Week 4 Flashcards
Mutation
All genome sequence variations are changes in sequence and therefore mutations
only a small proportion result in a change of phenotype
Four classes of genome sequence variations
Substitution
Indels
Inversion
Translocation
Substitution
Base subsituitions result in single nucleotide polymorphism (SNPs)
a base substitution results in a new allele
transition and transversion
Transition
Purine to purine
pyrimidine to a pyrimidine
Transversion
purine for a pyrimidine
pyrimidine for a purine
Transversion vs transition
for everyone transition there should be two traversions
transversions based on randomness should occur more frequently
but transitions occur more frequently
Indels
insertion and deletions
smallest: insertion and deletion of one base
define the break point at either end of the insertion
Deletions can remove a whole gene, insertions can be very large transposons.
Inversion
smallest inversion of two bases
look for breakpoints
Can be Mb in length.
Translocation
Movement of DNA between different chromosomes
look for breakdown
Mutation Rate
mutations over some measure of time
rate is concerning a measure of time, generation, cell, division
Two mutation rates
Gene mutation rate
Mutation rate = genome variation rate
Two mutation rates
Gene mutation rate
Mutation rate = genome variation rate
Gene mutation rate
mutation disrupts allele causing a detectable change in the phenotype
Bacterial gene rate: 2-8 10^-9/division
Drosophila gene: 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
Mutation Rate
Mutations over some measure time
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)
Consequence of Mutation Rate
1-Evolutionary change
2-Animal cloning
Mutations and evolutionary change
generation after generation genomes change
Clones of cells with somatic mutation. Different mutations occurring in different cells.
Ratio of transitions to transversions.
Predicted: 2 transversion for every transition
Observed: 2 transition for evert tranversion
changes in genome sequences are caused by mechanism
in coding DNA it is 3 transition for every transversions
Spontaneous Replications errors
Tautomeric shifts
Wobble
Strand Slippage
Unequal crossing over
Tautomeric shift
Aromatic rings can be tautomers not just one structure
protons can move between the nitrogen and oxygen
results in alternate base pairing; can result in replication errors,
A-C
T-G
Wobble
tRNA binding in codons
but we can get it in DNA
Thymine guanine wobble in which they line up slightly differently and in that different conformation hydrogen bonds are beginning to form
alternative base pairing mechanisms
T-G
A-C
Strand Slippage
Indels
during DNA replication when you replicate through areas of low complexity DNA polymerase can sometimes when its pulling strands apart and trying to synthesize DNA place this A down on the T casuing the loop out on the A. Insertion of an A to strand slipagge on the newly sequenced strand.
slippage of the template strand, deletion.
slippage of the newly synthesized strand, insertion
Unequal crossing over
Improper alignement of repeats
Spontaneous Chemical Changes
Deamination
Depurination
Deamination
Due to the instability of amine on cytosine
cytosine has a rate of deamination
deamination results in uracil
5-methylcytosine to thymine
results in a transition mutation
Depurination
Purines can spontaneously leave DNA
Apurinic site: sugar phosphate but no base
Mutagens
1-Base analogs 2-Alkylating Agents 3-Deaminating chemicals 4-Hydroxylamine 5-Oxidative radicals 6-Intercalating agents 7-UV light
Base Analogs
5-bromouracil
looks like thymine bu the methyl group has been exchanged with bromine
bromine is electron withdrawing
Bromine can create an ionized form of 5BU it can be recognized as a cytosine
A or G binding
Alkylating Agents
Ethyl-methylsulfonate
ethylates G and T
ehtylated guanine can bind thymine
Deaminating chemicals
Deamination can occur spontaneously at a determined rate but chemicals can increase the rate of deamination
Hydroxylamine
hydroxylamine of cytosine can bind to adenine
Oxidative radicals
eukaryotes generates ROS in the mitochondria, they can modify the bases in DNA
Transversion
Intercalating agents
flat benzene rings that slide very easily into the slight hydrophobic space between the stacked base pairs
results in insertion mutations
UV light
UV light induces thymine dimers resulting in covalent bonds between thymine bases (dimers)
DNA repair
Mismatch repair.
Direct repair.
Base-Excision repair.
Nucleotide-Excision Repair.
Mismatch repair
Bacteria can distinguish the newly synthesized strand from the template strand. Bacteria methylates their DNA at specific positions using methylases, when the template strand is replicated the other strand has no methyl group. When an error has occured it is able to travel back along the strand to the nearst methyl group and specifically nick the newly replicated strand and remove the DNA all the way past the mismatch and then have that DNA resynthesized removing the mismatch reinstated the original sequence because methylation takes time in bacteria.
