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Molecular Basis of Inheritance: DNA Structure, Replication, and Gene Expression, Lecture notes of Science education

Yashwantrao Chavan Maharashtra Open University Science education

This document offers a comprehensive overview of the molecular basis of inheritance, covering key concepts such as dna structure, replication, transcription, translation, the genetic code, and dna repair mechanisms. it details the processes involved in gene expression and regulation, including the roles of rna polymerase, trna, mrna, and ribosomes. the document also touches upon molecular techniques like pcr and dna fingerprinting, making it a valuable resource for students studying molecular biology or genetics.

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2024/2025

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Molecular Basis of Inheritance

DNA Structure and Replication

1. DNA Structure: Double helix model

(Watson and Crick)

DNA, or deoxyribonucleic acid, is a molecule that carries the genetic instructions for all

known organisms. It's a double-stranded helix, meaning it looks like a twisted ladder.

Each strand is made up of nucleotides, which consist of a sugar (deoxyribose), a phosphate

group, and a nitrogenous base. There are four types of nitrogenous bases: adenine (A),

guanine (G), cytosine (C), and thymine (T). The bases pair up in a specific way: A with T,

and C with G. These base pairs form the "rungs" of the DNA ladder, while the sugar-

phosphate backbone forms the "sides".

DNA replication is the process by which a DNA molecule makes a copy of itself. This is

essential for cell division and the transmission of genetic information. The process involves

several steps:

1. Unwinding: The DNA double helix unwinds, and the two strands separate.

2. Primer Binding: An enzyme called primase synthesizes short RNA primers that bind to

the DNA strands. These primers provide a starting point for DNA polymerase.

3. Elongation: DNA polymerase adds complementary nucleotides to the template strand,

forming a new DNA strand. The new strand is synthesized in the 5' to 3' direction.

4. Leading and Lagging Strands: Because DNA polymerase can only add nucleotides in

one direction, one strand (the leading strand) is synthesized continuously, while the other

strand (the lagging strand) is synthesized in short fragments called Okazaki fragments.

5. Joining: The Okazaki fragments are joined together by an enzyme called ligase.

6. Termination: The replication process continues until the entire DNA molecule has been

duplicated.

The result is two identical DNA molecules, each containing one original strand and one

newly synthesized strand. This is called semi-conservative replication.

2. DNA Replication:

Semi-conservative,

semi-discontinuous (Okazaki fragments)

DNA replication is a fundamental process in all living organisms, ensuring the accurate

duplication of the genetic material before cell division. The process is semi-conservative,

meaning each new DNA molecule contains one original strand and one newly synthesized

strand.

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Molecular Basis of Inheritance DNA Structure and Replication

DNA Structure: Double helix model (Watson and Crick) DNA, or deoxyribonucleic acid, is a molecule that carries the genetic instructions for all known organisms. It's a double-stranded helix, meaning it looks like a twisted ladder. Each strand is made up of nucleotides, which consist of a sugar (deoxyribose), a phosphate group, and a nitrogenous base. There are four types of nitrogenous bases: adenine (A), guanine (G), cytosine (C), and thymine (T). The bases pair up in a specific way: A with T, and C with G. These base pairs form the "rungs" of the DNA ladder, while the sugar- phosphate backbone forms the "sides". DNA replication is the process by which a DNA molecule makes a copy of itself. This is essential for cell division and the transmission of genetic information. The process involves several steps:
Unwinding: The DNA double helix unwinds, and the two strands separate.
Primer Binding: An enzyme called primase synthesizes short RNA primers that bind to the DNA strands. These primers provide a starting point for DNA polymerase.
Elongation: DNA polymerase adds complementary nucleotides to the template strand, forming a new DNA strand. The new strand is synthesized in the 5' to 3' direction.
Leading and Lagging Strands: Because DNA polymerase can only add nucleotides in one direction, one strand (the leading strand) is synthesized continuously, while the other strand (the lagging strand) is synthesized in short fragments called Okazaki fragments.
Joining: The Okazaki fragments are joined together by an enzyme called ligase.
Termination: The replication process continues until the entire DNA molecule has been duplicated. The result is two identical DNA molecules, each containing one original strand and one newly synthesized strand. This is called semi-conservative replication.
DNA Replication: Semi-conservative, semi-discontinuous (Okazaki fragments) DNA replication is a fundamental process in all living organisms, ensuring the accurate duplication of the genetic material before cell division. The process is semi-conservative, meaning each new DNA molecule contains one original strand and one newly synthesized strand.

