Genetic Materials and Genetic Code
 |
| Watson and Crick showing the three dimensional model of DNA prepared using metal scraps |
Genetic material is the substance or material that gets transformed from one generation to the next generation in order to express its characteristic parental characters.
The genetic material has following three main properties:
It is capable of replicating and being inherited to offspring.
It is able to carry out all the information necessary for the function of a cell.
It is able to change its sequence by mutation.
Nucleic acids are the genetic materials in living organisms. In almost all the organisms, DNA (deoxyribonucleic acid) is the genetic material. However, in some viruses, RNA (ribonucleic acid) is the genetic material.
Concept of Gene and Central Dogma of Molecular Biology
Gene is a segment of DNA molecule which encodes a character of an organism. The term gene was coined by a Danish Geneticist, Wilhelm Johannsen in 1909 from the Greek word ‘genesis’ meaning ‘to be born’. The gene transmits individual traits or characters.
According the classical concept of gene, gene is regarded as:
The unit of function: As this definition tells, genes are the unit of a chromosome responsible for the expression of a trait e.g. blue or brown eyes in humans.
The unit of mutation: Genes are the smallest segments of chromosomes capable of undergoing changes or mutation.
The unit of segregation in transmission: Genes are the smallest segments of chromosomes capable of undergoing segregation or exchange during crossing over.
Central dogma of molecular biology is the unidirectional flow of genetic information from DNA to protein through RNA. Here, the genetic information in DNA flows into mRNA (messenger RNA) and from mRNA to protein (See Figure 1). This concept of central dogma was advanced by Crick in 1958.
 |
| Figure 1 Graphic representation of central dogma of molecular biology |
In retroviruses, RNA is the genetic material. Such viruses contain reverse transcriptase, which makes DNA from RNA. So, the genetic information flows from RNA to DNA and from DNA to mRNA and finally into the protein. This is called reverse central dogma or reverse transcription or teminism. It was reported by Temin (1970) and Baltimore (1970) in RSV (Raus’s Sarcoma Virus, the retrovirus).
 |
| Figure 2 Reverse transcription or Reverse central dogma of molecular biology |
Nucleic acids
Nucleic acids are the most essential molecules of life. They are macromolecules containing C, O, H, N, and P. There are two types of nucleic acids - Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Nucleic acids serve as the repositories and transmitters of genetic materials.
Nucleic acids are the polymers of nucleotides held together by 3’ to 5’ phosphate bridges; they are polynucleotides.
Structure of a nucleotide
A nucleotide is formed by three components - nitrogen base, pentose sugar, and phosphate group. If the phosphate group is absent, the compound is called the nucleoside.
 |
| Figure 3 Structure of nucleotide |
1. Pentose sugars
In nucleotides, these are the five carbon monosaccharides (C5H10O5). The DNA contains deoxyribose sugar and the RNA contains ribose sugar. The deoxyribose has no oxygen at 2’ position whereas the ribose does have (See Figure 4).
 |
| Figure 4 Structure of pentose sugars in nucleotide Image source: OpenStax College, CC BY 3.0 <https://creativecommons.org/licenses/by/3.0>, via Wikimedia Commons |
2. Nitrogen bases
In nucleotides, nitrogen bases are the aromatic heterocyclic compounds. They are of two categories - purines and pyrimidines. Ring forming atoms in the purines are numbered anticlockwise while pyrimidines are numbered clockwise.
 |
| Figure 5 Nitrogen bases in nucleic acids Source: https://2012books.lardbucket.org/books/introduction-to-chemistry-general-organic-and-biological |
Purines have two carbon-nitrogen rings in their structures. Examples are adenine (A) and guanine (G).
Pyrimidines have one carbon-nitrogen ring in their structures. Examples are Cytosine (C), Thymine (T), or Uracil (U). In RNA, Uracil (U) is present in place of Thymine (T). Thymine is called methylated Uracil.
A purine base is attached to its specific pyrimidine base with hydrogen bonds. Adenine (A) combines with Thymine (T) by two hydrogen bonds while Cytosine (C) bonds with Guanine (G) by three hydrogen bonds. These bases are called complementary bases. Due to purine-pyrimidine base pairing, the total amount of purines is equal to the total amount of pyrimidines in the DNA of any species. This is called Chargaff’s rule, proposed by Erwin Chargaff in 1949.
A + G = T + C
3. Phosphoric acid
It contains a phosphate group. It combines two nucleotides together by a phosphodiester bond to form a backbone of nucleic acids.
Deoxyribonucleic acid (DNA)
DNA is found in the nucleus (nuclear DNA), mitochondria (mitochondrial DNA), and plastids (plastid DNA). DNA in the cytoplasmic organelles is collectively called organellar DNA.
