Class 12 Biology Notes Chapter 6 (Molecular Basis of Inheritance) – Examplar Problems Book

Alright class, let's delve into one of the most fundamental chapters, 'Molecular Basis of Inheritance'. Understanding this is crucial not just for your Class 12 exams, but forms the bedrock for many questions in competitive government exams involving Biology or General Science. We will cover the key concepts point-by-point.

Chapter 6: Molecular Basis of Inheritance - Detailed Notes

1. The DNA (Deoxyribonucleic Acid)

• Structure:
  • Polymer of Deoxyribonucleotides: Each nucleotide has three components: a nitrogenous base (Purines: Adenine-A, Guanine-G; Pyrimidines: Cytosine-C, Thymine-T), a deoxyribose sugar, and a phosphate group.
  • Linkages: Nucleoside = Nitrogenous base + Sugar (N-glycosidic linkage). Nucleotide = Nucleoside + Phosphate group (phosphoester linkage). Two nucleotides are linked by a 3'-5' phosphodiester linkage, forming a dinucleotide and subsequently a polynucleotide chain.
  • Watson-Crick Model (B-DNA):
    • Double helix structure with two polynucleotide chains.
    • Backbone: Formed by sugar-phosphate-sugar chain.
    • Bases project inwards.
    • Antiparallel Polarity: One chain runs 5'→3', the other runs 3'→5'.
    • Base Pairing: Specific pairing between bases: Adenine (A) pairs with Thymine (T) via two hydrogen bonds (A=T). Guanine (G) pairs with Cytosine (C) via three hydrogen bonds (G≡C). This is Chargaff's rule (%A=%T, %G=%C, Purines = Pyrimidines).
    • Helical Turn: Right-handed helix. Pitch = 3.4 nm (34 Å). Base pairs per turn ≈ 10 bp. Distance between adjacent base pairs ≈ 0.34 nm (3.4 Å).
    • Stability: Provided by H-bonds between bases and stacking interactions between base pairs.
• Packaging of DNA Helix:
  • Prokaryotes (e.g., E. coli): DNA is not scattered; it's held with some proteins (non-histone, positively charged) in a region called the 'nucleoid'. DNA is organised in large loops.
  • Eukaryotes: More complex packaging.
    • Histones: Set of positively charged, basic proteins (rich in lysine and arginine). Organised into an octamer (two molecules each of H2A, H2B, H3, H4).
    • Nucleosome: Negatively charged DNA wrapped around the positively charged histone octamer. A typical nucleosome contains ~200 bp of DNA helix. H1 histone acts as a linker protein outside the octamer.
    • Chromatin: Repeating units of nucleosomes form a thread-like structure. Appears as 'beads-on-string' under an electron microscope.
    • Further Condensation: Chromatin fibers coil and condense further (solenoid structure) to form chromosomes at metaphase. Requires Non-Histone Chromosomal (NHC) proteins.
    • Euchromatin: Loosely packed, transcriptionally active chromatin. Stains light.
    • Heterochromatin: Densely packed, transcriptionally inactive chromatin. Stains dark.

2. The Search for Genetic Material

• Griffith's Experiment (1928) - Transformation:
  • Used Streptococcus pneumoniae (bacteria causing pneumonia).
  • S strain (smooth, virulent, polysaccharide coat) & R strain (rough, non-virulent, no coat).
  • Conclusion: Some 'transforming principle' transferred from heat-killed S strain enabled R strain to synthesize a smooth coat and become virulent. The biochemical nature was not defined.
• Avery, MacLeod, McCarty Experiment (1933-44) - Biochemical Characterization:
  • Purified biochemicals (proteins, DNA, RNA) from heat-killed S cells.
  • Treated purified components with digestive enzymes (proteases, RNases, DNases).
  • Only DNase treatment inhibited transformation, indicating DNA was the transforming principle. Not universally accepted initially.
• Hershey-Chase Experiment (1952) - The 'Blender Experiment':
  • Used Bacteriophage T2 (virus infecting bacteria).
  • Grew phages on two media: one with radioactive phosphorus (³²P - labels DNA) and another with radioactive sulfur (³⁵S - labels protein coat).
  • Allowed radioactive phages to infect E. coli.
  • Blended to remove phage particles attached to bacteria surface.
  • Centrifuged to separate bacteria (pellet) and supernatant (lighter phage particles).
  • Results: Bacteria infected with ³²P-labelled phages were radioactive (DNA entered). Bacteria infected with ³⁵S-labelled phages were not radioactive (protein coat remained outside).
  • Conclusion: DNA is the genetic material that enters the host cell to direct synthesis of new viruses.

