lectures 44-53 Flashcards
define genomics
the branch of molecular biology concerned with the structure, function, evolution, and mapping of genomes
define genetics
the study of heredity and the variation of inherited characteristics
what is the holobiont?
a multicellular host and the associated beneficial microbiome
can plants have XY chromosomes?
yes but only some do
what are telomeres?
a repeat structure found at the ends of chromosomes that maintains their length
what is the centromere?
it is a spindle attachment containing satellite DNA
what are euchromatin and heterochromatin used for?
the packaging of DNA, RNA, and protein
what stain is commonly used to stain chromosomes?
Giemsa stain
what occurs in interphase?
the chromosomes and organelles replicate
give an overview of what occurs in prophase in mitosis
- the centrosomes duplicate and begin to move
- the chromosomes begin to condense
- the spindle begins extending from the poles and attaches to the centromeres
what occurs in metaphase in mitosis?
the centromeres align at the equator along the metaphase plate by bipolar attachment
what occurs in mitosis in anaphase?
- the sister chromatids separate into individual chromosomes and migrate to opposite poles
what occurs in telophase in mitosis?
- the chromosomes are now situated at the poles
- the spindle disassembles
- the nuclear membrane reforms
what occurs in cytokinesis?
- the chromosomes decondense
- cells divide
how are sister chromatids held together and separated?
- held together by cohesin
- cohesin is destroyed enzymatically by separase breakdown of cohesin proteins
what occurs in prophase 1 of meiosis?
- the centrosome splits and moves to the poles
- DNA condensing begins
- homologous chromosomes align and the synaptonemal complex forms
- double strand breaks arise and chiasmata form
- the nuclear membrane breaks down
what occurs in metaphase 1 of meiosis?
- kinetochores align at the equator
what happens in anaphase 1 of meiosis?
- each chromosome with 2 chromatids are pulled apart
- independent assortment occurs
what occurs in telophase 1?
- 2 haploid cells are formed
how does genetic variation occur in meiosis?
- independent assortment
- crossing over
what are the 5 stages of prophase 1 called?
1) leptotene
2) Zygotene
3) pachytene
4) diplotene
5) diakinesis
what occurs in the leptotene stage?
- also known as the thin thread stage
- chromosomes begin to condense and become visible
- homolog pairing begins
- double strand DNA breaks are introduced (potential sites for crossing over)
what happens in the zygotene stage?
- also known as paired thread stage
- a synaptonemal complex begins to form between homologous pairs - paired homologs are now referred to as bivalents
what happens in the pachytene stage?
- condensing of chromosomes continues
- the synaptonemal complex is complete
- bivalents now have 4 sister chromatids
- crossing over is completed
what occurs in the diplotene stage?
- the synaptonemal complex disassembles
- each pair of sister chromatids begin to separate
- chiasmata are visible (regions of crossing over between non-sister chromatids)
what happens in the diakinesis stage?
- chromosomes repel each other
- non-sister chromatids remain loosely associated via chiasmata
- nuclear membrane and nucleolus disappear
- monopolar attachment of chromosomes to spindle fibres occurs
what is the function of the synaptonemal complex?
it prevents different homolog pairs from getting entangled
define genotype
DNA based information
define phenotype
measurable expressions of the interaction between genes and the environment
what were the seven discrete traits studied by mendel?
- round or wrinkled ripe seeds
- yellow or green seed interiors
- green or yellow unripe pods
- purple or white petals
- inflated or pinched ripe pods
- axial or terminal flowers
- long or short stems
what is Mendel’s first law of inheritance?
heredity is controlled by paired factors or alleles of genes
what is frequency of recombination?
the hypothesis that a smaller number of non-parental type phenotypes will be produced
how does map based cloning occur?
1 - identify the gene locus from a genome-wide search of linkage to markers
2 - sequence the DNA across the locus, in both wild type and mutant variants
3 - verify function of the causal gene
what is a molecular marker?
a difference in DNA sequence between 2 individuals
in complete dominance, what genotypes are seen as maximum expression?
AA and Aa
are discrete traits usual or unusual in plants and animals?
unusual
define penetrance
the proportion of individuals carrying a particular variant of a gene that also expresses an associated trair
what does redundancy mean in the concept of genetics?
duplicate genes that provide the same function
what are complementary genes?
genes in which the phenotype depends on both of the genes being functional
how are the progeny chosen?
they are chose if they exhibit contrasting phenotypes and are polymorphic in many genes
what is the statistical test for linkage?
LoD = log10 (likelihood that 2 loci are linked/ likelihood that 2 loci are unlinked)
what is a simple mendelian genetic disease?
a single gene mutation associated with disease
what is pedigree analysis?
the use of a diagram to summarise the inheritance of discreet trait in a family history
what is the ethical limit on pedigree analysis?
controlled matings are not possible
what is the sampling limit with pedigree analysis?
small family sizes per generation
what are the characteristics of an autosomal recessive disease?
- the disease will typically not occur in every generation
- affected individuals can be born to unaffected parents
what are the characteristics of an autosomal dominant disease?