The process begins with the unwinding of the DNA double helix by enzymes like helicase, which separates the two strands. This creates a replication fork, where the replication machinery assembles. DNA replication is semi-discontinuous because the two strands are synthesized differently. One strand, the leading strand, is synthesized continuously in the 5' to 3' direction. The other strand, the lagging strand, is synthesized in short fragments called Okazaki fragments, also in the 5' to 3' direction, but away from the replication fork. RNA primers, synthesized by primase, provide a starting point for DNA polymerase, which adds complementary nucleotides to each strand. On the lagging strand, multiple primers are needed for each Okazaki fragment. After the fragments are synthesized, the RNA primers are removed and replaced with DNA. The Okazaki fragments are then joined together by DNA ligase, forming a continuous strand. This process ensures that each new cell receives a complete and accurate copy of the genetic information. Errors during replication are rare, but they can occur and are often corrected by DNA repair mechanisms. Central Dogma

Transcription: DNA RNA (mRNA, tRNA, rRNA) The central dogma of molecular biology explains the flow of genetic information within a biological system. It's a fundamental concept that describes the directional flow of information: DNA to RNA to protein. Transcription is the first step in this process. It's the synthesis of RNA from a DNA template. This process is carried out by enzymes called RNA polymerases. RNA polymerase binds to a specific region of the DNA called the promoter, which signals the start of a gene. The enzyme then unwinds the DNA double helix and uses one strand as a template to synthesize a complementary RNA molecule. There are different types of RNA molecules produced during transcription, each with a specific function:

Messenger RNA (mRNA): Carries the genetic code from DNA to the ribosomes, where proteins are synthesized.
Transfer RNA (tRNA): Brings amino acids to the ribosomes during protein synthesis, matching them to the mRNA codons.
Ribosomal RNA (rRNA): Forms part of the ribosome structure and helps catalyze peptide bond formation during protein synthesis. After transcription, the RNA molecule undergoes further processing before it can be used in protein synthesis. For example, in eukaryotic cells, mRNA undergoes splicing, where non- coding regions (introns) are removed, and the coding regions (exons) are joined together.

Codons: The genetic code is based on codons, which are sequences of three nucleotides (e.g., AUG, GGC, UUU). Each codon specifies a particular amino acid or a stop signal.
Universality: The genetic code is nearly universal, meaning that it is used by almost all organisms, from bacteria to humans. This suggests that the code originated early in the history of life and has been largely conserved over time.
Degeneracy: The genetic code is degenerate, meaning that most amino acids are encoded by more than one codon. This redundancy provides some protection against mutations, as a change in a single nucleotide may not always alter the amino acid specified by a codon.
Start and Stop Codons: The genetic code includes a start codon (AUG), which signals the beginning of protein synthesis. It also includes three stop codons (UAA, UAG, UGA), which signal the end of protein synthesis.
Reading Frame: The sequence of codons in mRNA is read in a specific reading frame, which is determined by the start codon. The reading frame is crucial because it determines how the codons are grouped together and, therefore, which amino acids are incorporated into the protein.
tRNA and Amino Acid Pairing: Each transfer RNA (tRNA) molecule carries a specific amino acid and has an anticodon that is complementary to a codon on the mRNA. During translation, the tRNA molecules bind to the mRNA codons, bringing the correct amino acids to the ribosome to be added to the growing polypeptide chain. The genetic code is a fundamental concept in biology and is essential for understanding how genetic information is used to build and maintain living organisms.
Degeneracy: Multiple codons for one amino acid The degeneracy of the genetic code refers to the fact that a single amino acid can be encoded by more than one codon. This is a key feature of the genetic code and has several implications:
Redundancy: Because multiple codons can code for the same amino acid, the genetic code is considered redundant. This redundancy provides a buffer against mutations.
Wobble Hypothesis: The wobble hypothesis explains how a single tRNA molecule can recognize multiple codons. The third base in a codon (the "wobble" position) can sometimes pair with different bases in the anticodon of the tRNA molecule. This allows for some flexibility in the codon-anticodon pairing.
Synonymous Codons: Codons that specify the same amino acid are called synonymous codons. The use of synonymous codons can vary between different organisms, which can affect the efficiency of protein synthesis.
Mutation Effects: Degeneracy can minimize the effects of certain mutations. If a mutation occurs in a DNA sequence and results in a synonymous codon, the amino acid sequence of the protein will not change. This is known as a silent mutation. In summary, the degeneracy of the genetic code is an important feature that contributes to the robustness and flexibility of the translation process. It allows for some tolerance of mutations and influences the efficiency of protein synthesis.
Universality: Almost universal across organisms

