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Biology 2581B Lecture Notes - Lecture 12: Southern Blot, Wild Type, Restriction Site

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pucespider269
6 Mar 2017
School
Western University
Department
Biology
Course
Biology 2581B
Professor
David R Smith

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Document Summary

Not all individuals within a species have identical genomes. Generally, an allele is labeled as the wild-type is more than 1% of the population express that allele. A polymorphic locus is one that has 2 or more alleles that are present in more than 1% of the population: alleles of a polymorphic locus are called genetic variants, rather than mutant or wild-types. A locus is any location within a genome that has a defined chromosome location. Polymorphic loci can have: single nucleotide polymorphisms (snps, insertions and deletions (indels or dips, simple sequence repeats (ssrs, copy number polymorphisms (cnps, complex variants. Most common genetic variation: single base pair substitutions. Can be spontaneous (occur during replication) or be induced (by a chemical mutagen) The mutant allele also happens to confer resistance to malaria. Need to use short probes, as probes that are too long will appear to bind specifically to mismatched dna even at high temperatures.

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Related Questions

If your biological parents are unrelated to one another, youprobably have about 3,000,000 sites in your genome that contain asingle nucleotide difference between maternal and paternalchromosomes. SNP arrays have been designed to survey about 500,000of the most commonly variable sites across the genome, and they candetect whether you contain allele A, allele B, or both, as well asthe copy number of each allele. If any segmental deletions orduplications exist in your genome, they would be detected bychanges in copy number and allele frequency for all SNPs within agenomic segment. Please describe how your SNP arrays would appearif your biological parents were biological brother and sister (thishappened by accident in England a few years ago between siblingswho grew up in different families). [Hint: you should pay attentionto the distribution and copy number of the alleles.]

1. Humans and chimpanzees share several polymorphic loci. Which is the LEAST plausible explanation for this fact?

A. Balancing selection has maintained polymorphism in both species

B. Incomplete lineage sorting left polymorphic loci and those have persisted since the speciation event.

C. Interbreeding has allowed introgression of alleles at theses loci in both directions.

D. Genetic variation provided by the polymorphic alleles enhances resistance to pathogens.

2. According to the social brain hypothesis, we should expect primates living in larger social groups to have:

A. Larger brains, specifically, a neocortex of relatively larger size

B. Lager incisors and canines, to defend against more social competitors

C. Smaller brains, because many individuals can work together to solve problems

D. Great variation in brain and neocortex size, with the dominant individuals having the largest

3. You extract DNA from human bones in an ancient village buried by volcanic ash. You discover that there is an extremely high frequency of the LCT allele for lactase persistence. What might you reasonably conclude about the population?

A. This population is likely the source of the high frequency of the LCT gene in Northern Europe

B. The village could not be more than 4,500 years old

C. The members of this population likely used domesticated livestock for their milk

D. villagers had a diet rich in wheat or another domesticated crop

4. Why do populations father from Africa have more deleterious mutations in their genome?

A. Repeated bottlenecks and founder effects made drift more intense more often

B. Populations farther from Africa have been exposed to more mutagens in the environment

C. As people migrated over the globe they interbred with Neanderthals and Denisovans

D. The populations are younger, so purifying selection has not had time to purge delirious mutations from the populations.

Expression vectors inprokaryotes do not make functional eukaryotic gene products inbacteria very well because

Answer Not sure which one ?!

· the codon sequence for prokaryotes is differentthan the codon sequence in eukaryotes

· there are no disulfide bridges formed in proteinsnormally made in prokaryotes

· prokaryotic expression vectors cannot translateeukarytic sequences

· eukaryotic genes have introns, and prokaryotesdon't

· eukaryotic genes have exons and prokaryotesdon't


I create a knockout mouseusing the agouti/black fur system \. When I cross the agoutioffspring of the originally engineered mouse, I find a ratio of 2agouti mice to 1 black furred mouse. What is the bestexplanation?

Answer not sure which one?!

· The gene knocked out was recessive.

· The gene knocked out was dominant.

· The gene knocked out was a lethalgene.

· The knockput was integrated into a random spot,and did not knockput the original gene.

A restriction enzyme cuts DNAand leaves the following end

xxCTGCA
xxG

Which of the following could be the sequence of the correspondingend of the other end of the cut DNA?

Answer

· xxG
xxCTGCA

· xxC
xxGTGCA

· xxCCGAT
xxG

· xxGGCTA
xxC


An SNP always occurs dueto

Answer

· a one base-pair change.

· a three base-pair change.

· a single restriction site change.

· a single amino acid change.

· None of these.


I PCR out a mutated gene in apatient with Lisenbee chorea (the inability to dance in acoordinated fashion) and I compare it to another patient with thatsame disease phenotype. One subject had a mutation on chromosome 4,and the other subject couldn't rock it because of a mutation onchromosome 5. This is an exampe of

Answer

· pleitropy

· locus heterogeneity

· allelic heterogeneity

· dominant negative mutation

· penetrance

In his experiments, Mendelnoted that when two traits are involved in a genetic cross, theyare inherited independently of each other. Though Mendel didn'tknow about chromosomes, this still holds true (mostly)because

Answer

· genes on the same chromosome are often mixedthrough meiotic crossover during the formation ofgametes.