3. Properties of Genetic Material

• Should be able to replicate itself accurately.
• Should be chemically and structurally stable. (DNA is more stable than RNA due to 2'-OH group absence and Thymine instead of Uracil).
• Should provide scope for slow changes (mutation) required for evolution.
• Should be able to express itself in the form of 'Mendelian characters'.

4. RNA World

• RNA was likely the first genetic material.
• Evidence: RNA can act as genetic material (e.g., some viruses like TMV, QB bacteriophage), RNA can act as a catalyst (ribozymes, e.g., in ribosomes, spliceosomes), essential life processes (metabolism, translation, splicing) evolved around RNA.
• DNA evolved from RNA for better stability, making RNA primarily functional in gene expression (adapter, structural, catalytic roles).

5. Replication

• Semi-conservative Replication: Proposed by Watson & Crick. Each new DNA molecule consists of one parental (conserved) strand and one newly synthesized strand.
• Meselson and Stahl Experiment (1958): Proved semi-conservative replication using heavy nitrogen isotope (¹⁵N) and E. coli. Used Cesium Chloride (CsCl) density gradient centrifugation.
• Mechanism:
  • Origin of Replication (ori): Replication begins at specific sites.
  • Activation of Deoxyribonucleotides: dAMP, dGMP, dCMP, dTMP are phosphorylated to ATP, dGTP, dCTP, dTTP (also provide energy).
  • Unwinding: Enzyme Helicase unwinds the DNA helix by breaking H-bonds, creating a Replication Fork. SSBPs (Single-Strand Binding Proteins) stabilize the separated strands. Topoisomerase relieves torsional stress.
  • Primer Synthesis: A short RNA primer is synthesized by Primase (a type of RNA polymerase). DNA polymerase requires a free 3'-OH end to initiate synthesis.
  • DNA Synthesis: Enzyme DNA-dependent DNA Polymerase catalyzes polymerization only in the 5'→3' direction.
    • Leading Strand: Synthesized continuously towards the replication fork (on 3'→5' template).
    • Lagging Strand: Synthesized discontinuously away from the fork in short fragments called Okazaki fragments (on 5'→3' template). Requires multiple primers.
  • Primer Removal & Gap Filling: RNA primers are removed (by DNA Polymerase I in prokaryotes). Gaps are filled with deoxyribonucleotides by DNA Polymerase.
  • Joining: Okazaki fragments are joined together by DNA Ligase, forming a continuous strand.
• Accuracy: High fidelity due to proofreading activity of DNA polymerase.

6. Transcription

• Process of copying genetic information from one strand of DNA (template strand) into RNA.
• Transcription Unit: A segment of DNA that is transcribed. Consists of:
  • Promoter: DNA sequence where RNA polymerase binds (upstream, 5'-end of structural gene).
  • Structural Gene: DNA sequence coding for RNA (polypeptide).
  • Terminator: DNA sequence specifying end of transcription (downstream, 3'-end of structural gene).
• Template Strand: DNA strand with polarity 3'→5', acts as a template for RNA synthesis.
• Coding Strand: DNA strand with polarity 5'→3', sequence same as RNA (except T instead of U), does not code for anything directly during transcription.
• Enzyme: DNA-dependent RNA Polymerase catalyzes polymerization in 5'→3' direction.
• Mechanism in Prokaryotes:
  • Single RNA Polymerase synthesizes all types of RNA (mRNA, tRNA, rRNA).
  • Initiation: RNA polymerase binds to promoter, aided by sigma (σ) factor. Unwinds DNA locally.
  • Elongation: RNA polymerase moves along DNA, adding ribonucleotides complementary to the template strand. Sigma factor dissociates.
  • Termination: Reaches terminator region. Nascent RNA and RNA polymerase fall off. Can be Rho-dependent (requires Rho protein) or Rho-independent (hairpin loop formation).
• Mechanism in Eukaryotes: More complex.
  • Three RNA Polymerases:
    • RNA Pol I: Transcribes rRNAs (28S, 18S, 5.8S).
    • RNA Pol II: Transcribes precursor of mRNA (hnRNA) and snRNAs.
    • RNA Pol III: Transcribes tRNA, 5S rRNA, and snRNAs.
  • Post-transcriptional Modifications (Processing): Primary transcript (hnRNA) undergoes modifications before becoming functional mRNA in the cytoplasm.
    • Splicing: Removal of non-coding sequences (introns) and joining of coding sequences (exons). Catalyzed by spliceosome (complex of snRNA and proteins).
    • Capping: Addition of an unusual nucleotide (methyl guanosine triphosphate) to the 5'-end. Protects from degradation, helps in ribosome binding.
    • Tailing: Addition of 200-300 adenylate residues (poly-A tail) at the 3'-end. Provides stability, aids in transport from nucleus.

