What is the gene pool?
All of the alleles for every gene in a population.
Cystic fibrosis shows autosomal recessive inheritance. The frequency of cystic fibrosis in the US is about 1 in 3500. What are the frequencies of the normal and affected alleles? What is the frequency of homozygous dominant individuals? MSU has approximat
q2 = 1/3500 = 0.000286
Therefore, q = sq. root 0.000286 = 0.0169
p = 1 - 0.0169 = 0.9831
p2 = (0.9831)2 = 0.966 (frequency of homozygous dominant individuals) Therefore 0.966 x 22000 = 21, 262 individuals
Red-green color blindness shows X-linked recessive inheritance. In a sample population of 210 000 males, 13 860 males were red-green color blind. What is the frequency of the affected allele in this population? If we also sampled 210 000 females in this p
For X-linked alleles, the allele frequency is equal to the genotype frequency in males. q = 13 860/210 000 = 0.066
In females q2 = 0.0044. Therefore, 0.0044 x 210 000 = 924
What is microevolution?
Changes in allele frequencies that occur in a population from one generation to the next.
What type of traits does natural selection select for and why?
Natural selection selects for traits that enhance survival and traits that enhance reproductive success (e.g. increase fertility or make an individual more appealing to the opposite sex) because such traits ensure that genes are passed to the next generat
What is fitness?
Fitness is the relative likelihood that a particular genotype will contribute genes to the next generation.
Lactose tolerance is inherited as a dominant trait (A = lactose tolerance; a = lactose intolerance). In early European populations, most individuals were aa, and only rare individuals were AA or Aa. Following domestication of cattle, individuals with the
Over many generations we would expect the frequency of the A allele to increase in the population and the frequency of the a allele to decrease in the population because individuals with the A allele are more likely to survive and pass on their alleles to
How does balancing selection due to the heterozygote advantage work to maintain two different alleles in a population?
Individuals with the heterozygous genotype have the highest fitness, so the heterozygotes are most likely to survive and pass on their alleles to the next generation. Heterozygotes pass on both alleles to the next generation ensuring both alleles are main
What effect does stabilizing selection have on the phenotype of a population? Which graph below best illustrates stabilizing selection (left, middle or right graph)?
In stabilizing selection, the mean phenotype has the greatest fitness, so the mean phenotype is naturally selected for and the extreme phenotypes are selected against. Over many generations of stabilizing selection, there will be a greater proportion of i
What effect does diversifying selection have on the phenotype of a population? Which graph below best illustrates diversifying selection (the left, middle or right graph)?
Diversifying selection selects for different phenotypes in different environments. For example, in early human populations we had the natural selection for dark skin pigmentation in areas with intense sunlight, and the selection for light skin pigmentatio
What is genetic drift? Is genetic drift more likely to alter allele frequencies in smaller populations or larger populations? How do the bottleneck effect and the founder effect act to promote genetic drift?
Genetic drift refers to changes in allele frequency due to random chance. Genetic drift is more likely to affect small populations (e.g., in a small population, there is a greater probability that all individuals will randomly pass on one allele more ofte
How does migration promote microevolution?
Migration results in gene flow, which is the transfer of alleles from one population into another. The introduction of new alleles may alter allele frequencies in the receiving population.
Suppose that a population composed of 100 individuals existed on an island. Two different alleles of the "A" gene were present in this population (a1 and a2) at equal frequency. The following events occurred to the population. Determine what evolutionary
(i)
Genetic drift (bottleneck effect), which may alter the allele frequencies due to random chance.
(ii)
Directional selection, which would increase the frequency of the a1 allele and decrease the frequency of the a2 allele.
(iii)
Genetic drift (bottlenec
What is a complex trait? What are the 3 categories of complex traits? What is a quantitative trait? What is a polygenic trait?
Complex traits: influenced by several genes as well as environmental factors. 3 categories of complex traits:
Continuous traits: do not fall into discrete categories.
Meristic traits: can be counted and expressed in whole numbers.
Threshold traits: traits
Complex continuous traits usually show normal distribution. What is normal distribution?
