Molecular Genetics

Question 1

What is Mendels law of independent assortment?

Answer 1

Inheritance of one gene not affected by inheritance of another

(Depends on distance between genes

Question 2

What is Mendels law of segregation?

Answer 2

A gene may exist in 2 forms

1 from mum and 1 from dad

1 can dominate the expression of another and this is known as linkage, genes that are close together are often inherited together.

Question 3

What does the genome consist of?

Answer 3

6 billion nucleotide base pairs

Two copies of each 22 autosomal

Plus the sex chromosomes X Y - females and X X males

Question 4

What is a gene!

Answer 4

A section of the DNA sequence that codes for protein

Question 5

How many genes do humans have?

Answer 5

Around 25000 (less than 2% of the genome sequence)

Large variation of the size of the genome and Number of genes across species (e.g. Some Plants have larger genomes than humans)

Question 6

What has recently been discovered about non coding DNA?

Answer 6

That it is transcribed but not translated and in which RNA regulates gene expression.

Question 7

What is the 1% of DNa variation between individuals responsible for?

Answer 7

Differences between people

Heredity (characteristics passed on from generation to generation)

Question 8

What is the biggest type of DNA sequence variability?

Answer 8

Single nucleotide polymorphisms

90%

Question 9

What is a linkage study?

Answer 9

This is a type of study that identifies genes (DNA polymorphisms) for specific traits by tracking genes in families by pinpointing those in affected individuals.

Question 10

What is an association study?

Answer 10

Case/control study

Genotype for a specific genes and compare those with and without a phenotype and see if there is a stronger correlation for specific genotype-phenotype in the case group relative to controls.

Question 11

What is ‘knocking out’?

Answer 11

This is a term used in animal studies which refers to knocking out or silencing genes in animals such as mice.

Question 12

What are problems with allelic association studies?

Answer 12

Stratification

Multiple testing

Type 1 error

Power

Question 13

What is population stratification and how is it a problem for association studies?

Answer 13

This is where certain genes may be more common in a certain population and therefore a correlation can be found that is just a coincidence not actually a cause.

Chopstick gene example.

This is a problem for association studies as positive associations have to be taken into consideration of this. When doing GWAS studies population stratification can be controlled for during the analysis.

Question 14

How is multiple testing an issue for association studies?

Answer 14

When an association study using multiple genes or genetic markers in a study multiple testing becomes and issue as if you genotype a million SNPs there is a greater opportunity to find significant results by chance and this is a potential reason why many molecular study’s are not able to be replicated. In order to combat this issue researchers have corrected the p value significance level (not as stringently as a bonferroni correction) but to the level to less than 10 to the -6. This is known as genome wide significance level and is used in GWAS and GCTA studies.

Question 15

What is type 1 error and how is it a problem for association studies?

Answer 15

Type 1 error is the probability of finding an effect that is not there by chance. This is the same issue as with multiple testing… More tests increases type 1 error rate so the p value is corrected to try and alleviate this.

Question 16

How is power an issue for association studies?

Answer 16

As the effects of any one genetic marker (excluding OGOD disorders) are very small they are often difficult to detect so studies need huge samples sizes to achieve enough power to detect them.

Question 17

What is allelic association?

Answer 17

Refers to the association between an allele and a trait.

Question 18

What is a quantitative trait loci?

Answer 18

Is a point on the genome which influences a phenotype in a small way, therefore there are many (quantitative) markers that together influence a phenotype (trait) and the loci refers to the position on the genome.

Question 19

Why are animal studies useful in the quest for QTLs?

Answer 19

remember that QTLs are many markers of small effect therefore they are difficult to find and identify and the issues around allelic associations are vast (power, stratification, multiple testing etc)

Animal studies are useful as they enable both genetics and environments to be manipulated neither of which are possible with human research.

Question 20

Briefly outline Flint et al., (1995) study on mice.

Answer 20

Looking at open field activity in mice.

Mice were selected for high and low open field activity and then inbred for 30 generations. Each mouse has an average combination of alleles from the original parental strains because there is an average of one recombination in each chromosome inherited from the first generation strain.

The most active and least active second generation mice were examined for 84 chromosomal regions that are associate with open field activity. This was to identify chromosomal regions associated with field activity. The analysis simply compared the frequencies of marker alleles for the most active and least active groups.

Open field activity may have specific genes influencing behaviour or it could be that genes influence fearfulness in the mice and this influences open field activity.

The results of the study show that there were QTLs that were associated with open field activity but not other measures of fearfulness (suggesting a potential gene specific to open field activity) and then also QTLs that were related to open-field activity and other domains of fearfulness.

Question 21

Discuss a limitation of Flint et al., (1995) mice study? This is also relevant to other animal studies using inbreeding to create generation 2

Answer 21

Because generation 2 mice have an average of only one crossover between maternal and paternal chromosomes this method has little power to pinpoint locus, it can only identify the chromosome linked with behaviour.

Question 22

Instead of inbreeding from one strain of mouse selected for a certain phenotype it is possible to create generations from multiple inbred strains this is called heterogenous stocks, what does it do?

