question

Taq polymerase

answer

Bacteria that lives in vents, chemotroph, flourishes at 70 degrees celcius - can live between 50 and 80 degrees celcius. Polymerase used in PCR that can keep on working at high temperatures

question

Chemotroph

answer

Organism that obtain energy by the oxidation of electron donors in their environments. These molecules can be organic or inorganic. The chemotroph designation is in contrast to phototrophs, which utilize solar energy.

question

Humans or PCR? RNA primers, helicase, dna polymerase, whole genome, nucleotides needed for elongation

answer

Humans

question

Humans or PCR? DNA primers, heat, taq, only part of the DNA, nucleotides needed for elongation

answer

PCR

question

Anneal

answer

To be capable of combining with complementary nucleic acid by a process of heating and cooling

question

Micro-Array

answer

Use cDNA instead of mRNA as in traditional PCR - this is expensive and takes more time to generate. Primer 2 = poly-T to bind to poly-A tail.

question

PCR Cycle Threshold

answer

A quantitative measurement for the amount of input material (as the end amount of PCR output is not a measure for initial amount of DNA)

question

After about 25 cycles experimentally, PCR amplification is no longer ______________

answer

Linear

question

How to get rid of unwanted products in PCR (longer is stronger)

answer

Increase temperature/make better primers

question

PCR temperatures during thermocycler

answer

95 degrees = separation DNA 50 degrees = primer 72 degrees = DNA polymerase

question

Thermocycler

answer

Device that can change temperatures quickly (used for PCR)

question

Virtual lab: DNA extraction

answer

http://learn.genetics.utah.edu/content/labs/extraction/

question

Virtual lab: PCR

answer

http://learn.genetics.utah.edu/content/labs/pcr/

question

Virtual lab: Electrophoresis

answer

http://learn.genetics.utah.edu/content/labs/gel/

question

Virtual lab: Microarray

answer

http://learn.genetics.utah.edu/content/labs/microarray/

question

Waarom zou je DNA kleuren met ethydium bromide

answer

Intercalates with DNA (binds with carcinogenes), fluorescent tag. Means you can visibly see potential carcinogenic elements in DNA with the naked eye under UV light.

question

Chromatography

answer

Separation on basis of colour. Gel electrophoresis is a form of this except with a negative and positive pole because DNA is a negative molecule.

question

>50bp mutatie PCR, what do you use?

answer

Agarose gel (gel electrophoresis)

question

<50bp mutatie PCR, what do you use

answer

Ontwikkel een selectieve primer voor de mutatie -> wildtype geen PCR product, mutatie wel PCR product (of vice versa afhankelijk van je primer design). Daarna gel electrophoresis

question

Gel electrophoresi

answer

The separation of nucleic acids or proteins, on the basis of their size and electrical charge, by measuring their rate of movement through an electrical field in a gel.(Sodium docyl sulfate & Mercaptoethanol & heating changes 3D structure and denatures DNA/RNA/protein, then agarose/polyacrylamide gel, separates on size in a gel 'matrix')

question

cDNA

answer

Complementary DNA. DNA produced synthetically by reverse transcribing mRNA. Because of eukaryotic mRNA splicing, it contains no introns.

question

In Western blotting gel electrophoresis charts: bigger molecules are on the..

answer

Top

question

In Western blotting gel electrophoresis charts: smaller molecules are on the..

answer

Bottom

question

Reverse transcriptase

answer

An enzyme encoded by some certain viruses (retroviruses) that uses RNA as a template for DNA synthesis. Very poor proofreading activity.

question

Integrase

answer

Inserts viral dna into the host chromosome

question

Protease

answer

any enzyme that performs proteolysis, that is, begins protein catabolism by hydrolysis of the peptide bonds that link amino acids together in a polypeptide chain

question

Vector

answer

Articifical construct used to insert foreign DNA into a cell. (circular DNA)

question

Plasmid

answer

Cloning vector: 15kb, propagates by plasmid reproduction, uses transformation

question

Phage lambda

answer

Cloning vector: 23kb, propagates by phage reproduction, uses phage infection

question

Cosmid

answer

Cloning vector: 44kb, propagates by plasmid reproduction, uses phage infection

question

Bacterial artificial chromosome

answer

Cloning vector: 300kb, propagates by plasmid reproduction, uses electroporation

question

Cloning vector

answer

DNA molecules that can carry foreign DNA into a host cell and replicate there.

