Michaelmas diversity of life

what is the molecular soup idea of the origin of life?

• organic molecules were formed in early oceans due to the release of heat by the reaction of atmospheric gases (catalysed by UV light and lightning)

• these condensed into polymers

• by chance, a self-replicating polymer formed, which took over the molecular soup due to exponential growth

• random changes that improved the speed of replication would be more successful and selected for by evolution

• most believe this polymer would have been RNA, because it can fold into ribozymes which can catalyse RNA replication (whereas DNA needs auxiliary protein catalysts)

what are the problems with the molecular soup idea and what is an alternative?

• the oceans would have been very dilute, to the point that it would be rare for two nucleotides to meet to polymerise, let alone enough nucleotides to form a catalytic chain (50-60 nucleotides) of RNA

• hence, the process would be very slow

• also, RNA is actually unstable in water (unlike DNA)- hydrolysis is more likely than condensation because it is exothermic

some believe clay mineral layers could be the formation site of RNA, instead of the ocean:

• molecules are able to bind to clay silicates, which concentrates them closer in order to polymerise

• repeat cycles of hydration and dehydration would reduce the likelihood of hydrolysis so that RNA formation is favourable

what are the problems with the RNA world theory?

• relying on wet-dry cycles would make the process incredibly slow

• many unwanted organic molecules would also be present in the molecular soup/minerals that would pollute the process- so why would RNA be made of just three components

• we don’t know how the formation of RNA would lead to the formation of cell membranes + metabolism to produce real life

what is an alternative to the RNA world theory?

• membranes could have come first because they are self-assembling structures

• amphiphiles (molecules that are both hydrophilic and hydrophobic) can form bilayers that can result in stable vesicles/micelles

• phospholipds are too complex to have formed independently but simpler amphiphiles like fatty acids could have

• however, the membrane of this proto-cell provides no functional advantage for RNA synthesis and replication

what is the spontaneous metabolism theory?

• life could have begun with a simplified metabolism that has been seen to occur spontaneously, without protein catalysts

• this process produces fatty acids (for membranes), pyruvate (for metabolism), RNA and proteins from CO2 and H2O

• however it requires very high temperatures and pressures and redox-active metals (like Fe and Ni) to act as catalysts, so the clay mineral theory can’t apply

• alkaline smokers are the main candidate as a place for this to occur:

  • minerals rich in iron and nickel are formed by serpentinization and assemble into networks of interconnected micropores

  • the reaction also generates heat, hydrogen gas, and hydroxide ions (alkaline)

  • there is high pressure due to being at the bottom of the ocean, so all the conditions for spontaneous metabolism are satisfied

  • the metabolism would be catalysed by the minerals and driven by a proton gradient between the acidic seawater (due to dissolved CO2) and the alkaline hydrothermal fluid

however, the self-assembly of membranes would immediately isolate the metabolites from the mineral catalysts

what are the different kinds of flagella organisation?

what are linkage equilibrium and disequilibrium?

• linkage equilibrium is found in sexual organisms- this is where different genes are randomly assorted in a population

• linkage disequilibrium is found in asexual organisms- this is where genes are associated non-randomly in a population eg. two genes are more likely to be found together because one parent organism has both, so its whole lineage will also have both- particular patterns will accumulate in different lineages

• in bacteria these exist on a continuum depending on the degree of horizontal gene transfer and recombination

what is Muller’s ratchet?

• Muller’s ratchet is a case of reductive evolution- small asexual populations (without recombination) are vulnerable to the accumulation of deleterious mutations

• ultimately these species will go extinct, because they evolve themselves into a corner and can’t be ‘rescued’ by recombination

• in asexual populations, genomes are inherited as indivisible blocks, so that an organism inherits the same mutations as its parent, more mutations occur, and it passes the entire increased mutational load onto its own offspring

• one generation will never have fewer mutations than the generation before, so they accumulate

• this is greater in small populations because they are more affected by genetic drift, so less mutated lineages may die out due to stochastic changes

as the prokaryotic genome size increases, how do the proportions of different kinds of genes change?

as the genome size increases:

• the proportion of genes for DNA translation, replication and repair decrease- new proteins (eg. kinds of polymerase) aren’t needed as the genome increases, the process doesn’t change

• the proportion of genes for metabolism and transport increases- the metabolic diversity increases so the organism can deal with a wider range of environments + becomes more resilient

• the proportion of regulatory genes increases- more structural genes mean more regulatory genes are needed to control transcription

why are bacterial coding sequences non-randomly arranged in the chromosome?

