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genomics notes > molecular evolution > Flashcards

molecular evolution Flashcards

1
Q

What is molecular evolution?

A
  • Charles Darwin (1859)
  • based on natural selection and fitness
  • explains the current variety of life on earth
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2
Q

What is natural selection?

A

-the effects of a wide range of factors on the frequency of heritable changes in a species.

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3
Q

What is fitness?

A
  • how well species are able to reproduce in its environment.

- anything that increases fitness is selected.

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4
Q

what is modern synthesis theory?

A
  • theory that explains evolution could be unified with genetics to explain the molecular process underlying evolution.
  • genetic variation is the main source of heritable changes in a species.
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5
Q

what factors affect frequencies of genetic variants?

A
  • selection
  • mutation
  • migration
  • genetic drift
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6
Q

What is selection?

A

-genetic variants that confer a positive advantage will be selected for, and vice versa.

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7
Q

give examples of variants that confer a positive advantage in selection.

A

-resistance to disease
-ability to metabolise a new food source
antibiotic resistance
-change in appearance that enhances mate chance.

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8
Q

Why are some parts of the genome resistant to change, give an example?

A
  • Some parts of genome are resistant to change because they contain vital sequences which need to be conserved.
  • Example : DNA that encodes active site of enzyme
  • conserved = dont change through time
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9
Q

Define mutation

A
  • process by which variation in the genome arises
  • genomic variants and their frequency depends on selection and when they first arose.
  • a rare variant may arise due to base deletion(because it is disadvantageous) and being selected against.
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10
Q

Define migration.

A
  • physical movement of people from different population results in new pools of variant being introduced to an existing population (admixture).
  • change in population can be due to admixture, not always due to disease.
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11
Q

Define genetic drift.

A
  • how frequency of a variant changes in a population due to chance.
  • not all organisms in population will pass on their genetic variant (one gene from each parent not both)
  • recombination will also result in not all variants being passed on
  • all variants are subject to genetic drift
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12
Q

What is sequence conservation?

A
  • DNA sequence that is vital to the survival of an organism does not normally show much evidence of variation
  • most variants in these regions will be selected against as they are likely to have strongly deleterious effect.(disadvantage)
  • flexibility for sequence conservation due to the variation in the third base of a codon codes for same amino acid, so same protein will be coded.
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13
Q

What are 3 levels of conservation?

A
  • high conservation : coding regions (not exons as these contain non-coding regions)
  • intermediate conservation - prometer, 5’ untranslated region (UTR), 3’ UTR, terminator.
  • low conservation : introns, 3rd base of codons , terminator.
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14
Q

What can we use sequence conservation for?

A
  1. cross species comparison : generate an evolutionary profile for a gene or gene family
  2. cross -species conservation allows us to identify the important regions of a gene (and its protein)
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15
Q

Define phylogenetics

A

‘tree of life’

-incorporates all living things on earth and tries to show their relatedness in terms of evolution.

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16
Q

what are 4 steps of studying phylogenetics?

A
  1. observe sequence
  2. reconstruct evolutionary history
  3. learn more about evolutionary processes
  4. develop better evolutionary models.
17
Q

What does the distance between two entities on the tree show?

A
  • how similar they are
  • distance is related to evolutionary pressures and time.
  • time is estimated by mutation rate
18
Q

what are uses of phylogenetic in disease?

A
  • it had been theorised that HIV had been introduced to human population via a contaminated polio vaccine in Africa.
  • Worobey et al (2004) investigated this using phylogenetic
  • sampled HIV and SIV of humans and chimpanzees
  • found : polio vaccine does not give HIV bc evolutionary distance
19
Q

What is unequal crossing over?

A

recombination between sequences are not the correct sequence but are very similar
-often low copy number repeat sequence

20
Q

Give an example of globin gene.

A
  • two clusters

- alpha like and beta like

21
Q

What chromosome are alpha like and beta like genes found?

A
  • alpha like are on chromosome 16- 3 genes and 3 pseudogenes

- beta like are on chromosome 11 - 5 genes and 1 pseudogene

22
Q

What order are globin genes arranged?

A
  • genes are arranged in the order of expression during development.
23
Q

What are pseudo genes?

A
  • non functioning genes that look similar to functioning genes but are non functioning.
  • complicate PCR/sequencing
24
Q

What are symptoms of sickle cell disease?

A

anaemia - fatigue, restlessness, jaundice
- acute pain episode
increased frequency of infection - spleen damage

25
Q

What is the genetics of sickle cells?

A
  • a single base change in the beta -globin gene haemoglobin
  • codon change is a GAG to GTG
  • this is Glu to Val in position 6
  • on chromosome 11
  • autosomal recessive gene
26
Q

What is the chance of a child having SCD if parents have one copy of the the gene (Ss)?

A

1/4 chance of child having 2 copies = sickle cell

27
Q

Why is sickle cell more common in African, middle eastern and Indian population?

A

natural selection and sickle cell:

  • two copies has extremely negative effects on reproductivity (bc it causes sickle cell disease)
  • one copy of HbS variant helps resistance of severe malaria
  • this heterozygous advantage means that HbS variant is maintained in the population when it would have otherwise been selected against.
28
Q

What does hemoglobin consist of?

A
  • 2 alpha proteins

- 2 beta proteins

29
Q

Define gene duplication.

A
  • duplication of a DNA sequence consisting a gene.
30
Q

What causes gene duplication?

A
  • the typical mechanism is unequal crossing over during meiosis
31
Q

What happens after duplication?

A
  • one copy can continue the original function

- the other copy can evolve new functions through changes in the coding sequence and control sequences.

32
Q

What does globin cluster evolution show?

A
  • globin genes have evolved through duplication and accumulation of mutations (divergence)
  • some are functioning genes and some are pseudogenes
  • divergence of promoters has occured so they bind different transcription factors and allow expression of genes at different stages of development (embryo > feotus > postnatal) .

genomics notes (18 decks)

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