Midterm Flashcards
What is HIV?
Human Immunodeficiency Virus, caused by a retrovirus.
What is a retrovirus? What is the enzyme responsible for aiding retroviruses?
A virus with an RNA genome that gets converted into DNA once it inserts into the host cell.
It uses reverse transcriptase for the conversion.
What are the two theories of origin for HIV1 and HIV2? Which theory is true?
1: HIV1+2 have a common recent ancestor and diverged due to host jumping (monkey to human)
2: HIV1+2 have independent origins; HIV1 came from chimps while HIV2 came from sooty mangabeys
Theory 2 has more proof backing it.
Why is reverse transcriptase so important in terms of evolution?
It converts RNA to DNA and the lack of proofreading ability leads to genetic variation, which may be beneficial to the organism.
What are the 3 factors that aid in genetic diversity among viruses?
- Mutations
- Recombination
- Reassortment
What are the genetic mechanisms that generate genetic diversity in HIV?
Mutations caused by reverse transcriptase
Recombination between 2+ viral strains
What are the genetic mechanisms that generate genetic diversity in influenza?
Mutations
Recombination
Reassortment (mix and match H and N antigens)
What makes influenza so dangerous to humans?
There are many different subtypes of H and N antigens, so by mix and matching the genes, antigenic shift occurs -> new strain.
The H and N antigens can also have point mutations -> antigenic drift.
What are the H and N antigens? What are their functions?
H - hemagluttinin antigen; host cell entry
N - neuraminidase antigen,lysis of the host cell
Why are HCN and formaldehyde important for abiotic synthesis?
HCN - nucleic acids and aldehydes
Formaldehyde - sugars.
What are the conditions for abiotic polymerization?
Monomers must be concentrated into one area, then condensation occurs with the help of a catalyst to turn them into polymers.
Why are scaffolds required for abiotic synthesis?
Scaffolds are surfaces that prefer the formation or accumulation of one enantiomer over another, they’re good for building up the concentration of certain enantiomers.
What makes deep sea vents attractive as an alternative to the early atmosphere as a site for abiotic synthesis of biomolecules?
They provided reducing conditions, energy, inorganic catalysts (FeS and NiS) and chemicals (CH4, NH4+, CO2, etc.).
What could be other sources of biomolecules during the early part of this planets evolution?
Meteorites - amino acids
Iron meteorites - NTPs
What is the relevance of stromatolites, microfossils and nanofossils to early evolution?
Stromatolites - rock-like formations of microbial mats
Microfossils - first signs of biological carbon assimilation
Nanofossils - 1/10th of the size of microfossils or “living cell types”
What type of deep sea vents are a source of thioesters?
White smokers
Why is there a recent interest in formamide for abiotic synthesis?
Dissociation of formamide can be used to make CN and NH radicals and produce all 4 nitrogenous bases (G, U, A, C) when simulating meteorite bombardment.
What compound allows for the abiotic formation of some nucleosides (without ribose)?
2-aminooxazole - can contribute atoms to both a sugar and a pyrimidine nucleobase, so no need for them to form separately
What is a black smoker?
Hydrothermal vents that generate sulfur-containing compounds.
What is a white smoker?
Hydrothermal vents that generate acetyl thioesters.
What is Wachtershauser’s iron-sulfur world theory?
Iron pyrite in deep hydrothermal vents could have provided scaffolding and energy through pressure/high temp for chemical reactions.
Some AAs, peptides and acetic acid can be produced under these conditions.
What is de Duve’s thioester world theory?
Thioesters could have provided the energy and catalytic framework for a protometabolic set of primitive chemical reactions.
What is the single origin theory?
The theory that metabolism and genetics evolved together in the prebiotic world. There are two different branches of this theory: metabolism first and replicators first.
Which researchers follow the “metabolism first” theory?
Wachterhauser, Oparin, Fox and Haldane
Which researchers follow the “replicators first” theory?
Orgel and Eigen
What is the double origin theory?
The theory that metabolism and replicators evolved separately then later merged together.
What are Freeman Dyson’s views on the origin of life?
He believed that life started out as two separate entities (double origin theory): metabolism and simple nucleic acid pools.
What is a viroid?
An infectious ssRNA that can replicate via rolling circle mechanism.
It relies on mechanical or insect activity for dispersal.
What is a virusoid?
An infectious ssRNA that can replicate via rolling circle mechanism.
It gets packed into other viral particles for dispersal (it’s a stowaway).
What is a coacervate?
Droplets of complex organic molecules.
