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week 4 Flashcards

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1
Q

Mutations

A

Genome sequence variation e.i changes in the sequence.

small proportionr result in a change in phenotype.

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2
Q

Four classes of genome sequence variation

A

Single bp substitutions
Indels
Inversions
Translocation

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3
Q

Substitution

A

Single base pair subsitution
snps
Alleles

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4
Q

Two classes of subsitution

A

Transition and Transversion

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5
Q

Transversion

A

Purine to Pyrimidine and vice versa (expected to occur more freuqently)

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5
Q

Transversion

A

Purine to Pyrimidine and vice versa (expected to occur more freuqently)

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6
Q

Transition

A

Purine to Purine and Pyrimidine to Pyrimidine

occurs more frequently

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7
Q

Indels

A

Insertions and Deletion

Look for break points.

If not done in multiplies of three can completement change the ORF

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8
Q

Missense

A

Wrong Amino Acid is introduce in the protein

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9
Q

Nonsense

A

Premature stop codon

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9
Q

Nonsense

A

Premature stop codon

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10
Q

Inversion

A

order of bases is flipped (smallest is two bases)

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11
Q

Translocation

A

Movement of DNA segement between different chromosomes

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12
Q

Mutation Rate

A

Mutations over some measure of times.

Gene mutation rate
Mutation rate (genome variation rate)
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13
Q

Gene mutation rate

A

observing the mutation disrupting the allele causing a detectable change in phenotype.

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14
Q

Mutation Rate

A

Mutations over some measure of time

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15
Q

Gene Mutation Rates

A

Bacterial gene rate 2-8 X 10-9/division

Drosophila gene rate 5-50 X 10-6/ gamete

Human gene rate 1-30 X 10-6/ gamete

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16
Q

Gene mutation rate varies

A

From gene to gene. Some genes are larger providing more location for a mutation to take place.

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17
Q

DNA seuqence mutation rates

A

Bacterial rate 1-10 X 10-10/ bp division

Eukaryotic rate 1 X 10-8/ bp gamete

Somatic rate 3 X 10-9/ bp mitosis

COVID 19 rate 8 X 10-4 / bp year (25 / year)

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18
Q

Conequences of Mutation Rate

A

Evolutionary change

Animal cloning

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19
Q

With a germ-line rate of 1 X 10-8 / bp gamete means that you inherited 1 X 10-8 / bp gamete X 2 parents providing 3 X 109 bp haploid genomes. Therefore, on average you have _ _ novel mutant alleles in your genome that will not be found in your parents’ genomes.

A

60

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20
Q

Somatic sequence variation

A

Clones of cells with somatic mutation. Different mutations occuring in different cells.

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21
Q

What is a practical consequence of mutation rate for cloning mammals?

A

Cloned animal cells acquire mutations renderering the clone different from the organism it came from.

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22
Q

Spontaneous Replication Errors

A

Tautomeric Shifts

Wobble

Strand Slipagge

Unequal crossing over

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23
Q

Tautomeric Shifts

A

Proton shift leads to another ring structure.

Consequence is alternate base pairing

Transition mutation

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24
Q

Wobble

A

Non watson crick base pairing.

Alternative base pairing

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25
Q

Strand Slippage

A

Create Indels

Template strand slippage: deletion

NSS slippage: insertion

Areas of low complexity

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26
Q

Unequal Crossing Over

A

Improper alignment of repeats.

One shortened and one long chromosome

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27
Q

Spontaneous Chemical Changes

A

Deamination

Depurination

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28
Q

Deamination

A

Lose of amine form cytosine results in a uracil.

Transversion

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29
Q

Deamination

A

Lose of amine form cytosine results in a uracil.

Transversion

30
Q

5 methylcytosine (5mC)

A

Loss of amine from 5 methylcytosine leads to thymine.

transition mutation

31
Q

Depurination

A

Loss of purines from DNA. Sugar phosphate backbone is still intact

DNA pol adds a random base (usually A) by default during replication of the strand.

32
Q

Mutagens

A

Base Analogs

Alkylating Agents

Deaminating Chemicals

Hydroxylamine

Oxidative radicals

Intercalating agents

UV light

33
Q

Base Analogs (5BU)

A

Thymine and 5 bromouracil

looks like thymine but methyl group has been exchanged with bromine (EWG).

Pairs with A or G (ionized)

Transition

34
Q

Alkylating Agents

A

Ethyl-methylsulfonate ethylates G and T

GT pairing

35
Q

Deaminating Chemicals

A

Nitrous Acid

Deamination occurs spontaneously at a determined rate but chemicals can increase the rate.

36
Q

Hydroxylamine

A

Hydroxylamine adds an OH to cytosein and it binds to Adenine

37
Q

Oxidative Radicals

A

Eukaryotes generate ROS in the mitochondria, they can modify the bases in DNA.

Transversion

38
Q

Intercalating agents

A

Hydrophobic benzene rings.

slide very easily into the slight hydrophobic space between stacked base pairs.

results insertion mutation

39
Q

UV Light

A

UV light induces thymine dimers resulting in covalent bonds between adjacent residues.

40
Q

DNA repair

A
  1. Mismatch repair.
  2. Direct repair.
  3. Base-Excision repair.
  4. Nucleotide-Excision Repair.
41
Q

Mismatch repair

A

Bacteria can distinguish which base was wrongfully incorporated by looking for the nearest methylated site.

methylation is only on the template strand.

