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SGUL - Genomics > Molecular Evolution > Flashcards

Molecular Evolution Flashcards

1
Q

What is Evolution?

A

On the origin of species
- A theory put forward to explain the current variety of life on earth
- Natural selection and Fitness
- Underpins our understanding of biology

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2
Q

Define “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

Define “Fitness”

A

How well a species is able to reproduce in its environment.

Anything that increases fitness is selected for, anything that deceases fitness is selected against and other neutral changes will vary randomly.

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4
Q

Describe the modern synthesis

A
  • It was realised that evolution could be linked to genetics to explain modular processes underlying evolution
  • Genetic variation is the main source of heritable changes in a species
  • Frequencies of genetic variants are affected by:
    Selection, Mutation, Migration, Genetic Drift
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5
Q

Describe how Selection affects genetic variants

A
  • Genetic variants that confer a POSITIVE advantage will be selected for (and vice versa)
  • Examples of + advantages include resistant to disease, ability to metabolise new food source, antibiotic resistance.
  • Some parts of the genome are resistant to change as they contain vital sequences - they are conserved
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6
Q

Describe how Mutation affects genetic variants

A
  • Mutation is the process by which Variation in the genome arises
  • We all carry large numbers of genomic variants and their frequency will depend on selection and when they first arose
  • A rare variant may have risen recently or be deleterious and being selected against or both
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7
Q

Describe how Migration affects genetic variants

A
  • Migration is the physical movement of people from a different population which results in new pools of variants being introduced to an existing population.
  • This is called Admixture
  • Population frequencies of specific variants can change purely due to admixture and not be disease related
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8
Q

Describe how Genetic Drift affects genetic variants

A
  • This is how the frequency of a variant changes in a population due to chance
  • Not all organisms in a population will pass on their genetic variants
  • Mechanisms such as recombination will also result in not all variants being passed on
  • All variants are subject to genetic drift
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9
Q

Describe Sequence Conservation

A
  • DNA sequence conservation is vital to the survival of an organism. Doesn’t show much evidence of variation.
  • Most variants in these regions will be selected against as they’re likely to have a strong deleterious effect.
  • There is some flexibility for variation in the third base of codons as some amino acids are encoded by multiple codons.
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10
Q

What are the different types of Sequence conservation in genes?

A
  • High conservation - Coding regions (not exons as these contain non coding regions)
  • Intermediate conservation - promoter, 5’ UTR, 3’ UTR, terminator
  • Low conservation - Introns, 3rd base of codons, terminator
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11
Q

What can Conservation be used for?

A

CROSS SPECIES COMPARISON
- Can be used to generate evolutionary profile for a gene or family
- Allows us to identify the important regions of a gene
- This allows us to concentrate on areas that appear to be important in novel genes

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12
Q

What is Phylogenetics?

A

Phylogenetics is the study of evolutionary relationships among biological entities

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13
Q

What is a phylogenetic tree? How can it be used?

A
  • Has multiple diagram types
  • Main aim is to illustrate the relatedness of different species or sequences
  • Distance between two entities on a tree is usually related to how similar they are
  • Distance is usually related to both evolutionary pressures and to time
  • Time estimated by measuring mutation rates
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14
Q

How has Phylogenetics been used in the past?

A
  • It had been theorised that HIV had been introduced to some of the human population via a contaminated polio vaccine in Africa
  • Some polio vaccines used to be produced using cultured chimpanzee cells, which could have been infected with HIV
  • Worobey eat al (2004) investigated this using phylogenetic
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15
Q

What is gene duplication?

A

The Duplication of the DNA sequence containing a gene

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16
Q

What is the typical mechanism for gene duplication?

A

The unequal crossing over during meiosis

17
Q

What happens after gene duplication?

A
  • One copy can continue the original function
  • The other copy can evolve new functions through changes in the coding sequence and/or control sequences.
18
Q

What is Unequal Crossing Over?

A
  • Recombination between sequences that are not the correct sequence but are very similar
  • Often low copy number repeat sequences
19
Q

Describe the Globin genes

A
  • Has 2 clusters
  • Alpha-like are on chromosome 16 - 3 genes and 3 pseudogenes
  • Beta-like are on chromosome 11 - 5 genes and 1 pseudogene
  • The genes are arranged in order of expression during development
20
Q

Describe the Alpha and Beta chromosome positioning???
Check over

A

Alpha: Haemoglobins in order of production during development
Beta: Symbols are Greek letters – Zeta, Epsilon, Alpha, Gamma, Delta and Beta
Green indicates DNA control elements

21
Q

Describe the Globin Cluster Evolution

A
  • Very clear that Globin genes have evolved through duplication and accumulation of mutations
  • Some are functioning and some are not (Pseudogenes)
  • Promoters have diverged so they bind to different transcription factors and allow expression of genes at different stages of development.
  • Embryo -> Foetus -> Postnatal
22
Q

What are Pseudogenes?

A
  • After gene duplication, One gene can maintain the original function and the other can diverge
  • Pseudogenes typically have many mutations and are non functional
  • There are many of them in the genome
  • They complicate PCR/sequencing
23
Q

Sickle Cell Disease. When do the symptoms typically start?

A

Typically start at 5-6 months of age

24
Q

What are the main symptoms of Sickle Cell Disease?

A
  • Anaemia: Fatigue, Restlessness, Juandice
  • Acute Pain Episodes: “Crises” x due to oxygen deprivation of tissues
  • Increased frequency of infections: Spleen damage
25
Q

What are the other symptoms of sickle cell disease?

A

Stroke, Pulmonary Hypertension, Gallstones, Liver and Kidney problems, Joint problems, Delayed Puberty

26
Q

Explain the genetics of Sickle Cell Disease

A
  • A single base change occurs in the beta Globin gene of Haemoglobin A = Haemoglobin S (HbS)
  • Codon Changes from GAG to GTG
  • This changes the amino acid from Glu -> Val at position 6 of the protein
  • An autosomal recessive genetic disease
  • The original mutation occurred 7300 years ago
27
Q

Describe how Sickle Cell Disease is passed on through genetics

A
  • If both parents have a copy of the HbS then each child has a 1 in 4 chance of having Sickle Cell Anaemia (2 copies of HbS)
  • Sickle trait is common in African, Middle Eastern, Mediterranean and Indian populations and very rare in Northern Europe
28
Q

Give an example of a heterozygote advantage

A
  • 2ncopies of the HbS variant has significant negative effects on reproductive ability - SCD
  • However one copy of the HbS variant confers resistance to severe Malaria
  • This “heterozygote advantage” means that the HbS variant is maintained in the population when otherwise it would have been selected against and lost.
29
Q

SUMMARY

A
  • Mutational processes can lead to genes being duplicated
  • They can also lead to new functions
  • Evolutionary pressure can be very strong and lead to maintenance of apparently damaging variants
  • Malaria and HbS are good examples of this

SGUL - Genomics (21 decks)

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