MGI 301 exam 2

Genome function

Stores DNA-encoded instructions for cellular structure, metabolism, stress responses, and reproduction.

Central dogma

Genomic DNA is transcribed into mRNA, which is translated into functional proteins.

Targeted sequencing

Examines a specific gene or region across multiple isolates.

Whole-genome sequencing

Maps entire genomes to investigate metabolic capabilities, novel genes, or uncultured microbes.

Open reading frame

A potential protein-coding region bounded by start and stop codons.

ORF annotation

Computers scan six reading frames, evaluate codon bias, and compare sequences with databases.

Parasitic bacterial genomes

Can be reduced because parasites rely on hosts for essential metabolites.

Metagenomics

Sequences environmental DNA to reveal microbial functions without laboratory cultivation.

Phylogenetic trees

Use sequence divergence in conserved genes to depict evolutionary relationships.

Core genome

Genes shared by all strains of a species.

Pan genome

All core and accessory genes found across strains of a species.

16S rRNA gene

Conserved and variable regions support microbial identification and evolutionary comparisons.

Southern blotting

Uses labeled probes to bind specific complementary DNA sequences.

DNA microarrays

Use thousands of probes to screen for genes or mutations simultaneously.

Ribotyping

Fingerprints bacterial strains using restriction digestion and Southern blotting of rRNA genes.

FISH

Uses fluorescent probes targeting rRNA to visualize specific microbes in intact cells.

Replication fork enzymes

Helicase unwinds DNA; primase provides primers; DNA polymerase synthesizes DNA 5′ to 3′.

Leading and lagging strands

The leading strand is synthesized continuously; the lagging strand forms Okazaki fragments.

DNA base pairing

A pairs with T, and G pairs with C; RNA uses U instead of T.

Transcriptional regulation

Conserves resources by preventing synthesis of unneeded mRNAs and proteins.

Rho-dependent termination

Rho binds RNA and catches paused RNA polymerase, terminating transcription.

Intrinsic termination

A GC-rich RNA hairpin followed by a U-rich tract destabilizes RNA polymerase.

Bacterial operon

Regulatory sites and structural genes organized for transcription as one polycistronic mRNA.

Regulon

Separate genes or operons controlled by one regulatory protein or sigma factor.

Coupled transcription and translation

Bacterial ribosomes translate mRNA while it is still being transcribed.

Polysome

Multiple ribosomes simultaneously translating a single mRNA.

Arginine operon

Abundant arginine activates a repressor that blocks transcription of its biosynthetic genes.

Lac operon negative control

Without lactose, a repressor blocks transcription; lactose inactivates the repressor.

Lac operon positive control

Low glucose raises cAMP, enabling CRP-cAMP to activate transcription.

Diauxic growth

Glucose utilization precedes a lag and subsequent lactose utilization.

Maltose operon

A maltose-bound activator promotes transcription initiation.

Small regulatory RNAs

Pair with target mRNAs to block translation or promote mRNA degradation.

Riboswitch

Metabolite binding changes mRNA structure, potentially blocking the Shine-Dalgarno sequence.

Feedback inhibition

A pathway's end product inhibits its first enzyme through an allosteric site.

Missense mutation

A base-pair change alters one amino acid.

Nonsense mutation

A codon changes into a stop codon, prematurely truncating the protein.

Silent mutation

A base-pair change leaves the encoded amino acid unchanged.

Frameshift mutation

An insertion or deletion not divisible by three shifts the reading frame.

Reversion mutation

A secondary mutation restores the wild-type phenotype or genotype.

Mutation causes

Replication errors or mutagens can alter DNA.

Direct selection

Uses conditions under which only the desired mutants can grow.

Indirect selection

Identifies mutants by comparing growth patterns, as in replica plating.

Plasmid

Extrachromosomal DNA ring that can confer auxiliary traits such as antibiotic resistance.

Transposon

Mobile DNA element that can carry resistance or metabolic genes.

Transformation

Uptake of extracellular DNA by a competent recipient cell.

