Home Brochure Contact

Biology: Gene its nature, expression and regulation

Topics are arranged as per SYLLABI published by Maharashtra State Board of Secondary and Higher Secondary Education.

Gene is units of inheritance. It is a segment of DNA that provides instructions for synthesis of a specific protein or a particular type of RNA. It may be defined as a segment of DNA which is responsible for inheritance and expression of a particular character.
Gene is specific segment of DNA consisting of three structural units; Seymour Benzer (1955) distinguished three structural units as Cistron, Muton and Recon.

Cistron (function) Muton (Mutation) Recon (Recombination)
The functional unit of gene which expresses phenotype. Unit of gene capable of undergoing changes called mutation. Unit of gene capable of recombination.
Largest sub-unit. Several hundred base pairs long. One to few base pairs long. Smallest unit of gene. There are more than one recon in a gene.
Further made up of two units: Introns (non-coding region) and Exons (coding region) Represented by a single Nitrogen base or a group of nitrogen bases. Participates in recombination through crossing over during meiosis.

  • DNA is the master molecule that carries genetic information for performing all the activities of cells.
  • George Beadly and Edward Tatuam in 1941 presented concept "One Gene - One Enzyme hypothesis" to explain how genetic information exists in the DNA molecule.
  • Vernon Ingram modified this concept in 1957 as "One Gene-One polypeptides" ; as gene code for proteins is not always a enzyme.
  • DNA contains all genetic information of an organism. The gene controls, regulate and express the characters through a specific protein.
  • Basic information of DNA is coded in a language of 4 alphabets A, G, C and T. They represent specific protein (genetic code).
  • Genetic code is the specific sequence of base pairs in the DNA which specifies the sequence of complementary bases on the m-RNA and the amino acids in proteins.
  • m-RNA acts as an agent in conveying information from DNA to cytoplasm.
  • The coded language on DNA and m-RNA is organized in triplets of nitrogen bases.
  • A triplet or 3 letter code for m-RNA called codon [Gamow in 1954].
  • Marshall Nirenberg, Heinrich Matthaei and Harbobind Khorana deciphered the genetic code by using artificial mRNA templates (homopolymers and co-polymers) and cell free system of protein synthesis.
  • Using four bases (A,U,C,G), a maximum 64 triplets (codons) can be possible (4 x 4 x 4 ) which determine 20 amino acids. This set of 64-triplet codon that specifies 20-acids is termed the dictionary of genetic code or coding dictionary.
  • The m-RNA language is used for the arrangement of the amino acids to form the polypeptide chain (protein molecule) ; this is called translation, cryptoanalysis or decoding.
  • The original sequence in the DNA is present in the form of DNA nucleotides (bases) i.e. A,T,C and G. It is copied by the m-RNA using complementary RNA nucleotides form A, U, C and G.
  • Out of 64 codons, three codons serve as termination codons. The remaining 61 codons are sense codons which codes for 20 essential amino acids required for protein synthesis.

Structure of DNA was discovered by James Watson and Francis Crick in 1953. According to Watson and Crick model, the DNA molecule is double-helix i.e. comprising of two polynucleotide strands which are antiparallel, complementary and spirally coiled around an imaginary central axis forming a right handed helix.

  • Structure on each strand
    • Deoxyribose sugar
    • Phosphate group
    • Nitrogen Base
      • Minor Groove
      • Major Groove
  • Complementary nature of strands
    • Purine base Adenine (A) always pairs with pyrimidine base Thymine (T) of the opposite strand with two hydrogen bonds.
    • Purine base Guanine (G) always pairs with pyrimidine base Cytosine (C ) of the opposite strand with three hydrogen bond.
  • Antiparallel nature of strands
    • Ascending strands
    • Descending strands

  • The DNA molecule is too long if not folded.
  • Bacteria have much less DNA in their cells than eukaryotes do, but even so the length of their DNA molecule if stretched out would be 1000x the length of the cell itself thus, even in the bacteria DNA must be "packaged", folded and coiled to make it fit in the cell eukaryotes have even more DNA, and use somewhat elaborate means to package the DNA even when it is in "decondensed" chromatin.
  • Nucleosomes are the main packaging mechanism for eukaryotic DNA.
  • Most of the time much of the DNA is packed tighter than just being wound on nucleosomes; this next packing step uses another histone, H1, that associates with the linker DNA regions; H1 binding leads to packing of nucleosomes into a 30 nm chromatin fiber.

