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The structure of DNA, Practice Problems and FAQs

Did anyone ever tell you that you look just like your mom or dad? What do you think might be the reason for the same? It is the DNA that we inherit from our parents that is responsible for our similarities with our parents. DNA stands for deoxyribonucleic acid and is a long chain made of deoxyribonucleotides. It is the genetic material present in every cell of our body and the decision maker for traits we inherit from our parents.

Did you know that DNA is one of the most stable compounds found in living organisms which is why it acts as the genetic material for almost all organisms, except a few viruses. But what does DNA look like? How does it carry the genetic information? What is it made up of? How big is the DNA? How do we measure the size of DNA? There are so many questions tht might be popping in your head right now. Let us get the answer to all these questions. 

Table of contents

  • What is DNA made up of?
  • How long is the DNA?
  • What does DNA look like?
  • Biological significance of Watson and Crick model of DNA
  • Coding and non-coding strands of DNA
  • Cistron
  • Types of DNA
  • Practice problems
  • FAQs

What is DNA made up of?

DNA is a long double helical chain made up of deoxyribonucleotides. Deoxyribonucleotides are monomeric units made up of a pentose sugar (deoxyribose), a phosphate and a nitrogenous base. 

The phosphate group is attached to the hydroxyl (-OH) group of the 5’ carbon of pentose sugar by a phosophoester bond. The nitrogenous base is attached to the 1’ carbon of the pentose sugar with the help of an N-glycosidic linkage.

Fig: Nucleotide

Fig: Nucleotide

There are four nitrogenous bases found in DNA - Adenine, Guanine, Cytosine and thymine. The four nitrogenous bases are categorised into two types - purines (adenine and guanine) and Pyrimidine (cytosine and thymine in DNA and uracil present only in RNA, in place of thymine).

How long is the DNA?

The length of DNA varies in different organisms and is measured by the number of nucleotides present in the cell of an organism. To quote some examples, DNA of bacteriophage has 5386 nucleotides, Escherichia coli has 4.6x106 base pairs and bacteriophage lambda has 48502 base pairs. Haploid content of human DNA constitutes 3.3x109 base pairs. 

What does DNA look like?

History

image

Fig: Timeline of DNA discovery

Before it was discovered that DNA is a double helical long polynucleotide chain, many scientists tried to figure out the structure of DNA. In 1869, Friedrich Miescher discovered DNA, which he then referred to as nuclein in the nucleus of white blood cells. In the late 1800s, Kossel Albrecht found out that DNA constitutes nitrogenous bases. Phoebus Levene, in 1900,proposed tetranucleotide theory. Studies of W.T Astbury in 1940s indicated that DNA is a polynucleotide structure in which the successive nucleotides are 3.4 Å apart.

In 1948, Erwin Chargaff and his colleagues discovered that nitrogenous bases are present in specific ratios in a DNA and proposed Chargaff’s rules which helped in understanding the structure of DNA better.

Fig: Watson and Crick

Fig: Watson and Crick

Maurice Wilkins and Rosalind Franklin extracted very clear X-ray diffraction images of DNA in 1951-1952 and said that it is a double helix. Based on the X-ray diffraction images, James Watson and Francis Crick proposed deduced the three-dimensional structure of the DNA double helix. Watson, Crick and Wilkins were awarded the nobel prize in 1962 for the discovery of DNA structure.

image

Fig: Wilkins and Franklin

Chargaff’s rules

Chargaff proposed certain rules that helped in understanding the structure of DNA. As per Chargaff’s rules, the amount of adenine is equal to that of thymine and the amount of guanine is equal to that of cytosine i.e., A=T and G=C. The sum of the quantity of purines is equal to that of pyrimidines i.e., A+G=C+T. Chargaff’s rules are only applicable to DNA.

image

Fig: Chargaff’s rules

He also said that base composition of DNA varies and is different in different species but is the same for all members of the same species. The base ratio of A+T/G+C varies in the DNA of different groups of organisms but remains constant for a specific species.