In a population, most individuals have the mean phenotype and there is symmetrical phenotypic variation at either side of the mean. When plotted on a graph (number of individuals vs. phenotype) the curve shows a bell shaped curve with symmetrical variatio
Complex traits show phenotypic variance in a population. What is variance? What is the relationship between variance and standard deviation?
Variance is a measure of how much phenotypic variation is present in a population. Standard deviation is the square root of variance.
Height was measured in 3 populations. Which population has the greatest variance?
Population 3 has the greatest variance as it has the broadest spread about the mean.
If a trait shows normal distribution, we can predict the proportion of individuals that will fall within 1 and 2 standard deviations from the mean.
The average US male is 69.1 inches tall and the standard deviation is 2.9 inches. How tall would a male hav
For normal distribution ~32% are outside 1 s.d. from the mean; of those 32%, ~16 are less than 1 s.d. and ~16% are more than 1 s.d. Therefore a height of 69.1 + 2.9 = 72 in would put a male in the top 16% for height.
For a normal distribution, 4.5% of ind
We determine the covariance of IQ score for 10 mother/daughter pairs.
Mother Daughter
135 121
127 131
124 112
120 115
115 99
112 118
104 106
96 89
94 92
85 90
a. What would it indicate if the correlation coefficient (r) is:
- Greater than 0:
- Equal to 0:
a. What would it indicate if the correlation coefficient (r) is:
- Greater than 0: daughter IQ score increases with mother IQ score
- Equal to 0: there is no relationship between daughter and mother IQ score
- Less than 0: daughter IQ score decreases as m
What is broad sense heritability? (represented by either H2 or hB2)
Broad sense heritability is an estimate of how much phenotypic variation about the mean is due to genetic factors (it is the ratio of variance due to genetic factors over total variance).
For which of the following traits does genetics have the greatest effect on variance in a population? Does this tell us that the trait can be predictable inherited?
Character H2
Stature 0.85
Body weight 0.62
Systolic blood pressure 0.57
Diastolic blood pr
Stature, because it has the highest broad-sense heritability value. Compared to the other traits, genetic factors have a greater influence on phenotypic variance about the mean. Although stature has a high broad-sense heritability, it does not tell us tha
Ten pairs of monozygotic twins separated at birth and raised apart were tested for their waist circumference. The variance in waist circumference within the twenty subjects (measured in in2) was 40. The covariance for waist circumference between twins was
Broad sense heritability (hB2) = COV/Vx = 20in2/40in2 = 0.5
The value of 0.5 tells us that variance in waist circumference is equally due to genetic factors
and environmental factors.
If the twins were raised in the same household, we would expect the bro
What is narrow sense heritability?
Narrow sense heritability is an estimate of how much phenotypic variance in a population can be predictably inherited (it is the ratio of variance due to additive genetic factors over total phenotypic variance).
Narrow sense heritability for heart rate in a particular study was calculated to be 0.17. Does this indicate that variance in heart rate can be predictably inherited?
A value of 0.17 tells us that only 17% of variance can be predictable inherited, so most of the phenotypic variance in heart rate is not predictably inherited.
The correlation coefficients for age of onset of Huntington disease were determined for 15 pairs of individuals with the following relationships. What is the narrow sense heritability for age of onset of Huntington disease in this study? Why is this value
Observed r values
Parent - offspring 0.10
Grandparent - grandchild 0.07
Sibling - sibling 0.42
Calculate robs/rexp
Parent-offspring 0.1/0.5 = 0.2
Grandparent-grandchild 0.07/0.25 = 0.28
Sibling-sibling 0.42/0.5 = 0.84
Average robs/rexp = (0.2+0.28+0.84)/3
What is polymerase chain reaction used for?
It is used to amplify a target DNA sequence to produce many copies.
What four components are required as starting material for any PCR reaction? What are the three basic steps that are repeated with each cycle?
The 4 components required for all PCR reactions are: template DNA (the sequence to be
amplified), DNA nucleotides, primers and Taq polymerase (a heat stable DNA polymerase).
Basic steps
Denaturation: The template DNA strands are separated by heating the D
Initially we have 10 copies of a DNA sequence. How many copies do we have after 3 cycles of PCR?
The DNA is doubled with each cycle, so the number of DNA copies present after n cycles is X(2n) (x = number of starting DNA copies; n = number of cycles), so there are 80 copies after 3 cycles (10 x 2 x 2 x 2 or 10(2)3).
