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Summer exams > MCO > Flashcards

MCO Flashcards

1
Q

reasons to understand genetics
UNDERSTANDING FUNCTION

A

we experiment to find the allele

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2
Q

Genomics

A

technology for sequecing

TECHNOLOGY used to generate LARGE DATASETS of digital information

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3
Q

Genetics

A

Method of experimentation (the methodology)

used to understand the cause and effect between genes and phenotypic variation

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4
Q

the centers goal

A

o apply genetic information to develop therapies and clinical risk assessment tools for diseases in individuals and the general population.

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5
Q

model organisms

A

are how we know about genome

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6
Q

Holobiont

A

Host (multicellular) + microbiome (beneficial)

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7
Q

viable systems model

A

urban eaters/eden/ eat

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8
Q

african globe lily

A

-has microtubules
-huge thicker chromosomes when condensed during mitosis
-thicker than the longest human chromosome

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9
Q

a human cell contains over

A

two metres of DNA

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10
Q

chromosome structure

A

telomeres
centromeres
euchromatin and heterochromatin

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11
Q

telomeres

A

-ends maintain length
-repeat structure

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12
Q

centromere

A

-spindle attachment
-satellite DNA

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13
Q

euchromatin and heterochromatin

A

packaging of DNA, RNA and protein

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14
Q

chromosomes - p

A

short arm

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15
Q

chromosomes - q

A

long arm

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16
Q

chromosome structure and staining

A

pink = nucleic acid banding patterns provides address because two pairs that look different with different number of bands

=small deletion of some infs
mapping related to trait

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17
Q

drosophila

A

polytene chromosomes from salivary glands

these arise because replicated DNA strands do not separate during interphase

visible bands provide high resolution physical Map position

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18
Q

the era of genome sequence

A

chromosome and position

physical size (base pairs)

gene names and position

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19
Q

genotype =

A

aligning chromosome pairs copying them

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20
Q

interphase

A

chromosomes and organelles replicate

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21
Q

prophase

A

nuclear membrane breaks down
spindle begins extending from poles and attaches to centromeres (kinetochore)

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22
Q

in mitosis it is _______ attachment

A

bipolar

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23
Q

in anaphase sister chromatids are now

A

chromosomes

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24
Q

cytokinesis

A

CHROMSOMES DECONDENSE
cells divide

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25
Q

cohesin

A

protein that provides attachment for sister chromatids

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26
Q

kinetochore

A

attaches to chromatids and spindle fibres

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27
Q

seperase

A

enzyme that breaks down cohesion

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28
Q

all cells are same ploidy

A

same number of chromosomes

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29
Q

prophase 1

A

-centrosome splits and move to poles
-DNA condensing
-homologous chromosomes align and synaptonemal complex forms
-double strand breaks arise and chiasmata form
-nuclear membrane breaks down
-spindle begins to form
-DNA fully condensed , synaptonemal complex breakdowns and monocular kinetochores attach chromosomes to spindle

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30
Q

metaphase 1

A

kinetochores have aligned at the equator (metaphase plate)

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31
Q

anaphase 1

A

monopoly attachment pulls homologous chromosomes to opposite poles

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32
Q

telophase 1 and cell division

A

haploid cells have formed
-shuffling the deck has occurred through independent assortment and crossing over

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33
Q

meiosis results in

A

four genetically distinct haploid cells

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34
Q

prophase stage 1- leptotene (thin thread stage)

A

-chromosomes start to condense and become visible
-homolog pairing begins
-double-stranded DNA breaks are introduced (potential sites for crossing over)

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35
Q

prophase stage 2-zygotene (paired threads stage)

A

-a synaptonemal complex begins to form between homologous pairs (synapsis)
-paired homologs now referred to as bivalents

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36
Q

prophase stage 3-pachytene (thick thread stage)

A

-condensing of chromosomes continues
-synaptonemal complex is complete
-bivalents now have four sister chromatids (tetrads)
-crossing over is completed

