2.6: Structure and Function - Nucleic Acids (2023)

Structure

A strand of DNA is a polymer of nucleoside monophosphates linked by phosphodiester bonds. Two of these paired strands make up the DNA molecule, which then twists into a helix. In the more common B form, the DNA helix has a repeat of 10.5 base pairs per turn, with the sugar and phosphate forming the covalent phosphodiester "backbone" of the molecule, and the bases adenine, guanine, cytosine and thymine line up in the middle, where the base pairs we know today are, which look like the rungs of a ladder.

building blocks

The term nucleotide refers to the building blocks of DNA (deoxyribonucleoside triphosphate, dNTP) and RNA (ribonucleoside triphosphate, NTP). To discuss this important group of molecules, it is necessary to define some terms.

Nucleotides contain three primary structural components. These are a nitrogenous base, a pentose sugar, and at least one phosphate. Molecules that contain only a sugar and a nitrogenous base (no phosphate) are called nucleosides. Nitrogenous bases found in nucleic acids include adenine and guanine (called purines) and cytosine, uracil, or thymine (called pyrimidines). There are two sugars found in nucleotides: deoxyribose and ribose (Figure 2.128). Conventionally, the carbons of these sugars are labeled 1' to 5'. (This is to distinguish the carbons of sugars from those of bases, whose carbons are simply labeled 1, 2, 3, etc.) Deoxyribose differs from ribose at the 2' position, where ribose has an OH group. , where deoxyribose has H

Nucleotides that contain deoxyribose are called deoxyribonucleotides and are the forms found in DNA. Nucleotides that contain ribose are called ribonucleotides and are found in RNA. Both DNA and RNA contain adenine, guanine, and cytosine nucleotides, but with few exceptions, RNA contains uracil nucleotides while DNA contains thymine nucleotides. When a base is attached to a sugar, the product, a nucleoside, is given a new name.

• contains uracil= uridine (bound to ribose) / deoxyuridine (bound to deoxyribose)
• shy= ribothymidine (linked to ribosa) / thymidine (linked to deoxyribose)
• containing cytosine= cytidine (linked to ribose - Figure 2.129) / deoxycytidine (linked to deoxyribose)
• that contains guanine= guanosine (bound to ribose) / deoxyguanosine (bound to deoxyribose)
• adenine= adenosine (linked to ribosa) / deoxyadenosine (linked to deoxyribose)

Of these, deoxyuridine and ribothymidine are the least common. The addition of one or more phosphates to a nucleoside makes it a nucleotide. For this reason, nucleotides are often called nucleoside phosphates. The number of phosphates in the nucleotide is indicated by the appropriate prefixes (mono, di, or tri).

For example, cytidine refers to a nucleoside (without phosphate), but cytidine monophosphate refers to a nucleotide (with phosphate). The addition of second and third phosphates to a nucleoside monophosphate requires energy due to the repulsion of negatively charged phosphates, and this chemical energy is the basis for the high-energy triphosphate nucleotides (like ATP) that power cells.

(Video) Structures And Functions of Nucleic Acids

Hint: ribonucleotides as energy sources

Although ATP is the most common and well-known cellular energy source, each of the four ribonucleotides plays an important role in energy supply. GTP, for example, is the source of energy for protein synthesis (translation) as well as some metabolic reactions. A link between UDP and glucose produces UDP-glucose, the building block for glycogen production. CDP is similarly linked to several important molecular components for the synthesis of glycerophospholipids (such as CDP-diacylglycerol).

