Eukaryotic Genetics (44-53) Flashcards
What is genomics?
Technology used to generate large data sets of digital information
What is genetics?
Method of experimentation used to understand cause ad effect between genes and phenotypic variation
What is a holobiont?
Host + Microbiome
→ extends our genome
How much DNA does a human cell contain?
Over 2 meters
What are telomeres?
A region of repetitive DNA sequences at the end of a chromosome
→ prevents the ends from becoming tangled and frayed
→ gets shorter each time a cell divides
What is a centromere?
Links sister chromatids together
→ spindle fibres attach via the kinetochore
→ contains satellite DNA - non-coding repeating regions
What is the difference between euchromatin and heterochromatin?
Euchromatin → lightly packed DNA, gene rich, often under active transcription
Heterochromatin → tightly coiled DNA, not good place for genes as too tight for transcription
What is mitosis?
For tissue repair, multiplication and growth
→ generates two identical daughter cells
What is meiosis?
For gametes
→ four genetically distinct daughter cells
→ sexual reproduction ‘shuffles the deck’
What happens during interphase?
Chromosomes and organelles replicate
What happens during prophase?
Nuclear membrane breaks down
→ spindle begins extending from poles and attaches to centromeres
→ centrosome splits to two poles
→ DNA begins to condense
What happens during metaphase?
Centromeres align at the equator (metaphase plate)
→ bipolar attachment
What happens during anaphase?
Chromosomes migrate to opposite poles
(sister chromatids are now chromosomes)
→ chromosomes with two strands of identical information - chromatids
What happens during telophase?
Chromosomes at poles
→ spindle disassembles
→ nuclear membrane reforms
What is cytokinesis?
Chromosomes decondense
→ cell divide
→ same genetic information in both cells
How are sister chromatids joined?
Cohesin
→ cohesion destroyed enzymatically by separase breakdown of cohesin protein
What happens during prophase 1?
Centrosome splits and move to poles
→ DNA condensing begins
→ 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, monopolar kinetochore attach chromosomes to spindle
What are sister chromatids?
Identical copies of a single chromosome
→ temporarily held together by a centromere during cell devision
What are homologous chromosomes?
Pairs of chromosomes of similar size, shape and gene content
→ inherited from both parents
→ carry same genes at corresponding locations, although alleles differ between the two
→ undergo crossing over - creates genetic diversity
What happens during metaphase 1?
Kinetochores aligned at the equator (metaphase plate)
→ spindle fibres attach to the centromeres of homologous chromosomes
What happens during anaphase 1?
Monopolar attachment pulls homologue chromosomes to the opposite poles
→ pairs in opposite directions
→ sister chromatids remain attached
What happens during telophase 1 and cell devision?
Haploid cells have formed (half the number of chromosome)
→ nuclear envelope reforms
What happens during meiosis II?
Prophase 2 → chromosomes recondense
Metaphase 2 → line up at metaphase plate
Anaphase 2 → sister chromatids separate to opposite poles
Telophase 2 → chromosomes arrive at poles
+ cytokinesis
→ results in 4 genetically unique haploid cells
What is leptotene stage?
1st stage of prophase 1: ‘thin thread’ stage
→ chromosomes start to condense and become visible
→ homolog pairing begins
→ double-stranded DNA breaks are introduced
→ each chromosome consists of two sister chromatids joined by centromere
What is zygotene stage?
2nd stage of prophase 1: ‘paired threads’ stage
→ a synaptonemal complex beings to form - a protein structure that holds homologous chromosomes together
→ paired homologs now referred to as bivalents
→ crossing-over starts to occur at chiasmata
What is pachytene stage?
3rd stage of prophase 1: ‘thick thread’ stage
→ condensing of chromosomes continues
→ synaptonemal complex is complete - homologous chromosomes held together tightly
→ bivalents have 4 sister chromatids
→ crossing-over is completed
What is diplotene stage?
4th stage of prophase 1: ‘two thread’ stage
→ synaptonemal complex dissembles - homologous chromosomes separate slightly but are held at chiasmata
What is diakinesis stage?
5th stage of prophase 1: ‘moving apart’ 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
What is the synaptonemal complex function?
Protein structure formed during meiosis 1 that holds together homologous chromosomes
→ facilitates late stages of recombination
→ prevents different homolog pairs form getting entangled
When does genetic shuffling occur?
During meiosis 1 by:
→ independent assortment of homologous chromosomes
→ crossing-over of chromosomes arms between non-sister chromatids
What are discrete alleles?
