Page 1: Introduction to Nucleic Acids

Lecture Overview

• Instructor: Dr. Kourosh Ebrahimi

• Course Code: 4BBP0131

• Primary Text: "Molecular Biology of the Cell" by Bruce Alberts et al.

• Additional Reading: "Genes and Common Diseases: Genetics in Modern Medicine"

Page 2: Gene and Pharmacy

Gene-Drug Interactions

• Impact on Treatment: Understand how genes affect drug responses.

• Study Requirements: Information can be gathered both orally and in writing with informed consent is essential.

• Pharmacogenetic Testing:

  • Check for gene-drug interactions.

  • Adjust drug regimen accordingly (e.g., switch, stop, dose).

• Gene Therapy: Discuss relevance with nephrologists.

• Targeted Medicine: Focus on precision in drug development and the role of pharmacogenetics.

Page 3: Learning Objectives

• Develop an understanding of:

  • Genes and the human karyotype.

  • Mechanisms of inheritance and genetic disorders.

  • Chemistry of DNA and structure.

  • Features of the human genome.

  • DNA replication processes.

  • Recent advances in pharmacy and medicine.

Page 4: Section 1 - Chemistry of DNA

• Introduction to the core chemical aspects of DNA's structure and function.

Page 5: Building Blocks of DNA

Key Components

• Deoxynucleoside Triphosphate (dNTP): Building blocks of DNA.

• Deoxynucleoside Structure:

  • Includes a sugar (deoxyribose), a phosphate group, and a nucleobase.

Page 6: Nucleobases of DNA

Types of Nucleobases

• Purines:

  • Adenine (A)

  • Guanine (G)

• Pyrimidines:

  • Cytosine (C)

  • Thymine (T)

• Composition: Deoxyribose sugar forms the backbone of DNA along with nucleobases.

Page 7: DNA and RNA Polymers

Structure

• Polymers of Nucleotides: Both DNA and RNA are long chains of nucleotides.

• Key Differences Between DNA and RNA:

  • RNA contains uracil instead of thymine and has ribose in place of deoxyribose.

• Base Pairing: Adenine pairs with thymine (or uracil in RNA) and guanine pairs with cytosine.

Page 8: X-Ray Diffraction Studies

Key Contributions

• Rosalind Franklin & Maurice Wilkins: Led critical studies that characterized DNA as helical through X-ray diffraction, yielding insights into base pairing and helix structure.

• Photo 51: Provides substantial evidence of the DNA double helix structure.

Page 9: Watson and Crick's Model

DNA Structure Elucidation

• Key Figures: James Watson and Francis Crick (1953)

• Chargaff's Rules:

  • G = C and A = T ratios inform DNA pairing.

• Molecular Diversity: Varies among species but adheres to pairing rules.

Page 10: Structure of DNA

Characteristics of Helix

• Dimensions:

  • Each full twist is approximately 3.4 nm with a diameter of 2.0 nm.

• Polynucleotide Chains: DNA consists of two strands forming a right-hand double helix.

Page 11: Base Pairing and Backbone

Detailed Structure

• Adjacent Bases: Bases are perpendicular to the helical axis and hydrogen bonded.

• Sugar-Phosphate Backbone: Maintains structural integrity of DNA while bases complete the genetic code.

Page 12: Orientation of DNA Strands

Directionality

• Antiparallel Strands: The two DNA strands run in opposite directions crucial for replication and functionality.

Page 13: DNA in Heredity

Characteristics for Genetic Role

• Information Storage: DNA encodes hereditary information through base sequences.

• Replication Mechanism: Suggested by Watson and Crick, reflecting how information is copied and passed to progeny.

Page 14: Section 2 - DNA Replication

Page 15: Prokaryotic vs Eukaryotic Genes

Differences in Gene Structure

• Prokaryotic Genes: Simpler structure with coding regions known as exons and non-coding regions identified as introns.

• Eukaryotic Genes: More complex with introns interrupting coding sequences.

Page 16: Prokaryotic DNA Replication

Overview of Process

• Daughter Strand Synthesis: Employs parent strands as templates.

• Semi-conservative Replication: Each DNA molecule manufactured contains one old and one new strand.

Page 17: Initiation & Unwinding

Role of Helicase

• Helicase Function: Unwinds double helix at the replication fork, allowing access to bases for protein synthesis.

• Single-Strand Binding Proteins: Prevent immediate re-formation of double helix.

Page 18: Topoisomerase Function

Prevention of DNA Damage

• Topoisomerase Role: Prevents tension and potential breaks caused by unwinding, ensuring replication can progress without damage.

Page 19: Synthesizing New Strands

DNA Polymerase Action

• Direction of Synthesis: New DNA strands are synthesized exclusively in the 5' to 3' direction.

• Fork Dynamics: Guiding the unwinding and replication process for efficient DNA duplication.

Page 20: Lagging and Leading Strand Synthesis

Different Modes of Synthesis

• Leading Strands: Continuously synthesized.

• Lagging Strands: Discontinuous synthesis using Okazaki fragments that are ultimately joined together.

Page 21: Role of Primase

Initiating DNA Synthesis

• Primase Function: Synthesizes short RNA primers allowing DNA polymerase to extend a new strand starting from an existing template.

Page 22: DNA Bond Formation

Phosphodiester Bonds

• Formation Process: DNA polymerase facilitates the formation of phosphodiester bonds, securing the structure of the DNA chain.

Page 23: Polymerase Functionality

Restaurant Reference

• Reference video on DNA polymerase providing insights on its functional capacity during replication.

Page 24: Error Correcting Mechanisms

Role of Exonuclease

• Incorporation of Nucleotides: DNA polymerase can make errors; exonuclease helps remove incorrectly incorporated nucleotides, mitigating mutations.

Page 25: Joining Okazaki Fragments

Required Enzymatic Action

• DNA Ligase: Enzyme responsible for sealing gaps between Okazaki fragments to create a continuous strand.

Page 26: Finalizing DNA Synthesis

Continuation of Synthesis

• Attachment of Adjacent Fragments: DNA polymerase continues adding nucleotides beyond gaps left by RNA primers once they are degraded.

Page 27: Summary of Replication Enzymes

Key Players in Prokaryotic Replication

• Helicase: Unwinds double helix.

• Topoisomerase: Relieves DNA tension.

• Primase: Initiates RNA primer synthesis.

• DNA Polymerase: Synthesizes DNA strands.

• Exonucleases: Remove RNA primers,

• DNA Ligase: Joins Okazaki fragments.

Page 28: Coordination of Synthesis

Leading vs Lagging Strand

• Exploration of how replication is organized despite contradicting synthesis directions.

Page 29: Topoisomerase Activity

Importance and Risks

• Discusses essential and potentially harmful effects of topoisomerase activity and inquires about mitigating enzymes.

Page 30: Section 3 - Advances in Pharmacy & Medicine

Page 31: Treatment Approaches for Cancer

Targeting DNA Replication

• Cancer Treatments: Explores drug targeting mechanisms including polymerase inhibitors and examples such as Cisplatin and Gemcitabine.

Page 32: Polymerase Chain Reaction (PCR)

Applications

• PCR Uses: Diagnostic tools in biotechnology and medicine.

Page 33: CRISPR-Cas9 Technology

Genome Editing

• Overview: Describe the bacterial immune system’s role in genetic editing.

Page 34: CRISPR for Treating Disorders

Therapeutic Applications

• Genome Editing: Focuses on using CRISPR/Cas9 for treating hereditary hematological disorders.

Page 35: Summary of the Lecture

Concluding Remarks

• Overview of key topics covered and the importance of nucleic acids in molecular biology.