13.3 Genetic Variability and Disease

Question 1

How many genes in the human mitochondrial genome

Answer 1

37

Question 2

Define genetic variation

Answer 2

Differences in DNA sequences between individuals in a population

Question 3

What is a genetic polymorphism?

Answer 3

A DNA sequence variation that is common in the population

Question 4

What is a single nucleotide polymorphism?

Answer 4

DNA sequence variation that exists within a population and is caused by the change in a single nucleotide

Question 5

What is a haplotype?

Answer 5

Set of polymorphisms close together on a chromosome that are typically passed from one parent more often than expected by chance

Question 6

What type of DNA mutations are known as “structural variants”?

Answer 6

Variation in a region of DNA that is 1kb and larger in size

Question 7

What are the two mechanisms by which DNA sequence can be altered?

Answer 7

• Mutation (short region of genome by alteration in a nucleotide sequence)
• Recombination (restructuring a large part of the genome, such as in crossing over)

Question 8

What is meant by the type of recombination known as translocation?

Answer 8

Lengths of DNA exchanged between non-homologous chromosome (e.g. 1 and 8)

Question 9

How does the position of a mutation in a DNA codon affect severity?

Answer 9

Later in codon, less severe, since the mutation is less likely to alter the amino acid that the entire codon codes for

Question 10

What is a synonymous mutation?

Answer 10

Change in DNA, no change in amino acid

Question 11

What is a nonsense mutation?

Answer 11

Change in DNA sequence that encodes “stop”

Question 12

What is a non-synonymous mutation?

Answer 12

Change in DNA, change in amino acid

Question 13

Conservative vs non-conservative non-synonymous mutation

Answer 13

Cons: similar properties
Non-Cons: different properties

Question 14

What is a readthrough mutation?

Answer 14

Stop codon is replaced with another codon, causing gene to be extended beyond its typical end

Question 15

What are five types of structural variation of DNA sequence?

Answer 15

• Inversion
• Copy number variation
• Deletion
• Insertion
• Duplication

Question 16

What is meant by “epigenome”?

Answer 16

All epigenetic modifications within the genome that regulate the activity/expression of genesd (AKA epigenetic marks)

Question 17

List three main types of epigenetic modification

Answer 17

• Histone modifications
• DNA methylation
• RNA regulation

Question 18

What is a 2x2x2 bundle of eight histones with DNA coiled around it called?

Answer 18

Nucleosome

Question 19

Which amino acids in the n-terminal tails of histones are most commonly modified?

Answer 19

Lysine and arginine

Question 20

How do histone modifications impact gene expression?

Answer 20

They change whether a gene is wrapped or unwrapped, making them more or less accessible to transcriptional machinery and hence impacting gene expression

Question 21

Which nitrogenous base is most commonly methylated?

Answer 21

Cysotine

Question 22

Which enzyme is required for DNA methylation?

Answer 22

Methyltransferase

Question 23

Which dinucleotide is most commonly methylated?

Answer 23

CpG (Cytosine phosphate Guanine)

Question 24

Generally, which of methylation and demethylation turn genes on or off?

Answer 24

Methylation: off
Demethylation: on

Question 25

What are CpG islands?

Answer 25

Regions of genome that contains large number of CpG dinucleotide repeats

Question 26

Give an example where CpG islands in promoter regions of DNA might be used in gene silencing?

Answer 26

X inactivation

Question 27

If a gene promoter region is unmethylated, does that mean the gene will definitely be expressed?

Answer 27

No; the gene itself (or one section of it) could be methylated

Question 28

What is ncRNA?

Answer 28

- Non-coding RNA - RNA that is not translated into a protein

Question 29

What is the role of regulatory nCRNA?

Answer 29

Regulate gene expression at epigenetic, post and pre-translational levels

Question 30

What are the two size classifications of ncRNA?

Answer 30

Small: <200nt Long ncRONA: >200nt

Question 31

In what two ways can ncRNA influence gene expression?

Answer 31

- Recruit proteins to modify histones - Influencing translation and stability of mRNA

Question 32

Are epigenetic marks passed down to offspring?

Answer 32

No

Question 33

Are epigenetic marks carried across generations of cells within an organism once differentiation occurs?

Answer 33

Yes

Question 34

What is epigenetic inheritance?

Answer 34

Only one copy of a gene is switched on (i.e. only from one parent), which can lead to a vast range of syndromes

Question 35

What is a fluorophore?

Answer 35

Fluorescent compound that can re-emit light upon excitation

Question 36

How can DNA polymerase allow for amplification of specific regions of target DNA?

Answer 36

By selecting primers which are complementary to the target sequence

Question 37

Describe PCR

Answer 37

- DNA is heated with primers, taq polymerase and free nucleotides (denaturation) - Temperature is decreased to the level of the specific primer being used, enabling primer to anneal to DNA; needs to be high enough that no non-complementary linkage will be tolerated (annealing) - Temperature is increased to the right level for polymerase, which synthesises complementary strands using free nucleotides

Question 38

How is PCR used in cervical screening tests?

Answer 38

- Detection of Human Papillomavirus (HPV) DNA - Identify strain - Test is more than just sensitive detection when used to differentiate between strains

Question 39

Describe chromosome microarray

Answer 39

Patient DNA and reference DNA (labelled with different fluorophore colours) are added to a slide. Depending on the resulting colour in different regions, we can infer whether there are any deletions or insertions in patient DNA relative to reference.

Question 40

What are some limits of chromosome microarray?

Answer 40

- Cannot detect single gene mutations - Almost all genes have some variation, and so it is not always clear whether changes in copy number are pathogenic or not

Question 41

What are some strengths of chromosomal microarrays?

Answer 41

- Good at detecting anything that changes in copy number (including trisomies and monosomies) - Can detect these changes on any size within probe resolution

Question 42

How does FISH work?

Answer 42

- DNA in cells is denatured - Incubated with fluorophoric probes to see where they can successfully binds

Question 43

What does FISH stand for?

Answer 43

Fluorescent in Situ Hybridisation

Question 44

Does FISH have to occur in prophase?

Answer 44

No, it can also occur in metaphase, when chromosomes are condensed

Question 45

What can karyotype analysis detect?

Answer 45

- Monosomies/trisomies - Translocations - Insertions - Deletions

Question 46

What are some limitations of karyotype analysis?

Answer 46

- Low resolution - Requires culturing of cells to get at start of mitosis

Question 47

Why might whole genome sequencing be of limited clinical value

Answer 47

We don't have the medical understanding to interpret all of the thousands of changes between two haploid genomes, and so we can't use the data to its full potential

Question 48

Do all pathogenic DNA changes occur in exons within the exome?

Answer 48

No; but most do

Question 49

How does genome sequencing differ from exon sequencing?

Answer 49

Before sequencing, the genome is processed to enrich exon content

Question 50

How does Non Invasive Prenatal Testing (NIPT) work?

Answer 50

During pregnancy, small amounts of foetal DNA are in a mother's blood. This can be used to assess changes in copy number between maternal and foetal DNA, enabling us to assess for monosomies, trisomies, and even sex identification

Question 51

Is NIPT considered diagnostic?

Answer 51

No