, while adenine binds to thymine. This complementary bonding pattern, known as Watson-Crick base pairing, forms the basis of DNA's double helical structure. Although exceptions to these rules exist, they are not typically tested on.

Furthermore, when guanine and cytosine form a base pair, three hydrogen bonds are established between them that provide stability to the DNA molecule. In contrast, when adenine and thymine bond, only two hydrogen bonds are formed. These hydrogen bonds play a critical role in maintaining the structural integrity of DNA and facilitating its replication and transcription processes.

FIGURE 2: HYDROGEN BONDS PROVIDE STABILITY BETWEEN BONDED BASES AND PREVENT ROTATION OF BONDED NUCLEOTIDES — **FIGURE 2:** HYDROGEN BONDS PROVIDE STABILITY BETWEEN BONDED BASES AND PREVENT ROTATION OF BONDED NUCLEOTIDES

The stability of DNA is enhanced by these hydrogen bonds, favoring the pairing of guanine with cytosine and adenine with thymine. A simple way to recall the nucleotides that bond together is by associating the letters AT and GC. This reminds us that adenine (A) pairs with thymine (T), whereas guanine (G) pairs with cytosine (C).

b) Phosphate backbone

Consider a ladder lacking its side rails, consisting only of rungs—it would hardly serve its purpose as a ladder! Similarly, DNA requires a backbone to uphold its double helix structure. This backbone, known as the sugar-phosphate backbone, is made up of a repetitive arrangement of sugar and phosphate groups bonded together.

Recalling the structure of a nucleotide, each nucleotide base contains a phosphate group and a pentose sugar. The phosphate group attaches to the 5’ carbon of the pentose sugar. Within the sugar-phosphate backbone, the phosphate group of one nucleotide forms a phosphodiester bond with the 3’ carbon of the pentose sugar on the adjacent nucleotide. Examine the diagram below to pinpoint the locations of the phosphodiester bonds.

FIGURE 3: PHOSPHODIESTER BONDS IN THE SUGAR PHOSPHATE BACKBONE — **FIGURE 3:** PHOSPHODIESTER BONDS IN THE SUGAR PHOSPHATE BACKBONE

Phosphodiester bonds form the backbone of DNA by linking adjacent nucleotides. It's crucial to understand that DNA's backbone carries a negative charge, primarily due to the presence of phosphate groups containing charged oxygen atoms. This negative charge creates an attractive force between the DNA molecule and the surrounding aqueous, polar environment.

Now, let's consider what would occur if the negatively charged backbone were situated in the interior of the molecule, with the aromatic bases positioned on the exterior. Such an arrangement would result in an energetically unfavorable conformation. The negative charges on either side of the backbone would repel each other, leading to instability. Moreover, the aromatic bases would not be soluble in water, rendering the molecule insoluble and unable to function effectively.

c) G-C content

Analyzing the nucleotide composition of DNA often involves calculating its G-C content, which denotes the percentage of nucleotide bases containing guanine or cytosine within a DNA fragment. This metric holds significance due to the stability of G-C bonds compared to A-T bonds. G-C bonds, characterized by three hydrogen bonds, are more stable and require more energy to break.

The G-C content plays a pivotal role in determining DNA's melting point and accessibility to polymerases. Higher G-C content indicates a greater number of guanine-cytosine base pairs, thereby increasing the number of hydrogen bonds and necessitating more energy for strand dissociation. A higher G-C content therefore leads to a higher melting point. Conversely, lower G-C content implies reduced stability, lower energy requirements for strand dissociation, and enhanced accessibility to polymerases.

In the context of the DAT, understanding nucleotide composition involves applying Chargaff’s rules, which state a 1-to-1 ratio of purine to pyrimidine nucleotides in DNA. Specifically, the ratios of guanine to cytosine and adenine to thymine are each 1-to-1. These rules stem from the consistent pairing of adenine with thymine and guanine with cytosine, ensuring a balanced nucleotide distribution in DNA strands.