Most of the ATP produced in cells does not derive from directly coupled biochemical metabolism, but from the combined processes of electron transport and oxidative phosphorylation in mitochondria and/or photophosphorylation that occurs in the chloroplasts of photosynthetic organisms. The energy from the triphosphate in ATP is transferred to the other nucleosides/nucleotides through the action of enzymes called kinases. For example, nucleoside diphosphokinase (NDPK) catalyzes the following reaction

See Also

IB DP Biology Topic 2: Molecular Biology 2.6 Structure of DNA and RNA Study NotesStructure of DNA and RNA (2.5.1) | Biology DP IB: SL 2016 Revision NotesStructure of DNA and RNA (2.5.1) | Biology DP IB: HL 2016 Revision NotesRNA and Protein Synthesis | Notes on the A-Level Biology Review

\[\ce{ATP + NDP <-> ADP + NTP}\]

where "N" of "NDP" and "NTP" is any base. Other kinases can link individual phosphates to nucleosides or to nucleoside monophosphates using energy from ATP.

Structure of DNA strands

Each DNA strand is assembled from dNTPs by the formation of a phosphodiester bond, catalyzed by DNA polymerase, between the 3'-OH of one nucleotide and the 5'-phosphate of the next. The result of this directed chain growth is that one end of the chain has a free 5'-phosphate and the other a free 3'-hydroxyl group (Fig. 2.130). These are known as the 5' and 3' ends of the tape.

Figure 2.131 shows two strands of DNA (left and right). The left strand from 5' to 3' is T-C-G-A, while the right strand from 5' to 3' is T-C-G-A. The strands of double-stranded DNA are arranged in an antiparallel fashion, with the 5' end of one strand opposite the 3' end of the other.

hydrogen bonds

Hydrogen bonds between base pairs hold a nucleic acid duplex together, with two hydrogen bonds per A-T pair (or per A-U pair in RNA) and three hydrogen bonds per G-C pair. Form B DNA has a prominent major groove and minor groove that trace the path of the helix (Figure 2.132). Proteins, such as transcription factors, bind to these grooves and access the base pair hydrogen bonds to "read" the internal sequence.

In addition to the B form (Movie 2.5), other forms of DNA are also known (Fig. 2.133). One of these, Form A, was identified by Rosalind Franklin in the same issue of Nature as the Watson and Crick article. Although the structure of form A is a relatively smaller form of DNA and resembles form B, it is important in the duplex form of RNA and in RNA-DNA hybrids. BothformIt's inForm BDNA oriented the helix in the so-called right-handed shape.

Movie 2.5 - B-shaped DNA duplex spinning in space Wikipedia

superhelicidio

Short stretches of linear DNA duplexes are in B form and are 10.5 base pairs per turn. DNA duplexes in the cell can vary in the number of base pairs per turn they contain. There are many reasons for this. For example, during DNA replication, DNA strands are unwound at the replication site at a speed of 6000 rpm by an enzyme called helicase. The effect of such local unwinding at a site in the DNA has the effect of increasing the previous unwinding. If not relieved, this "strain" on a DNA duplex can lead to structural obstacles to replication.

These adjustments can be made in three ways. First, voltage can provide energy to "reverse" the structure of DNA. Z-DNA may emerge as a means of relaxation. Second, DNA can "supercoil" to relieve tension (Fig.Figures 2.134 and 2.135). In this method, the duplex is crisscrossed over and over again, like a rubber band unwinding when you hold one section and twist another part. Third, enzymes called topoisomerases can relieve or, in some cases, increase tension by adding or removing twists in DNA.

Parameter

To understand topologies, we introduce the concepts of registration and connection number. First, imagine you open a closed circle of DNA and remove one twist or add one twist and then re-form the circle. Since the cables do not have free ends, they cannot relieve the induced stress by adding or removing twists at their ends again. Instead, the tension is relieved by "supercoils" that form when the double filaments intersect (Figure 8 structures in Figure 2.136). Although not apparent, each crossing of the double threads in this way allows the twists to be increased or decreased accordingly. Thus, the superhelicity of the double helix allows it to resume 10.5 base pairs per turn by adding or removing turns and replacing them with turns as needed.

