Exam 3 - Review Flashcards
(129 cards)
1
Q
The study of distribution and change in frequency of alleles within populations.
A
Populaiton genetics
2
Q
A change in gene frequency over time in a population (i.e. leads to speciation and divergence).
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Evolution
3
Q
of individuals possessing the genotype over the total # of individuals in the sample.
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Genotypic frequency
4
Q
of copies of a particular allele present in a sample over the total # of alleles
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Allelic frequency
5
Q
States that allele and genotype frequencies are constant within a population from generation to generation (i.e. Absent of other evolutionary influences).
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Hardy-Weinberg Law
6
Q
Assumptions of Hardy-Weinberg Law.
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Population = Large, Mating = Random, Mutations/Migration/Natural selection = Not present
7
Q
Measure of probability, determines whether two alleles are identical by descent
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Inbreeding
8
Q
Alleles descended from the same copy in a common ancestor (i.e. seen in inbreeding, small populations).
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Alleles identical by descent
9
Q
The avoidance of mating between related individuals.
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Outcrossing
10
Q
Conditions that favor inbreeding.
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Can uncover/eliminate harful alleles. Can preserve good combinations of genes that may otherwise be broken up by outcrossing.
11
Q
Observance of different rates of survival/reproduction due to differences in phenotype.
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Natural selection
12
Q
Phenomena where two individuals have a higher probability of mating as opposed to the rest of the individuals in the population.
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Nonrandom mating
13
Q
A permanent alteration in the DNA sequence that makes up a gene.
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Mutation
14
Q
Movement of a group/population/individual.
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Migration
15
Q
A change in the frequency of an allele in a small population, due to chance disappearance of particular genes (i.e. individuals die do not reproduce)
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Genetic drift (i.e. bottleneck effect and founder effect)
16
Q
Natural selection, nonrandoming mating, mutaiton, migration, and genetic drift are all forces of what?
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Evolution
17
Q
Phenomena that occurs when members of one biological sex compete in order to choose mates of the other sex to mate with.
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Sexual selection
18
Q
Potential effect of introducing genes from an outside populaltion into another population.
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Dramatic change in allele frequency.
19
Q
What happens when the environment of a population changes?
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Population will adapt to new environment through natural selection or will suffer.
20
Q
Why are the characteristics of a small isolated population useful for genetic studies?
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Can be utilized to study/identify rare disease variants. Have a reduced genetic diversity some of which drift to a high frequency of a rare disease.
21
Q
Relative intensity of selection against a genotype.
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Selection coefficient
22
Q
Phenomena where heterozygotes are favored over homozygotes (i.e. provide a reproductive advantage) thus both alleles are maintained in a population.
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Overdominance/Heterozygote advantage
23
Q
A genetic change in a group of organisms, a change in gene frequency within a population.
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Biological evolution
24
Q
Type of biological evolution, takes place in a single group/lineage with the passage of time.
A
Anagenesis
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Type of biological evolution, splitting of one lineage into two leading to arise of new species.
Cladogenesis
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Reproductive isolating mechanism, acts before zygote has formed.
Prezygotic
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Reproductive isolating mechanism, acts after zygote has formed.
Postzygotic
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Examples of prezygotic reproductive isolating mechanisms.
Ecological (i.e. differences in habitats thus individuals do not meet); Temporal (i.e. reproduction takes places at different times)
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Postzygotic, hybrid zygote does not survive to reproduction.
Hybrid inviability
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Postzygotic, hybrid is steril.
Hybrid sterility
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Postzygotic, first generation is viable and fertile, but second generation is inviable or sterile.
Hybrid breakdown
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The evolutionary relationships among a group of organisms.
Phylogeny
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Most prominent idea today, states that populations that were able to deal with a rapidly change environment survived best (i.e. ability to make tools, social structure, and upright walking)
Variability selection hypothesis
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Protein evolution is relatively constant therefore observation of the amount of molecular change can be used as a clock.
Molecular clock
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Functional domains encoded by individual exons can be shuffled to create mosaic genes of different but related function.
Exon shuffling
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Tumor remains localized.
Benign tumor
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Tumor cell invades other tissues.
Malignant tumor
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Tumor cell induces secondary tumors
Metastasis
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Notion that a singlular mutaiton event is not in of itself the result of cancer but rather it is an accumulaiton of issues.
Knudson's multistep model of cancer
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Two somatic mutations in a cell leading to a tumor.
Sporadic cancer
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Person is predisposed to cancer (i.e. inherits one mutation) only one somatic mutation is required to produce cancerous cells.
Hereditary cancer
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Initiating event of sporadic cancer.
May be deregulation of growth-regulating genes leading to DNA damage and DNA replicaiton stress
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Initiating event of sporadic cancer.
Genomic instability
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Most cancers (i.e. if not all) have a genetic basis yet few are hereditary. Why is this the case?
Cancer tends to result as an individual ages and is exposued to carinogens. These mutations are commonly occ
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Deals with phenotypes that vary continuously (i.e. such as height or mass).
Quantitative genetics
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Phenomena that describes that control of quantitative characteristics being controlled by the sum effects of multiple genes
Polygenic inheritance
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What would have happened if he studied traits with continuous phenotypes?
