RNA World Flashcards
What are the three great biological macromolecules?
DNA, RNA, protein
What is encoded in DNA?
proteins
proteins are encoded in…
…dna.
the first replicator is unlikely to have been…
…dna.
Why was the first replicator unlikely to have been dna?
it has no ability to do anything other than encode – it requires proteins to replicate
What does dna require to replicate?
DNA requires protein to replicate
Proteins are good at doing things but…
…need to be encoded – they can’t just assemble by themselves
the problem with postulating that DNA was the first replicating molecule is that…
its replication requires so many other things – many protein enzymes plus RNA molecules – something similar must have preceded this?
Some scientists propose that prior to the DNA-based cellular life that we see today there was…
…a period where ‘life’ was based on RNA
what did Miller find after his experiment?
loads of organic molecules
Some of the organic compounds that Miller isolated were…
…sugars
What ribose or deoxyribose easier for Miller to isolate?
he found that it was easier to isolate ribose than deoxyribose
RNA molecules form…
…secondary structure
RNA molecules can fold up with…
intra-chain base pairing
A with U, C with G
forms the basis of tRNA and rRNA
RNA molecules exhibit…
…catalytic properties.
Other than just being intermediary molecules (mRNA, rRNA, and tRNA)…
…the importance of RNA molecules in the cell is that they are also able to catalyse chemical reactions
Describe RNA catalysis.
1) Ribozyme mediated cut introduced into RNA message.
2) Cut (cleaved) RNA messages.
What did Thomas Cech win the Nobel Prize for?
won the Nobel Prize for demonstrating the catalytic qualities of an RNA molecule in cleaving a mRNA.
above left:
the three-dimensional structure of the original ribozyme - the self-splicing intron of Tetrahymena.
What do green and blue ribbons indicate?
green and blue ribbons indicate the path of the RNA backbone in the two major domains of the RNA and the red star marks the active site
What did Sidney Altman and Cech share the nobel prize for?
his work on RNase P
What is RNase P?
a protein-RNA complex involved in the maturation of tRNA molecules – the catalytic property of the complex lies in the H1 RNA component
The catalytic function of the ribosome…
…is RNA-based
Joining amino acids to form proteins is…
…catalysed by RNA is the ribosome.
What is catalysed by RNA in the ribosome?
joining amino acids to form proteins
We see no instances of…
…DNA-mediated construction of proteins in cells
proteins are always built using RNA intermediate molecules
Coenzymes are mostly..
…nucleotides.
It is suggested that coenzymes are…
…the remnants of the active site of various small ribozymes
In what direction does the dna chain grow?
5’ to 3’ by addition of nucleotides to a free 3’ OH end
is there a fundamental difference in DNA replication between Archaea and Bacteria?
Whilst the principles of DNA replication are the same - some of the proteins that do this differ and are not phylogenetically related – think about the session on phylogeny
How can we explain the differences in DNA replication between bacteria and archaea?
to suggest that there are two independent evolutionary events and that life started with RNA (all life), went through a RNA-DNA hybrid phase (all life) then to a DNA phase (after the split between archaea/eukaryotes and bacteria)
when was the evolution of dna replication (DNA -dependent DNA polymerisation)?
after bacteria split from Archaea/ eukaryotes
What things are common between all 3 domains in the tree of life?
RNA polymerisation, basic metabolism, Krebs Cycle, chemiosmosis
While some things are in common between all three domains …
… some things are different.
There are examples of viruses that have…
…both DNA and RNA phases of their life cycle
In certain systems in some viruses, RNA acts both as…
…a template to make DNA and a message to make proteins
What is needed for the RNA hypothesis to work?
a replicase
Whats a replicase do?
An RNA molecule that can synthesize the polymerization of itself.
How many views are there on how RNA replication was accomplished in an RNA world?
There are two competing views.
What is the first competing view on how RNA replication was accomplished in an RNA world?
the first view is reminiscent of DNA polymerisation as bases are added one by one
What is the second competing view on how RNA replication was accomplished in an RNA world?
the second view is more akin to DNA ligation as smaller molecules are joined together to make larger ones
where are the RNA-dependent RNA polymerase ribozymes?
whilst nobody has managed to make a replicase that replicates itself it has been possible to construct ribozymes with RNA ligase activity that are able to process by adding ribonucletotides
What do E’ base pair with and what do they form?