Alleles Mendel studies
→ environment doesn’t matter
→ phenotype good prediction
What is Mendel’s First Law of Inheritance?
During the formation of gametes (sex cells), the paired alleles for a trait separate (segregate) from each other, so that each gamete receives only one allele for a particular trait.
Heredity is controlled by paired factors or ALLELES of genes
→ used experimental method to explain 3.15:1 ratio of purple to white flowers
How did Roland Biffen do the first demonstration of applied genetics?
Produced wheat variety that contained resistance to yellow rust disease
→ identified as a simple mendelian trait
What is translational genetics?
Application of genetic research to clinal practice or new therapies
→ from model organisms like:
Arabidopsis thaliana → innate immunity
Drosophila (fruit fly) → multicellular development, innate immunity
Mice → mammalian acquired immunity
What is the chromosome theory?
Chromosomes are the unit of heredity
→ genes are located on chromosomes
→ chromosomes are the carriers of genetic information - DNA
→ not true - genes are unit of heredity
What two things should be true if chromosomes are the unit of heredity?
→ traits on different chromosomes should independently assort
→ traits in the same chromosome should be inherited together
Why was the chromosome theory not holding up with Thomas Hunt-Moragn’s experiments with drosophila?
The ratio of normal and vestigial wings didn’t match predictions (if they were on the same of different chromosomes?
→ recombination
Does the frequency of recombination depend on the physical distance between genes?
Yes
→ genes that are located farther apart on the chromosome have a higher probability of experiencing a crossover event during meiosis
What is the unit of heredity?
Genes are the unit of heredity
→ genes are ‘physically’ locally located in a linear manner along a chromosome
What is map-based cloning?
Molecularly identify a gene that is responsible for a Mendelian trait on the basis of its physical location in the organism genome
Step 1 → identify genes location from a genome-wide search of linkage markers
Step 2 → sequence the DNA across the locus in both wt and mutant variants
Step 3 → verify the function of the causal gene
What is a molecular marker?
A difference in DNA sequence (DNA polymorphism) between two individuals
→ can’t see through karyotyping - need base sequence
How to verify whether a candidate gene is causal?
Mutational analysis → loss-of-function experiment
Genetic transformation → gain-of-function experiment
What is artificial mutation used for?
The main source of genetic information used for research in experimental genetic models
What is gene penetrance?
The proportion of individuals carrying a particular variant of a gene and also expressing the associated trait
What causes primordial dwarfism?
Pericentrin gene mutations
→ affecting mitosis (chromosome segregation and cell division)
What is gibberellic acid?
Like human growth hormone for plants
→ some dwarf mutants in plants are GA-responsive, theres are not
What are complementary genes?
Presence of phenotype depends on both alleles being present - both genes being functional
What is linkage mapping population?
Used to localise genes that underline a phenotype on the basis of correlation with DNA sequence variation
→ progeny derived from controlled cross of known parents (chosen because they exhibit contrasting phenotypes and are polymorphic in many genome-wide DNA markers)
What is a LOD score?
A statistical test for linkage
→ LOD = logarithm of the odds
= log10 (likelihood that two loci are linked/likelihood that two loci are unlinked)
What did Ronald A Fisher develop?
Mathematical approach to explain Mendelian factors - as the basis of quantitative traits
→ focused on inheritance of complex traits influenced by multiple genes and environmental factors - statistical methods and models to study inheritance
→ also contributed to the understanding of genetic linkage and mapping
What are some examples of diseases demonstrating simple mendelian genetics?
Autosomal dominant → Huntington’s disease
Autosomal recessive → cystic fibrosis
X-linked recessive → Duchenne muscular dystrophy
→ tractable and easy to investigate
→ single gene mutation associated with disease
→ typically causes by rare allele in the population
Why are complex/multifactorial genetic diseases difficult to investigate?
Allelic variation in multiple genes are associated with the disease
→ cumulative affect of weakly expressed common alleles
→ disease risk typically influences by non-genetic factors
→ e.g. various cancers, heart-related diseases, IBS, diabetes, Parkinson’s, alzheimers
What is pedigree analysis?
Use of diagram to summarise the inheritance of discrete traits in a a family history
square → male
circle → female
filled → affected
half filled → heterozygous recessive
What are some limitations of pedigree analysis?
Ethical limits → controlled matings are not possible - can’t force mating
Sampling → limited sample size due to small family size per genertaion
Inaccurate/incomplete data → fale info, missing records
Demographics → migration and intermitting
What are the aims of pedigree analysis?
