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5.3: The Double Helix of DNA - Biology

5.3: The Double Helix of DNA - Biology


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This structure of DNA was worked out by Francis Crick and James D. Watson in 1953. It could be replicated and so passed on from generation to generation. For this epochal work, they shared a Nobel Prize in 1962.


The 5' and 3' mean "five prime" and "three prime", which indicate the carbon numbers in the DNA's sugar backbone. The 5' carbon has a phosphate group attached to it and the 3' carbon a hydroxyl (-OH) group. This asymmetry gives a DNA strand a "direction". For example, DNA polymerase works in a 5' -> 3' direction, that is, it adds nucleotides to the 3' end of the molecule (the -OH group is not shown in diagram), thus advancing to that direction (downwards).

The no 5 and 3 are the carbon no of the carbon skeleton ring of deoxyribose as similar as any other organic compound. In any nucleic acid, RNA or DNA 3' refers to the 3rd carbon of sugar ribose or deoxyribose which is linked to OH group and 5' linked to a triple phosphate group. So these 5' and 3' group provide a directional polarity to the DNA or RNA molecule. Now a good question would be y 3' and 5' not 3 and 5. It is simply to differentiate sugar carbons from that of the bases which are also having a carbon skeleton and thus nos for their carbon


3.5 Nucleic Acids

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 3.31). 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 3.31). 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 3.31). 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 3.32). 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 3.33 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.

Visual Connection

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 3.34).

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. Table 3.2 summarizes DNA and RNA features.

DNA RNA
FunctionCarries genetic informationInvolved in protein synthesis
LocationRemains in the nucleusLeaves the nucleus
StructureDouble helixUsually single-stranded
SugarDeoxyriboseRibose
PyrimidinesCytosine, thymineCytosine, uracil
PurinesAdenine, guanineAdenine, 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.

Link to Learning

To learn more about DNA, explore the Howard Hughes Medical Institute BioInteractive animations on the topic of DNA.


DNA Replication

During DNA replication, each strand is copied, resulting in a daughter DNA double helix containing one parental DNA strand and a newly synthesized strand. At this time it is possible a mutation may occur. A mutation is a change in the sequence of the nitrogen bases. For example, in the sequence AATTGGCC, a mutation may cause the second T to change to a G. Most of the time when this happens the DNA is able to fix itself and return the original base to the sequence. However, sometimes the repair is unsuccessful, resulting in different proteins being created.

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High School Biology : Understanding the Double Helix

Who is credited for the discovery of the DNA double helix?

Rosalind Franklin and Albert Einstein

James Watson and Francis Crick

James Watson and Francis Crick

Watson and Crick are credited with discovering the DNA double helix and built a model that explains the shape of DNA. Rosalind Franklin was the crystallographer who found the structure of DNA, but it was Watson and Crick who looked at this scan and realized the shape of DNA. Since Watson and Crick's shunning of Franklin from the discovery, the topic has become a point of controversy. Franklin had died by the time Watson and Crick were awarded the Nobel Prize for their work.

It is important to know that Watson and Crick are credited for the discovery of DNA structure, but selecting Franklin for the question is acceptable.

Understanding The Double Helix : Example Question #2

Which of the following is a characteristic of DNA?

Uracil pairs with adenine in DNA

Each DNA nucleotide has a nitrogen group surrounded by oxygen atoms

Each DNA helix consists of two long chains of nucleotides

The ribose sugar is identical in all DNA nucleotides

Each DNA helix consists of two long chains of nucleotides

DNA is an organic compound that is made up of repeating subunits call nucleotides. Each DNA nucleotide is composed of three parts: a deoxyribose sugar molecule, a phosphate group, and a nitrogen-containing base. Phosphate groups are formed by a phosphorus atom bonded to four oxygen atoms. The deoxyribose sugar and the phosphate group are identical in all DNA nucleotides and form the backbone of the DNA. There are four possible nitrogenous bases: adenine, guanine, cytosine, and thymine. In double-stranded DNA, adenine pairs with thymine and guanine with cytosine via hydrogen bonding to create the DNA helix.

During transcription, uracil is added to RNA to complement adenine. DNA does not contain ribose sugar or uracil, but RNA does.