· variant alleles of the same gene do not interferewith the phenotypic expression of the gentoype in different geneticloci.

· most higher organisms are diploid, making only twoalleles available for every genetic locus, and there is a 50/50chance of geting either allele from a single parent.

· expression of phenotypes can vary from thegenotypes because of encironmantal influences.

· chromosomes often recombine

Anticipation is caused by amutation that increases in expressivity over subsequentgenerations.

Answer

· True

· False

Question 44

I have a genotype that shouldproduce a specific phenotype, but some of the individuals with thegenotype do not demonstrate any evidence of the phenotype. I wouldconsider this an example of

Answer

· allelic heterogeneity.

· locus heterogeneity.

· penetrance.

· expressitivity.

· sheer luck.

Question

Which of the following doesnot occur during the PCR reactions?

Answer

· Changes in the reaction temperature by athermocycler

· Denaturation at high temperatures

· Synthesis of oligonucleotide primers

· Extension of primers by DNA polymerase

· Annealing of oligonucleotide primers

Question

DNA markers, or variantnon-coding regions of DNA, are DNA polymorphisms that are usefulfor genetic mapping.

Answer

· True

· False

A mosaic is an organismwith

Answer

· multiple genotypes within one organism

· multiple alleles within one genotype

· more than one color of fur

· transgenes added to the zygote beforedevelopement

· a wt phenotype but a mutated genotype

Question

Genotype causesphenotype.

Answer

· No, gentoype just influences phenotype.

· Yes, genotype is the DNA sequence that createsphenotype.

Question

A true genetic chimera can becreated by

Answer

· mutating a gene early on in the development of anorganism resulting in different alleles being present in theadult

· multiple fertilized eggs or zygotes fusing to formone embryo

· adding a transgene to the genome of an organismduring fetal development only

· adding cells of a different species to an adultorganism

· adding a transgene to the genome of an animal atany stage in development

Question

The ABO blood group can bestbe explained by the concept of _______.

Answer

· dominant traits

· recessive traits

· allelic heterogeneity

· locus heterogeneity

· vampirism

If a loss of functionmutation creates a dominant phenotype, it may be becauseof

Answer

· haploinsufficiency

· penetrance

· expressivity

· allelic heterogeneity

· locus heterogeneity

Please select the best matchfor each.

Answer

· PCR: Technique used to generatecopies of a DNA fragment

· Southern blot : Screeningprocedure used to assay DNA fragments

· RFLPs : DNA fragments generatedby restriction enzymes that vary in length betweenindividuals

· Northern blot : Screeningprocedure used to assay mRNA fragments

· Electrophoresis Movement ofmacromolecules in an electrical field

Answer

A.

Screening procedure used toassay DNA fragments

B.

Movement ofmacromolecules in an electrical field

C.

Screening procedure used toassay mRNA fragments

D.

DNA fragments generated byrestriction enzymes that vary in length betweenindividuals

E.

Technique used to generatecopies of a DNA fragment

A gene mutates, and theprotein produced has a novel way of interacting with the cell, andcreates a new phenotype because of this new functionality. This iscalled

Answer

· pleitropy

· locus heterogeneity

· allelic heterogeneity

· dominant negative mutation

· gain of function dominant mutation

Question 62

Mutations in the somaticchromosomes may be inherited by the next generation.

Answer

· True

· False


A degenerate PCR primer withmany variant sequences must be used to make multiple copies of agene

Answer

· if only the protein sequence of the gene productis known to construct the primers

· if the DNA you are using is cDNA to constructthe primers

· if the DNA you are using is genomic DNA to becopied

· if the DNA you are trying to copy iscDNA

· if the vector is prokaryotic and the transformedcell is eukarytotic

Question

Please select the best matchfor each term.

Answer

· Restriction enzyme


· PCR C

· Plasmid

· YAC A

· Dideoxynucleotide

Answer

A.

Endonuclease isolated frombacteria

B.

Eukaryotic cloningvector

C.

Method for amplification ofDNA sequences

D.

Small circular fragment ofDNA

E.

Molecule used in DNAsequencing

Question

A couple goes on MauryPovitch, and the results are in: you are not the father. But noother man impregnated the female (granted, unlikely for a MauryPovitch guest, but work with me here) and he must be the father.DNA analysis claims otherwise, though the child definitely wasmom's (poor thing). What may be going on here?

Answer

· the child is parthenogenic because the motheractually impregnated herself like a shark, and the child's DNA isall mom's

· the child had a mutation that changed the genethat is used to trace paternity

· the child is a mosaic because he is actually a setof twins fused early during fetal development, and therefore camefrom 2 eggs and 2 sperm

· the dad may have germ-line mosaicism, meaning thatthe genotype of his sperm is different from his somaticgenotype

· mitochondrial DNA only comes from mom, so there isno way to tell whobthe baby's father is