cellular clone
All the individuals derived by nonsexual propagation from a single original parent
What virus allows the human and mouse cells to fuse to create a hybrid cell?
sendai virus
What is the term for the cells when the two cytoplasm fuse?
heterokaryon
What is the term for the hybrid cell when the human and mouse nuclei fuse?
synkaryon
what kind of mutant are the mouse cells (what gene)? What kind of mutant are the human cells?
mouse-tk gene; human-hpr gene??
Based on the somatic cell hybridization data in your class slides, which chromosome appears to code for the enzyme thymidine kinase?
chromosome 17
linkage
the association of genes that are physically located on the same chromosome
crossing over
the exchange of chromatin material between nonsister chromatids of homologous chromosomes
Explain the Holliday Model of Crossing Over. Include the following enzymes in your explanation: a. Endonuclease, DNA binding and/or DNA unwinding proteins (aka gyrase and helicase), proteins such as recA, Exonuclease, DNA polymerase, and DNA ligase
First enzyme is endonuclease that causes break in two inside strands. DNA unwinding protein. Forms hydrogen bonds with the other strand. Recombinant A protein. Strands rotate then break again. Then reunite. See slide 6
Label the ratios as Independent Assortment, Complete Linkage, or Normal Linkage:
a. 6:1:7:2
b. 1:1:1:1
c. 1:1
a. normal linkage(has 4#s with crazy ratios)
b independent assortment
c. complete linkage
In a normal linkage situation, which testcross offspring are the in highest percentage: the parental or the recombinant types? Why?
Parental % is always higher than recombinant types
how to determine cis or trans
looking at the parental types
if a genotype has both dominant alleles it is cis ex) AaBb aabb
if the dominant alleles are on different chromosomes then it is trans ex) Aabb aaBb
What is the maximum percentage of crossing over between two genes?
50%
How do you calculate the percentage cross-over/recombination when given the numbers of each of the genotypes of the offspring resulting from a cross between an F1 parent and a testcross parent?
add the ratios of the recombinant genotypes
divide by total number of offspring multiple by 100
What is the map unit distance between two genes (aka what does the map unit distance indicate to a geneticist)?
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When does the percentage cross over equal the map unit distance?
when the percentage of cross over is less than 20
As the distance between two genes increases, there is a tendency for the percent cross over to increase or decrease
increase
Does crossing-over occur in male Drosophila melanogaster?
no
Please explain the importance of a three factor cross.
give more accurate estimate of map unit distance for the 2nd crossover event
helps correct underestimation
mutation
sudden heritable changes in genetic material and the processes by which these changes occur
What is the name of the shortened chromosome 22 that causes chronic myeloid leukemia?
philadelphia chromosome
involves a translocation of part of chromosome 22 to chromosome 9 resulting in an abnormally shortened chromosome 22
When could a mutation be a good thing?
introduce variation
drive natural selection
can mutation occur in any cell type
yes
spontaneous mutations v. induced mutations
Spontaneous mutations-mutations that are not under the control of man
Induced mutations- mutations produced by man with a mutagen
mutagen
An environmental agent that is capable of inducing a mutation
What is the minimal level of DNA base pair mistakes allowed naturally without causing problems associated with mutations?
1 X 10^-10 errors per synthesized nucleotide
List the three examples of ionizing radiation that could cause mutations in DNA.
x-rays
alpha, beta, gamma, radation
cosmic rays
What is an example of non-ionizing radiation that can cause mutations?
ultraviolet light
List examples of chemical mutagens
Mustard gas
Formaldehyde
benzene
What naturally causes mutations?
viruses
Who in 1927 used x-rays to show that external factors could cause DNA mutations using Drosophila melanogaster?
Herman J Muller
low intensity over a long period of time = ?
high intensity over a short period of time
dosage of ionizing radiation is cumulative
point mutation
Mutations involving changes in single base pairs
mis-sense mutation
A change in one of the first two nucleotides in the codon
describe what happens in deletions and insertions.
Insertion or deletion of nucleotides that cause a frame shit and alter protein function
can involve single nucleotide or many
Are silent mutations, mis-sense mutations, non-sense mutations, and deletions and insertions all also considered point mutations?
If they only involve one nucleotide. Deletions and insertions can be of any size
What are the three general steps of DNA repair?
excision of the defective
nucleotide(s) from one strand of the duplex, replacement of the nucleotide by DNA polymerase I, phosphodiester bond formation by DNA ligase
What occurs during Depurination DNA damage? What nucleotide bases are involved? What bond is broken?
lose of a purine bass (A/G)
spontaneous hydrolysis
breaks glycosidic bond
What occurs during deamination? What nucleotide bases are involved?
amino groups removed via random water collison
(C,A,G)
How is depurination damage repaired (recall the three general steps of DNA repair)? Note the specific enzymes involved in each of the repair steps.
