Genetics

Question 1

What is the relevance of genetics to modern science and society?

Answer 1

• E.g. engineered bacterial genes to plants to improve their photosynthetic ability
• E.g. found link between obesity and dementia using gene association
• Green revolution used genetic techniques to develop new high-yielding strains of crops
• Green revolution is responsible for most of the crops we have now
• Disadvantage: high yield crops are exhausting land of nutrients so lots of fertiliser and weed killer needed
• Biotechnology industry uses molecular genetic methods to produce substances of economic value

Question 2

How related are we to all organisms in terms of genes and gene function?

Answer 2

• Many aspects of human biology are conserved in other species
• Example: the eye
• Eye structure is not conserved between species
• Example of convergent evolution
• Humans have one lens
• Insect eyes have 700 lenses in a compound eye
• Mice have allele for small eye or normal eye
• Heterozygous mouse has small eye
• ‘Eyeless’ flies have a much smaller eye or no eye
• Humans can have normal eyes or eyes with no pupil
• Mutant phenotypes of mice, fruit flies and humans have mutations to Pax6/eyeless gene
• If cells express eyeless gene they will develop as eye even if they aren’t in the eye, forming ectopic eye
• Human Pax6 gene can be expressed in drosophila
• Eyeless gene is a drosophila analogue of Pax6
• Pax6 gene causes ectopic eye in tadpoles, does the same when expressing eyeless gene
• Genes are much more highly conserved between species than you would expect
• “Master” genes involved in fundamental biological and biochemical processes are conserved between species
• The PAX-6/ eyeless gene tells us that there is an evolutionary connection between all the myriad eye forms in nature
• The study of genes in one species is likely to tell us about the biochemistry and biology of all species
• E.g. information flow in e.coli

Question 3

The experimental basis to Mendel’s observations

Answer 3

• He used pure breeding lines: all individuals the same generation after generation
• All genes in homozygous state
• He used single pairs of clearly distinguishable alternatives
• He collected numerical data
• His rigorous collection of significant amounts of data allowed him to propose 2 rules to predict types of progeny and proportions of each type, knowing certain information about the parents
• He used two types of crosses, cross-pollination and selfing
• He transferred pollen with brush onto stigma
• Removed anthers so flowers can’t self fertilise
• Or in selfing he brushed pollen from plant directly onto stigmata
• Sealed a bag around the plants so they can’t be fertilised by insects

Question 4

What do we mean by Mendelian monohybrid ratios?

Answer 4

• Law of segregation-during formation of germ cells, 2 versions segregate so only one appears in the germ cells
• Monohybrid cross is one gene
• Mendelssohn results show that fertilisation is random

Question 5

• Dihybrid ratios:

Answer 5

• Looks at 2 traits
• All 4 possible combinations of alleles were displayed in the peas
• Frequency was not the same
• Traits present in parents only show the dominant one in F1
• 9/16 in F2 show same phenotype as F1
• 3/16 showed one of the dominant characteristics but not the other
• 3/16 showed the other
• 1/16 showed double recessive

Question 6

What is the chromosomal basis to Mendel’s observations?

Answer 6

• In meiosis I homologous chromosomes are pulled apart
• In meiosis II sister chromatids are pulled apart
• Gives haploid gametes
• In haploid cells the daughter cells can fuse to form diploid then immediately undergo mitosis
• Independent segregation of homologous chromosomes
• Independent assortment of chromosomes
• The trait that is shown in a heterozygote is called the dominant trait
• The trait that is hidden in a heterozygote is recessive
• In the case of Mendels peas, they showed complete dominance – the heterozygote has the same phenotype as the homozygous dominant
• This is not always the case
• E.g. snapdragons show codominance, red and white form pink intermediates
• Codominace doesnt invalidate Mendels findings
• Mendels work allows proportions of progeny to be predicted from a particular genetic cross

Question 7

How crossing over generates new combinations of alleles

Answer 7

• Chromosomes break and rejoin at exactly homologous positions between homologous chromosomes in meiosis I
• Gives recombinant chromosome with new combinations of alleles
• Every time you make a recombinant chromosome you also make the reciprocal

Question 8

What is pedigree analysis?

Answer 8

• Human genetics doesn’t exist as we don’t perform crosses on humans
• Instead we infer inheritance from analysing existing matings in pedigrees
• Uses standard symbols and terminology

Question 9

How do dominant and recessive traits appear in pedigrees?

Answer 9

• In dominant pedigrees individuals In every generation display the phenotype
• Affected individuals can have normal offspring
• In recessive pedigrees an affected individual can be born of two parents that don’t show the phenotype
• Usually only see affected individual once in the pedigree
• Matings between first cousins greatly increases rate at which recessive phenotype appears

Question 10

What do we mean by the terms mutant and wild type?

Answer 10

• Mutant has nothing to do with ‘normal’ or not, only to do with frequency
• Often, one allele is much more frequent than others
• This allel is called the wild type and all other alleles are mutant
• In some cases such as Ia, Ib and Io alleles that determine ABO blood groups, several alleles are all frequent
• Here none is picked as the wild type and gene is said to be polymorphic

Question 11

How is X linked inheritance different to autosomal inheritance?

Answer 11

• In many species, one pair of chromosomes do not look alike – heteromorphic
• In one sex you find the heteromorphic pair
• In the other sex you find two copies of one member of the pair
• Presence of these chromosomes correlated with sex, so called sex chromosomes
• The other chromosomes which are identical in both sexes are called the autonomies
• Genes on X chromosomes behave differently to genes on autosomes
• Males only have 1 X chromosome so will always display recessive phenotype

Question 12

What is the effect of lethal alleles on inheritance?