What is quantitative PCR (qPCR)? What additional component is needed for qPCR that is not needed for regular PCR? What is the threshold cycle? How does the level of fluorescence correlate with the number of DNA copies in the starting sample?
It is a quantitative version of regular PCR. By including standards of known concentration, we can quantify the number of starting DNA copies in a sample.
In addition to the four components needed for regular PCR, we additionally need to add a fluorescent
qPCR is conducted on samples 1 - 8 to determine the number of viral copies present in the samples. Which sample has the greatest number of viral DNA copies present in the starting sample? Are all of the samples positive for viral DNA?
Sample 1 has the greatest number of viral DNA copies because it has the earliest threshold cycle value. Samples 6 - 8 are negative for viral DNA because fluorescence is not detected above threshold (i.e., above background). If we wanted to quantify the nu
What is cDNA? Which enzyme makes cDNA from mRNA?
cDNA is a DNA copy of mRNA. Therefore, it is the coding sequence of a gene without the introns. The enzyme reverse transcriptase converts mRNA to cDNA.
What is DNA fingerprinting?
DNA fingerprinting compares the DNA fingerprint of different samples. There are many sites in the genome that are highly variable between different individuals in the population. For example, there are many sites that contain a short repetitive sequence,
DNA fingerprinting was performed on blood from a crime scene. Does DNA taken from blood at the crime scene match either of the suspects 1 - 3? (The gel is on the next page).
DNA taken from the crime scene matches the DNA sample from suspect #2.
In the fingerprinting analysis below, several DNA sequences were amplified simultaneously by PCR, and then the mixture of resulting DNA sequences was separated on a gel. On what basis are DNA sequences separated in gel electrophoresis (i.e., based on shap
DNA sequences have a uniform negative charge. When a voltage is applied to the gel, the DNA sequences migrate from the cathode (negatively charged) to the anode (positively charged) and DNA molecules are separated based on size. Larger sequences migrate s
In the paternity test below, do either of the potential fathers (F1 or F2) have a DNA fingerprint that is a match with the child?
Father F2. If a band in the child does not line up with the mother then it lines up with father F2.
What are dideoxy nucleotides (ddNTPs). Opposite which base would dideoxy cytosine (ddCTP) terminate replication?
ddNTPs are DNA nucleotides that have a H at the 3' position instead of an OH. When incorporated into a DNA strand being synthesized, they will terminate replication because nucleotides cannot be added to the 3' end. A DNA strand is synthesized according t
What is the sequence of DNA (below) that was synthesized from the DNA template that was used for dideoxy sequencing? Remember to indicate the 5' and 3' ends.
(Note: we can use either DNA strand for sequencing, and often use both). (Yellow = G; red = T; bl
The fragments are separated on a gel, and the color of each band tells us which base terminated the strand based on the color of the fluorescent signal associated with the dideoxy nucleotide that terminated the strand.
5' - CAC CGT AAG GAC TG - 3'
(The 5'
The following readout from dideoxy sequencing shows the sequence of the coding DNA strand for a small stretch of the wild type BRAF gene and a mutant BRAF gene (V600E mutation) found in melanoma cells. What is the mutation?
(orange = A; black = G; purple
The mutation is a T to A base substitution.
What is a Southern blot, and what is it/was it used for?
A DNA probe is used to locate a target DNA molecule; the DNA probe will hybridize to a complimentary DNA sequence. Some applications of Southern blotting include:
- Finding homologous genes (genes that are derived from the same ancestral gene) including o
What is a Northern blot and what is it/was it used for?
A DNA or RNA probe is used to locate a target RNA molecule; the probe will hybridize to a complimentary RNA sequence. Some applications of Northern blotting include:
- Determining if a particular gene is expressed in a particular cell type or during a
par
What is a western blot and what is it used for?
To determine if a particular protein is present in a sample. Proteins are extracted from a sample and run on a gel. Commonly an antibody specific for the target protein of interest is used as probe.
Question E22 from the textbook. If the same amount of total cDNA is loaded for each sample, then the intensity of the band indicates the relative amounts of cDNA present in each sample.