Understanding The Double Helix : Example Question #3

Which of the following scientists is credited with discovering the double-helix structure of DNA?

The double-helix structure of DNA was discovered by James Watson and Francis Crick, as well as Rosalind Franklin. They published an article titled "Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid" that described the three-dimensional structure of DNA.

Linus Pauling was the first scientist to propose a helical structure for DNA however, he proposed that DNA was a triple helix. His work regarding DNA structure heavily influenced Watson and Crick who won the Nobel Prize for their model of DNA.

Understanding The Double Helix : Example Question #4

Which of the following is false regarding the DNA double-helix?

The backbone of the double-helix is held together by covalent bonds

The major groove is the region of the double-helix where the two DNA backbones are closest to each other

Base pairing in the double-helix can be broken down by adding heat

A double-helix occurs in both double-stranded DNA and double-stranded RNA molecules

The major groove is the region of the double-helix where the two DNA backbones are closest to each other

The double-helix is the three dimensional structure of a DNA molecule. This structure arises due to the interaction (hydrogen bonding of base pairs) between the two strands of a DNA molecule. A double-helix can occur in any double-stranded molecule therefore, a double-stranded RNA molecule can also form a double-helix if there is proper base pairing between the strands.

The base pairing in the double-helix involves hydrogen bonds, a type of noncovalent bond or intermolecular force. Since it is a noncovalent bond, hydrogen bonds between bases can be broken down by adding energy in the form of heat. Recall that the DNA backbone contains a series of pentose sugars that have a phosphate group attached to their 5' carbon. These pentose sugars in the DNA backbone are held together by covalent bonds called phosphodiester bonds therefore, the DNA backbone is held together by covalent bonds.

One of the characteristics of double-helix is the presence of the major groove and the minor groove. The major groove is the region of the double-helix where the distance between the two DNA strands is largest. The minor groove, on the other hand, is the region of double-helix where the distance between the two strands is smallest.


Major Steps Involved in the Mechanism of DNA Replication | Biology

During this process a whole range of enzymes is required to take care of various steps. The DNA replication in procaryotic cells (bacteria) starts at a single point known as origin of replication, and moves bidirectionally.

Image Courtesy : cnx.org/content/m46073/latest/0323_DNA_Replication.jpg

On the other hand, in eucaryotic cells there are several points of origin on the length of DNA per chromosome.

The first requirement before any type of synthesis is to unwind the double helix of DNA, so that the two strands become free to act as templates.

This function of unwinding of double helix is carried out by the enzyme helicase, which unzips the two strands beginning at the origin site.

As soon as unwinding takes place, other proteins called single-stranded binding proteins, associate with single strands and make this condition stable.

Unwinding also creates a coiling tension ahead of the moving replication fork, a structure that will be formed when DNA replication begins.

The coiling tension created by unwinding of double helix is reduced by the enzymes known as topoisomerases.

One of the most important DNA synthesizing enzyme is DNA polymerase III. This enzyme along with other DNA polymerases (i.e., I and II) can elongate an existing DNA strand but cannot initiate the synthesis of DNA.

All the above mentioned three DNA polymerases (i.e., I, II, and III) function in 5′ to 3′ direction only for DNA polymerisation and have 5′ to 3′ direction for exonuclease activity.

Now, to initiate DNA synthesis, a small segment of RNA, known as RNA primer complementary to the template DNA is synthesized by an unique RNA polymerase known as primase.

It is to this RNA primer, that DNA polymerase III adds 5′ deoxyribonucleotides and extends the DNA.

A problem arises, when two strands of DNA run antiparallel to each other and DNA polymerase III can act only in 5′ —> 3′ direction. This problem is solved as follows:

While on the one strand, the DNA synthesis goes on continuously in 5′ —> 3′ direction, on the other strand, DNA is synthesised in small stretches resulting in discontinuous DNA synthesis.

This process takes place in the opposite direction to the first strand but maintains the overall 5′ 3′ direction as required and such a process is sometimes called semi-discontinuous replication.

The short stretches of DNA, each primed by RNA are called Okazaki fragments, named after Japanese scientist who discovered them.

