Lectures 12-15 Flashcards
Why are ‘fundamental’ characteristics present in all modern day organisms not necessarily representative of the first living ones?
Mass extinction event where 1 lineage survived which had the single characteristic
What is the Hadean?
The eon that started 4.6 Ga with a supernova that created the earth.
- was a series of meteorite impacts - created moon 4.5 Ga
- probably continued until 3.8Ga
ENDED AT 3.5Ga
What is the archaean?
Eon started 3.5Ga - 2.5Ga
- maybe first microfossils (controversial)
- Microbial activity 3.5 Ga
- Photosynthesis (maybe not oxygen producing) at 3 Ga
- oxygenic photosynthesis 2.7Ga
How does isotope geochemistry help with identifying life?
Living organisms have preference for certain isotopes and so differing concentrations tell a lot
- like C12 vs C13
What rocks suggest microbial activity in 3.5Ga?
The rocks from North Pole, Australia (sulphide containing rocks)
Which rocks suggest photosynthesis at 3 Ga and then oxygenic at 2.7Ga?
Zimbabwe, South Africa and Canada show certain chemical balances
- also in Zimbabwe the carbon isotope fractionation shows oxygenic at 2.7Ga
- Stromatolites support these inferences
What are stromatolites?
thought to be the remains of algal mats
What is the Proterozoic?
- 4Ga to 0.54 Ga
- 2.4 Ga is the great oxidation event
- oxygen released before but was not increasing in the atmosphere as most likely oxidising
2.3 and 0.7 Ga = Global snowballs where much colder and then reversed by volcanic activity
Eukaryotes at 1.5 Ga from fossil record
0.6Ga oxygen levels close to present and complex life existed
What is the Phanerozoic?
eon from 0.54ga to present
What does the origin of life require? (chemically?)
x 3
- Liquid water
- Tectonic activity (to supply metals)
- Temperature - not too hot or cold
4 different ideas for origin of life
- Panspermia
- Lightning flashed in atmosphere
- Hydrothermal vents
- Lost city systems
What is the panspermia hypothesis?
Life transferred from elsewhere by meteoritic bombardment
What experiment was used to try to illustrate lightning flashes in the atmosphere
Miller and Urey 1950s
- CH4 NH3 H2O and H2
- organic material formed - some but not all amino acids
- problem is that geologist say most likely wasnt right mix of gases and also that pools of these most likely wouldnt have existed
Hydrothermal vent hypothesis
sea-floor spreading means black smokers are where hot liquid released
- though some say too hot
Lost city systems
too hot at hydrothermal vents to at warm springs away from the central vents
Iron sulphide layers in membranous froth hypothesis
- act as a surface for polymerisation of molecules
- gradients across and redox gradients
- lipids at this point line up along
- nucleotides formed and then leading to primitive protein synthesis systems
Why is RNA assumed to be the first of RNA, DNA proteins
- catalytic activity and self-replicate
- DNA can’t self-replicate but is catalytically active
- Protein is catalytically active but can’t self-replicate
What experiments first showed RNA ability to catalyse?
Splicing experiments
- shown that removal of intron sequence of RNA can occur auto-catalytically using
- guanosine nucleotide co-factor
- though could argue than they were changed at the end and so not a ‘catalyst’
What is the estimated Km and Kcat of ribozymes?
42μM = Km
so high affinity
2 min^-1 = Kcat which is slow
Example of RNA catalysing RNA molecule replication
x 2
Johnston et al (2001)
100 11-nucleotide extension products were sequenced
- of the 1100 nucleotides there were 1088 correct
- accuracy 96-99%
Attwater et al (2013)
Developed an RNA polymerase ribozyme that could copt a molecule longer than itself
Error rates in ribozymes
RNA replication has a relatively high error rate
- places upper limit on size of ‘genome’
What is the eigen paradox?
The idea of mutational melt-down as change increases error rate which leads to more errors and so on
What is the Darwin-Eigen cycle?
Positive feedback hypothesis that opposes eigen paradox
- larger genome size —>new function evolves—>selection increases fidelity—>larger genome size
etc
What is the RNP world?
the world of RNA and protein (no DNA)
How can protein synthesis be catalysed by
Peptidyl transferase
- makes peptide bonds
- has been a ribozyme that has peptidyl transferase activity
(Zhang & Cech) 1997
Hypothesis for the origin of the ribosome
- maybe originally an RNA replicase
- lines up short nucleotide chains on a template
- this then evolves into something that lines up short nucleotide chains with something attached (amino acids) on a template and then attaches amino acids
Steps involved in creating DNA world
- development of a DNA polymerase
- most likely alteration of RNA polymerase - Development of deoxyribonucleotides
- reduction of of OH to H
- involves acquisition of an enzymes though could be from another enzyme
Why and when was U turned into T?
WHY?
- C spontaneously deaminates to U
- so don’t know if to correct it
WHEN?
- After DNA made as not present in RNA even though it would be advantageous
Origin of metabolic pathways
- may have been established spontaneously
- simply heating many metabolic intermediates allows non-enzymatic formation of other ones—like pyruvate
What increases non-enzymatic formation of metabolic intermediates?
anoxic conditions
Fe(II)
like Archaean ocean
- so later enzymes to increase efficiency and evolve into new niches
What is LUCA?
The last Universal Common Ancestor
- probably had some kinds of DNA, RNA, Protein and metabolic pathways
what are the two possible explanations for the presence of genetic material in chloroplasts?
- endosymbiosis
- results of partitioning specialised photosynthetic region
most likely 1 from genomics
what group have chloroplasts most likely evolved from within?
cyanobacteria
- unclear is within group or sister though most point to within
why do we think came from prokaryotes? - chloroplasts
many clusters of genes in chloroplast genomes are the same as in prokaryotes
- most likely evolved from rather than by chance
what was the endosymbiont for chloroplasts?
- cyanobacteria
- chlorophyll a but not b
- but only differ by oxidation state of 1 carbon
- but present at time of chloroplast evolution - prochlorophytes - now considered part of cyanobacteria
- both a and b
- but sequence based trees show not closely related
- so most likely b evolved separately
How did chlorophyll b evolve?
most likely gained independently rather than widespread loss
- prochlorophytes most likely got CB after chloroplasts evolved
What were the advantages of chloroplasts?
x 2
- fixed carbon for host whilst gaining nutrients/ protection for endosymbiote
- other possibilities - like provision of fixed nitrogen or vitamines
Why do chloroplast have less genes then modern cyanobacteria
cyanobacteria = thousands chloroplasts = 100 1. some redundant after endosymbiosis 2. transported to nucleus and then protein products transported back when required 3. moved and now used for other purposed
why do genes move to the nucleus from the chloroplasts?
x 3
- Muller’s ratchet
- nucleus is a sexual population but chloroplast not so increase fitness by moving to nucleus - DNA protection
- photosynthesis generates reactive species which damage DNA - no reason
- can move to nucleus but not back so random process
why don’t all genes go to nucleus?
- individual needs of chloroplasts and mitochondria - no waiting
- possibility of transfer may have stopped before all transferred
- if only 1 in a cell then cant
How do the number of membranes of chloroplasts differ and why?
- green algae and plants = 2 so primary endosymbiosis where it happened once
- 4 membranes like in diatoms = two endosymbiosis events = secondary
- presence of nucleomorph between 3 and 4 - 3 membranes where nucleomorph lost and one of the membranes degrades
- can even be tertiary (3 events)