Salient features of Watson and Crick’s model of DNA

DNA is a double helix which constitutes two polynucleotide chains helically wrapped around each other. 

In a polynucleotide chain, phosphodiester bond is the ester bond that connects the phosphate group linked to the 5’ carbon of the pentose sugar of one nucleotide with the hydroxyl group linked to the 3’ carbon of the pentose sugar of the adjacent nucleotide.

Fig: Phosphodiester bond between nucleotides

Fig: Phosphodiester bond between nucleotides

Each chain has a sugar phosphate backbone and the nitrogenous bases are present on the inside of the double helix. 

Fig: Double helical structure of DNA

Fig: Double helical structure of DNA

The coiling of the double helix is in a right handed direction. 

Fig: Right handed coiling of DNA double helix

Fig: Right handed coiling of DNA double helix

One end of the polynucleotide chain has a sugar residue with a free 5’ carbon attached to a phosphate group that is not linked. This is the 5’ end. The other end has a sugar residue with a free 3’ carbon attached to a -OH group that is not linked. This is the 3’ end.

Fig: 5’ and 3’ ends of DNA double helix

Fig: 5’ and 3’ ends of DNA double helix

The two polynucleotide chains are antiparallel to each other. The two DNA strands are said to be antiparallel as they run parallel but are oriented in opposite directions, i.e, the 3’ end of one polynucleotide chain lies opposite to the 5’ end of the other. 

Fig: Antiparallel polynucleotide chains of DNA

Fig: Antiparallel polynucleotide chains of DNA

The nitrogenous bases are connected with each other with the help of hydrogen bonds. 

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Fig: Hydrogen bonds between nitrogenous bases

The purines (Adenine and Guanine) and pyrimidines (Cytosine and thymine) cannot pair with themselves so the hydrogen bond is always present between purines and pyrimidines. 

Fig: Bonding of purine with pyrimidine in the DNA double helix

Fig: Bonding of purine with pyrimidine in the DNA double helix

Adenine always bonds with thymine with the help of double hydrogen bonds while guanine and cytosine are linked together with the help of three hydrogen bonds.

Fig: Hydrogen bonds with different nitrogenous bases

Fig: Hydrogen bonds with different nitrogenous bases

There are approximately 10 base pairs present in each turn of a double helix. The diameter of the helix is approximately 2nm. Thus, the pitch of the helix, i.e, the length of one complete turn, is 3.4 nm and the distance between two base pairs is 0.34 nm. 

Fig: Dimensions of the DNA helix

Fig: Dimensions of the DNA helix

DNA helix has two groves- major groove is the grove where the backbones are far from each other and the minor groove is where the backbones are closer to each other. One complete turn of the DNA helix is considered to be the distance between two major grooves or two minor grooves. The major groove is around 2.2nm wide and the minor groove is about 1.2nm wide.

Fig: Major and Minor Groove

Fig: Major and Minor Groove

In addition to the hydrogen bonds, the double helix is held stable with the help of attraction forces between the bases stacked over each other.

Fig: Attraction Forces in DNA

Fig: Attraction Forces in DNA

Biological significance of Watson and Crick model of DNA

The Watson and Crick model of DNA explains the following basic functions of DNA as a hereditary material:

Replication

The double helical structure of DNA indicates that each strand of DNA can easily build its complementary strand and can replicate faithfully.

Storage of hereditary information

Genetic material acts as the repository of all hereditary information. It should be able to determine the composition of a polypeptide chain by specifically dictating the sequence of amino acids. The same is done by the triplet codons of DNA, i.e, a cluster of 3 adjacent nucleotides on the DNA which act as a code for specific amino acids. Thus, DNA is considered as a tape of coded information for the sequence of amino acids.

