Genetics

Front 1

What is the mutagenic action of 5-bromouracil?

Back 1

A modified from f thymine which a 5 methyl group. In the keto form it can base pair with Adenine but in the enrol/ionised form the bromine extends the are of delocalised electrons allowing it to base pair with Guanine

Front 2

What is the mutagenic action of Nitrous Acid?

Back 2

It promotes the oxidative deamination of bases (converts amino groups to keto groups). This allows:
C->U (then bp with T)
A->hypoxanthine (then bp with C)
Guanine->xanthine (bp with C, not mutagenic)

Front 3

What is the mutagenic action of Ethylmethanesulfonate (EMS) and Nitrosoguanidine (NMG)?

Back 3

They are both alkylating agents. They add methyl or ethyl groups to multiple positions across all four bases but particularly G and T.

EMS is more likely to occur to an oxygen at group 6 in G making O-6-alkylgunaine (BP with T).

Front 4

What mutagenic damage can UV light cause?

Back 4

254nm is the most mutagenic wavelength as DNA absorbs it most strongly.
It causes dimmers between adjacent pyridines (T and C).
T=T or T=C cause a knick in the DNA.
If not repaired, the wrong base can be inserted opposite them.

Front 5

What is excision repair and what disease exists where is is defective?

Back 5

Repair enzymes recognize the kink and cuts it and some more DNA out. DNA pol and ligase then act.

For a wrong bp, e.g. G=T 13 bases are excised in prokaryotes and 29 in eukaryotes.

Xerderma pigmentosum is an autosomal recessive disease where sufferers are deficient in repair enzymes. They get skin cancer very easily.

Front 6

What is SOS repair?

Back 6

This is a last resort in E.coli, it is better to pass on SOME DNA, even if it is highly mutated rather than none at all.
UmuC and UmuD (subunits of DNA pol V) enable the polymerase to be more error prone. They are normally negatively regulated by LexA which binds to the SOS box in their operator region. DNA pol III stops at a noncoding lesion (e.g. A T-C photodimer) here SSBP accumulate and RecA forms a filament around the ssDNA in an ATP dependent way and is activated. Upon activation RecA interacts with LexA causing self-cleavage. Levels of LexA decrease gradually and so does their repression of the SOS genes allowing their sequential activation.

UmuD is preduced and cleaved by Rec A to become UmuD’ . UmuC can then form a complex with UmuD’ and allows DNA polymerisation to proceed.

Front 7

What mutagenic damage is caused by ionising radiation?

Back 7

Leads to free radical formation that can lead to DNA damage or adducts (bases chemically bonded to a cancer causing agent.

Front 8

What are intercalating agents?

Back 8

Flat planar molecules that mimic that mimic bp and slip between adjacent purines. Include proflavin and acridine dyes
These induce frame shift mutations as they cause an insertion or deletion of a bp during replication
A frame shift mutation is hard to alter.

Front 9

What are the three modes of action for a mutagen?

Back 9

1. Replacement of a base
2. Altering a base resulting in miss pair
3. Damaging a base so it can't pair.

Front 10

What was the Luria and Delbruck Test?

Back 10

A test to show that mutations are spontaneous.

Separate colonies were plated onto plates with page and the number of resistant individuals was compared. They found huge differences (therefore it is spontaneous!)

Front 11

What are the three mechanisms of spontaneous mutation?

Back 11

1. Spontaneous lesions
2. Errors in DNA replication
3. Insertion of transposable elements

Front 12

What kinds of spontaneous mutations are there?

Back 12

Deamination
Deamination of 5-methylcytosine also generates thymine (C->T transition). Methylation can occur as a control for expression such as in the lac operon and so provides hotspots for mutations.

Depurination (the loss of the purine base)
This can result in damage as during replication these sites don’t specify any type of base. Sometimes a base is inserted resulting in mutation.

Front 13

What kind of replication errors are there?

