Mcb 104 Midterm #3 Flash Cards

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gene expression

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when and where genes are transcribed

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molecular enhancer

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a region of DNA that positively regulates gene expression (transcription) often in a spatial and/or temporal manner (also called a cis-regulatory element)

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in situ hybridization

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looks for expression of a SINGLE gene using a labeled anti-sense RNA probe. The probe will bind to complementary sequence in fixed embryos or tissues

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immunolocalization

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detects protein - use an antibody to tag protein of interest and amplify signal with additional probes

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homeosis

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changes in segmental identity

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contigs

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overlapping sequences (continguous sequence)

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scaffold

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two contigs connected (supercontig)

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synteny

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allows you to compare regions of the DNA between organisms

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ESTs

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expressed sequence tags = sequence reads from both ends of a cDNA; ESTs are used to annotate where exons are

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homolog

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closely related genes in different organisms

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paralogs

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genes related by gene duplication

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synteny

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the conserved order of orthologous sequences

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orthologs

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genes in which the same genetic locus has been inherited from a common ancestor

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point mutation

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alteration of a single base pair

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synonymous mutation

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altered codon specifies the same amino acid

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missense mutation (conservative)

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altered codon specifies a chemically similar amino acid

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missense mutation (non-conservative)

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altered codon specifies a chemically dissimilar amino acid

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nonsense mutation

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altered codon signals chain termination

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single nucleotide polymorphism

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one nucleotide changes anywhere in the genome

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types of chromosome mutations

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1. translocation
2. deletion
3. missing chromosomes
4. extra chromosomes
5. duplication
6. inversion

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translocation

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a chunk of one chromosome is moved onto another chromosome

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reciprocal translocation

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re-arrangement where two nonhomologous chromosomes trade acentric fragments

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Robertsonian translocation

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rearrangement involving fusion of two acrocentric chromosomes

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metacentric chromosomes

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have centromeres in the middle

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submetacentric

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off-center centromeres which results in one longer and one shorter arm

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acrocentric

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centromeres near the end (Robertsonian translocations most common in these)

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comparative genome hybridization

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used to detect duplications, deletions, and tandem amplifications in an individual's genome

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population genetics

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the study of genetic variation and how it changes in time and space

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Hardy-Weinburg equilibrium

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in the absence of disturbing forces, the amount of genetic variation remains constant generation after generation

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disturbing forces

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1. non-random mating
2. mutation
3. migration
4. selection
5. genetic drift

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haplotype

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tightly linked polymorphisms not separated by historical meioses in a natural population (they do not follow Mendel's laws because they are linked)

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quantitative genetics

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the genetic analysis of complex traits

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discontinous (Mendelian) trait

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a discontinuous trait only exhibits a few, easily distinguished phenotypes

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continuous (qualitative) trait

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a continuous trait characteristic exhibits a range of phenotypes

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meristic

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determined by multiple genetic and environmental factors and can be measured in whole numbers

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threshold traits

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measured by presence or absence

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polygenic inheritance

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refers to quantitative traits controlled by the cumulative effects of many genes

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frequency distribution

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show the distribution of a trait within a population

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normal distribution

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bell-shaped curve

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population

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group of interested individuals

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sample

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collection of individuals from the population

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mean

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average

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variance

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variability of a group of measurements

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standard deviation

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square root of the variance

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quantitative trait loci

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chromosome regions containing a gene or genes that influence a quantitative trait

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correlation

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when two variables are correlated, a change in one characteristic is likely to be associated with a change in the other

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correlation coefficient

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measures the strength of the association between two variables

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regression

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predicting the value of one variable if the value of the other is given

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regression coefficient

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represents the slope of the regression line, indicating how much one value changes on average per increase in the value of another variable

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heritability

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the proportion of the total phenotypic variation that is due to genetic differences

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broad-sense heritability

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proportion of the phenotypic variance that is due to genetic variance

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narrow-sense heritability

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proportion of the phenotypic variance that is due to additive genetic variance

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response to selection

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the amount that a quantiative characteristic changes in a single generation when subjected to selection (the response to selection) is directly related to the selection differential and narrow-sense heritability

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pseudogene

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open reading frame or partial open reading frame that are nonfunctional or inactive due to mutations

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copy number variant

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a segment of DNA that is 1 kb or larger and is present at a variable copy number in comparison with a reference genome (classes of CNVs include insertions, deletions, and duplications)

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segmental duplication

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a segment of DNA greater than 1 kb in size that occurs in TWO or more copies per haploid genome with the different copies sharing more than 90% sequence identity

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whole mount ISH

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detects mRNA gene expression in tissue

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Fluorescent ISH (FISH)

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detects specific DNA sequences in chromosomes in cells

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Fiber fluorescent ISH

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detects specific DNA sequences in chromosomes in cells at high resolution by stretching out chromosomes

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Genome-wide association studies

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test of the association between markers (SNPs) across the genome and disease or quantitative trait phenotype, usually involving hundreds of thousands of SNPs spread throughout the genome

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tagSNPs

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minimal set of SNPs that tag most common haplotypes

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linkage disequilibrium

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the deviation in the frequency of haplotypes in a population from the frequency expected if the alleles at different loci are associated at random

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odds ration

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basically the odds you would get cancer if you have a certain allele compared to people without the allele

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Bonferroni correction

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p value divided by number of tests performed

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common disease-common variant hypothesis

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many common disease are caused by common alleles that individually have little effect but in concert confer a high risk