question

Limitations of PCR

answer

<2kb fragments & must know target DNA for primers

question

Shot gun sequencing

answer

Make small fragments, sequence all samples in parallel, assemble golden path "contigs" (side by side, touching; near), put all together for final genome

question

Contig

answer

Components van shotgun sequence die aan elkaar gelijmd worden

question

Genetic chimera

answer

An organism in which some cells have a different genotype than others, and will transmit transgenes to progeny only of embryonic germ cells carry a copy of the transgene.

question

DNA restriction enzymes do what

answer

Recognize palindromic sequences & cleave them

question

DNA Ligase does what

answer

Anneals 2 DNA strands with cohesive or blunt ends back together (can only anneal sequences which are complementary)

question

Cohesive 'sticky' end

answer

Fragments with short, single-stranded overhanging ends, can easily realign

question

Blunt end

answer

Even-length ends from both single strands

question

Transfection

answer

transformation of bacteria with DNA extracted from a bacterial virus

question

Sanger sequencing

answer

Dideoxynucleotides halt DNA polymerization at each base, generating sequences of various lengths that encompass the entire original sequence. Terminated fragments are electrophoresed and the original sequence can be deduced. (4 different reaction tubes)

question

ddNTP

answer

Dideoxynucleotide has 2 Hs at 2' and 3' position. Use to stop PCR, principle of sanger sequencing (new nucleotides cannot be added)

question

Genome grab

answer

Ethical conflict surrounding patents on genes. i.e. if you want to get tested for a certain genetic disturbance you'd have to pay for it. Synthetic DNA is allowed to be patented (modified cDNA)

question

TIGR vs HGS

answer

The Institute for Genomic Research (for-profit, developed whole genome shotgun sequencing) vs Human Genome Sciences (nonprofit). TIGR: computerintensief. Shotgun alles in een keer. HGP: Arbeidsintensief, genetische kaart, verdeling chromosomen in segmenten, shotgun sequence segmenten HGP benadering beter omdat je met whole genome shotgun waarschijnlijk gaten krijgt.

question

Pyrosequencing (454 sequencing)

answer

less accurate than Sanger, but is faster and cheaper; sequencing is done on randomly sheared fragments that will overlap for assembly (contigs); DNA from more than one organism can be sorted into different genomes. Als nucleotide ingebouwd wordt komt pyro los, via ATP ; luciferase komt er een licht flits. Zie je in parallel allemaal flitsjes.

question

Ideal population eigenschappen

answer

1. No mutation 2. Infinitely large 3. No genetic interaction with other populations 4. Random pairing (no paringsvoorkeur) 5. No selection (all alleles equal fitness) AN IDEAL POPULATION DOES NOT EVOLVE!!

question

Hardy-Weinberg equilibrium

answer

All our allele frequencies stay the same from generation to generation unless evolutionary occurences take place (nonideal population)

question

Genetic drift

answer

Genetische veranderingen door toevallige gebeurtenissen - non-adaptive evolutie. Treed vaker op in kleine populaties.

question

Bottleneck phenomenon

answer

Population bottlenecks occur when a population's size is reduced for at least one generation. Afname variatie in populatie.

question

Founder effect

answer

the reduced genetic diversity which results when a population is descended from a small number of colonizing ancestors.

question

Positive assortative pairing

answer

Mate with individuals LIKE yourself. Decreases heterozygotes, increases homozygotes

question

Negative assortative pairing

answer

mate with individuals UNLIKE self' increases heterozygotes, decreases homozygotes

question

Inteeltdepressie

answer

Afname fitness van een populatie (minder heterozygoten -; meer lethal alleles)

question

Tay-Sachs

answer

An inherited genetic disease that is caused by lack of and enzyme necessary to break down lipids necessary for normal brain function and results in seizures, blindness, and early death; common in Ashkenazi Jews. INTEELTDEPRESSIE

question

Coefficient of inbreeding

answer

Kans dat 2 kopieen van een gen van dezelfde voorouder komen

question

Coefficient of inbreeding for different family members

answer

Unrelated parents, F = 0 Parent-offspring or brother/sister = 1/4 Half-sibling = 1/8 First cousin = 1/16 Second cousin = 1/64

question

Heterozygote advantage

answer

When the heterozygote genotype has a higher relative fitness than either the homozygote dominant or homozygote recessive genotype. (i.e. sickle cell anemics heterozygotes malaria resistant)

question

Hoeveel verschillende dieren, planten ; schimmels bestaan er op aarde?