- in most cases DD will be lethal, so all diseased individuals will be Dd
- disease will be found in every generation
- males and females are equally affected
which offspring will be affected in x chromosome sex linked recessive inheritance if the mother is a carrier?
- half of the daughters will be carriers
- half of the sons will be affected
which offspring will be affected in x chromosome sex linked recessive inheritance if the father is a carrier?
- all the daughters will be carriers
- none of the sons will be affected
which offspring will be affected in x chromosome sex linked dominant inheritance if the father is affected?
- all daughters are affected
- no sons are affected
which offspring will be affected in x chromosome sex linked dominant inheritance if the mother is affected?
- half the daughters will be affected
- half of the sons will be affected
how is linkage mapping with SSRs carried out?
1 - collect pedigree info from a family with history of a genetic disease and blood samples for DNA from living family members
2 - use PCR and gel electrophoresis to determine genotype of family members for several hundred SSR loci distributed throughout the genome
3 - use statistical linkage analysis to identify SSRs that are linked to inheritance of the disease allele
4 - identify how molecular markers from within the locus and repeat the linkage analysis with additional families to resolve a narrower map interval
how do you find the causal gene of a genetic disease?
1 - define the locus with flanking molecular markers to a region of below 50 candidate genes
2 - identify the candidate genes within the interval that are allelic between diseased an unaffected individuals
3 - identify loss of function using knock-out analysis of genes within locus of an experimental organisms
4 = identify gain of function by genetic transformation of knock-out mutants with functional alleles
what LoD score indicates a likelihood that a marker is located with the candidate gene?
above 3
what is linkage disequilibrium?
a physical region observed a a non-random association of mutations amongst individuals in a population
what is a transposable element?
a DNA sequence that can change in position within the genome
define epigenetics
heritable changes in gene expression that are not caused by changes in DNA sequence
what is methylation
methyl groups which can tag DNA and activate or repress genes
what are histones?
proteins around which DNA can wind for compaction and gene regulation
describe histone modification
the binding of epigenetic factors to histone ‘tails’ alters the extent to which DNA is wrapped around histones and the availability of genes in the DNA to be activated
what biochemical evidence of mitochondrial symbiosis is there?
mitochondria communicate with the nucleus via trafficking of proteins and RNAs
what genetic evidence of mitochondrial symbiosis is there?
the nucleus contains genes that encode mitochondrial proteins
is the mitochondrial genome circular or linear?
circular
what genes does the mitochondrial genome have?
it contains genes for:
- tRNAs
-rRNAs
- cytochrome oxidase
- ATPase subunits
- NADH dehydrogenase
is the chloroplast genome circular or linear?
circular
what genes does the chloroplast genome contain?
it contains genes for redox proteins involved in electron transport for photosynthesis
does the chloroplast genome contain a very small or very large amount of non-coding DNA?
a lot
does extranuclear inheritance involve meiotic segregation?
no
how are organelles acquired in extranuclear inheritance?
- organelles are acquired at cell division from the maternal cytoplasm
why are organelles only acquired from the mother in extranuclear inheritance?
there are no mitochondria in the sperm head
what are the uses of mitochondrial genome sequencing?
- maternity analysis
- phylogenetic analysis
- population genetics
what is genomic imprinting?
- a 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 the offspring
what is a chromosomal mutation?
changes in the chromosome number per cell
are chromosomal mutations visible by microscopy?
yes
what are the reasons that we would investigate chromosomal mutations?
- cytological insight into meiosis
- medical insight into causes of genetic disease
- molecular insight of how genes interact throughout a genome
- evolutionary insight
define aneuploid
change in the number of some but not all chromosomes
by which mechanism do autopolyploids come about?
endoreduplication
by which mechanisms do allopolyploids come about?
hybridisation and endoreduplication
what chemical can be used to disrupt spindle assembly and block chromosomal segregation?
colchicine
what gametes are produced when meiosis occurs in a triploid?
aneuploid gametes
does nondisjunction occur in meiosis one or two? what are its effects?
- occurs in both meiosis 1 and 2
- in 1, it will be lethal to all daughter cells
- in 2, it will be lethal to half the daughter cells
does paracentric inversion encompass the centromere?
no
how can the study of population genetics be applied in real-world scenarios?
- species conservation and utilisation of biodiversity
- it is essential for genome wide association mapping
what are the assumptions needed for Hardy Weinberg?
- infinitely large population
- random mating amongst individuals
- no new mutations, migration, or natural selection
what is directional selection?
- it favours individuals at one extreme of a phenotype distribution which have greater reproductive success in a particular environment
initiator: introduction of a new favoured allele, prolonged environmental change
what is stabilising selection?
- favours survival of individuals with intermediate phenotypes
- extreme phenotypes are selected against
what is disruptive selection?
- 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
what is balancing selection?
- two or more alleles are kept in balance and therefore are maintained in a population over many generations
what is genetic drift?
random loss of alleles from a population due to chance events
what is a genetic bottleneck?
a sudden decrease in population size caused by adverse environmental factors
define the founder effect
dispersal and migration that establish new populations with low genetic diversity
what is assortative mating?
individuals with similar phenotypes are more likely to mate
what is disassortative mating?
dissimilar phenotypes mate preferentially