7. Genetic Code

• The relationship between the sequence of nucleotides in mRNA and the sequence of amino acids in a polypeptide.
• Features:
  • Triplet Code: Three adjacent nucleotides (codon) specify one amino acid. 64 possible codons (4³).
  • Unambiguous: One codon specifies only one particular amino acid.
  • Degenerate: Some amino acids are coded by more than one codon (e.g., Leucine has 6 codons).
  • Commaless: Code is read continuously without any punctuation.
  • Nearly Universal: Same codons specify the same amino acids in almost all organisms (some exceptions in mitochondria, protozoa).
  • Start Codon: AUG codes for Methionine and also acts as the initiation codon.
  • Stop Codons: UAA, UAG, UGA are termination codons; they do not code for any amino acid.
• Wobble Hypothesis (Crick): The base pairing between the third base of a codon (mRNA) and the first base of an anticodon (tRNA) is less stringent, allowing some tRNAs to recognize more than one codon.
• Mutations and Genetic Code: Point mutations (change in single base pair) can cause:
  • Silent mutation: No change in amino acid.
  • Missense mutation: Change in amino acid. (e.g., Sickle cell anemia: GAG -> GUG, Glu -> Val)
  • Nonsense mutation: Formation of a stop codon, leading to premature termination.
  • Frameshift mutation: Insertion or deletion of one or two bases changes the reading frame from that point onwards, leading to a completely different protein.

8. Translation (Protein Synthesis)

• Process of polymerization of amino acids to form a polypeptide, based on the sequence of codons in mRNA.
• Location: Ribosomes in the cytoplasm.
• Requirements:
  • mRNA: Template carrying the genetic code.
  • Ribosomes: Cellular factories for protein synthesis (made of rRNA and proteins). Prokaryotes: 70S (50S + 30S). Eukaryotes: 80S (60S + 40S). Provide sites for tRNA binding (A, P, E sites) and catalyze peptide bond formation (peptidyl transferase activity - rRNA acts as ribozyme).
  • tRNA (Transfer RNA): Adapter molecule. Reads codons on mRNA (via anticodon loop) and carries specific amino acids (at amino acid acceptor end).
  • Aminoacylation of tRNA (Charging): Attachment of specific amino acid to its cognate tRNA. Catalyzed by aminoacyl-tRNA synthetase. Requires ATP.
  • Energy: ATP (for charging tRNA), GTP (for initiation, elongation, translocation).
  • Protein Factors: Initiation, elongation, and release factors.
• Steps:
  • Initiation: Binding of mRNA to the small ribosomal subunit. Initiator tRNA (carrying Met in eukaryotes, fMet in prokaryotes) recognizes the start codon (AUG) and binds to the P-site. Large subunit binds to form the initiation complex. Requires initiation factors and GTP.
  • Elongation:
    • Codon Recognition: Charged tRNA with anticodon complementary to the codon at the A-site binds. Requires elongation factors and GTP.
    • Peptide Bond Formation: Peptide bond formed between the amino acid at the A-site and the polypeptide chain attached to the tRNA at the P-site. Catalyzed by peptidyl transferase (activity of rRNA in large subunit). Polypeptide chain is transferred to the tRNA at the A-site.
    • Translocation: Ribosome moves one codon ahead on the mRNA (5'→3'). tRNA carrying the polypeptide chain moves from A-site to P-site. Uncharged tRNA moves from P-site to E-site (exit site) and is released. Requires elongation factors and GTP. Cycle repeats.
  • Termination: Ribosome reaches a stop codon (UAA, UAG, UGA) at the A-site. No tRNA recognizes stop codons. Release factors bind to the A-site, promoting hydrolysis of the bond between the polypeptide and the tRNA at the P-site. Polypeptide is released. Ribosomal subunits dissociate.

