CHAPTER 5 - MOLECULAR BASIS OF INHERITANCE
Molecular Basis of Inheritance - During inheritance, chromosome pass on genes from a generation to next generations but it is not chromosome, it is DNA (deoxyribonucleic acid) which is the genetic material. Hence molecular basis of inheritance is DNA (deoxyribonucleic acid).
The DNA (DeoxyriboNucleic Acid)
- DNA is a long polymer of deoxyribonucleotides.
- The length of DNA is usually defined as number of nucleotides (or a pair of nucleotide referred to as base pairs) present in it.
- This also is the characteristic of an organism.
- For example -
- a bacteriophage known as ϕ×174 has 5386 nucleotides
- Bacteriophage lambda has 48502 base pairs (bp)
- Escherichia coli has 4.6 × 106 bp
- haploid content of human DNA is 3.3 × 109 bp
Structure of Polynucleotide Chain (DNA or RNA)
- A nucleotide has three components –
- a nitrogenous base
- a pentose sugar (ribose in case of RNA and deoxyribose for DNA)
- a phosphate group.
- There are two types of nitrogenous bases –
- Purines (Adenine and Guanine)
- Pyrimidines (Cytosine, Uracil and Thymine)
- Cytosine is common for both DNA and RNA.
- Thymine is present in DNA.
- Uracil is present in RNA at the place of Thymine.
- Nucleoside - A nitrogenous base is linked to the OH of 1'C pentose sugar through a N-glycosidic linkage to form a nucleoside, such as
- adenosine or deoxyadenosine
- guanosine or deoxyguanosine
- cytidine or deoxycytidine
- uridine or deoxythymidine
- Nucleotide - When a phosphate group is linked to OH of 5' C of a nucleoside through phosphoester linkage, a corresponding nucleotide (or deoxynucleotide) is formed.
- Dinucleotide - Two nucleotides are linked through 3'-5' phosphodiester linkage to form a dinucleotide.
- Polynucleotide - More nucleotides can be joined through 3'-5' phosphodiester linkage to form a polynucleotide chain.
- A polymer (polynucleotide chain) has two end
- a free phosphate moiety at 5'-end of sugar, which is referred to as 5’-end of
polynucleotide chain - a free OH of 3'C group which is referred to as 3'-end of the polynucleotide chain
- a free phosphate moiety at 5'-end of sugar, which is referred to as 5’-end of
- The backbone of a polynucleotide chain is formed due to sugar and phosphates.
- The nitrogenous bases linked to sugar moiety project from the backbone.
- RNA -
- Every nucleotide residue in RNA has an additional –OH group present at 2' -position in the ribose.
- Also, in RNA the uracil is found at the place of thymine.
The DNA (DeoxyriboNucleic Acid)
- This is an acidic substance present in nucleus.
- This was first identified by Friedrich Meischer in 1869.
- X-ray diffraction data was produced by Maurice Wilkins and Rosalind Franklin.
- In 1953, James Watson and Francis Crick, based on the X-ray diffraction data proposed 'Double Helix structure of DNA'.
- There was base pairing between the two strands of polynucleotide chains.
- Erwin Chargaff observed that for a double stranded DNA, the ratios between Adenine and Thymine and Guanine and Cytosine are constant and equals one.
The salient features of the Double-helix structure of DNA
- It is made of two polynucleotide chains, where the backbone is constituted by sugar-phosphate, and the bases project inside.
- The two chains have anti-parallel polarity. It means, if one chain has the polarity 5'→3' , the other has 3'→5' .
- The bases in two strands are paired through hydrogen bond (H-bonds) forming base pairs (bp).
- Adenine forms two hydrogen bonds with Thymine from opposite strand and vice-versa.
- Guanine is bonded with Cytosine with three H-bonds.
- As a result, always a purine comes opposite to a pyrimidine.
- This generates approximately uniform distance between the two strands of the helix.
- The two chains are coiled in a right-handed fashion.
- The pitch of the helix is 3.4 nm (a nanometre is one billionth of a metre, that is 10-9 m) and
- there are roughly 10 bp in each turn.
- Consequently, the distance between a bp in a helix is approximately 0.34 nm.
- The plane of one base pair stacks over the other in double helix. This, in addition to H-bonds, confers stability of the helical structure.