Back 13

Substitution: (Occurs when an illegitimate nucleotide pair (e.gT-G) forms during synthesis; can occur due to a tauatomer shift in either existing or newly incorporated bases.)

Indels (when not divisible by three this results in a frameshift)

Replication slippage (Loops in ss regions become stabilized by adjacent sequences where there is a slipped miss-pairing of repeated sequences.

In E.coli the lac I gene there are hotspots due to CTGG repeats. The majority of mutations result from the addition of an extra CTGG and the minority from CTGG. Whether a deletion or insertion occurs is dependent on whether the slippage occurs on the original template or a newly synthesized strand respectively. )

Unequal Crossover (can happen due to simple tandem repeat polymorphisms and leads to deletions and duplications).

Front 14

What is fragile X chromosome syndrome?

Back 14

The most common form a of mental retardation. This is the most common form of mental retardation. This is due to repeats in the FMR-1(fragile mental retardation) gene.

<200 CTG repeats are needed to be affected.

Front 15

What is Huttington's disease?

Back 15

Variable with age (25-60 yr onset)
Dementia, involuntary jerky movements and death
Dominant form of the gene, normally make huttington’s protein which aggregates in cells in the hippocampus and cerebral cortex
Normal=1-29 CAG in exon 1. Instable=30-35 CAG Affected=36-39 CAG
25% risk for 36 repeats but 91% for 39. Huge increase over just a few more repeats.

Front 16

What causes Sickle Cell Anaemia?

Back 16

Affects 1/500 people of african descent.
Due to a missense mutation at codon 6 of the beta-globin gene (Glutamate->valine)
The deoxygenated form of the mutant pro is insoluble and so forms crystals altering the shape of the R.B.C.
Maintained in the population by heterozygous advantage.

Front 17

What causes Retinoblastoma?

Back 17

Rb protein is key in the cell cycle, and is lacking resulting in over proliferation.
A tumour results from the inherence of a mutated allele and then a second mutation in the somatic cell of the other allele. However, a double mutation could happen in somatic cells but is rarer and is known as sporadic retinoblastoma.

Front 18

What is the cir-du chat syndrome?

Back 18

Heterozygous deletion of the tip of the short arm of chromosome 5 (specifically=5p15.2 and 5p15.3). Infected individuals have a cat like mewing cry, a moonlike face and mental retardation.
Fatality rates are low so individuals can reach adult hood.

Front 19

What is Williams Syndrome?

Back 19

Autosomal dominant, reduced brain size and poor cognitive development.
1.5Mb deletion (contains 17 genes) in one homolog of chromosome 7.
Normally the sequence is delimited by repeated copies of postmeiotic segregation (PMS), encoding a DNA repair enzyme.
Unequal crossing over between the copies leads to a duplication and deletion-1/1000 people.
Arises spontaneously in germ-line cells.

Front 20

What are Bacterial Insertion Sequences? Give an example

Back 20

Sections of DNA that move around the chromosome and can insert into genes or promoters (affect numbers genes). They are shorter than transposons and do not contain any additional genes (and so aren't transposons) There are two types:

Composite/Complex. There are several genes between two IS sites and the transposes gene is divided. Tn10 is an example of this; a gene coding for tetracylcine resistance is sandwiched between two IS10 elements.

Simple. 2.Simple. Flanked by IR sequences which are short and do not contain a transposase enzyme but the intervening space does as well as genes. An example is Tn3

Front 21

What are P elements in Drosophila?

Back 21

P elements are transposes which encode P transposes. They are observed in wild populations but not lab populations (they were separated off before it evolved)

Wild females can suppress the activity of the P element and so have viable offspring whilst the lab types don't and so when they are mated with wild males hybrid dysgenesis is observed.

Front 22

What is isolation (filtration enrichment)?

