genet 270 lec 1
What is the genetic material in cells?
DNA is the genetic material, organized in linear base sequences (not proteins)
What is the Central Dogma of molecular biology?
DNA → RNA → Protein. DNA bases: A, T, C, G; RNA bases: A, U, C, G; Proteins: amino acid sequence
How are bacterial genes named?
3 lowercase italicized letters (pathway) + capital letter (specific gene). Example: lacZ = gene for β-galactosidase
What do gene name symbols mean?
+ = wild-type, – = mutant, Δ = deleted
How are proteins named compared to genes?
Proteins are not italicized, first letter capitalized. Example: LacZ = β-galactosidase enzyme
Why study bacterial genetics?
They are model systems, surprisingly complex, ecologically essential, symbiotic, and relevant in disease
Name two major contributions of bacteria/phages to biology.
Watson & Crick → DNA structure; Meselson & Stahl → DNA replication
What are the three domains of life?
Archaea, Bacteria, Eukaryotes
Key features of bacterial genomes?
Haploid, single circular chromosome, supercoiled loops, condensed into nucleoid
Gram-positive vs. Gram-negative bacteria?
Gram+ = thick peptidoglycan, purple stain. Gram– = thin peptidoglycan + outer membrane, pink stain, often more antibiotic resistant
What is generation time?
Time for an organism to reach maturity and produce offspring; in E. coli, ~20 minutes
What are prototrophs vs. auxotrophs?
Prototrophs grow on minimal media. Auxotrophs require additional organic substances
Define colony in microbiology.
A visible cluster of bacteria derived from a single bacterium
Why are bacteria good genetic models?
Haploid genome, short generation time, asexual reproduction, easy to count, easy to screen/select
What are bacteriophages?
Viruses that infect bacteria; most numerous “organisms” on Earth (10³¹ particles)
Why are bacteriophages important ecologically?
They turn over ~40% of all bacteria daily, major role in carbon/nutrient cycling
What are the two main bacteriophage life cycles?
Lytic (phage replicates, lyses host) and Lysogenic (phage integrates as prophage, can be induced later)
Define prophage and lysogen.
Prophage = phage DNA integrated into bacterial chromosome; Lysogen = bacterium carrying a prophage
What is a plaque in phage biology?
A clear region in a bacterial lawn caused by lytic phage infection
Why are phages good genetic models?
Haploid, short generation time, clonal multiplication, easy to cross strains, easy to select mutants
Name two foundational discoveries made with microbes.
DNA as genetic material (Griffith; Hershey & Chase); DNA replication mechanism (Meselson & Stahl).
Who elucidated DNA structure?
Watson & Crick.
Who uncovered gene regulation in bacteria?
Jacob & Monod.
What are the three domains of life?
Archaea, Bacteria, Eukaryotes.
How were domains distinguished?
By rRNA sequence comparisons.
How divergent are bacterial lineages vs mammals?
Bacteria diverged billions of years ago; mammals millions.
What notable traits does Streptomyces coelicolor have?
forms spore stalks (hyphae) and produces antibiotics.
What’s notable about E. coli?
Single-celled rod; both a model organism and pathogen.
List three structural/functional hallmarks of bacteria.
Prokaryotic (no nuclear membrane), transcription & translation are simultaneous, usually one chromosome.
What ploidy are bacteria and why is it useful?
Haploid—mutations show immediate phenotypes, facilitating genetic analysis.
Name key eukaryotic features.
Organelles (mitochondria, chloroplasts, ER); diverse lineages; similar macromolecular synthesis.
origin of mitochondria and chloroplasts?
Derived from endosymbiosis (alpha-proteobacterium; cyanobacterium).
In bacteria, how are transcription and translation related?
Tightly coupled; ribosomes translate mRNA as it’s synthesized, forming polyribosomes.
What’s a take-home from the coupling diagram?
Spatial/temporal coupling in prokaryotes enables rapid responses.
Describe the bacterial chromosome.
Single, supercoiled, double-stranded circular DNA.
What is the nucleoid?
Condensed DNA region composed of supercoiled loops.
Which group often shows greater intrinsic antibiotic resistance and why?
Gram–, due to the additional outer membrane barrier that is very impermeable due to LPS
what is periplasmic space
soluble space dense with proteins
Why do haploid genomes aid genetic analysis?