Central dogma
Francis Crick proposed the Central dogma in molecular biology, which states that the genetic information flows from DNA→RNA→Protein.
Packaging of DNA Helix
- The distance between two consecutive base pairs = 0.34×10–9 m (0.34 nm)
- the total number of bp in a typical mammalian cell = 6.6 × 109 bp
- the length of DNA double helix in mammalian cell = 2.2 metres (approximately)
- A length that is far greater than the dimension of a typical nucleus (approximately 10–6 m).
In prokaryotes
- They do not have a defined nucleus but the DNA is not scattered throughout the cell.
- DNA (-ve charge) is held with some proteins (+ve charges) in a region termed as ‘nucleoid’.
- The DNA in nucleoid is organised in large loops held by proteins.
In Eukaryotes
- This organisation is much more complex.
- Histones -
- A set of positively charged, basic proteins is called histones.
- A protein acquires charge from charged side chains of amino acids residues.
- Histones are rich in the basic amino acid residues lysine (+ve) and arginine (+ve).
- Histone Octamer -
- Histones are organised to form a unit of eight molecules called histone octamer.
- Nucleosome -
- The negatively charged DNA is wrapped around the positively charged histone octamer to form a structure called nucleosome.
- A typical nucleosome contains 200 bp of DNA helix.
- Chromatin -
- Nucleosomes constitute the repeating unit of a structure in nucleus called chromatin.
- It is thread-like stained (coloured) bodies seen in nucleus.
- The nucleosomes in chromatin are seen as ‘beads-on-string’ structure when viewed under electron microscope (EM).
- Chromatin Fibers -
- The beads-on-string structure in chromatin is packaged to form
chromatin fibers.
- The beads-on-string structure in chromatin is packaged to form
- Chromosomes -
- They are further coiled and condensed at metaphase stage of cell division to form chromosomes.
- Non-histone Chromosomal (NHC) proteins -
- The packaging of chromatin at higher level requires additional set of proteins that collectively are referred to as Non-histone Chromosomal (NHC) proteins.
- Euchromatin -
- In a typical nucleus, some region of chromatin are loosely packed (and stains light) and are referred to as euchromatin.
- Heterochromatin -
- The chromatin that is more densely packed and stains dark are called as Heterochromatin.
- Euchromatin is said to be transcriptionally active chromatin, whereas heterochromatin is inactive.
Griffith Experiment
- In 1928, Frederick Griffith, in a series of experiments, he grew Streptococcus pneumoniae (pneumococcus) bacteria are grown on a culture plate.
- Some produce smooth shiny colonies (S) due to mucous (polysaccharide) coat
- while others produce rough colonies (R) without mucous coat
- When he injected mice with
- the S strain (virulent), mice die from pneumonia infection
- but mice infected with the R strain (non virulent) do not develop pneumonia.
- Griffith was able to kill bacteria by heating them. He observed that heat-killed S strain bacteria injected into mice did not kill them.
- When he injected a mixture of heat-killed S and live R bacteria, the mice died. Moreover, he recovered living S bacteria from the dead mice.
- He concluded that the R strain bacteria had been transformed by the heat-killed S strain bacteria to synthesise a smooth polysaccharide coat and become virulent.
- This was thought to be transforming principle.
Biochemical Characterisation of Transforming Principle
- It was thought that the genetic material was a protein.
- Oswald Avery, Colin MacLeod and Maclyn McCarty purified biochemicals (proteins, DNA, RNA, etc.) from the heat-killed S cells to determine the biochemical nature of ‘transforming principle’ in Griffith's experiment.
- They discovered that protein-digesting enzymes (proteases) and RNA-digesting enzymes (RNases) did not affect transformation, so the transforming substance was not a protein or RNA.
- Digestion with DNase inhibited transformation, suggesting that the DNA caused the transformation.
- DNA alone from S bacteria caused R bacteria to become transformed.
- They concluded that DNA is the hereditary material.
The Genetic Material is DNA
Hershey-Chase Experiment
- Alfred Hershey and Martha Chase (1952) worked with viruses that infect bacteria called bacteriophages.
- They grew some viruses on a medium that contained radioactive phosphorus and some others on medium that contained radioactive sulfur.
- Viruses grown in the presence of radioactive phosphorus contained radioactive DNA but not radioactive protein because DNA contains phosphorus but protein does not.