Transposon
Selfish DNA
Jumping genes
Transposable element
Transposon
parasitic elements that only think of themselves and replicate to throughout the genome
some transposons can jump between organisms
Consequence of Transposition
Increase in genome sizes
Disruption of genes
Altered expression
Genome rearrangement
Genome size
variation of sizes in eukaryotic genomes, the difference is in the amount of noncoding DNA, transposon
as genome size increases %non-coding DNA increases
Why is there a lot of non-coding DNA?
non-coding DNA can sometimes have a function
a lot of the noncoding DNA is just transposable elements that have moved through the genome
race to replicate
reducing consequences of transposition
The mass mobilization of transposons is suppressed in most organisms.
there are active mechanisms that surpress transposition
How can transposition alter genes
disrupt genes
interrupt regulatory sequences of genes
Can alter the location of the gene expression, can decrease the expression of the gene in particular cells.
genome rearrangement: homologous transposon sequences can pair with one another due to similar complimentary sequences resulting in rearrangement of areas in the genome
Orientation
Direct orientation
Inverted Orientation
Orientation of the transposons relative ot one another can determine how they will cross over and the subsequent rearrangement.
Direct the sequence read from transposon one is the same as the sequence read from transposon 2
Genome rearrangement: direct orientation
Deletion
Genome rearrangement: inverted regions
inversion of sequences between the two recobination sites
Genome rearrangement: direct orientation on the same chromosome misagned with another chromosome
deletion and duplication
insertion of segments in the loop into the other chromosome
Direction orientation on different chromosomes
Rarely during meiosis the transposons will pair with one another.
translocation
Mechanisms of Transposition
1-Duplication of target sequence 2-Type II transposons -replicative -cut and paste 3- Type I -retrotransposition
Duplication of target sequence
when a transposon is supposed to be inserted in a specific target site transposases will come and introduce a double stranded breaks, the break is staggared
single stranded gaps are filled by DNA polymerase
here is the creating of a direct repeat of five bases
Structure of transposons
exicision 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: Flanking direct repeats
Transposable element: terminal inverted repeat
Flaking direct repeat
Type II transposons
replicative
cut and paste
Type II: Replicative
during transposition the original transposon is replicated into a new insertion sites
original transposon is maintained, the transposon is replicated to its new site
Type II: cut and paste
during transposition, the transposon is cut out and reinserted at a different point
transposon is cut out of its site leacing double stranded break that needs to be repaired
Type I: Retrotransposition
Transposase using an RNA intermediate
Have long terminal direct repeats (LTR)
Eukaryote specific
Steps of retrotransposition
1-LTRs and transposon is transcribed into mRNA
2-Reverse transcriptase makes a DNA copy
3-DNA copy is inserted into the genome
Observation the retrotransposons with LTRs look similar to retroviruses in the genome so this led to the suggestion that retrotransposons and the LTR in the genome were transposing using a retrovirus like mechanism
Experiment determining the mRNA intermediate
intron placed in the DNA and is spliced out before being included into the genome
Genomes are not stable
In a growing population of genomes with no selelction pressure, the total number of alleles increase every generation
SNP
Single nucleotide polymorphisms
serve as genetic markers
medellian alleles
differences, polymorphisms, the SNPs are very close to one another the chances that a recombination event will occur between them are very low.
they are in linkage disequilibrium they tend to segregate together
very little chances of exchange between the homologous
haplotype comes from haploid, we consider one homologous chromosome and the other homologous chromosome
Affected vs Unaffected
we could expect that mutational changes would be found in the group of affected individuals with a specific set of alleles
Haplotypes and disease
SNPs that are close to one another and therefore rarely seperated by recombination resulting in linkage disequilibrium
any mutation causing a change in phenotype can be linked to a haplotype
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
How do you 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.
on the x-axis we indicate the position of the SNP on the chromosome
low distribution on the plot: these SNPs are not associated they are not in linkage disequilibrium and randomly associate with phenotype
How do you 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.
on the x-axis we indicate the position of the SNP on the chromosome
low distribution on the plot: these SNPs are not associated they are not in linkage disequilibrium and randomly associate with phenotype
Use SNPs to
determine relatedness
the more snps you have the more distantly related you are
MSTN gene and horse speed
Myostatin is a protein that suppresses muscle development.
slow horses have high levels of myostatin expression
fast horse lower level of myostatin expression. SINE transposon in the regulatory region.
Human evolution
Homo erectus
Homo Heidelbergensis
Neanderthal, Denisovans, Homo sapiens
migration
homo heidelbergenesis left africa and moved to greece
neanderthal move to europe
denisovans to asia
This occurs after they have migrated this populations grow and generation after generation mutations arise in hteir genomes and they start to have particular haplotypes.
Homo sapiens interbreed; therefore, Neanderthals are not distinct species because we can find the Neanderthal and Denisovan haplotypes in European and Asian Homo sapiens.
A strong association and a high linkage desiquilibrium around this reigon of the chromosome 3, this region in chromosome three that shows up in individuals that have a s severe covid-19 infection came from neanderthal.