Answer 22

It creates a generation with a greater number of recombined chromosomes which enables the study to have enough power to identify specific locus linked with behaviour.

Question 23

What does the QTL model for common complex disorders suggest?

Answer 23

That phenotypes lie on a normal distribution, many genetic markers influence a phenotype and ability and disability are at either end of that distribution. Most people will have some risk alleles and some protective alleles and will fall in the middle of the distribution. Then those with more risk alleles will be pushed to the lower end and those with more protective/enhancing alleles will be pushed to the high end. It’s QTLs as its many genes of small effect influencing a trait, this is known as polygenicity.

Question 24

Describe phenylketonuria (PKU)

Answer 24

Affects 1 in 12000 births

Used to account for 1% of the institutionalised mentally retarded populations

Different mutations in a gene on chromosome 12

Recessive allele

The gene was easier to find because it’s enzyme was known. Faulty enzyme that cannot break down phenylalanine (which comes from food), so it builds up and damages the developing brain.

All newborns are screened for elevated phenylalanine levels in their blood. DNS test has been hampered by the finding of many mutations

Early diagnosis can prevent retardation by Serving low phenylalanine diets.

Total genetic cause total environmental intervention.

Question 25

Discuss microarrays

Answer 25

Microarrays or gene chips are used for genotyping many DNa markers often SNPs at the same time. A small chip with up to a million glass rods where small single stranded fragments of DNA containing the SNP of in interest are positioned. Then a persons Dna is copied to its complementary RNA strand and this is chopped up and is washed over the chip. Fluorescent markers are attached to the sample RNA fragments by a chemical called biotin.

and using a machine the chip is hybridised and the fragments of a persons DNA move to the complementary strand and then a computer can read the chip and identify what variant and individual has in what position by shining a laser which shows the fluorescent markers.

Question 26

What is missing heritability?

Answer 26

Heritability estimates from twin studies are mostly between 40-60 %

Largest GWAS association = less than 1%

Putting all know SNP associations together accounts for very little variance

Gap between heritability and GWAS findings = missing heritability problem.

Question 27

How do you find the phenotypic similarity in a GCTA study?

Answer 27

The genetic similarity in unrelated pairs vary from +2% - 2%

The phenotypic similarity is calculated by each individual being correlated with every other individual in the sample and this is correlated with the genotyping correlation between them

Question 28

What is gene expression?

Answer 28

This is the process by which the DNA sequence of a gene is converted into functional protein structures

Question 29

What is the transcriptome?

Answer 29

Transcriptome is the set of all messenger RNA (mRNA) molecules or transcripts produced in one or a population of cells

The transcriptome reflects the genes that are being actively expressed at any given time

Unlike the genome, which is roughly fixed at birth. The transcriptome can vary with external environmental conditions (only partially stable).

Question 30

What is epigenetics?

Answer 30

Epigenetics is the regulation of genomic activities

The DNA sequence determines what specific mRNA molecules are synthesised

Epigenetics determines how much of the mRNA is made, and where and when it is synthesised

Question 31

Discuss gene expression in the context of methylation

Answer 31

In its basic form methyl marks attached to a gene suppresses expression.

No methyl - significant expression - large amounts of protein expressed

Lots of methyl - no expression - no protein

Question 32

Discuss epigenetics in more depth

Answer 32

• DNA modifications that are stable over rounds of cell division but do not involve changes in the underlying DNA sequence of the organism

Involved in cellular differentiation, allowing cells to stably maintain different characteristics despite containing the same genomic material

Heritable traits:
Over rounds of cell division (descendants of a cell inherit cell activity even though the original stimulus for gene activation is no longer present)

Sometimes transgenerationally

Question 33

Briefly explain the agouti mice example

Answer 33

Two nice are genetically identical and have an identical mutation (inserted DNA) in the agouti gene - leading to unmethylation in what should be a highly methylated region

One is big and yellow the other develops normally by mothers being placed on a high or none methyl rich diet. In the context of epigenetics the mouse on the methyl diet is showing a response to an environmental exposure affecting gene expression. This is an epigenetics process

Extras
Epigenetic features may play a role in short-term adaptations of species by allowing for reversible phenotype variability.

Both hyper-methylation and hypo-methylation can be detrimental

Question 34

Is there a connection between agouti mice and human obesity levels rising?

Answer 34

Very few studies on optimal levels and combinations of nutrients

• possible connection between the increase in plastic in out environment and the rising incidence of obesity in humans: exposure to pregnant mice to bisohenol a (bra), a building block of polycarbonate plastics and epoxy resins - reduces DNA methylation in mice - resulting in birth of more yellow offspring, obesity and higher incidence of diabetes and cancer in adults

Question 35

What is the initial product of genome expression?

Answer 35

Transcriptome, a collection of RNA molecules derived from this protein-coding genes whose biological information is required by the cell at a particular time

These RNA molecules direct synthesis of the final product of genome expression, the proteome the cells repertoire of proteins, which specified the nature of the biochemical
Reactions that the cell is able to carry out