The universality of the genetic code is a fundamental principle in biology, referring to the fact that the same codons (sequences of three nucleotides) generally code for the same amino acids in almost all known organisms. Here's a breakdown of why this is important:

Common Ancestry: The near-universal nature of the genetic code strongly supports the theory of a common ancestor for all life on Earth. It suggests that the genetic code evolved early in the history of life and has been conserved across vast evolutionary distances.
Protein Synthesis: The universality of the code allows for the transfer of genetic information between different organisms. For example, a gene from a bacterium can be expressed in a human cell because the cellular machinery recognizes and translates the codons in the same way.
Exceptions: While the genetic code is remarkably universal, there are a few exceptions. These variations are typically found in the mitochondria of some eukaryotes, where some codons have different meanings compared to the standard code. These variations are thought to have arisen independently during evolution.
Implications for Biotechnology: The universality of the genetic code has significant implications for biotechnology. It allows scientists to use genetic engineering techniques to introduce genes from one organism into another, enabling the production of valuable proteins and other products.
Evolutionary Perspective: The universality of the genetic code also provides insights into the evolutionary history of life. The conservation of the code suggests that once established, it was highly advantageous and resistant to change, likely due to the complexity of the translation machinery and the need for accurate protein synthesis. In essence, the universality of the genetic code is a testament to the interconnectedness of life on Earth and a cornerstone of modern biology. Gene Expression
Regulation: Lac operon, gene regulation in prokaryotes and eukaryotes Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein-coding genes such as RNA genes, the product is a functional RNA. The process of gene expression is used by all known life—including eukaryotes and prokaryotes—to generate the macromolecular machinery for life.
Regulation: The lac operon is a classic example of gene regulation in prokaryotes, specifically in E. coli. It controls the expression of genes involved in lactose metabolism. The lac operon is regulated by several factors, including the presence of lactose and glucose. When lactose is present, it binds to the repressor protein, preventing it from binding to the operator region of the operon, which allows for the transcription of the genes needed for lactose metabolism. In contrast, when glucose is present, the cell prefers to use glucose as an energy source, and the lac operon is repressed, even if lactose is also present. Gene regulation in eukaryotes is more complex, involving multiple levels of control. This includes chromatin structure, transcription factors, RNA processing, and translation.

DNA polymerase, the enzyme responsible for DNA replication, has a proofreading function.
During DNA replication, if an incorrect base is added, the polymerase can detect the error.
The polymerase then reverses its direction, using its exonuclease activity to remove the incorrect base.
The polymerase then resumes replication, adding the correct base.
Proofreading significantly reduces the error rate during DNA replication.
Mismatch Repair (MMR):
MMR corrects errors that escape proofreading, such as mismatched base pairs that were not caught during replication.
MMR involves several steps:

Recognition of the mismatch: MMR proteins recognize the mismatched base pair.
Strand discrimination: The MMR system must distinguish between the correct and incorrect DNA strands. In bacteria, this is often achieved by recognizing the methylation pattern on the DNA. The original (template) strand is methylated, while the newly synthesized strand is not.
Excision: The incorrect base is removed from the newly synthesized strand.
Resynthesis: DNA polymerase fills in the gap, using the correct strand as a template.
Ligation: DNA ligase seals the nick in the DNA.