• coding sequences, particularly of more essential genes, are more likely to be encoded on the leading strand of the chromosome- there is a bias of coding locations in the chromosome

• this is because when simultaneously replicating and transcribing DNA, head-on collisions between the machinery are much less likely in the leading strand than the lagging strand- this forms truncated products, so it is selected against

• ie. DNA polymerase from replicating the lagging strand (forming the Okazaki fragments) can collide head-on with RNA polymerase from transcribing the newly formed DNA

what are pangenomes?

• the pangenome is the entire array of genes available to a bacterium- essentially, the gene pool of a species/group

• bacteria have a core genome and an accessory genome, comprising the genes in the population which each individual/strain may or may not have

• most bacteria have an open genome (along a continuum) because horizontal gene transfer is widespread (compared to human closed genomes, where most of our genes are the same, and the differences are pretty superficial)

how can bacteria be characterised?

• staining + microscopy to observe morphology

• responses to anti-microbial compounds, pHs and temperatures

• serology- applying antibodies and determining responses

• metabolic phenotyping- using strips with different metabolites to produce a metabolic fingerprint

• MALDI-TOF- mass spectrometry of all proteins found to obtain a protein fingerprint

• DNA sequencing- comparing single genes, multiple loci or whole genomes using gel electrophoresis/Sanger sequencing

what is a single locus that is often sequenced for bacterial classification?

• the 16S rRNA gene- codes for a highly conserved ribosomal RNA strand

  • contains universal regions that can be easily used to generate primers for PCR and Sanger sequencing

  • however, this high conservation means it has a limited resolution- to species level at best

• it is a single gene so it is rapid, but for a higher resolution multi-locus sequencing is needed (normally conserved housekeeping genes are used)

• sometimes there can be multiple gene copies in a cell, so there may be variation within an isolate

what do we predict luca was like?

• anaerobic- all oxygen was reduced into water in the early world

• CO₂ fixing

• H₂ dependent

• N₂ fixing

• thermophilic

• dependent on transition metals

these traits are all consistent with a hydrothermal setting

why is the surface origin of life hypothesis not valid?

• UV light, low pressures and the possibility of drying up makes them unstable and unfavourable environments for the origin of life

• subsurface hydrothermal vents are actually ideal, they produce large temperature gradients, mineral gradients etc

what are the mitochondria early and mitochondria late hypotheses?

• these are two hypotheses describing the endosymbiotic event introducing an aerobic bacterium into another host, resulting in a eukaryotic cell containing a mitochondrion

• the mitochondrion late hypothesis (A) assumes that the host, a protoeukaryote, was already quite developed (endosymbiotic event occurred late in its development), as it had evolved the process of phagocytosis of the bacteria

  • however, in this theory, the host would have had to exist and evolve for a long period, solely living off of fermentation as its metabolism, which is very weak

• the mitochondrion early hypothesis (B) assumes that the host, an archaeal cell, was not very developed (no nucleus yet), and instead it lived in a metabolic symbiosis with a bacterium

  • this bacterium would have produced CO₂ and H₂ in its metabolism, and this hydrogen provided vital fuel for the metabolism (methane-producing) of the archaea, in a highly dependent relationship, until eventually they merged

what are lichens and what are the roles of the symbionts?

• lichens are mutualistic associations of a fungus with a cyanobacteria or algae

• the mycobiont (fungus) is a macrobe, so it can form a large structure which protects the photobiont and absorbs minerals

• the photobiont (bacteria or algae) photosynthesises, fixes nitrogen and synthesises organic nutrients

what are the roles of legumes and Rhizobium in their symbiosis?

