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Introduction to Evolution and Genetics > RNA World > Flashcards

RNA World Flashcards

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Biology 101 flashcards
1
Q

What are the three great biological macromolecules?

A

DNA, RNA, protein

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2
Q

What is encoded in DNA?

A

proteins

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3
Q

proteins are encoded in…

A

…dna.

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4
Q

the first replicator is unlikely to have been…

A

…dna.

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5
Q

Why was the first replicator unlikely to have been dna?

A

it has no ability to do anything other than encode – it requires proteins to replicate

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6
Q

What does dna require to replicate?

A

DNA requires protein to replicate

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7
Q

Proteins are good at doing things but…

A

…need to be encoded – they can’t just assemble by themselves

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8
Q

the problem with postulating that DNA was the first replicating molecule is that…

A

its replication requires so many other things – many protein enzymes plus RNA molecules – something similar must have preceded this?

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9
Q

Some scientists propose that prior to the DNA-based cellular life that we see today there was…

A

…a period where ‘life’ was based on RNA

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10
Q

what did Miller find after his experiment?

A

loads of organic molecules

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11
Q

Some of the organic compounds that Miller isolated were…

A

…sugars

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12
Q

What ribose or deoxyribose easier for Miller to isolate?

A

he found that it was easier to isolate ribose than deoxyribose

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13
Q

RNA molecules form…

A

…secondary structure

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14
Q

RNA molecules can fold up with…

A

intra-chain base pairing

A with U, C with G
forms the basis of tRNA and rRNA

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15
Q

RNA molecules exhibit…

A

…catalytic properties.

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16
Q

Other than just being intermediary molecules (mRNA, rRNA, and tRNA)…

A

…the importance of RNA molecules in the cell is that they are also able to catalyse chemical reactions

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17
Q

Describe RNA catalysis.

A

1) Ribozyme mediated cut introduced into RNA message.
2) Cut (cleaved) RNA messages.

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18
Q

What did Thomas Cech win the Nobel Prize for?

A

won the Nobel Prize for demonstrating the catalytic qualities of an RNA molecule in cleaving a mRNA.

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19
Q

above left:

A

the three-dimensional structure of the original ribozyme - the self-splicing intron of Tetrahymena.

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20
Q

What do green and blue ribbons indicate?

A

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

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21
Q

What did Sidney Altman and Cech share the nobel prize for?

A

his work on RNase P

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22
Q

What is RNase P?

A

a protein-RNA complex involved in the maturation of tRNA molecules – the catalytic property of the complex lies in the H1 RNA component

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23
Q

The catalytic function of the ribosome…

A

…is RNA-based

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24
Q

Joining amino acids to form proteins is…

A

…catalysed by RNA is the ribosome.

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25
Q

What is catalysed by RNA in the ribosome?

A

joining amino acids to form proteins

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26
Q

We see no instances of…

A

…DNA-mediated construction of proteins in cells

proteins are always built using RNA intermediate molecules

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27
Q

Coenzymes are mostly..

A

…nucleotides.

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28
Q

It is suggested that coenzymes are…

A

…the remnants of the active site of various small ribozymes

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29
Q

In what direction does the dna chain grow?

A

5’ to 3’ by addition of nucleotides to a free 3’ OH end

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30
Q

is there a fundamental difference in DNA replication between Archaea and Bacteria?

A

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

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31
Q

How can we explain the differences in DNA replication between bacteria and archaea?

A

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)

32
Q

when was the evolution of dna replication (DNA -dependent DNA polymerisation)?

A

after bacteria split from Archaea/ eukaryotes

33
Q

What things are common between all 3 domains in the tree of life?

A

RNA polymerisation, basic metabolism, Krebs Cycle, chemiosmosis

34
Q

While some things are in common between all three domains …

A

… some things are different.

35
Q

There are examples of viruses that have…

A

…both DNA and RNA phases of their life cycle

36
Q

In certain systems in some viruses, RNA acts both as…

A

…a template to make DNA and a message to make proteins

37
Q

What is needed for the RNA hypothesis to work?