What is a proteinoid?
Peptides that assemble into microspheres.
What is a liposome?
Droplets of lipids. Certain lipids can self-assemble into lipid bilayers.
What is an abiotic compartment? Why is it relevant for early molecular evolution?
Clay/crystal scaffolding that provides information (ie: inorganic replicator/information) to go along with the metabolism.
Explain how Eigen rationalized his RNA first theory.
RNA is more ancient than DNA:
- RNA doesn’t need primers
- Ribose is more common than deoxyribose
- RNA can fold into more thermodynamically stable structures
- RNA is the genetic material for some viruses
- RNA is an important intermediate for some biological processes (mRNA, tRNA, rRNA, RNAi)
- Both RNA sequence and structure can be used to do things like alter gene expression
What are Eigen’s hypercycles? What are some issues with it?
A hypercycle is a group of RNA pools (quasispecies) that promote and stabilize each others’ replication.
Some issues with hypercycles:
- a member of the hypercycle can be skipped over
- one member can be selfish and ignore the other members
- members must work at the same rate for the hypercycle to be efficient
- error rate too high
- parasites can compete for raw materials, space, catalysts
What is a quasispecies?
A mathematical model that describes the Darwinian evolution of self-replicating entities.
- allows for mutations/variation
- selection for efficient replication
- assumes raw materials are always present
What is Cairns-Smith’s clay first concept?
Clay provides a scaffold for organizing biological complexity.
- Can concentrate/organize biomolecules
- Crystals act as abiotic replicators
- Clay can act as physical barriers for isolating reactions, as well as provide scaffolds for catalysis
Elaborate on Higg’s concept of transitioning from a “dead” to a “living state”.
Monomers and polymers can convert to each other in a spontaneous reaction, but spontaneous decay also occurs.
The polymers need a catalyst to stay as polymers and transition from a dead state to a living state.
What is the Darwinian evolution of RNA molecules in terms of Spiegelman’s Q-beta system experiments?
Darwinian evolution in this experiment is the selection pressure exhibited by the RNA molecules in the continuous culture tubes growing shorter and shorter so that they could replicate faster. They lost their infectivity genes since the only selection pressure in the tubes was to replicate faster.
What are introns and exons?
Intron - segments of RNA that are removed during processing into mRNAs
Exon - segments of RNA that are kept during processing into mRNAs; encode for proteins
What was unusual about T. Cech’s self-splicing introns in Tetrahymena?
He found that ribosomes made entirely of RNA could assemble short peptides. They also required GTP and Mg2+.
What are the features of group 1 introns?
Need external GTP for self-splicing
Intron RNA is catalytically active and goes through 2 fragmentation reactions
-intron gets spliced out
-exons join together
Have homing endonucleases
Needs a complementary sequence to the IGS
What are the features of group 2 introns?
Does not need external GTP for self-splicing
Has an internal branch point A, where the intron lariat forms
Have reverse transcriptases
Needs homologous region to recombine
Why is it important to generate pools of genetically diverse RNA molecules?
Cover more niches
Improve efficiency
More robustness to changes in the environment
Based on natural and “in vitro evolved” ribozymes: list some of the catalytic properties we discussed in class that can be attributed to RNA molecules.
Intron core - can grab and donate:
- NTPs
- Phosphate groups
- Ligate RNA segments
RNA folding - facilitated by IGS so that exons can be pushed closer together
Are there “experimental” hypercycles that have been generated in the lab? If so what are they based on?
The Azoarcus group 1 intron ribozyme.
It was fragmented into 4 pieces and tested whether the pieces could stick back together into a function ribozyme and if this ribozyme could self-replicate. (Yes it can.)
They also tried making 3 variations of the fragments to see if they could make other ribozyme variations. The individual variations didn’t work that well, but mixed together, they could assemble into functional enzymes (worked like a hypercycle).
What was Woese’s opinion about LUCA?
The Last Universal Common Ancestor or LUCA is a pool of “cells” that shared genetic info and biochemical intermediates. The cells were open systems or the membranes were leaky so lots of things could be passed around.
What are progenotes?
Organisms with RNA genomes, leaky compartments, lots of HGT
What are genotes?
Organisms with DNA genomes (had more stable replication and repair process than progenotes), better membranes, can still share info and components, but less frequent HGT.
What is the Darwinian threshold?
The point at which a single organism can “make it on its own” and no longer needs to rely on other members of its community for biochemical intermediates.
(limited HGT, more VGT or descent with modification)
What’s the difference between natural selection and mutual enhancement?