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37
Q

prophase stage 4- Diplotene (two thread)

A

-synaptonemal complex dissembles
-each pair of sister chromatids begins to separate
-chiasmata = visible regions of cross-over between non-sister chromatids

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38
Q

prophase stage 5-Diakinesis (moving apart stage)

A

-chromsomes repel each other
-non-siter chromatids remain loosely associated via chiasmata
-nuclear membrane and nucleolus disappear
-monopolar attachment of chromosomes to spindle fibres

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39
Q

synaptonemal complex

A

function: facilitates late stages of recombination

prevents different homolog pairs from getting entangled

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40
Q

meiosis 1 maintain

A

policy level for sexual reproduction

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41
Q

genetic shuffling

A

occurs in meiosis 1 by independent assortment of homologous chromsomse and by cross over of chromosome arms between sister chromatids

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42
Q

studying genetics look at

A

variation in progeny

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43
Q

biochemistry studying genetics

A

study proteins in test tube

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44
Q

molecular biology upstanding genetics

A

DNA/RNA in a test tube

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45
Q

Eric lander

A

mission of improving medicine with genome-based evidence

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46
Q

Gregor mendel author of

A

experiments in plant hybridisation in 1865

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47
Q

experimental method genetics to reveal cause and effect

A

1)assemble robust experimental system
2)design and perform first experiment and generate lots of quantitative data
3)repeat same experiment with different starting material
4)analyse the collective data and derive a predictive model
5)devise and execute experiment to test predictions

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48
Q

F1 =

A

first generation PRODUCED

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49
Q

first law of inheritance

A

heredity is controlled by paired factors or alleles of genes

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50
Q

Bateson (1861-1926)

A

coined terms genetics and epistasis
-looked at different organisms and conducted controlled crosses looked at progeny

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51
Q

Roland biffen 1879-1949

A

resistance to yellow rust wheat plants was identified as a ingle mendelian trait
-FIRST DEMONSTRATION OF APPLIED GENETICS

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52
Q

phenotypic dominance and first law of inheritance demonstrated the importance of

A

experimental model organisms

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53
Q

experimental genetic models are how we understand

A

immunity (plant and animal)

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54
Q

Discrete traits

A

-complete full dominance
-environmentally stable phenotypes

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55
Q

artificial mutation

A

main source of genetic variation used for research in experimental genetic models

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56
Q

natural variation

A

the main resource for translational genetics

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57
Q

discrete traits are unusual

A

in a species

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58
Q

complete dominance

A

maximum expression
AA

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59
Q

incomplete dominance

A

maximum + intermediate
AAAa

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60
Q

overdominace

A

intermediate Maximum

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61
Q

penetrance

A

the extent to which a particular gene or set of genes is expressed in the phenotypes of individuals carrying it, measured by the proportion of carriers showing the characteristic phenotype.

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62
Q

genetype x environment [rimoridial dwarfism

A

primordial = genetic cause as it is a gene mutation

hypopituitary dwarfism is mutation but can be treated with growth hormone therapy

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63
Q

gibberrellic acid (GA)

A

like human growth hormone for plants

some dwarf mutants in plants are GA-responsive

other dwarf mutants are not GA-responsive

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64
Q

redundancy

A

duplicate genes that provide the same function

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65
Q

complementary genes

A

the phenotype depends on both genes being functional

(e.g., different steps in same biochemical pathway)

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66
Q

polygenic variation

A

1918 fisher developed mathematical approach to explain mendelian factors as the basis of quantitative (polygenic) traits

1920 drosophila (truncate wings) shown to arise from mutations in multiple unlinked factors

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67
Q

Ronald A fisher (1890-1962)

A

found number of F2 in each genotype was distributed normally

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68
Q

Genetic mapping of complex traits
objective

A

to localize (map) genes that underlie a phenotype on the basis of correlation with DNA sequence variation.

