Molecular Biology Flashcards

1
Q

What is the definition of a mutation

A

A change in the genetic material of a cell or virus

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2
Q

What is the definition of a gene

A

A genomic sequence directly encoding for functional products (proteins or RNA)

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3
Q

What is a De Novo mutation

A

Mutations present in your genome but not your parents.

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4
Q

What causes mutations

A

Replication/repair errors, metabolism, ionizing radiation, mutagens in food.

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5
Q

Where do De Novo mutations happen

A

In the parents germ cells or in the early stages of embryogenesis

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6
Q

How can net DNA mutation rate be lowered

A

Decreasing the rate of DNA damage or increasing the DNA repair efficiency.

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7
Q

Why do most mutations not affect the phenotype

A
  1. Most mutations fall in unimportant regions like between exons or genes
  2. Most mutations are recessive, so two copies are needed to effect phenotype
  3. Mutations may be silent or conservative resulting in the same or a very similar protein being produced
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8
Q

Why are mutations not typically passed onto the next generation

A

Only mutations that occur in the germ line cells are passed onto the next generation and the mutation rate in the germ line is a much lower

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9
Q

Why are mutations important for evolution

A

Natural selection relies on variation, which is acquired through sex and spontaneous mutations

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10
Q

How much of the genome codes for phenotypic traits

A

1-2%

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11
Q

What are the different outcomes of point mutation?

A
  1. Silent- A change in an nucleotide that does not result in a different amino acid
  2. Nonsense- Change results in a stop codon
  3. Missense: Change in nucleotide which results in a different amino acid being produced, this can be conservative: amino acid replace with a chemically similar one, or nonconservative: amino acid changed with a chemically different one.
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12
Q

Why do recessive mutations require inbreeding to show?

A

Recessive mutations must have a copy on both alleles, it would be very rare for someone else to mutate the exact same so they must both come from one ancestor

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13
Q

How do recessive mutations affect gene products

A

Recessive mutations are usually loss of function mutations, so protein functions worse than before

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14
Q

How can a recessive mutation effect a phenotype

A

Through having too little product or too much substrate in the pathway of the mutated protein

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15
Q

What type of mutation is albinism and how does it effect phenotype

A

Albinism is a recessive, loss of function mutation. The phenotype arises due to too little product.
The mutation effects the protein tyrosinase which controls the pathway between tyrosine and melanin. Tyrosinase is working less than normal resulting in too little melanin, which causes the white appearance.

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16
Q

What type of mutation is phenylketonuria and how does this effect the phenotype?

A

Phenylketonuria is a recessive, loss of function mutation. The phenotype is caused by too much substrate. The mutation effects phenylalanine hydroxylase which controls the pathway between phenylalanine and tyrosine. Phenylalanine hydroxylase functions less that normal so there is a build up of phenylalanine which is converted to phenylpyruvic acid. Too much phenylpyruvic acid leads to progressive brain disfuction. This can be diagnosed using a birthtest and treated with a low phenylalanine diet.

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17
Q

What is incomplete dominance?

A

When having one mutated allele is enough to show the phenotype but having two mutated alleles is worse. When one allele is wildtype, it still contributes to the protein pool.

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18
Q

How is dominance and recessiveness determined

A

When two different alleles contribute to a protein pool, if there is enough wildtype to show the wildtype phenotype, the the mutated allele is recessive. And vice versa

19
Q

Why are recessive mutations not normally an issue for wildtype functioning

A

One functioning allele is typically enough to function normally.

20
Q

What different types of dominant mutation are there?

A

Gain of the normal function (more efficient- this is more common) or gain of new function (rose colours).

21
Q

What type of mutation is achondroplasia and how does this effect the phenotype?

A

Achondroplasia is a gain of normal function dominant mutation. It is due to 1 or 2 point mutations of FGFR3 resulting in the receptor getting locked in an active state. This receptor normally acts to inhibit limb growth, turned off by FGF binding. The mutated gene is always turned on irrespective of FGF binding so bone growth is always inhibited.

22
Q

What is weird about achondroplasia heritability?

A

Achondroplasia is a very common De Novo mutation, only 20% of cases have a parent with the condition. Having a homozygous dominant genotype results in death.