Now, let's consider a DNA fragment with a G-C content of 30%. The relatively low G-C content indicates a correspondingly low melting point and heightened accessibility to polymerases. Applying Chargaff’s rules, we deduce that the DNA must have 15% guanine and 15% cytosine. With adenine and thymine constituting the remaining nucleotides in the DNA, totaling 70% collectively, each must account for 35%.

In summary, our DNA fragment encompasses 15% guanine, 15% cytosine, 35% adenine, and 35% thymine. When combining the percentages of purine nucleotides and pyrimidine nucleotides, as stipulated by Chargaff’s rule, we observe an equal distribution. This distribution results in a 1-to-1 ratio that is consistent with Chargaff's principles.

d) DNA synthesis

As cells undergo growth and division, the need for DNA replication arises. How do cells precisely duplicate extensive sequences of nucleotide bases? First, let's look at the directional aspect of DNA. Each end of the DNA molecule is designated as 5’ or 3’, based on the orientation of the pentose sugar in the nucleotides. The 5’ end marks the termination of the backbone chain, where the phosphate group attaches to the 5’ carbon of the pentose sugar. The 3’ end denotes the site where the 3’ carbon forms a phosphodiester bond with the adjacent nucleotide.

The two strands of DNA run in opposite directions, a configuration known as antiparallel. One strand progresses in the 5’ to 3’ direction, while its complementary strand proceeds in the 3’ to 5’ direction. DNA replication necessitates temporary unzipping of the helix to expose its nucleotides. Since single-stranded DNA is prone to degradation, this unzipping occurs in small intervals that begin at the origin of replication. The origin is a region rich in adenine-thymine bonds. Eukaryotic chromosomes often feature multiple origins of replication, enabling concurrent replication at distinct sites.

Vital enzymes, such as helicase and DNA topoisomerase, initiate the unzipping process and alleviate DNA coiling, respectively. As DNA unwinds, it can form tangled structures called supercoils, which topoisomerases resolve by selectively cutting and repairing the phosphate backbone. The unzipping proceeds bidirectionally away from the origin of replication, facilitating replication in both directions and expediting the process.

DNA polymerase, a key enzyme, continuously adds nucleotides to synthesize a new daughter strand, while ligase seals the nucleotides together. Notably, DNA polymerase synthesizes DNA in a 5’ to 3’ direction, necessitating that the template strand it operates on runs in the 3’ to 5’ direction. While this applies to one of the strands, known as the leading strand, it's essential to remember that the two DNA strands are antiparallel. The other strand, then, is termed the lagging strand and runs in the 5’ to 3’ direction.

Replication of the leading parent strand proceeds smoothly, while replication of the lagging parent strand occurs discontinuously. Due to the polymerase's directional constraint, DNA primase continuously generates new primers along the lagging strand. DNA polymerase utilizes these primers to produce short DNA sequences called Okazaki fragments. Finally, DNA ligase seals these fragments and fills in any remaining gaps, completing the formation of a new daughter strand.

FIGURE 5: DNA REPLICATION — **FIGURE 5:** DNA REPLICATION

DNA replication occurs in a semiconservative manner, wherein each strand serves as a template for the synthesis of a new DNA molecule. After one round of replication and mitosis, each daughter cell harbors one original DNA strand from the parent cell and one newly synthesized DNA strand.

During replication, DNA polymerase not only synthesizes the new daughter strand but also meticulously proofreads it. This process ensures accurate pairing of complementary nucleotides between the new and parent strands.

The majority of errors made by DNA polymerase are rectified promptly through proofreading. For any remaining mistakes, mismatch repair mechanisms come into play during the G2 phase of the cell cycle. Enzymes like MSH2 and MLH1 detect, excise, and replace incorrectly paired nucleotides.

Repeated DNA replication leads to progressive shortening of DNA molecule ends, termed telomeres. Telomeres function to safeguard and stabilize DNA coding regions. As telomeres diminish in length, they eventually reach a critical threshold, signaling the end of replication in the cell—a phenomenon known as the Hayflick limit.

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DNA and RNA for the DAT

Learn key concepts related to DNA and RNA for the DAT, plus practice questions and answers

Table of Contents

Part 1: Introduction to DNA and RNA