answer

10-15 miljoen

question

Kritisch moment ontstaan nieuwe soort

answer

Overgang van gemeenschappelijke ouderstammen -; 2 groepen

question

Morfologische soort

answer

Groep van individuen die qua uiterlijk op elkaar lijken

question

Biologische soort

answer

Groep van individuen die actueel of potentieel vruchtbare nakomelingen kunnen produceren Problem: asexual organisms not encompassed by this definition ; kruisbaarheid not always test-able

question

Fylogenetische soort

answer

Groep van individuen die afstammen van dezelfde genetische lijn

question

Cryptysche soort

answer

Groep van individuen die qua genotype op elkaar lijken. Het kleinst mogelijke verzameling van organismen met een gemeenschappelijke voorouder.

question

Aseksuele soort

answer

Groep van individuen die voortplanten zonder partner

question

Reproductive isolation

answer

Separation of a species or population so that they no longer interbreed and evolve into two separate species

question

Premating

answer

Reproductive isolation (prezygotic isolation 1) i.e. mechanical isolation, chemical isolation, ecological isolation.

question

Mechanical isolation

answer

Morphological differences prevent fertilization. Form of prezygotic isolation (premating)

question

Chemical isolation

answer

Based on pheromones, only some males will attract the females.

question

Ecological isolation

answer

Isolation in space and time, live on ; feed off different environments, reproduction in different seasons etc. Example is geographic isolation.

question

Na bestuiving/inseminatie

answer

Reproductive isolation (prezygotic isolation 2 - zelfincompatibiliteit

question

Postzygotische isolatie

answer

Reproductive isolation (prezygotic isolation 3) i.e. meiotic problems (chromosomes don't line up properly due to different #)

question

Dobzhansky-Muller incompatibility

answer

Disharmonious interactions between the different genes inherited from the two parents. Leads to inferior fitness due to dimer enzymes & epistasis.

question

Haldane's Rule

answer

States that the pattern of sterility is in heterogametic sex, regardless of which is male or female

question

Speciation genes

answer

Gene duplication ; selfish genes

question

Gene duplication

answer

The generation of extra copies of a gene in a genome over evolutionary time. A mechanism by which genomes can acquire new functions.

question

Selfish genes

answer

Parasitic DNA sequences that survive and reproduce but that do not increase the fitness of the host genome.

question

Soortvorming is een bijproduct van....

answer

genetische isolatie

question

Allopatrische soortvorming

answer

Populaties raken geografisch gescheiden (vicariantie)

question

Peripatrische soortvorming

answer

Populaties koloniseren nieuwe gebieden (dispersal)

question

Sympatrische soortvorming

answer

Disruptieve selectie en ecologische soortvorming

question

Disruptieve selectie

answer

also called diversifying selection, describes changes in population genetics in which extreme values for a trait are favored over intermediate values. In this case, the variance of the trait increases and the population is divided into two distinct groups.

question

Outcomes of secondary contact between branched sorts

answer

Hybrid zone: Reinforcement, fusion, stability

question

Phylogeny

answer

The sequence of events involved in the evolutionary development of a species or taxonomic group of organisms

question

Taxonomy

answer

Discipline of classifying organisms and assigning each organism a universally accepted name

question

Systematics

answer

A scientific discipline focused on classifying organisms and determining their evolutionary relationships.

question

Homology

answer

Similarity resulting from common ancestry.

question

Analogy

answer

Similarity resulting from function. (no common ancestor)

question

Example character vs. character state

answer

colour of the abdomen vs. red, white, yellow

question

Maximum parsimony

answer

"Occam's Razor." A principle that states that when considering multiple explanations for an observation, one should first investigate the simplest explanation that is consistent with the facts.

