Central Dogma & Gene Regulation

Overview of the Central Dogma

The central dogma of molecular biology describes the flow of genetic information within a cell, from DNA to RNA to protein. This process is fundamental to all living organisms and underpins cellular function and heredity.

• Transcription: DNA is transcribed into messenger RNA (mRNA) by RNA polymerase, which reads the DNA template strand in the 3’ → 5’ direction.

• Translation: Ribosomes translate mRNA into proteins, with transfer RNA (tRNA) delivering the correct amino acids based on codons.

• Replication: DNA is replicated before cell division. Enzymes such as topoisomerase and DNA gyrase relax the chromosome, while helicase creates the replication fork. DNA polymerase synthesizes new DNA strands in the 5’ → 3’ direction, using the old strand as a template.

• Eukaryotes: DNA replication and transcription occur in the nucleus; translation occurs in the cytoplasm or rough endoplasmic reticulum.

Example: In Escherichia coli, the lac operon is transcribed into mRNA, which is then translated into enzymes for lactose metabolism.

Gene Regulation: Operons

• Inducible Operon (lac operon): Activated by the presence of an inducer (lactose), which binds to the repressor and prevents it from binding to the operator site, allowing transcription.

• Repressible Operon (trp operon): Shut down by a co-repressor (tryptophan), which binds to the repressor, enabling it to bind to the operator and block transcription.

Example: The lac operon is induced in the presence of lactose; the trp operon is repressed when tryptophan is abundant.

Microbial Genetics

Mutations and Their Effects

Mutations are changes in the DNA sequence that can occur spontaneously or due to external factors. They are a major source of genetic variation and can impact microbial evolution.

• Spontaneous mutations: Occur during DNA replication.

• Induced mutations: Caused by chemical mutagens (e.g., ethidium bromide) or physical factors (e.g., UV light).

• Types of mutations:

  • Base substitution: One nucleotide is replaced by another.

  • Frameshift mutation: Insertion or deletion of nucleotides, altering the reading frame.

• Mutation outcomes:

  • Silent mutation: No change in amino acid.

  • Missense mutation: Change in amino acid.

  • Nonsense mutation: Premature stop codon.

Example: UV light can cause thymine dimers, leading to frameshift mutations.

Genetic Exchange in Bacteria

• Transformation: Uptake of naked DNA from the environment.

• Conjugation: Transfer of DNA between bacteria via a pilus.

• Transduction: Transfer of DNA via bacteriophage infection.

Example: Streptococcus pneumoniae can acquire antibiotic resistance genes through transformation.

Microbial Evolution

• Mutations and genetic exchange contribute to microbial evolution, such as the development of antibiotic resistance.

Biotechnology

Microbial Applications in Biotechnology

Biotechnology harnesses microbes and genetic techniques to produce desired products, such as pharmaceuticals, enzymes, and genetically modified organisms.

• Restriction enzymes: Used to cut plasmids and genes for ligation and insertion into microbes.

• Site-directed mutagenesis: Introduces specific mutations into genes.

• Prokaryotic cells: Efficient and inexpensive for gene product production, but may lack post-translational modifications.

• Eukaryotic cells: More similar to human cells, but production is expensive and complex.

• DNA technology: Used for gene editing, genome editing, and production of products for human use.

• Genome projects: Aim to sequence entire genomes to aid in treatment and vaccine development.

• Ethical and ecological concerns: DNA modification can have unpredictable effects and raise ethical issues.

Example: Insulin production using recombinant Escherichia coli.

Classification of Microorganisms

Principles and Methods of Classification

Classification organizes organisms to aid in identification and understanding evolutionary relationships. It is based on genetic, biochemical, and structural characteristics.

• Genetic methods: rRNA sequencing, DNA hybridization.

• Biochemical tests: Identify metabolic capabilities.

• Fatty acid profiles: Analyze membrane lipids.

• Phage typing: Use of bacteriophages to identify bacteria.

• Dichotomous keys: Series of yes/no questions to identify unknown microbes.

• Cladograms: Diagrams showing evolutionary relationships.

Example: rRNA sequencing distinguishes between Staphylococcus and Streptococcus.

