Molecular Biology: Transcription and RNA Processing

DNA Structure and Replication

• DNA is essential for all organisms, carrying the necessary information for building and functioning.
• It transmits information from parents to offspring.
• It replicates to create copies for inheritance.
• It exhibits variation to explain phenotypic diversity.

Central Dogma

• DNA acts as a template for RNA production (transcription).
• RNA then directs protein synthesis (translation).
• Epigenetics involves modifications to DNA that can be inherited.
• Non-coding RNAs (miRNA, siRNA, IncRNA, piRNA) play diverse regulatory roles.

Key Experiments

• Griffith (1928): Demonstrated transformation in bacteria, implying a genetic material.
• Avery, MacLeod, and McCarty (1944): Confirmed DNA's role as the transforming agent.
• Hershey and Chase (1952): Provided evidence that DNA, not protein, enters bacteria during viral infection.

DNA Structure (1953)

• Watson and Crick's model: DNA is a double helix with two strands running antiparallel (5' to 3' and 3' to 5').
• Nucleotides are the building blocks, each consisting of a phosphate group, deoxyribose sugar, and a nitrogenous base (A, T, C, G).
• A pairs with T, and C pairs with G through hydrogen bonds.

DNA Double Helix

• Two antiparallel strands are coiled around each other.
• Key interactions: hydrogen bonds between base pairs and hydrophobic interactions between stacked bases.
• DNA has a hydrophilic sugar-phosphate backbone that interacts with water and proteins.

DNA Replication

• Semiconservative Replication: Each new DNA molecule consists of one original strand and one new strand.
• Enzymes like helicase, DNA polymerase, primase, and ligase are crucial for this process.
• Replication proceeds in both directions along the replication fork.

DNA Replication Speed and Accuracy

• DNA polymerase III synthesizes 2,000 nucleotides per second.
• Proofreading mechanisms ensure high accuracy (approximately 1 error in 10^10 nucleotides).
• DNA Polymerases in E. coli: Pol I (repair), Pol II (backup), Pol III (main replication).

Key Enzymes and Proteins in DNA Replication

• Helicase: unwinds DNA double helix ahead of replication fork.
• DNA gyrase (topoisomerase): relieves supercoiling tension.
• Primase: synthesizes RNA primers (starting points for DNA synthesis).
• DNA polymerase III: extends RNA primers with new DNA.
• DNA polymerase I: removes RNA primers and replaces them with DNA.
• Ligase: joins Okazaki fragments on the lagging strand.
• Single-strand binding protein (SSB): prevents re-annealing of separated DNA strands.

DNA Replication in Eukaryotes

• Multiple origins of replication along each chromosome
• Replication occurs during S phase of the cell cycle.
• Telomeres are involved in protecting the ends of linear chromosomes.

Key Concepts of DNA Replication

• DNA replication fork location where DNA unwinding occurs
• RNA primer as starting point for replication by DNA polymerase
• Leading strand synthesizes continuously 5’-> 3’
• Lagging strand synthesizes in short fragments (Okazaki fragments).

RNA Structure and Function

• RNA consists of ribose sugar, a phosphate group, and uracil instead of thymine.
• Various RNA types have diverse roles: mRNA (template for protein synthesis), tRNA (transfers amino acids), rRNA (part of ribosome), and non-coding RNAs.
• RNA plays a crucial role in gene expression.

RNA Synthesis and Translation, Prokaryotic and Eukaryotic

• RNA synthesis occurs in the cytoplasm for prokaryotes and in the nucleus for eukaryotes.
• Transcription and translation are coupled in prokaryotes.
• Processing steps are needed before translation in eukaryotes.

RNA Replication, Process and Function

• RNA polymerase utilizes one strand as a template for transcription.
• Synthesizes new RNA from 5’-> 3’,
• RNA is produced and exported to the cytoplasm from the nucleus
• RNA is processed through different steps and functions in different ways in various processes.

RNA vs DNA

• RNA has ribose, DNA has deoxyribose
• RNA is typically single-stranded, DNA is double-stranded
• RNA is less stable than DNA.

RNA Polymerase in Eukaryotes

• Three types utilized (Pol I, Pol II, and Pol III).
• Pol I synthesizes rRNA; Pol II synthesizes mRNA, and Pol III synthesizes tRNA and other small RNAs.

RNA Polymerase II Transcribed Genes

• Promoter and control elements play a role in gene-specific expression.

Transcription Initiation

• Pre-initiation complex (PIC) comprises multiple transcription factors and RNA polymerase II.

Transcription in a eukaryotic organism

• RNA is produced, processed and exported out of the nucleus.
• Transcription Initiation factors recruit the transcription machinery to the promotor region and RNA polymerase.
• Transcription Elongation by RNA polymerase elongates the mRNA.
• Termination mechanisms cause the release of RNA and transcription machinery from the DNA.

Protein Protein Interactions

• Yeast two-hybrid system is used to screen libraries of proteins to find interactions.
• This system is able to find protein-protein partners.
• Screening protein-protein interactions may help to better understand complicated biological systems.

Comparative Genomics

• Comparisons between genomes of pathogens and non-pathogens, and between humans and other species provide insights into gene function and evolution.
• Gene duplications through retroviral insertions,
• Changes between multiple species can reveal relationships and evolutionary pathways.

Protein Structure

• Primary structure: amino acid sequence.
• Secondary structure: alpha helix, beta sheet.
• Tertiary structure: 3D shape of a single polypeptide chain.
• Quaternary structure: arrangement of multiple polypeptide chains to form a functional protein.

Point Mutations

• Transition (purine to purine or pyrimidine to pyrimidine).
• Transversion (purine to pyrimidine or vice versa).
• Effects on protein structure and function can vary from no effect to complete loss of function.

Gene mutations and regulation

• Mutations can affect gene expression by altering regulatory regions (enhancers, promoters), splicing sites, and microRNA binding sites.
• Spontaneous mutations can occur due to errors in DNA replication, tautomeric shifts, deamination, etc.
• Trinucleotide repeats cause genetic disorders.

DNA Damage and Repair

• DNA can be damaged by physical or chemical agents, leading to mutations and severe problems.
• Cells utilize dedicated repair mechanisms to correct these damages.
• Defects in DNA repair systems lead to certain genetic diseases.

Gene Cloning and PCR

• Gene cloning involves isolating a specific gene and creating multiple identical copies.
• Polymerase Chain Reaction (PCR) is a method for amplifying DNA sequences.
• These methods have critical applications in research, medicine, etc.

Other genetic concepts

• Other details involved in mutations, replication, and gene cloning

Chromosomal Rearrangements

• Deletions, duplications, inversions, and translocations: changes in chromosome structure
• these disrupt genes, potentially leading to disease.
• these events can bring distant genes together.

This quiz examines the key concepts of transcription and RNA processing in prokaryotes and eukaryotes. Participants will explore differences in mRNA processing, RNA polymerases, and the structural elements of DNA. Test your understanding of these fundamental biological processes!