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69
Q

Genetic mapping of complex traits
Methods

A
  • Linkage mapping population: progeny derived from a controlled cross of known parents (chosen because they exhibit contrasting phenotypes and are polymorphic in many genome-wide DNA markers
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70
Q

mapping populations pros and cons

A

Pros:
1)No question of dominance
2)Immortal lines
3)Powerful data accumulation
4)Reproducibility
5)GxE experiments possible
6)Inter-mating inbreds, to test
genetic models

cons = finite resources

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71
Q

LOD score: a statistical test for linkage
logarithm of the odds

A

= Log10 (likelihood that two loci are linked)/(likelihood that two loci are unlinked)

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72
Q

simple medelian (tractable-easy to investigate)

A

-single gene mutation associated with disease
-disease is due to a typically rare allele in the population (1 in >2000 individuals)

-readily defined pattern of inheritance

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73
Q

complex or multifactorial (difficult to investigate

A

-alleic variation in multiple genes associated with disease
-cumulative affect of weakly expressed common alleles
-disease risk is typically influenced by non-genetic factors

74
Q

What is pedigree analysis?

A

-use of diagram to summarise the inheritance of discrete trait (phenotype) in a family history

75
Q

coloured in square on pedigree charts

A

usually has phenotype of interest

76
Q

diamond shape on pedigree charts

A

unknown sex

77
Q

half coloured shape on pedigree charts

A

heterozygote

78
Q

why do pedigree analysis?

A

Knowledge about simple ‘Mendelian’ traits

ethical limits (controlled matings are not possible)

limits
-small sampes
-inaccurate or incomplete data

79
Q

aims of pedigree analysis

A

Determine the mode of inheritance
Sex-linked or autosomal
Dominant or recessive

Calculate the probability of an affected individual based on recent family history
(e.g., for genetic counseling)

80
Q

Autosomal recessive inheritance

A

dd = disease

81
Q

Autosomal dominant inheritance

A

DD can be lethal so all heterozygotes will be Dd

82
Q

If two affected parents have unaffected children, then recessiveness can be ruled out

A

True for both autosomal and sex-linked traits

83
Q

If unaffected parents have an affected child,
then dominance can be ruled out

A

true for both autosomal and sex-liked traits

84
Q

If unaffected parents have an affected daughter,
then

A

dominate and x-linked recessive disorder can be ruled out

85
Q

types of molecular markers
SSR

A

Simple Sequence Repeats

micro satellites (2-4 base pair repeats)
minisatlleties (variable number tandem repeats)

86
Q

Types of molecular markers SNP

A

Single Nucleotide Polymorphisms

87
Q

Sir

more and fewer sequence repeats

A

more = bigger PCR product

Fewer = Smaller PCR product

88
Q

linkage mapping with SSrs

A

1)collect pedigree information
2)ue PCR and blood samples from living family members use gene electrophoresis
3)statistical linkage
4)identify new molecular markers from within the locus

89
Q

Barbara McClinktock 1983 Nobel prize for

A

discovering transposable elements

-looked at maize in two different places
-then found mutations can be turned on or off

90
Q

Transposable element

A

DNA sequence that can change position within its genome

91
Q

umping occurs during mitosis and is affected by

A

the environment

92
Q

transposable elements can enter

A

promotors =switching gene on or off

exons = non-functional

Not in gene = no effect

93
Q

Jumping genes effect ..

A

generate transposable elements in plants and animals

94
Q

epigenetics

A

heritable changes in gene expression not caused by changes in DNA sequence

methylation = methyl group an epigenetic factor can tag or repress genes

95
Q

Ruth Sager =

A

discovered DNA in mitochondria and early pioneer in cancer genetics

INHERITANCE VIA CYTOPLASM TYPICALLY FROM MOTHER ONLY

96
Q

biochemical evidence of symbiosis

A

mitochondria communicate with the nucleus via trafficking of proteins and RNAs

97
Q

genetic evidence of symbiosis

A

the nucleus contains genes that encode mitochondrial proteins

98
Q

mitochondrial genome

A

circular genome

contains genes for tRNAs, r RNAs, cytochrome oxidase …

humans small genome as 16 kb

99
Q

chloroplast genome

A

contains genes for redox proteins involved in electron transport for photosynthesis

