RNA world Flashcards
Is the public’s acceptance of evolution varied across the countries of the world or not?
Very varied
Give 3 countries that have a public acceptance of evolution of around 80%
Iceland
Denmark
Sweden
Give 3 countries that have a public acceptance of evolution of around 50%
Poland
Greece
Bulgaria
Give 3 countries that have a public acceptance of evolution of around 30-40%
Turkey
United States
Cyprus
What are the obvious problems with the literal interpretation of the Bible?
Where did the daughter-in-laws of Adam and Eve arise? Or did Cain and Seth have children with Eve?
What is the genomic sequence difference percentage between man and gorilla?
1.6%
What is the genomic sequence difference percentage between man and chimp?
1.2%
Do small differences in DNA sequence cause small or large differences in phenotype?
Large differences in phenotype
What are the theories that lack substantial evidence for how life on Earth began?
Divine intervention as ‘intelligent design’
Extraterrestrial intervention
Define irreducible complexity
‘A single system which is composed of several interacting parts that contribute to the basic function, and where the removal of any one of the parts causes the system to effectively cease functioning’ M. Behe
What does ‘directed Panspermia’ suggest?
That life may be distributed by an advanced extraterrestrial civilisation
What did Crick and Orgel argue for in 1973?
‘Directed Panspermia’
That DNA encapsulated within small grains could be fired in all directions by an advanced extraterrestrial civilisation in order to spread life within the universe
What is the issue with the Panspermia hypothesis?
It simply shifts the problem - how did DNA-based extraterrestrials evolve?
What does the ‘prebiotic soup’ give rise to?
RNA
What remained unanswered for a long time from the ‘prebiotic soup’ theory?
Why was RNA favoured?: what chemical biases led to RNA? Or was there something else before RNA?
Can RNA replicate?
What is considered ‘clutter’ in the ‘prebiotic soup’?
The RNA alternatives
Why are RNA alternatives not favoured in the ‘prebiotic soup’?
They are not as stable.
Some condense in sunlight, some is destroyed by UV etc.
Why is the formation of RNA in the ‘prebiotic soup’ stable?
Because ribose is formed in the presence of borate - stabilises RNA
Relatively simple chemistry can generate building blocks of what?
RNA and proteins
What are cynobacteria?
Photosynthetic bacteria that generate oxygen
What is the term used to describe biology of the cosmos?
Exobiology
Which scientist was the first to generate the ‘building blocks of life’ from an experiment?
Miller
Which nucleotides are characteristic of RNA?
A, G, and U
Which molecule is the suggested earliest molecule to arrive on planet earth?
RNA
What does HCN stand for?
Hydrogencyanide
What are aldehydes important for making?
Sugars
What did the Cambrian explosion lead to?
The diversification of life
The RNA on earth was more resistant to destruction than ‘clutter’, but what was this ‘clutter’ destroyed by?
UV
What is borate?
A catalyst
What question can paleogenetics answer?
Can RNA generate ‘life’?
What organism is generated from RNA?
Tetrahymena thermophila
Who discovered Tetrahymena?
Tom Cech
What did Cech found out about the Tetrahymena intron in 1992?
It could:
Make and break bonds between tRNA and amino acid
Generate a poly-Cytosine nucleotide strand, make and break phosphodiester bonds between nucleotides
Might it be a ‘fossil’ of the early RNA world?
What is the traditional view of how the ribosome works?
Translational complex of proteins and rRNA. Peptidyl transfer reaction to make growing polypeptide chain. rRNA binds catalytic proteins together - ‘string’
What did Carl Woese found out in 1987?
Found that rRNA genes are more conserved than ribosomal protein coding genes.
Also, drugs inhibit protein synthesis. Mutants found that were resistant to drugs. Mutations mapped to rRNA, not proteins!!
What did Noller found out in 1992?
Removed all protein from the ribosome (40% of bulk is protein, 60% rRNA), still got peptidyl transferase reaction. Peptidyl transferase centre was Woese’s conserved rRNA region. So rRNAs provide the catalytic component for protein elongation, proteins provide scaffold.
Essentially, what does ‘life’ mean?
Replication
Is it a conceivable idea that RNA was catalytic?
Yes
What would you need to prove that RNA could replicate itself in the prebiotic ‘soup’ and that it was the first replicase?