23
Q

What type of mutation is Huntington’s and how does this affect the phenotype

A

Huntington’s is gain of new function dominant mutation. It is a result of the extension of a CAG codon repeat at the start of the open reading frame on the Huntington gene. This codes for more glutamine and the increase in the polyglutamine tract is neurotoxic. This mutation is an example of a variable number tandem repeat: microsatellite.

24
Q

How could wing growth be inhibited by a recessive or a dominant mutation?

A

Recessive: mutation of gene which promotes wing growth
Dominant: mutation of gene which inhibits wing growth

25
Q

Why is the nature of a mutation important for treatment therapies?

A

Treatment strategies are opposite depending on the mutation effect:
1. Gene therapy: introduce a wildtype allele (recessive) or inactivate the mutated allele (dominant)
2. Develop an agonist (activator) or an antagonist (inhibitor).

26
Q

How much of our genome is exons and what is the rest

A

Over half of our genome is intergenic DNA and only a small amount of our gene related DNA are exons (1.5%). Most of the genome is comprised of genome wide repeats (LINES, SINES, LTR elements and Transposons.

27
Q

What are homologous genes?

A

Genes of high similarity between and within species, inherited from a common ancestor

28
Q

What is the difference between an ortholog and a paralog?

A
  1. Orthologs are genes in different species that are very similar and have the same function/role
  2. Paralogs are copies of a single gene within a species that arose through gene duplication
29
Q

Why are orthologs important in genetics?

A

Orthologs which we share with a model species allow us to study a gene in another organism and apply it to our genome.

30
Q

How much of our genome varies across the population?

A

Humans typically show 99.5% similarity across the population. Only differ by 0.5% due to mutations.

31
Q

What are INDELS

A

INDELS are insertion/deletion mutations. This is when one or multiple nucleotides base pairs get added or deleted. They can have a major effect on the protein due to frameshift mutations if they occur in the open reading frame. These mutations can also effect non-coding RNA and regulatory regions. Most occur outside of genes so do not effect gene function.

32
Q

Why are most genes recessive?

A

Mutations are random so are more likely to cause damage than improvement.

33
Q

What are variable number tandem repeats?

A

These are regions of nucleotide repeats that vary widely across the population. These are pretty stable across generations. A repeat of 1-9bp is a microsatellite- these are known as short tandem repeats in forensics. A repeat of 10-100bp is a minisatellite.

34
Q

What are copy number variants?

A

Copy number variants are variations in the number of copies of a DNA sequence/chromosomal segment. A segment of a chromosome may be duplicated or deleted, can vary in length.

35
Q

What is the different between variant and polymorphism mutations?

A

Variants have frequency of less than 1% and polymorphisms have a frequency of greater than 1%.

36
Q

What are single nucleotide polymorphisms?

A

SNPs are a single base pair change which has a frequency of greater than 1% in the population. There can be rare SNPs (1-5%) or common (5%+). Can be silent, missense or nonsense mutations or occur outside the open reading frame. Most SNPs are in hardy Weinberg equilibrium and are not evolving.

37
Q

What is evolution in molecular terms?

A

Evolution is the change of allele frequency in a gene pool over time

38
Q

How can evolution be measured at one time point?

A

Evolution is a process which happens over a long period of time, it can be measured in a single time point using the hardy Weinberg equilibrium.

39
Q

What does the hardy weinberg equilibrium predict?

A

The hardy weinberg equilibrium predicts the genotype frequencies present in a population will stay the same if all conditions are met. The equation can be used to work out the genotype and allele frequencies of a population.

40
Q

What are the 5 hardy weinberg assumptions?

A
  1. No mutations
  2. Random mating
  3. No gene flow in or out of population
  4. Very large population size
  5. No natural selection
41
Q

What is PTC and how does its taste differ across the population?

A

Phenylthiocarbamide is a bitter tasting chemical which has a resemblance to many bitter tasting chemicals such as those is brassica vegetables. 70% of the population perceive PTC as bitter.

42
Q

How do tastebuds work?

A

Taste buds are elongated epithelial cells. Chemicals that bind to taste buds start an intracellular signaling cascade. This sends a signal to the brain which produces the taste depending on the tastebud.

43
Q

What is the nucleotide and amino acid change at SNP 785 to go from taster to non-taster?

A

Cytosine to a thymine-
Alanine to a Valine