Comprehensive Study Guide on DNA, RNA, and Genetic Processes

School

University of Wisconsin, Madison**We aren't endorsed by this school

Course

MICROBIO 470

Subject

Biology

Date

Dec 12, 2024

Pages

Uploaded by ChiefLapwing4669

Study GuideSection 1 & Section 2 (total 25%)DNA structure and replicationNucleic acid structure – reactive chemical groups; types of chemicalbonds Differences between DNA and RNADifferent enzymatic activities of DNA polymerase that perform distinct functions during DNA replicationDirection of DNA synthesis; leading/lagging strand synthesisStart and end signals/sequences of DNA replicationmultifork replicationChromosome translocation, segregation and DNA supercoilingDNA methylation as a way to control replication initiationA way to study essential gene functions: temperature sensitive mutantsTranscriptionTranscription initiation: promoter recognition; closed/open complex;promoter melting; promoter escapeTranscription elongation: channels in elongation complexesTranscription termination: Rho-independent termination – hairpin RNA secondary structure; Rho-dependent termination – Rho utilization sites (rut)Translation3 main types of RNA: mRNA, tRNA and rRNAgenetic code degeneracy and wobble pairingRibosome translocation, A, P, E sites, position of tRNA and mRNA onthe ribosomeTranslation start/stop signals: SD sequence, start/stop codons, accessory factors (IF, EF, TF)Trans-translation by tmRNA: mechanism and benefitMutations and basic genetics methods

Types of mutations: spontaneous vs induced; duplication/deletion vs inversion; base substitution (transition/transversion) vs frameshift mutationsConsequences of mutations: missense, nonsense, silence (synonymous)Genetic selection vs screenMutant phenotypes and selection method: Prototrophy vs auxotrophy, alternative carbon utilization, antibiotic resistanceReversion vs suppressionNonsense mutation suppressorComplementation (dominant vs recessive, cis vs trans, complementation group)PlasmidsPlasmids are DNA molecules that can exist separately from the chromosome.Understand plasmid replicate from its own origin of replication.Differentiate Theta or Rolling Circle replication.Understand that plasmids have different copy numbers in the cellUnderstand that plasmids are maintained because they provide selective advantageHorizontal gene transfer (conjugation, transformation and transduction)What happens to the cells (donor/recipient) and DNAHow to perform genetic manipulation with themHow to differentiate them (e.g Davis U-tube)Calculate their efficiency of transfer and understand factors that contributes to the (in)efficiency.Conjugation:Definition and characteristics of F+, F’, Hfr.Structure and function of F plasmid.Formation of F’ and Hfr.Process of conjugation by F+, F’ and Hfr.

Recombination (crossover) in conjugation.Hfr-initiated conjugation and interrupted-mating mapping (process, gene order, directionality…).Understand how to map chromosomes with interrupted-mating mappingTransformation:Definition of natural transformation and competence.Calculate Efficiency of TransformationUnderstand that ssDNA is recombined to form heteroduplex during transformationTransduction and Phage:Understand MOI, plaque, headful DNA packing.Calculate efficiency of transduction and co-transduction.Understand how to map genetic distance using co-transduction.Differentiate lytic / lysogenic cycles.Understand the role of processive antitermination in lambda lytic cycle.Understand how decision making between lytic and lysogeny is achieved.Understand the differences between generalized and specialized transduction.Understand λ phage immunity.Understand zygotic induction in conjugational transfer of prophage.Recombination:Understand site-specific recombination (λ phage incorporation, cre recombinase)Identify and draw Holliday junctionSection 3 (75%)

Regulation of genes and operons:Repressors, activators and their allosteric regulation by small molecule effectors1.Understand negative regulation of operon transcription by repressor2.Understand positive regulation of operon transcription by activator3.Operators and activator binding site sequences (cis-acting elements)4.Understand why mutants of repressor, activator have their respective phenotypes5.Inducers, co-repressors, co-activators, inhibitors6.Understand how to use genetic analyses to differentiate repressors from activators in a gene regulatory circuit7.How cis and trans acting element behave in complementation; complementation group; dominant vs recessive8.Understand how small molecule effectors regulate biosynthesis operons (eg. trp operon) via negative feedback. Mutants in these operons are auxotrophs.9.understand how alternative carbon source positively regulates carbon utilization operons (eg. lac operon). Mutants in these operons are not auxotrophsRepressors sensing DNA damage via RecA1. lambda CI repressor cleavage2. SOS response: LexA repressor cleavagePost-initiation: Attenuation, the riboswitch, and processive antitermination1.Trp attenuator: structure, function, mechanism2.Combination of trp repressor and attenuation3.Metabolite-binding riboswitch: transcription termination vs translation initiation4.Understand how to use genetics to differentiate the mechanisms of regulation and characterize attenuation and riboswitch.5.Processive antitermination in phage lytic cycleSignaling nucleotides: second messengers (cAMP, 2'3' cNMP, ppGpp)1.cAMP and carbon catabolite regulation incoli2.Definition and explanation of diauxic growth3.Synthesis and function of ppGpp after amino acid starvation4.ppGpp and purine nucleotide synthesis regulation inB. subtilis5.initiating NTP concentrations regulates transcription initiation

Alternative sigma factors1.Sigma N in nitrogen regulation2.Sigma H in heat shock response3.Alternative sigma factors in sporulationTwo component system1. Sensor kinase and response regulator2. phosphorelayEpistasis in bacterial development (differentiating from complementation)