Would need two almost complementary RNA molecules, one as the template and one as the enzyme (the ribozyme)
How can nucleotides spontaneously polymerise and form phosphodiester bonds?
Montmorrillonite clay is mineral rich and attracts nucleotides promoting polynucleotide formation, even in dilute solutions. Also promotes vesicle assembly - membranes and encapsulation
What is needed for the replication of RNA?
Requires two similar RNA molecules, one to act as template, the other as enzyme.
Need errors in copying - evolution
Stabilise replicase RNA with amino acid (+ charge) - selection for the first tRNA. Beginning of RNP world and ribosome.
How big is the shortest ribozyme?
52 nucleotides (currently)
What does RNP stand for?
Ribonucleoprotein
What is the complex called when an RNA replicase is stabilised by amino acids associated with it?
Protoribosome
What does Darwinian selection for more efficient replication allow for?
Positive feedback and rapid evolution
What did the initial ‘tRNA’ function in?
Replication
What do many modern retroviruses have as a signal for replication?
A 3’ tag with terminal CCA
Where are ancient CCA repeats often found now?
In chromosome telomeres, CCA, TTG
Who came up with the genomic tag hypothesis in 1987?
Weiner and Maizels
What is the genomic tag hypothesis?
RNA replicase have affinity for 3’ end of other molecule - tag hypothesis - 3’ loop plus terminal CCA identifies molecule as substrate for replication. Replication initiates on first C of CCA
The tRNA role in modern replication could have evolved before its role in what?
Protein synthesis
Give an example where tRNA acts as a template for cDNA synthesis
In neurospora mitochondrial retroplasmids
Give two examples where tRNA acts as a primer for cDNA synthesis
In the cauliflower mosaic virus
In integrating retroviruses
Give an example where tRNA acts as a template for telomere synthesis
In the eukaryotic chromosome
If you had a random RNA of 40 nucleotides that can act as a ribozyme, and E24 possible 40 nucleotides weigh about 1kg, what would you need to replicate it?
A template that will bind to it having a complementary sequence (E48) or 1028 gms (mass of the Earth)
Primeval soup model has replication of RNA coming way before the evolution of translation, true or false?
True
What is the opposing view to the primeval soup model?
The ‘iron-sulphur world’
What was done in 1997 to provide more evidence for the ‘iron-sulphur world’ model for the origin of life?
NiS and FeS catalyse acetic acid formation
What was done in 2000 to provide more evidence for the ‘iron-sulphur world’ model for the origin of life?
Pyruvate generated, central to biosynthetic pathways
What was done in 2006 to provide more evidence for the ‘iron-sulphur world’ model for the origin of life?
Amino acids generated, glycine, dipeptides Gly-Gly
What is autocatalysis?
Products (ligands) increase catalytic potential of metal sulphides which increase rate of product etc. etc…
Effectively ‘reproduction’, with variation (‘mutation’), i.e. evolvable - chemoautotrophic origin of life before RNA
What does COS stand for?
Carbonyl sulphide
What is COS?
A volcanic gas
What does COS mediate in the presence of L-phenyl alanine?
The condensation to a dipeptide
What else can COS mediate?
Also mediates mixed peptide condensation with metal sulphides from single mixture of L, F, S, A, Y - get mixed tripeptides and dipeptides
What compound found in volcanic gases can hydrolyse to phosphorylation agents?
P4O10 pyrophosphates
Define double feedback
Interlocked feedback loops. One product starts to have a new metabolism, which feeds back onto its own new metabolism plus the pioneer metabolism, e.g. extant coenzmes catalyse reactions plus their own synthesis
Define metabolic inheritance
Initial pathway dependent on environment. Once feedbacks kick in they become independent of the environment
What part of a cell might have evolved pre-RNA/DNA?
Membranes
What did the RNA world give way to?
The RNP world and protein enzymes
What did the first RNA replicases evolve into?
The first protoribosomes, then the DNA world
How is DNA far more stable and a better replicator than RNA?
Ribonucleotide reductase mediates deoxyribose from ribose and reverse transcriptase copies RNA to DNA
What is ribonucleotide reductase?
An ancient enzyme found in all cellular life
What are the three classes of ribonucleotide reductase enzymes that have distinct radical-generating mechanisms?
I - aerobic
II - independent of O2 but cobalt-dependent
III - anaerobic
What part of the riboucleotide reductase enzyme is conserved and so indicates that it has only evolved once?
