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BS3000 Evolutionary Genetics > Introns > Flashcards

Introns Flashcards

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Biology 101 flashcards
1
Q

Give examples of genes that have arisen by intron gain

A

Rice catalaseA gene

Midge globin genes

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2
Q

What does an introns early model suggest happened with introns?

A

Loss of introns in many lineages

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3
Q

What does an introns late model suggest happened with introns?

A

Sporadical transposition of introns into few lineages

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4
Q

What do functional introns contain?

A

snoRNAs or miRNAs

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5
Q

When do phylogenetic analyses suggest that functional introns were present?

A

In early metazoans

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6
Q

What does snoRNAs stand for?

A

Small nucleolar RNAs

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7
Q

Do bacteria contain snoRNAs?

A

Not found (yet)

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8
Q

Are introns junk?

A

Maybe, but also have enhancer sequences determining when and where a gene is expressed
Have other properties apart from abilities to splice themselves out of genes, e.g. Tetrahymena group 1 intron

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9
Q

What types of introns are there?

A 
Group I introns
Group II introns
Spliceosomal introns
tRNA
Group III twintrons
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10
Q

What are group III twintrons?

A

Introns within introns

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11
Q

Give examples of group III twintrons

A

Chloroplasts

Euglena

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12
Q

RNA splicing is catalysed by a spliceosome formed from the assembly of what?

A

U1, U2, U5 and U4/U6 snRNPs plus other components

> 150 proteins > ribosome

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13
Q

When were introns discovered?

A

1977

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14
Q

What did Gilbert propose about introns in 1978?

A

Proposed ‘exon shuffling’ for protein evolution

Introns EARLY

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15
Q

What do Go plots define?

A

A compact protein module

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16
Q

What gave rise to mitochondria?

A

Purple bacteria

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17
Q

Describe group I introns

A

Self splicers
In rRNA of lower eukaryotes, e.g. Tetrahymena
Also tRNA, rRNA and mRNA genes of bacteria and higher plants
In eukaryotes found in mitochondria and chloroplasts

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18
Q

Describe group II introns

A

Mitochondrial and chloroplasts reverse transcriptase ORF, self-splicers, different splice mechanism from eukaryote pre-mRNAs (5’ GU, 3’ A- any purine, AG)

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19
Q

Describe spliceosomal introns

A

5’ GU, 3’ AG

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20
Q

Describe tRNA introns

A

Any base for donors/acceptors

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21
Q

What did Blake suggest about introns in 1978?

A

Exon = globular protein domain with compact structure.

Shuffling domains to make new proteins helped by introns which separate domains.

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22
Q

What are introns more common in, eukaryotes or prokaryotes?

A

Introns are more common in higher eukaryotes

Rare in lower eukaryotes and prokaryotes

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23
Q

What do Go domains define?

A

Exons

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24
Q

What does the limited intron distribution suggest about introns?

A

It is much more likely that they came in later sporadically

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25
Q

What did further analysis into introns and compact domains by Gilbert in 1998 reveal?

A

That there is a correlation between intron position and protein domain only for introns in phase zero, i.e. between codons ~40% introns

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26
Q

What percentage of introns are ancient compared to those due to later insertions?

A

~40% introns are ancient whereas ~60% might be due to later insertions

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27
Q

Are phase zero introns in more ancient or recent parts of genes?

A

More ancient

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28
Q

Is there any correlation for introns that fall within codon, phase 1 and 2?

A

No correlation

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29
Q

Which introns would be lost more readily, functional or non-functional?

A

Non-functional

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30
Q

What is the function of snoRNAs?

A

To methylate rRNA

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31
Q

What does each individual gene in split tRNA genes encode?

A

A hairpin

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32
Q

Recent phylogenetic analysis reveals several split tRNA genes sporadically in archaeobacteria. What does sequence analysis suggest about this?

A

Arisen through recent acquisition through mobile elements

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33
Q

What is the take home message about introns?

A

Introns may have provided an ancient mechanism for bringing sequences together, so intron/exon boundaries could be a very early evolutionary development

34
Q

What do other complex features of the split genes also suggest?

A

An ancient origin

35
Q

What is Carpediemonas?

A

A free living soil anaerobic eukaryote

36
Q

Does Carpediemonas have identifiable mitochondria?

A

No

37
Q

What does Carpediemonas have in its carbamate kinase genes? And what is the significance of this?

A

A splicesomal intron

Pushes back origins of introns even earlier but still after eukaryotic evolution

38
Q

What was discovered about Trichomonas in 2005?

A

It has spliceosomal introns

39
Q

Were introns and spliceosomal proteins present in the earliest eukaryotes?

A

Yes, but as the spliceosome is very complex is must have evolved much earlier

40
Q

How many species revealed positional conservation in functional versus non-functional introns?

A

28 species

41
Q

Was introns late before or after protein synthesis was established?

A

After

42
Q

Was introns early before or after protein synthesis was established?

