Midterm 2 - Notes 3 (Part 1)

Question 1

What is molecular evolution mediated by?

Answer 1

Transposons

- but doesnt have to be

Question 2

What are 4 major models of genetic innovations?

Answer 2

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

Question 3

What is the most common model for genetic innovations?

Answer 3

Intragenic mutations

Question 4

Where do intragenic mutations occur?

Answer 4

Within protein coding regions

Question 5

What happens with intragentic mutations?

Answer 5

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

Question 6

What is gene duplication?

Answer 6

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

Question 7

What does gene duplication allow?

Answer 7

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

Question 8

What is DNA segment shuffling?

Answer 8

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

- contains parts of old genes in recombination

Question 9

What is vertical transfer?

Answer 9

Transfer from one generation to the next in the same genome

- this is a slow process

Question 10

What is horizontal transfer?

Answer 10

Transfer from one genome to another

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

Question 11

Exon shuffling

Answer 11

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

Question 12

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

Answer 12

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

Question 13

What are cis elements needed for?

Answer 13

Expression and processing

Question 14

What is transposition of a retrotransposon mediated by?

Answer 14

RNA transposon

Question 15

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

Answer 15

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

Question 16

What does retrotransposons involve?

Answer 16

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

Question 17

What may or may not be included with retrotransposons?

Answer 17

Cis regulatory elements

Question 18

What does homologous recombination between TE not involve?

Answer 18

Transposition

- can use any type of TE

Question 19

What does homologous recombination between TE need?

Answer 19

TE

Question 20

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

Answer 20

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

Question 21

What does homologous recombination between TE involve?

Answer 21

Double cross over between identical TE sequences

Question 22

What is the problem in homologous recombination between TE?

Answer 22

The segments are very similar

Question 23

What do most proteins contain?

Answer 23

Multiple domains

Question 24

What can domain shuffling via transposons do?

Answer 24

Combine exons from distinct proteins

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

Question 25

What can combinations create?

Answer 25

New functions

Question 26

EGF

Answer 26

Epidermal growth factor

Question 27

What does an EGF initiate?

Answer 27

Signalling cascade

- binds to a receptor

Question 28

What does chymotrypsin do?

Answer 28

Its a protease (for digestion)

• it cleaves peptide bonds
• unspecific

Question 29

What does urokinase do?

Answer 29

It is a plasminogen activator

- it cleaves plasminogen and activates the formation of blood clods

Question 30

What does Factor IX(9) do?

Answer 30

It cleaves factor X(10)

- allows blood clod generation

Question 31

What does plasminogen do?

Answer 31

It cleaves fibrin

• it dissolves blood clods
• protein protein interaction domain

Question 32

What are retro-copies?

Answer 32

Copies of regular genes

- via transposition of “normal” cellular gene transcripts

Question 33

What may RT of non-LTR transposons act on?

Answer 33

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

Question 34

What do retropsons (retro-copies) differ from?

Answer 34

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

Question 35

What are retro-copies prone to become? (2)

Answer 35

1. Processed pseudogene

2. Neo-functionalization

Question 36

What are 4 things that are needed in order to become successful is a retro-copy?

Answer 36

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

Question 37

Pseudogene

Answer 37

A section of a chromosome that is an imperfect copy of a functional gene
- evolves neutrally