Chromosome Structure

Question 1

Facultative heterochromatin

Answer 1

Heterochromatin that can be both active (decondensed) or inactive (condensed)

Question 2

Constitutive heterochromatin

Answer 2

Highly condensed heterochromatin that shows little or no evidence of active gene expression.

Question 3

Alpha satellite DNA

Answer 3

171 monomer unit tandemly repeated to form a large array. Role in centromere development.

Question 4

Beta satellite

Answer 4

68bp monomer repeat unit

Question 5

Gamma satellite

Answer 5

Mostly observed on X chromosome. Prevents spread of heterochromatin.

Question 6

Inversion variants

Answer 6

inv(2)(p11.2q13)
inv(3)(p11q12)
inv(3)(p13q12)
inv(5)(p13q13)
inv(10)(p11.2q21.2)
inv(Y)(p11.2q11.2)

Question 7

What is a fragile site?

Answer 7

Segments of uncoiled chromatin likely to show gaps and chromosome breaks. Line in gene content and high in LINE content. Sites where genes can be silenced by hypermethylation. Disruption of the DNA due to a) DNA elongation inhibition by folate sensitivity b) DNA polymerase inhibition by BrdU c) starving cells of thymidine.

Question 8

What type of culture conditions induce fragile sites?

Answer 8

Folate sensitivity, thymidine starvation, BrdU or distamycin A exposure.

Question 9

What is the incidence of a rare fragile site?

Answer 9

1/several hundred individuals (less than 5% of pop), Rare ones tend to be folate sensitive.

Question 10

Intermediate fragile sites (1-5% of population)

Answer 10

fra(10)(q25)

fra(16)(q22)

Question 11

What is FRA11B?

Answer 11

A fragile site at 11q23.3 within proto-oncogene CBL2. CCG repeat which behaves similar to FRAXA. Expansion of this repeat in mothers can be a vulnerable point for de novo del (11q) - Jacobsen syndrome.

Question 12

Euchromatic variants

Answer 12

var(4)(p16.1p16.1) - resembles a dup

var(8)(p23.1 p23.1) - can appear cytogenetically indistinguishable from 8p23.1 dup syndrome which includes dup of GATA4. Distinguish by FISH or MLPA

var(9)(p12p12) - can appear as dup or trp

var(15)(q11.2q11.2) - difficult to distinguish between PWS/AS critical region.

Question 13

Why do some euchromatic variants show no phenotypic effect?

Answer 13

• low gene content
• absence of dosage sensitive loci
• psuedogenes (copy of a gene that lacks introns or other essential DNA sequences essential for function)
• functional compensation elsewhere in the genome
• positional effect e.g. inactivation of a duplicated gene
• may be a small phenotypic effect but patient within the normal range so difficult to detect

Question 14

Transposable elements

Answer 14

Units of DNA that move within the genome. e.g. LINES (long interspersed nuclear elements) and SINES (short interspersed nuclear elements),
Reterotranspons are transposons that have done a copy and paste.
As transposons accumulate over evolution they can result in repetitive sequences of DNA interspersed throughout the genome.
Transposons can be associated with disease if they insert within a gene or disrupt homologoius recombination and/or mismatch repair resulting in structural rearrangements.

Question 15

VNTRs

Answer 15

variable number tandem repeats aka satellite DNA

Question 16

Where do you find minisatellites?

Answer 16

Cluster at telomere, but can be found throughout the genome. (10-50bp)

Question 17

How long are microsatellites (STRs)?

Question 18

What is restriction lenth polymorphism analysis?

Answer 18

The cleavage of DNA is done by restriction enzymes. Individuals can have different lengths of DNA due to the existence of VNTR or SNP mutations at the cleavage site, which can be separated by electrophoresis. This is one of the first fingerprinting techniques.

Question 19

Synonymous SNP

Answer 19

Does not change the amino acid sequence

Question 20

Non-synonymous SNP

Answer 20

Changes the amino acid sequence

Question 21

What is contained within a nucleotide unit?