Endonuclease detects absence of base and nicks phosphodiester bond
DNA polymerase I removes affected ribose without a base and replaces nucleotide
DNA ligase fixes phosphodiester bond
How is deamination damage repaired?
DNA Glycosidase cleaves glycosidic bond
Endonuclease detects absence of base and nicks phosphodiester bond
DNA polymerase I removes affected ribose without a base and replaces nucleotide
DNA ligase fixes phosphodiester bond
Deamination and depurination events are considered hydrolytic reactions. What molecule causes the DNA damage?
water
When DNA ligase repairs a phosphodiester bond in the sugar phosphate backbone of DNA, what molecule is produced?
water
How specifically does UV light affect/damage DNA?
causes dimers
forms covalent bonds between adjacent pyrimidine bases (C,T)
How is UV light DNA damage repaired?
UV specific endonuclease clips affected strand of DNA and removes it
DNA polymerase I replaces nucleotides
DNA ligase fixes phosphodiester bond
Can DNA replication and transcription proceed if a pyrimidine dimer is formed?
no
Xeroderma pigmentation
A genetic disorder of DNA repair in which the body's normal ability to remove damage caused by ultraviolet light is deficient. This leads to multiple basaliomas and other skin malignancies at a young age. In severe cases, it is necessary to avoid sunlight
There are the multiple alleles (three or more allelic forms of a gene) present in the population. How many alleles are present per gene in a somatic cell of an individual organism in that population?
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When working with multiple alleles, what formula is used to determine the number of different genotypes possible? What does the letter "n" represent in the formula?
n(n+1)/2 = # of genotypes
n= # of alleles in population
48. List the two examples of multiple alleles discussion in class.
rabbit fur color
blood types
Have a general understanding of the immunology associated with blood types. Why can't you give someone with type A blood a blood transfusion using type B blood? What blood type is the universal donor? What blood type is the universal recipient?
different blood types have different antigens
Type A has A, Type B has B, Type AB has A and B, Type O has none
Body will attack any antigens it does not already have as foreign
Type O is the universal donor
TYpe AB is the universal recipient
What are quantitative traits? List a few examples of quantitative traits.
trait governed by many genes, each contributing such a small amount to the phenotype that their individual effects cannot be detected by Mendelian methods.
ex??
Quantitative traits exhibit continuous variation (as compared to discrete variation which is a one-or-the-other situation such as "yes" or "no"). What shape does a graph have when the frequency (percentage) of individuals is plotted on the y axis and the
bell curve??
What happens to the graph as the number of additive genes (genes all interacting on the single trait) increases?
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What is another term for multiple genes working in conjunction to influence a single trait?
polygene?
How do you determine the number of genes that interact to control a particular quantitative trait (aka what is the formula used in quantitative traits)? What does the letter "n" represent in the formula?
2n+1 = # of phenotypes
n= # of genes interacting to influence a single trait
What is heterosis (aka hybrid vigor)? How do you calculate heterosis
superiority of heterozygous genotypes in comparison with corresponding homozygous genotypes in respect to one or more traits
(avg. of hybrid offspring- avg. of crossed breeds)/avg. of crossed breeds, then multiply by 100
What is heritability? How do you calculate heritability?
degree to which a given trait is controlled by inheritance
h2=delta G/Sd
As selection occurs on a quantitative trait, will the curve become narrower or wider
narrower
population
the total of all individuals in a breed or species or as those individuals that inhabit a particular area
population genetics
branch of genetics that deals with frequencies of alleles and genotypes in breeding populations
What is gene frequency within a population? How can gene frequency be modified in a population?
the relative abundance or relative rarity of a particular gene in a population as compared with its own alleles in a population
List the formulas for determining genotypic frequencies and allelic frequencies
allelic frequency
p+q=1
genotypic frequency
p2+2pq+q2=1
hardy-weinberg equilibrium
ideal
over generations allele frequencies in a population do not change
What are the five assumptions that must be met in Hardy-Weinberg Law in order for allele frequencies in a population to remain constant over the generations?
no selection
no migration
no mutations
no genetic drift
have to have random mating
Hardy-Weinberg Law utilizes the two equations listed below. Please describe what p and q represent. What do p2, 2pq, and q2 represent? a. p + q = 1
b. p2 + 2pq + q2 = 1
p-dominant allele
q-recessive allele
p2-# of homozygous dominant individual
2pq- # of heterozygous individuals
q2- # of homozygous recessive individuals
What is the formula for the Chi-Square test?
x2=summation of [(obs-exp)2/exp]
In a Chi-Square goodness of fit test evaluating Hardy-Weinberg Equilibrium/Law (aka that the allele frequencies do not change over the generations) what is the null hypothesis and the alternative hypothesis? What degree of freedom will you use in this par
1 degree of freedom
????????