Determine the role of inheritance
→ sex-linked or autosomal?
→ dominant or recessive
Calculate the probability of an affected individual based on family history
Whats some samples of autosomal recessive diseases?
Cystic fibrosis → abnormal CFTR, sodium chloride transport across epithelium
Tay-Sachs disease → neurodegenerative disorder in children
dd = affected
DD = unaffected
Dd = carrier
Whats some exampled of autosomal dominant diseases?
Huntington’s disease → neurodegenerative disorder affecting muscle coordination and cognition
Hereditary retinoblastoma → retinal cancer affecting children
Achondroplasia → common genetic cause of dwarfism
dd = unaffected
DD = mostly lethal
Dd = affected
What are some examples of sex-linked recessive X chromosome diseases?
Haemophilia → impaired control on blood clotting
Red-green vision deficiency → light receptor defect
Christianson syndrome → nervous system disability in children
Fragile X syndrome → learning disability and cognitive impairment
Duchenne muscular dystrophy → muscular degeneration
What are some examples of sex-linked recessive Y chromosome diseases?
Y chromosome infertility → males without viable sperm production
Swyer syndrome → female (XY without functional ovaries)
What are some examples of sex-linked dominant X chromosome diseases?
Incontinentia pigmenti → disorder affecting skin, hair, teeth, nails and CNS, lethal in males
Charcot-Marie tooth neuropathy → progressive loss of muscle tissue and touch sensation in various parts of the body
Coffin-Lowry syndrome → intellectual disability
Hypophophatemic rickets → vit D resistant rickets
What are some examples of sex-linked dominant Y chromosome diseases?
None discovered yet
What are the types of molecules markers used today?
SSR → simple sequence repeats
SNP → single nucleotide polymorphisms
What are the steps for linkage mapping with SSRs?
- collect pedigree info from family with genetic disease + blood samples/DNA
- use PCR and gel electrophoresis to determine genotype for 100s SSR loci
- use statistical linkage analysis to identify SSRs that are linked to inheritance
- identify new molecular markers form within loci, repeat and resolve narrower map interval
In linkage mapping with SSR what does a low recombination % mean?
Indicates gene for diseases is close
→ no examples of recombinant - even closer
Why map human disease-related genes?
First step towards identifying the causal protein
→ leads to determining the nature of normal and abnormal biochemical function involving the causal protein
→ developing diagnostics tests, target specific drugs, gene therapy
What are SNPs?
Single nucleotide polymorphisms
→ molecular marker based on single base-pair substitutions
→ arise from random mutagenesis
→ mutation rate 1x10^-9 per locus per generation
→ most occur in non-coding sequence within introns
→ most in exons will be synonymous - won’t alter amino acid
→ over 10mil SNP loci in human genome
What is linkage disequilibrium on association mapping?
A physical region observed as non-random association of mutations amongst individuals in a population
→ sequences not broken up, not randomised by recombination
What is a haplotype block?
A block of sequence with non-random association
→ not independent
What are some examples of complex inherited disorders that are common in the general human population?
Diabetes, Alzheimer’s disease, several cancers, arthritis, coronary disease, asthma, lupus, IBD, celiac
What are the steps of experimental biology from Mendel’s legacy?
- assemble robust experimental material
- generate lots of data from first experiment
- repeat with different starting material
- analyse data and derive predicative model
- test predications with further experiments
- revise model
What are ‘jumping’ genes?
Transposable elements or transposons - segments of DNA that have the ability to move or jump within a genome
→ discovered by Barbara McClintock in 1940’s using corn
→ jumping occurs during mitosis and can be affectedly environment (e.g. temp stress)
What is epigenetic?
Heritbale changes in gene expression that are not caused by changes in DNA sequence
→ effects coiling of DNA
→ DNA wrapped around histone proteins, if too tight can’t transcribe: histone modification blocks uncoiling
→ DNA methylation: adds methyl group can tag DNA and activate or repress genes
Why do mitochondria and chloroplasts have DNA?
Endosymbiosis of an aerobic bacterium and cyanobacteria within the ancestral eukaryotic cell
What is the biochemical evidence of symbiosis?
Mitochondria communicate with the nucleus via trafficking of the proteins and RNA
What is the structure of the mitochondrial genome?
Circular genome
→ contains genes for tRNAs, rRNAs, cytochrome oxidase, ATPase subunit and NADH-dehydrogenase
How are mitochondria/chloroplasts inherited?
The organelles are acquired at cell division from the maternal cytoplasm
→ genotype and phenotype same as the mother
What are the uses of mitochondrial genome sequencing?
