Gene Loss, Base Composition Evolution, and Trannsposition

Question 1

What is the most common fate of duplicated genes

Answer 1

Gene loss

Question 2

Two main mechanisms of gene loss

Answer 2

1. Abrupt mutational event leads to sudden deletion of a gene (unequal crossing over, incorrect non-homologous end joining)
2. slower process of nonfunctionalisation, an acculuation of loss-of-function mutations that eventually result in a non-processed pseudogene

Question 3

The road to nonfunctionalisation

Answer 3

1. Malfunctional gene product can still be expressed
2. Truncated protein product or altered essential AA can sometimes have deleterious effect

Question 4

Unitary pseudogenes

Answer 4

A single copy gene that is nonfunctionalisaed. No paralogs exist in the genome - fewer than 100 in human genome.

Question 5

What gene have humans, old word and new world monkeys lost that causes scurvy?

Answer 5

L-gulano-y-lactone oxidase gene

Question 6

How many of the exons are deleted in L-gulano-y-lactone oxidase gene?

Answer 6

7/12

Question 7

What gene is responsible for sweet taste perception?

Answer 7

Tas1r2

Question 8

Effect of the loss of the MYH16 gene in humans?

Answer 8

two bp deletion causes smaller jaw muscles which are potentially more beneficial for speech and cranial capacity

Question 9

Caspase 12

Answer 9

Polymorphic in humans- we have function version and pseudogenes.
Normal function is in inflammation and innate immunity. Loss of gene possibility results in a reduced risk of sepsis

Question 10

2 hypotheses for variation in GC contents

Answer 10

1. Mutationist - GC biases are just a reflection of mutation patterns
2. Selectionists - GC biases are a adaption to selective pressure

Question 11

Can mutation bias alone explain the variation in GC contents in bacteria?

Answer 11

The fact that GC contents can be high should prove that selection is playing a role

Question 12

what kind of genomes are more thermodynamically stable?

Answer 12

GC rich genomes

Question 13

What does UV radiation produce?

Answer 13

Thymidine dimers - GC rich sequences are more protected

Question 14

Leading strands tend to be enriched for

Answer 14

G and T

Question 15

Lagging strands tend to be enriched for

Answer 15

C and A

Question 16

What was the breakage at C9 of maize caused by?

Answer 16

Ds (Dissociation at the breakage site
Ac (Activator) impossible to map

Question 17

Transposable elements (TE)

Answer 17

Mobile genetic element that is able to move or propagate within a genome and some move between genomes

Question 18

Transposition

Answer 18

Movementt of genetic material from one genomic location to another within the same genome

Question 19

Are plasmids that can be transferred horizontally TEs?

Answer 19

No

Question 20

Classification of TEs - what they move

Answer 20

1. Conservative - cut and paste transposition
2. Replicative - copy and paste transposition

Question 21

Conservative transposition

Answer 21

Cut and paste

Donor element excised from donor site and transposed into new element. The donor no longer has the transposable element

Question 22

Replicative transposition

Answer 22

Copy and paste

Both the donor and the target have the TE

Question 23

Classification of TEs - how they move

Answer 23

1. Class I or retrotransposable elements
2. Class II elements

Question 24

Class I or retrotransposable elements

Answer 24

Move via an RNA intermediate and reverse transcriptase - and integrase They always replicate

Question 25

Class II elements

Answer 25

DNA-mediated transposition. No RNA involved
Can be conservative or replicate - only requires transposase

Question 26

Classification of TEs - autonomy

Answer 26

1. Active - encode all parts of the transposition machinery themselves (e.g. transposase in class II and reverse transcriptase and integrase in Class I)
2. Fossil - no longer transposable - made immobile by some type of mutation

Question 27

Where and when can TEs transpose themselves - species

Answer 27

Some TEs are species-specific, others can travel across different hosts and even different kingdoms of life

Question 28

Where and when can TEs transpose themselves - Cell type and developmental stage

Answer 28

Some TEs can transpose in all cells, others are highly specific. Some of the only mobile germ cells or during meoisis

Question 29

Where and when can TEs transpose themselves - Genomic regions

Answer 29

Majority of TEs show little or no target site specificity, although a few are highly specific

Question 30

Effect of TEs on target sites

Answer 30

Almost always causes duplication of a small stetch of DNA at a target site - this is due to a staggered cut made by the transposase before inserting the element. The fill-in repair of these gaps results in direct repeats flanking the TE

Question 31

What is the hallmark of transposition?

Answer 31

Direct repeats flanking the TE

Question 32

What do transposons normally travel on?

Answer 32

Plasmids

Question 33

The exogenous genes carried by bacterial transposons can confer resitance to

Answer 33

Antibiotics, heavy metals and heat

Question 34

Retroelement

Answer 34

Any sequence that contains reverse transcriptase

Question 35

Retroviruses

Answer 35

ssRNA viruses that infect vertebrates

1. Viral genomic RNA is reverse-transcribed into cDNA after invasion of a host cell
2. Integrase pastes cDNA into host genome - provirus
3. Viral coding region is flanked by long terminal repeats (LTRs) which contain promoters for transcription and reverse transcription
4. Most are mobile elements (can integreate within genome) a few are transposable (move within the genome)

Question 36

Endogenous retroviruses

Answer 36

Retroviruses that have infected the germline and can be transmitted through vertical descent
Make up 8% of human genome

Question 37

Retrotransposons

Answer 37

RT-mediated transposable elements that do not construct virion particles. They lack the env (envelope) gene

Question 38

Retrotransposons

Answer 38

RT-mediated transposable elements that do not construct virion particles. They lack the env (envelope) gene

Question 39

What is likely to have given rise to a retrovirus?

Answer 39

LTR-retrotransposon

Question 40

LINEs

Answer 40

Autonomous non-LTR retrotransposons
3k-7k bp repeated sequence
approx 20% of human genome

Question 41

SINEs

Answer 41

Non-autonomous non-LTR retrotransposons - non-autonomous LINEs
75-500bp and don’t code for any protein
13% of human genome
Mostly derive from tRNA
Don’t have their own reverse-transcriptase so steal it from LINEs
Have a region of its sequence that matches the corresponding LINE

Question 42

Why are retrosequences usually called “dead on arrival”?

Answer 42

1. Reverse transcription is very inaccurate - can introduce loss-of-function mutations
2. They are inserted somewhere without necessary regulatory sequences - they never get expressed