We write the equation L = T + W, where T is the number of turns in a DNA, W is the number of turns, and L is the junction number. The junction number is therefore the sum of the twists and turns. Interestingly, the DNA inside cells normally exists in a supercoiled form. Supercoiling affects the size of the DNA (by compressing it) and also the expression of genes in the DNA, with some expression increased and some expression decreased when supercoiling is present. Enzymes called topoisomerases alter the density of the DNA supercoil and play a role in DNA replication, transcription, and control of gene expression. They work by making cuts on one strand (type I topoisomerases) or both strands (type II topoisomerases) and then adding or removing turns depending on the target DNA. Once this process is complete, the topoisomerase religates the nick/cut made in the DNA in the first step.

Topoisomerases can be targets for antibiotics. The family of antibiotics known as fluoroquinolones works by interfering with the action of type II bacterial topoisomerases. Ciprofloxacin also preferentially targets type II bacterial topoisomerases. Other topoisomerase inhibitors target eukaryotic topoisomerases and are used in the treatment of cancer.

RNS

The structure of RNA (Fig. 2.137) is very similar to that of a single strand of DNA. RNA is made up of ribonucleotides linked together by the same type of phosphodiester bonds as DNA and uses uracil instead of thymine. In cells, RNA is assembled by RNA polymerases, which copy a DNA template in the same way that DNA polymerases replicate a leading strand. During RNA synthesis, uracil is used instead of adenine in the DNA template. The construction of messenger RNAs by copying a DNA template is a fundamental step in translating information from DNA into a form that directs protein synthesis. In addition, ribosomal and transfer RNAs play important roles in "reading" information in mRNA codons and in polypeptide synthesis. RNAs are also known to play an important role in the regulation of gene expression.

ARN-Welt

The discovery in 1990 that RNAs could play a role in catalysis, a role previously thought to be unique to proteins, was followed by the discovery of many more called ribozymes, RNAs that function like enzymes. This suggested the answer to an old chicken-and-egg puzzle: if DNA codes for protein, but DNA replication requires protein, then how did a replicator system arise? This problem could be solved if the first replicator were RNA, a molecule capable of encoding information and carrying out catalysis. Dubbed the “RNA world” hypothesis, this idea suggests that DNA as genetic material and proteins as catalysts came later and became popular because of their advantages. The lack of a 2'OH in deoxyribose makes DNA more stable than RNA. The double-stranded structure of DNA also provides an elegant way to replicate it easily. However, the RNA catalysts are still remnants of this primitive world. In fact, the formation of peptide bonds, essential for protein synthesis, is catalyzed by RNA.

secondary structure

In terms of structure, RNAs are more diverse than their DNA cousins. Cellular RNAs, created by copying regions of DNA, are synthesized as single strands, but often have self-complementary regions resulting in "bends" containing duplex regions. These are most easily visualized on ribosomal RNAs (rRNA) and transfer RNAs (tRNAs) (Fig. 2.138), although other RNAs, including messenger RNAs (mRNAs), small nuclear RNAs (snRNAs), microRNAs (fig. 2.139) and small interfering RNAs (siRNAs) may also have double-stranded regions.

Basenpaarung

Base pairing in RNA is slightly different from that in DNA. This is due to the presence of the uracil base in RNA instead of thymine in DNA. Like thymine, uracil's base pairs with adenine, but unlike thymine, uracil can also pair with guanine to some degree, leading to many more pairing opportunities within a single RNA strand. .

These extra base-pairing opportunities mean that RNA has many opportunities to fold back on itself, which single-stranded DNA cannot. Folding is obviously crucial to protein function, and we now know that some RNAs in their folded form can catalyze reactions like proteins and enzymes. These RNAs are called ribozymes. Because of this, scientists believe that RNA was the first genetic material because it could not only carry information but also catalyze reactions. Such a scheme could allow certain RNAs to make copies of themselves, which in turn would make more copies of themselves, allowing for positive selection.

