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Organismal genetics > L 1-8 > Flashcards

L 1-8 Flashcards

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Biology 101 flashcards
1
Q

what are common model organisms

A
  • yeast
  • C. elegans
  • drosophila melanogaster
  • arabidopsis thaliana
  • mouse
  • human
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2
Q

why is yeast a good model organism

A
  • have a haploid and diploid stages of life
  • can introduce DNA into yeast to create mutants
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3
Q

why is c. elegans a good model organism

A
  • can add DNA via microinjections
  • can reduce gene function via RNAi
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4
Q

why is drosophila melanogaster a goood model organism

A
  • transposable elements
  • amenable to mutagenesis and chromosomal rearrangements such as deletions and inversions
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5
Q

why is arabidopsis thaliana a good model organism

A
  • 6 week lifecycle
  • amenable to mutagenesis
  • transformation via plasmids
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6
Q

why is mus musculus a good model organism

A
  • great similarities in gene content and genome organisation with humans
  • physiology and developement similarity to humans
  • amenable to genetic manipulation: mutagenesis, transgenics, knockouts, knockin, conditional alterations of gene activity
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7
Q

why are humans good model organisms

A
  • haplotype analysis
  • pedigree analysis and positional cloning
  • large scale genomic projects
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8
Q

what are the mendelian phenotypes

A
  • Variation in singe gene causes phenotype change
  • Pathological change = monogenic disease
  • Expected inheritance pattern
  • Dominant and recessive alleles
  • Autosomal and sex linked
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9
Q

what is phenylketonuria (PKU)

A
  • autosomal recessive
  • error of metabilsm
  • profound conginitive defects
  • deficiency of phenylalanine hydroxylase
  • deficiency blocks tyrosine production
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10
Q

what are the problems confounding pedigree analysis in humans

A
  • small family size
  • participation in molecular analysis
  • uncertain/misreported paternity
  • phentype/genotype variations (mild disease, multipple seperate diseases, pleiotropy)
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11
Q

what are the reasons for genotype/phenotype vatiations

A
  • penetrance
  • expressivity
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12
Q

what is penetrance

A

the probabaility that a disease will appear in an individual when a disease allele is present
- 100% penetrence = 100% diseased
- 25% penetrence = 25% penetrence

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13
Q

what is expressivity

A

difference in severity and symptoms of a disease

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14
Q

what is pleiotropy

A
  • one gene has many functions
  • may be required for different reasons in different tissues
  • loss of function causes phenotype affecting multiple systems
  • different mutations may affect function in specific tissues or a subset of functions
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15
Q

what is nail-patella syndrome (NPS) and what is it an example of

A
  • pleiotropy
  • nail abnormalities, patella absent or poorly developed, glaucoma, kidney disease
  • LMX1B mutation
  • multi-tissue expression
  • the gene has roles in each of these different tissues during developement and this is why different parts of the body are affected
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16
Q

maternal effect

A
  • genotype and phenotype mismatch
  • phenotype depends on gene expression/actvity early in devopement
  • embryonic gene expression/function provided by mother prior to zygotic expression
  • mothers genotype dictates offspring phenotype rather than offsprings own genotype
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17
Q

what is an allelic series

A
  • different mutations in the same gene have different phenotypes
    -each allele affects protein function in a different manner
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18
Q

what is an example of an allelic disease

A

fibroblast growth factor receptor mutations

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19
Q

what is a fibroblast growth factor receptor

A
  • family creates paracrine factors acting in developement
  • responsible for:
  • introducing specific cells to become mesoderm
  • production of blood vessels
  • limb outgrowth
  • growth and differentiation of numerous cell types
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20
Q

explain the allelic series of fibroblast growth factor receptors mutations

A

-receptor proteins contain multiple domains, many isforms (growth, differentiation, growth arrest, motility)
- disruption of different parts of the amino acid and protein changes disease type
- thanataphoric dysplasia
- muenke syndrome
- achondroplasia
- crouzondermoskeletal syndrome
- hypochondroplasia
- thanataphoric dysplasia
- SADDAN

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21
Q

what is genetic heterogeneity

A
  • different mutations cause same phenotype
  • mutations in same gene (allelic heterogeneity)
  • mutations in different genes - locus heterogeneity
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22
Q

what are some examples of genetic heterogeneity

A

Disease examples:
- Cystic Fibrosis – many mutations in CFTR cause same phenotype (allelic)
- Retinitis Pigmentosa – many different genes cause RP when
mutated (locus)
- multiple epiphyseal dypslatia (locus)
- pseudochondroplasia

