Genetics Quiz 3 + video questions

factors that case genetic drift ____ effect: a drastic reduction in population that creates reduced genetic variation, and smaller population may not be able to adapt to new selection pressure what species experienced a large population bottleneck?

bottleneck effect cheetahs

what is the central dogman of molecular biology

dna to mrna (transcription) mrna to protein (translation)

____: 1 copy of allele results in trait (genotype could be AA or Aa) ___: requires 2 copies of allele (genotype must be aa) ____: heterozygote results in an intermediate example blood typing

dominant reccessive codominant

factors that case genetic drift ____ effect: occurs when a new colony is started by a few members of the original population Reduced genetic variation May lead to speciation

founder effect

___ number Standardized number for genomic variation, unless new will have this number in the National Center for Biotechnology Information

Reference Sequence (RS) number

Impact of slurring/branding due to an individual's genetic differences.

Stigmatization

Population genetics is what?

The study of the change of allele frequencies, genotype frequencies, and phenotype frequencies

If SNP1 and SNP2 are completely linked 100% of the time, what is their r2 value? 1.00 0.00 0.50 Cannot be determined

1.00

APOE is a major cholesterol carrier that supports liid transport and injury repair in the brain APOE4 are the main genetic determinant of what disease? SNPs in this disease also reported less effect of what drugs? Important as it effects multiple things

Alzheimer's disease cholesterol

___ ____: measures the degree to which alleles at two sites are linked and occurs when two mutations are completely co-inherited what value indicates perfect LD? what value indicates no LD tagging can be used in SNPs with ___ LD

Linkage Disequilibrium (LD) 1 0 high LD

types of mutations ___: changes which exons expressed ___: change gene expression ___: shifts codon/ amino acid sequence

Splice site Promoter frame shift (worst most likely to express protein function)

In a population, there are the following number of individuals: 150 homozygous for the minor allele, 250 heterozygotes, and 650 homozygous for the major allele. What is the frequency of the minor allele? 0.26 0.74 0.38 0.62

0.26

ASSUMPTIONS of HWE 1) ____ organism (2 copies of each chromosome) 2) ____ reproduction 3) generations are non-___ 4) mating occurs at ___ 5) large population size 6) negligible ___ 7) negligible ___ 8) __ selection on genes

1) diploid organism (2 copies of each chromosome) 2) sexual reproduction 3) generations are non-overlapping 4) mating occurs at random 5) large population size 6) negligible migration 7) negligible mutation 8) no selection on genes

How many genes code for proteins in human? Each diploid cell contains how many chromosomes? How many are sex chromosomes in a diploid cell? What about a haploid?

20000-25000 genes 46 chromosomes 2 sex chromosomes 23 and 1

structure of a gene always go from what to what? what occurs before the coding region and determines whether of not a gene will be transcribed? changes in what is the most important in the coding region?

5 to 3 promoter exons these are what are translated into protein

two strands of a double-stranded DNA molecule. Both complementary strands may encode important information

Forward and reverse strands

What does allele frequency of 0 mean? what about 1?

Frequency of 0 means complete absence of that allele or genotype from the population (no individual in the population carries that allele or genotype) 1 means complete fixation of the allele or genotype (fixation means that every individual in the population is homozygous for the allele -- i.e., has the same genotype at that locus).

Star allele nomneclature Generally, *__ represents the reference sequence or "wild type" Generally numbered in order of ___

Generally, *1 represents the reference sequence or "wild type" Generally numbered in order of discovery

The combination of two alleles at a particular location in the genome. Each of these two alleles comes from a different chromosome. My ___ at that position is A/C

Genotype

A set of DNA variations, or polymorphisms, that tend to be inherited together.

Haplotype

Which of the following is false regarding the Myriad Genetics case? The case dealt with testing for mutations in BRCA1 and BRCA2 genes, which greatly increase breast and ovarian cancer susceptibility. Myriad was awarded patents on the BRCA1 and BRCA2 genes in the 1990s. In 2013, the US Supreme Court ruled that isolated, naturally existing human genes can be patented. DNA molecules engineered by man are eligible for patents.