Thereafter RNA primers are removed, and the gap is filled by DNA synthesis. Both these steps are performed by DNA polymerase I.

Now the Okazaki fragments are sealed by the enzyme ligase.

The strand which supports the continuous DNA synthesis is the leading strand and one which is replicated in short stretches is called the lagging strand.

The process of DNA replication ensures the accuracy to maintain the nucleotide sequence of the original DNA.

DNA synthesis is slower in eucaryotes, as larger DNA’s need to be replicated.

The general steps of DNA replication are similar both in eucaryotes and procaryotes.


Structure of DNA by Watson and Crick

Watson and Crick displayed the structure of DNA after studying the manuscript of the two scientists Linus Pauling and Corey. In 1953, Linus Pauling and Corey gave the 3D-structure of nucleic acid, which was not successful. Then, (in early 1953) Watson and Crick together combined the data of physical and chemical properties and proposed a double-helical structure of DNA. The main characteristics of Watson and Crick model of DNA include:


Physical Properties of DNA

  • According to the Watson and Crick model, the DNA is a double-stranded helix, which consists of two polynucleotide chains. The two polynucleotide chain are spirally or helically twisted, which gives it a twisted ladder-like look.
  • Both the polynucleotide strands of DNA have the opposite polarities, which mean that the two strands will run in the antiparallel direction, i.e. one in 5’-3’ and other in 3’-5’ direction.
  • The diameter of ds-stranded DNA helix is 20Å.
  • The distance between the two nucleotidesor internuclear distance is 3.4Å. The length of DNA helix is 34Å after a full turn and it possesses 10 base pairs per turn.
  • The DNA is twisted in “Right-handed direction” or we can say in a “Clockwise direction”.
  • Turning of DNA causes a formation of wide indentations, i.e. “Major groove”. The distance between the two strands forms a narrow indentation, i.e. “Minor groove”. The formation of major and minor grooves result after the DNA coiling and the grooves also act as a site of DNA binding proteins.

Chemical Properties of DNA

  • There are four nucleotide bases present in the polynucleotide chain like adenine, guanine, cytosine and thymine. Adenine and guanine are the two purine bases, which have a single ring structure. Cytosine and thymine are the two pyrimidine bases, which have the double-ring structure.
  • The two strands are joined together by the “Complementary base pairing” of the nitrogenous bases. Therefore, a purine base will complementarily pair with the pyrimidine base, in which ‘Adenine’ pairs with ‘Thymine’ and ‘Guanine’ pairs with ‘Cytosine’.
  • The nucleotide bases in the polynucleotide strands of DNA will join with each other through a strong hydrogen bond.
  • Adenine complementarily pairs with thymine through two hydrogen bonds, whereas guanine complementarily pairs with cytosine by means of three hydrogen bonds.
  • The nucleotide base composition of DNA follows the Chargaff’s rule where the sum of purines is equal to the number of pyrimidines. The base composition of A + G = T + C obeys the Chargaff’s rule, but the base composition of A + T is not equal to the G + C.
  • Polynucleotide strands of DNA consist of three major components, namely nitrogenous bases, deoxyribose sugar and a phosphate group.
  • The backbone of DNA consists of the sugar-phosphate backbone. The sugar-phosphate backbone holds both the polynucleotide strands of DNA by means of “Phosphodiester bond”. Therefore, the bonding between sugar and phosphates, i.e. phosphodiester bond and the bonding between nitrogenous bases, i.e. hydrogen bond contributes to the “DNAStability”.

Conclusion

The DNA is a supermodel proposed by Watson and Crick in the year 1953. The discovery of double helix DNA was not possible without the collaboration of Maurice Wilkins and Rosalind Franklin. Maurice Wilkins and Rosalind Franklin discovered the picture of DNA through X-ray crystallography. The X-ray diffraction picture of DNA helped Watson and Crick to further study the DNA structure and components. By this, Watson and Crick proposed a model for DNA known as Watson and Crick’s model of double-helical DNA.

The DNA is the largest biomolecule which contains all the genetic information of the person to build an organism or a life form. The study of DNA double-helical structure helps us to know about the chemical and physical properties of DNA, apart from the property of DNA being a “Genetic material”.