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23
Q

what is multiple epiphyseal dypslatia

A
  • short stature and early onset osteoarthritis
  • locus heterogeneity
  • the reason is due to protein protein interaction network involved in the cartilage structure
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24
Q

what is pseudoachondroplasia

A
  • more servere than multiple epephyseal dysplasia
  • mutations generate structurally abnormal COMP protein
  • COMP protein expressed in chondrocytes and tendons - generates defects in those tissues
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25
Q

what are allelic series and locus heterogeneity simplified

A

Allelic series - one gene - several disorders
locus heterogeneity - several genes - one disorder

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26
Q

what is a linkage map

A
  • based on recombination during meiosis
  • during meiosis, recombination of furthar apart markers/sequences is more than those closer together
  • not always related to phsical distance some recombination hot/ cold spots
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27
Q

what is pre-genome analysis

A
  • identify genetic markers whose genotype correlates with presence of disease/phenotype
  • mandelian inheritance (diseased genotype the same in all patients)
  • genotype in this region is not shared with healthy individuals
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28
Q

what is post genome linkage analysis

A
  • human polymorphic markers with known location
  • (SNP) single nucleotide polymorphisms
  • assess markers over region of chromosome
  • combination of alleles presnt on same chromosome homolog = haplotype
  • shared haplotype indicate potential similarities in phenotype
  • large scale analysis of haplotype, provides genome differeing between populations
  • haplotype block in linkage diequilibrium - recombination events between close markers are rare
    -can analyse just a few SNPs to determine haplotype
    can ask if haplotype is associated with disease
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29
Q

what is exome sequencing

A
  • Applicable to human disease
  • Applicable to identify phenotypes in other organisms
  • Many genome sequences available – not just common models
  • Capture and isolation of all exons from genome
  • Direct sequencing of coding regions
  • Identify variations (mutations?)
30
Q

what is next generation sequencing

A
  • sequencing of many DNA molecules in parellel
  • uses PCR amplification and coloured labells
31
Q

what are the major modifications of next generation sequencing

A
  • dont need gene specific primers
  • parallel sequencing of pool samples
  • rapid data generation of large datasets
  • short read (50bp-450bp)
    -alignment ot genome needed
32
Q

what are the exome sequence limitations

A
  • only samples known coding regions (1% of genome)
  • doesnt identify chromosomal stractural alterations, only sequence alterations
  • many variations in each individual
  • false positives and negatives due to PCR amplification
33
Q

what are polygenic phenotypes

A
  • many phenotypes affected by multiple different genes, each making a small contribution to phenotype
  • linkage hard to identify
  • each allele has different degree of influence over phenotype
    environmental behavioural influence
34
Q

give examples of phylogenic diseases

A
  • hypertension
  • alcoholism
  • psychiatric disease
35
Q

what is the difference between heterogeneity and polygenic disease

A
35
Q

what is the difference between heterogeneity and polygenic disease

A
  • locus heterogeneity, many genes cause same disease through individual mutations (eacch has mandelian inheritance pattern
  • polygenic disease, multiple genes cause disease through combined action of alleles
36
Q

what is a genome wide assiciation study

A
  • use SNP markers to generate haplotype for all genomic regions
  • identify common haplotype from affected pools and unaffected pools
  • assess genes in region for links to phenotype
37
Q

what are the advantages of GWAS

A
  • compare large groups, identify regions contributing to small amount of variation of phenotype
    -useful for common diseases with polygenic basis
38
Q

what are the advantages of GWAS

A
  • compare large groups, identify regions contributing to small amount of variation of phenotype
    -useful for common diseases with polygenic basisa
39
Q

what are the disadvantages of GWAS

A
  • need large nunmber of individuals in each group
  • associated regions often contain on genes or unlikely candidates
  • association to causation difficult to demonstrate (need functional experiments to validate)
40
Q

what are the principles of independent assortment

A
  • traits are inherited independent of each other
    -if traits analysed individually each shows 3:1 inheritance - concluded 2 dominant 2 recessive
  • ratio of offspring from a two-trait cross 9:3:3:1
41
Q

what were the contradictions found in mendels observations

A
  • plant height
  • seed diemeter
42
Q

what did francis galton discover

A
  • studied seed size in pea plants
  • saw no clear phenotype of large vs small, however did have a variation of 1-2%
  • observed offspring with no clear hertible impact
43
Q

conflict between mendelian genetics and biometrics

A
  • mendelieans, variation in discrete characters drives evolution, new mutants have large effects
  • biometricians, evolution is natural selection acting on continously distributed characters
44
Q

what is the modern theory of inheritence

A
  • some phenotypes controlled by one gene
  • many alleles (based changes can be observed for each gene
  • some phenotypes controlled by many genes and interactions
45
Q

what is a quantitative trait

A
  • phenotypes are not one or two choices but rather, vary along a range of values
  • controlled by interactions between genes and environment
46
Q

what is an example of a quantitative trait

A

hypercholesterolemia

47
Q

what is a quantitative trait loci

A

genetic regions that influence phenotypic variation of a complex trait, often through genetic interactions with each other and the environment.

