R14 Life cycle of a gene

Question 1

How is evolution of a genome shown?

Answer 1

The size, proportion of non-coding, repeats and coding parts always changes

Question 2

What does an expanded and contracted genome mean ?

Answer 2

Gained or lost genes

Question 3

Where do genes come from ?

Answer 3

Horizontal gene transfer (HGT), duplication or de novo

Question 4

What is horiztonal gene transfer (HGT)

Answer 4

o When genetic material is shared between organisms that are not parents nor offspring.
o Antimicrobial and other chemical resistance, virulence and degradation of rare substances genes are created via this.
o Vertical gene transfer is between generations.
o Uptake from the environment (transformation), transferred to other bacteria (conjugation), injected by viruses (transduction)
o transfer of genes into the nuclear genome (mtDNA, Chloroplast DNA, endosymbionts, ingested prokaryotes)
o Genes imported by the organelles into the nuclear genome, the genes in the organelles for formation are already in the nucleas, so those genes are lost in the organelle.

Question 5

How does duplication allow new genes to form ?

Answer 5

o Most common in eukaryotes
o Duplication of whole genomes, chromosomes or DNA segments like genes and exons
o Whole genome Duplication by aneuploidy (number of chromosomes) leads to autopolyploidisation. There will be different outcomes depending on when the non-disjunction occurs in the 2 steps of meisosis.

o Whole genome duplication through hybridisation (allopolyploidisation), combination of 2 different species into one genome
o Replication error, loop may form on the nascent strand so that when it is used as a template then the gene will be duplicated.
o Unequal crossover – crossing over of the wrong arm leads to genes being gained and lost in homologous chromosomes.

o Retrotransposition, reverse transcription of RNA to DNA, then when the DNA is integrated back into the genome then 2 of the genes will be present.

Question 6

What is a de novo gene ?

Answer 6

A non-coding region of DNA acquiring a mutation that enables transcription by RNA pol II. The protein must benefit the organism

Question 7

How can new genes be lost?

Answer 7

o Deletion
 When the loop forms on the template strand it may be deleted
o Genetic drift
 Loss by chance
o Selection against
 Gene product may be deleterious
o Loss of function by mutation (pseudogenisation)

Question 8

How can a new gene be preserved ?

Answer 8

o Compensation
 One copy of the gene is silenced by transcription (like X), or transcription factors are split between the copies so that gene dosage doesn’t exceed optimum.
o Neofunctionalization
 New function
o Subfunctionalisation (temporal/ specialisation)
 Similar function, but subset a different use of that function. They may limit the use of that function or use it at a different time
 Similar to how haemoglobin changes as the embryo develops into a fetus then an adult
o Lack of selection against
o Selection for

Question 9

What is the two classes of transposable elements ?

Answer 9

Retrotransposon (class 1) – gets transcribed, then reverse transcribed to a DNA intermediate and then is integrated back into the genome. Usually far away, (copy and paste mechanism)
- Only transposable element that results in gene duplication
- they can be detected as they have no introns in as splicing occurs then integration back into the genome

DNA Transposon (class 2) – excision of the gene then integrated into the DNA, far away from the donor site. (cut and paste mechanisms)

Question 10

What will happen if the transposable element copies itself into another transposable element ?

Answer 10

• When they are duplicated, they are mutated and lose their ability to duplicate (pseudogenisation), they copy themselves into another TE and then causing a different base order leading to a major mutation.

Question 11

What causes the shortening of telomeres?

Answer 11

• Aging
• Cancer
• Immune diseases
• Cardiovascular diseases
• Metabolic diseases
• Psychiatric diseases

Question 12

How are telomeres transcriptionally silenced ?

Answer 12

They are made from heterochromatin

Question 13

How will transposable elements that copy themselves onto the end of chromosomes affect the genomic evolution ?

Answer 13

o Chromosomes will accumulate copies of these TEs over generations as long as there is not strong selection against the copies and there is no pseudogenisation of the TE transposable genes
o The telomeres are transcriptionally silent so we don’t need dosage compensation