Chromosome Organisation - Eukaryotes

Question 1

What do the labels refer to?
*    * ------A
 *  *
   * -------B
 *  *
*    * ---------C
  |/
  D

Answer 1

A - Telomere
B - Centromere
C - Telomere
D - Sister Chromatids

Question 2

How many chromosomes do humans have?

Answer 2

23 pairs:
22 pairs of autosomes
and
1 pair of sex chromsomes

Question 3

Does chromosome number tell us anything about the organism?

Answer 3

No

Question 4

How are autosomes numbered?

Answer 4

Largest to smallest

Question 5

How are chromosomes classified?

Answer 5

Telocentric - no chromosome arm (p arm) above centromere (not in humans)
Arocentric - small chromosome arm (p arm) above centromere
Submetacentric - medium sized chromosome arm (p arm) above centromere
Metacentric - chromosome arms same length either side of centromere

Question 6

What technique can be used to distinguish chromosomes?

Answer 6

G-banding

Uses Giemsa staining to produce dark bands (gene poor) and light bands (gene rich)

Question 7

What technique can be used to map genes to chromosomal regions?

Answer 7

FISH (Fluorescence in situ Hybridisation)
Make fluorescent copy of probe sequence
Denature sequences
Probe and target sequences mixed
Probe hybridises to target sequence
Can detect presence of probe using a fluorescent microscope

Question 8

Name the types of numerical abnormalities

Answer 8

Polyploidy - many copies of entire karyotype (not in humans)
Aneuploidy:
Monosomy, loss of one chromosome (not in humans except Turner Syndrome)
Trisomy, gain of one chromosome

Question 9

What syndromes result from aneuploidy in humans?

Answer 9

Sex chromosomes:
Turner syndrome - XO
Trisomy X - XXX
Klinefelter syndrome - XXY
Autosomes:
Down syndrome - +21
Edwards syndrome - +18 (lethal at infancy)

Question 10

What are the 4 main classes of rearrangements?

Answer 10

Duplication, Deletion, Inversion, Translocation

Question 11

What are the causes and consequences of rearranged chromosomes?

Answer 11

Causes:
ds breaks
Non-allelic homologous recombination (NAHR)
Consequences:
Change to gene dosage
Unbalanced
Gene disruption
Centromere not preserved
Meiotic pairing affected

Question 12

What is a robertsonian translocation?

Answer 12

Centric fusion of arocentric chromosomes 13, 14, 15, 21, or 22
Can cause Down syndrome in progeny of carrier

Question 13

What is a reciprocal translocation?

Answer 13

Exchange of parts between two non-homologous chromosomes

Can produce Philadelphia chromosome - exchange of 9q with 22q, causes Chronic myeloid leukemia

Question 14

What condition can gene duplication cause and how is it detected?

Answer 14

Charcot-Marie-Tooth syndrome type 1 from duplication including PMP22
Detected using FISH on interphase nuclei

Question 15

What are copy number variations? (CNVs)?

Answer 15

Duplications and deletions not microscopically visible
Main source of human variation
Associated with human phenotypes but can be neutral
Often fixed segmental duplications

Question 16

How so segmental duplications allow for evolution?

Answer 16

Generate redundant genes free to evolve

Can also generate further de novo rearrangements

Question 17

What is a syntenic block?

Answer 17

Collection of contiguous genes located on the same chromosome, traits by the genes inherited together

Question 18

What does the number of conserved syntenic blocks indicate?

Answer 18

Larger number = more evolutionary arrangements

Question 19

What is the average gene composed of?

Answer 19

Non-coding intervening sequences
Non-coding control sequences (promoters, enhancers, etc.)
CpG islands
Small coding sequence

Question 20

What indicates the presence of genes?

Answer 20

High GC content signifies areas with more concentrated genes

Question 21

Are genes dispersed evenly throughout the genome?

Answer 21

No

Question 22

What is a Cot renaturation curve?

Answer 22

Measures how much repetitive DNA is in a DNA sample

Used to study genome structure and organisation

Question 23

What is repetitive DNA?

Answer 23

A sequence present more than once in a haploid genome

Question 24

What is a gene family?

Answer 24

Genes present in more than one copy in a haploid genome

Question 25

What's an example of gene families providing variant proteins?

Answer 25

Beta globin cluster, change of expression throughout development All carry oxygen in blood but decrease in oxygen affinity as human ages

Question 26

What's an example of gene families making a large amount of gene product?

Answer 26

Histone repeating units in sea urchins

Question 27

What are the 2 types of interspersed repeats?

