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Nucleic Acids*# - Biology

Nucleic Acids*# - Biology


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Nucleic acids

Nucleic acids are molecules made up of nucleotides that carry the genetic blueprint of a cell. Interactions known as "base stacking" interactions also help stabilize the double helix. microRNA regulates the use of mRNA for protein synthesis.

Nucleotide structure

The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). The main common difference between these two types of nucleic acids is the presence or absence of a hydroxyl group at the C2 position, also called the 2' position, of the ribose. DNA lacks the ribose and contains a hydrogen atom at that position, hence the name, "deoxy" ribonucleic acid whereas RNA has a hydroxyl functional group at that position.

DNA and RNA are made up of monomers known as nucleotides. Individual nucleotides condense with one another to form a nucleic acid polymer. Each nucleotide is made up of three components: a nitrogenous base (for which there are five different types), a pentose (five-carbon) sugar, and a phosphate group. These are depicted below.

Figure 1. A nucleotide is made up of three components: a nitrogenous base, a pentose sugar, and one or more phosphate groups. Carbon residues in the pentose are numbered 1′ through 5′ (the prime distinguishes these residues from those in the base, which are numbered without using a prime notation). The base is attached to the 1′ position of the ribose, and the phosphate is attached to the 5′ position. When a polynucleotide is formed, the 5′ phosphate of the incoming nucleotide attaches to the 3′ hydroxyl group at the end of the growing chain. Two types of pentose are found in nucleotides, deoxyribose (found in DNA) and ribose (found in RNA). Deoxyribose is similar in structure to ribose, but it has an -H instead of an -OH at the 2′ position. Bases can be divided into two categories: purines and pyrimidines. Purines have a double ring structure, and pyrimidines have a single ring.
Attribution: Marc T. Facciotti (original work)

The nitrogenous base

The nitrogenous bases of nucleotides are organic molecules and are so named because they contain carbon and nitrogen. They are bases because they contain an amino group that has the potential of binding an extra hydrogen, and thus acting as a base by decreasing the hydrogen ion concentration in the local environment. Each nucleotide in DNA contains one of four possible nitrogenous bases: adenine (A), guanine (G) cytosine (C), and thymine (T). RNA contains adenine (A), guanine (G) cytosine (C), and uracil (U) instead of thymine (T).

Adenine and guanine are classified as purines. The primary distinguishing feature of the structure of a purine is double carbon-nitrogen ring. Cytosine, thymine, and uracil are classified as pyrimidines. These are distinguished structurally by a single carbon-nitrogen ring. You will be expected to recognize that each of these ring structures is decorated by functional groups that may be involved in a variety of chemistries and interactions.

Note: practice

Take a moment to review the nitrogenous base in Figure 1. Identify functional groups as described in class. For each functional group identified, describe what type of chemistry you expect it to be involved in. If hydrogen bonded, does the functional group act as a donor or acceptor?

The pentose sugar

The pentose sugar contains five carbon atoms. Each carbon atom of the sugar molecule are numbered as 1′, 2′, 3′, 4′, and 5′ (1′ is read as “one prime”). The two main functional groups that are attached to the sugar are often referred in reference to the carbon number they are bound to. For example, the phosphate residue is attached to the 5′ carbon of the sugar and the hydroxyl group is attached to the 3′ carbon of the sugar. We will often use the carbon number to refer to functional groups on nucleotides so be very familiar with the structure of the pentose sugar.

The pentose sugar in DNA is called deoxyribose, and in RNA, the sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the 2' carbon of the ribose and its absence on the 2' carbon of the deoxyribose. Hence you can determine if you are looking at a DNA or RNA nucleotide by the presence or absence of the hydroxyl group on the 2' carbon atom—you will likely be asked to do so on numerous occasions (including exams).

The phosphate group

There can be anywhere between one and three phosphate groups bound to the 5' carbon of the sugar. When one phosphate is bound, the nucleotide is referred to as a Nucleotide MonoPhosphate (NMP). If two phosphates are bound the nucleotide is referred to as Nucleotide DiPhosphate (NDP). When three phosphates are bound to the nucleotide it is referred to as a Nucleotide TriPhosphate (NTP). The phosphoanhydride bonds between that link the phosphate groups to each other have specific chemical properties that make them good for various biological functions. The hydrolysis of the bonds between the phosphate groups is thermodynamically exergonic in biological conditions and nature has evolved numerous mechanisms to couple this negative change in free energy to help drive many reactions in the cell. Figure 2 shows an example of the hydrolysis of the nucleotide triphosphate ATP.

