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BIOL 322 > Midterm #1 > Flashcards

Midterm #1 Flashcards

1
Q

What are the characteristics of cells that point to LUCA?

A
  • DNA as genetic material
  • A,C,T,G and A,C,U,G for DNA and RNA bases
  • Three letter genetic code
  • Lipoprotein membranes in cell envelope
  • 20 core amino acids compose proteins
  • Translation: small subunit RNA, large subunit RNA, ribosomal proteins, tRNA
  • Transcription: RNA polymerase
  • Membrane transport systems: ABC transporters
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2
Q

What indications do we have that archaea are more closely related to eukarya than they are to bacteria?

A
  • Archaea and eukarya share more fundamental similarities
  • E.g., sensitivity to antibiotics means archaea and eukarya have similar ribosomes
  • E.g., more similar RNA polymerase
  • Transcription and translation
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3
Q

In terms of energy metabolism, what are the different types of energy sources?

A
  • Light (photo)

- Chemicals (chemo)

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4
Q

In terms of energy metabolism, what are the different types of electron donors?

A
  • Inorganic compounds (litho)

- Organic compounds (organo)

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5
Q

In terms of energy metabolism, what are the different sources of carbon?

A
  • Inorganic (mostly carbon dioxide) (autotroph)

- Organic (heterotroph)

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6
Q

Which photosynthetic reaction centres are in the following organisms?

  • Heliobacillus
  • Chloroflexi
  • Purple bacteria
  • Chlorobi
  • Cyanobacteria
A
  • Heliobacillus = RC1
  • Chloroflexi = RC2
  • Purple bacteria = RC2
  • Chlorobi = RC1
  • Cyanobacteria = RC1, RC2, chlorophyll
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7
Q

Describe the differences between reaction centre 1 and reaction centre 2

A
  • RC1 = Capacity to catalyze oxidation of hydrogen and highly reduced electron donors, likely first one to evolve
  • RC2 = Does not work with very reduced substrates like hydrogen, has higher affinity for sulfur or water
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8
Q

What are orthologs? What are paralogs?

A
  • Orthologs = same gene in two different species (separated by speciation event)
  • Paralogs = One cell has two copies of a gene (separated by duplication event)
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9
Q

Difference in bacteria/eukaryote membrane and archaea membrane

A
  • Bacteria/eukaryote: Ester-linked, G3P, fatty acids, bilayer
  • Archaea: Ether-linked, G1P, isoprenoid, can form monolayer
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10
Q

What are the two types of phototrophy?

A
  • Oxygenic: Produces oxygen (oxygen is terminal electron acceptor); electrons from ETC come from water
  • Anoxygenic: No oxygen production; electrons come from sources other than water
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11
Q

What are the two types of base pair substitutions?

A
  • Synonymous (silent): Codes for same amino acid

- Non-synonymous: Codes for different amino acid (missense) or codes for stop codon (nonsense)

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12
Q

In base pair substitutions, what are transitions and transversions?

A
  • Transitions: Interchanges of 2-ring purines or one-ring pyrimidines
  • Transversions: Interchanges of purines and pyrimidines
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13
Q

What are the three ways to exchange DNA during lateral gene transfer?

A
  • Conjugation
  • Transduction
  • Transformation
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14
Q

What are the two main steps involved in lateral gene transfer?

A
  • Foreign DNA must penetrate cellular envelope via transformation, conjugation, or transduction
  • Integration into the host genome via homologous recombination, heterologous recombination, of extrachromosomal maintenance and repair
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15
Q

Describe conjugation and the different ways it can occur

A
  • Exchange DNA through cellular contact
  • Bacterial donor with conjugative plasmid forms a connection with neighbouring cell (pilus)
  • DNA is sent through pilus and a complementary strand of the plasmid is made
  • Genomic material essentially “hitchhikes” on plasmid
  • In thermoacidophilic archaea, a UV inducible pilus promotes DNA exchange (stress inducible evolution)
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16
Q

