lecture 5 Flashcards
What are four sources of DNA?
Blood, semen, hair, saliva/buccal swabs
Briefly, describe the process of PCR (3 main steps).
First step is Denaturation solution is heated allowing DNA strand to separate
Second step is Annealing solution is cooled allowing DNA primers to bind
Third step is Elongation DNA polymerase binds and synthesizes new DNA strand
Describe a study that uses next-generation sequencing technology to understand the genetic basis of disease (focus on what is known already, the method of the study, populations studied, results, and conclusions)
What is known already: Uterine Serous Carcinoma (USC), constitutes ~10% of all endometrial cases, and the survival rate can be as low as 50%. African American women have a 3-fold greater incidence of USC compared to European American women, and they tend to die early and quickly from this disease
Method: genome wide coding sequence variation looking at genetic mutations (500,000 SNPS) and performing a Cluster analysis on data
Population: African American women (N=13) with average age of 57.5 and European American (N= 21) women with an average age of 66.9 with a total of 34 individuals.
Results: observed general clustering of individuals by ethnicity. Identified a rare mutation (rs33935154) is associated with endometrial cancer in African American individuals but it wasn’t found in European American individuals.
Conclusions: globally rs33935154 occurs at a low frequency and about 10% in African descent populations which implies a potential ethno specific biomarker. This data reinforces the need for more research into specific regions of the genome enriched for west African ancestry to identify novel mutations that likely play a role in the differential onset and/or progression of USC in African American populations
. List four public databases used for the storage of genetic variants.
UCSC Genome Browser (genome.ucsc.edu): sequence information can be found here, as well as genomic information from other species (e.g. chimpanzee)
HapMap: a subset of SNPs from across the genome typed in several human populations
1000 Genomes Project browser: access to variation data for a particular segment of the genome
ALFRED: anthropologically based database with allele and frequency information (for ALlele FREquency Database)
Describe Mendel’s monohybrid cross experiment (select a characteristic). In your answer, start with the parental generation, and state the trait and the underlying genotype at each step in the cross
The parent generation in Mendel’s monohybrid cross starts with two parents where one is homozygous dominant (RR) for round seeds, and one is homozygous recessive (rr) for wrinkled seeds. At the first generation all of the 4 offspring are round seeds where all of the genotypes are heterozygous (Rr). The second-generation results in ¾ round seeds where the genotype was homozygous dominant (RR) or heterozygous (Rr) and ¼ wrinkled seeds that were homozygous recessive (rr).
Know the Table of Important Genetic Terms.
Gene: an inherited region of DNA that helps determine a characteristics
Allele: alternative forms of a gene
Locus: a specific place on a chromosome occupied by an allele
Genotype: set of alleles possessed by an individual organism
Phenotype or trait: appearance or manifestation of a characteristic
Hetero: 2 different alleles at a locus
Homo: two of the same alleles at a locus
Characteristic: attribute or feature possessed by an organism
Describe Mendel’s 4 important conclusions from the results of his monohybrid crosses (8 points).
- Each plant must posses two alleles encoding for a characteristic, inherited genetic factors from each of their parents.
- alleles in each plant separate into gametes and one allele goes into each gamete.
- When dominant and recessive alleles are present together the recessive alleles is masked or suppressed.
- The two alleles of an individual plant separate with equal probability into the gametes.
Understand how to construct a Punnett square and predict the genotypes of uniting gametes. Expect to see a problem on the exam
Take the two genotypes and separate them into alleles and put on the square and distribute the alleles into the boxes to find the offspring’s possible genotypes and phenotypes.
What is probability?
Probability expresses the likelihood of the occurrence of a particular event.
What is the multiplication rule? What is the addition rule?
Multiplication rule: The probability of two or more independent events taking place together is calculated by multiplying their independent probabilities.
Addition rule: The probability of any one of two or more mutually exclusive events is calculated by adding the probabilities of these events
You will have to apply the multiplication and addition rules on the exam. Specifically, use these two rules to calculate the probability of obtaining the expected genotypes and phenotypes in a monohybrid cross.
Addition rule: Tall = ¼ + ¼ + ¼ = ¾ and short = ¼
Multiplication rule used: To calculate the probability of obtaining TT progeny, we multiply the probability of receiving a T allele from the first parent (½) times the probability of receiving a T allele from the second parent (½). ½ x ½ = ¼ for TT
what is population genetics
Population genetics: genetic makeup of groups of individuals and how a group’s genetic composition changes with time
Because it is not practical to determine the genotypes of all individuals in a large population, what strategy can population geneticist use to estimate allelic and/or genotypic frequencies in large populations?
They take samples of a population then the genotypic and allelic frequencies of the sample are then used to represent the gene pool of that population.
How do genotypic frequencies and allele frequencies differ in terms of how they are calculated?
Genotypic frequencies: # of individuals with that genotype/ total # of individuals in that sample
Allelic frequencies: # of copies of that allele/ # of copies of all alleles at the locus
p = f(A) = (2nAA + nAa)/2N
q = f(a) = (2naa + nAa)/2N
p + q = 1
what is a mathmatical model?
Mathematical model: is a representation of how the real-world works, describes a process as an equation, factors that influence that process are represented as variables in equation, equation defines the way in which the variables influence the process