also contain lots of introns

100
Q

extranuclear inheritance

A

does not involve meiotic segregation

organelles are acquired at cell division from teh maternal cyctoplasm

GENOTYPE AND PHENOTYPES OF OFFSPRING IS THE SAME AS THE MOTHER

101
Q

chloroplast inheritance and who found that

A

maternal inheritance following mitosis

CORREN who found that by observing chloroplasts and leucoplasts (no chlorophyll production)
no contribution from pollen

102
Q

yeast mitochondrial inheritance *IMPORTANT

A

most yeast is haploid
normal vs petite

genetic evidence from two types of mutants

segregational mutants = mendelian segregation following meiosis and genes are located in the nucleus PREDICTABLE RATIO

vegatative mutants = non-mendelian pattern of inheritance and genes are located in teh mitochondria

103
Q

segregational petites

A

two haploid cells create zygote then meiosis resulting in a tetrad of progeny each
resulting tetrad shows a 2 : 2 ratio of wild type to petite this result indicates mendelian inheritance in yeast

104
Q

vegetative petites (non mendielian)

A

neutral or suppressive

each tetrad produces a 4:0 ratio of allwild type to petite

all petites produce a 0:4 ratio of wild type to petite

105
Q

yeast petite mutants

A

neutral petites lack most of their mitochondria DNA

-suppressive petites lack only small segment of mtDNA
-yeast offspring inherit mitochondria from both parents

106
Q

why petite colonies

A

suppressive petite mitochondria replicate faster and dominate

107
Q

heteroplasmy

A

occurrence of both forms of mitochondria in teh same cell results in variable levels of expressivity

108
Q

maternity analysis phylogenetic systematics ad population genetics WHY

A

-easy to isolate and PCR amplify mtDNA due to high copy number per cell
-maternal inheritance mtDNA enables analysis of maternal population structure without confusion of male-mediated gene flow
-no recombination of mtDNA so very slow to evolve
-mutations that do occur are rapidly fixed in a population

109
Q

maternal inheritance

A

for example shells in snails maternal factors(protein or mRNA) that are deposited in the oocyte prior to fertilisation these are typically important for development

110
Q

genomic imprinting

A

A form of gene expression in which an allele of the affected gene is marked imprinted in one of the parents and can be passed on through meiosis to the offspring

111
Q

chromosomal mutation

A

-changes in the chromosome number per cell
-large-scale (segmental) change in chromosome structure
-VISIBLE BY MICROSCOPE

112
Q

why investigate chromosomal mutations?

A

-cytological insight into meiosis
-medical insight in causes of genetic disease
-molecular insight of how genes interact through a genome
-evolutionary insight

113
Q

terms indicating number of chromosomes

A

-monoploid - n
-diploid - 2n
-triploid - 3n
-tetraploid- 4n

114
Q

Aneuploid

A

change in number of some but not all chromosomes

115
Q

monoploidy

A

-non viable in most animal species
-deleterious mutations would be effective (as any mutation is expressed)
exception: social insects males are monoploid and develop by PARTHENOGENESIS (gametes from mitosis)

116
Q

paleotetraploid

A

functionally diploid but 1000s of years ago were tetra but over time genomes seperated

117
Q

polyploidy and size

A

size increases with higher policy (not number of)

118
Q

two origins of polyploidy

A

autoplyploid = derived from teh SAME diploid species
Allopolyploid = different progenitor species

119
Q

organ of hexaploid wheat

A

-42 chromosomes
-derived from three ancestral diploid species

120
Q

chemically induced polyploidy is done by

A

colchicine which can be used to disrupt spindle assembly and thereby block chromosomal segregation

121
Q

meiosis in a triploid

A

produces aneuploid gametes consequence = highly sterile

122
Q

what causes change in chromosome number?