MMR is essential for maintaining genomic stability.
Excision Repair:
Excision repair involves removing damaged or modified bases and replacing them with the correct ones. There are two main types:
Base Excision Repair (BER):
BER repairs damage to a single base.
It involves:

Recognition of the damaged base by a DNA glycosylase.
Removal of the damaged base by the glycosylase, leaving an apurinic/apyrimidinic (AP) site.
AP endonuclease cuts the DNA backbone at the AP site.
DNA polymerase adds the correct base.
DNA ligase seals the nick.

Nucleotide Excision Repair (NER):
NER repairs larger lesions, such as those caused by UV radiation (e.g., pyrimidine dimers).
It involves:

Recognition of the damage.
Unwinding of the DNA around the damage.
Cutting of the DNA backbone on both sides of the damage.
Removal of the damaged DNA segment.
DNA polymerase fills in the gap.
DNA ligase seals the nick.

Excision repair is critical for removing various types of DNA damage caused by environmental factors or cellular processes.

Importance: Maintaining genome stability Here's more detailed information on each of the DNA repair mechanisms:

Proofreading:
- DNA polymerase has a 3' to 5' exonuclease activity that allows it to remove incorrectly incorporated nucleotides.
- This activity is separate from the polymerase's main function of adding nucleotides.
- When an incorrect base is added, the polymerase stalls, and the exonuclease activity removes the mismatched base.
- The polymerase then resumes DNA synthesis, incorporating the correct base.
- Proofreading significantly increases the fidelity of DNA replication, reducing the error rate.
Mismatch Repair (MMR):
- MMR recognizes and repairs base mismatches and small insertion/deletion loops that escape proofreading.
- In bacteria, the MMR system involves the MutS, MutL, and MutH proteins.
  - MutS recognizes the mismatch.
  - MutL and MutH are recruited.
  - MutH cuts the newly synthesized strand near the mismatch.
  - An exonuclease removes the DNA segment containing the mismatch.
  - DNA polymerase fills the gap, and DNA ligase seals the nick.
- In eukaryotes, the MMR system is similar but involves different proteins.
  - MSH2 and MSH6 (or MSH2 and MSH3) recognize the mismatch.
  - MLH1 and PMS2 are recruited.
  - Exonucleases remove the DNA segment.
  - DNA polymerase fills the gap, and DNA ligase seals the nick.
- MMR is essential for preventing mutations and maintaining genomic stability.
Excision Repair:
- Base Excision Repair (BER):
  - DNA glycosylases recognize and remove specific damaged bases, such as those caused by oxidation, alkylation, or deamination.
- An AP endonuclease cuts the DNA backbone at the AP site (a site lacking a base).
- DNA polymerase adds the correct base, and DNA ligase seals the nick.
- BER is the primary pathway for repairing damaged bases.
- Nucleotide Excision Repair (NER):
  - NER removes larger DNA lesions, such as those caused by UV radiation (pyrimidine dimers) and bulky adducts.
- NER involves several steps:
  1. Recognition of the damage.
  2. Recruitment of repair proteins.
  3. Unwinding of the DNA around the damage.
  4. Cutting of the DNA backbone on both sides of the damage.