Natural selection - organisms compete with each other for resources/survival; whoever can get the most resources will have a higher chance of proliferation
Mutual enhancement - organisms cooperate so that everyone can proliferate
Though both methods of mutual enhancement, how are hypercycles and communal ancestors different?
Hypercycles - each member of the cycle helps the next member replicate
If one member becomes selfish or dies off, everyone in the cycle suffers
Communal ancestor - each member produced a biochemical intermediate that another member could convert into another one to produce a product
Precursor to biochemical pathways.
What is the benefit of communal ancestors over hypercycles?
Communal ancestors aren’t as reliant on other members like hypercycles are. They won’t collapse like hypercycles would if one member fails.
What are the functions of elongation factors EF-Tu and EF-G?
EF-Tu - delivers charged tRNA to the ribosome
EF-G - removes tRNA after it delivers the AA to the peptide
They originated from a gene duplication event.
What are homologs, paralogs, orthologs and analogs?
Homologs - share a distant common ancestor
Paralogs - a type of homolog that arose from a duplication event
Orthologs - same gene in different species
Analogs - different origin but similar function in different species (not a homolog)
What does the phylogenetic analysis of the EF sequences show with regard to the three domains of life?
Confirms Woese’s 3 domain theory.
Bacterial Tu and G are homologous to Archaean and Eukaryotic Tu and G.
Archaean Tu and G are more closely related to Eukaryotic Tu and G than they are to Bacterial.
What does the phylogenetic analysis of the EF sequences show with regards to the evolution of the EF genes?
They are paralogous and follow the same branching pattern between Tu and G for all three domains.
Recently with more genes being analyzed - are the three domains well defined or are we actually looking at two domains?
Eukaryotes may have been a result of the merging of Archaea (Asgard superphylum) and Bacteria (alphaproteobacteria)
- Bacteria gave rise to endosymbiotic organelles
- Archaea became a host cell for mitochondrial endosymbiont
Oxygen appeared about 2.5 billion years ago, why is this significant for life on this planet?
Oxygen was released as a by-product of the first bacteria’s developing the ability to photosynthesize -> oxygen concentration increase which gave rise to newer organisms that made use of oxygen.
Allowed organisms to grow bigger, more diverse and more complex by providing a more efficient method of getting energy.
What is syntrophy?
The act of sharing biochemical intermediates, aka cross-feeding.
What is horizontal gene transfer (HGT)?
The act of sharing genetic information between two organisms (but not through inheritance or VGT).
Why has PCR and the 16S and 18S rRNA gene sequences revolutionized studies on microbial diversity and taxonomy?
rRNA can be used as markers for species identification. We can identify species just by their genomic content (good if that organism can’t be cultured in lab), separate them into operational taxonomic units (OTUs).
We can also use PCR->NGS metagenomics to see who are the members in a community and how much of them there are.
What are targetrons?
Group 2 introns, ancestors to spliceosomal introns/snRNPs. They can be used for gene editing (can be used for knockout mutations by programming a new “home” and remove the self-splicing feature).
Targetrons work well in bacteria but not in eukaryotes bc of their Mg2+ content.
What are twin-ribozymes?
RNA molecules with two or more domains that have different functions.
The inner group 2 intron interrupts the expression of the outer group 1 intron. Once the group 2 intron is removed, expression is restored to the group 1 intron.
Another case is that one group 1 intron acts as a cap for another group 1 intron. Splicing the first intron makes it act like a cap to fool the host into using the second intron -> makes homing endonuclease.
What are hammerhead ribozymes?
RNA scissors that recognize folding patterns instead of sequences.
List 3 examples of RNA contributing to the regulation of gene expression.
Riboswitches - in bacteria, these can determine whether TS starts or not
Attenuation - can be affected by RNA folding state
RNA interference - can affect TS and TL regulation
Why are group II introns attractive as elements that were able to easily move from an RNA world to the DNA based “world”?
They have reverse transcriptases - used to convert RNA to DNA
Compare Eigen’s view on the “origin of information” vs Higgs ideas about the “origin of RNA pools” and cooperation.
Eigen: Hypercycles are multiple RNA pools (quasispecies) that interact to form a larger beast. These quasispecies can replicate, generate variations and cooperate with other quasispecies to further stabilize info.
Higgs:
Patches of RNA polymers start evolving different abilities (each patch maintains its own replication). The patches could cooperate to start a biochemical interaction. They’re not reliant on other patches for replication but they team up to make a product that benefits everyone.