Maternit analysis
Phylogenetic systematics
Population genetics
Why is mitochondrial genome sequencing used?
→ easy to isolate and pCR amplify mtDNA due to high copy number per cell
→ maternal inheritance of 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
How is mtDNA analysis used in phylogenetics?
Way to track migration of generations
What is genomic imprinting?
A form of gene expression in which an allele of the affected gene is marker or ‘imprinted’ in one of the parents and can be passed on through meiosis to the offspring
→ epigenetic mechanism: marked by methylation or histone modification
e.g. mouse lgf2 - makes by methylation causes wars phenotype
What is a chromosomal mutation?
Changes in the chromosome number per cell
→ large scale change in chromosome structure
→ visible by microscopy
Why investigate chromosome mutations?
Cytological → provided good examples for stages of meiosis
Medical → insist into genetic disease, testing for chromosome abnormality
Molecular → insight into how genes interact throughout a genome
Evolutionary → insight
What are the names indicating the number of chromosome sets?
Monoploid (haploid) - n
Diploid - 2n
Triploid - 3n
Tetraploid - 4n
→ aneuploid: change no. of some but not all chromosomes - particular chromosome with extra copy
Is monoploidy viable in most animals?
No
→ deleterious mutations would be effective
exception: social insects like male honey bees
Is polyploidy common in plants?
Yes e.g.
Triploid → banana
Tetraploid → coffee, cotton, peanut, potato
Hexaploid → oat, wheat
Octaploid → strawberry
→ rare in animals
→ size increase with high ploidy
What are the two origins of polyploidy?
Autopolyploid → derived from the same diploid species
Allopolyploid → derived from different progenitor species
How is polyploidy chemically induced?
Colchicine → used to disrupt spindle assembly and thereby block chromosomal segregation, stops cytokinesis
What does meiosis in a triploid lead to?
Produces aneuploid gametes
2 pairing possibilities
→ trivalent or bivalent + univalent
→ consequence sterility or death
What is non-disjunction?
Occurs when meiosis malfunctions
→ synaptonemal complex
→ leads to triatomic and monosomic embryos - lethal
What is the consequence of miss-aligned repeat sequences?
Unequal crossing-over
→ gain or loss of repeats
What are the two types of large segmental inversions?
Pericentric inversion → encompasses the centromere
Paracentric inversion → does not encompass the centromere
What is reciprocal translocation?
Type of chromosome rearrangement
→ segments of DNA at different break points resulting in genetic exchange between two non-homologous chromosomes
What is a population?
A group of individuals of the same species that are able to interbreed
→ species that occupy a large geographical area are divided into sub-populations
What is the purpose of population genetics?
Find out the genetic structure of a population
→ the no. of alleles and frequency
Geographical patterns in distribution of allelic variation
Temporal changes in genetic structure of a population
What is the Hardy-Weinberg principle for genetics?
Method for investigating the movement of alleles in populations
→ essential for understanding mechanisms of evolutionary change
→ assumes: infinitely large population, random mating, no new mutations
(if a stat doesn’t fit with HW you can ask why?)
What is the equation for the total of genotype frequencies?
p^2 + 2pq + q^2 = 1
p = frequency of allele A
q (1-p) = frequency of allele a
How does mutation change genetic structure?
Creates new alleles
→ lethal, neutral, beneficial
→ ultimate source of genetic variation
How does migration change genetic structure?
New individuals move into population
→ introduction of new alleles
→ ‘gene flow’
How does natural selection change genetic structure?
Some genotypes produce more offspring
→ differences in survival or reproduction leads to adaption
→ due to selection pressure
What are the types of natural selection?
Directional selection → favours individuals at one extreme phenotype, advantage with selection pressure
Stabilising selection → favours induces with intermediate phenotypes
Disruptive selection → favours two or more different phenotypes, diverse environments
Balancing selection → two or more allele kept in balance, maintained over many generations
How doe genetic drift change genetic structure?
Random loss of alleles from a population due to chance events
→ large populations are more stable than small populations
→ results in loss of genetic variation
→ random sudden shift away from expected allele frequency
What contributes to genetic drift?
Genetic bottlenecks → a sudden decrease in population size cause be adverse environments, makes pop. vulnerable
Founder effects → dispersal and migration that establish new populations with low genetic diversity
How does non-random mating change genetic structure?
Assortative mating → individuals with similar phenotypes more likely to mate, increase freq. of homozygotes
Disassortative mating → favours heterozygotes
