Week 3: microbial classification/ evolution

Question 1

taxonomy

Answer 1

classification of organisms into groups

Question 2

classification def

Answer 2

arranging groups into taxa

Question 3

nomenclature

Answer 3

assignment of names to taxonomic groups, following published rules

Question 4

identification def

Answer 4

process of defining that a particular isolate belongs to a taxon

Question 5

phylogeny def

Answer 5

evolutionary relatedness of species

Question 6

bacterial taxonomy

Answer 6

domain, phylum, class, order, family, genus, species

Question 7

microbial species

Answer 7

collection of strains that share many stable properties and differ significantly from other groups

Question 8

biovars

Answer 8

biochemical variants

Question 9

morphovars

Answer 9

morphological variants

Question 10

serovars

Answer 10

serogenic (immunologically reactive variants

Question 11

pathovars

Answer 11

pathogenic variants

Question 12

core genome

Answer 12

set of genes found in all members of a species
minimal set of genes required by microbes to live

Question 13

accessory genes

Answer 13

more recently acquired non-essential genes
enables colonisation of new niches
not possessed by all strains of a species

Question 14

Pan genome

Answer 14

combination of all genes found within a species

Question 15

horizontal gene transfer transformation

Answer 15

bacterium picks up genetic material through cell wall from external surroundnings

Question 16

horizontal gene transfer transduction

Answer 16

DNA transmitted via a bacteriophage

Question 17

horizontal gene transfer conjugation

Answer 17

direct contact, exchange of plasmids

Question 18

phenetic classification

Answer 18

compares phenotypic similarities between organisms

Question 19

Genotypic classification

Answer 19

compares genetic similarity between organisms

Question 20

types of phenetic class

Answer 20

morphological, physiology, metabolic, biochemical, ecological

Question 21

types of genotypic class

Answer 21

nucleic acid base composition, nucleic acid hybridization, genomic fingerprinting, nucleic acid sequencing, multiocus sequence analysis and typing, 16s rRNA sequencing

Question 22

viruses classification system

Answer 22

baltimore which classfies on genome type and replication strategy

Question 23

class 1 dsDNA viruses

Answer 23

large genomes
Most replicate in the host cell nucleus, some replicate in the cytoplasm (bacteriophages and poxviruses replicate in the cytoplasm)

Question 24

class 2 ssDNA viruses

Answer 24

Genome contains one strand of DNA, can have linear, circular genomes or circular multicomponent genomes
Infect bacteria, mammals and plants

Question 25

class 3 dsRNA viruses

Answer 25

Genome two RNA annealed together and can be split into parts
Infect bacteria, animals plants, fungi and protozoa
cannot function as mRNA for translation, transcription must first occur to produce ssRNA molecules, use and carry viral encoded RNA-dependent and RNA polymerase for transcription and replication

Question 26

class 4 + sense ssRNA viruses

Answer 26

Viral genome has same polarity as mRNA
Many can be translated directly by ribosome into proteins, use virus encoded RNA dependent RNA polymerase to replicate their genome (do not carry) , replication often occurs in cytoplasm of infected cell

Question 27

class 5 - sense ssRNA viruses

Answer 27

Genome consists of ssRNA of opposite polarity to mRNA, cannot be directly translated into a protein, before it can occur, it must be copied into +ve sense mRNA
Need to carry RdRp in virus particle

Question 28

class 6 RNA reverse transcribing viruses

Answer 28

Retroviruses have ssRNA but replicate via dsDNA intermediate
E.g. HIV, carry reverse transcriptase and intergrase in virus particle, RT converts the ssRNA to dsDNA and intergrase intergrates into host chromosome

Question 29

class 7 DNA reverse transcribing viruses

Answer 29

Have a cccDNA genome but replicate via a ssRNA
Need to carry reverse transcriptase but occurs inside the virus particle

Question 30

how do ICTV classify viruses

Answer 30

families classified on nucleic acid type, presence or absence of envelope, symmetry of capsid, dimesnions of viroid