week 4 Flashcards
Mutations
Genome sequence variation e.i changes in the sequence.
small proportionr result in a change in phenotype.
Four classes of genome sequence variation
Single bp substitutions
Indels
Inversions
Translocation
Substitution
Single base pair subsitution
snps
Alleles
Two classes of subsitution
Transition and Transversion
Transversion
Purine to Pyrimidine and vice versa (expected to occur more freuqently)
Transversion
Purine to Pyrimidine and vice versa (expected to occur more freuqently)
Transition
Purine to Purine and Pyrimidine to Pyrimidine
occurs more frequently
Indels
Insertions and Deletion
Look for break points.
If not done in multiplies of three can completement change the ORF
Missense
Wrong Amino Acid is introduce in the protein
Nonsense
Premature stop codon
Nonsense
Premature stop codon
Inversion
order of bases is flipped (smallest is two bases)
Translocation
Movement of DNA segement between different chromosomes
Mutation Rate
Mutations over some measure of times.
Gene mutation rate Mutation rate (genome variation rate)
Gene mutation rate
observing the mutation disrupting the allele causing a detectable change in phenotype.
Mutation Rate
Mutations over some measure of time
Gene Mutation Rates
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
Gene mutation rate varies
From gene to gene. Some genes are larger providing more location for a mutation to take place.
DNA seuqence mutation rates
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)
Conequences of Mutation Rate
Evolutionary change
Animal cloning
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.
60
Somatic sequence variation
Clones of cells with somatic mutation. Different mutations occuring in different cells.
What is a practical consequence of mutation rate for cloning mammals?
Cloned animal cells acquire mutations renderering the clone different from the organism it came from.
Spontaneous Replication Errors
Tautomeric Shifts
Wobble
Strand Slipagge
Unequal crossing over
Tautomeric Shifts
Proton shift leads to another ring structure.
Consequence is alternate base pairing
Transition mutation
Wobble
Non watson crick base pairing.
Alternative base pairing
Strand Slippage
Create Indels
Template strand slippage: deletion
NSS slippage: insertion
Areas of low complexity
Unequal Crossing Over
Improper alignment of repeats.
One shortened and one long chromosome
Spontaneous Chemical Changes
Deamination
Depurination
Deamination
Lose of amine form cytosine results in a uracil.
Transversion
Deamination
Lose of amine form cytosine results in a uracil.
Transversion
5 methylcytosine (5mC)
Loss of amine from 5 methylcytosine leads to thymine.
transition mutation
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.
Mutagens
Base Analogs
Alkylating Agents
Deaminating Chemicals
Hydroxylamine
Oxidative radicals
Intercalating agents
UV light
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
Alkylating Agents
Ethyl-methylsulfonate ethylates G and T
GT pairing
Deaminating Chemicals
Nitrous Acid
Deamination occurs spontaneously at a determined rate but chemicals can increase the rate.
Hydroxylamine
Hydroxylamine adds an OH to cytosein and it binds to Adenine
Oxidative Radicals
Eukaryotes generate ROS in the mitochondria, they can modify the bases in DNA.
Transversion
Intercalating agents
Hydrophobic benzene rings.
slide very easily into the slight hydrophobic space between stacked base pairs.
results insertion mutation
UV Light
UV light induces thymine dimers resulting in covalent bonds between adjacent residues.
DNA repair
- Mismatch repair.
- Direct repair.
- Base-Excision repair.
- Nucleotide-Excision Repair.
Mismatch repair
Bacteria can distinguish which base was wrongfully incorporated by looking for the nearest methylated site.
methylation is only on the template strand.
Atomic Bomb
Somatic mutation rate increased.
Germline mutation rate remained the same.
3x10^-6
Transposons
Mobile elements that move freely within the genome
Consequence of Transposition
Increase in genome size
Disruption of genes
Altered Expression
Genome rearrangement
How do transposons contributed to the genome?
they increase the amount of non-coding DNA, increasing the genome size.
Mass Mobilization of transposons
is surpressed in most organisms.
There are active mechanisms that supress transposition (piwiRNA)
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.
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.
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.
Direction orientation on the same chromosome
Deletion
one transposon is left
Inverted orientation on the same chromosome.
Inversion + two translocons
Direct orientation on the same chromsome. Misaligned
Deletions and duplications.
Two chromosome segments.
One transposon removed.
Mechanisms of Transposition
Duplication of target sequence
Type II:
replicative
cut and paste
Type I: retrotransposition
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.
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.
Type II transposons
Transpose with DNA intermediates and have short inverted repeats at the end.
Binding sites for transposase
inverted repeats
Replicative Transposon (Type II)
During transposition the original transposon is replicateed into a new insertion site.
increases the number of transposons
Cut and Paste (Type II)
During transposition the transposon is cut out and reinserted at a different point.
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
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
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.
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.
Single Nucleotide Polymorphism are
Are genetic markers (Alleles)
Linkage disequilibrium
Non random association between genetic elements on a chromosome
Haplotype
Haploid set of genetic elements on one chromosome (one for each chromosome)
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
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.
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.
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.
Traditional Horse Breeding
Dilution of genes, offspring recieve half and offspring of offspring recieve 1/4
Geography of neanderthals and denisovans
Denisovans went east
Neanderthals went west
each population develops their own haplotypes.
Geography of neanderthals and denisovans
Denisovans went east
Neanderthals went west
each population develops their own haplotypes.
Homo sapiens
have interbred with neanderthals and denisovans. shared haplotypes between the groups.