Answer 21

5 carbon deoxyribose sugar, a phosphate and one of four nitrogenous bases (A,T,G,C)

Question 22

Purines

Answer 22

A and G (two interlocked rings)

Question 23

Pyrimidines

Answer 23

C and T (single ring)

Question 24

Length of a single pitch (complete turn of DNA)

Answer 24

3.6nm

Question 25

Hydrogen bonds for DNA

Answer 25

2 for A joining to T

3 for G joining to C

Question 26

Define A, B, H and Z DNA

Answer 26

A-DNA: right handed helix with 11bp per turn. Not found in vivo.
B-DNA: right handed helix with 10bp per turn. Most DNA in bacterial and eukaryotic cells adopt this.
Z-DNA: left handed, 12bp per turn. HIgh GD rich favours this form. Conformation occurs during transcription of genes.
H-DNA - triple helix structure caused by inverted repeats of polypurine/polypyrimidine DNA stretches. May have a role of functional regulation of gene exp.

Question 27

Hairpin structure

Answer 27

inverted repeats of polypurine and polypyrimidine DNA stretches that form hairpin structures through intra strand pairing (DNA folds back on itself).

Question 28

Cruciform

Answer 28

Two hairpin loops arranged in a 4 way junction (such as holliday junction formed during recombination)

Question 29

Promotor region of DNA

Answer 29

TATA box (so called because of its 8bp conserved sequence made solely of AT pairs). It lies 30bp up from the mRNA start site. This sequence is recognised by the transcription factor TATA binding protein (TBP).

Question 30

5’ untranslated region (5UTR)

Answer 30

The region of a gene from the transcription start site to the nucleotide before the start codon (usually 100 to 220bp, but vary across species). High GC content (approx 60%) is highly conserved. The 5’UTR is an important binding site for ribosomal RNA that initiates mRNA translocation and as such this region is important in regulation of protein expression.

Question 31

Translation initiation codon

Answer 31

ATG (codes for methionine)

Question 32

Majority of introns start and end with what base sequence?

Answer 32

Start GT (becoming GU in intronic RNA)
End AG

Question 33

Largest gene is what?

Answer 33

Dystrophin gene, which is involved in muscular dystrophy. 99% of it is intronic, with 79 introns.

Question 34

Translation stop site codons

Answer 34

TAA, TAG or TGA

Question 35

3’ untranslated region

Answer 35

Regulator elements within the 3UTR can influence mRNA polyadenylation, translation efficiency, localisation and stability and thus ultimately control protein expression. 3UTR contains the polyadenylation primary signal for the poly A tail to be added to the mRNA to control nuclear export, translation and stability of mRNA.

Question 36

Mitochondrial gene

Answer 36

Circular DNA containing 37 genes. Maternally inherited.

Question 37

Mutations can arise by?

Answer 37

1) DNA damage
2) failure to to DNA damage
3) errors in DNA replication
4) recombination

Question 38

MMR

Answer 38

Mismatch repair. Carried out by MutSa and MutSB, which recognise mismatched base pairs. Recurits MutL complex which excises the mismatched DNA. When MMR is lost there is a decrease in apoptosis and a 100 to 1000 fold increase in mutation rates.

Question 39

BER

Answer 39

Base excision repair. Principal repair pathway for oxidative damage. DNA glycosylases recognise and remove damaged bases and inserts new ones. Either short patch (single nucleotide) or long patch (multiple)

Question 40

NER

Answer 40

Nucleotide excision repair. Removes pyrimidine dimers caused by UV radiation.

Question 41

DSBs - how are they repaired?

Answer 41

1) homologous recombination repair (HRR): a single strand from the homologous chromosome invades the damaged DNA and acts as a template for accurate repair. Involves Rad51.
2) non homologous end joining (NHEJ): Ku and DNA dependent protein kinase complexes bind to the end of the DSB. Ku unwinds the ends, by chance revealing short homologous sequences in the two DNAs, which base pair to yield a region of microhomology. The unpaired single stranded 5’ends are removed and the two double stranded molecules ligate together. As a result the DNA is repaired, but several base pairs at the site of breakage are removed. Leads to permanent change in DNA.