- Similarly, viruses grown on radioactive sulfur contained radioactive protein but not radioactive DNA because DNA does not contain sulfur.
- Radioactive phages were allowed to attach to E. coli bacteria.
- Then, as the infection proceeded, the viral coats were removed from the bacteria by agitating them in a blender.
- The virus particles were separated from the bacteria by spinning them in a centrifuge.
- Bacteria which was infected with viruses that had radioactive DNA were radioactive, indicating that DNA was the material that passed from the virus to the bacteria.
- Bacteria that were infected with viruses that had radioactive proteins were not radioactive.
- This indicates that proteins did not enter the bacteria from the viruses.
- Hence DNA is the genetic material that is passed from virus to bacteria.
Properties of Genetic Material
- A molecule that can act as a genetic material must fulfill the following criteria:
- It should be able to generate its replica (Replication).
- It should be stable chemically and structurally.
- It should provide the scope for slow changes (mutation) that are required for evolution.
- It should be able to express itself in the form of 'Mendelian Characters’.
RNA
- RNA was the first genetic material.
- RNA used to act as a genetic material as well as a catalyst.
- RNA being a catalyst was reactive and hence unstable.
- Essential life processes (e.g. metabolism, translation, splicing, etc.), evolved around RNA.
- Important biochemical reactions are catalysed by RNA catalysts and not by protein enzymes.
Replication
- Watson and Crick (1953) had proposed a scheme for replication of DNA.
- The scheme suggested that the two strands would separate and act as a template for the synthesis of new complementary strands.
- After the completion of replication, each DNA molecule would have one parental and one newly synthesised strand.
- This scheme was termed as semiconservative DNA replication.
- It is now proven that DNA replicates semiconservative.
- It was shown first in Escherichia coli and subsequently in higher organisms, such as plants and human cells.
Meselson and Stahl's Experiment
- Matthew Meselson and Franklin Stahl performed the following experiment in 1958 in support of semiconservative nature of DNA:
- They grew E. coli in a medium containing 15NH4Cl (15N is the heavy isotope of nitrogen) as the only nitrogen source for many generations.
- The result was that 15N was incorporated into newly synthesised DNA (as well as other nitrogen containing compounds).
- This heavy DNA molecule could be distinguished from the normal DNA by centrifugation in a cesium chloride (CsCl) density gradient.
- Then they transferred the cells into a medium with normal 14NH4Cl and took samples at various definite time intervals as the cells multiplied, and extracted the DNA that remained as double-stranded helices.
- The various samples were separated independently on CsCl gradients to measure the densities of DNA.
- Thus, the DNA that was extracted from the culture one generation after the transfer from 15N to 14N medium had a hybrid or intermediate density.
- DNA extracted from the culture after 2nd generation was composed of equal amounts of this hybrid DNA and of ‘light’ DNA.
Taylor and colleagues Experiment
- Very similar experiments was done by Taylor and colleagues in 1958 to detect semiconservative nature of DNA.
- Use of radioactive thymidine to detect distribution of newly synthesised DNA in the chromosomes was performed on Vicia faba (faba beans).
- The experiments proved that the DNA in chromosomes also replicate semiconservatively.
The Machinery and the Enzymes
Enzymes
- In living cells, such as E. coli, the process of replication requires a set of catalysts (enzymes).
- DNA Helicase
- DNA gyrase
- DNA polymerase
- DNA ligase
- DNA Helicase -
- It unwind the DNA helix to replicate.
- DNA gyrase -
- It prevent DNA to supercoil or rewind.
- DNA polymerase -
- It uses a DNA template to catalyse the polymerisation of deoxynucleotides.
- These enzymes are highly efficient enzymes as they have to catalyse polymerisation of a large number of nucleotides in a very short time.
- They are very fast to catalyse the reaction with high degree of accuracy.
- DNA ligase -
- The DNA fragments are joined by the enzyme DNA ligase.
The Mechanism of Replication
For Long DNA Molecule
- DNA ( Whloe genome) -
- Since the two strands of DNA cannot be separated in its entire length due to very high energy requirement.
- Deoxyribonucleoside triphosphate -
- It acts as substrates.
- They provide energy for polymerisation reaction.