stability

RNA is chemically less stable than DNA. The presence of the 2'-hydroxyl in ribose makes RNA much more prone to hydrolysis than DNA, which has a hydrogen instead of a hydroxyl. Also, RNA contains uracil instead of thymine. It turns out that cytosine is the chemically least stable base of nucleic acids. It can spontaneously deaminate and, in turn, is converted to uracil. This reaction occurs in both DNA and RNA, but because DNA normally contains thymine instead of uracil, the presence of uracil in the DNA indicates that cytosine deamination has occurred and that the uracil must be replaced. for a cytokine. Such an event occurring in RNA would be essentially undetectable, since uracil is a normal constituent of RNA. RNA mutations are much less consequential than DNA mutations because they are not transmitted between dividing cells.

catalysis

RNA structure, like protein structure, is important for catalytic function in some cases. Like the random coils of proteins that give rise to tertiary structure, the regions of single-stranded RNA that connect the duplex regions also impart tertiary structure to these molecules. Catalytic RNAs, called ribozymes, catalyze important cellular reactions, including peptide bond formation in ribosomes (Fig. 2.114). DNA, which normally exists in cells in strictly double-stranded form (not in tertiary structure per se), is not known to participate in catalysis.

RNA structures are important for reasons other than catalysis. The 3D arrangement of tRNAs is necessary for the enzymes that bind them to amino acids to do so correctly. In addition, small RNAs, called siRNAs, found in the cell nucleus appear to play a role in both gene regulation and cellular defense against viruses. The key to the mechanisms of these actions is the formation of short RNA folding structures that are recognized by cellular proteins and then cut into smaller units. One strand is copied and used to base-pair with specific mRNAs to prevent protein synthesis from them.

denaturing nucleic acids

Like proteins, nucleic acids can be denatured. The forces that hold duplexes together include hydrogen bonds between the bases of each strand, which, like hydrogen bonds in proteins, can be broken by heat or urea. (Another important stabilizing force for DNA arises from the stacking interactions between the bases of a strand.) Single strands absorb light at 260 nm more than double strands. This is called the hyperchromic effect (Figure 2.141) and results from the disruption of the interactions between the stacked bases. Changes in absorbance make it easy to follow the course of DNA denaturation. Denatured duplexes can be easily renatured if the temperature is lowered below the "melting temperature" or Tm, the temperature at which half of the DNA strands are in duplex form. Under such conditions, the two strands can reform the hydrogen bonds between the complementary sequences and restore the duplex to its original state. With DNA, strand separation and reannealing are important to the technique known as polymerase chain reaction (PCR). Strand separation of DNA duplexes is achieved in the process by heating them to boiling point. Hybridization is an important aspect of the method, which requires single-stranded primers to "find" matching sequences in the template DNA and form a duplex. Considerations for efficient hybridization (also called hybridization) include temperature, salt concentration, strand concentration, and magnesium ion levels (see HERE for more information on PCR).

DNA packaging

DNA is by far the largest macromolecule in a cell. For example, the single chromosome in small bacterial cells can have a molecular weight of more than a billion daltons. If you were to take all of the human chromosomal DNA from a single cell and place them side by side, they would be over 2.1 meters long. Such a large molecule requires careful packaging to fit within the confines of a nucleus (eukaryotes) or a tiny cell (bacteria). The eukaryotic chromatin system is the best known, but bacteria also have a system for condensing DNA.

DNA in bacteria

In bacteria, there is no nucleus for DNA. Instead, DNA is contained in a structure called a nucleoid (Figure 2.142). It contains about 60% DNA, with much of the rest being RNA and transcription factors. Bacteria do not have histone proteins for DNA to wind around, but they do have proteins that help organize DNA in the cell, primarily by forming loop structures.