(Note: expression of alternatively spliced mRNAs may also be investig
See answers to textbook study questions.
There is evidence that elevated intraocular (in the eye) pressure is involved in the pathogenesis of glaucoma. This microarray array compares gene expression in cells from eye tissue under normal conditions and cells from eye tissue under six different ex
Decreased expression: VEGFC, KIAA1718 and perhaps slightly SULT1B1 (higher fluorescent signal in control cells compared to experimental cells).
Increased expression: IRFD1, ZNF146, Apg4B, ZNF288, DDO and slightly DUSP5 and SMA3.
What is a recombinant DNA molecule?
A DNA molecule that contains DNA from two different sources.
What is a vector, and what are vectors used for? What are two examples of vectors?
Vectors are used to carry foreign DNA into a host cell. Two examples of vectors are plasmids and viruses.
What is a restriction enzyme, and how is it useful for creating a recombinant DNA molecule?
An enzyme that cuts DNA. Many restriction enzymes cut DNA at a specific base sequence. If two different DNA molecules are cut with the same restriction enzyme then they will have complimentary ends that can hybridize together.
Which of the following DNA molecules has an 8 bp palindromic sequence that could be cut by a restriction enzyme to produce sticky ends? (i.e., the 2 strands must have the same 8 bp sequence when read 5' - 3'). The complimentary partner strands are shown s
5' - GATCGATC - 3' 3' - CTAGCTAG - 5'
After bacteria have been transformed with a recombinant plasmid to produce many copies of the plasmid, explain how the ampicillin resistance gene and the LacZ gene can be used as selectable markers to detect bacterial colonies that contain the recombinant
A plasmid is used that carries the ampicillin resistance gene and the lacZ gene. However, the insertion site for the gene of interest is in the middle of the LacZ gene, so insertion of our target gene in the plasmid will inactivate the LacZ gene. Bacteria
What is a transgenic organism?
A transgenic organism is an organism that has been genetically modified.
What is molecular pharming?
The genetic modification of organisms to produce pharmaceutical proteins that they don't normally produce. For example, in class we looked at the genetic modification of bacteria to produce human insulin and the genetic modification of livestock to secret
What is a knockout mouse? What is a knockin mouse? What are a couple of uses of transgenic mice?
A knockout mouse has had a particular gene inactivated by homologous recombination, which replaced the normal gene copy with an inactivated gene copy. A knockin mouse has had a particular gene inserted into its genome without any original genes being repl
How is a cloned gene containing a knockout mutation inserted into a target location in the genome of mouse embryonic stem (ES) cells? How are the ampicillin resistance and thymidine kinase genes used to select for the embryonic stem (ES) cells that have a
First of all the target gene is disrupted by insertion of the ampicillin resistance gene. The disrupted gene is also cloned into a vector containing the thymidine kinase gene (confers susceptibility to the drug ganciclovir). In some ES cells, the vector D
What is a chimeric mouse? After transferring genetically modified ES cells into the early blastocyst of a donor mouse, how can we select for chimeric offspring that contain cells with the knockout gene? Once we have selected chimeric offspring, how do we
A chimeric mouse is a mouse produced from cells derived from two or more zygotes.
The ES cells to be genetically modified are obtained from a zygote made from parents with brown fur. The blastocyst in the donor female is made from parents with white fur.
What is the aim of gene therapy? Why is a virus a logical choice of vector for gene therapy?
A vector is used to deliver a gene to a patient's cells. Once the gene has been incorporated into the patient's cells, the patient's cells will produce the functional gene product.
Viruses naturally infect human cells and deliver their genome to human cel
What are stem cells? What is the difference between totipotent, pluripotent, and multipotent stem cells?
Stem cell are cells that have the ability to self-renew and differentiate into one or more specialized cell types.
Totipotent stem cells are at the earliest developmental stage and can give rise to any cell type in the body as well as extraembryonic tissu
Other than embryonic stem cells, what are two other sources of pluripotent stem cells that have been programmed to differentiate to cells of all three germ layers in the laboratory?
Embryonic-like stem cells from umbilical cord blood, and induced pluripotent stem cells (iPSCs) that have been reprogrammed from adult differentiated cells back to a pluripotent state.