last test Flashcards
Dan Barber
different flavoured wheat
genomics vs genetics
genomics is technology used to generate large datasets of digital info (materials)
genetics is method of experimentation used to understand cause and effect between genes and phenotypic variation
what things can be understood with genetic methods
cancer diabetes/obesity eye disorders heart disorders infectious disease nervous system digestive system
model organisms
mice experiments led understanding of human genome
Norman Borlaug
interested in cereals
can change architecture of plant through genetics, to improve and produce more food - increased yield
plant breeding limits
high yields, less starvation, wealth
but high inputs so not very sustainable
John Beddington
by 2030 we need to be producing 50% more food and energy and 30% more fresh water
chromosomes
coloured bodies
most of the time DNA is decondensed because need to be accessed by machinery to transcribe and translate
only during division is it condensed to chromosomes
plant chromosomes
are flexible in terms of number of them
chromosome structure
telomeres - ends
centromere - spindle attachment
euchromatin - lot genetic info
heterochromatin - structural movement, little genetic info
kinetochore - where microtubules attached
2 copies, 2 sister chromatids make up chromosome
centromere position
telocentric - at end so only 1 arm
acrocentric - bit below end
submetacentric - almost centre
metacentric - in the middle
Giemsa stain
banding pattern
shows more info on location of what’s on chromosome
drosophila polytene chromosomes
replicated DNA strands do not separate during interphase
cell cycle
most of the time in interphase
short time in division phase (mitosis/meiosis)
prophase
centrosome duplicates and begins to move to poles
chromosomes condense
nuclear membrane breaks
spindle forms from centrosome to centromere
bipolar attachment
both side of chromosomes attached by microtubules
when do chromatids become chromosomes
sister chromatids separate from each other during anaphase and when separate, are now chromosomes
cohesin
attaches chromatids in chromosome
destroyed enzymaticaly by separase breakdown
synaptonemal complex
homologous chromosomes brought together, attached along full length
crossing over
nicks along length of chromatid in prophase, repaired or 2 chromatids swap segments
chiasmata
microscopy term
see where crossing over has occurred
monopolar kinetochores
chromosomes attached to spindle
1 side of microtubule to 1 chromosomes, other side to other chromosome
female gamete
only 1 gamete goes onto next generation
5 stages of prophase
leptotene zygotene pachytene diplotene diakinesis
leptotene
chromosomes condense and become visible
homolog pairing
double-stranded DNA breaks for crossing over
zygotene
synaptonemal complex between homologous pairs
paird homologs now are bivalents
pachytene
condensing
synaptonemal complex complete
tetrads - bivalents have 4 chromatids
crossing over complete
diplotene
synaptonemal complex disassembles
pair of chromatids begin to separate
chiasmata visible
diakinesis
chromosomes repel each other
non-sister chromatids loosely associated via chiasmata
nuclear membrane disappear
monopolar attachment
total no. possible gamete combinations
2^ no. chromosomes
experimental method
assemble robust experimental system
carefully design and perform first experiment and quantify results to generate lots data
repeat with diff starting materials
analyse data and derive predictive model
devise experiments to test predictions
Mendel’s experimental method
self pollination to make sure they’re true bred
1st experiment - 1st generation outcross
repeat with diff things - seed shape/colour
analyse data to get model - ratio
test ratio
first law of inheritance
heredity is controlled by paired factors (alleles) that separate in gametes and are joined upon fertilisation in offspring
size of human genome
size of wheat genome
3,300
16,000
Barbara McClintock
discovery of gene switches in maize
Transposable element
DNA sequence that can change its position within the genome
jumping occurs during mitosis
different outcomes depending on position of transposable element
element inserted into coding region of gene - protein produced not expressed/not functional
in promoter - not being transcribed
other region - no effect
promoter region vulnerable to…
and what does this mean?
methylation (no changes in base pair sequence, adding of methyl group doesn’t allow transcription)
epigenetics
heritable changes in gene expression that are not caused by changes in DNA sequences
types of epigenetics
methylation
histone protein stopped from uncoiling (can’t access to transcribe)
Ruth Sager
discovered DNA in mitochondria (so inherit them but not like mendelian inheritance)
early pioneer in cancer genetics
biochemical evidence of symbiosis
mitochondria communicate with the nucleus via trafficking proteins and RNAs
genetic evidence of symbiosis
nucleus contains genes that encode mitochondrial proteins
mitochondrial genome
wide variation on size (16kb humans, 80 yeast, 100kb to 2Mb plants)
circular genome
contains genes for tRNAs, rRNAs, cytochrome oxidase, ATPase subunit, NADh-dehydrogenase
chloroplast genome
80-600 kb
circular genome
genes for redox proteins involved in electron transport for photosynthesis
lots of non-coding DNA
mitochondrial variation only comes from mother because…
more space for mitochondria in egg than sperm
does not involve meiotic segregation but organelles acquired at cell division from maternal cytoplasm
Variegation
diversity of colours
genetic evidence from 2 types of Petite mutants
segregational mutants - mendelian segregation following meiosis, genes located in nucleus
vegetative mutants - non mendelian pattern, genes located on mitochondria
2 categories of vegetative petites
neutral - cross with wild type and all wild type offspring (4:0 ratio), lack most of their mitochondrial DNA
suppressive - cross with wild type and all petites offspring (0:4 ratio), lack only small segments of mtDNA
yeast inherit mitochondria…
from both parents
why do suppressive petite mitochondria produce all petites when crossed with wild type even though mitochondria inherited from both parents in yeast?
suppressive petite mitochondria replicate faster and dominate
mitochondrial genome sequencing
maternity analysis
phylogenetic systematics
population genetics
why do we use mitochondrial genome sequencing?