He would not have been able to make that mathematical conclusions he derived from his studies.
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Demonstrated as only two possible phenotypes (i.e. present of absent) although they are quantitative. As susceptibility increases and reaches threshold the phenotype will be present
Threshold characteristics
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Graph that displays the # or proportion of different phenotypes.
Frequency distribution
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Average of a set of values.
Mean
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Information provided via mean.
Approximate center of distribution.
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Variability within a group of measurement.
Variance (i.e. larger variance = larger spread)
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Information provided via variance.
Variability of a group of phenotypes, how big the "tails" of distribution are
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The square root of the variance.
Standard deviation
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What does variance and standard deviation tell you about a population?
Variance measures the variability of a population, standard deviation is another measure of variability therefore they both are calculating information related the spread or variability of data.
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Characteristics that are associated thus a change in one will result in a change in the other.
Correlated characteristics
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True/False: Correlation demonstrated cause-and-effect relation.
False
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Statistical measure of the strength of associate.
Correlation coefficient
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Statistical method, predicts the value of one variable if the value of another variable is given.
Regression
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Statistical measure, slope of a regression line, demonstrates the change in one variable on average as another variable increases.
Regression coefficient
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Measurement of the proportion of the total phenotypic variation that is due to genetic factors for a population in a given environment.
Heritability (i.e. note thie estimate is for a POPULATION)
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Ratio of additive genetic variance to the total phenotypic variance.
Narrow sense heritability (i.e. will be on exam)
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Ratio of total genetic variance to the total phenotypic variance.
Broad sense heritability (i.e. will be on exam)
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Phenotypes/characteristics that vary in degree may be due to polygenic effects (i.e. the product of two or more genes and their environment)
Quantitative traits
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Limitations of heritability.
Cannot determine degree to which a characteristic is genetically determined. Individuals do not have heritability.
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Can any quantitative trait increase forever? If not, why not?
No, quantitative traits tend to level over due to physiological limits on the trait.
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Difficulties with statistical methods.
Claims are often refuted due to lack of consistency in results, segregation analysis, and association analysis.
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Study, used to identify the correlation between sequence variants and phenotypes of interest such as complex disease.
Genome wide association
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Heritable change in phenotype that does not involve changes in the DNA sequence.
Epigenetics
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How does epigenetics and Lamarkianism relate to each other?
Lamarkianism was the notion that aquired traits are heritable. Epigenetics is quite similiar by definition.
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Thrifty phenotype theory.
Proposes that parental exposure to poor environment conditions triggers internal biological response that calculate that the environment of their offspring will be poor as well (i.e. parent with a food shortage may have a child that is metabolically thrifty, eating as much as possible while minimizing energy expenditure, and conserves calories).
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Addition of methyl groups to nucleotide bases (i.e. commonly cytosine which produced CpG islands), generally associated with deactivation/gene repression and chromatin condensation.
DNA methylation
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Generally associated with gene activity and open chromatin structure.
Acetylated histones
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Associated with variable gene activity depending on the lysine methylated.
Methylated histones
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Attempt to understand how biochemical modifications on histones and the impact that they have on gene expression/function, shows that these modifications work together.
Histone code
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Epigenetic phenomena, the expression of an allele depends on whether it is inherited from the male of the female.
Genomic imprinting
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Inheriting two copies of a chromosome from one parent.
Uniparental disomy
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Why are some regions of the human genome differentially imprinted?
Different evolutionary pressures on males versus females (i.e. female need to provide longevity and nutrition meanwhile mean are simiply looking to reproduce).
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A biosensor for environmental epigenomic studies investigating the developmental origins of health and disease.
Agouti mouse
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Overall pattern of chromatin modification possessed by each individual.
Epigenome
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Tools for detecting DNA methylation.
Restriction enzymes and bisulfate sequencing
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Tools for detecting histone modifications.
ChIP
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What is the significance of folate as it pertains to epigenetics?
Source of carbons used by methylases in epigenetic mechanisms and prevents birth defects
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What implications may epigenetics have on insurance?
Insurance companies can use this data to determine the cost of your plan.
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Key event of cancer
Genomic instability (i.e. mutations that activate all the secondary hallmark events)
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Mutated gene, only a single allele needs to be mutated (i.e. dominant) can induce excessive cell proliferation.
Oncogene
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Normally produce factors that stimulate cell division however when mutated they become oncogenes
Proto-oncogene
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Normally produce factors that inhibit cell division, both alleles must be mutated (i.e. recessive) to induce excessive cell division.
Tumor-suppresor genes
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A gross chromosomal event that results in the loss of the entire gene and the surrounding chromosomal region
Loss of heterozygosity
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What is the point of pan-cancer analysis? What is the logic behind it?
Pan-cancer analysis aims to determine similarities and differences among the genomic and cellular alterations found across different tumor types. Logically by identifying similarities between various tumors could reveal potential targets for treatment.
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Tumor-suppressor gene, regulates cell division/apoptosis/DNA repair/inhibit angiogenesis
p53
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Why don't elephants get cancer?
Elephants have 20 copies of p53 in comparison to humans who only have one.