question

Sexual selection

answer

A form of natural selection in which individuals with certain inherited characteristics are more likely than other individuals to obtain mates.

question

Cryptic female choice

answer

the ability of a female in receipt of sperm from more than one male to choose whose sperm get to fertilize her eggs

question

Waarom zijn sommige mutaties neutraal?

answer

- Derde letter in codon vaak zelfde aminozuur (geen effect op eiwitstructuur) - Veel aminozuren zelfde eigenschappen - Delen van aminozuur niet cruciaal voor functie

question

Mutatiesnelheid is groter in ______________ dan in niet-____________ posities

answer

Synonieme

question

Hoe bereken je het aantal mutaties

answer

Aantal kopieen X mutatiesnelheid = 2N*mu (diploide). Als mutaties neutraal zijn is P(fixatie) = 1/2N (of 1/N voor haploid). Substitutiesnelheid K = # mutaties * P(fixatie). k = (2N*mu)*1/2N = mu

question

Hoe bereken je divergentie (het aantal neutrale substituties wat is opgetreden vanaf de splitsing A en B)

answer

d = 2tk =; t = d/2k

question

Methods of dating evolution

answer

Radioactive isotopes in rocks and fossils, stratification (relative sequence of events) and molecular clock calculations.

question

Voordelige mutaties (positieve selectie) relatie tussen K en Mu

answer

k ; mu (als mutaties sneller gaan dan verwacht, bevorderd het waarschijnlijk de voortplanting)

question

Nadelige mutaties (negatieve selectie) relatie tussen K en Mu

answer

k ; mu (als mutaties sneller gaan dan verwacht, bevorderd het waarschijnlijk niet de voortplanting)

question

NS/S ratio en betekenis als het gelijk aan 0, 1 of ;1 is

answer

Niet-synonieme substituties/synonieme substituties = 0 (of bijna 0) purifying selection, gen is essentieel = 1 mutaties neutraal, sequentie codeert nergens voor ; 1 positieve selectie op de sequentie, gen veranderd door natuurlijke selectie

question

Purifying selection

answer

Natural selection that removes deleterious variants of a DNA or protein sequence, thus reducing genetic diversity. Conservation of 'nuttige' eigenschappen maar leidt tot slechte fitness

question

Selective sweep

answer

Strong selection can "sweep" a favorable allele to fixation with a population so fast that there is little opportunity for recombination

question

Assortative mating

answer

the type of mating that occurs when an organism selects a mating partner that resembles itself i.e. in Darwin's finches to prevent 'medium' sized beak (big beak mates with big beak etc)

question

Irreducible complexity

answer

Organic systems incorporating several parts each necessary for the functioning of the system and each of which cannot be accounted for apart from the system; no functional advantage. Ex: bacterial flagellum; human eye

question

The eye is a bad example of ________________

answer

Intelligent design because it's an accumulation of mutations and there was probably a smarter way of putting together the eye.

question

Possible explanation for red-green colour blindness

answer

Mutation that allows for more distinction between khaki colours - possibly voordelig in east africa grasslands. Or the mutation is just a mutation.

question

Frequency dependent selection

answer

the more frequent an allele, the more it will be selected against

question

Heterozygotic advantage

answer

the manifestation of higher fitness by heterozygotes than by homozygotes at a specific locus, homozygote recessive causes disease. i.e. sickle cell anemia vs malaria.

question

Pseudogenization

answer

when one copy of a duplicated gene is inactivated, be invisible to natural selection, and thus mutate at a faster rate

question

Neofunctionalization

answer

Divergence of duplicate genes whereby one acquires a new function.

question

Subfunctionalization

answer

The process, following gene duplication, whereby mutations in each of the two copies can result in the two genes having complementary activities such that their combined activity is the same as the activity of the gene before duplication

question

Adaptive walks

answer

pathway of a stepwise evolutionary change that results from natural selection and the accumulation of a series of mutations

question

Quantitative Trait Loci

answer

Genes that have relatively small effects and influence likelihood of some characteristic in a population. Like genetic markers. Follow them throughout a selection line - associations between markers and associations.

