Micro Final Exam

Class 1

dsDNA genomes - Genome replication and transcription utilize the same mechanism as host cells; depending on cell types infected can often use the host's DdDp and DdRp.

Class 2

ssDNA (+ and -) genomes, most are (+)ssDNA - Transcription would yield (-)mRNA so need to form a replicative intermediate = dsDNA -> used as template for transcription and genome replication.

Class 3

dsRNA genomes - Must encode and carry RdRp for transcription and genome replication.

Class 4

(+)ssRNA genomes - Must encode RdRp for transcription and genome replication; Genome = mRNA but only 1 copy enters cell; upon entry, the RdRp gene is immediately translated -> copies genome to (-)ssRNA, then to (+)ssRNA.

Class 5

(-)ssRNA genomes - Must encode and carry RdRp for transcription and genome replication; RdRp carried in virion makes (+)ssRNA copies of genome following entry = mRNAs and used as templated to produce (-)ssRNA genomes.

Class 6

Retroviruses, (+)ssRNA genomes - Must encode and carry RdDp (reverse transcriptase) enzyme to convert genome to dsDNA following entry; dsDNA provirus integrated into the host genome; transcription and genome replication are performed using the host DdRp.

Class 7

Reverse-transcribing DNA viruses, dsDNA genomes - Transcription performed by the host DdRp; Virus encodes RdDp that synthesizes DNA genomes from genome-length transcripts.

Viruses first appearance

~4 billion years ago - after cells.

RNA world hypothesis

Where RNA was the main genetic material, and they may have played a role in the transition from RNA to DNA.

Gene transfer mechanism

Viruses could have evolved to facilitate gene transfer among organisms, enhancing genetic diversity and host fitness, mostly in prokaryotes.

Lytic and latent evolution

May have been primarily latent, evolving lytic capabilities later to spread more effectively to new hosts.

φX174 replication

Uses rolling circle replication to convert its ssDNA genome into a double-stranded form, which then serves as a template for producing more ssDNA genomes; causes lysis of the host cell through inhibition of peptidoglycan synthesis, leading to the release of new virions.

M13 replication

Also employs rolling circle replication, BUT, maintains its ssDNA form throughout the process; releases virions without lysing the host cell, allowing the infected cells to continue growing and resulting in chronic infection.

T7 replication

Utilizes rolling circle replication to form concatemeric DNA with terminal repeats; a phage-encoded nuclease cuts the concatemer into individual linear dsDNA genomes for packaging into capsids; causes cell lysis through phage-encoded holin and lysozyme, releasing new virions.

Mu replication

Can replicate via lytic or lysogenic pathways; in the lytic cycle, it causes cell lysis; in lysogeny, it integrates into the host genome; replication involved transposition, where the Mu transposase integrates the viral genome into multiple sites in the host DNA.

Pox Viruses replication

Replicate entirely in the host cell cytoplasm; they carry their machinery for DNA replication and transcription, as they cannot rely on the host's nuclear processes.

Adenoviruses replication

Replicate in the nucleus of the host cell; they utilize a unique mechanism involving leading strand synthesis on both DNA template strands.

SV40 replication

SV40 is a circular dsDNA virus that replicates in the nucleus using the host's DNA polymerase; it involved both leading and lagging strand synthesis, with early viral genes expressed first to produce proteins necessary for replication.

Herpesviruses replication

Herpesviruses are large, enveloped dsDNA viruses that also replicate in the nucleus; they utilize a rolling circle mechanism to produce concatemeric DNA.

Poliovirus replication

Entry: endocytosis after receptor binding; Replication: translated into a polyprotein in the cytoplasm; RdRp synthesizes (-)ssRNA for new (+)ssRNA genomes; Release: cell lysis.

Coronaviruses replication

Entry: endocytosis after receptor binding; Replication: similar to poliovirus; polyprotein is cleaved, and RdRp synthesizes (-)ssRNA; Release: budding from the cell membrane.

Rabies virus replication

Entry: endocytosis after receptor binding; Replication: viral RNA is transcribed into mRNA and (+)ssRNA in the cytoplasm; Release: budding.

Influenza virus replication

Entry: endocytosis after binding to sialic acid receptors; Replication: transcription occurs in the nucleus; segmented genome allows reassortment; Release: budding.

Hepadnaviruses replication

Entry: nucleocapsid enters the nucleus; Replication: the viral genome is completed and transcribed into mRNAs; RdRp synthesizes (-)ssDNA; Release: budding.

Reoviruses replication

Entry: endocytosis; Replication: transcription occurs within the viral particle; mRNA is translated, the new dsRNA is synthesized; Release: cell lysis.

Phages contribution to ocean ecology

Regulation of bacterial populations: Phages act as natural predators of bacteria, controlling their populations and maintaining microbial balance.

Nutrient cycling

When phages lyse bacterial cells, they release organic matter, which provides nutrients for other microbes, enhancing nutrient cycling.

Genetic exchange

Phages facilitate horizontal gene transfer among bacteria, increasing genetic diversity and allowing for rapid adaptation to environmental changes.

Impact on microbial food webs

By influencing bacterial abundance, phages affect the structure and dynamic of microbial food webs, which are crucial for oceanic primary production.

Biogeochemical processes

Phages contribute to biogeochemical cycles, such as carbon and nitrogen cycles, by enhancing the turnover of organic material.