EASY to isolate and PCR amplify mtDNA due to high copy number per cell
maternal inheritence mtDNA enables analysis of MATERNAL POPULATION STRUCTURE w/o confusion of male-mediated gene flow
no recombination of mtDNA so very SLOW TO EVOLVE
mutations that do occur are rapidly FIXED in population
genomic imprinting
form of gene expression in which an allele of the affected gene is marked or imprinted in one of the parents, and can be passed on through meiosis to offspring
marked by methylation or histone modification
why investigate chromosomal mutations?
cytological insight into meiosis
medical insight in causes of genetic disease (down syndrome)
molecular insight of how genes interact throughout a genome
evolutionary insight
monoploid/haploid
diploid
triploid
tetraploid
aneuploid
n
2n
3n
4n
change in number of some but not all chromosomes
monoploidy
non-viable in most animal species
deleterious mutations would be effective (no other chromosome to overcome mutation in 1 chromosome)
some social insect males are monoploid, develop by parthenogenesis
polyploidy examples
triploid - bananas
tetraploid - coffee, cotton, peanut, potato, oilseed rape
hexaploid - oat, wheat
octaploid - strawberry
paleotetraploid - cabbage, soybean (act as diploid)
rare polyploidy animals
tetra - african clawed frog,viscacha rat, rainbow trout
Brassicacea species
polyploidy and speciation
size…. with…… ploidy
increases
higher
autopolyploid
derived from same diploid species (diploid duplicated but doesn’t divide, stays in 1 cell)
allopolyploid
derived from different progenitor species (2 diploid species merged)
colchicine
used to disrupt spindle assembly and thereby block chromosomal segregation
meiosis of triploid
produces aneuploid gametes
highly sterile
separate into bivalent (2 chromosomes) and univalent (1)
non-disjunction
meiosis malfunctions e.g. dont separate in opposite but come together so monosomic (no pairs, 1 chromosome so lethal) and trisomic (3 chromosomes, lethal)
miss-aligned repeat sequences
unequal crossing-over and gain/loss of repeats
large segmental inversions
break and repair with inversion
pericentric inversion
encompasses the centromere (with centromere in middle of segment that’s inverted)
paracentric inversion
doesn’t encompass centromere, so segment to the side not involving centromere
meiosis with inverted heterozygotes
1 chromosome needs to form inversion loop so that pair correctly with other chromosome (loops to flip)
crossing over will create dicentric and acentric chromosomes
Mendel’s first law of inheritence
discrete trait
complete dominance
environmentally stable phenotype (easy to work with)
are chromosomes the unit of heredity?
NO
crosses show non-parental recombinant phenotypes which wouldn’t be seen if chromosomes were unit of heredity
the chromosome theory is consistent with…..but
Mendel’s second law
this isn’t proof
Thomas Hunt-Morgan
established fruit fly as model for genetics
actually observed that non-parental phenotypes almost don’t show up so doesn’t meet either hypothesis (not equal but not 0) - 17% non-parental types
frequency of recombination
frequency at which alleles are co-inherited
what hypothesis drawn from Thomas Hunt-Morgan’s experiments?
not on different chromosomes because not all equal phenotypes like 1st hypothesis
maybe on same chromosome but recombination occurs - frequency to do with distance between alleles
far enough apart - crossing over occurs like independent assortment
Alfred Sturtevant experiment to test new hypothesis
3rd gene 8% recombination so fits in between 2 other genes because b–vg (17%) and b–cn (9%)
can map out linear order of genes
double recombination
take distance between the 2 and multiply to get percentage of recombination
far enough apart that cross can happen twice
linear model
genes are physically located in a linear manner along a chromosome
0% recombination
50% rec.
1% rec.
genes tightly linked or possibly the same gene
independently assorting/ unlinked/ on diff chromosomes/ far apart on same chromosome
1 Map Unit = 1 centiMorgan (cM)
positional cloning
narrow down region where gene occurs (mendelian trait)
1) identify genes location (locus) from genome-wide search of linkage to markers
2) sequence the DNA across the locus, in both wild type and mutant
3) verify function of the causal gene
molecular marker
difference in DNA sequence (DNA polymorphism) between 2 individuals
differences due to mutation
segmental rearrangement
flipped part of sequence
Muriel Wheldale
snapdragon colours unpredictable, new colours come out of nowhere, cross breed and count number of flowers of each colour, multiple genes work together
discrete traits are……… in a species and most…..
