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Evolution and Behaviour > Lectures 12-15 > Flashcards

Lectures 12-15 Flashcards

1
Q

Why are ‘fundamental’ characteristics present in all modern day organisms not necessarily representative of the first living ones?

A

Mass extinction event where 1 lineage survived which had the single characteristic

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2
Q

What is the Hadean?

A

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

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3
Q

What is the archaean?

A

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
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4
Q

How does isotope geochemistry help with identifying life?

A

Living organisms have preference for certain isotopes and so differing concentrations tell a lot
- like C12 vs C13

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5
Q

What rocks suggest microbial activity in 3.5Ga?

A

The rocks from North Pole, Australia (sulphide containing rocks)

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6
Q

Which rocks suggest photosynthesis at 3 Ga and then oxygenic at 2.7Ga?

A

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
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7
Q

What are stromatolites?

A

thought to be the remains of algal mats

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8
Q

What is the Proterozoic?

A
  1. 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

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9
Q

What is the Phanerozoic?

A

eon from 0.54ga to present

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10
Q

What does the origin of life require? (chemically?)

x 3

A
  1. Liquid water
  2. Tectonic activity (to supply metals)
  3. Temperature - not too hot or cold
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11
Q

4 different ideas for origin of life

A
  1. Panspermia
  2. Lightning flashed in atmosphere
  3. Hydrothermal vents
  4. Lost city systems
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12
Q

What is the panspermia hypothesis?

A

Life transferred from elsewhere by meteoritic bombardment

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13
Q

What experiment was used to try to illustrate lightning flashes in the atmosphere

A

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
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14
Q

Hydrothermal vent hypothesis

A

sea-floor spreading means black smokers are where hot liquid released
- though some say too hot

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15
Q

Lost city systems

A

too hot at hydrothermal vents to at warm springs away from the central vents

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16
Q

Iron sulphide layers in membranous froth hypothesis

A
  • 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
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17
Q

Why is RNA assumed to be the first of RNA, DNA proteins

A
  • catalytic activity and self-replicate
  • DNA can’t self-replicate but is catalytically active
  • Protein is catalytically active but can’t self-replicate
18
Q

What experiments first showed RNA ability to catalyse?

A

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’
19
Q

What is the estimated Km and Kcat of ribozymes?

A

42μM = Km
so high affinity

2 min^-1 = Kcat which is slow

20
Q

Example of RNA catalysing RNA molecule replication

x 2

A

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

21
Q

Error rates in ribozymes

A

RNA replication has a relatively high error rate

- places upper limit on size of ‘genome’

22
Q

What is the eigen paradox?

A

The idea of mutational melt-down as change increases error rate which leads to more errors and so on

23
Q

What is the Darwin-Eigen cycle?

A

Positive feedback hypothesis that opposes eigen paradox

  • larger genome size —>new function evolves—>selection increases fidelity—>larger genome size

etc

24
Q

What is the RNP world?

A

the world of RNA and protein (no DNA)

25
Q

How can protein synthesis be catalysed by

A

Peptidyl transferase

  • makes peptide bonds
  • has been a ribozyme that has peptidyl transferase activity

(Zhang & Cech) 1997

26
Q

Hypothesis for the origin of the ribosome

A
  • 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
27
Q

Steps involved in creating DNA world

A
  1. development of a DNA polymerase
    - most likely alteration of RNA polymerase
  2. Development of deoxyribonucleotides
    - reduction of of OH to H
    - involves acquisition of an enzymes though could be from another enzyme
28
Q

Why and when was U turned into T?

A

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

29
Q

Origin of metabolic pathways

A
  • may have been established spontaneously

- simply heating many metabolic intermediates allows non-enzymatic formation of other ones—like pyruvate

30
Q

What increases non-enzymatic formation of metabolic intermediates?

A

anoxic conditions
Fe(II)
like Archaean ocean
- so later enzymes to increase efficiency and evolve into new niches

31
Q

What is LUCA?

A

The last Universal Common Ancestor

- probably had some kinds of DNA, RNA, Protein and metabolic pathways

32
Q

what are the two possible explanations for the presence of genetic material in chloroplasts?

A
  1. endosymbiosis
  2. results of partitioning specialised photosynthetic region

most likely 1 from genomics

33
Q

what group have chloroplasts most likely evolved from within?

A

cyanobacteria

- unclear is within group or sister though most point to within

34
Q

why do we think came from prokaryotes? - chloroplasts

A

many clusters of genes in chloroplast genomes are the same as in prokaryotes
- most likely evolved from rather than by chance

35
Q

what was the endosymbiont for chloroplasts?

A
  1. cyanobacteria
    - chlorophyll a but not b
    - but only differ by oxidation state of 1 carbon
    - but present at time of chloroplast evolution
  2. prochlorophytes - now considered part of cyanobacteria
    - both a and b
    - but sequence based trees show not closely related
    - so most likely b evolved separately
36
Q

How did chlorophyll b evolve?

A

most likely gained independently rather than widespread loss

- prochlorophytes most likely got CB after chloroplasts evolved

37
Q

What were the advantages of chloroplasts?

x 2

A
  1. fixed carbon for host whilst gaining nutrients/ protection for endosymbiote
  2. other possibilities - like provision of fixed nitrogen or vitamines
38
Q

Why do chloroplast have less genes then modern cyanobacteria

A 
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
39
Q

why do genes move to the nucleus from the chloroplasts?

x 3

A
  1. Muller’s ratchet
    - nucleus is a sexual population but chloroplast not so increase fitness by moving to nucleus
  2. DNA protection
    - photosynthesis generates reactive species which damage DNA
  3. no reason
    - can move to nucleus but not back so random process
40
Q

why don’t all genes go to nucleus?

A
  1. individual needs of chloroplasts and mitochondria - no waiting
  2. possibility of transfer may have stopped before all transferred
    - if only 1 in a cell then cant
41
Q

How do the number of membranes of chloroplasts differ and why?

A
  1. green algae and plants = 2 so primary endosymbiosis where it happened once
  2. 4 membranes like in diatoms = two endosymbiosis events = secondary
    - presence of nucleomorph between 3 and 4
  3. 3 membranes where nucleomorph lost and one of the membranes degrades
  • can even be tertiary (3 events)

Evolution and Behaviour (8 decks)

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