DNA was discovered by Friedrich Miescher as nucleins from the pus cells in 1868. Fisher (1880) discovered the presence of purine and pyrimidine bases in nucleic acids. Chargaff (1949) found the equal amount of purine and pyrimidine in DNA. James Watson and Francis Crick (1953) proposed the double helical model of DNA.
Structure of DNA
According to Watson and Crick's model, the DNA is a double helix with other remarkable features. It consists of two poly-deoxyribonucleotide chains or strands spirally twisted around each other on a common axis. These two spiral strands of DNA are collectively called the DNA duplex.
Each strand contains a polynucleotide chain of many nucleotides linked one after another by phosphodiester bonds. Such a polynucleotide chain contains the phosphate groups outside and the nitrogen bases inside.
These two strands are antiparallel i.e. one strand runs in the 5’ to 3’ (5’→3’) while the other in 3’ to 5’ (3’→5’) direction. There is an opposite orientation with respect to each other with 3’-hydroxyl terminus of one strand opposite to the 5’-phosphate terminus of the other strand.
The diameter of the double helix or width between two strands is 20 Ã… (Angstrom) and the length of one complete turn is 34 Ã…. There are 10.4 base pairs on a complete turn of double helix. The adjacent base pairs are 3.4 Ã… apart.
The two strands are not identical but are complementary to each other due to the base pairing. The two strands are held together by the hydrogen bonds between complementary bases. Two hydrogen bonds hold A and T base pairs whereas three hydrogen bonds G and C base pairs. Sugar and phosphate molecules form the backbone of the DNA strand without concealing the nitrogen bases inside.
The double helix has two grooves along the surface of the DNA molecule. The wide and deep groove is called the major groove and the narrow and shallow groove is called the minor groove.
 |
| Figure 6 Watson and Crick model of of DNA Image from with modification: OpenStax College, CC BY 3.0 <https://creativecommons.org/licenses/by/3.0>, via Wikimedia Commons |
On the basis of the number of base pairs in a turn, DNA exists as A-DNA, B-DNA, C-DNA, D-DNA, and Z-DNA.
A-DNA has 11 base pairs in a turn and is with right-handed duplex. Its major grooves are very deep while minor grooves are very shallow.
B-DNA is the DNA described by Watson and Crick. It has 10 base pairs (on average 10.4 nucleotides) in a turn and is with right-handed duplex. It is metabolically the most stable form of DNA.
C-DNA has 9 base pairs (on average 9.3 nucleotides) per turn and is with right-handed duplex. The axis lies close to the minor groove.
D-DNA has 8 base pairs per turn and is with right-handed duplex.
Z-DNA has 12 base pairs per turn and is left-handed. It has a zig-zag sugar-phosphate backbone in antiparallel organization. One complete helix is of 4.5 anglestron. The adjacent nucleotides are oppositely oriented with respect to one another.
Functions of DNA
DNA is a genetic material that carries the hereditary information from one generation to another.
It controls all the biological activities of the cells as it dictates the synthesis of proteins, enzymes, and other biochemicals.
It synthesizes RNA by transcription.
It determines the type of protein to be synthesized during the protein synthesis in the cell.
Ribonucleic acid (RNA)
RNA is the genetic material of some viruses like animal viruses and bacteriophages. It is synthesized in the nucleus but is found in nucleolus, cytoplasm, and on the membranes of ribosomes.
Structure of RNA
RNA is a single stranded nucleic acid. In viruses, it is double stranded but never exists as the double helix. It consists of poly-ribonucleotides. Each ribonucleotide consists of a pentose sugar, phosphate, and nitrogen bases. Nitrogen bases in ribonucleotides are the same as in deoxyribonucleotides of DNA, except uracil in place of thymine. Nucleotides are joined together by the phosphodiester bonds. It forms the backbone of the RNA strand.
Functions of RNA
RNA helps in protein synthesis.
It serves as the hereditary material in some viruses.
Types of RNA
Based on molecular size and functions, RNA remains as messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA).
1. Messenger RNA (mRNA)
Messenger RNA is synthesized in the nucleus as the heterogenous nuclear RNA (hnRNA). It constitutes 2-5% of total RNA. It carries the genetic information from DNA in the form of codons of three bases to the ribosome in the cytoplasm. It is translated into protein in ribosomes. As it acts as a template for protein synthesis, it is unstable.