Transmission of information 

Due to the presence of complementary base-pairing in DNA, one of the two strands is capable of copying down the base sequence into an mRNA by the process of transcription. The mRNA moves out of the nucleus, into the cytoplasm, where it is translated by ribosomes into a polypeptide chain. The nucleotide or nitrogenous base sequence of the mRNA provides the codons for the amino acid sequence in the polypeptide.

Stability and repair

DNA is one of the most stable molecules due to the presence of stacked base pairs and the hydrogen bonds between the base pairs that hold it together. Thus, it is most suited for the long term preservation of coded genetic information. 

If by chance, one of the strands is damaged, the base sequence of the complementary strand can be used to correct the error and repair the damaged chain.

Coding and non-coding strands of DNA

The 5’-3’ strand of the DNA double helix is known as the coding strand or sense strand as the nucleotide sequence of this strand matches with the nucleotide sequence of the mRNA and hence determines the amino acid sequence of the polypeptide chain. This indicates that this strand is not complementary to the mRNA and is not used as a template for mRNA synthesis. Thus, this strand is also known as the non-template strand.

The 3’-5’ strand of the DNA double helix acts as a template for mRNA synthesis and is termed as the template strand. As the nucleotide sequence of this strand is complementary to the mRNA sequence and does not directly determine the amino acid sequence in the polypeptide, it is also termed as the non-coding strand or antisense strand.

Cistron

The segment of DNA that codes for a specific polypeptide chain is termed as a cistron or a gene. The cistron consists of all the codons required for the synthesis of a polypeptide. 

In prokaryotes, each cistron or gene is a continuous stretch of DNA in which codons correspond exactly with the sequence of amino acids in the polypeptide.

In eukaryotes, the cistron is discontinuous, i.e, stretches of coding segments are interrupted by non-coding segments. The coding segments are termed as exons whereas the non-coding segments are termed as introns. In a function mRNA molecule of eukaryotes, the introns are removed by mRNA splicing.

Types of DNA

Fig: Types of DNA

Fig: Types of DNA

A-DNA

The dehydrated form of B-DNA forms A-DNA. The structure and orientation of A-DNA is similar to that of B-DNA. In order to survive, B-DNA modifies itself into A-DNA under stress conditions.

The diameter of the helix in A-DNA is 2.3nm, pitch is 3.4nm and the number of base pairs per turn is 11. The distance between successive bases is 0.27nm. It is a right-handed helix with a smooth sugar-phosphate backbone.

B-DNA

This DNA is found in organisms in normal physiological conditions. It is believed that B-DNA helps in gene regulation.

The diameter of the helix in B-DNA is 2nm, pitch is 3.4nm and the number of base pairs per turn is 10. The distance between successive bases is 0.34nm. It is a right-handed helix with a smooth sugar-phosphate backbone.

Z-DNA

This DNA is found in a very small amount. Similar to B-DNA, the bases are arranged in a zigzag pattern. This DNA is also believed to have some role in gene regulation in a cell. It occurs in cells in dehydrated and high salt conditions.

The diameter of the helix in Z-DNA is 1.8nm, pitch is 4.5nm and the number of base pairs per turn is 12. The distance between successive bases is 0.37nm. It is a left-handed helix with a zig-zag sugar-phosphate backbone.

Practice problems

Q1. The length of a DNA is 2.04 mm. Find out the number of base pairs in the given DNA.

A. 6 x 106 bp
B. 2 x 106 bp
C. 2.44 x 106 bp
D. 1.66 x 106 bp

Solution: The distance between two base pairs is 0.34 nm which is equal to 0.34 x 10-6 mm. Total number of base pairs= Length of DNA/ distance between two base pairs

=2.04/0.34 x 10-6 mm

=6 x 106 bp

Hence, the correct option is a.

Q2. In DNA, it was found that there are 29 adenine and 29 guanine residues. What is the total number of pyrimidine found in the DNA?

A. 58
B. 29
C. 62
D. 54

Solution: It is given that the number of adenine and guanine are 29 each. According to the Chargaff’s rules, total number of purines is equal to the number of pyrimidines, i.e., A+G=T+C. 