If your calculated Chi-Square value is less than the table Chi-Square value, will you accept or reject the null hypothesis? If you accept the null hypothesis, what does that indicate in terms of Hardy-Weinberg Equilibrium/Law?
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If you wish to select for a particular trait, what three characteristics must the trait possess in the population?
heritable
must have genetic variation
reproductive potential is greater than the carrying capacity-more offspring are produced than are able to live
Describe the two main purposes of DNA cloning
artificial production of commercially important gene products
increasing amounts of DNa that can be used for determining the nucleotide sequence of the gene of interest
Name the two means by which DNA is derived for cloning.
use DNA of known character
shot-gun approach
If you are using DNA of known character, you could create a cDNA library to enable you to study parts of the DNA of interest. cDNA is double stranded DNA made from single stranded mRNA of your DNA or gene(s) of interest. Describe the steps (and enzymes) i
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What kinds of enzymes does the "shotgun approach" use? List an example of this kind of enzyme
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Define vector and host cell. List at least one example of a vector. List an example of a prokaryotic and a eukaryotic host cell.
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In order for a DNA fragment to be inserted into a specific vector, should both the DNA and the vector be cleaved with the same restriction endonuclease? Why or why not?
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What enzyme forms the covalent linkage between the DNA fragment and the vector's DNA (such as a plasmid)?
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What is the polylinker region on a plasmid vector?
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recombinant DNA
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How can recombinant DNA be taken up by a host cell?
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Not all host cells will take up the recombinant DNA, so we have to select or screen for cells that have taken up the recombinant DNA (because we aren't interested in host cells that don't contain the DNA of interest). Describe the techniques used to scree
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What is the purpose of PCR (Polymerase Chain Reaction)? What happens to the DNA during the PCR reaction? How is a specific segment of DNA amplified?
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Name the three main steps in PCR (Polymerase Chain Reaction).
Denaturation-occurs at 90-95 degrees C
Annealing- occurs at 50-70 degrees C
Extension- occurs at 70-75 degrees C
What specific polymerase is commonly used for PCR reactions? Why is this polymerase used for this reaction?
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Who won the Nobel Prize in 1993 for the use of Taq Polymerase in PCR?
Kary Mullis
What is Real Time PCR?
is a sensitive method for the detection of mRNA expression levels
involves two steps:RT reaction and PCR amplification
Name the two kinds of gels we discussed that are used in gel electrophoresis? Aka what are the gels made of?
agarose
polyacrylamide
plants??
What kind of liquid needs to be pored over (and submerges) the gel during gel electrophoresis?
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Describe how gel electrophoresis works. Do smaller or larger DNA fragments move through the gel faster? What charge is DNA? So where would you place the cathode (negative charge) and the anode (positive charge) in relation to a gel with DNA samples placed
smaller
???????
How are the bands on the gel visualized? What is ethidium bromide? How can you visualize bands on a gel that has been stained with ethidium bromide?
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What are the steps of Southern Blotting?
digestion with restriction endonuclease enzymes
electrophoresis
use of radioactive probe
autoradiography
What information does restriction mapping and chain termination sequencing give us?
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Describe the restriction mapping technique. What kinds of enzymes are used? How many tubes will you need? Why?
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How do you read the DNA sequence on the gel after performing the restriction mapping technique? Which end of the DNA (5' or 3') is at the bottom of the gel? Do you know the first nucleotide using this technique?
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Chain termination sequencing uses small amounts of dideoxyriboneucleotide triphosphate precursors (ddNTPs). Dideoxy means there are two hydroxyl groups (-OH) missing from the ribose sugar instead of the usual one in DNA (at carbon #2). At which carbon pos
the third carbon; this stops DNA synthesis because DNA polymerase has to add nucleotides to a free hydroxyl group
Chain termination sequencing can use radioactive labeling with four different tubes and four different lanes on the gel OR it can be done using one tube and one lane on the electrophoretic gel. How is it possible to use only one tube and lane? What are th
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Why is only a small amount of ddNTPs added to the chain termination sequencing reaction? Describe the competitive exclusion process.
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How do you read the DNA sequence on the gel after performing the chain termination sequencing using radioactive labeling (so you have four lanes on the gel)? Which end of the DNA (5' or 3') is at the bottom of the gel? Are you reading the sequence of your
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How do you read the DNA sequence after performing the chain termination sequencing in a single tube (using fluorescent dyes)? Are the peaks the sequence of the original DNA strand or its complementary strand sequence?
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List all of the DNA technologies we discussed that used 32P (radioactive)
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