- Origin of replication -
- A definite region in E. coli DNA where the replication originates is termed as origin of replication.
- Replication fork -
- The replication occur within a small opening of the DNA helix, referred to as replication fork.
- The DNA-dependent DNA polymerases -
- This catalyse polymerisation only in one direction, that is 5'→3'.
- Leading strand -
- On one strand (the template with polarity 3'→5' ), the replication is continuous only in 5'→3' direction.
- This strand is called leading strand.
- Lagging strand -
- On the other (the template with polarity 5'→3' ), the replication is discontinuous.
- This strand is called lagging strand.
- Okazaki fragments -
- The discontinuously synthesised fragments are called okazaki fragments.
- DNA ligase -
- Okazaki fragments are later joined by the enzyme DNA ligase.
Transcription
- The process of copying genetic information from one strand of the DNA into RNA is termed as transcription.
- In transcription only a segment of DNA and only one of the strands is copied into RNA.
- The adenosine complements now forms base pair with uracil instead of thymine.
- Why are both the strands not copied during transcription?
- If both strands act as a template, they would code for RNA molecule with different sequences for two different proteins.
- If the two RNA molecules produced simultaneously, they would be complementary to each other, hence would form a double stranded RNA. This would prevent RNA from being translated into protein.
Transcription Unit
- A transcription unit - In DNA this is defined primarily by the three regions in the DNA :
- (i) A Promoter
- (ii) The Structural gene
- (iii) A Terminator
Two strands of the DNA for Transcription
- Template strand or antisense strand (minus strand) or a non-coding strand -
- This strand code for mRNA transcription.
- The template strand is directed in the 5’→3’ direction.
- This strand contains anticodons.
- Coding strand or sense strand (plus strand) -
- This strand does not code for anything.
- The coding strand is directed in the 3’→5’ direction.
- This strand contains codons.
DNA-dependent RNA polymerase
- This catalyse the polymerisation in only one direction, i,e., 5'→3'.
Structure of a Transcription Unit
- The promoter and terminator flank the structural gene in a transcription unit.
- The promoter -
- This is said to be located towards 5'-end (upstream) of the structural gene (the reference is made with respect to the polarity of coding strand).
- It is a DNA sequence that provides binding site for RNA polymerase.
- It is the presence of a promoter in a transcription unit that also defines the template and coding strands.
- By switching its position with terminator, the definition of coding and template strands could be reversed.
- The terminator -
- This is located towards 3'-end (downstream) of the coding strand.
- It usually defines the end of the process of transcription.
- There are additional regulatory sequences that may be present further upstream or downstream to the promoter.
Gene
- Definition -
- A gene is defined as the functional unit of inheritance.
- The DNA sequence coding for tRNA or rRNA molecule is also a gene.
- Location - They are located on the DNA.
- Cistron - This is a segment of DNA coding for a polypeptide. It may be -
- monocistron - the structural gene in a transcription unit coding for one polypeptide.
- polycistron - the structural gene in a transcription unit coding for more polypeptide.
- Exons - The coding sequences or expressed sequences that appear in mature or processed RNA.
- Introns - Introns or intervening sequences do not appear in mature or processed RNA.
- Regulatory genes - The regulatory sequences of a structural gene that do not code for any RNA or protein.
Types of RNA
- There are three major types of RNAs:
- mRNA (messenger RNA) - This provides the template.
- tRNA (transfer RNA) - This brings aminoacids and reads the genetic code.
- rRNA (ribosomal RNA) - This play structural and catalytic role during translation.
- All three RNAs are needed to synthesise a protein in a cell.
The process of Transcription in Bacteria
- DNA-dependent RNA polymerase -
- This catalyses transcription of all types of RNA in bacteria.
- It binds to promoter and initiates transcription (Initiation).
- It uses nucleoside triphosphates as substrate and polymerises the amino acid.
- It also facilitates opening of the helix and continues elongation.
- Only a short stretch of RNA remains bound to the RNA polymerase.
- Once the RNA polymerases reaches the terminator region, the nascent RNA falls off, so also the RNA polymerase.
- This results in termination of transcription.
- The RNA polymerases are able to catalyse all the three steps, which are initiation, elongation and termination.
The process of Transcription in Eukaryotes
- RNA polymerases -
- There are at least three RNA polymerases in the nucleus (in addition to the RNA polymerase found in the organelles). There is a clear cut division of labour.