Answer 27

SINEs (short interspersed nuclear element) - Alu most abundant 11% genome LINEs (long interspersed nuclear element) - L1 most abundant 17% genome

Question 28

Where can SINEs be interspersed?

Answer 28

Within and between genes

Question 29

How do most interspersed repeats spread?

Answer 29

Retrotransposition | Integrated using reverse transcription - LINE encodes RT

Question 30

What are negative effects of interspersed repeats?

Answer 30

Can cause insertional mutagenesis and genome rearrangements

Question 31

What are VNTRs?

Answer 31

``` Variable number tandem repeats Can be: Satellite - >100 bp Minisatellite - 15-100bp Microsatellite - <15bp ```

Question 32

Why are VNTR repeats variable in number?

Answer 32

Unequal crossing over DNA replication slippage DNA repair

Question 33

What is genetic fingerprinting?

Answer 33

Detected repeat numbers in individuals eg. using minisatellites - generated 1st fingerprints Microsatellite VNTRs now amplified by PCR so they can be detected, held as genetic profiles Repeat number is reliably inherited throughout pedigrees

Question 34

What causes triplet repeat diseases?

Answer 34

Length variation in specific unstable trinucleotide repeats (microsatellites) Expansion beyond a critical number is associated with disease Eg. neurogenerative disorders like Huntington's disease

Question 35

What does epigenetic mean?

Answer 35

Mitotically heritable states of gene expression that cannot be explained by changes in DNA sequence

Question 36

What makes up chromatin?

Answer 36

The nucleosome, made up of a core histone ocatamer plus DNA

Question 37

What is heterochromatin?

Answer 37

Tightly packed DNA, transcriptionally inactive | Constitutive and facultative forms

Question 38

What is euchromatin?

Answer 38

Open and active DNA, nucleosomes look like a bead on a string

Question 39

What part of the chromatin can be modified to alter its structure?

Answer 39

The histone tail

Question 40

What does acetylation of lysine do?

Answer 40

Acetylated chromatin on H3 and H4 tails opens up chromatin making it transcriptionally active HAT acetylises, HDAC deacetylises

Question 41

What does methylation of lysine residues do?

Answer 41

Context specific: H3K4 tri-methylation associated with active genes H3K9 tri-methylation associated with chromatin condensation (recognised by HP1)

Question 42

What is ChIP?

Answer 42

Chromatin Immunoprecipitation | Detects DNA sequences associated with specific chromatin modifications

Question 43

Steps of ChIP

Answer 43

``` Cell lysis Sonication Fragmented chromatin Immunoprecipitation with antibody DNA purification Analysis - eg. sequencing ```

Question 44

What are the 3 chromatin changes associated with gene activity change?

Answer 44

Histone modification Histone re-modelling (moving nucleosomes) Variant histones

Question 45

How is specificity achieved for kinetochore assembly?

Answer 45

Centromeric chromatin contains CENP-A (variant H3) and is flanked by pericentromeric chromatin (H3K9 tri-methylated)

Question 46

What causes Position Effect Variegation (PEV) in Drosophila?

Answer 46

Chromosomal inversion can result in the w+ gene being located close to the heterochromatic region - can cause gene silencing

Question 47

What do Suvar genes do?

Answer 47

Have a role in forming heterochromatin with HP1

Question 48

What are examples of highly methylated sequences?

Answer 48

Satellite DNAs, repetitive elements, intergenic DNA, exons of genes

Question 49

What does DNA methylation usually signify?

Answer 49

Repression

Question 50

Which sites are mostly methylated?

Answer 50

CG sites (70-80%)

Question 51

What CG sites aren't methylated?

Answer 51

``` CpG islands: Around 1kb long Mark promoters and 5' regions of genes Open chromatin Normally unmethylated even if not expressed ```

Question 52

How does methylation lead to chromatin modification?

Answer 52

Methyl-CpG recognised by proteins with methyl DNA-binding domain Recruit chromatin repressor complexes Unmethylated CpG recognised by other proteins Recruit chromatin activating complexes

Question 53

Why and how does X inactivation occur?

Answer 53

Would have double gene expression in females (XX) so inactivated in dosage compensation Inactivation occurs through heterochromatin formation

Question 54

What happens to CpG island in inactivated X

Answer 54

Become methylated, except X inactive specific transcript (Xist), CpG island methylated on active X instead

Question 55

What does Xist do?

Answer 55

Coats the inactive X chromosome and recruits chromatin modifications and DNA methylation