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Genomics > Molecular Evolution > Flashcards

Molecular Evolution Flashcards

1
Q

What is creationism?

A

The idea that species are made by a supernatural intelligent creator

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2
Q

Explain how supernatural explanations and science work

A

Science cannot disprove supernatural explanations
Whatever observations are made, they could be explained by supernatural forces
But equally it is impossible to carry out science, once you allow supernatural explanations

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3
Q

What are the assumptions science has to make regarding supernaturalism

A
  • Natural phenomena have natural explanations

- Which can be studied by scientific experiment

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4
Q

What are the assumptions made in religious terms?

A
  • God works through natural laws

- Not individual miracles

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5
Q

What constitutes a scientific theory?

A

To be a scientific theory, the theory must:
- Make testable predictions
- Stand / fall according to whether predictions are
confirmed or refuted

“a scientific theory must be falsifiable”

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6
Q

What are Darwin’s theory predictions?

A

Evolutionary theory says that man and apes descend from a common ancestor. Therefore intermediate forms must be present in the fossil record

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7
Q

What does natural selection predict?

A
  1. Spontaneous natural variation occurs

2. These variations are stably inherited

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8
Q

What is the modern synthesis of evolution?

A

Natural Selection
Is not simply a hypothesis based on a finite set of data
But a logical deduction from our knowledge of molecular genetics and ecology

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9
Q

What is variation?

A

mutation, due to changes in DNA sequence
mostly mistakes during DNA synthesis
rare because DNA synthesis is exceedingly accurate
most mutations are neutral or deleterious, a minority are beneficial

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10
Q

What is selection?

A

the idea those organisms better adapted to their environment due to desirable alleles survive and produce more offspring

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11
Q

What is reproductive success dependent upon?

A

Observation of nature and science of Ecology shows
Individuals are in competition with Predators, prey and members of own species

new alleles may increase or decrease reproductive success

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12
Q

What is relative fitness (W)?

A

The average number of surviving progeny of a genotype (compared with competing genotypes) after one generation

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13
Q

What does W<1 mean for the allele frequency?

A

If w < 1, the frequency of the allele

  • will decrease with each generation
  • until the allele disappears (negative selection)
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14
Q

What does a W > 1 mean?

A

If w > 1 the frequency of the allele

  • will increase with each generation
  • until the allele reaches fixation (positive selection)
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15
Q

What are the different types of small mutations that occur?

A
  • Base substitutions
  • Small insertions
  • Small deletions
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16
Q

What are the larger mutations that occur?

A
  • Large deletions
  • Large DNA duplications
  • Insertions of transposable elements
  • Viral insertions
  • Chromosome rearrangements
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17
Q

How can we use molecular phylogeny to identify ancestors of species?

A

DNA mutations accumulate over time, so species that share a recent common ancestor will have fewer differences than species that are more distantly related

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18
Q

How do we create a phylogenic family tree?

A

Sequence data can be used to generate evolutionary family trees

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19
Q

What are the medical implications of phylogenic trees?

A

substances produced by fungi, which are toxic to bacteria, but not fungi, able to be identified - antibiotics

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20
Q

Explain why there are consistently more differences (per unit length of DNA) in intron sequences than in exon sequences?

A

Introns removed during splicing, exon include coding sequences
Any changes in exon coding sequence likely due to a change in protein structure which cause faulty proteins - removed via negative selection over generations

As introns don’t have such functional significance, their removal by negative selection is less likely to occur and so remain in DNA

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21
Q

When looking at coding sequences, there are more differences in every 3rd nucleotide compared to the first two. Explain Why?

A

First two nucleotides are important in defining amino acids
If these are changed the amino acid changes (mostly bad effects)
3rd nucleotide is often redundant and ∴ doesn’t change amino acid sequence - no major effect

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22
Q

What sets the reading frame?

A

The reading frame is set by the first codon which is always AUG

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23
Q

What is a synonymous substitution?

A

A substitution that doesn’t cause a change in amino acid sequence

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24
Q

What is a non-synonymous substitution ?

A

Nucleotide mutation that alters the amino acid sequence

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25
Q

Which sequences of DNA are most highly conserved?

A

Enzyme active sites

Structural regions of proteins

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26
Q

Which DNA sequences are moderately conserved?

A

Signal regions in 5’ and 3’UTRs

Promoters

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27
Q

Why are some sequences less highly conserved than others?

A

in low conserved areas the base changes have little/no effect as less functional DNA

28
Q

Which sequences are weakly conserved?

A

Enhancers (in introns and intergenic DNA)

Other intronic and intergenic DNA

29
Q

What is the significance of Gene evolution?

A

Gene duplication is a major driving force of evolution.

30
Q

What occurs once a gene has been duplicated?

A
  • one copy continues to maintain original function
  • the other can evolve new functions

Likely to be changes in both the coding sequence (i.e. in amino acid sequence) and in control sequences

31
Q

How did β globin gene locus evolution provide us with Hb?

A

Haemoglobins (Hb) are ancient in evolution.

Duplication of an ancestral gene gave rise to myoglobin and haemoglobin.

32
Q

Outline the features of myoglobin

A
  • In skeletal muscle
  • monomeric protein
  • Hyperbolic oxygen dissociation curve
  • Function: Oxygen storage
33
Q

outline the features of haemoglobin

A
  • In RBCs
  • Tetrameric protein
  • Sigmoidal Oxygen dissociation curve
  • Fucntion: Oxygen transport
34
Q

Why is myoglobin oxugen dissociation curve hyperbolic?