• the bacterium fixes nitrogen from the atmosphere into bioavailable nutrients

• the plant provides the bacterium with carbohydrates, protects it within root nodule structures, and creates a specific microenvironment

  • it produces the leghaemoglobin protein, which buffers the free oxygen concentration- this keeps it high enough to allow for aerobic respiration, but low enough to allow the oxygen-sensitive nitrogenase enzyme to work

what are the three types of insect endosymbionts?

obligate mutualists:

• these are domesticated within the host and can’t survive outside it (next best thing to an organelle/organ)

• they are restricted in bacteriomes produced by the host

• dependent on host-based mechanisms for transmission

facultative symbionts:

• resemble pathogens as they invade cells in uninfected hosts (and can establish maternal inheritance) and are erratically distributed

• not required for host reproduction but may confer benefits

reproductive manipulators:

• parasites that spread by maternal inheritance, and manipulate proportions of female offspring to spread through a population

• eg. infected males sterilise uninfected females, so that offspring from infected females individuals are more successful

what are two examples of a intracellular insect endosymbionts?

• Buchnera are an obligate intracellular endosymbiont of aphids (mutualist)

• these are vertically transmitted through the ovary cells

• they live in specialised bacteriocyte cells (obligate- they are unculturable)

• the host aphid supplies energy, carbon and nitrogen

• the symbiont produces amino acids, especially tryptophan

• Wolbachia is a large and highly prevalent group of intracellular endosymbionts

• in some cases (eg. nematodes) they are mutualists

• often they are reproductive manipulators, altering host sex ratios

how do Wolbachia alter host sex ratios?

1. feminisation of genetic males from infected mothers

2. causing parthenogenesis (where only female offspring can be produced)

3. killing of infected males

4. cytoplasmic incompatibility so that infected males can’t mate with uninfected females

these methods all increase the proportion of infected females in the population, because vertical transmission can only occur through infected females

what are holobionts?

• the macrobe and its microbiome combined comprise the holobiont (metaorganism)

how do the measles and varicella zoster viruses behave differently?

measles is an acute infection:

• hosts infected with the measles virus develop life-long immunity to it, so it can only survive in large populations

• otherwise it runs out of susceptible hosts and dies out as it has no other reservoir

chickenpox/shingles is a chronic infection:

• hosts infected with the varicella zoster virus (VZV) develop chickenpox

• the pathogen then remains in a quiescent state in the host

• it can be reactivated to cause shingles

how can microbes cause cancers?

• certain viruses and bacteria can cause cancers directly or indirectly eg. by the alteration of host cells or the production of toxic substances

• eg. human papillomaviruses (HPV), which cause cervical cancer

• eg. devil facial tumour disease (DFTD) and canine transmissible venereal tumour (CTVT)

what are prions?

what is the osmotrophic mode of nutrition?

• most fungi (excluding microsporidia and cyptomycota, no osmotrophism or hyphae, hence debatable) secrete enzymes into their environment to depolymerise + digest nutrients extracellularly

• eg. cellulose, proteins and lignin (partially)

• this relies on a high surface area to volume ratio- restricts hyphal diameter

what is the structure of the fungal cell wall?

• thick, rigid chitin inner layer

• glucan layer

• glycoprotein-rich outer layer

• the lipid bilayer normally contains ergosterol

what is the structure of fungal hyphae?

• tube-like eukaryotic cell structures that extend at the tips and branch

• can be compartmentalised with septa that allow for isolation, differentiation and mechanical strength

• non-septated hyphae are coenocytic and have multiple nuclei in one cell

• when branching, two adjacent hyphae can avoid eachother by negative autotropism or can rejoin together during anastomosis by positive autotropism

how is hyphal colony growth regulated?