Generalized transduction

A lytic bacteriophage transfers randomly packaged host DNA.

Specialized transduction

Imprecise prophage excision transfers host genes adjacent to the integration site.

Conjugation

Direct cell-to-cell DNA transfer through a conjugative pilus.

Homologous recombination

RecA and other proteins mediate exchange between homologous DNA segments.

F⁺ and F⁻ cells

F⁺ cells carry an independent F plasmid; F⁻ cells lack it.

Hfr cells

Contain an F plasmid integrated into the bacterial chromosome.

F⁺ conjugation outcome

The F⁻ recipient typically acquires the F plasmid and becomes F⁺.

Hfr conjugation outcome

The recipient may acquire chromosomal genes but usually remains F⁻.

Viruses

Acellular infectious agents that depend on host machinery for replication.

Naked virions

Capsid-enclosed genomes are environmentally stable and typically exit by lysis.

Enveloped virions

Host-derived lipid envelopes contain viral glycoproteins; these virions typically exit by budding.

Viral polymerases

Some RNA viruses carry specialized enzymes to replicate or reverse-transcribe their genomes.

Lytic phage cycle

Phage replication uses host machinery and culminates in cell lysis.

Lysogenic phage cycle

Viral DNA persists as a prophage until induction into the lytic cycle.

SARS-CoV-2 genome

Enveloped virus with a positive-sense single-stranded RNA genome.

SARS-CoV-2 entry

Spike proteins bind host ACE2 receptors to mediate entry.

COVID-19 mRNA vaccines

Deliver instructions for host cells to produce the spike antigen.

HPV genome and target

A naked, circular double-stranded DNA virus infecting basal epithelial cells.

HPV E6 protein

Degrades the p53 tumor suppressor.

HPV E7 protein

Binds and inactivates retinoblastoma protein.

Influenza genome

Enveloped virus with eight segments of negative-sense single-stranded RNA.

Influenza hemagglutinin

Promotes viral attachment to host cells.

Influenza neuraminidase

Promotes release of newly produced viruses.

Antigenic drift

Minor influenza mutations alter surface antigens and necessitate updated vaccines.

Antigenic shift

Reassortment between influenza strains can produce pandemic strains.

HIV reverse transcription

Reverse transcriptase converts viral RNA into complementary DNA.

HIV integration

Integrase inserts viral DNA into the host chromosome, establishing lifelong latency.

HIV immune impact

Destruction of CD4⁺ T cells weakens adaptive immunity and can lead to AIDS.

Autoclaving

Steam under pressure at 121°C and 15 psi for 15 minutes destroys endospores.

Batch pasteurization

Heats food to 63°C for 30 minutes.

Flash pasteurization

Heats food to 72°C for 15 seconds.

Ultraviolet radiation

Induces thymine dimers and is used for surface and air sterilization.

Ionizing radiation

Generates reactive free radicals that damage DNA and proteins.

Microbial filtration

Membrane or HEPA filters remove microbes from heat-sensitive liquids or gases.

Bacteriostatic agents

Inhibit bacterial division without killing cells.

Bactericidal agents

Kill bacterial cells without necessarily destroying their structures.

Bacteriolytic agents

Kill bacterial cells through lysis, reducing both viable and total counts.

Chemical antimicrobial categories

Sterilizers kill all life; disinfectants treat surfaces; antiseptics treat tissue; sanitizers reduce counts.

Diagnostic sensitivity

Ability to correctly identify true positive cases.

Diagnostic specificity

Ability to correctly identify true negative cases.

Bacteremia

Presence of viable bacteria circulating in the blood.

Selective and differential media

Selective media inhibit nontargets; differential media distinguish microbes using observable traits.

Antibody titer

Concentration of specific antibodies in serum; a rising titer suggests recent or current infection.

Direct and indirect EIA

Direct EIA detects patient antigens; indirect EIA detects patient antibodies.

PCR and qPCR

PCR amplifies target DNA; qPCR monitors amplification in real time to quantify pathogen load.