A

Myoglobin shows hyperbolic curve (steeper) for oxygen dissociation. Depending on Pk, doesn’t readily offload O₂ at low concentrations

35
Q

Explain why Hb has a sigmoidal oxygen dissociation curve

A

Hb has sigmoidal curve which at high PpO₂ becomes highly saturated but offloads O₂ readily at low PpO₂ - functionally required for humans

36
Q

Why is Hb the evolutionary globin used for Oxygen transport?

A

If we had myoglobin it would bind strongly in the lungs and not offload readily in the tissues - not functional

37
Q

How is the human β-globin gene evolved to what it is today?

A

Ancestral globin gene has undergone multiple duplications + modifications to give rise to α-globin gene complex on human chromosome 16, and the β-globin gene complex (chrom.11)

38
Q

What are the adult Hb compositions ?

A

alpha-2-beta-2
alpha-2-delta-2
alpha-2-gamma-2

39
Q

Why has HbF has evolved to have a higher oxygen affinity than HbA?

A

allows Foetal Hb to load O₂ from mothers placenta

40
Q

How did HbF evolve to have a higher Oxygen affinity than adult Hb?

A

Changes to the amino acid sequence of the gamma globin protein gives a high O₂ affinity

41
Q

How many gamma genes are there?

A

2
coding for proteins that differ by one a.a. residue
function differences are unknown

42
Q

How does gamma gene coding sequence change at birth?

A

γ-gene coding sequence changes by mutation in structure and regulatory sequence

43
Q

What changes occur to gamma gene from HbF to HbA?

A

the γ gene control sequences have evolved
so that γ-genes are expressed during foetal life
while the β-gene is expressed during postnatal life

44
Q

How do the changes to Gamma coding sequence in HbF occur at birth?

A

Promoter duplicated along with coding sequence
Promoter sequence evolved so β and γ promoters bind different transcription factors
Interact differently with gene enhancers
Differential control of β and γ genes

45
Q

How does the globin gene expression change at birth?

A

At birth β expression increases, γ decreases

46
Q

Explain how globin gene expression is altered at birth

A

due to controlling region (enhancer element) interacts with foetal globin promoter => causing γ expression
Then around birth there are changes in transcription factors causing interaction with β globin promoter increasing its expression.

47
Q

What is an LCR?

A

Locus control region

48
Q

What is Ψβ?

A

a pseudogene
It has clear sequence homology to the β-globin gene, but we know it can’t make a functional protein (many stop codons, mutations in key regulatory sequences)

49
Q

Outline the statistics on cystic fibrosis

A

CF

  • northern europe
  • 4/10,000 live births
  • 2% allele frequency
50
Q

Outline the features of β-thalassaemia

A

β-Thalassemia

  • Cyprus
  • 80/10,000 live births
  • 9% allele frequency
51
Q

Outline the features of Sickle Cell Anaemia

A

SCA

  • Tropical West Africa
  • 100-1600/10,000 live births
  • 10-40% allele frequency
52
Q

Outline the statistical features of Fanconi’s Anaemia

A

Fanconi’s Anaemia

  • 0.03/10,0000 live births
  • 0/2% allele frequency
53
Q

What is Fanconi’s Anaemia?

A 
Recessive lethal genetic disorder
Most affected patients die of bone marrow failure during childhood
Do not reproduce
Gene arises by random mutation
Eliminated by natural selection
Very low allele frequency
54
Q

How does SCA arise?

A
  • Point mutation in the β globin gene
    or
  • Mutant haemoglobin molecules
55
Q

Descrieb the point mutation in β globin gene causing SCA

A

Single amino acid substitution

a hydrophilic a.a. (glutamic acid) is replaced by a hydrophobic a.a. (valine) at position 6

56
Q

How do mutant Hb molecules cause Sickle cell shape?

A

Mutant haemoglobin molecules aggregate and form crystals when deoxygenated
Force red cells into characteristic “sickle” shape

57
Q

How do the mutant Hb cell crystals cause anaemia?

A

Cell lysis causing anaemia

Cell adhesion, causing blockage of small blood vessels, followed by tissue infarction

58
Q

What is the incidence of inheritance pf SCA?

A

Autosomal recessive inheritance

In tropical West Africa, and without modern medical care, few homozygotes survive childhood

59
Q

What ws JBS Haldane’s theory about SCA and thalassemia?

A

J.B.S.Haldane noted that thalassaemia and SCA are common in areas of endemic malaria. He hypothesized that heterozygotes for these alleles have resistance to malaria.

60
Q

What did the epidemiological studies carried out by A. Allison deduct about SCA and Malaria?

A

There is now excellent direct evidence for improved survival of SCA heterozygote carriers (up to 95% protection), due to lower parasitaemia and fewer severe complications.
Heterozygotes still catch malaria but are much less likely to die of malaria

61
Q

Describe the heterozygote advantage

A

AA

  • homozygous AA
  • don’t die of SCA
  • likely to die of Malaria

AS

  • Heterozygote AS
  • don’t die of SCA
  • less likely to die of Malaria

SS

  • Homozygous SS
  • die of SCA
62
Q

What is the main source of heritable changes in a species?

A

Genetic variation

63
Q

What is the frequency of genetic variation affected by?

A

Selection
Mutation
Migration
Genetic Drift

64
Q

What is migration?

A

The physical movement of people from a different population results in new pools of variants being introduced to an existing population
> called admixture

65
Q

What may be a cause of population frequency changes?

A

Population frequencies of specific variants can change purely due to admixture and not be disease-related.

66
Q

What are the symptoms of sickle cell disease?

A

Anaemia – fatigue, restlessness, jaundice

Acute pain episodes – “crises” – due to oxygen deprivation of tissues

Increased frequency of infections – spleen damage

Genomics (20 decks)

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