A

Before

43
Q

Is the intron early view intron loss or intron gain?

A

Intron loss

44
Q

Is the intron late view intron loss or intron gain?

A

Intron gain

45
Q

What type of intron does the Giardia lamblia ferrodoxin gene have?

A

Spliceosomal introns

46
Q

What type of organism is the Giardia lamblia?

A

A primitive gut eukaryote

47
Q

Describe the metabolism of Giardia lamblia

A

Anaerobic, does not have identifiable mitochondria

48
Q

What does the finding of the spliceosomal protein genes Sm (Prp8p, Prp11p) suggest about Giardia lamblia?

A

It has deep phylogenetic roots

If introns added late, then date is pushed back to earliest common eukaryotic ancestor

49
Q

Describe what is meant by intron conservation

A

Different lineages show different rate of gain and loss but ancestor was intron rich irrespective of phylogeny

50
Q

What was the rate of intron loss 1.5-2 billion years ago?

A

2E-9 to 2E-10 per year

51
Q

What was the rate of intron gain 1.5-2 billion years ago?

A

6E-13 to 4E-12 per year

52
Q

When scientists took 450 human genes that have snoRNAs or miRNAs containing introns, they found orthologues in how many other species?

A

27

53
Q

It is thought that introns could be functional or non-functional, true or false?

A

True

54
Q

According to the introns first theory, if the spliceosome was found in early eukaryotes, and took a long time to evolve, what must there have been?

A

A lot of introns in the earliest eukaryotic ancestors.. prokaryotes?

55
Q

Are spliceosomal proteins ancient or modern?

A

Ancient and found in the most primitive eukaryotes

56
Q

Are spliceosomes small or large?

A

Huge! - took a long time to evolve

Have U1-6snRNAs, but >150 other proteins

57
Q

Where are snoRNAs preferentially encoded?

A

Within spliceosomal introns of genes encoding chaperones (heat shock proteins) and ribosomal proteins

58
Q

Why must introns be older than the exons surrounding them?

A

Because they are critical to maturing the ribosome: must be older than the origin of proteins

59
Q

What kingdom, other than eukaryotes, are snoRNAs found in and what does this mean about its ancestry?

A

Found in archaea! (no nucleolus, no introns, no spliceosome)

Thus must have been in eukaryotic/archaen ancestor

60
Q

If introns predate proteins, the spliceosome must have been around in ancestors of archaea/eukaryotes, therefore archaea must have lost..

A

The spliceosome

61
Q

Why would you need spliceosomal sno/RNAs in archaea if you do not have introns or a spliceosome?

A

Back to RNA world. Maybe as replicators became more efficient, longer RNA molecules would be generated. Need to keep the catalytic part and remove the junk RNA

62
Q

When not in chaperone/ribosomal protein genes, where are snoRNAs often found?

A

In introns where exons are non-coding, i.e. exon is junk

63
Q

What is the suggested theory for the origin of translation?

A

Maybe unused junk RNA became exons?

64
Q

What is the smallest microorganism known (1% volume of E. coli)?

A

Nanoarchaeum equitans

65
Q

What is the genome size of Nanoarchaeum equitans?

A

0.5Mb

66
Q

Where are Nanoarchaeum equitans found and with what other hyperthermophile?

A

Found in submarine Icelandic hot geysers (100 degrees centigrade) with Ignicoccus hospitalis

67
Q

Why has Nanoarchaeum equitans been studied?

A

To investigate other roles for introns, particularly the function of ancient introns

68
Q

Where is the split of the tRNA split gene?

A

After position 37, one nucleotide downstream of anticodon, and in position of tRNA intron

69
Q

Do tRNA split genes have the same or different promoters?

A

Same promoter (for RNA polymerase III) found in 5’ half and 3’ half

70
Q

For tRNA split genes, sequences upstream of 3’ half (GC rich) are the reverse complement of sequences found..

A

Downstream of 5’ half

71
Q

Which type of introns are mobile?

A

Group III

72
Q

Which is more complicated, the ribosome or the spliceosome?

A

The spliceosome

73
Q

Introns must have evolved early as without recombination there would be..

A

Phase issues

74
Q

When was the eukaryotic/prokaryotic split?

A

Very early, around 2-3 billion years

75
Q

Which is the more accepted theory, introns early or introns late? Why?

A

Introns early
Common ancestors are intron rich
More evidence

76
Q

Which is the more accepted idea, RNA life started before chemical life, or chemical life started before RNA life?

A

RNA life started before chemical life

77
Q

Where is an intronic sequence normally located?

A

Just downstream of the anticodon site

78
Q

What are the three theories for introns?

A

Introns late
Introns early
Introns first

79
Q

Briefly describe what a cladogram shows

A

No time on it

Lengths of branches don’t reflect time

80
Q

Briefly describe what a phylogenetic tree shows

A

Time associated with branches

81
Q

What can bias the view of evolution?

A

Natural selection

BS3000 Evolutionary Genetics (5 decks)

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