Gene cloning is a molecular technique used to create multiple identical copies of a specific gene. This process involves inserting the gene of interest into a vector, such as a plasmid, which is then introduced into a host cell, like bacteria. As the host cell multiplies, it replicates the vector, including the cloned gene, resulting in multiple copies of the gene. Here's a deeper dive into gene cloning:

Isolation of the Gene: The gene of interest is first identified and isolated from the source DNA.
Insertion into a Vector: The gene is inserted into a cloning vector, such as a plasmid (a small, circular DNA molecule found in bacteria). This often involves cutting both the gene and the vector with the same restriction enzymes (which act like molecular scissors) and then joining them together using DNA ligase (an enzyme that acts like molecular glue).
Transformation: The recombinant vector (the vector with the gene of interest inserted) is introduced into a host cell, often bacteria. This process is called transformation.
Selection: The host cells that have taken up the recombinant vector are selected, usually using antibiotic resistance genes carried on the vector.
Multiplication/Cloning: The host cells are grown in culture, allowing the vector and the cloned gene to replicate, producing multiple copies of the gene.
Gene Expression (Optional): The cloned gene can be further manipulated to make the host cell produce the protein encoded by the gene. Gene cloning is a fundamental technique in molecular biology with applications in various fields, including medicine, agriculture, and biotechnology. Alright, here's a breakdown of those key concepts for NEET, with some extra details to help you out:
DNA structure and replication:
- DNA Structure:
  - DNA is a double helix composed of two strands of nucleotides.
  - Each nucleotide consists of a deoxyribose sugar, a phosphate group, and a nitrogenous base (adenine, guanine, cytosine, or thymine).
- The two strands are antiparallel (run in opposite directions) and held together by hydrogen bonds between the bases (A with T, G with C).
- DNA Replication:
  - The process of copying DNA, occurring during the S phase of the cell cycle.
  - It's a semi-conservative process, meaning each new DNA molecule has one original strand and one newly synthesized strand.
- Involves enzymes like DNA polymerase (adds nucleotides), helicase (unzips the DNA), and ligase (joins DNA fragments).
Central dogma (transcription, translation):
- Central Dogma: The flow of genetic information from DNA to RNA to protein.
- Transcription:
  - The process of synthesizing RNA from a DNA template.

RNA polymerase binds to a promoter region on the DNA and synthesizes an mRNA molecule.
mRNA carries the genetic code from the DNA to the ribosomes.
Translation:
The process of synthesizing a protein from an mRNA template.
Occurs in ribosomes.
tRNA molecules bring amino acids to the ribosome, where they are linked together in the order specified by the mRNA codons.

Genetic code and its characteristics:
- Genetic Code: The set of rules by which information encoded in genetic material (DNA or mRNA) is translated into proteins.
- Characteristics:
  - Triplet code: Three nucleotides (a codon) code for one amino acid.
  - Unambiguous: Each codon specifies only one amino acid.
  - Degenerate: Most amino acids are coded for by more than one codon.
  - Universal: The genetic code is nearly universal across all organisms.
  - Start codon: AUG (methionine) initiates translation.
  - Stop codons: UAA, UAG, UGA signal the end of translation.
Gene expression and regulation:
- Gene Expression: The process by which the information encoded in a gene is used to synthesize a functional gene product (usually a protein).
- Regulation:
  - Gene expression is tightly regulated to ensure that the correct proteins are produced at the right time and in the right amounts.
- Regulation can occur at various levels, including transcription (e.g., through transcription factors), RNA processing, translation, and post-translational modifications.
DNA repair mechanisms:
- DNA Repair: A collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome.
- Types of Repair:
  - Base excision repair (BER): Removes damaged or inappropriate bases.
  - Nucleotide excision repair (NER): Removes bulky DNA lesions.
  - Mismatch repair (MMR): Corrects errors that occur during DNA replication.
  - Double-strand break repair: Repairs breaks in both DNA strands (e.g., homologous recombination, non-homologous end joining). 6. Molecular techniques (PCR, DNA fingerprinting, gene cloning):
- PCR (Polymerase Chain Reaction): Amplifies a specific DNA sequence. (See previous responses for more detail).
- DNA Fingerprinting: Identifies individuals based on their unique DNA profiles. (See previous responses for more detail).

Molecular Basis of Inheritance: DNA Structure, Replication, and Gene Expression, Lecture notes of Science education

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