2. Ribosomal RNA (rRNA)
Ribosomal RNA is the most stable and abundant RNA. It constitutes about 70-80% of total RNA. It is synthesized in the nucleus and is carried out to the cytoplasm. In the cytoplasm, it combines with proteins to form ribosomes. It helps in binding mRNA to ribosomes during protein synthesis.
3. Transfer RNA (tRNA)
Transfer RNA is the smallest RNA with about 70-90 nucleotides. It accounts for about 10-15% of total RNA. It is also known as soluble RNA. Single tRNA carries only one amino acid to the ribosome during protein synthesis.
Structure of tRNA
According to the model proposed by Holley (1965), the tRNA coils over itself to form double stranded RNA looking like a clover leaf. The single polynucleotide chain of tRNA is folded upon itself to form five arms. Each arm consists of a stem and ends in a loop. The loops are acceptor arm, anticodon arm, DHU-arm, TψC arm, and extra arm.
Acceptor arm: This arm is capped with a sequence CCA (5’ to 3’). Amino acid is attached to the acceptor arm as it has an amino acid binding site.
Anticodon arm: It is 5-base pair long. The anticodon represents an amino acid in tRNA.
DHU-arm: It is made up of 8-12 bases. It contains dihydrouridine. It is the binding site for aminoacyl synthetase.
TψC arm: It contains a sequence of T, pseudouridine (represented by psi, ψ), and C. It is the site for binding tRNA to the ribosomes.
Extra arm: It lies between the TψC arm and anticodon arm. It may have five bases in the loop. Its exact function is still unknown.
 |
| Figure 7 Structure of tRNA (two dimensional) |
Replication of DNA
Replication is the process of making an exact copy or replica of DNA. So, the replication of DNA can be defined as the process of synthesis of DNA on its own. During replication, each strand of DNA acts as a template strand for the formation of a new and complementary DNA strand. A template strand and a newly synthesized complementary strand form a new DNA duplex which is identical to the parent DNA molecule.
The most relevant explanation tells that the DNA replication occurs by semi-conservative mode. By semiconservative mode of replication, each strand synthesizes its complementary strand. As a result, a new DNA is synthesized in which one parent DNA strand is conserved and a daughter strand is newly synthesized. So, the newly synthesized DNA is a hybrid DNA.
Basic requirements and components for the replication of DNA in both the prokaryotes and eukaryotes are the same. Different enzymes, protein factors, metal ions, and substrates are essential to occur DNA replication. Those enzymes are DNA helicase (separates DNA strands), primase (synthesizes RNA primers), DNA polymerase (catalyzes DNA synthesis), topoisomerase (causes nick in the DNA), DNA ligase (seals gap in the synthesized DNA fragments), and RNAse (digests RNA primers after the DNA synthesis). Protein factors are single stranded binding (SSB) proteins (stabilizes single stranded DNA long enough for replication). Metal ions are Mg2+ and Mn2+ ions. Substrates are deoxyribonucleoside triphosphate (dNTPs) and folic acid.
Mechanism of DNA replication
The mechanism of DNA replication includes origin of replication site, activation of deoxyribonucleotides, unwinding of DNA helix, formation of RNA primer, polymerisation of new strand, joining of Okazaki fragments, and proofreading.
 |
| Figure 8 The process of DNA replication (proposed by Watson and Crick) |
1. Origin of replication site
As DNA is a long chain of polynucleotides, it has many replication units called replicons. At each replicon, a nick (a cut) is produced in one strand at a specific initiation point, which is called ‘Ori-site’. This nick or cut is produced by an enzyme endonuclease.
2. Activation of deoxyribonucleotides
Deoxyribonucleoside monophosphates (dNMPs: dAMP, dGMP, dCMP, dTMP) present freely in the nucleoplasm are activated into deoxyribonucleoside triphosphates (dNTPs: dATP, dGTP, dCTP, dTTP) by the ATP in presence of an enzyme phosphorylase. The process is known as phosphorylation.
3. Unwinding of DNA helix
An enzyme DNA helicase unwinds the two DNA strands by breaking the hydrogen bonds between nucleotides. Then, the Y-shaped replication fork is formed. Both the separated DNA strands are templates for new DNA synthesis.
4. Formation of RNA primer
A small strand of RNA, called primer, is synthesized by an enzyme primase. The primer is attached to the template DNA at an initiation site. Then, DNA synthesis begins from the 5’ to 3’ direction of a primer and the 3’ to 5’ direction of the template strand.
5. Elongation of new strand
Once the RNA primer is formed and attached to the template strand, DNA polymerase III (in prokaryotes) and DNA polymerases (in eukaryotes) carry out DNA replication by using ATP and Mg2+ ions.