Note: "high-energy" bonds

The term "high-energy bond" is used A LOT in biology. It is, however, one of those shortcuts we referred to earlier. The term refers to the amount of negative free energy associated with the HYDROLYSIS of that bond! The water is important. While we have tried to minimize the use of the vernacular "high energy" when referring to bonds, keep the above in mind when you are reading or listening to discussions in biology.

Figure 2. ATP (adenosine triphosphate) has three phosphate groups that can be removed by hydrolysis to form ADP (adenosine diphosphate) or AMP (adenosine monophosphate).The negative charges on the phosphate group naturally repel each other, requiring energy to bond them together and releasing energy when these bonds are broken.
Attribution: Marc T. Facciotti (original work)

Double helix structure of DNA

DNA has a double helix structure (shown below). The sugar and phosphate lie on the outside of the helix, forming the backbone of the DNA. The nitrogenous bases are stacked in the interior, like the steps of a staircase in pairs; the pairs are bound to each other by hydrogen bonds. Every base pair in the double helix is separated from the next base pair by 0.34 nm. The two strands of the helix run in opposite directions, meaning that the 5′ carbon end of one strand will face the 3′ carbon end of its matching strand. This is referred to as antiparallel orientation.

Figure 3. Native DNA is an antiparallel double helix. The phosphate backbone (indicated by the curvy lines) is on the outside, and the bases are on the inside. Each base from one strand interacts via hydrogen bonding with a base from the opposing strand.
Attribution: Marc T. Facciotti (original work)

In a double helix, certain combinations of base pairing are chemically more favored than others based on the types and locations of functional groups on the nitrogenous bases of each nucleotide. In biology we find that adenine (A) is chemically complementary with thymidine (T) and guanine (G) is chemically complementary with cytosine (C), as shown below. We often refer to this pattern as "base complementarity" and say that the antiparallel strands are complementary to each other. For example, if the sequence of one strand is of DNA is 5'-AATTGGCC-3', the complementary strand would have the sequence 5'-GGCCAATT-3'.

Figure 4. In a double-stranded DNA molecule, the two strands run antiparallel to one another so that one strand runs 5′ to 3′ and the other 3′ to 5′. The phosphate backbone is located on the outside, and the bases are in the middle. Adenine forms hydrogen bonds (or base pairs) with thymine, and guanine base pairs with cytosine.
Created by Ivy Jose

Functions and roles of nucleic acids and nucleotides

Nucleic acids play a variety of roles in in cellular process besides being the information storage molecule. Nucleic acids, RNA in particular, are believed to be the first biologically active molecules during a period referred to as the "RNA world" when catalytic RNA were thought to serve the dual role as catalysts and information storing molecules. Remnants of the RNA world can be seen in many riboprotein complexes essential for life. In these RNA-Protein complexes, the RNA serves both catalytic and structural roles. Examples of such complexes include, ribosomes, RNases, splicesosome complexes, and telomerase. Nucleotides such as ATP and GTP also serve as mobile short-term energy transport units for the cell. Nucleotides also play important roles as co-factors (in addition to energy vehicles) for many enzymatic reactions. Like lipids, proteins, and carbohydrates, nucleic acids and nucleotides play a wide variety of roles in the cell.


Nucleic Acids

Nucleic acids are key macromolecules in the continuity of life. They carry the genetic blueprint of a cell and carry instructions for the functioning of the cell. The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material found in all living organisms, ranging from single-celled bacteria to multicellular mammals. The other type of nucleic acid, RNA, is mostly involved in protein synthesis. The DNA molecules never leave the nucleus, but instead use an RNA intermediary to communicate with the rest of the cell. Other types of RNA are also involved in protein synthesis and its regulation. We will be going into more detail about nucleic acids in a later section.

DNA and RNA are made up of monomers known as nucleotides connected together in a chain with covalent bonds. Each nucleotide is made up of three components: a nitrogenous base, five-carbon sugar, and a phosphate group (Figure 1). The nitrogenous base in one nucleotide is attached to the sugar molecule, which is attached to the phosphate group.

Figure 1 A nucleotide is made up of three components: a nitrogenous base, a pentose sugar, and one or more phosphate groups.

The nitrogenous bases, important components of nucleotides, are organic molecules and are so named because they contain carbon and nitrogen. They are bases because they contain an amino group that has the potential of binding an extra hydrogen, and thus, decreases the hydrogen ion concentration in its environment, making it more basic. Each nucleotide in DNA contains one of four possible nitrogenous bases: adenine (A), guanine (G) cytosine (C), and thymine (T). RNA contains the base uracil (U) instead of thymine. The order of the bases in a nucleic acid determines the information that the molecule of DNA or RNA carries. This is because the order of the bases in a DNA gene determines the order that amino acids will be assembled together to form a protein.