Classifying Prokaryotes

Gram Negative Bacteria

Gram negative bacteria have a thin peptidoglycan layer and an outer membrane containing lipopolysaccharide (LPS), providing extra protection.

• Examples: Azospirillum (nitrogen fixation), Rickettsia (obligate intracellular parasite), Rhizobium (nitrogen fixation), Bordetella (whooping cough), Neisseria (gonorrhea, meningitis), Pseudomonas (nosocomial infections), Vibrio (cholera), Escherichia (UTI), Salmonella (foodborne illness), Yersinia (plague), Enterobacter (UTI), Bdellovibrio (lives inside Gram negative cells), Helicobacter (peptic ulcers), Chlamydia (STD), Fusobacterium (dental caries), Treponema (syphilis), Borrelia (Lyme disease).

Gram Positive Bacteria

Gram positive bacteria have a thick peptidoglycan layer with embedded teichoic acids.

• Examples: Clostridium (endospore forming – tetanus), Bacillus (endospore forming – anthrax), Staphylococcus (wound infections), Lactobacillus (food production), Streptococcus (strep throat), Listeria (food contamination), Mycoplasma (no cell wall), Mycobacterium (TB, leprosy), Propionibacterium (acne), Streptomyces (antibiotics).

Archaea

Archaea are prokaryotes that live in extreme environments, such as high salt, heat, cold, or pressure.

Classifying Eukaryotes

Fungi

Fungi include multicellular molds and unicellular yeasts. They digest organic matter and can survive in diverse environments.

Lichens

Lichens are symbiotic associations between a fungus and an alga or cyanobacterium. The fungus provides structure and protection, while the alga/cyanobacterium photosynthesizes to produce nutrients.

• Ecological role: Serve as food for herbivores and contribute to soil formation.

Algae

Algae are photosynthetic organisms living in aquatic environments. They vary in color and type.

• Diatoms: Store oil.

• Dinoflagellates: Cause paralytic shellfish poisoning.

• Algal blooms: Can produce toxins harmful to aquatic life and humans.

Protozoans

Protozoans are unicellular eukaryotes with animal-like behaviors, including complex life cycles, feeding, and excretion.

• Example: Plasmodium (malaria parasite) is transmitted from mosquitoes (definitive host) to humans (intermediate host).

Helminths

Helminths are parasitic worms, including flatworms (incomplete digestive system) and roundworms (complete digestive system).

• Some are segmented, with each segment containing reproductive organs.

• Many are spread by vectors (mosquitoes, flies) either biologically or mechanically.

Viruses, Viroids, & Prions

Viruses

Viruses are obligate intracellular parasites that require a host cell for replication. They consist of a protein coat (capsid) housing the genome (DNA or RNA), and some have an envelope derived from the host cell membrane.

• Growth: Viruses are grown on bacteria (bacteriophages) or eukaryotic cells.

• Identification: Viral genomic assays and antibody testing.

• Bacteriophage infection: DNA is inserted into the host bacterial cell.

• Animal virus infection: Virus enters the host cell.

Viral Replication Cycles

• Lytic cycle: Virus multiplies in the host cell and lyses it.

• Lysogenic cycle: Viral DNA integrates into the host chromosome and can later excise to enter the lytic cycle.

Animal Virus Replication

• DNA viruses: Replicate, transcribe, and translate their DNA to produce viral proteins.

• RNA viruses: Synthesize complementary RNA strands, then translate mRNA into proteins.

• Retroviruses: Insert their genome into the host genome, potentially leading to cancer.

• Chronic viral infections: Can cause cancer through persistent inflammation and immune reactions.

Viroids and Prions

• Viroids: Infectious RNA molecules affecting plants (not detailed in original notes).

• Prions: Infectious proteins that induce misfolding of normal proteins in the brain, causing spongiform encephalopathies.

Example: Prion diseases include Creutzfeldt-Jakob disease and mad cow disease.

Table: Comparison of Gram Positive and Gram Negative Bacteria

Table: Types of Mutations and Their Effects

Key Equations

• DNA Replication Direction:

• Central Dogma:

Additional info: Viroids are infectious RNA molecules affecting plants, not detailed in the original notes but included for completeness. Some details about classification methods and examples were expanded for academic context.