Micro Final Exam

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89 Terms

1

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.

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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.

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3

Class 3

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

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4

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.

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5

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.

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6

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.

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7

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.

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8

Viruses first appearance

~4 billion years ago - after cells.

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9

RNA world hypothesis

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

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10

Gene transfer mechanism

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

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11

Lytic and latent evolution

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

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12

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.

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13

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.

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14

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.

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15

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.

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16

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.

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17

Adenoviruses replication

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

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18

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.

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19

Herpesviruses replication

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

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20

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.

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Coronaviruses replication

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

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22

Rabies virus replication

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

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23

Influenza virus replication

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

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24

Hepadnaviruses replication

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

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25

Reoviruses replication

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

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26

Phages contribution to ocean ecology

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

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27

Nutrient cycling

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

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28

Genetic exchange

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

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29

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.

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30

Biogeochemical processes

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

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31

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.

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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.

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33

PAMP and DAMP

What is a PAMP and DAMP?

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34

PAMP

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

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35

DAMP

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

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36

Bacteriophages

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

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37

Adenoviruses

DNA viruses that cause respiratory infections.

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38

Herpesviruses

DNA viruses that cause herpes.

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39

Papillomaviruses

DNA viruses that cause skin warts and cervical cancer.

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40

Rhinoviruses

RNA viruses that cause the common cold.

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41

Coronaviruses

RNA viruses that cause COVID-19.

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42

Influenza viruses

RNA viruses that cause the flu.

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43

Animal viruses

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

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44

Plant viruses

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

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45

Vibrio cholerae

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

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46

Viriods

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

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47

Prions

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

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48

Mutation

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

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49

Mutant

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

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50

Genotype

Genetic composition of an organism (genetic blueprint).

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51

Phenotype

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

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52

Selection

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

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53

Screening

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

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54

Silent mutation

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

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Missense mutation

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

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Nonsense mutation

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

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Same-site revertants

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

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58

Second-site revertants

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

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59

Suppressor tRNAs

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

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60

Chemical mutagens

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

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61

Radiation

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

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62

Transformation

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

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63

Transduction

DNA transfer mediated by a virus

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64

Conjugation

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

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65

Homologous recombination

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

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66

RecA

Essential protein for homologous recombination

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67

Holliday junction

Intermediate during homologous recombination that can be resolved in either direction

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68

Molecular Koch's postulate

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

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69

Transduction frequency

Used in the past to map genes on the chromosome

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70

Phage conversion

Alteration of the phenotype of a host cell by lysogeny

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71

Hfr strains

Strains that facilitate conjugation and DNA transfer

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72

F plasmid

An episome that can integrate into the host chromosome

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73

Insertion elements

Simplest transposable elements, ~1000 nucleotides long with inverted repeats

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74

Transposons

Larger than IS elements but have the same two essential components

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75

Conservative transposition

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

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Replicative transposition

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

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77

Transposon mutagenesis

Used to identify genes involved in biofilm formation

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78

Genetic engineering

Using in vitro techniques to alter genes in the laboratory

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79

Insulin

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

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80

Human growth hormone

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

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81

Erythropoietin

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

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82

Transgenic organisms

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

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83

Gene mining

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

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84

GMO biocontainment mechanism

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

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85

TAG codons

Stop codons that can be replaced to facilitate biocontainment in GMOs

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86

Transposon insertion

Causes a change in the gene sequence leading to mutation

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87

Biofuel production

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

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88

Antibodies in microbes

Certain antibodies can be produced in microbial systems for therapeutic purposes

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89

Vaccines from engineered microbes

Produced using genetically engineered microbes that express specific antigens

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