The pentose sugar in DNA is deoxyribose, and in RNA, the sugar is ribose (Figure 1). The difference between the sugars is the presence of the hydroxyl group on the second carbon of the ribose and hydrogen on the second carbon of the deoxyribose. The carbon atoms of the sugar molecule are numbered as 1′, 2′, 3′, 4′, and 5′ (1′ is read as “one prime”). The phosphate residue is attached to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms a 5′–3′ phosphodiester linkage (a specific type of covalent bond). A polynucleotide may have thousands of such phosphodiester linkages.


Nucleic Acids: DNA and RNA

Living organisms are complex systems. Hundreds of thousands of proteins exist inside each one of us to help carry out our daily functions (see our Fats and Proteins module for more information). These proteins are produced locally, assembled piece-by-piece to exact specifications. An enormous amount of information is required to manage this complex system correctly. This information, detailing the specific structure of the proteins inside of our bodies, is stored in a set of molecules called nucleic acids.

The nucleic acids are very large molecules that have two main parts. The backbone of a nucleic acid is made of alternating sugar and phosphate molecules bonded together in a long chain, represented below:

Each of the sugar groups in the backbone is attached (via the bond shown in red) to a third type of molecule called a nucleotide base:

Though only four different nucleotide bases can occur in a nucleic acid, each nucleic acid contains millions of bases bonded to it. The order in which these nucleotide bases appear in the nucleic acid is the coding for the information carried in the molecule. In other words, the nucleotide bases serve as a sort of genetic alphabet on which the structure of each protein in our bodies is encoded.

In most living organisms (except for viruses), genetic information is stored in the molecule deoxyribonucleic acid, or DNA. DNA is made and resides in the nucleus of living cells. DNA gets its name from the sugar molecule contained in its backbone(deoxyribose) however, it gets its significance from its unique structure. Four different nucleotide bases occur in DNA: adenine (A), cytosine (C), guanine (G), and thymine (T).

Interactive Animation:Chemical Structure of the DNA Nucleotides

These nucleotides bind to the sugar backbone of the molecule as follows:

The versatility of DNA comes from the fact that the molecule is actually double-stranded. The nucleotide bases of the DNA molecule form complementary pairs: The nucleotides hydrogen bond to another nucleotide base in a strand of DNA opposite to the original. This bonding is specific, and adenine always bonds to thymine (and vice versa) and guanine always bonds to cytosine (and vice versa). This bonding occurs across the molecule, leading to a double-stranded system as pictured below:

sugar phosphate sugar phosphate sugar phosphate sugar .
T A C G
¦ ¦ ¦ ¦
A T G C
sugar phosphate sugar phosphate sugar phosphate sugar .


In the early 1950s, four scientists, James Watson and Francis Crick at Cambridge University and Maurice Wilkins and Rosalind Franklin at King's College, determined the true structure of DNA from data and X-ray pictures of the molecule that Franklin had taken. In 1953, Watson and Crick published a paper in the scientific journal Nature describing this research. Watson, Crick, Wilkins and Franklin had shown that not only is the DNA molecule double-stranded, but the two strands wrap around each other forming a coil, or helix. The true structure of the DNA molecule is a double helix, as shown at right.

The double-stranded DNA molecule has the unique ability that it can make exact copies of itself, or self-replicate. When more DNA is required by an organism (such as during reproduction or cell growth) the hydrogen bonds between the nucleotide bases break and the two single strands of DNA separate. New complementary bases are brought in by the cell and paired up with each of the two separate strands, thus forming two new, identical, double-stranded DNA molecules. This concept is illustrated in the animation below.

Interactive Animation: The Replication of DNA

Ribonucleic acid, or RNA, gets its name from the sugar group in the molecule's backbone - ribose. Several important similarities and differences exist between RNA and DNA. Like DNA, RNA has a sugar-phosphate backbone with nucleotide bases attached to it. Like DNA, RNA contains the bases adenine (A), cytosine (C), and guanine (G) however, RNA does not contain thymine, instead, RNA's fourth nucleotide is the base uracil (U). Unlike the double-stranded DNA molecule, RNA is a single-stranded molecule. RNA is the main genetic material used in the organisms called viruses, and RNA is also important in the production of proteins in other living organisms. RNA can move around the cells of living organisms and thus serves as a sort of genetic messenger, relaying the information stored in the cell's DNA out from the nucleus to other parts of the cell where it is used to help make proteins.