Question : 2. The double-helix model of DNA The double-helix model of DNA is shown here. One strand points upward in the 5’ to 3’ direction. In the image, label which direction the other arrow points. A Hydrogen bonds between bases on opposite strands hold this DNA helix together. How many hydrogen bonds form between a single guanine (G) and its

The double-helix model of DNA is shown here. One strand points upward in the 5’ to 3’ direction. In the image, label which direction the other arrow points.

Hydrogen bonds between bases on opposite strands hold this DNA helix together. How many hydrogen bonds form between a single guanine (G) and its complementary base?

Examine the distance between base pairs and the length of one full twist of the double helix. How many base pairs long is one full twist of the helix?

You can represent a DNA segment by writing out the sequence of its base pairs. Which of the following sequences represents a correct DNA segment?

Ernest Chargaff helped Watson and Crick determine the base-pairing rules of DNA. Some of his data measuring the relative amount of the four bases of DNA.


During cell division, each daughter cell receives a copy of each molecule of DNA by a process known as DNA replication. The single chromosome of a prokaryote or each chromosome of a eukaryote consists of a single continuous double helix. The model for DNA replication suggests that the two strands of the double helix separate during replication, and each strand serves as a template from which the new complementary strand is copied. In the conservative model of replication, the parental DNA is conserved, and the daughter DNA is newly synthesized. The semi-conservative model suggests that each of the two parental DNA strands acts as template for new DNA to be synthesized after replication, each double-stranded DNA retains the parental or “old” strand and one “new” strand. The dispersive model suggested that the two copies of the DNA would have segments of parental DNA and newly synthesized DNA. The Meselson and Stahl experiment supported the semi-conservative model of replication, in which an entire replicated chromosome consists of one parental strand and one newly synthesized strand of DNA.

Meselson and Stahl's experiments proved that DNA replicates by which mode?


Lk number components — Wr and Tw numbers

The curve that runs along the centre of the ribbon is called the axis of the ribbon. Although it doesn’t model a part of the molecule, it does tell us how contorted theme molecule is in space. It is possible to choose an orientation on the axis and then give the two boundaries of the ribbon orientations that match it.

First, we define the twist number of the ribbon, denoted Tw(R). It measures how much the ribbon twists around its axis. When the axis lies flat in the plane, without crossing itself, the twist of the ribbon is simply one-half of the sum of the +1s and -1s occurring at the crossings between the axis and a particular one of the two link components bounding the ribbon.

Next, we define the writhe number of the ribbon, denoted Wr(R). It measures how much the axis of the ribbon is contorted in space. For any particular projection of the axis, define the signed crossover number to be the sum of all the ±1s occurring at crossings where the axis crosses itself. It becomes trickier to compute the writhe when the axis is not in a plane, as some projections will have crossings and others will not.

Finally, we can treat the two boundaries of the ribbon as components of a link and then compute the linking number of the two components, denoting the result by Lk(R). Remember the linking number is just one half of the sum of the ±1s occurring at the crossings between the two components.

Lk(R) = Tw(R) + Wr(R)

Remember the linking number is just one half of the sum of the ±1s occurring at the crossings between the two components. This last invariant does not depend on the particular placement of the link in space.

Therefore when we achieve supercoiling phenomena, the absolute values of each of these three numbers will increase.

Experimentally separation of supercoiled molecules from a normal is possible — the molecules place in a gel and then pass electricity through the gel to attract the molecules toward an electrode. The molecules with greater supercoiling are more compact and hence move more quickly through the gel, allowing their separation.

Now we can return to the original question, which was how to determine
the action of an enzyme on DNA. We discuss a particular type of action by an enzyme called site-specific recombination, which is a process whereby an enzyme attaches to two specific sites on two strands of DNA, called recombination sites, each of which corresponds to a particular sequence of base pairs that the enzyme recognizes.

There are two types of coiling: negative and positive supercoils as we can see in Figure 35. Negative supercoils favour local unwinding of the DNA, allowing processes such as transcription, DNA replication, and recombination.


Watch the video: 4. Η ανακάλυψη της διπλής έλικας του DNA 4 1ο κεφ. - Βιολογία Γ λυκείου. (May 2022).