The biosynthesis process by which DNA produces daughter DNA molecule which are exact copies of the original DNA is called replication DNA. The process of replication in eukaryotes was discovered by Watson and Crick in 1953. The most common method of DNA replication is semi-conservative method of replication.
Site: In Eukaryotic cell, it takes place in the nucleus, where the DNA is present in the chromosomes. The deoxyribose nucleotides needed for the formation of the new DNA strands are present in the nucleoplasm (pool of nucleotides). In prokaryotes, the process of replication occurs in cytoplasm.
Period: Replication takes place during the S-phase of interphase nucleus before cell division (mitosis and meiosis).
Due to replication, the quantity of DNA doubles. There is equal distribution of genetic material in the two daughter cells when the cell divides. Therefore each daughter cells receives the same genetic information.

  • Unwinding or Uncoding or Unzipping of DNA
    • Activation of nucleotides
    • Origin of replication and Incision.
    • Unwinding and Replicating fork
    • SSBP
    • DNA Gyrase
  • Biosynthesis of new strands
    • Template
    • Base Pairing (Replication)
    • Formation of new strand
    • Leading and Lagging strands
    • Leading Strand
    • Lagging Strand
  • Coiling or Winding or Zipping of DNA

  • It is a nucleic acid containing robose sugar.
  • Consist of single strand of polynucleotides formed by polymerization of many ribonucleotides joined by phosphor-diester bond.
  • It is found in the nucleus as well as cytoplasm of living cells.
  • It is present in all organisms except some viruses.

It is a polymer of many ribonucleoties or ribotides linked by phospo-diester linkage. A strand of RNA contains 70-12000 nucleotides. Being single stranded, it can be linear, straight or can be folded upon itself. Each ribonucleotide has the following three components.

  • Cycling Pentose Sugar C5H10O5
  • Phosphoric Acid : Inorganic molecule present in RNA.
  • Nitrogen Bases
    • Purines (Double Ring Structure)
      • Adenine (A)
      • Guanine (G)
    • Pyrimidines (Single Ring Structure)
      • Cytosine (C)
      • Uracil (U)
In a nucleotide, the nitrogen base is attached to the first carbon atom of the sugar by a glycosidic linkage. Phosphate group is attached to the fifth carbon atom of the sugar by ester bond. The ribonucleotides are linked with each other by phosphor-dister bonds in 5 Genes 3 direction to form a single polynucleotide strand.

RNA is single stranded, it does not show base pairing but base pairing may occur if the RNA gets folded upon itself in certain regions and forms loops. In linear RNA, the base are exposed or unpaired. Therefore, nitrogen bases are paired in the loops and remain unpaired in unfolded regions.

There are two main types of RNA

Genetic RNA Non-Genetic RNA
Carries genetic information and functions as genetic material. Neither carry any genetic information nor function as genetic material.
Found only in certain viruses (ex: Riboviruses). Also called as Genomic RNA. Present in all organisms where DNA is genetic material. Called as cellular RNA.
It can replicate. It cannot replicate.
It is single or double stranded. It is usually single stranded.
As a genetic material, it controls heredity. It is present in viruses where DNA is absent. They are of three types (based on functions performed) : m-RNA, r-RNA, t-RNA

  • Protein Synthesis: All the three types of non-genetic RNA : m-RNA, t-RNA and r-RNA are involved in protein synthesis. They bring about synthesis of polypeptide chain according to the coded information given by DNA.
  • RNA Primer : It is a small polymer of RNA containing 15-20 ribonucleotides which is essential for DNA replication.
  • Ribosomes: Ribosomal RNA are the main constituents of ribosomes. Ribosomes are the main sites of protein synthesis.
  • Genomic RNA : In some viruses, RNA is hereditary material. It is called genetic RNA.