48
Q

what causes pigmentation differences

A
  • melanosomes, cellular compartments that store melanin
  • eumelanin - black/brown
  • pheomelanin - red/yellow
49
Q

what is the evolutionary function of melanin

A

protection against UV radiation, reduces synthesis of vitamin D

50
Q

how to do QTL identification in mice

A
  • identify phenotype of interest
  • test inbred strains for phenotype
  • determine genetic region that contributes to phenotype (major effect)
  • evaluate genes in region as candidates
51
Q

what were the conclusions of the alcoholic study

A
  • stxbp1 is likely to be gene that causes ethanol preference QTL on mouse chromosome 2
  • further studies into role of protein structure change are needed to determine molecular basis of phenotype
52
Q

what is transgenic rescue

A

add wild type allel to mutant and see phenotype disappear

53
Q

what is a knock in

A

generate same sequence change in wild type mice and induce same phenotype

54
Q

what is epigenetics

A
  • conrad waddington (1905-1975) “the branch of biology which studies the causal interactions between genes and their products, which bring the phenotype into being”
  • epigenetics regerto the study of heritable changes that occur without a modificaiton in DNA sequence of the genes
55
Q

what are the four types of epigenetic mechanisms

A
  • DNA methylation
  • histone modification
  • nucleosome remodelling
    -non-coding RNA-methylation
56
Q

what is DNA methylation

A
  • serves as a signal to how that DNA should be packed within the nucleus whether or not it should be present or easy for transcription
  • blocks transcription of methylated gene
  • imprint can differ depending on parental chromosome
    opposite to acetylation
57
Q

what diseases are due to imprinting

A
  • Prader-Willi syndrome
  • Angelman syndrome
58
Q

what is Prader-Willi syndrome

A
  • failure to thrive, short stature, impared conitive developement , respiratory distress, excessive eating and obesity
  • micro deletions of chromosome 15
  • imprinting center on chromosome 15, stop and increase transcription
59
Q

what is Angelmans syndrome

A
  • developmental delay, hyperactivity, impaired cognitive developement, seizures
  • microdeletions of chromosome 15
  • imprinting center on chromosome 15, stop and increase transcription
60
Q

how does the imprint marking change

A
  • During fertilisation there is an epigenetic reprogramming cycle
  • Adult have differentiated cells
  • The adult forms germ cells that are not imprinted
  • After fertilisation a new marking of the imprints occurs
61
Q

how is imprinting established

A
  • Differentiated gametes must undergo widespread epigenetic reprogramming upon fertilisation
  • After the mammalian 8 cell stage the zygotic genome is activated
  • Two cell lineages form in mammalian embryo - inner cell mass and trophectoderm
  • The inner cell mass is what gives rise to the embryo itself
  • The trophectoderm gives rise to the placenta
  • ICM further forms into epiblast (EPI) and primitive endoderm
    Genes have different degree of methylation in inner cell mass and trophectoderm
62
Q

how does cloning work

A
  • take adult cell
  • remove nucleus
  • transfer to oocyte with nucleus removed
  • implant into mother
63
Q

what is the common dyndrome associated with cloning

A

large offspring syndrome, due to adult imprinting

64
Q

what are the symptoms of large offspring syndrome

A
  • respiratory distress
  • up to 2-fold increase in birth weight
  • skeletal defects
  • immunological defects
  • placental defects
65
Q

what are the causes of large offspring syndrome

A
  • improper placental developement due to imprinting defect in epigenetic markers
  • abnormal gene expression in developement
  • imprinted genes especially effected
  • genes required for pluripotency affected
  • gene expression changes, some genes not expressed
66
Q

is epigenetics the cause of clone abnormalities

A
  • methylation defects at imprinted locus in cloned cattle with large offspring syndrome showed: large loss of methylation
  • cloned female and male animals used in natural matings have pups that show no defects like LOS
  • offspring have same genotype but different epigenetic imprint
67
Q

in what organisms does imprinting occur

A

mammals and plants

68
Q

how are histone proteins modified

A

lysine residues can be acetylated (causeing packing)

69
Q

what is the barker hypothesis

A

he believed nutrient restriction caused increased mortality rates and cardiovascular disease from 1910 to 1970 due to epigenetics

70
Q

what is a thriftly phenotype

A

nutrient conditions during pregnancy have effect on health in adult life

71
Q

how does a thrifty phenotype occor

A
  • programming (persisting changes in phsiology and metabolism causes histone modification
  • experience adequate nutrition after birth, modified physiology cannot compensate and causes obesity and cardiovascular disease

Organismal genetics (4 decks)

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