- The RNA polymerase I - It transcribes rRNA (28S, 18S, and 5.8S).
- The RNA polymerase III - It is responsible for transcription of tRNA, 5srRNA, and snRNAs (small nuclear RNAs).
- The RNA polymerase II - It transcribes precursor of mRNA, the heterogeneous nuclear RNA (hnRNA).
- The primary transcripts contain both the exons and the introns and are non-functional.
- Splicing - A process of removing introns and joining exons in a defined order are called splicing. hnRNA undergoes additional processing called as capping and tailing.
- Capping - In capping an unusual nucleotide (methyl guanosine triphosphate) is added to the 5'-end of hnRNA.
- Tailing - In tailing, adenylate residues (200-300) are added at 3'-end in a template independent manner.
- It is the fully processed hnRNA, now called mRNA, that is transported out of the nucleus for translation
Genetic Code
- Definition -
- Genetic code is genetic information from a polymer of nucleotides that could synthesise the sequence of amino acids during synthesis of proteins.
- History -
- George Gamow, a physicist -
- the code should constitute a combination of bases.
- the code should be made up of three nucleotides.
- Har Gobind Khorana, a Biochemist and Nobel Prize for Physiology (1968) -
- Synthesise RNA molecules with defined combinations of bases (homopolymers and copolymers)
- Marshall Nirenberg’s, a Biochemist and Nobel Prize for Physiology (1968) -
- protein synthesis in laboratory i.e. cell-free system
- Severo Ochoa, a Physician -
- Severo Ochoa enzyme (polynucleotide phosphorylase) was also helpful in polymerising RNA with defined sequences in a template independent manner.
- George Gamow, a physicist -
The salient features of genetic code
- The salient features of genetic code are as follows:
- (i) The codon is triplet. 61 codons code for amino acids and 3 codons do not code for any amino acids, hence they function as stop codons.
- (ii) Some amino acids are coded by more than one codon, hence the code is degenerate.
- (iii) The codon is read in mRNA in a contiguous fashion. There are no punctuations.
- (iv) The code is nearly universal: for example, from bacteria to human UUU would code for Phenylalanine (phe). Some exceptions to this rule have been found in mitochondrial codons, and in some protozoans.
- (v) AUG has dual functions.
- It codes for Methionine (met).
- It also act as initiator codon.
- (vi) UAA, UAG, UGA are stop terminator codons.
- (vii) Any change in the sequence of genetic code results in mutation.
Translation
- Translation refers to the process of polymerisation of amino acids to form a polypeptide.
- The order and sequence of amino acids are defined by the sequence of bases in the mRNA.
- Amino acids have no structural specialities to read the code uniquely.
- There must be an adapter molecule that would on one hand read the code and on other hand would bind to specific amino acids.
- That adapter molecule is tRNA.
Structure of tRNA– the Adapter Molecule
- tRNA has following structure -
- Anticodon loop - It has bases complementary to the code of mRNA.
- Amino acid acceptor end - It binds to amino acids.
- tRNAs are specific for each amino acid.
- Initiator tRNA -
- The specific tRNA for initiation is referred as initiator tRNA.
- Charging of tRNA or aminoacylation of tRNA -
- In the first phase of translation amino acids are activated in the presence of ATP and linked to their cognate tRNA – a process commonly called as charging of tRNA.
Ribosome
- The cellular factory responsible for synthesising proteins is the ribosome.
- The ribosome consists of structural RNAs and about 80 different proteins.
- In its inactive state, it exists as two subunits;
- a large subunit and
- a small subunit
- When the small subunit encounters an mRNA, the process of translation of the mRNA to protein begins.
- There are two sites in the large subunit, for subsequent amino acids to bind to and thus, be close enough to each other for the formation of a peptide bond.
- The ribosome also acts as a catalyst (23S rRNA in bacteria is the enzyme- ribozyme) for the formation of peptide bond.
- A translational unit in mRNA is the sequence of RNA that is flanked by the start codon (AUG) and the stop codon and codes for a polypeptide.
- Untranslated regions (UTR) -
- An mRNA also has some additional sequences that are not translated and are referred as untranslated regions (UTR).
- The UTRs are present at both 5' -end (before start codon) and at 3' -end (after stop codon).