1.5 Nucleic Acids Overview

The big picture in this section of the AP Biology curriculum is that heritable information provides for continuity of life. “Heritable” means that it can be passed from one generation to the next, while the “continuity of life” describes the ongoing process of organisms growing, replicating their DNA, and creating a new generation of organisms that share that DNA. This section focuses more specifically on DNA and RNA. We will be looking at how they are similar, how they are different, and the various roles they serve in cells.

The structure of DNA was first worked out in 1953, by researchers Watson and Crick. The team used x-ray crystallography images produced by Rosalind Franklin, who unfortunately died of cancer before she was awarded the Nobel Prize like the rest of the team. Her method of using X-rays to view the structure of DNA ultimately led to the model we still use today.

DNA actually stands for “deoxyribonucleic acid” – a name that references the sugar ribose and the nucleotide bases that are at the heart of every DNA molecule. “Deoxy” references the fact that unlike normal ribose, deoxyribose has lost an oxygen atom. At the molecular level, DNA gets its structure through two main features – the sugar-phosphate backbone and the hydrogen bonds formed between complementary nucleotide bases.

Each nucleotide in the sequence is bonded to the next through a phosphodiester bond, which is created through a dehydration reaction facilitated by the enzyme DNA polymerase. In this bond, the hydroxyl group on the pentose sugar molecule connects to the phosphate group on the new nucleotide. Thus, the new strand is constructed from the 5’ end (with a phosphate group) to the 3’ end (with a hydroxyl). The DNA polymerase molecule moves along the template strand in the opposite direction, from 3’ to 5’, since the two strands run antiparallel.

Within the structure of a DNA molecule, the nitrogenous bases stick out perpendicularly from the sugar-phosphate backbone. The sugar-phosphate backbone creates a helix structure, due to the angle of the bonds it is made out of. With the addition of nitrogenous bases that form hydrogen bonds with the antiparallel strand, this molecule takes on a double-helix structure – also called a duplex.

This duplex has two grooves that wind their way up the molecule. The first groove, the major groove, is formed by the structure of the sugar-phosphate backbone. As the second strand is synthesized, another groove is created. The minor groove is formed by the gap between the two strands, which is filled with nitrogenous bases. Enzymes that interact with DNA use these grooves to recognize DNA molecules, attach to them, and complete their function.

RNA molecules are slightly different than DNA molecules. “RNA” stands for ribonucleic acid. Unlike DNA, the sugar molecule used in RNA is ribose – complete with that extra oxygen atom that deoxyribose is missing.

While this is just one tiny atomic change in the structure of a much larger molecule, the oxygen atom actually causes many changes in the function of RNA. For one, RNA is a less stable molecule. The oxygen atom is much more reactive than a single hydrogen and often engages in hydrolysis reactions that disrupt the structure of RNA. Second, RNA is most commonly a single-stranded molecule in part due to the physical presence of the oxygen atom. The oxygen atom bonded with the hydrogen creates a large hydroxyl group that sits just above the nitrogenous base from the nucleotide below. This hinders the ability of the nitrogenous bases to form hydrogen bonds with each other.

The other difference that makes RNA different from DNA is that it uses Uracil instead of thymine. While all of the other nitrogenous bases are the same, RNA may use uracil for a few different reasons. Uracil is easier to create, though it is very similar to cytosine and can degrade quickly. Since RNA is short-lived, this is not an issue. DNA requires a more stable base to help store information correctly for long periods of time.

While DNA is pretty much only found as a duplex in nature, RNA can take on many different forms. In addition to the single-stranded, single-helix structure most commonly seen as messenger RNA (mRNA), other common secondary structures include transfer RNA (tRNA) and ribosomal RNA (rRNA).

Transfer RNA, or tRNA for short, is used to add new amino acids to a growing peptide chain. tRNA is created when a single-stranded RNA molecule folds back on itself to create small structures known as ‘hairpins.’ On one side of a tRNA molecule, 3 nitrogenous bases are left exposed. These bases will hydrogen bond with a codon on an mRNA molecule, allowing a ribosome to know it has selected the right amino acid. The other end of the tRNA carries a specific amino acid, and can only bind to one amino acid and no others. The other parts of a tRNA molecule ensure the molecule can be processed by a ribosome.

While ribosomes themselves are mostly made of protein, they have an RNA component that intertwines with the protein structure – known as rRNA – that aids in the process of translation. rRNA helps the ribosome hold mRNA and tRNA in place as the translation process unfolds. It also helps catalyze the dehydration reaction needed to form new peptide bonds between amino acids!