question

Eisen voor quantitative trait loci analysis

answer

1. Inbreeding lines (we want homozygoot crosses) 2. Genetic markers bijvoorbeeld SNPs. SNPs kan je vinden via microarray 3. Family tree (Stamboom) -; backcross met crossing over

question

DNA Marker

answer

Een stukje DNA die we makkelijk kunnen herkennen en waar de locus van bekend is

question

Fine mapping

answer

Process using very closely linked markers (~1 or more centimorgan apart usually) that flank a particular trait to search for a gene of interest. Involves identifying individuals with a rare crossover event that occurred between the two regions of interest (requires large number of progeny, esp successful w/ plants). Can reveal what parent the trait was inherited from, whether the mutation is dominant/recessive, etc. Allows for the mapping of a mutation/disease trait and is important for isolation of defective disease causing genes.

question

Genome Wide Association mapping

answer

Utilize molecular markers that are spread throughout the genome. Determine genotypes for a generally large number of individuals. Look for alleles of markers that are more often associated with the disease phenotype than the control phenotype. Does not require the use of a genomic library.

question

Linkage disequilibrium

answer

Tendency for certain alleles at 2 linked loci to occur together more often than expected by chance. Measured in a population, not in a family, and often varies in different populations. Value is called D. What is the genetic term?

question

Formula for linkage disequilibrium

answer

D = P(AB)-P(A)*P(B)

question

Manhattan plot

answer

Seen in a GWAS: highest point is MOST significant SNP with disease state

question

Population stratification

answer

A false positive association that results from a population's subgroups that tend to remain genetically separate from each other. i.e. investigating smokers and nonsmokers, the smokers group probably has a higher genetic risk factor of addiction. Confounding variable.

question

Genome Wide Association effectiveness

answer

That one graph you couldn't find anywhere

question

Holometabolous

answer

Complete metamorphosis during life cycle (transition from larva to adult)

question

Hemimetabolous

answer

Having no pupal stage in the transition from larva to adult.

question

Syncytium

answer

A large multinucleate cell, typically formed by the fusion of many smaller cells during development (e.g. a skeletal muscle cell), or formed by nuclear division in the absence of cellular division.

question

Imaginal discs

answer

Clusters of undifferentiated tissue that form adult tissues pupae are known as this

question

In-situ hybridization

answer

a method to detect DNA or messenger RNA directly in tissue labeled probes; is often performed directly in tissue embedded in paraffin; may be used to detect underlying genetic abnormalities

question

Immunolocalization

answer

fluorescent visualization of the protein in a cell, where its localized

question

Segmentation

answer

Body is made up of a series of fused rings; external and internal structures are repeated segment by segment

question

Threshold/Liability trait

answer

A trait which is inherited quantitatively, but is expressed qualitatively. i.e. type-2 diabetes. Requires environmental 'threshold'.

question

Threshold dimorphism example

answer

Salmon mating: grote mannetjes en sneaky mannetjes. Threshold is body size, fat percentage. Environmental factor is population density.

question

Meristic

answer

a trait in which the phenotype is determined by counting, such as number of ears on a stock of corn or number of eggs laid by a hen.

question

Examples of complex traits in humans

answer

IQ, depression, schizophrenia, alzheimer, height, weight, blood pressure, cancer risk

question

Polygenic traits: how many genotypes/phenotypes per 1, 2, 3, 4 genes

answer

1 gene -; 3 geno, 3 feno 2 gene -; 9 geno, 5 feno 3 gene -; 27 geno, 7 feno 4 gene -; 81 geno, 9 feno

question

Central limit theorem

answer

The averages of samples have approximately normal distributions, with a narrower distribution as sample sizes increase.

question

Broad sense heritability

answer

heritability that is due to total genetic variation

question

Narrow sense heritability

answer

the proportion of trait variation that contributes to genetically-based resemblance between parents and offspring

question

Types of peoples and times when they lived

answer

Ardipithecus 4-7 million years ago H. Habilis 2 million years ago H. erectus 1 million years ago H. heidelberg 0.5 million years ago H. sapiens current

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