Bacterial strategies against phages

Bacteria use enzymes to cut foreign phage DNA; incorporate phage DNA sequences to recognize and target phages in future infections; mutate surface receptors to prevent phage binding; create protective biofilms that shield them from phage attacks; produce a polysaccharide capsule to block phage access.

Phage strategies against bacteria

Some phages evolve proteins to inhibit bacterial CRISPR defenses; adapt their binding proteins to attach to various bacterial strains; choose to destroy the host or integrate into its genome, allowing persistence; rapidly adapt through genetic changes, enhancing their ability to infect hosts.

PAMP and DAMP

What is a PAMP and DAMP?

PAMP

Conserved molecular structures found on pathogens that are recognized by the immune system.

DAMP

Molecules released by damaged or dying cells that signal tissue injury and activate the immune response.

Bacteriophages

Viruses that infect bacteria, found in the gut and microbiome.

Adenoviruses

DNA viruses that cause respiratory infections.

Herpesviruses

DNA viruses that cause herpes.

Papillomaviruses

DNA viruses that cause skin warts and cervical cancer.

Rhinoviruses

RNA viruses that cause the common cold.

Coronaviruses

RNA viruses that cause COVID-19.

Influenza viruses

RNA viruses that cause the flu.

Animal viruses

Viruses that can be transmitted from animals to humans, known as zoonotic viruses.

Plant viruses

Viruses that infect plants and are often ingested through dietary intake.

Vibrio cholerae

A phage that is harmful to humans and is the causative agent of cholera.

Viriods

The smallest known infectious agents, consisting of a short strand of circular, single-stranded RNA without a protein coat.

Prions

Infectious agents that consist entirely of protein and cause diseases in animals and humans.

Mutation

Heritable change in a DNA sequence that can lead to a change in phenotype; can occur spontaneously or via horizontal gene transfer.

Mutant

A cell or virus derived from the wild-type strain that carries a nucleotide sequence change.

Genotype

Genetic composition of an organism (genetic blueprint).

Phenotype

Observable physical or biochemical traits of an organism (observable characteristics).

Selection

A powerful genetic tool that allows the isolation of a single mutant from a population of millions/billions of cells (selectable mutations).

Screening

Isolation of non-selectable mutants requires laborious, time-consuming screening (examining large numbers and looking for differences).

Silent mutation

Change the nucleotide sequence, but do not affect the amino acid sequence of the encoded polypeptide so do not change the phenotype.

Missense mutation

Change the sequence of amino acids in a polypeptide as a result of nucleotide changes; can affect protein structure -> change the phenotype.

Nonsense mutation

Change the nucleotide sequence to a stop codon; typically results in truncated (incomplete) proteins that lack normal activity.

Same-site revertants

Phenotype/activity-restoring mutation occurs at the same site as the original mutation.

Second-site revertants

Phenotype/activity-restoring mutation occurs at a different site in the DNA than the original mutation.

Suppressor tRNAs

tRNAs that can suppress nonsense mutations by changing the anticodon sequence to base-pair with a stop codon.

Chemical mutagens

Substances that cause mutations through nucleotide base analogs or alkylating agents, leading to DNA sequence changes.

Radiation

Energy that can cause mutations in DNA, including nonionizing (UV) and ionizing radiation (X-rays, cosmic rays, gamma rays).

Transformation

free DNA released by one cell is taken up by another cell

Transduction

DNA transfer mediated by a virus

Conjugation

DNA transfer involving cell-to-cell contact and a conjugative plasmid in the donor cell

Homologous recombination

Process that results in genetic exchange between homologous DNA sequences from two different sources

RecA

Essential protein for homologous recombination

Holliday junction

Intermediate during homologous recombination that can be resolved in either direction

Molecular Koch's postulate

The suspected causative agent must be absent from all healthy organisms but present in all diseased organisms

Transduction frequency

Used in the past to map genes on the chromosome

Phage conversion

Alteration of the phenotype of a host cell by lysogeny

Hfr strains

Strains that facilitate conjugation and DNA transfer

F plasmid

An episome that can integrate into the host chromosome

Insertion elements

Simplest transposable elements, ~1000 nucleotides long with inverted repeats

Transposons

Larger than IS elements but have the same two essential components

Conservative transposition

Transposon is excised from one location and reinserted at a second location; copy number remains constant

Replicative transposition

A new copy of the transposon is produced and inserted at a second location while the original remains

Transposon mutagenesis

Used to identify genes involved in biofilm formation

Genetic engineering

Using in vitro techniques to alter genes in the laboratory

Insulin

The first human protein produced in bacteria, crucial for treating diabetes

Human growth hormone

Used to treat growth abnormalities, cloned from mRNA and expressed in bacterial systems

Erythropoietin

Hormone that stimulates red blood cell production, produced in engineered microbes

Transgenic organisms

Genetically engineered plants or animals containing a gene or genes from other organisms

Gene mining

The process of identifying and isolating potentially useful genes from the environment

GMO biocontainment mechanism

Genetically engineered to code for synthetic amino acids which must be supplied

TAG codons

Stop codons that can be replaced to facilitate biocontainment in GMOs

Transposon insertion

Causes a change in the gene sequence leading to mutation

Biofuel production

Engineering microbes to convert cellulose to sugars and ferment them to ethanol

Antibodies in microbes

Certain antibodies can be produced in microbial systems for therapeutic purposes

Vaccines from engineered microbes

Produced using genetically engineered microbes that express specific antigens