Describe transduction and the three ways that it can occur

A
  • Exchange of DNA through a vesicle
  • Gene transfer agent can be used (phage-like particles that release without lysing the host)
  • DNA can be transported in cell vesicles (bud from cell membrane and transfers its contents when it finds another cell membrane)
  • Phage (this is the most common - transports DNA between two cells in protected vesicle)
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17
Q

Describe transformation and the necessary qualities of cells for this to occur

A
  • Uptake of “naked”/free DNA
  • Cells take up free DNA and insert it into their cytoplasm. This free DNA recombines with the chromosome
  • Cell needs to be naturally competent (needs a mechanism to uptake DNA from the environment - can take up DNA for food, repair, or genetic diversity)
  • Cells can also be artificially competent (pores made in membrane via lightning or calcium)
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18
Q

What are the four types of lateral gene transfer?

A
  • Novel acquisition (Gene x –> selection for function x –> novel adaptation)
  • Loss and regain (X function not needed –> gene lost –> X function needed again –> X function supplied by Y gene)
  • Homologous replacement (Antibiotic pressure –> Resistant form of X –> Possible recombination (2 gene copies) –> Loss of old X + hybrid copy) (gene is essential in this case)
  • Analogous replacement (Gene with the same function but a different protein sequence)
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19
Q

What are the two ways that DNA can get into chromosomes? What are the differences between these?

A
  • Homologous recombination: Requires sequence similarity (RecA will only bind similar sequences - only mechanism to do this)
  • Heterologous recombination: Does not require sequence similarity (uses a phage or integron to transfer DNA - many different mechanisms)
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20
Q

What are some examples of the interdependence of replication, recombination, and mutation?

A
  • Repairs stalled replication forks (homologous recombination)
  • Replication is required for many heterologous recombination events
  • Many mutations are caused by biosynthetic errors during DNA replication
  • Every type of mutation can occur during DNA replication
  • Same system is responsible for ensuring the accuracy of DNA replication and limiting homologous recombination (e.g., mismatch repair system)
  • No mobile genetic element is purely extra-chromosomal (integrons, lytic phages etc.)
  • Extra-chromosomal elements segregation is often coupled to chromosomal segregation (plasmids)
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21
Q

What is constitutive mutability? What does it lead to?

A
  • Permanently increase mutation rates
  • Leads to: Defects in mismatch repair system; changes in DNA polymerase (rare); changes in other proteins involved in DNA replication
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22
Q

The mismatch only recognizes strands of DNA that are what?

A
  • Methylated

- Non-methylated strands are destroyed

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23
Q

Give two examples of inducible mutability

A
  • The SOS response: Stress bacteria activates SOS system, leads to LexA being turned off and no longer regulating other genes, makes cell a temporary mutator by increasing homologous recombination etc…cell mutates fast = stress-induced mutation
  • The Growth Advantage in Stationary Phase (GASP) response: Specific to starvation, cells maintained at low concentrations, induction of Pol IV (mutate to cope with starving)
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24
Q

What are the three species concepts?

A
  • Biological (biospecies): Interbreeding natural populations (LGT in bacteria); recombination to mutation ration > 1; higher the ratio, greater the recombination
  • Ecological (ecospecies): Lineage occupying an adaptive zone (same niche); e.g., grouping by pathogenecity
  • Phylogenetic (phylospecies): Biological species forming a diagnosable monophyletic; take all genes that bacteria have in common and make phylogenetic tree based on ALL this information
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25
Q

Species definition: Morphospecies

A
  • Based on shape/movement
26
Q

Species definition: Taxospecies

A
  • Based on numerical taxonomy (battery of biochemical tests) - see how culture reacts
27
Q

Species definition: Genomospecies

A
  • “Strains with around 70% or greater DNA-DNA relatedness and with 5C or less change in melting temperature”
28
Q

Species definition: ribosomal rRNA (+ advantages and disadvantages?)