In 2013, the US Supreme Court ruled that isolated, naturally existing human genes can be patented. (cannot patent existing human genes)

__ ___: is when two mutations are completely random with respect to each other - free flowing equilibrium of mutations

Linkage equilibrium

More cross-over (meiosis) means ___ linkage disequilibrium (LD) Less LD between variants if they are ____ apart (more cross-over) Less LD if the have been ____ generations (i.e. African populations)

More cross-over (meiosis) means less linkage disequilibrium (LD) Less LD between variants if they are far apart (more cross-over) Less LD if the have been more generations (i.e. African populations since founder population)

What kind of mutation is Lys102Leu? Non-synonymous Non-sense Splice site Frame shift

Non-synonymous

What is the use of information about an individual, including their family history, diseases, environmental factors and genetic information to personalize or individualize care

Personalized medicine

the study of influences of specific variants or variation in specific genes on drug disposition and response

Pharmacogenetics

the study of influences of variation in the human genome on drug disposition and response

Pharmacogenomics (this one is broader)

What is the need to prevent fairness in the use of genetic information by insurers, employers, courts, schools, adoption agencies, the military, among others.

Prevention of Genetic Discrimination

Variation in a single nucleotide of the genetic sequence; a common form of variation in the human genome.

SNP

types of mutations and describe what they are SNPs Indel Copy number variant structural rearrangements

SNP- switch one base for another Indel- Insertion or deletion of based Copy number variant- multiple copies example CYP2D6 structural rearrangement: translocation of a part of a chromosome to a different chromosome

What is an example of the heterozygote advantage

Sickle cell anemia Homozygotes exhibit severe anemia, have abnormal blood cell shape, and usually die before reproductive age. •Heterozygotes are less susceptible to malaria

types of mutations ___: SNP in coding region but no amino acid change ___: change amino acid ___: premature stop of transcription

Synonymous Missense/nonsynonymous Nonsense

What does the HWE mean? t/f Natural populations are expected to actually be in Hardy-Weinberg equilibrium

The gene pool of a non-evolving population remains constant over multiple generations (allele frequency doesn't change) false- will not be follow as they are evolving

What does HLA-B*1502 refer to? a specific allele and amino acid sequence for HLA a single nucleotide polymorphism (SNP) in HLA-B the 1502nd star allele (*) for HLA-B a substitution at amino acid number 1502 in HLA-B

a specific allele and amino acid sequence for HLA HLA-B= HLA gene 1502= specific allele

definition combination of one or more base pairs of DNA on a particular chromosome

allele

what is a characteristic that is objectively measured and evaluated as an indicator of normal biological processes, pathogenic processes, or pharmacologic responses to a therapeutic intervention. could be a metabolite, dna, rna, protein or image

biomarker

The Genetic Information Nondiscrimination Act of 2008 prohibits genetic discrimination associated with employment disability insurance life insurance long-term care insurance

employment Does not include protections from genetic discrimination in life, disability, or long-term care insurance, but does cover regular insurance

single pathway to bioactivation example a prodrug that is metabolized to an active metabolite examples of high risk pharmacokinetics medications

encainide clopidogrel tamoxifen codeine- metabolized to morphine by CYP2D6 can cause issues if poor metabolizer or rapid metabolizer

portion of a gene that encodes an amino acid

exon

The fundamental physical and functional unit of heredity. A __ is an ordered sequence of nucleotides located in a particular position on a particular chromosome that encodes a specific functional product

gene

____: genetic change by chance alone due to sampling error such as mirepresentation and small populations

genetic drift

if two mutations are co-inherited this is known as what? this implies that they are usually close to each other and both mutation are either major allele (A) or minor allele (a) all the time

genetic linkage

The entire set of genetic instructions found in a cell (in humans), including 23 pairs of chromosomes, found in the nucleus, as well as a small mitochondrial chromosome.

genome

calculate genotype and allele 200 white rr 500 pink Rr 300 red RR

genotype frequency 200/1000= 0.2 rr 500/1000=0.5 Rr 300/1000=0.3 RR allele frequncy 200rr= 400r 500Rr= 500r 500R 300RR= 600R 2000 total alleles 900/2000=0.45r 1100/2000=0.55R