Back 22

Used on filamentous fungi. The spores are mutagenised and grown in a liquid minimal media.
The suspension is passed through a membrane filter, big enough to let spores through. Therefore the non-growing spores (auxotrophs) will pass through and the grown filaments won't.
This is repeated a number of times before being plated.

Front 23

What is killing enrichment isolation?

Back 23

Used for filamentous fungi, yeast and bacteria. The growing medium contains anti fungal or antibiotics that kills fast growing individuals (e.g penicillin). The dead cells are centrifuged out

Front 24

What is Phenylketonuria (PKN)?

Back 24

Autosomal recessive. Sufferers cannot convert phenylalanine to tyrosine so phenylalanine builds ip in the blood and the excess is converted into phenylpyruvic acid which damages the developing brain.

Front 25

What is negative/dis-assortative mating?

Back 25

AAxaa, unlike individuals mate, increases the number of heterozygotes and decreases the number of homozygotes e.g self incompatibility systems

Front 26

What is positive or assortative mating?

Back 26

AAxAA, like mates with like, increases the number of homozygotes and decreases the number of heterozygotes e.g human height.

Front 27

Describe the experiment using the red flour beetle and how it shows directional selection.

Back 27

Tribolium castaneum (red flour beetle). A locus with two alleles, the recessive is lethal (w=0) Initially two lab populations were stated off with equal allele frequencies. The model described above was used to predict the frequency of the two alleles after each generation.

Front 28

Describe an experiment with mosquitos that exemplifies directional selection in a natural population.

Back 28

Culex pipiens resistance to he insecticide chlorpyrifos, which interferes acetylcholinesterase (Ace).

AceR allele gives immunity to chlorpyrifos. The control was the aspartate amino transferase 1 (supposed to be neutral in terms of insecticide resistance) 4 populations were exposed to the insecticide and 5 weren’t over 22 years. They found a higher frequency of resistance genes in the exposed alleles over the unexposed ones. The Aat1 allele did not change.

Front 29

Describe the evolution of lactose tolerance in humans and what a selective sweep is.

Back 29

In most mammals the lactase-phlorizin hydrolase gene is inactivated around 4yrs
However, due to the domestication of cattle in certain human populations, it is advantageous for humans to have it switched back on.


A mutated gene will be selected for
The surrounding genes are likely to be inherited with it due to linkage hence you get a selective sweep.
Over time they will eventually be seperated in recombination.
This can be used to calculate when the original mutation arose
Predicted to be around 2,200-20,700 yrs ago (cattle domestication ~9,000 ya).

Front 30

Describe the case study of the Great Prairie Chicken.

Back 30

These are a north American species of limited dispersal.
In Illinois in the 20th century, there was a massive decrease in populations size (from millions to 10s) the allelic diversity also fell hugely.
There was a continual decline, even after the habitat was repaired
There were other non threatened populations where the allelic diversity was almost double.
Hybrid vigor was introduced and the population was saved!!

Front 31

Describe the case study of the Floridian mountain lion.

Back 31

The populations had lots of (nearly) fixed deleterious traits from drift
Kinked tail, undescended testes, very low molecular diversity, poor semen quality
A texan cougar was introduced and the deleterious traits started to disappear.

Front 32

Describe the case study of the mountain Ibex.

Back 32

The alpine population crashed in the 19th century was “restored with the turkish and nubian races
This didn’t work as both populations had local adaptations (the times when babies were born) so the hybrid ended up being less fit.

Front 33

Describe the case study of the Dusky Sea-side sparrow.

Back 33

There was very few left (6 and the were all male)
Mated them with their nearest geographical relative
But this was later found out to not be it’s closest genetic relative!!!

Front 34

How can genetics be used to date the florida Peninsular?

Back 34

A separation event in ultrametric phylogenies of species that lived near the peninsular can be used to date it.

Front 35

Give an example of a behavioural barrier that results in divergent populations.

Back 35

Turtles have natural homing sites and won't mate with turtles on the same beach (continuous geography) if they are too far way, even though they can genetically.

