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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
Tautomeric Shifts
Proton shift leads to another ring structure. Consequence is alternate base pairing Transition mutation
24
Wobble
Non watson crick base pairing. Alternative base pairing
25
Strand Slippage
Create Indels Template strand slippage: deletion NSS slippage: insertion Areas of low complexity
26
Unequal Crossing Over
Improper alignment of repeats. One shortened and one long chromosome
27
Spontaneous Chemical Changes
Deamination Depurination
28
Deamination
Lose of amine form cytosine results in a uracil. Transversion
29
Deamination
Lose of amine form cytosine results in a uracil. Transversion
30
5 methylcytosine (5mC)
Loss of amine from 5 methylcytosine leads to thymine. transition mutation
31
Depurination
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
Mutagens
Base Analogs Alkylating Agents Deaminating Chemicals Hydroxylamine Oxidative radicals Intercalating agents UV light
33
Base Analogs (5BU)
Thymine and 5 bromouracil looks like thymine but methyl group has been exchanged with bromine (EWG). Pairs with A or G (ionized) Transition
34
Alkylating Agents
Ethyl-methylsulfonate ethylates G and T GT pairing
35
Deaminating Chemicals
Nitrous Acid Deamination occurs spontaneously at a determined rate but chemicals can increase the rate.
36
Hydroxylamine
Hydroxylamine adds an OH to cytosein and it binds to Adenine
37
Oxidative Radicals
Eukaryotes generate ROS in the mitochondria, they can modify the bases in DNA. Transversion
38
Intercalating agents
Hydrophobic benzene rings. slide very easily into the slight hydrophobic space between stacked base pairs. results insertion mutation
39
UV Light
UV light induces thymine dimers resulting in covalent bonds between adjacent residues.
40
DNA repair
1. Mismatch repair. 2. Direct repair. 3. Base-Excision repair. 4. Nucleotide-Excision Repair.
41
Mismatch repair
Bacteria can distinguish which base was wrongfully incorporated by looking for the nearest methylated site. methylation is only on the template strand.
42
Atomic Bomb
Somatic mutation rate increased. Germline mutation rate remained the same. 3x10^-6
43
Transposons
Mobile elements that move freely within the genome
44
Consequence of Transposition
Increase in genome size Disruption of genes Altered Expression Genome rearrangement
45
How do transposons contributed to the genome?
they increase the amount of non-coding DNA, increasing the genome size.
46
Mass Mobilization of transposons
is surpressed in most organisms. There are active mechanisms that supress transposition (piwiRNA)
47
Genome Rearrangement (Transposition)
Transposons contain homologous sequences and can pair with one another due to similar complementary sequences resulting in reearrangement of areas in the genome.
47
Genome Rearrangement (Transposition)
Transposons contain homologous sequences and can pair with one another due to similar complementary sequences resulting in reearrangement of areas in the genome.
48
Orientation of Transposon Combination
Direct or inverted Orientation of the transposons relative to one another can determine how they will cross over and the subsequent rearrangement.
49
Direction orientation on the same chromosome
Deletion one transposon is left
50
Inverted orientation on the same chromosome.
Inversion + two translocons
51
Direct orientation on the same chromsome. Misaligned
Deletions and duplications. Two chromosome segments. One transposon removed.
52
Mechanisms of Transposition
Duplication of target sequence Type II: replicative cut and paste Type I: retrotransposition
53
Duplication of target sequence
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
Cutting out transposon
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
Type II transposons
Transpose with DNA intermediates and have short inverted repeats at the end.
56
Binding sites for transposase
inverted repeats
57
Replicative Transposon (Type II)
During transposition the original transposon is replicateed into a new insertion site. increases the number of transposons
58
Cut and Paste (Type II)
During transposition the transposon is cut out and reinserted at a different point.
59
Retrotransposition (Type I)
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
Retrotransposition (Type I)
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
Retrotransposons mechanism resembles
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
Retrotransposons mechanism resembles
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
Single Nucleotide Polymorphism are
Are genetic markers (Alleles)
62
Linkage disequilibrium
Non random association between genetic elements on a chromosome
63
Haplotype
Haploid set of genetic elements on one chromosome (one for each chromosome)
64
Haplotypes can be associated with
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
Represent the association with large datasets of 100,000 of SNPs
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
What Makes horses fast?
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
What Makes horses fast?
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
Traditional Horse Breeding
Dilution of genes, offspring recieve half and offspring of offspring recieve 1/4
68
Geography of neanderthals and denisovans
Denisovans went east Neanderthals went west each population develops their own haplotypes.
68
Geography of neanderthals and denisovans
Denisovans went east Neanderthals went west each population develops their own haplotypes.
69
Homo sapiens
have interbred with neanderthals and denisovans. shared haplotypes between the groups.

Genetics (16 decks)

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