Answer 12

• Mendelian predicts 3;1 ratio dominant to recessive
• If one phenotype is lethal, it will be a 2:1 ratio
• Not a departure from Mendel, the third phenotype is accounted for in the deaths

Question 13

How can the environment influence Mendelian genetics?

Answer 13

• E.g. Phenylketonuria (PKU) is a rare recessive allele
• Homozygtotes have severe mental retardation
• Codes for phenylalanine hydroxylase
• Affected individuals can’t convert Phe to Tyr
• Phe can easily pass in and out of cells so accumulates in cerebrospinal fluid
• Intereferes with neurotransmitters
• Can diagnose lack of enzyme at birth with an antibody test
• Changing diet of PKU individuals at birth to low protein allows them to be virtually normal (wild type)
• Example where change in environments can affect the way a genotype presents as a phenotype

Question 14

How changes in Mendelian di-hybrid ratios can be explained by gene interaction

Answer 14

• Genotypes can mask phenotypes
• E.g. Labrador’s
• Called recessive epistasis – the recessive ee genotype masks all genotypes of the B gene

Question 15

How alleles of genes on the same chromosome tend to be inherited together

Answer 15

• Linkage
• When genes are on the same chromosome there is a tendency for alleles of those genes to be inherited together
• Parental combinations outnumber recombinant types
• Strength of linkage depends what genes you look at and how far apart they are on the chromosome

Question 16

How have genetic maps helped in whole genome sequencing?

Answer 16

• Recombination or genetic exchange allows for the construction of genetic maps
• Genes are placed in the map as a result of linkage to other genes whose position is already known
• Can measure strength of linkage by frequency of recombinant progeny
• The map distance is the unit of recombination, 1% of recombination frequency or 1cM

Question 17

How can linkage be observed in human pedigrees?

Answer 17

• Both haemophilia and colour blindness are X linked disorders, therefore the genes are linked
• In rare pedigrees, with both conditions segregating, you see evidence of the linkage
• Because the progeny numbers are small, can’t calculate recombination frequency directly
• If we do see recombination, the frequency would be artificially high if calculated from that pedigree
• Instead we use probability theory
• What are the odds of observing a particular pedigree given linkage at a particular distance
• Take info from a large number of pedigrees
• Chance of seeing this pedigree if genes are at x distance
• Allows you to take the log of the odds and add them together to give a score to tell the genetic distance
• Farther apart genes are, the closer their recombination frequency is to 50% (Mendelian)

Question 18

What is dna sequence variation for linkage analysis

Answer 18

• Since there are so few genetic markers in humans, we use dna sequence variation to detect molecular alleles
• Forms the basis of the genetic map of the human genome
• This was a necessary pre-requisite to whole genome sequencing since the genetic markers acted as landmarks for the sequencing
• Through hybridisation and sequencing we can identify homologous sequences
• Southern blot technique is used to identify sequences homologous to probe
• Probe binds to marker
• Some people will have RE site on chromosome and some people won’t
• We wont see same RE fragment pattern between 2 people as site is changed as we have different DNA sequences
• Gives measurement of recombination
• Can southern blot all individuals
• Probe is a marker
• Can measure distance between gene and marker

Question 19

How did positional cloning alow the identification of the Cystic Fibrosis gene?

Answer 19

• DNA based markers have allowed for the identification of disease genes such as the cystic fibrosis transmembrane conductance regulator (CFTR)
• Finding several closely linked markers eventually allowed the gene to be identified by positional cloning
• Analysis is repeated with more markers
• Measure strength of linkage of markers with CF to find the smallest distance
• Closely linked DNA markers can be used in prenatal diagnosis
• KM19 marker is close to CF so very tightly linked, can be used to find CF gene

Question 20

Linkage analysis for finding CF gene

Answer 20

• Linkage analysis was carried out on families with cystic fibrosis and an association was found between the inheritance of molecular markers from chromosome 7 and CF
• Linkage studies with additional markers indicated that the CF locus is close to the marker KM19
• Use pedigrees to show linkage between markers and CF
• Hybridise probes for markers to chromosome to find physical position
• Get close to CF gene
• Take probe for closest marker and hybridise to genomic DNA libraries
• Restriction map clones and work out order in which they overlap
• Make probes for ends and hybridise to library (chromosome walking)
• If you use larger clones then make end probes its chromosome jumping
• Clones from the region were isolated by chromosome walking and jumping
• Analysis of DNA sequences within clones revealed 4 candidate genes
• Look for pieces of DNA that correspond to mRNA using northern blotting to find genes
• Additional studies eliminated three of the candidate genes
• Look at sequences of genes and where they are expresssed until you find best candidate
• DNA sequencing of normal and KS individuals revealed the presence of a 3bp deletion in the gene of the CF patient

Question 21

SNP:

Answer 21

• SNPs are the most common type of genetic variation among people
• They are single nucleotide polymorphisms and can be used as DNA markers
• Can be used in gene association studies
• Don’t require pedigree analysis
• Instead, just compare SNPs of case studies against controls
• Looks for SNP alleles that associate with the trait of interest
• This defines a region of the genome that may contain a candidate gene

Question 22

Linkage disequilibrium:

Answer 22

• 2 alleles on same chromosome tend to be inherited together
• Recombination is the engine of evolutionary change allowing for new combinations of alleles in offspring
• But its slow
• Groups of alleles of closely linked genes remain stuck together
• Call the phenomenon where pairs of alleles are more common linkage disequilibrium
• Groups of alleles tightly linked are locked in a haplotype
• If we genotype position with know what will be around there

Question 23

What is the future for identifying genes involved in disease or other phenotypes?

Answer 23

• The approach to identifying genes which predispose individuals to getting cancer has changed significantly
• As the cost of whole genome sequencing plummets, this will take over from other approaches