The catalytic core is conserved
Was the ribonucleotide reductase enzyme present in LUCA?
Phylogenies are inconclusive so don’t know if LUCA was DNA or RNA based. Probability of horizontal transfer from bacteria to archaea and eukaryotes
What does LUCA stand for?
Last universal common ancestor
Reverse transcriptase encoded in mRNA that looks like a ribozyme shows common descent, true or false?
True
Why are ribozymes big business for therapeutics?
They can cut themselves and they can cut invading viruses
Apart from autoreplicating FeS mediated peptides, what else may have kick-started replication?
RNA-peptide world
What do ribozymes show about RNA?
That it is a very flexible molecule that can catalyse many reactions
Can RNA catalyse self replication which is the definition of ‘life’?
So far, not demonstrated in the laboratory.
Also, PCR based synthetic ribozymes bear no resemblance of anything found in life
What do urzymes catalyse?
tRNA acylation ~E9
Is there any evidence in extant organisms that ribozymes can acylate?
No, except in synthetic biology
What problem does the RNA world have?
A fidelity problem
What does the peptide-RNA world accelerate?
Codon directed translation
What type of structure does poly-lysine in droplets show?
Secondary structure:
Beta strand and alpha helices
At what pH do protocell droplets form?
7.2
At what pH do protocell droplets disassemble?
Alkaline pHs
Which statement is correct?:
There was an independent evolution of two types of lipid membranes.
OR
G1PDH/G3PDH evolved by recruiting domains from other ancestral dehydrogenases.
It is still not clear which of the two happened
Do G1PDH and G3PDH belong to the same or two separate families of dehydrogenases?
Two separate
What questions can you ask about the membrane of the first cells?
How did lipid membranes arise?
How was encapsulation achieved?
Was it before or after the evolution of translation apparatus?
What is the reasoning behind the suggestion that there was an early encapsulation or simultaneous evolution of replication and membranes?
Lipid-like FeS membranes can form in hydrothermal vents. Have affinity for formaldehyde, phosphates and cyanide!!
Lipid biolayers are relatively impermeable, so how are molecules and signals able to pass?
Molecules use special protein channels and pumps to move through or receptors to transduce signals
Define coacervation
Liquid-liquid separation
Spontaneous sequestration of polyelectrolytes and macromolecules into liquid droplets - no lipid membrane
How can you mimic the primitive ‘soup’ and what happens when you do?
Make liquid suspensions with nucleotide triphosphates, ATP, CTP, TTP, GTP, UTP, deoxynucleotide triphosphates dATP, dCTP and mono and poly-lysines.
Found that poly-Lys and ATP spontaneously formed droplets within the aqueous solution
What do protocells attract?
Other molecules
You need growth of membrane/cell before division and amphiphiles to grow membrane and entry of nucleotides for non-enzymatic copying of template, true or false?
True
What is an amphiphile?
A water and lipid loving molecule
Are there the same or different phospholipids built on different glycerols in kingdoms?
Different
How many ways are there of making bacterial sn-glycerol-3 phosphatase?
Two
What proportion of archaea have G1PDH?
All
What is the function of bacterial G1PDH?
Unknown
What proportion of eukaryotes have G1PDH?
None
What proportion of bacteria have G1PDH?
Very few
Do G1PDH and G3PDH look the same or different?
Very different
Is Tetrahymena thermophila a eukaryote or prokaryote?
A simple eukaryote
Why was the Tetrahymena intron looked at in the first place?
Because the intron forms a complicated shape similar to that of an enzyme
(Which it did - it splices itself out of RNA)
What is a ribozyme?
A piece of RNA with catalytic activity
What were the first introns?
Flexible catalytic molecules that, with some tweaking, can generate novel RNAs
What is the A site of a ribosome?
Acylation site
What is the E site of the ribosome?
Exit site
What is the role of the peptidyl transfer reaction?
For the elongation of the growing chain
Can rRNA function as a ribozyme?
Yes
Where are archea often found?
In hydrothermal vents
Is the peptide cycle an example of a positive or negative feedback loop?
Positive feedback loop
At the beginning of life on Earth, what events meant that there was an abundance of phosphates available?
Meteor impacts
What are the biproducts of the peptide cycle?
Digonucleotides
Why is R18 replicase named the way it is?
Because there are 18 rounds of replication
What is the key to translation?
The anti-codon