Process of Translation
- At first, initiator tRNA detects the start codon (AUG) of mRNA.
- Then the ribosome binds to the mRNA at the start codon (AUG).
- The ribosome proceeds to the elongation phase of protein synthesis.
- During this stage, complexes composed of an amino acid linked to tRNA, sequentially bind to the appropriate codon in mRNA by forming complementary base pairs with the tRNA anticodon.
- The ribosome moves from codon to codon along the mRNA.
- Amino acids are added one by one, translated into Polypeptide sequences dictated by DNA and represented by mRNA.
- At the end, a release factor binds to the stop codon, terminating translation and releasing the complete polypeptide from the ribosome.
Regulation of gene expression
- Gene expression may be regulated at following levels -
- transcriptional level (formation of primary transcript)
- processing level (regulation of splicing)
- transport of mRNA from nucleus to the cytoplasm
- translational level
The Lac operon
- The lac operon consists of
- one regulatory gene (the i gene – inhibitor gene)
- three structural genes (z, y, and a)
- The i gene -
- It codes for the repressor of the lac operon.
- The z gene -
- It codes for beta-galactosidase (β-gal), which is primarily responsible for the hydrolysis of the disaccharide, lactose into its monomeric units, galactose and glucose.
- The y gene -
- It codes for permease, which increases permeability of the cell to β-galactosides.
- The a gene -
- It encodes a transacetylase.
- Inducer -
- Lactose is the substrate for the enzyme beta-galactosidase
- It regulates switching on and off of the operon. Hence, it is termed as inducer.
- In the presence of an inducer, such as lactose or allolactose, the repressor is inactivated by interaction with the inducer.
- Enzyme permease -
- Lactose is transported into the cells through the action of permease.
Process of The Lac operon
- The repressor of the operon is synthesised from the i gene.
- The repressor protein binds to the operator region of the operon and prevents RNA polymerase from transcribing the operon.
- In the presence of an inducer, the repressor is inactivated by interaction with the inducer.
- This allows RNA polymerase access to the promoter and transcription proceeds.
- Regulation of lac operon by repressor is referred to as negative regulation.
Human Genome Project (HGP)
- It was launched in 1990 to find out the complete DNA sequence of human genome.
- It was completed in 2003.
Goals of HGP
- Identify all the approximately 20,000-25,000 genes in human DNA
- Determine the sequences of the 3 billion chemical base pairs that make up human DNA
- Store this information in databases
- Improve tools for data analysis
- Transfer related technologies to other sectors, such as industries
- Address the ethical, legal, and social issues (ELSI) that may arise from the project
Salient Features of Human Genome
- The human genome contains 3164.7 million bp.
- The average gene consists of 3000 bases, but sizes vary greatly, with the largest known human gene being dystrophin at 2.4 million bases.
- The total number of genes is estimated at 30,000– much lower than previous estimates of 80,000 to 1,40,000 genes. Almost all (99.9 per cent) nucleotide bases are exactly the same in all people.
- The functions are unknown for over 50 per cent of the discovered genes.
- Less than 2 per cent of the genome codes for proteins.
- Repeated sequences make up very large portion of the human genome.
- Repetitive sequences are stretches of DNA sequences that are repeated many times, sometimes hundred to thousand times. They are thought to have no direct coding functions, but they shed light on chromosome structure, dynamics and evolution.
- Chromosome 1 has most genes (2968), and the Y has the fewest (231).
- Scientists have identified about 1.4 million locations where single-base DNA differences (SNPs – single nucleotide polymorphism, pronounced as ‘snips’) occur in humans.
- This information promises to revolutionise the processes of finding chromosomal locations for disease-associated sequences and tracing human history.
DNA fingerprinting
- DNA Fingerprinting is a technique to find out variations in individuals of a population at DNA level.
- It works on the principle of polymorphism in DNA sequences.
- It has immense applications in the field of forensic science, genetic biodiversity and evolutionary biology.
One Mark Questions
Q1. When was HGP completed?
Ans. HGP was completed in 2003.
Q2. What is inducer?
Ans. Inducer regulates switching on and off of the operon.
Q3. Which Indian scientist got Nobel Prize in Medicines?
Ans. Har Gobind Khorana (a Biochemist) got Nobel Prize for Physiology (1968).
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