Most mutations show immediate effects (no second allele masks them).
What’s a challenge with haploid genetics?
Lethal mutations are hard to maintain.
Define generation time.
Time to reach maturity and produce offspring.
Approximate generation time of E. coli under optimal conditions?
~20 minutes.
What does asexual reproduction produce in bacteria?
Clones—progeny genetically identical to the parent and each other.
what is complex media?
complex extract of bio material, rich in organic molecules.
what is minimal media?
no organic compounds other than carbon source.
Define a colony.
A visible cluster derived from a single bacterium.
Formula to estimate viable cell concentration (CFU/mL)?
CFU/mL = (number of colonies × dilution factor) ÷ volume plated (mL).
What is colony purification?
Picking a single colony and re-streaking (e.g., twice) to obtain a pure culture.
Screen vs selection?
Screen: both WT and mutants grow but look different. selection: only desired mutants grow under selective conditions (e.g., antibiotic/temperatures)
List archaeal traits.
Single-celled; no nucleus (like bacteria) but core processes (transcription/translation/replication) resemble eukaryotes.
What are extremophiles?
Organisms thriving in extreme conditions (high temp, high salinity/osmolarity, ocean floor, etc.). Many archaea are extremophiles.
What are bacteriophages?
Viruses that infect bacteria; foundational tools for genetics.
Name one ecological role of phages.
Major players in carbon/nutrient cycling; can move genes between hosts (drive evolution).
List minimal functions a phage must accomplish.
Protect nucleic acid; deliver it into a bacterium; convert host into a phage factory; release progeny.
What nucleic acids do phages use?
DNA or RNA; single- or double-stranded; linear or circular.
What is the phage capsid?
Protein coat surrounding nucleic acid; shapes include helical or isometric (often icosahedral).
What is an obligate bacterial parasite?
Can only multiply in an actively metabolizing bacterium.
what is a lysogeny and what is a phage capable of lysogeny called
process of integration/ temperate bacteriophage.
Define a virulent (lytic) phage.
A phage that only undergoes lytic growth (replicate and lyse host).
Define a temperate (lysogenic) phage.
A phage capable of integrating into the host genome as a prophage and remaining silent until induced.
What is a lysogen?
A bacterium carrying a prophage
Name early steps of the lytic cycle.
Adsorption to specific receptors; injection of DNA; early genes enable DNA replication.
what are later steps of lytic cyle
new virus made using bac cell machinery then cell lyses
What do late genes encode?
Structural proteins for head and tail.
How are new phages released?
Assembly (morphogenesis) then lysis via holin (protein that disrupts cytoplasmic membrane) and lysozyme ( protein that degrades cell wall). Burst size = phage released per cell.
what is a lysate
collection of lysed cells and new phages
what happens during lysogenic lifecyle
viral dna is intergated into bac chromo, brief period of transcription occurs where a repressor protein and site specific recomb enzyme is made, the phage dna molecule recombines intoo bac chromo mediated by integrase, phage dna replicated into bac chromo as bac grows, lytic growth can be triggered gens after through induction
what advantages does lysogenic lifecyle provide
selective growth advantage
What is a plaque?
A clear zone in a bacterial lawn where lytic phage have killed cells; one plaque originates from one infectious phage.
What is EOP (Efficiency of Plating)?
Fraction of phage particles that can form a plaque, usually close to 1
What is MOI (Multiplicity of Infection)?
Average number of adsorbed phage per bacterium, determines how many bac will be infected by phage
Why do mixed phage/bacteria often yield a lysate?
Phage amplify rapidly (e.g., ~100 per generation), overwhelming bacteria (2 per generation).
what are plaques useful for
Can examine plaques to study interaction of genes.
List four reasons phages are excellent genetic models.
Haploid (mutations show immediately), short generation times, clonal multiplication (pure stocks), easy crosses (co-infect at high MOI), and strong selections- easier to select for mutants.
Name five reasons bacteria make good genetic models.
Haploid genomes, short generation times, asexual/clonal reproduction, easy counting (CFU), easy screens/selections & colony purification.
Define “prototroph” vs “auxotroph.”
prototroph: grows on min media. Auzotroph: requires additional organic compounds beyond a carbon source
What is “colony purification”?
Picking an individual colony and re-streaking to obtain a pure strain.