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HMB265H1 Lecture Notes - Lecture 3: Single-Nucleotide Polymorphism, Allele Frequency, Dna Replication

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emeraldcrow840
20 May 2018
School
UTSG
Department
Human Biology
Course
HMB265H1
Professor
Maria Papaconstantinou

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Lecture 3: Molecular Basis of Genetic Polymorphisms & Their Detection
Mutations are the source of allelic variation
• Mutation is the process whereby genes change from one allelic form to another. The creation of entirely new
alleles can occur
o Creates variation
• Genes mutate randomly, at any time and in any cell of an organism
• Can arise spontaneously during normal replication, or can be induced by a mutagen
• Only mutations in germ line cells can be transmitted to progeny. Somatic mutations can not be transmitted
• Inherited mutations appear as alleles in populations of individuals
• Allele frequency is the percentage of the total number of gene copies represented by one allele
o Wild-type: allele whose frequency is ≥ 1%
o Mutant allele: allele whose frequency is < 1%
o Monomorphic: gene with only one wild-type allele
o Polymorphic: gene with more than one wild-type allele
▪ Detectable change (difference) in a given locus/gene
• Forward mutation: changes wild-type allele to a different allele
• Reverse mutation: causes novel mutation to revert back to wild-type (reversion)
• Mutations affecting phenotype occur very rarely
• Different genes mutate at different rates
o Mutation rate varies from 1 in 1000 to 1 in 1,000,000,000 per gamete per generation
• Rate of forward mutation is almost always higher than rate of reverse mutation
• Mutation can occur during normal DNA replication
• Mutation rate can increase after exposure to mutagen
o UV light, chemicals
Classification of Mutations
• Wild type: is the starting sequence
• Substitution: base is replaced by one of the other three bases
• Deletion: block of one or more DNA pairs is lost
• Insertion: block of one or more DNA pairs is added
• Inversion: rotation of piece of DNA
• Reciprocal translocation: parts of nonhomologous chromosomes change places
• Chromosomal rearrangements: affect many genes at one time
• SNP’s are single nucleotide polymorphisms
o They are alleles where only a single base is changed
Gene Expression and Alleles
• Allelic differences at the DNA level can influence mRNA expression and/or protein function, and thus the
phenotype
• Important domain of an enzyme is the active site
o If there is a mutation in the mRNA code than a different protein could be made and result in a disease due
to the non-functional protein
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Expression vectors inprokaryotes do not make functional eukaryotic gene products inbacteria very well because

Answer Not sure which one ?!

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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?

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A restriction enzyme cuts DNAand leaves the following end

xxCTGCA
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Answer

· xxG
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· xxC
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· a one base-pair change.

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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

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

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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.

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· 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

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· 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

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Answer

· multiple genotypes within one organism

· multiple alleles within one genotype

· more than one color of fur

· transgenes added to the zygote beforedevelopement

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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

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Question

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

Answer

· dominant traits

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

Answer

· haploinsufficiency

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Please select the best matchfor each.

Answer

· PCR: Technique used to generatecopies of a DNA fragment

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· 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

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· pleitropy

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Question 62

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

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· True

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Answer

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

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· if the vector is prokaryotic and the transformedcell is eukarytotic

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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?

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

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