Front 36

What is allopatric speciation?

Back 36

Allopatric speciation or geographic speciation is speciation that occurs when biological populations of the same species become isolated due to geographical changes such as mountain building or social changes such as emigration.

Front 37

What is parametric speciation?

Back 37

Parapatric speciation is a form of speciation that occurs due to apparition of dimorphism between populations of a species, and simultaneous Niches in this habitat can differ along an environmental gradient, hampering gene flow, and thus creating a cline variation in the mating habits, within a continuous geographical area. This example is of fire ants.

Front 38

What is peripatric speciation?

Back 38

In this form, new species are formed in isolated peripheral populations; this is similar to allopatric speciation in that populations are isolated and prevented from exchanging genes. However, peripatric speciation, unlike allopatric speciation, proposes that one of the populations is much smaller than the other.

Front 39

What is sympatric speciation?

Back 39

The process through which new species evolve from a single ancestral species while inhabiting the same geographic region, homozygous individuals may, under particular environmental conditions, have a greater fitness than those with alleles heterozygous for a certain trait. Under the mechanism of natural selection, therefore, homozygosity would be favoured over heterozygosity, eventually leading to speciation.

Front 40

Give an example of a good co-phylogeny.

Back 40

Gophers and lice show very similar phylogenies, although the lice exhibit faster rates of evolution. There are some examples of horizontal transfer events.

Front 41

What is a molecular clock?

Back 41

A protein with a constant rate of substitution/evolution (not mutation-which is always pretty constant) and so can be used to calibrate.


A protein with a constant rate of substitution/evolution (not mutation-which is always pretty constant) and so can be used to calibrate.

Front 42

What are the 5 ways in which sequence divergence can be underestimated?

Back 42

1)Multiple substitution (A->C and then C->T only shows as one difference)
2)Coincidental substitution (A->G on one line and A->C on the other. Two changes but appears as one.)

3)Parallel substitution. 2 changes but they are the same so there is no difference)

4)Convergent Substitution. A->T on one strand and the same result on another send but through 2 or more changes)

5) Back substitution.

Front 43

What is a synapomorphy?

Back 43

A trait that is shared due to relation to a common ancestor.

Front 44

What is homeoplasy?

Back 44

Appears like a synapomorphy but isn't as the trait doesn't have a common origin. It can occur through different mechanisms:

1) Convergent evolution. The trait evolved from the different ancestral conditions

2) Parallel evolution. The trait has evolved from different ancestral traits

3) Reversal. There is a reversion to the ancestral state.

Front 45

What is maximum parsimony?

Back 45

Aims to minimise the number of evolutionary steps needed to fit data to a tree. Assumes that all changes are equally likely and more change is rarer than few changes. It doesn't use all the data available.

Front 46

What is Maximum Likelihood?

Back 46

Takes into account that there re different levels of evolution (which is modelled, and can be wrong and should be tested). This then searches for that is most likely.

Front 47

What are the symptoms of Prader-Willi Syndrome and what causes it?

Back 47

Low muscle tone, obesity (chronic feeling of hunger) and intellectual disabilities.

Normally, the several paternal genes on chromosome 15 are active and the maternal ones are inactive. If the paternal ones become deleted or inactivated then the maternal ones can't compensate.

Another near by gene, (UBE3A) which is paternally inactivated and maternally activated and if it is deleted you get Angelman's Syndrome. Describe the symptoms of Angelman's Syndrome.

Hint 47

Mental disability, lack of seizures, unusually happy demeanour.

Front 48

What is Rett syndrome and what are the symptoms?

Back 48

Symptoms develop 6-18 months onwards and you get developmental regression (no motor or speech skills). Allmost exclusively in females (males die as embryos)
It is X-linked do you get mosaic expression.

There is a mutation in the mecp2 gene (on the x chromosome which binds to methyl CpG islands and is very abundant in the brain. The levels of expression have been shown to be very important for development.