A
  • Small ribosomal subunit (higher than 97% sequence identity + DNA relatedness to be the same species)
  • Advantages: Universal, functionally conserved, slow and fast evolving regions, encodes an RNA molecule (not a protein), abundant in cells
  • Disadvantages: Limited resolution at fine phylogenetic scale, multiple copies, intragenomic heterogeneity, does not represent the whole genome
29
Q

MLSA and MLST?

A
  • Multi-locus sequence typing: Genotypic characterization of prokaryotes at infraspecific level (allelic mismatches of a small number of housekeeping genes to recognize distinct strains)
  • Multi-locus sequence analysis: Genotypic characterization of more diverse groups of prokaryotes using sequences of multiple protein-coding genes (uses cocatenated phylogenetic tree - puts genes together like one big gene and see how closely related strains are)
30
Q

In MLST, what are sequence types and single-locus variants (in allelic profiles)?

A
  • Sequence type (ST) = Unique set of alleles. Two bacteria with a single allele that is different (even if due to a single point mutation) belong to different sequence types
  • Single-locus variants (SLVs) = Two isolates differing at a single allele
31
Q

Recombination to mutation ratios: = 1 ; > 1 ; < 1 ?

A
  • = 1 : 50% mutation; 50% recombination
  • > 1 : Recombination causes more change that mutation
  • < 1 : Mutation causes more change than recombination
32
Q

Species definition: Whole genome

A
  • “Core” set of genes found in all strains of species

- “Auxilliary” set of genes found in different subset of all strains

33
Q

Species definition: Average Nucleotide Identity

A
  • Average nucleotide identity of all protein-coding genes shared by two different bacteria (core genome comparison). Greater resolution that 16S rRNA sequencing and MLST
  • Species with 95% ANI correlate very well with DNA:DNA hybridization (70%) (much easier to get ANI)
34
Q

Species definition: Core genome phylogeny

A
  • Concatenated phylogeny based on all protein-coding genes shared by two organisms
  • All genes the have in common put onto phylogenetic tree
35
Q

Species definition: Genome composition

A
  • Express as a % of conserved genes between two organisms
  • Calculated by # genes in core genome / # genes in whole genome
  • Gene content similarity / conserved DNA
  • Does not correlate well with ANI
36
Q

What does high ANI and high gene content similarity reflect in bacterial populations?

A
  • High ANI = evolutionary relatedness

- High gene content similarity = ecological relatedness

37
Q

What is a polyphasic taxonomy?

A
  • Assembles and assimilates many levels of information and incorporates many distinct portions of information to yield a multi-dimensional taxonomy
  • 95% 16S rRNA, 70% gene content, 95% ANI and phenotypic features that agree with genotypic definition
38
Q

Vibrio sp.

A
  • V. coralliilitycus (bleaches corals - regulated by temperature)
  • V. fischeri (found in squids, creates light to match light of moon to mask shadow)
  • V. cholera (toxin makes cells lose water)
39
Q

Different intracellular parasites and symbionts?

A
  • Mycoplasma, Sulcia, Chlamydia, Proteobacteria, Rickettsia, Buchnera, Baumannia
40
Q

Buchnera aphidicola

A
  • Obligate symbiont
  • Very small genome
  • Lives in specialized aphid cells
  • Overproduces amino acids from sugars (can’t repair DNA, no lipopolysaccharides)
41
Q

Sulcia muelleri and Baumannia cicadellinicola

A
  • Leafhopper symbionts
  • Sulcia supplies amino acids
  • Baumannia supplies vitamins and cofactors
42
Q

Chlamydia

A
  • Obligate intracellular parasite
  • Requires host eukaryotic cell to replicate (elementary bodies (can’t replicate) infect host, form into reticular bodies (can replicate), binary fission, transformed back into elementary body, released)
43
Q

Mycoplasma and Cytoplasma

A
  • “Gracilicutes” = thin cell wall, little peptidoglycan, gram negative
  • “Firmacutes” = thicker cell wall, more peptidoglycan, gram positive
  • “Mollicutes” = no cell wall
44
Q

Rickettsia

A
  • Closely related to mitochondria

- Requires animal host cell to be able to replicate (can only replicate in host cytosol)