A

non-disjunction = when meiosis malfunctions

triatomic possibly lethal
monosomic = lethal

123
Q

miss-aligned repeat sequences

A

consequence = unequal crossing over
gain or loss of repeats

124
Q

pericentric inversion

A

encompasses teh centromere

125
Q

aracentric invesion

A

does not encompass the centromere

126
Q

invasion heterozygote

A

twisting of chromosomes large segments creates inversion loop visible in meiosis

127
Q

large segmental inversions

A

if no recombination within an inversion loop

then no deletion of duplication possible

128
Q

a crossover within an inversion loop creates

A

dicentric and eccentric chromosomes

129
Q

reciprocal translocation

A

heterozygous translocation one pair interchanges and one pair normal

homozygous translocation = both pairs interchanged

130
Q

cancer by somatic translocation

A

ABL encodes a protein kinase that transduce a signal for cell proliferation which is inherited by a growth factor

chimeric protein is always active therefore cancerous

131
Q

population

A

a group of individuals of the same species that are able to interbreed

some species occupy a wide geographic range and are divided into sub-populations

132
Q

purpose of population genetics

A

-genetic structure of a population
(number of alleles within a gene pool)
-geographic patterns in a distribution of allelic variation within and amongst sub-populations
-temporal changes in genetic structure of a ppulations

133
Q

application of population genetics

A

-species conservation and utilisation of biodiversity
-essential for Genome-Wide association mapping (GWAM)

134
Q

genetic structure

A

-genotype frequencies

number of characteristic / total in population

135
Q

genetic structure allele frequecies

A

-total number of a specific gene (r) / number of alleles

136
Q

hardy Weinberg principle

A

method for investigating the movement of alleles in a population

essential for understanding the mechanisms isms of evolutionary change

assumes several starting parameters

-infenetly large population
-random mating amongst infdividuals
-no new mutations, migration or natural selction

137
Q

hardy Weinberg principle

A

look up on good notes on computer

138
Q

change in genetic structure
Mutation

A

-creates new alleles
-ultimate source of genetic variation

139
Q

change in genetic structure
migration

A

-new individuals move into teh population
-introduces new alleles (gene flow)

140
Q

change in genetic structure natural slection

A

-some genotype produce more offspring
-differences in survival or reproduction
-leads to adaptatio

141
Q

directional selection

A

-favours individuals at one extreme of a phenotypic distribution which have a greater reproductive success in a particular environment

142
Q

stabilising selection

A

-favours survival of individuals with intermediate phenotypes
-extreme phenotypes are selected against

143
Q

initiator

A

introduction of new favoured allele

144
Q

disruptive selection

A

-favours the survival of two or more different genotypes that each produce different phenotypes
-likely to occur in populations that occupy diverse environments
-members of the populations can freely interbreed

145
Q

balancing selection

A

two or more alleles are kept in balance therefore maintained over genertions

heterozygote advantage

146
Q

change in genetic structure

genetic drift

A

-random loss of alleles from a population due to a chance event
-large populations are more stable than small populations
-result in loss of genetic variation

147
Q

genetic drift is a

A

random event does not select for a phenotype

148
Q

genetic bottlenecks

A

-sudden decrease in population size caused by adverse environmental factors

-serious concern for endangered species
-the black plague eliminated 75% of some European populations during the mid 1300s

149
Q

founder effect

A

dispersal and migration that establish new populations with low genetic diversity

150
Q

non random mating

assortative mating

A

-individuals with similar phenotypes are more likely to mate

-increases frequency of homozygotes

151
Q

non-random mating

disassortative mating

A

-dissimilar phenotypes mate preferentially
-favors heterozygosity

152
Q

Dawn of the hominins

A

-found in the sahal area shows that the earliest hominids were wide ranging across Africa (eastern and southern)

153
Q

hominids =

A

great apes + gibbons

after the split with pan

154
Q

early hominid sites

A

-austrolopith sites of eastern and southern africa

-A ramidus and Ar kadabba in middle awash possibly stem group from which all hominids evolved
-first australopithecine was found by Raymond dart