In addition to these forms of RNA, scientists are constantly discovering new uses for RNA within cells. For instance, there is also microRNA that has functions in regulating genes within the nucleus, RNAs that function as enzymes for certain reactions, and many other special-function RNAs that are still being discovered!

Besides a few viruses that use RNA as their main information molecule, organisms on Earth overwhelmingly use DNA to store information and RNA to translate that information into proteins. Let’s consider the structure of each molecule to see why they serve these roles well.

The duplex structure of DNA is very stable. Not only are the two strands held together by hydrogen bonds between complementary bases, but the sugar used (deoxyribose) is also much less likely to react with other molecules because it does not have the reactive oxygen atom present in RNA. This structure makes DNA strong and ensures it will last a long time without damage. Further, DNA is strong enough to be stored in a complex manner.

If we were to stretch out all of the DNA contained in 1 cell of your body, it would be around 5 feet long. But, DNA can be wrapped around storage proteins called histones to create nucleosomes. Nucleosomes can be packed tightly together into a fiber called chromatin, which can then be packed even further into a chromosome. This allows 6 billion nucleotides to be stored within the nucleus of a cell – that’s only about 1/500th of an inch!

By contrast, RNA is not a very stable molecule. But, it serves its many roles in the cell that DNA could not complete. RNA polymerase – an enzyme that makes RNA from the DNA template – can quickly create an RNA transcript that can carry the information out of the nucleus. RNA can interact with ribosomes to create new proteins, and these molecules can fold into protein-like shapes that serve as enzymes and gene regulators within cells. Because RNA uses uracil and has an extra oxygen atom in the ribose sugar, RNAs break down quickly. That is okay, since each RNA molecule is only needed for a short time and more can easily be made through transcription of the DNA code!


Biology 171

By the end of this section, you will be able to do the following:

  • Describe nucleic acids’ structure and define the two types of nucleic acids
  • Explain DNA’s structure and role
  • Explain RNA’s structure and roles

Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell’s genetic blueprint and carry instructions for its functioning.

DNA and RNA

The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) . DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes, the DNA is not enclosed in a membranous envelope.

The cell’s entire genetic content is its genome, and the study of genomes is genomics. In eukaryotic cells but not in prokaryotes, DNA forms a complex with histone proteins to form chromatin, the substance of eukaryotic chromosomes. A chromosome may contain tens of thousands of genes. Many genes contain the information to make protein products. Other genes code for RNA products. DNA controls all of the cellular activities by turning the genes “on” or “off.”

The other type of nucleic acid, RNA, is mostly involved in protein synthesis. The DNA molecules never leave the nucleus but instead use an intermediary to communicate with the rest of the cell. This intermediary is the messenger RNA (mRNA) . Other types of RNA—like rRNA, tRNA, and microRNA—are involved in protein synthesis and its regulation.

DNA and RNA are comprised of monomers that scientists call nucleotides . The nucleotides combine with each other to form a polynucleotide , DNA or RNA. Three components comprise each nucleotide: a nitrogenous base, a pentose (five-carbon) sugar, and a phosphate group ((Figure)). Each nitrogenous base in a nucleotide is attached to a sugar molecule, which is attached to one or more phosphate groups.


The nitrogenous bases, important components of nucleotides, are organic molecules and are so named because they contain carbon and nitrogen. They are bases because they contain an amino group that has the potential of binding an extra hydrogen, and thus decreasing the hydrogen ion concentration in its environment, making it more basic. Each nucleotide in DNA contains one of four possible nitrogenous bases: adenine (A), guanine (G) cytosine (C), and thymine (T).

Scientists classify adenine and guanine as purines . The purine’s primary structure is two carbon-nitrogen rings. Scientists classify cytosine, thymine, and uracil as pyrimidines which have a single carbon-nitrogen ring as their primary structure ((Figure)). Each of these basic carbon-nitrogen rings has different functional groups attached to it. In molecular biology shorthand, we know the nitrogenous bases by their symbols A, T, G, C, and U. DNA contains A, T, G, and C whereas, RNA contains A, U, G, and C.

The pentose sugar in DNA is deoxyribose, and in RNA, the sugar is ribose ((Figure)). The difference between the sugars is the presence of the hydroxyl group on the ribose’s second carbon and hydrogen on the deoxyribose’s second carbon. The carbon atoms of the sugar molecule are numbered as 1′, 2′, 3′, 4′, and 5′ (1′ is read as “one prime”). The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms a 5′–3′ phosphodiester linkage. A simple dehydration reaction like the other linkages connecting monomers in macromolecules does not form the phosphodiester linkage. Its formation involves removing two phosphate groups. A polynucleotide may have thousands of such phosphodiester linkages.