____ mutations (i.e. SNPs) occur in the eggs and sperm and can be passed on to offspring

germ line

what are pharmacokinetic targets?

get drug to where it needs to be and its metabolism Transporters •Plasma protein binding •Phase 1 metabolism •Phase 2 metabolism

_____: individuals move into population, introduces new alleles through "gene flow"

migration

ancestral mapping and can show human migration based on ___ dna also for crime scene investigation as it is very resistant and long living

mitochondrial dna

A change in a DNA sequence

mutation

____ : spontaneous change in dna, this creates new alleles and is the ultimate source of all genetic variation

mutation

pharmacogenomics could matter in drugs with ___ theraputic windows examples of this type of drug

narrow • warfarin • lithium • digoxin • some antibiotics (vancomycin)

The FDA shutdown of 23andme in 2013 was primarily a result of the fact that the company offered: genetic counseling carrier status for disease non-validated disease risk earwax type

non-validated disease risk now more carrier status like eye color, hair color, earwax type

pharmacogenomics could matter in drugs with ___ target adverse effects examples

off target serious adverse effects like SJS carbamazepine clozapine haloperidol abacavir (HLAB5701) antibiotics

an emerging approach for disease treatment and prevention that takes into account individual variability in genes, environment, and lifestyle for each person

precision medicine

Hardy- Weinberg ___ mating then allele frequency remain unchanged over time p= freq (A) q= freq (a) AA=__ Aa= __ aa=__

random mating AA=p2 (% homozygous wild type) Aa= 2pq (% heterozygotes) aa=q2 (% homozygous)

legal issues for pharmacogenomics

regulatory approval, informed consent (pt awareness), disclosure and reporting (will new knowledge be reported to patients), data and sample ownership (biobank samples without pt consent), intellectual property (can you own biomarkers)

Factors causing genotype frequency changes or evolutionary principles ___: variation in fitness; heritable ____: change in DNA of genes ______: movement of genes across populations ___: pollen, spores, airplanes _____: exchange of gene segments ____: mating between neighbors rather than by chance _______: if populations are small enough, by chance, sampling will result in a different allele frequency from one generation to the next.

selection mutation migration vectors recombination non-random mating random genetic drift

____ mutations (i.e. chromosome rearrangements) occur in body cells and are not passed on

somatic

t/f mating combines alleles into genotypes non-random mating causes non-random allele combinations

t/f

what protects the ends of chromosomes making sure that valuable chromosomal dna is not lost

telomere

In the equation for Hardy Weinberg Equilibrium, what does "2pq" indicate? the percentage of heterozygotes the percentage of major allele homozygotes the percentage of minor allele homozygotes 2pq always equals 1

the percentage of heterozygotes

what are pharmacodynamic targets?

the physical target of the drug where it will illicit a response receptors, ion channels, enzymes, immune molecues

t/f In genetic studies, there is typically a bias towards including persons with European ancestry and excluding persons with non-European ancestry.

true

t/f Privacy and confidentiality of genetic information is an ethical issue for pharmacogenomics

true

t/f Reproductive issues - complex and potentially controversial procedures, use of genetic information in reproductive decision making, and reproductive rights are a huge ethical issue for pharmacogenomics

true

t/f there are dramatic genetic differences and different pharmacogenomic markers between ethnic groups

true

t/f there are Uncertainties associated with gene tests for susceptibilities and complex conditions (e.g., heart disease) linked to multiple genes and gene-environment interactions.

true do risk benefit analysis

Most studies in pharmacogenetics has occurred in what population?

white peple

typical trait or genotype that occurs most abundantly in nature.

wild type

Which of these 5 causes allele frequency change? • mutation • migration • natural selection • genetic drift • non-random mating

• mutation • migration • natural selection • genetic drift

5 ways genetic structure changes

• mutation • migration • natural selection • genetic drift • non-random mating

what makes up pharmacogenomics?

genetics and pharmacology

____ certain genotypes produce more offspring- have higher fitness and will lead to adaptation (why we shouldn't use antibacterial soap)

natural selection

The observable traits of an individual person

phenotype