E’ base pairs with molecules A and B and ligates them to form E
What do E base pair with and what do they form?
E base pairs with molecules A’ and B’ and ligates them to form E’
What do RNA molecules exhibit in vitro?
RNA molecules exhibit ‘natural selection’ in vitro
What happens when mutations are introduced into RNA?
this makes some molecules better replicators than others
What happens in RNA as a result of mutations?
some molecules will start outcompeting others in competition for resources
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What is the issue of primordial soup?
the issue about the idea of a primordial soup is that there is no ‘dynamism’ – the ingredients are there (in a dilute form) and if they react – what then?
there needs to be a continuous flow of new ‘ingredients’ and energy in order to make life more likely
purines can be synthesised from …
…simple inorganic compounds relatively easily
starting with HCN adenine can be made – but these are not yet attached to ribose sugars or phosphate groups
In the primordial soups favour…
… it has been shown that nucleotides (base + ribose + phosphate) can form in aqueous solution from UV radiation.
however – RNA polymerisation requires energy and a constant supply of a high concentration of nucleotides
What occurs in a hypothetical bowl of primordial soup?
in a hypothetical bowl of primordial soup RNA polymers might be formed but UV radiation destroys as well as creates
What happens in primordial soup once RNA replicates?
once an RNA molecule replicates – the pool of nucleotides necessarily falls – it needs to be at a much higher concentration – the solution has reached thermodynamic equilibrium
What do all cells require?
all cells require a carbon source and energy plus water as well as sources of other essential elements (e.g. nitrogen, phosphorus, iron)
What is vital within a membrane?
the concentration of energy and ‘convertible matter’ within a membrane is vital
What does the metabolic conversion of carbon and energy result in?
the metabolic conversion of carbon and energy results in cellular growth
Cell growth is followed by…
…division whereby daughter cells each retain the information to convert energy … ad infinitum
life couples…
…chemical reactions.
exergonic reactions…
…provide energy
endergonic reactions…
…utilize energy.
What chemical reactions are coupled?
exergonic and endergonic reactions.
What are the two ways of looking at lifes origins?
top-down and bottom-up.
Describe top down way of looking at lifes origins?
looking from the top downwards to see what we have today and strip things back to their bare minimum
we have already seen an example of this in a way by comparing DNA polymerisation machinery – examine the differences between Bacteria and Archaea – what is common?
Describe bottom up way of looking at lifes origins?
looking from the bottom upwards seeks to figure what happened by inferring what was there to start life
this is like Miller’s experiment
One arguement is that LUCA used…
…fermentation.
but – the enzymes that allow fermentation in Bacteria and Archaea are different – likely to have evolved independently
What does LUCA stand for?
Last Universal Common Ancestor
What were the most talked about hydrothermal vents known as?
black smokers
the hydrothermal vents known as ‘black smokers’ are often cited as…
… possible sources of life
Arguements against hydrothermal vents being the possible sources of life?
1) they are at very high temperature (may break down organic molecules)
2) they have a short lifetime
3) they lack compartmentalisation – everything spills into the sea
What is the other type of hydrothermal vents recently discovered?
alkaline vents
What temp are alkaline vents?
At a lower temperature (70 degrees C)
What are alkaline vents full of?
full of dissolved hydrogen
they are also full of cell-sized pores
What is the life span of alkaline vents compared to black smokers?
Alkaline vents are longer lived.
What do alkaline vents result from?
result from thermal expansion of olivine rocks by hydroxylation (serpentinisation)
Alkaline vents seem like…
good candidates
Why are alkaline vents seen to be good candidates to be the source of life?
1) have the ability to form reduced nitrogen compounds needed for life
2) they are likely to be able to concentrate nucleotides in cooler parts of the vent
3) alternate warming and cooling – like PCR?
4) bring together CO2 and H2
5) high amount of CO2 likely to produce an acidic ocean – proton flux? i.e. chemiosmosis