DNA Double-Helix Structure

DNA has a double-helix structure ((Figure)). The sugar and phosphate lie on the outside of the helix, forming the DNA’s backbone. The nitrogenous bases are stacked in the interior, like a pair of staircase steps. Hydrogen bonds bind the pairs to each other. Every base pair in the double helix is separated from the next base pair by 0.34 nm. The helix’s two strands run in opposite directions, meaning that the 5′ carbon end of one strand will face the 3′ carbon end of its matching strand. (Scientists call this an antiparallel orientation and is important to DNA replication and in many nucleic acid interactions.)


Only certain types of base pairing are allowed. For example, a certain purine can only pair with a certain pyrimidine. This means A can pair with T, and G can pair with C, as (Figure) shows. This is the base complementary rule. In other words, the DNA strands are complementary to each other. If the sequence of one strand is AATTGGCC, the complementary strand would have the sequence TTAACCGG. During DNA replication, each strand copies itself, resulting in a daughter DNA double helix containing one parental DNA strand and a newly synthesized strand.


A mutation occurs, and adenine replaces cytosine. What impact do you think this will have on the DNA structure?

Ribonucleic acid, or RNA, is mainly involved in the process of protein synthesis under the direction of DNA. RNA is usually single-stranded and is comprised of ribonucleotides that are linked by phosphodiester bonds. A ribonucleotide in the RNA chain contains ribose (the pentose sugar), one of the four nitrogenous bases (A, U, G, and C), and the phosphate group.

There are four major types of RNA: messenger RNA (mRNA), ribosomal RNA (rRNA), transfer RNA (tRNA), and microRNA (miRNA). The first, mRNA, carries the message from DNA, which controls all of the cellular activities in a cell. If a cell requires synthesizing a certain protein, the gene for this product turns “on” and the messenger RNA synthesizes in the nucleus. The RNA base sequence is complementary to the DNA’s coding sequence from which it has been copied. However, in RNA, the base T is absent and U is present instead. If the DNA strand has a sequence AATTGCGC, the sequence of the complementary RNA is UUAACGCG. In the cytoplasm, the mRNA interacts with ribosomes and other cellular machinery ((Figure)).


The mRNA is read in sets of three bases known as codons. Each codon codes for a single amino acid. In this way, the mRNA is read and the protein product is made. Ribosomal RNA (rRNA) is a major constituent of ribosomes on which the mRNA binds. The rRNA ensures the proper alignment of the mRNA and the Ribosomes. The ribosome’s rRNA also has an enzymatic activity (peptidyl transferase) and catalyzes peptide bond formation between two aligned amino acids. Transfer RNA (tRNA) is one of the smallest of the four types of RNA, usually 70–90 nucleotides long. It carries the correct amino acid to the protein synthesis site. It is the base pairing between the tRNA and mRNA that allows for the correct amino acid to insert itself in the polypeptide chain. MicroRNAs are the smallest RNA molecules and their role involves regulating gene expression by interfering with the expression of certain mRNA messages. (Figure) summarizes DNA and RNA features.

DNA and RNA Features
DNA RNA
Function Carries genetic information Involved in protein synthesis
Location Remains in the nucleus Leaves the nucleus
Structure Double helix Usually single-stranded
Sugar Deoxyribose Ribose
Pyrimidines Cytosine, thymine Cytosine, uracil
Purines Adenine, guanine Adenine, guanine

Even though the RNA is single stranded, most RNA types show extensive intramolecular base pairing between complementary sequences, creating a predictable three-dimensional structure essential for their function.

As you have learned, information flow in an organism takes place from DNA to RNA to protein. DNA dictates the structure of mRNA in a process scientists call transcription , and RNA dictates the protein’s structure in a process scientists call translation . This is the Central Dogma of Life, which holds true for all organisms however, exceptions to the rule occur in connection with viral infections.

To learn more about DNA, explore the Howard Hughes Medical Institute BioInteractive resources on DNA (videos, animations, interactives).

