Lecture Overview Lecture 6: Focus on the Molecular Biology of Microorganisms.

Transfer Genetic Information

• Replication: Essential for transferring genetic information between generations, relying on multiple enzymes to unwind DNA, synthesize new strands, and correct errors. Proper segregation ensures each daughter cell receives an identical genome.

• Cell Division: Following accurate segregation, cell division occurs through binary fission in prokaryotes and mitosis in eukaryotes, ensuring new cells inherit a complete genetic copy.

Flow of Genetic Information

• Central Dogma: Describes the pathway DNA → RNA → Protein, highlighting the unidirectional flow of information.

• Transcription: The synthesis of RNA from DNA, primarily by RNA polymerase, with transcription factors influencing gene expression.

• Translation: The nucleotide sequence in mRNA is translated into amino acids at ribosomes, involving tRNA and rRNA in assembling polypeptides.

Prokaryotic vs. Eukaryotic Gene Expression

• Polycistronic messages: In prokaryotes, multiple genes are transcribed into a single mRNA, unlike the monocistronic mRNAs in eukaryotes.

• Non-coding sequences in ORFs: Prokaryotic ORFs have uninterrupted coding sequences, while eukaryotic genes contain introns that must be spliced out.

• mRNA Processing: Eukaryotic mRNAs undergo 5' capping, polyadenylation, and splicing; prokaryotic mRNAs don't require such modifications.

• 5' and 3' ends: Modifications at both ends protect against degradation and enhance stability and translation.

Base Pairing

• Pairing Rules: Nucleotides pair via hydrogen bonding, with G-C pairs forming three bonds for greater stability than A-T pairs with two.

• Significance of A-U Base Pair: Important in RNA structures, especially in transcription termination.

• Structure of DNA Ends: Distinct 5' (phosphate group) and 3' (hydroxyl group) ends are critical for replication.

• Antiparallel Strands: Ensures proper base pairing and supports replication and transcription.

Base Pairing Gives DNA its Structure

• Double Helix: DNA's double helix structure features anti-parallel, complementary strands crucial for genetic encoding and replication.

• Grove Regions: Major groove allows for sequence-specific protein binding; the minor groove permits non-specific interactions.

Sequence Dependent Nucleic Acid Structures

• Inverted Repeats: Essential for forming secondary structures like hairpins that affect gene regulation.

• Stem-loop Structures: Significant for regulating gene expression and transcription termination.

Organization of the Bacterial Chromosome

• Nucleoid: A region in prokaryotes where the chromosome is densely packed, lacking a surrounding membrane.

• Chromosome Packaging: Due to its larger size, the bacterial chromosome organizes in supercoiled loops affecting gene expression and replication.

• Lysis Evidence: Observable chromosome extents beyond the cell indicate organized loop formations vital for function.

Extrachromosomal Genetic Elements

• Plasmids: Circular DNA molecules that replicate independently of chromosomal DNA, often carrying genes for traits like antibiotic resistance, crucial in biotechnology.

Synthesis of DNA Requires Coordination of Many Enzymes

• Multiple Enzymatic Steps: Involves helicases, primases, DNA polymerases, and ligases, working in concert to ensure accuracy and efficiency in DNA synthesis.

DNA Replication

• Helicase Activity: DnaB enzyme unwinds DNA using ATP energy to create single-stranded templates.

• Leading and Lagging Strands: Leading strand synthesized continuously; lagging strand forms in Okazaki fragments, necessitating complex coordination.

Termination of DNA Synthesis

• Cis-acting factors: Termination relies on specific motifs and protein interactions, indicating sophisticated control mechanisms.

Manipulation of DNA

• Restriction Enzymes: Cut DNA at palindromic sequences, creating “sticky” or “blunt” ends for recombinant DNA technology.

What is an Operon?

• Operons: Clusters of co-regulated genes producing polycistronic mRNA, enabling simultaneous expression under a single promoter—characteristic of prokaryotic regulation.

Deciphering the Genetic Code

• mRNA Codons: Three nucleotide sets representing specific amino acids or termination signals; among 64 codons, some denote start and stop.

• Degeneracy: Multiple codons can correspond to a single amino acid, providing mutation tolerance.

Attributes of tRNA

• L Structure: All tRNAs adopt an L-shaped structure crucial for amino acid binding and ribosome interaction for translation.

Stages of Protein Synthesis

• Three Stages: Consist of initiation, elongation, and termination, with specific factors aiding in both prokaryotic and eukaryotic systems, which differ in molecular players and timing.

Coupled Transcription and Translation in Prokaryotes

• No Compartmentalization: In prokaryotes, absence of a nuclear membrane allows simultaneous transcription and translation, enabling rapid responses to environmental changes.

Chaperones and Protein Folding

• Role of Chaperones: Assist nascent polypeptides in folding correctly during synthesis, preventing misfolding, with distinct types for co- and post-translational processes.