Midterm 2 - Notes 3 (Part 1) Flashcards

1
Q

What is molecular evolution mediated by?

A

Transposons

- but doesnt have to be

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2
Q

What are 4 major models of genetic innovations?

A
  1. Intragenic mutation
  2. Gene duplication
  3. DNA segment shuffling
  4. Horizontal transfer
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3
Q

What is the most common model for genetic innovations?

A

Intragenic mutations

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4
Q

Where do intragenic mutations occur?

A

Within protein coding regions

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5
Q

What happens with intragentic mutations?

A

Slightly changes the codon and possibly changes the function
- this occurs gradually

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6
Q

What is gene duplication?

A

Creates a 2nd copy that can be identical to the original gene in the genome

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7
Q

What does gene duplication allow?

A

Allows one copy to evolve while maintains the original function at the same time

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8
Q

What is DNA segment shuffling?

A

Mixing 2 parts of a genes in order to create a new gene

- contains parts of old genes in recombination

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9
Q

What is vertical transfer?

A

Transfer from one generation to the next in the same genome

- this is a slow process

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10
Q

What is horizontal transfer?

A

Transfer from one genome to another

  • this is a rapid process
  • novel function from distinct transfer
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11
Q

Exon shuffling

A

Is an evolutionary process for creating new genes form pre-existing ones by recombination between introns of 2 separated genes or by transposition of mobile DNA elements

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12
Q

Where are TE located via transposition of 2 integrated DNA transposons?

A

On either side of the gene (that wants to be cut out)

  • this is for translocation or duplication
  • its on either side the the exon for exon shuffling
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13
Q

What are cis elements needed for?

A

Expression and processing

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14
Q

What is transposition of a retrotransposon mediated by?

A

RNA transposon

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15
Q

Where are TEs located via transposition of a retrotransposon? (2)

A
  1. Upstream of the gene
    - gene duplication
  2. In an intron
    - exon shuffling
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16
Q

What does retrotransposons involve?

A

Run through transcription but utilizing the poly A signal on the TE

17
Q

What may or may not be included with retrotransposons?

A

Cis regulatory elements

18
Q

What does homologous recombination between TE not involve?

A

Transposition

- can use any type of TE

19
Q

What does homologous recombination between TE need?

20
Q

Where are the 2 pairs of TEs of the same type located on 2 different genomic location?

A
  1. On either side of the gene
    - gene translocation
  2. On either side of introns
    - exon shuffling
21
Q

What does homologous recombination between TE involve?

A

Double cross over between identical TE sequences

22
Q

What is the problem in homologous recombination between TE?

A

The segments are very similar

23
Q

What do most proteins contain?

A

Multiple domains

24
Q

What can domain shuffling via transposons do?

A

Combine exons from distinct proteins

- can have a drastic effect on the new types of proteins

25
What can combinations create?
New functions
26
EGF
Epidermal growth factor
27
What does an EGF initiate?
Signalling cascade | - binds to a receptor
28
What does chymotrypsin do?
Its a protease (for digestion) - it cleaves peptide bonds - unspecific
29
What does urokinase do?
It is a plasminogen activator | - it cleaves plasminogen and activates the formation of blood clods
30
What does Factor IX(9) do?
It cleaves factor X(10) | - allows blood clod generation
31
What does plasminogen do?
It cleaves fibrin - it dissolves blood clods - protein protein interaction domain
32
What are retro-copies?
Copies of regular genes | - via transposition of "normal" cellular gene transcripts
33
What may RT of non-LTR transposons act on?
May act on any RNA with a poly A tail - binds and acts on a regular mRNA on the cell and brings it back into the cell and preforms RT and brings it into the genome
34
What do retropsons (retro-copies) differ from?
Other gene duplicates - direct repeats and a poly A tail remainder - no introns because they would have been spliced out during RNA processing - no regulatory elements duplicated because they occur further upstream so they are not part of the duplication site and get a different expression pattern than the parent
35
What are retro-copies prone to become? (2)
1. Processed pseudogene | 2. Neo-functionalization
36
What are 4 things that are needed in order to become successful is a retro-copy?
1. Needs to be inserted completely - needs to have a complete genome - needs to be downstream of the promoter so it gets duplcicated 2. Must originate from a gene expressed - expressed in the germ line 3. Must gain regulatory elements - needs a promoter and a terminator 4. New regulatory modules must be advantageous - need an adaptive advantage to be able to be maintained
37
Pseudogene
A section of a chromosome that is an imperfect copy of a functional gene - evolves neutrally