42
Q

Atomic Bomb

A

Somatic mutation rate increased.

Germline mutation rate remained the same.

3x10^-6

43
Q

Transposons

A

Mobile elements that move freely within the genome

44
Q

Consequence of Transposition

A

Increase in genome size

Disruption of genes

Altered Expression

Genome rearrangement

45
Q

How do transposons contributed to the genome?

A

they increase the amount of non-coding DNA, increasing the genome size.

46
Q

Mass Mobilization of transposons

A

is surpressed in most organisms.

There are active mechanisms that supress transposition (piwiRNA)

47
Q

Genome Rearrangement (Transposition)

A

Transposons contain homologous sequences and can pair with one another due to similar complementary sequences resulting in reearrangement of areas in the genome.

47
Q

Genome Rearrangement (Transposition)

A

Transposons contain homologous sequences and can pair with one another due to similar complementary sequences resulting in reearrangement of areas in the genome.

48
Q

Orientation of Transposon Combination

A

Direct or inverted

Orientation of the transposons relative to one another can determine how they will cross over and the subsequent rearrangement.

49
Q

Direction orientation on the same chromosome

A

Deletion

one transposon is left

50
Q

Inverted orientation on the same chromosome.

A

Inversion + two translocons

51
Q

Direct orientation on the same chromsome. Misaligned

A

Deletions and duplications.

Two chromosome segments.

One transposon removed.

52
Q

Mechanisms of Transposition

A

Duplication of target sequence

Type II:
replicative
cut and paste

Type I: retrotransposition

53
Q

Duplication of target sequence

A

Transposase introduces a double stranded staggered break into the DNA strand where the DNA is supposed to be inserted.

Insert transposon at the opposite overhang corners

Single stranded gaps are filled by DNA polymerase.

Here is the creation of a direct repeat five bases.

54
Q

Cutting out transposon

A

Excision of a transposon leads to the creation of a scar in the genomic DNA sequence.

Transposase comes in and it will cut out the transposon leaving these duplicated regions that are fused back together.

5 nucleotide repeats flanking.

55
Q

Type II transposons

A

Transpose with DNA intermediates and have short inverted repeats at the end.

56
Q

Binding sites for transposase

A

inverted repeats

57
Q

Replicative Transposon (Type II)

A

During transposition the original transposon is replicateed into a new insertion site.

increases the number of transposons

58
Q

Cut and Paste (Type II)

A

During transposition the transposon is cut out and reinserted at a different point.

59
Q

Retrotransposition (Type I)

A

Transposes using RNA intermediates

Have long terminal direct repeats (LTR); direct orientation

Eukaryote specific

mRNA copy of transposon is transcribed

mRNA is reverse transcribed into a DNA copy.

DNA copy is inserted into a staggered cut site

59
Q

Retrotransposition (Type I)

A

Transposes using RNA intermediates

Have long terminal direct repeats (LTR); direct orientation

Eukaryote specific

mRNA copy of transposon is transcribed

mRNA is reverse transcribed into a DNA copy.

DNA copy is inserted into a staggered cut site

60
Q

Retrotransposons mechanism resembles

A

RT with LTRs look similar to retroviruses in the genome so this led to the suggestion that retrotranspsons and the LTR in the genome were transposed using a retrovirus like mechanism.

60
Q

Retrotransposons mechanism resembles

A

RT with LTRs look similar to retroviruses in the genome so this led to the suggestion that retrotranspsons and the LTR in the genome were transposed using a retrovirus like mechanism.

61
Q

Single Nucleotide Polymorphism are

A

Are genetic markers (Alleles)

62
Q

Linkage disequilibrium

A

Non random association between genetic elements on a chromosome

63
Q

Haplotype

A

Haploid set of genetic elements on one chromosome (one for each chromosome)

64
Q

Haplotypes can be associated with

A

Phenotypes caused by a mutation or allele.

Association is looking for known haplotypes and we assume that if the haplotypes show up with the affected individuals that either of these SNPs cause that phenotype or that there is a change near by that are associated due to linkage desquilibrium

65
Q

Represent the association with large datasets of 100,000 of SNPs

A

Manhattan Plot

Plot the probability that an association is not random, the higher the number the less likely it is going to occur by random chance.

66
Q

What Makes horses fast?

A

Myostatin is a protein that supresses muscle development faster horses have low myostatin levels.

insertion of sine transposon in the promotor region of the gene reduces expression of myostatin.

66
Q

What Makes horses fast?

A

Myostatin is a protein that supresses muscle development faster horses have low myostatin levels.

insertion of sine transposon in the promotor region of the gene reduces expression of myostatin.

67
Q

Traditional Horse Breeding

A

Dilution of genes, offspring recieve half and offspring of offspring recieve 1/4

68
Q

Geography of neanderthals and denisovans

A

Denisovans went east

Neanderthals went west

each population develops their own haplotypes.

68
Q

Geography of neanderthals and denisovans

A

Denisovans went east

Neanderthals went west

each population develops their own haplotypes.

69
Q

Homo sapiens

A

have interbred with neanderthals and denisovans. shared haplotypes between the groups.

Genetics (16 decks)

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