9. Regulation of Gene Expression

• Control of the rate at which gene products (RNA or protein) are synthesized. Crucial for efficiency, adaptation, and development.
• Regulation in Prokaryotes: Primarily at the transcriptional initiation level.
  • Operon Concept (Jacob & Monod): A unit of gene expression and regulation in prokaryotes, including structural genes, operator, promoter, and regulator gene.
  • Lac Operon (Inducible System): Regulates lactose metabolism in E. coli.
    • Components:
      • Regulator gene (i): Codes for repressor protein.
      • Promoter (p): Binding site for RNA polymerase.
      • Operator (o): Binding site for repressor protein. Overlaps with promoter.
      • Structural genes: z (β-galactosidase), y (permease), a (transacetylase).
    • Mechanism:
      • Absence of Inducer (Lactose): Repressor protein binds to the operator, blocking RNA polymerase access to structural genes. Transcription OFF.
      • Presence of Inducer (Lactose/Allolactose): Inducer binds to the repressor, causing conformational change. Repressor cannot bind to the operator. RNA polymerase binds to the promoter and transcribes structural genes. Transcription ON.
  • Also involves positive regulation (e.g., Catabolite repression involving CAP protein and cAMP).
• Regulation in Eukaryotes: More complex, occurs at multiple levels:
  • Transcriptional level: Chromatin remodeling (acetylation/deacetylation of histones), DNA methylation, binding of transcription factors (activators/repressors) to promoter and enhancer/silencer sequences.
  • Processing level: Regulation of splicing, capping, tailing. Alternative splicing can produce different proteins from the same gene.
  • Transport level: Regulation of mRNA transport from nucleus to cytoplasm.
  • Translational level: Regulation of mRNA stability, binding of mRNA to ribosome, availability of initiation factors.

10. Human Genome Project (HGP)

• International research effort (1990-2003) to sequence the entire human genome.
• Goals:
  • Identify all human genes (~20,000-25,000).
  • Determine the sequence of the 3 billion chemical base pairs.
  • Store this information in databases.
  • Improve tools for data analysis.
  • Address Ethical, Legal, and Social Issues (ELSI).
• Methodologies:
  • Expressed Sequence Tags (ESTs): Identifying all genes expressed as RNA.
  • Sequence Annotation: Sequencing the whole genome (coding and non-coding) and assigning functions to different regions.
  • Techniques: DNA sequencing (Sanger sequencing was predominant), Bioinformatics (computational tools for data storage, retrieval, analysis).
• Salient Features of Human Genome:
  • Genome contains 3164.7 million nucleotide bases.
  • Average gene consists of 3000 bases, but sizes vary greatly (largest: dystrophin - 2.4 million bases).
  • Total number of genes estimated at ~20,000-25,000 (much lower than previous estimates).
  • Almost all (99.9%) nucleotide bases are exactly the same in all people.
  • Functions are unknown for over 50% of discovered genes.
  • Less than 2% of the genome codes for proteins.
  • Repeated sequences make up a very large portion of the genome (important for chromosome structure, dynamics, evolution).
  • Chromosome 1 has the most genes (2968), Y has the fewest (231).
  • Identified ~1.4 million locations with single-base DNA differences (Single Nucleotide Polymorphisms - SNPs), useful in disease association studies and human history tracing.
• Applications: Disease diagnosis, treatment development, understanding human evolution, forensics.