m-RNA t-RNA / s-RNA r-RNA
Messenger RNA Transfer RNA / Soluble RNA Ribosomal RNA
About Name was given by Jacob & Monod due to function. Cannot be separated from the cell even by ultracentrifugation. Associated with Ribosomes
Position Produced in the nucleus on one of the strand of DNA by the process of transcription using enzyme RNA polymerase and the transfer to the cytoplasm for use. Produced in the nucleus on DNA by the process of transcription using enzyme RNA polymerase but is organized in the cytoplasm free floating for function. Present in the cytoplasm as ribosomes. Visible only during interphase.
Percentage Constitutes 3-5% of total cellular RNA Constitutes 10-15% of total cellular RNA Constitutes 80% of total cellular RNA
Shape Linear, straight or unfolded Single stranded but folded upon itself: Hairpin : One Loop Clover Leaf : Three Loop Single Stranded which is folded upon itself forming hair pin loops.
Length Depends upon the gene and the coded information of the protein. Not fixed. Single stranded polymer containing 73-93 nucleotides. It is long polymer containing thousands of ribonucleotides.
Size Variable, as length is not fixed. Smallest Longest and largest of all RNAs
Molecular Weight Variable
Life Span 2 mins - 4 hours (Shortest life among other RNAs) Remains in the cell till cell dies or divides. Appears in nucleus as nucleolus
Structure Polymer of ribonucleotides linked by phosphor-diester bonds having a polarity Genes. t-RNA gets folded upon itself forming a hair pin structure or clover leaf structure. Single stranded molecule of r-RNA is variously folded and twisted upon itself to form hair-pin loops.
Key Points One m-RNA is specific for one specific protein, as it carries information of particular protein) One t-RNA is specific for one specific amino acid as it carries one particular amino acid at the 3 end. Nitrogen pairing occurs in folded regions. Adenine pairs with uracil with 2 Hydrogen bonds, while Guanine pairs with cytosine by three hydrogen bonds.
Functions Carries specific Message.
Provides sequence of amino acids
Reads codon of m-RNA
Carries specific amino acid from cell cytoplasm to the ribosome.
Provides suitable binding site for m-RNA (for reading)
Protects m-RNA
Releases t-RNA
Helps in protein formation.

Protein Synthesis is the most important, essential and significant metabolic activity of the living world taking place in every living cell continuously. Biochemical reactions are essential for the actual phenotypic expression of any character in a living cell or in the body of an organism. Each biochemical reaction is catalyzed by a specific enzyme which initiates and complete the chemical reaction. Almost all enzymes are proteins. The cell also needs other structural proteins. Thousands of structural protein and catalytic proteins are required by cell continuously for its proper functioning.

Protein synthesis is directly under genetic control. A central dogma was formulatd by Crick, which states that the biological information flows in a unidirectional pattern. i.e. there is flow of information from DNA to RNA and from RNA into that of proteins. Genes
Exception to central dogma is reverse transcription which was first reported by American scientist H. Temin and D. Baltimore. They discovered that DNA is synthesized over the RNA template in RNA tumor virus - Rous Sarcoma virus. They were awarded Nobel prize for the discovery of reverse transcriptase enzyme. Genes
Proteins in the food are digested to form amino acids which ultimately reach the cells (move freely in the cytoplasm). Within the cell, these amino acids resynthesize proteins which then form enzymes and hormones. These enzymes and hormones control all the metabolic activities of life.

It is initiated by the DNA in the nucleus and build up by the RNA on the ribosomes in the cytoplasm.
Structure: Proteins are polypeptide chains formed by the polymerization of amino acids. The bonds between the amino acids is a peptide bond in which the carboxyl group of the amino acids is linked with the amino group of the second amino acid with the elimination of water. Only 20 amino acids are biologically important for the formation of different proteins in the cells.

  • 20 amino acids that are specified by the genetic code.
  • DNA (to provide base sequence)
  • Non-Genetic RNA (m-RNA, t-RNA, r-RNA)
  • Ribosomes (site of protein synthesis)
  • Various enzymes (factor)
  • Energy in the form of ATP and GTP.