These proteins are known as Nucleoid Associated Proteins and include those designated HU, H-NS, Fis, CbpA and Dps. Of these, HU most closely resembles eukaryotic histone H2B and binds non-specifically to DNA. Proteins associate with DNA and can also form clumps, which can be the source of loops. It is likely that these proteins play a role in the regulation of transcription and the response to DNA damage. They may also be involved in recombination.

eukaryotes

The method eukaryotes use to compress DNA in the nucleus differs significantly, and for good reason: eukaryotic DNAs are typically much larger than prokaryotic DNAs, but they must fit in a nucleus not much larger than a cell. prokaryote. For example, human DNA is about 1,000 times longer than cDNA. The strategy employed in eukaryotic cells is winding: DNA is wound around positively charged proteins called histones. These proteins, which are very similar in sequence in cells as diverse as yeast and humans, come in four types called H1, H2a, H2b, H3, and H4. A sixth type, called H5, is actually an isoform of H1 and is rare. Two each of H2a, H2b, H3 and H4 are found in the central structure of what is called the basic unit of chromatin: the nucleosome (Fig. 2.143).

octave number

The core of 8 proteins is called an octamer. The stretch of DNA wrapped around the octamer totals about 147 base pairs and wraps around it 1 2/3 times. This complex is called the central particle (Figure 2.144). A junction region of approximately 50 to 80 base pairs separates the particles from the core. The term nucleosome then refers to a core particle plus a linker region (Fig. 2.143). Histone H1 is near the junction of the incoming DNA and the histone core. It is often referred to as the linker histone. In the absence of H1, unfused nucleosomes appear "beads on a string" when viewed under the electron microscope.

Histona

Histones have a similar structure and are rich in basic amino acids such as lysine and arginine (Fig. 2.145). These amino acids are positively charged at physiological pH, which allows them to form strong ionic bonds with the negatively charged phosphate backbone of DNA.

In the case of DNA, compression occurs at different levels (Fig. 2.146). The first level is at the nucleosomal level. Nucleosomes are stacked and coiled into higher order structures. 10 nm fibers are the simplest higher order structure (beads on a string) and become progressively more complex. The 30 nm fibers consist of densely packed, stacked nucleosomes. Higher level packing produces the metaphase chromosome which is found in meiosis and mitosis.

The chromatin complex is a logistical problem for DNA replication and (particularly) gene expression processes, where specific regions of DNA need to be transcribed. The alteration of the chromatin structure is, therefore, an essential function for the activation of transcription in eukaryotes. One strategy is to add acetyl groups to positively charged lysine side chains to "loosen" their grip on negatively charged DNA, allowing proteins involved in activating transcription better access to the DNA. The mechanisms involved in the expression of eukaryotic genes are

Ames test

The Ames test (Fig. 2.147) is an analytical method that can be used to determine whether or not a compound causes DNA mutations (is mutagenic). The test is according to Dr. Bruce Ames, a UC Berkeley professor emeritus who was instrumental in its development. In the method, a single base pair of a selectable marker from an organism is mutated on a plasmid to render it inoperable. In the example, a Salmonella strain is generated that does not have the ability to grow in the absence of histidine. Without histidine, the organism will not grow, but when that histidine gene base on the plasmid is converted back to its original base, a functional gene is produced and the organism can grow without histidine.

A culture of the bacterium lacking the functional gene is grown with the necessary supply of histidine. It is divided into two bottles. A compound whose mutagenicity is to be tested is placed in one of the vials. Nothing is added to the other vial. Bacteria from each flask are spread on histidine-free plates. Bacteria will not grow without mutation. The more bacterial colonies grow, the more mutations occur. Note that some colonies will also grow in the flask without the potential mutagenic compound due to mutations unrelated to the potential mutagenic compound.

Mutations occur at low levels in all cells. If the plate of cells in the compound flask has more colonies than the cells in the control (no compound) flask, this would be evidence that the compound is causing more mutations than would normally occur and is therefore a mutagen. . On the other hand, if there is no significant difference in the number of colonies on each plate, this would indicate that it is not mutagenic. The test is not perfect, identifying about 90% of known mutagens, but its simplicity and inexpensive design make it an excellent choice for initial compound screening.