Section Summary

Nucleic acids are molecules comprised of nucleotides that direct cellular activities such as cell division and protein synthesis. Pentose sugar, a nitrogenous base, and a phosphate group comprise each nucleotide. There are two types of nucleic acids: DNA and RNA. DNA carries the cell’s genetic blueprint and passes it on from parents to offspring (in the form of chromosomes). It has a double-helical structure with the two strands running in opposite directions, connected by hydrogen bonds, and complementary to each other. RNA is a single-stranded polymer composed of linked nucleotides made up of a pentose sugar (ribose), a nitrogenous base, and a phosphate group. RNA is involved in protein synthesis and its regulation. Messenger RNA (mRNA) copies from the DNA, exports itself from the nucleus to the cytoplasm, and contains information for constructing proteins. Ribosomal RNA (rRNA) is a part of the ribosomes at the site of protein synthesis whereas, transfer RNA (tRNA) carries the amino acid to the site of protein synthesis. The microRNA regulates using mRNA for protein synthesis.

Art Connections

(Figure) A mutation occurs, and cytosine is replaced with adenine. What impact do you think this will have on the DNA structure?

(Figure) Adenine is larger than cytosine and will not be able to base pair properly with the guanine on the opposing strand. This will cause the DNA to bulge. DNA repair enzymes may recognize the bulge and replace the incorrect nucleotide.

Free Response

What are the structural differences between RNA and DNA?

DNA has a double-helix structure. The sugar and the phosphate are on the outside of the helix and the nitrogenous bases are in the interior. The monomers of DNA are nucleotides containing deoxyribose, one of the four nitrogenous bases (A, T, G and C), and a phosphate group. RNA is usually single-stranded and is made of ribonucleotides that are linked by phosphodiester linkages. A ribonucleotide contains ribose (the pentose sugar), one of the four nitrogenous bases (A,U, G, and C), and the phosphate group.

What are the four types of RNA and how do they function?

The four types of RNA are messenger RNA, ribosomal RNA, transfer RNA, and microRNA. Messenger RNA carries the information from the DNA that controls all cellular activities. The mRNA binds to the ribosomes that are constructed of proteins and rRNA, and tRNA transfers the correct amino acid to the site of protein synthesis. microRNA regulates the availability of mRNA for translation.

Glossary


DNA Double-Helical Structure

DNA has a double-helical structure (Figure 2). It is composed of two strands, or chains, of nucleotides. The double helix of DNA is often compared to a twisted ladder. The strands (the outside parts of the ladder) are formed by linking the phosphates and sugars of adjacent nucleotides with strong chemical bonds, called covalent bonds. The rungs of the twisted ladder are made up of the two bases attached together with a weak chemical bond, called a hydrogen bonds. Two bases hydrogen bonded together is called a base pair. The ladder twists along its length, hence the “double helix” description, which means a double spiral.

Figure 2 The double-helix model shows DNA as two parallel strands of intertwining molecules. (credit: Jerome Walker, Dennis Myts).

The alternating sugar and phosphate groups lie on the outside of each strand, forming the backbone of the DNA. The nitrogenous bases are stacked in the interior, like the steps of a staircase, and these bases pair the pairs are bound to each other by hydrogen bonds. The bases pair in such a way that the distance between the backbones of the two strands is the same all along the molecule.

In a molecule of DNA, adenine (A) always pairs with thymine (T), and cytosine (C) always pairs with guanine (G). This means that the sequence of one strand of the DNA double helix can always be used to determine the other strand.

Figure 3 A diagram of the structure of a DNA molecule, showing the pairing of the nitrogenous bases, which are connected by hydrogen bonds. In DNA, A always pairs (hydrogen bonds) with T, C always pairs with G. Picture by Awedashsome Wikimedia, CC SA 4.0.


Nucleic Acids

The polymerization reaction is mediated by an enzyme, but the overall reaction is basically an esterification reaction between an alcohol and a phospho acid. The alcohol group is located on the 3 end of the sugar of the nucleotide, and the phospho acid group is on the 5 end of the next reacting nucleotide.

Lets say nucleotide 1 will be the first nucleotide. It has a 3` OH on its sugar, and this OH will act as the alcohol group.

Nucleotide 2 has a HOPO3-Sugar-OH linkage (just like nucleotide 1), and the HO part of HOPO3 on nucleotide 2 reacts with the 3` OH on nucleotide 1 and you get an esterification reaction in which a phosphodiester bond is formed

Nuc1-O-P-O3-Nuc2, and now the two nucleotides are linked. This reaction happens over and over and over to make a long single strand chain of DNA or RNA.

In the cell, the HO-PO3-sugar group is actually a triphosphate (HO-PO3-PO3-PO3-sugar), and the extra phosphate groups just provide the needed energy to get the process moving.

Because the genes that make you a human, that allow you to do everything a human can do, including live, are stored in your DNA. And the DNA is converted to RNA to make the gene products of those genes, which are called proteins (usually). DNA and RNA are both nucleic acids (Deoxyribo nucleic Acid. and Ribo nuclei acid).