The process of protein synthesis follows central dogma which involves two main steps in protein synthesis. They are transcription and translation:

  • Transcription
    • Initiation of m-RNA formation
    • Elongation of m-RNA
    • Termination of mRNA formation
    • Final Movements
  • Translation
    • Activation of amino acids
    • Attachment to t-RNA
    • Formation of polypeptide chain
      • Initiation
      • Elongation
      • Termination
    • Final Movements

Transcription Translation
The process of involving the synthesis of m-RNA from DNA is called transcription. The process involving the decoding of the sequence of nucleotides present on m-RNA into the sequence of polypeptide chain is called translation.
Occurs in Nucleus. Occurs in Cytoplasm.
One of the DNA strand acts as a template for synthesis of m-RNA. The codons of the m-RNA act as template for the synthesis of proteins.
Takes place in presence of RNA polymerase. Takes place in presence of amino acyl synthetase enzyme.
No participation of t-RNA, r-RNA , ribosome and nonsense codon Involves the participation of t-RNA, r-RNA, ribosomes and nonsense codons.
Gene Expression and Gene Regulation (The Lac operon as a typical model of gene regulation).

  • It is the mechanism at the molecular level by which a gene is able to express itself in the phenotype of an organism.
  • The mechanism of gene expression involves biochemical genetics. It consists of synthesis of specific RNAs, polypeptides, structural proteins, proteinaceous biochemicals / enzymes which control the structure or functioning of specific traits.
  • Most of the times genes are inactive and not expressed. At certain times, genes are switched on to produce their particular products. The activation of the gene to produce their respective products is called as gene expression.
  • Gene expression takes place in two main steps
    • Transcription
    • Translation
  • If an enzyme called beta-galactosidase is produced by E. coli, it is used for catalyzing hydrolysis of disachharide lactose into glucose and glactose. These molecules are used by the bacteria as source of energy. Similarly, if there is no lactose in the surrounding of the bacteria, then there will be no requirement of enzyme beta-galactosidase. Therefore, it is metabolic, physiological or environmental conditions that regulates the gene expression.
  • Transcriptional regulation of gene is controlled by a cluster of genes called operons. They usually transcribes single mRNA molecule. [In E. coli there are 260 genes that are grouped in 75 different operons]

  • Each operon is a unit of gene expression and regulation which includes structural gene and their control elements - promoters and operators.
  • Structural genes have encoded information of the synthesis of chemical substances required for cellular machinery.
  • They either produces mRNA for synthesis of polypeptides, several proteins (polycistronic mRNAs) or nonconding RNAs.
  • Regulatory genes do not transcribe RNA and therefore produce no chemicals. They are meant for controlling the functions of structural genes. The important regulatory genes are promoters, terminators, operators and repressors producing / regulator genes.
    • Promotoers : These signal sequences in DNA that starts the process of RNA synthesis. These are the sites where the RNA polymerase binds during transcription.
    • Operators : These are present in between the promoters and structural genes. The repressor binds to the operator region of the opron.
  • Regulatory genes are responsible for the formation of repressors which interact with operators.

Operons are of two types:
  • Inducible Operon – Lac Operon
  • Repressible operon system - Tryptophan operon
Inducible operon system regulate genetic material which remains switched off normally but becomes operational in the presence of inducer, eg: Lac operon system. Inducible operon system occurs in catabolic pathway.

The Lac (Lactose) operon is an organized region of the genome that is present in E. coli bacteria. It is mainly concerned with metabolism of lactose sugar. It is important in the history of genetics as it was the first transcriptional regulated system that was elucidated.
First Lac-operon was discorved by Francois Jacob and Jacques Manad (1961) in E. coli . They studied the structure and explained the mechanism of the action for which they received the Nobel Prize for Medicine.
Lac Operon consists for following parts:

  • Structural genes
  • Operator gene
  • Regulator gene
  • Promoter gene
Inductor for Lac operon of E. coli is lactose. CAP is activator called catabolic activator protein. It exerts a positive control in lac operon because in its absence RNA polymerase is unable to recognize promoter gene. CAP activates lac gene only when glucose is absent. The expression of these genes depends upon, whether the operon is switched on or off.