11. DNA Fingerprinting

• Technique to identify differences in specific regions of DNA sequence called repetitive DNA, which vary from person to person (polymorphism). Basis of paternity testing, forensic identification.
• Developed by: Alec Jeffreys.
• Principle: Relies on variations in satellite DNA, specifically Variable Number of Tandem Repeats (VNTRs). VNTRs are short nucleotide sequences repeated many times, and the number of repeats is unique to an individual (except identical twins).
• Technique (Southern Blotting Hybridization):
  • Isolation of DNA: From cells (blood, hair follicle, skin, saliva, semen).
  • Digestion of DNA: Using Restriction Endonucleases (RE) which cut DNA at specific recognition sites flanking the VNTRs. Generates fragments of varying lengths depending on the number of repeats.
  • Separation of DNA fragments: By Gel Electrophoresis (agarose gel). Fragments separate based on size.
  • Transferring (Blotting): Separated DNA fragments are transferred from the gel to a synthetic membrane (nitrocellulose or nylon) - called Southern Blotting.
  • Hybridization: Membrane is incubated with a radioactive or fluorescently labelled VNTR probe (a short DNA sequence complementary to the VNTR). The probe binds specifically to complementary VNTR sequences on the membrane.
  • Detection: Location of probe binding is detected by Autoradiography (for radioactive probes) or fluorescence detection. This reveals a pattern of bands unique to the individual.
• Applications: Forensic science (crime investigation), Paternity/Maternity testing, Diagnosis of genetic disorders, Conservation of wildlife, Studying population genetics and evolution.

Multiple Choice Questions (MCQs)

1. Which enzyme is responsible for removing RNA primers during DNA replication in prokaryotes?
   (a) DNA Polymerase III
   (b) DNA Ligase
   (c) Primase
   (d) DNA Polymerase I

2. In the Lac operon model, the product of the regulator gene (i) acts as a:
   (a) Inducer
   (b) Repressor
   (c) Aporepressor
   (d) Activator

3. The experiment conducted by Hershey and Chase using bacteriophage T2 definitively proved that DNA is the genetic material because:
   (a) Radioactive phosphorus (³²P) was found in the supernatant after centrifugation.
   (b) Radioactive sulfur (³⁵S) was found in the bacterial pellet after centrifugation.
   (c) Radioactive phosphorus (³²P) was found in the bacterial pellet after centrifugation.
   (d) Both ³²P and ³⁵S were found equally distributed between the pellet and supernatant.

4. Which of the following features of the genetic code allows some tRNAs to recognize more than one codon?
   (a) Unambiguity
   (b) Degeneracy
   (c) Universality
   (d) Wobble hypothesis

5. During eukaryotic transcription, the primary transcript (hnRNA) undergoes processing. Which process involves the removal of introns?
   (a) Capping
   (b) Tailing
   (c) Splicing
   (d) Aminoacylation

6. The core structure of a nucleosome is formed by:
   (a) H1 histone only
   (b) Histone octamer (2 each of H2A, H2B, H3, H4)
   (c) Non-histone chromosomal proteins
   (d) DNA wrapped around H1 histone

7. Which RNA polymerase is responsible for transcribing tRNA and 5S rRNA in eukaryotes?
   (a) RNA Polymerase I
   (b) RNA Polymerase II
   (c) RNA Polymerase III
   (d) Primase

8. A single base change in a gene leads to the codon UCA (Serine) becoming UAA (Stop). This type of mutation is called:
   (a) Silent mutation
   (b) Missense mutation
   (c) Nonsense mutation
   (d) Frameshift mutation

9. The technique of DNA fingerprinting relies on variations in:
   (a) Coding sequences (exons)
   (b) Single Nucleotide Polymorphisms (SNPs) within genes
   (c) Variable Number of Tandem Repeats (VNTRs) in non-coding DNA
   (d) Mitochondrial DNA sequences only

10. According to the salient features identified by the Human Genome Project (HGP), approximately what percentage of the human genome codes for proteins?
    (a) Less than 2%
    (b) About 10%
    (c) About 25%
    (d) More than 50%

Answer Key for MCQs:

1. (d) DNA Polymerase I
2. (b) Repressor
3. (c) Radioactive phosphorus (³²P) was found in the bacterial pellet after centrifugation.
4. (d) Wobble hypothesis (Note: Degeneracy is the property explained by wobble, but wobble itself is the mechanism allowing flexible pairing).
5. (c) Splicing
6. (b) Histone octamer (2 each of H2A, H2B, H3, H4)
7. (c) RNA Polymerase III
8. (c) Nonsense mutation
9. (c) Variable Number of Tandem Repeats (VNTRs) in non-coding DNA
10. (a) Less than 2%

Study these notes thoroughly. Focus on the experiments, enzymes, processes, and key definitions. Good luck with your preparation!