155
Q

The taung child

A

-originally rejected as ancestor of humans because of LOW brain capacity

156
Q

the laetoli footprints

A

-3.6 MYA definitive evidence of bipedalism

157
Q

Lucy

A

-small brain
-highly sexually dimorphic species
-climber and walker

158
Q

Pelvic evolution for bipedalism - a bucket for your guts

A

-pelvis is Lucy has turned round to form a shallow support of the viscera of the body

-legs are still quite lateral (waddle going on)

159
Q

Obstetrical consequences of bipedalism LUCY

A

-would have been able to give birth to a baby with brain weight limited to 140-160 g

160
Q

less developed birth linked to changes in life history

A

-by observing dental development differences between humans and chimps

-less developed infants means more care required longer development phase

161
Q

Why stand up?

A

Arboreal bipedalism gaining favour

-prevents ranging on ground(dragging knuckles)

162
Q

features of robust morphology Hominds

A

Australopithecine trend towards heavier grinding with stronger muscle attachments and a flattening and deepening of the face

163
Q

`hominis evolved during a changing climate

A

-robusts seems to have been better adapted to the savannah environment the more gracile environment

-robustus persisted while the genus homo evolved from either Africans or ferns lineages

164
Q

many hominis?

A

-much debate still about whether various lineages should be grouped together and just represented wide range of phenotypes

165
Q

broad trend to increasing brain capacity

A

-increased brain size for given body weight over time

166
Q

cultural evolution :stone traditions

A

-oldowan started with australopithecians 2.5 MYA

-acheullian industry more complex is associated with homo Erectus beginning 1.7 MYA

167
Q

Homo habilis- one or two species

A

-many think morphological distance between Australopithecus and homo Erectus is too narrow another species

some say dimorphism is observed may actually be two species

168
Q

why did the brain enlarge?

A

beneficial for
male hunting
expensive tissue hypothesis = posits that in order for brains to grow

scavenging = what h. Habilis was capable of

-plant use = hunting is ecologically risky

169
Q

Java man the first missing link

A

-Haeckel coined the term pithecanthropus (ape man) from Darwins prediction of a missing link
-dubois found this missing link in java in 1984 rejected as it was insisted it was a gibbon

170
Q

H erectus expansion into SE asia

A

-Dtaes now suggest that H erectus reached java as much as 1.7 MYA meaning very early dispersal out of africa

171
Q

The enigma of flores

A

-flores has H erectus bu 800 Kya which would have required seafaring which is incredible in itself

172
Q

More SE asian hoinins

A

-homo luzonensis 67,000 years oldest homo in philipines
-tooth morphometrics place it as direct from archaic humans

173
Q

Divergence of African and asian H erectus

A

-oldest African H erectus dates from 1.89-1.95 MYA from e Africa older than Asian

174
Q

Asian H erectus lacked acheulian industry

A

-archeulian industry begins 1.5 MYA with h erectus in Africa
-asian does not have this which suggests it left before (fits with JAVA dates)
-means they left africa early

175
Q

Turkana boy

A

-most complete H erectus skeleton (1.65 MYA) would-be 6 foot
-had modern body proportions

176
Q

Locomotor evolution

A

-tall sim proportions there by 1.8 MYA in H erectus long legs for running
-SA:V allow loss of heat

177
Q

Archaic humans

A

hard to define groups between erectus and neandrathals

178
Q

Oldest homo sapians

A

-morphometric analysis shows it be like recent modern humans (RMH) but still evolving

179
Q

Oldest European H sapiens

A

modern h sapiens mixture of neandrathals an modern human features.

180
Q

Upper paleolithic revolution

A

-industries changed dramatically to become more aggressive use of handles and blades
-that quickly over ran the known world occurred 50,000 years ago

181
Q

did the anatomically modern human from Africa replace all regional archaic forms?

A

washer genetic input from regional archaic forms

Summer exams (6 decks)

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