  • It is extensively studied in prokaryotes especially E. coli.
  • The possible candidates for regulation of gene activity are the proteins associated with DNA in the chromosomes.
  • These include histone and non-histone chromosomal proteins.
  • It has been suggested that histone s probably mask DNA in a non-specific manner because histones are rich in lysine and arginine , they have a net positive charge and are basic proteins.
  • The positively charged groups, which appear to be arranged in clusters, could interact with the negative charge of the phosphate backbone of DNA. This would greatly reduce the charge repulsion of the phosphate groups and would facilitate supercoiling of DNA.
  • The control over the functioning of genes is called regulation of gene expression. In eukaryotes regulation of gene expression can be exerted at four levels.
    • Transcriptional level during formation of primary transcript.
    • Processing levels like splicing, terminal additions or modifications.
    • Transport of RNAs from nucleus to cytoplasm.
    • Translation level.

  • Length of DNA double helix in a typical mammalian cells is approximately 2.2 m.
  • RNA : Adenine pairs with uracil (two H-bonds) Guanine with Cytosine (three H-bonds).
  • The entire function of t-RNA is called as translation or crypto-analysis..
  • Meselson and Stahl performed experiments on E. coli using heavy isotope of nitrogen Gene: its nature, expression and regulation and proved that the DNA replication is semiconservative in prokaryotes.
  • Levene identified five carbon sugar, ribose in RNA and de-oxyribose in DNA.
  • H. Harries is associated with DNA-RNA hybridization technique. .
  • Nucleic acids are polymers of nucleotides ; which are called as "Secrets of Life".
  • The chromosome consists of two longitudinal halves called chromatids, which are joined at the single point called centromere. Each chromatid is 700nm in length and is made up of the coiled helical DNA, which winds upon itself as telephone chord and twisted into series of secondary coils or super coils to accommodate itself in small space of chromosomes .
  • Mendel was the pioneer to put forward the idea that heredity units are present as definite particles and referred to them as factors, which were later on called as genes.
  • Prokaryotes have 70S ribosomes and Eukaryotes have 80S ribosomes. [S stands for Swedberg Unit. Ie.e Rate of Sedimentation].
  • Ribosomes are called as protein factories as well as site of protein synthesis.
  • Ribosomes are only cell organelles which are not membrane bounded and therefore are found in prokaryotes as well as eukaryotes.
  • Khorana et all (1970) synthesized alanine tRNA having 97 nucleotides. Non Functional.
  • Khorana et all (1979) synthesized tyrosine tRNA having 207 nucleotides.
  • C. Value is the amount of DNA in picograms (pg) present in a genome.
  • Transposons or jumping genes are those DNA segments which can pass from one place to another in the genome. At their ends, transposons have similar or inverted repetitive DNA sequences. The sequences can be cleaved by an enzyme transposase.
  • Most common human transposon is Alu-Family .
  • Phragmoplast are persistent spindle apparatus in dividing plant cells where the spindle fibres develop an interdigitated array of microtubules, especially in the equatorial region.
  • Synzetic Knot is a leptotene arrangement found in certain plants (ex: Lilium), corresponding to bouquet stage of some animals (leptotene chromosomes found to be converged towards the side of centriole), where all chromosomes are observed to come together in one spot and then diverge again.
  • Go Phase is the arrest of cell cycle and onste of differentiation.
  • Nuclear Envelope = Karyotheca
  • Nuclear Matrix is a network of proteinaceous fibrils which is thickened towards the outside to from fibrous lamina or nuclear lamina in contact with inner membrane of nuclear envelope. The proteins here are acidic in nature.
  • Chargaff’s Rules are applicable to only DNA and not RNA. Chargaff discovered that in DNA.
    • Purines and pyrimidines occur in equal amounts.
    • Phosphate and deoxyribose sugar occur in equal number.
    • Molar amount of adenine is equal to that of thymine and cytosine equal to guanine.
    • Base Ratio A + T/C + G is specific for a species. It is rarely one. The ratio is high in advanced organisms and low in primitive organism.
  • Due to sequential opening of parent DNA duplex and its replication to form two DNA double chains, DNA replication is also called zipper duplication.
  • In the Mechanism of DNA Replication; The strands formed by joining Okazaki segments is called lagging (discontinuous) strand. Okazaki segments are joined by means of DNA ligase.
  • Garrod established the connection between gene and enzyme.
  • Beadle & Tatum proposed One-gene One-Enzyme hypothesis (Biomedical Genetics).