A

a replicase

38
Q

Whats a replicase do?

A

An RNA molecule that can synthesize the polymerization of itself.

39
Q

How many views are there on how RNA replication was accomplished in an RNA world?

A

There are two competing views.

40
Q

What is the first competing view on how RNA replication was accomplished in an RNA world?

A

the first view is reminiscent of DNA polymerisation as bases are added one by one

41
Q

What is the second competing view on how RNA replication was accomplished in an RNA world?

A

the second view is more akin to DNA ligation as smaller molecules are joined together to make larger ones

42
Q

where are the RNA-dependent RNA polymerase ribozymes?

A

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

43
Q

What do E’ base pair with and what do they form?

A

E’ base pairs with molecules A and B and ligates them to form E

44
Q

What do E base pair with and what do they form?

A

E base pairs with molecules A’ and B’ and ligates them to form E’

45
Q

What do RNA molecules exhibit in vitro?

A

RNA molecules exhibit ‘natural selection’ in vitro

46
Q

What happens when mutations are introduced into RNA?

A

this makes some molecules better replicators than others

47
Q

What happens in RNA as a result of mutations?

A

some molecules will start outcompeting others in competition for resources

48
Q

W

A
49
Q

What is the issue of primordial soup?

A

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

50
Q

purines can be synthesised from …

A

…simple inorganic compounds relatively easily
starting with HCN adenine can be made – but these are not yet attached to ribose sugars or phosphate groups

51
Q

In the primordial soups favour…

A

… 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

52
Q

What occurs in a hypothetical bowl of primordial soup?

A

in a hypothetical bowl of primordial soup RNA polymers might be formed but UV radiation destroys as well as creates

53
Q

What happens in primordial soup once RNA replicates?

A

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

54
Q

What do all cells require?

A

all cells require a carbon source and energy plus water as well as sources of other essential elements (e.g. nitrogen, phosphorus, iron)

55
Q

What is vital within a membrane?

A

the concentration of energy and ‘convertible matter’ within a membrane is vital

56
Q

What does the metabolic conversion of carbon and energy result in?

A

the metabolic conversion of carbon and energy results in cellular growth

57
Q

Cell growth is followed by…

A

…division whereby daughter cells each retain the information to convert energy … ad infinitum

58
Q

life couples…

A

…chemical reactions.

59
Q

exergonic reactions…

A

…provide energy

60
Q

endergonic reactions…

A

…utilize energy.

61
Q

What chemical reactions are coupled?

A

exergonic and endergonic reactions.

62
Q

What are the two ways of looking at lifes origins?

A

top-down and bottom-up.

63
Q

Describe top down way of looking at lifes origins?

A

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?
64
Q

Describe bottom up way of looking at lifes origins?

A

looking from the bottom upwards seeks to figure what happened by inferring what was there to start life

   this is like Miller’s experiment
65
Q

One arguement is that LUCA used…

A

…fermentation.

but – the enzymes that allow fermentation in Bacteria and Archaea are different – likely to have evolved independently

66
Q

What does LUCA stand for?

A

Last Universal Common Ancestor

67
Q

What were the most talked about hydrothermal vents known as?

A

black smokers

68
Q

the hydrothermal vents known as ‘black smokers’ are often cited as…

A

… possible sources of life

69
Q

Arguements against hydrothermal vents being the possible sources of life?

A

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

70
Q

What is the other type of hydrothermal vents recently discovered?

A

alkaline vents

71
Q

What temp are alkaline vents?

A

At a lower temperature (70 degrees C)

72
Q

What are alkaline vents full of?

A

full of dissolved hydrogen
they are also full of cell-sized pores

73
Q

What is the life span of alkaline vents compared to black smokers?

A

Alkaline vents are longer lived.

74
Q

What do alkaline vents result from?

A

result from thermal expansion of olivine rocks by hydroxylation (serpentinisation)

75
Q

Alkaline vents seem like…

A

good candidates

76
Q

Why are alkaline vents seen to be good candidates to be the source of life?

A

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

Introduction to Evolution and Genetics (18 decks)

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