Nucleotide chain formation proceeds from the initiation site by adding new bases, with the base specificity, only from the 5’ to 3’ direction on the template strand 3’ to 5’ direction.
The replication is bidirectional i.e. proceeds on both the template strands in opposite directions.
Replication is continuous on one template strand i.e. single RNA primer helps the formation of the whole strand. The new strand formed by continuous replication is called a leading strand. However, the replication is not continuous in another template strand, which means multiple primers are responsible for the formation of a complete strand. So, the many small fragments of DNA, called Okazaki fragments, are formed. The gap between the newly synthesized Okazaki fragments are sealed by a DNA ligase; a complete daughter strand is formed. Such daughter strands formed by joining Okazaki fragments are called lagging strands.
After a new nucleotide chain is formed, RNA primer is removed from the template strand and its gap is sealed with the complementary bases by an enzyme DNA ligase.
6. Termination
Once the replication forks have met, the replication is terminated.
7. Proofreading and DNA repair
During replication, wrong bases may be inserted on a daughter strand. The probability of inserting such wrong bases is once per 100, 000 nucleotides. Such an error is corrected by inserting the correct nucleotide; the process is called proofreading. The exonuclease activity of DNA polymerase removes the incorrectly paired nucleotide and inserts the correct nucleotide.
Finally, the daughter DNA is synthesized. Each daughter DNA molecule has one strand from the parent and the other is newly synthesized. Half of the original DNA is conserved and half is newly synthesized. Hence, this replication is called semi-conservative mode of DNA replication.
Genetic code
The nitrogen bases in DNA or RNA are represented by alphabets A, G, C, and T or U for Adenine, Guanine, Cytosine, and Thymine or Uracil, respectively . Those alphabets in DNA are A, G, C, and T. Similarly, in RNA, the alphabets are A, G, C, and U. These four alphabets encode the hereditary messages and are called code letters or codons.
Those codes can be single, double, and triple base codes. However, only three base codes in a sequence (triplet) are required for determining the sequence of amino acids. These triplets represent genetic code or codons.
The genetic code is defined as a dictionary of nucleotide bases (A,G,C, and U) that determines the sequence of amino acids in the proteins of a cell. In other words, the genetic code is the dictionary that helps in translating the language of the nucleic acid into the language of protein. The term genetic code was coined by George Gamow. Marshall Nirenberg, Hargovind Khorana, Francis Crick, and many scientists did research on genetic code. Nirenberg and Khorana received the Nobel Prize in 1968.
Triplet codon
Four nucleotide bases make 64 different combinations of three base codons (See Figure 9). Out of 64 codons, 61 codons are for the 20 amino acids in proteins. The remaining three codons UAA, UAG, and UGA act as stop signals during protein synthesis. These three codons are called termination codons or nonsense codons. The codons - AUG and GUG are the initiating codons and code for amino acids.
 |
| Figure 9 Triplet genetic code |
Characteristics of genetic code
The genetic code has following characteristics:
The code is triplet
A codon is a triplet i.e. it is with three nucleotide bases. For any amino acid, it is necessary to have a triplet codon. A triplet codon encodes for a particular amino acid. The 64 triplets would be enough to code for 20 amino acids.
The code is degenerate
Most of the amino acids have more than one triplet codon. For illustration, glycine has four triplet codons. Likewise, arginine has six triplet codons. This is called degenerate codon.
The codon is non-overlapping
A base is a part of only one codon. Same base letter is not for two different codons. For example, a nucleotide sequence CATGAT is read as CAT and GAT. It represents two codons i.e. CAT and GAT when it is not overlapped. However, when it is overlapped more than two codons appear, which cannot be the genetic codes.
The code is commaless or punctuationless
The genetic code is continuous; it does not have any pause or gap after the triplets. If a nucleotide is deleted or added, the whole genetic code will be read differently.
The code is non-ambiguous
A particular codon always codes for the same amino acid except one codon. The genetic code is highly specific or unambiguous. For example UGG is the codon for tryptophan. The exception for non-ambiguous genetic code is GGA which codes for glycine and glutamine; this code is ambiguous code.
The code is universal
The genetic code is applicable universally i.e. a codon specifies for the same amino acid from viruses to a plant and human beings.
The code is collinear
The genetic code works on the principle of collinearity. So, it explains the specific relationship between DNA, RNA, and polypeptide chains. The linear order of nucleotides in DNA determines the linear order of codons in mRNA which in turn determines the linear order of the amino acids in a polypeptide chain.
 |
| Figure 10 Genetic codes and amino acids Image source: OpenStax, CC BY 4.0 <https://creativecommons.org/licenses/by/4.0>, via Wikimedia Commons |
Comments
Post a Comment