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Enzyme, can be activated by cancer cells, prevents genomic instability of the cancer cell thus allowing infinite mitosis.
Telomerase
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Why is mutation the roof of development of resistance to chemotherapy?
Mutations provide genetic variability for cancer cells thus a cancer cell that is resistant to the chemotherapy will survive and reproduce.
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General feature of cancer cells (i.e. deletions, inversions, and translocations).
Chromosomal instability
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Translocation that is found in follicular lymphoma.
Translocation between chromosome 14 and 18.
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Result of translocation between chromosome 14 and 18 that causes follicular lymphoma.
BCL2 is placed behind strong promoter.
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Anti-apoptotic protein, oncogene, found in mitochondrial membrane, controls mitochondrial permeability and inhibits apoptosis, upregulation leads to decrease in apoptosis.
Anti-apoptotic protein
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Ubiquitous small non-coding RNA molecules that function in RNA silencing and post-transcriptional regulation of gene expression
miRNA
100
How can cancer interact with miRNA?
Can utilize miRNA to turn off tumor suppressor genes. Can inhibit/eliminate miRNA in order to activate oncogenes (i.e. miRNA that is inhibiting/regulating oncogene).
101
General cancer-causing mechanism of retroviruses.
Inserts strong promoters near proto-oncogenes or deactivates tumor suppressor genes or mutates and rearranges proto-oncogenes.
102
Why might a virus be associated with a specific cancer?
Viral infections probably have various route of infection ∴ a virus is likely causing cancers associated with the tissues/organs it is infecting.
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Where do monoclonal antibodies come from?
Mouse challenged with antigen, spleen cells are taken removed and fused with myeloma cells. Hybridoma is formed and can produce monoclonal antibodies.
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How are monoclonal antibody used?
Target cancer cells specific antigens and induce an immunological antibodies.
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Monocloal antibody, destroys B cells, utilized to treat diseases which are characterized by excessive numbers of B cells/overactive B cells/dysfunctional B cells (i.e. lymphomas, leukemias, transplant rejection, and autoimmune disorders)
Rituximab
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What does rituximab target?
Protein CD20
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Attraction of killer T cells/macrophages, binding leads to the recruitment of complimentary proteins, and apoptosis signaling are all proposed mechanisms of what?
Function of monoclonal antibodies to cure cancer.
108
Specialized blood filtration process used when taking a patient’s white blood cells (i.e. CAR T-cell therapy)
Leukapheresis
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General process of CAR T-cell therapy.
Leukapheresis, cells are reprogrammed (i.e. via viral vector and CRISPR-CAS9), cell expansion, quality check, lymphodepleting chemotherapy, and cell infusion.
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Enzymes, recognize and cut DNA at specific nucleotide sequences.
Restriction enzymes
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Method of gel eletrophoresis.
DNA has a negative charge thus it will migrate towards the + electrode.
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DNA or RNA with a base sequence complementary to a sequence in the gene of interest and with a radioactive or chemiluminescent molecule attached allows visualization.
Probe
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Amplifying a specific piece of DNA via a bacteria cell.
Gene cloning
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A replicating DNA molecule incorporating a foreign DNA sequence to be introduced into a cell.
Cloning vector
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Five chemical components required for PCR.
DNA template, DNA polymerase enzyme, primers, nucleotides, and reaction buffer
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DNA polymerase stable at boiling temperatures.
Taq polymerase
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General procedure of PCR.
DNA is heated – Allows DNA to separate, DNA is cooled – Allows primers to anneal (i.e. bind/pair with) complementary sequence, DNA is heated again – DNA polymerase synthesizes new DNA strands = Two new dsDNA molecules, Cycle is repeated
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RNA template is first converted into a complementary DNA via reverse transcriptase then the complementary DNA can be used as a template for exponential amplification using PCR
Reverse-transcription PCR
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Quantitatively determining the amount of DNA amplified as the reaction proceeds.
Quantitative real-time PCR
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PCR inhibitors
Hemoglobin, urea, heparin
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PCR enhances
DMSA, glycerol, BSA
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Various uses of PCR.
Detection of viruses in blood samples, identify genetic variation, and isolate DNA from ancient sources
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Limitations of PCR
Can amplify a single molecule therefore susceptible to contamination increasing the risk of a false positive.
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A collection of clones containing all the DNA of the DNA fragments from one source.
DNA library
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Sequencing fragments from a point near to a gene of interest, used in genomic mapping.
Chromosome walking
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A large fragment is circularized, and the junction is sequenced, used in genomic mapping.
Chromosome jumping
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DNA sequencing, dideoxyribonucleoside lacks a 3′ OH group which terminates DNA synthesis, terminates extension of DNA fragment.
Sanger's dideoxy-sequencing method
128
What happened to cause a mummified skeleton discovered in Chile to be only six inches tall.
Using whole genome sequence, Ata was determined to be female of Chilean descent, more importantly the genome demonstrated mutations in genes linked with disease resulting in - Small stature, rib, anomalies, cranial malformations, premature joint fusion, and osteochondrodysplasic
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A mouse carrying function human genes/cells/tissues.
Humanized mouse