• at the centre, the hyphae are more densely packed and fused together by anastomosis + positive autotrophy for transport and exchange

• moving further out, the hyphae become exploratory, unbranched and sparser, governed by negative autotrophy for space-filling

• these are called radial colonies

• as such, branching frequency is controlled by environmental conditions

  • under stress more exploratory hyphae are produced

  • under excess colonies become more dense

other growth forms exist- unicellular division by budding and binary fission in yeasts, though some species are dimorphic and change their growth form depending on the environment

what are the forms of asexual and sexual reproduction in fungi?

asexual:

• asexual production of spores

• anastomosis of genetically identical hyphae

• unicellular division in budding yeasts

sexual:

• spore production by fusion of gametes/2 haploid cells

• anastomosis, plasmogamy (cytoplasm fusion) and karyogamy (nuclear fusion) of genetically distinct but compatible hyphae

how do fungi survive in a haploid state?

• mutations are visible since genes are single copy

• but many hyphae are coenocytic, containing multiple nuclei- mutations can exist in the different nuclei, so multiple genotypes can exist at once and locally complement each other

• these heterokaryons are produced by anastomosis

  • the different nuclei increase genetic variation, so the phenotype depends on the interactions between the nuclei and can be spatially different/localised

  • however, hyphae may not be vegetatively compatible for anastomosis, dependent on the het (heterokaryon) loci and may die instead

what are viruses?

• obligate intracellular parasites

• viruses are infectious microbes consisting of a segment of nucleic acid surrounded by a protein coat

• they can’t replicate alone, they must infect cells and use the host cell machinery to replicate

• metabolically inert, so they rely on host cells for energy, metabolites and protein synthesis

what are the structures of viruses?

• tightly packed viral DNA/RNA is surrounded by a protein capsid

• viruses that infect eukaryotic cells normally have an envelope around the capsid (derived from the host cell) and spikes to attach to specific cell surfaces

• whereas viruses that infect prokaryotes normally have a ‘naked’ capsid

• some viruses, bacteriophages, have mechanisms to inject their viral genome into the host

on what basis are viruses classified under baltimore classification? what are other methods of classification?

• based on the route of information transmission from the genome to the mRNA

• dependent on whether they use double/single (sense/antisense) stranded DNA/RNA

• different pathways and proteins are used by each class

• viruses in a class aren’t necessarily closely related, but behave in the same way and have similar mutation rates:

  • viruses which use reverse transcriptase or RNA-dependent RNA polymerase (RdRp) are very error-prone and have higher mutation rates

  • double stranded DNA viruses have lower mutation rates

• alternatively, taxonomy and phylogeny can be used by tracking mutations in superviral hallmark genes (VHGs), which encode for core viral replication proteins

what are the three hypotheses for where new zoonotic viral variants come from?

• the virus circulates and mutates in an unsampled population, then spills over into a surveilled population

• the virus spills over into other species, mutates then spills back into humans

• long chronic infections of immunocompromised individuals allow for the rapid evolution of the virus- this is the favoured hypothesis

this is how we believe new variants of concern (now called major variants) of covid-19 evolved

• this hypothesis is most popular because it is the only one which favours mutations in the spike genes that allow new variants to cause waves of infections by binding to host cells and evading host antibodies better

what is reassortment and how does it occur in viral DNA?

• the genome of the virus is segmented (eg. influenza genome is in 8 segments)

• the host cell is coinfected by two different strains of virus

• this produces viruses with a mixture of segments from each virus

• reassortment is a kind of recombination (recombination refers to the exchange of fragments of genes)

• recombination creates mosaic genes, while reassortment creates novel combinations of existing genes (chimeric genomes)

what are antigenic drift and shift and which forms of influenza use each?

antigentic shift is only seen in influenza A (because B only infects humans), and is much less common

• new subtypes are created due to reassortment (coinfection of a host cell by two different strains, usually strains that have different target host species)

• this usually causes pandemics due to little immunity in the host population

antigenic drift is seen in influenza A and B, and is why we need new vaccines each year

• small changes driven by mutations result in gradual change

what kind of virus is faba bean necrotic stunt virus?