Nucleic Acids

Nucleic acids are composed of linked nucleotides. DNA includes the sugar, deoxyribose, combined with phosphate groups and combinations of thymine, cytosine, guanine, and adenine. RNA includes the sugar, ribose with phosphate groups and combinations of uracil, cytosine, guanine, and adenine.

DNA and RNA are nucleic acids and make up the genetic instructions of an organism. Their monomers are called nucleotides , which are made up of individual subunits. Nucleotides consist of a 5-Carbon sugar (a pentose ), a charged phosphate and a nitrogenous base (Adenine, Guanine, Thymine, Cytosine or Uracil). Each carbon of the pentose has a position designation from 1 through 5. One major difference between DNA and RNA is that DNA contains deoxyribose, and RNA contains ribose. The discriminating feature between these pentoses is at the 2′ position where a hydroxyl group in ribose is substituted with a hydrogen.

DNA has a double helical structure. Two anti-parallel strands are bound by hydrogen bonds. There are 10 bases for every complete turn in the double helix of DNA.

DNA is a double helical molecule. Two anti-parallel strands are bound together by hydrogen bonds. Adenine forms 2 H-bonds with Thymine. Guanine forms 3 H-bonds with Cytosine. This AT & GC matching is referred to as complementarity . While the nitrogenous bases are found on the interior of the double helix (like rungs on a ladder), the repeating backbone of pentose sugar and phosphate form the backbone of the molecule. Notice that phosphate has a negative charge. This makes DNA and RNA, overall negatively charged.

DNA can be identified chemically with the Dische diphenylamine test . Acidic conditions convert deoxyribose to a molecule that binds with diphenylamine to form a blue complex. The intensity of the blue color is proportional to the concentration of DNA. The Dische’s Test will detect the deoxyribose of DNA and will not interact with the ribose in RNA. The amount of blue corresponds to the amount of DNA in solution.

The diphenylamine compound of the Dische’s test interacts with the deoxyribose of DNA to yield a blue coloration.


Biology OER

Nucleic acids are composed of linked nucleotides. DNA includes the sugar, deoxyribose, combined with phosphate groups and combinations of thymine, cytosine, guanine, and adenine. RNA includes the sugar, ribose with phosphate groups and combinations of uracil, cytosine, guanine, and adenine.

DNA and RNA are nucleic acids and make up the genetic instructions of an organism. Their monomers are called nucleotides , which are made up of individual subunits. Nucleotides consist of a 5-Carbon sugar (a pentose ), a charged phosphate and a nitrogenous base (Adenine, Guanine, Thymine, Cytosine or Uracil). Each carbon of the pentose has a position designation from 1 through 5. One major difference between DNA and RNA is that DNA contains deoxyribose, and RNA contains ribose. The discriminating feature between these pentoses is at the 2&prime position where a hydroxyl group in ribose is substituted with a hydrogen.

DNA has a double helical structure. Two anti-parallel strands are bound by hydrogen bonds.
The following video illustrates the structure and properties of DNA

There are 10 bases for every complete turn in the double helix of DNA.

DNA is a double helical molecule. Two anti-parallel strands are bound together by hydrogen bonds. Adenine forms 2 H-bonds with Thymine. Guanine forms 3 H-bonds with Cytosine. This AT & GC matching is referred to as complementarity . While the nitrogenous bases are found on the interior of the double helix (like rungs on a ladder), the repeating backbone of pentose sugar and phosphate form the backbone of the molecule. Notice that phosphate has a negative charge. This makes DNA and RNA, overall negatively charged.


What are the structural differences between RNA and DNA?

DNA has a double-helix structure. The sugar and the phosphate are on the outside of the helix and the nitrogenous bases are in the interior. The monomers of DNA are nucleotides containing deoxyribose, one of the four nitrogenous bases (A, T, G and C), and a phosphate group. RNA is usually single-stranded and is made of ribonucleotides that are linked by phosphodiester linkages. A ribonucleotide contains ribose (the pentose sugar), one of the four nitrogenous bases (A,U, G, and C), and the phosphate group.

What are the four types of RNA and how do they function?

The four types of RNA are messenger RNA, ribosomal RNA, transfer RNA, and microRNA. Messenger RNA carries the information from the DNA that controls all cellular activities. The mRNA binds to the ribosomes that are constructed of proteins and rRNA, and tRNA transfers the correct amino acid to the site of protein synthesis. microRNA regulates the availability of mRNA for translation.