Total number of pyrimidines (T+C) = Total number of purine (A+G)

=29+29

=58

Hence, the correct option is a.

Q3. In the given figure, A represents adenine, T represents thymine, G represents guanine and C represents cytosine. Identify X labelled in the figure.

Fig: Identify X labelled

Fig: Identify X labelled

Fig: Identify X labelled

Fig: Identify X labelled

A. Covalent bond
B. Electrostatic bond
C. Hydrogen bond
D. Coordinate bond

Solution: The given figure represents the double helical structure of DNA. Adenine, guanine, cytosine and thymine are the nitrogenous bases present on the inner side of the double helix linked with the help of hydrogen bonds.

Hence, the correct option is c.

Q4. Given below is the sequence of DNA on the 5’ to 3’ strand of DNA. 

5’- ATGCGATCGTAC -3’

What should be the sequence on the 3’ to 5’ strands of DNA?

A. 3’- TACGCTAATTTG - 5’
B. 3’- TACGCTTATATG - 5’
C. 3’- TACGAATGCATG - 5’
D. 3’- TACGCTAGCATG - 5’

Solution: In a double helix, purines pair with pyrimidine. Adenine always pairs with thymine and cytosine always pairs with guanine. The two strands will be complementary to each other. The sequence on the 3’ to 5’ strand should be:

5’- ATGCGATCGTAC -3’

3’- TACGCTAGCATG - 5’

Hence, the correct option is d.

FAQs

Question 1. What is satellite DNA?
Answer: Satellite DNA represents thousands of tandem repeats of 5 to 1000 base pairs which either occur as a single copy dispersed throughout the genome or as closely spaced clusters. In humans, satellite DNA constitutes more than 45% of the genome.

Minisatellite DNAs represent 5 to 50 tandem repeats of around 15 base pairs or more.

Microsatellite DNAs are formed of around 100 tandem repeats of 2-5 base pairs.

Question 2. Why can’t Adenine pair with Cytosine or Guanine?
Answer: The diameter of the DNA is fixed and is around 2nm for B-DNA usually found in cells. This leaves around 1.1nm space for the nitrogenous base pairs which can accommodate one purine and one pyrimidine but not two purines (double rings would occupy too much space) or two pyrimidines ( single rings would occupy very little space). Thus Adenine can only pair with a pyrimidine and not with Guanine which is a purine.

The reason why Adenine specifically pairs with Thymine and not with cytosine is that Adenine and Thymine share the perfect match between hydrogen donor and acceptor sites for the formation of a hydrogen bond.

Question 3. Is it possible for two people to have the same DNA?
Answer: No two individual humans can have identical DNA. Approximately 99.9% of the human genome is the same for all humans and 0.1% is responsible for the variations which reflect in the form of variations in our appearance, health conditions, etc. Related individuals share more similarities in their DNA compared to unrelated individuals but even twins do not share identical DNA. 

Question 4. Where is DNA found in organisms?
Answer: In prokaryotic organisms, a well-defined nucleus is absent and DNA is found lying naked in the cytoplasm.

In eukaryotic organisms, DNA is found within the nucleus of the cells of the organism’s body. The DNA in eukaryotic cells is packaged in the form of chromatin fibres with the help of histone proteins and supercoiling.

Question 5. Which other animals share similarity in genome with humans?
Answer: Humans share maximum similarity in genome with chimpanzees which is approximately 98.8%. Around 98.4% and 96.9% similarity in DNA sequence is shared by humans with gorillas and orangutans, respectively. Mice and dogs share around 90% and 84% similarity with the human genome.

Question 6. What is DNA fingerprinting?
Answer: DNA fingerprinting is a method of identifying DNA of different individuals by locating differences in the arrangement of nucleotides the specific regions of repetitive DNA. It is used in the field of forensics and paternity testing. Even a small sample of spit, blood, human ash or semen can be used for the identification of an individual with the help of DNA fingerprinting.

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