• fbnsv is multipartite- each gene segment is packaged into a different virion

• all the separate virions need to infect one plant, so that all segments are present, for a productive infection

• we think that each infected cell rarely receives the full set of segments (low multiplicity of infection), but complementation across the cells allows the virus to be produced

• this virus is transmitted by aphids

what is the life cycle of the lambda phage?

in the lysogenic cycle:

• the virus attaches to its target cell, E.coli and viral contents are released into the cytoplasm

• the viral DNA integrates into the host genome where it stays dormant and is replicated as the host genome is replicated

• this is favoured when host abundance is low, as killing host cells is unfavourable

in the lytic cycle:

• the viral DNA is excised from the host genome

• proteins eg. polymerases are synthesised from the viral DNA, which are used to replicate the genetic material

• new virus particles are assembled and are released when the cell lyses

the switch from the dormant lysogenic cycle to the productive lytic cycle can be spontaneous or caused by a stimulus

in the chronic life cycle:

• the virions are continually released by exocytosis, so that the cell is not killed and continues to make new viruses

what are viral shunts and shuttles?

• viruses that infect plankton are involved in marine carbon and nutrient cycling

• viral shunt is when infected phytoplankton cells are lysed, releasing the cellular contents as dissolved organic matter in the nutrient cycling loop

• viral shuttle is when the lysis of infected cells releases large polymers that aggregate and sink to the deep ocean, cycling carbon

what are virophages and satellite viruses?

• virophages require co-infection with a giant virus and replicate inside this giant virus’s ‘factory’ (and the giant virus replication is reduced) eg. sputnik

• satellite viruses require co-infection with a helper virus that provides a certain protein (and the helper virus infection becomes more severe) eg. Hep D

what are the different hypotheses for why multicellularity evolved multiple times?

hypothesis 1: it’s sometimes better to be a big organism

• swimming further?- unlikely, cells mostly moved by currents

• harder to be eaten?- unlikely, there weren’t many bigger cells to at as predators

• catching more food?- yes, could set up a local water current to funnel cells for food eg. choanoflagellate protist changes from single-cell to colonies when given specific bacteria as food

hypothesis 2: it’s sometimes better to split up cell functions

• the germ cells are the most important and this genetic material must be protected from damage eg. UV radiation

• germ cells also seem to be modified to have a lower rate of mutations per mitotic cycle than somatic cells

hypothesis 3: it’s less efficient for flagellated cells to be the ones dividing- ‘flagellar constraint’

• when an animal cell divides, it has to depolymerise its flagellum because the flagellar basal body microtubules are the same structure as the centrosome needed for mitosis- both can’t be present at the same time

• the cell would have to retract the flagellum, divide, and re-grow the flagellum

• in this process motility is lost, so the cell might sink/not get any food

• unlikely, some single-celled organisms can overcome this by doing mitosis without the same centrosome, so not proven

hypothesis 4: it allows for self-cannibalism in famine situations

• when food becomes scarce, a single-celled variant would just die

• however, a multicellular variant could self-cannibalise certain cells by transferring nutrients to ensure at least a few survive, which can regrow when food returns

• this is the case for some animals eg. flatworms and hibernating mammals (fat cells are used in scarcity conditions)

since multicellularity evolved multiple times, different hypotheses could be true for different species

what are choanoflagellates?

• choanoflagellates are the closest living single-celled relatives to animals

• they are marine/freshwater protists that feed on bacteria

• they have a long flagellum surrounded by a collar of actin-supported tentacles, which is a similar structure to sponge choanocytes (feeding cells) inside chambers

• under certain conditions (eg. specific bacteria supplied), choanocytes can switch from a single-celled to a colony lifestyle, but are not multicellular

what makes animals true multicellular organisms?

• they have many cells, and many different types of cells

• they have specialised haploid sperm and egg cells of very different sizes

• this allows for different investment of resources

• epithelial cells are very unique and only found in animals:

  • they can form watertight sheets with tight junctions that solutes can’t pass, so solutes have to pass through the cells

  • this means ion concentrations can be tightly controlled and biochemical reactions can be compartmentalised

• this transition to produce multicellular organisms potentially required a thousand new genes