Week 4

Question 1

Mutation

Answer 1

All genome sequence variations are changes in sequence and therefore mutations

only a small proportion result in a change of phenotype

Question 2

Four classes of genome sequence variations

Answer 2

Substitution
Indels
Inversion
Translocation

Question 3

Substitution

Answer 3

Base subsituitions result in single nucleotide polymorphism (SNPs)

a base substitution results in a new allele

transition and transversion

Question 4

Transition

Answer 4

Purine to purine

pyrimidine to a pyrimidine

Question 5

Transversion

Answer 5

purine for a pyrimidine

pyrimidine for a purine

Question 6

Transversion vs transition

Answer 6

for everyone transition there should be two traversions

transversions based on randomness should occur more frequently

but transitions occur more frequently

Question 7

Indels

Answer 7

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.

Question 8

Inversion

Answer 8

smallest inversion of two bases

look for breakpoints

Can be Mb in length.

Question 9

Translocation

Answer 9

Movement of DNA between different chromosomes

look for breakdown

Question 10

Mutation Rate

Answer 10

mutations over some measure of time

rate is concerning a measure of time, generation, cell, division

Question 11

Two mutation rates

Answer 11

Gene mutation rate

Mutation rate = genome variation rate

Question 11

Two mutation rates

Answer 11

Gene mutation rate

Mutation rate = genome variation rate

Question 12

Gene mutation rate

Answer 12

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

Question 13

Mutation Rate

Answer 13

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)

Question 14

Consequence of Mutation Rate

Answer 14

1-Evolutionary change

2-Animal cloning

Question 15

Mutations and evolutionary change

Answer 15

generation after generation genomes change

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

Question 16

Ratio of transitions to transversions.

Answer 16

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

Question 17

Spontaneous Replications errors

Answer 17

Tautomeric shifts
Wobble
Strand Slippage
Unequal crossing over

Question 18

Tautomeric shift

Answer 18

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

Question 19

Wobble

Answer 19

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

Question 20

Strand Slippage

Answer 20

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

Question 21

Unequal crossing over

Answer 21

Improper alignement of repeats

Question 22

Spontaneous Chemical Changes

Answer 22

Deamination

Depurination

Question 23

Deamination

Answer 23

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

Question 24

Depurination

Answer 24

Purines can spontaneously leave DNA Apurinic site: sugar phosphate but no base

Question 25

Mutagens

Answer 25

``` 1-Base analogs 2-Alkylating Agents 3-Deaminating chemicals 4-Hydroxylamine 5-Oxidative radicals 6-Intercalating agents 7-UV light ```

Question 26

Base Analogs

Answer 26

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

Question 27

Alkylating Agents

Answer 27

Ethyl-methylsulfonate ethylates G and T ehtylated guanine can bind thymine

Question 28

Deaminating chemicals

Answer 28

Deamination can occur spontaneously at a determined rate but chemicals can increase the rate of deamination

Question 29

Hydroxylamine

Answer 29

hydroxylamine of cytosine can bind to adenine

Question 30

Oxidative radicals

Answer 30

eukaryotes generates ROS in the mitochondria, they can modify the bases in DNA Transversion

Question 31

Intercalating agents

Answer 31

flat benzene rings that slide very easily into the slight hydrophobic space between the stacked base pairs results in insertion mutations

Question 32

UV light

Answer 32

UV light induces thymine dimers resulting in covalent bonds between thymine bases (dimers)

Question 33

DNA repair

Answer 33

Mismatch repair. Direct repair. Base-Excision repair. Nucleotide-Excision Repair.

Question 34

Mismatch repair

Answer 34

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.

Question 35

Transposon

Answer 35

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

Question 36

Consequence of Transposition

Answer 36

Increase in genome sizes Disruption of genes Altered expression Genome rearrangement

Question 37

Genome size

Answer 37

variation of sizes in eukaryotic genomes, the difference is in the amount of noncoding DNA, transposon as genome size increases %non-coding DNA increases

Question 38

Why is there a lot of non-coding DNA?

Answer 38

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

Question 39

reducing consequences of transposition

Answer 39

The mass mobilization of transposons is suppressed in most organisms. there are active mechanisms that surpress transposition

Question 40

How can transposition alter genes

Answer 40

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

Question 41

Orientation

Answer 41

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

Question 42

Genome rearrangement: direct orientation

Answer 42

Deletion

Question 43

Genome rearrangement: inverted regions

Answer 43

inversion of sequences between the two recobination sites

Question 44

Genome rearrangement: direct orientation on the same chromosome misagned with another chromosome

Answer 44

deletion and duplication insertion of segments in the loop into the other chromosome

Question 45

Direction orientation on different chromosomes

Answer 45

Rarely during meiosis the transposons will pair with one another. translocation

Question 46

Mechanisms of Transposition

Answer 46

``` 1-Duplication of target sequence 2-Type II transposons -replicative -cut and paste 3- Type I -retrotransposition ```

Question 47

Duplication of target sequence

Answer 47

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

Question 48

Structure of transposons

Answer 48

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

Question 49

Type II transposons

Answer 49

replicative | cut and paste

Question 50

Type II: Replicative

Answer 50

during transposition the original transposon is replicated into a new insertion sites original transposon is maintained, the transposon is replicated to its new site

Question 51

Type II: cut and paste

Answer 51

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

Question 52

Type I: Retrotransposition

Answer 52

Transposase using an RNA intermediate Have long terminal direct repeats (LTR) Eukaryote specific

Question 53

Steps of retrotransposition

Answer 53

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

Question 54

Experiment determining the mRNA intermediate

Answer 54

intron placed in the DNA and is spliced out before being included into the genome

Question 55

Genomes are not stable

Answer 55

In a growing population of genomes with no selelction pressure, the total number of alleles increase every generation

Question 56

SNP

Answer 56

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

Question 57

Affected vs Unaffected

Answer 57

we could expect that mutational changes would be found in the group of affected individuals with a specific set of alleles

Question 58

Haplotypes and disease

Answer 58

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

Question 59

How do you represent the association with large datasets of 100,000 of SNPS?

Answer 59

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

Question 59

How do you represent the association with large datasets of 100,000 of SNPS?

Answer 59

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

Question 60

Use SNPs to

Answer 60

determine relatedness | the more snps you have the more distantly related you are

Question 61

MSTN gene and horse speed

Answer 61

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.

Question 62

Human evolution

Answer 62

Homo erectus Homo Heidelbergensis Neanderthal, Denisovans, Homo sapiens

Question 63

migration

Answer 63

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.