unusual
discrete genes will be lethal so unusual to see
complete dominance
incomplete dominance
overdominance
AA and Aa max expression
AA max, Aa is intermediate (like medium height not tall)
Aa max, AA intermediate (maybe to do with interaction between both alleles, provides bigger effect)
full penetrance
partial penetrace
AA and Aa max
AA medium, Aa weak
redundancy
duplicate genes that provide the same function
complementary genes
phenotype depends on both genes being functional
bean seed colour
offspring contains only 1 that’s white like parent and no like brown parent
lots of genes involved produce lots diff combinations of colours
Fisher
developed mathematical approach to explain Mendelian factors as basis of quantitative traits
complexity of genes creates smooth curve
linkage mapping
derived from a controlled cross of known parentage, that exhibit contrasting phenotype and are polymorphic in many DNA markers (genome-wide)
so find where gene locus is by finding markers that define interval
linkage mapping pros
no question of dominance immortal lines powerful data accumulation reproducibility GxE experiments possible inter-mating inbreds, to test genetic models
linkage mapping cons
finite resource
selfing
2 same chromosomes so all homozygous but different from other offspring
MAGIC LINES
Multiparent Advanced Generation Inter Cross
more parents means more alleles for more genes
LOD score
Logarithm Of the Odds
statistical test for linkage
=log10(likelihood that 2 loci are linked/likelihood that 2 loci are unlinked)
artificial mutation vs natural variation
artificial is the main source of genetic variation used for research in experimental genetic models
natural is the main resource for translational genetics
simple Mendelian genetic disease variation
easy to investigate
single mutation associated with disease
rare allele
Huntignton’s, CF, Duchenne muscular dystrophy, BRCA1 breast cancer
complex or multifactorial genetic disease variation
difficult to investigate
multiple genes involved
cumulative affect of weakly expressed common alleles
disease risk influenced by non-genetic factors
various cancers, heart diseases, IBS, diabetes, Parkinsons, Alzheimers
pedigree analysis
use diagram to summarise inheritance of discrete trait in family history
female circle, male square, unknown diamond
phenotype of interest is coloured
autosomal dominant disease exampes
Huntington’s
Hereditary retinoblastoma
Achondroplasia
X chromosome sex-linked recessive examples
Haemophilia Red-green vision Christianson syndrome Fragile X syndrome Duchenne muscular dystrophy
Y chromosome sex-linked recessive examples
Y chromosome infertility
Swyer syndrome
X chromosome sex-linked dominant examples
Incontinentia pigmenti
Charcot-Marie tooth neuropathy
Coffin-Lowry syndrome
Hypophosphatemic rickets
types of molecular markers
RFLP - no one uses it anymore
SSR - Simple Sequence Repeats
SNP - Single Nucleotide Polymorphisms
SSR
in between genes are repeating sequences
repeats vary in terms of copy number
more repeats = bigger PCR product
linkage mapping with SSRs
1) collect info (genetic disease family)
2) PCR - determine genotypes
3) statistical linkage analysis - identify SSRs linked to disease
4) identify new molecular markers from within locus
Z max
highest LOD score
how to find causal gene of genetic disease
1) define fine map interval
2) identify candidate genes - within interval
3) loss-of-function
4) gain-of-function (knock out mutant)
SNP
molecular marker based on single base-pair substitutions
mutation rate 1x10^-9 per locus per generation
Most SNPs in non-coding sequence (because affecting function is selected against)
SNPs within exon will not alter AA (synonymous mutations)
synonymous mutations
in exon but won’t alter AA
association mapping
need high resolution of genetic variation located on a physical map of a reference genome
need large set of phenotypic data
linkage disequilibrium
sequence variation
coloured block smaller if older species because more time for variation
genetic structure of a population
number of alleles and frequency of each within a population (gene pool)
genotype frequency/allele frequency
geographic patterns
in distribution of allelic variation within and amongst sub-populations
temporal changes
in genetic structure of populations
Hardy-Weinberg principle
investigating movement of genes and alleles in populations
understanding mechanisms of evolution
p^2 + 2pq + q^2 = 1
Hardy-Weinberg assumptions
infinitely large population
random mating
no new mutations, migration, natural selection
so entirely theoretical - no population is like this
gene flow
introduces new alleles from migration
types of natural selection
directional
stabilizing
disruptive
balancing
directional selection
favours individuals at one phenotypic extreme, greater reproductive success in particular env.
stabilizing selection
favours intermediate phenotypes - heterozygous, combined alleles
optimum
disruptive selections
favours survival of 2 or more different genotypes each produce diff phenotypes
diverse env. so are diff but can still interbreed
2 optimums on graph
balancing selection
2/more alleles kept in balance, maintained in population over many generations
heterozygote advantage e.g. sickle cell allele
genetic drift
random loss of alleles from a population due to chance events
large populations more stable than small
results in loss of genetic variation
genetic bottleneck
example?
sudden decrease in population size caused by adverse env. factors
e.g. black plague eliminated 75% of some populations
founder effect
dispersal and migration that establish new populations with low genetic diversity
non-random mating
assortative mating - similar phenotype so increase homozygotes
dissasortive mating - different phenotypes, favours heterozygotes