45
Q

Pelagibacter ubique

A
  • Alphaproteobacteria
  • 50% of cells in temperate water
  • Photosynthetic (important in carbon cycle) - not a normal photosynthetic apparatus though, proteorhodopsin based phototrophy
  • Very small genome for free-living bacteria
  • Carotenoid pigments
46
Q

Myxobacteria (deltaproteobacterium) - Sorangium cellulosum

A
  • Very large genome because it encodes complex behaviour
  • Forms very complex structures
  • Complex, multicellular structures with different cell types in bacteria = cellular differentiation (fruiting bodies!)
  • Independently evolved in bacteria and eukarya
  • Can remotely sense objects and hunts prey in coordinated fashion
47
Q

Deinococcus radiodurans

A
  • Highly pigmented
  • 4 chromosomes (condensed nucleoid maintains structure after irradiation)
  • Active DNA repair systems
  • High levels of manganese
  • Keeps DNA double stranded
  • Convergent evolution with other radiation resistant species (but not lateral gene transfer because it is not the same gene encoding this)
48
Q

Shigella

A
  • Human pathogen (destroys epithelial cells that form intestinal mucosa)
  • Releases toxin
  • Only differentiated from E. coli because of a virulent phenotype (acquired plasmid that allowed it to be pathogenic to humans - lateral gene transfer)
  • Gained functions by losing genes (Evolution by loss)
49
Q

Thermotoga

A
  • Heterotrophs that live at a variety of temperatures
  • Complex trait that has evolved from convergent evolution
  • No isolates
  • Low temp = mesothermotoga
50
Q

Caulobacter - Caulobacter crescentus

A
  • Alphaproteobacteria
  • Cellular differentiation (stalk and flagella) = derived trait
  • Complex life cycle
  • Asymmetrical division (also found in Bacillus subtilis)
51
Q

Bacillus

A
  • Model system for sporulation

- Triggered by lack of food (no other environmental stress)

52
Q

Paenibacillus

A
  • Complex social behaviour
  • Form vortexes (leave high density areas)
  • Cell to cell signaling
53
Q

Helicobacter pylori

A
  • Epsilon proteobacteria
  • Gastric ulcer patients
  • Chemotaxis through mucous toward epithelial cells in stomach (higher pH)
  • Pathogenecity from Cag pathogenecity island (type IV secretion systems inject toxins; cagA encodes protein that disrupts host cell activity)
54
Q

Bdellovibrio and Daptobacter

A
  • Predatory bacteria
  • Kill other bacteria
  • Likely convergent evolution between the two
55
Q

Streptomyces

A
  • Actinobacteria
  • Filamentous bacteria with linear chromosomes
  • Hyphae is reproductive structure
  • Produces multiple spores for reproduction (different from Bacillus spores)
  • Incredible secondary metabolite producers - source of many antibiotics today
56
Q

Cyanobacteria

A
  • Evolve spores (independent of Bacillus)
  • Some can fix nitrogen (heterocysts) = cellular differentiation and complex behaviour
  • Connections between cells…multicellular?
57
Q

Symbiotic relationship between ANME-2 and Desulfovibrio?

A
  • Methane-oxidizing archaea (produces energy)

- Sulfate-reducing bacteria (“breathe” sulfate)

58
Q

Thermoplasma

A
  • Facultative anaerobe
  • Grows best at 55-60C and pH 0.5-4
  • Can change shape
  • No cell wall, just a cell membrane
59
Q

Haloarchaea (Haloquadratum walsbyi)

A
  • Survives at 5M salt concentration
  • Proteorhodopsin - creates a proton gradient and uses phototaxis
  • H. walsbyi: Square cell shape, hard to cultivate, strict aerobe, gas vesicles made out of protein to help it float (non-motile)
60
Q

Ignicoccus (and nanoarchaea)

A
  • Lives at high pressure, high temperature (hydrothermal vents)
  • Nanoarchaea = small archaea that attaches itself to Ignicoccus (so divergent that no primers can amplify it)

BIOL 322 (2 decks)

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