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MOG > Chromosome Organisation - Eukaryotes > Flashcards

Chromosome Organisation - Eukaryotes Flashcards

1
Q 
What do the labels refer to?
*    * ------A
 *  *
   * -------B
 *  *
*    * ---------C
  |/
  D
A

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

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2
Q

How many chromosomes do humans have?

A

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

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3
Q

Does chromosome number tell us anything about the organism?

A

No

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4
Q

How are autosomes numbered?

A

Largest to smallest

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5
Q

How are chromosomes classified?

A

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

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6
Q

What technique can be used to distinguish chromosomes?

A

G-banding

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

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7
Q

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

A

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

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8
Q

Name the types of numerical abnormalities

A

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

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9
Q

What syndromes result from aneuploidy in humans?

A 
Sex chromosomes:
Turner syndrome - XO
Trisomy X - XXX
Klinefelter syndrome - XXY
Autosomes:
Down syndrome - +21
Edwards syndrome - +18 (lethal at infancy)
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10
Q

What are the 4 main classes of rearrangements?

A

Duplication, Deletion, Inversion, Translocation

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11
Q

What are the causes and consequences of rearranged chromosomes?

A 
Causes:
ds breaks
Non-allelic homologous recombination (NAHR)
Consequences:
Change to gene dosage
Unbalanced
Gene disruption
Centromere not preserved
Meiotic pairing affected
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12
Q

What is a robertsonian translocation?

A

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

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13
Q

What is a reciprocal translocation?

A

Exchange of parts between two non-homologous chromosomes

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

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14
Q

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

A

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

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15
Q

What are copy number variations? (CNVs)?

A

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

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16
Q

How so segmental duplications allow for evolution?

A

Generate redundant genes free to evolve

Can also generate further de novo rearrangements

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17
Q

What is a syntenic block?

A

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

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18
Q

What does the number of conserved syntenic blocks indicate?

A

Larger number = more evolutionary arrangements

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19
Q

What is the average gene composed of?

A

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

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20
Q

What indicates the presence of genes?

A

High GC content signifies areas with more concentrated genes

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21
Q

Are genes dispersed evenly throughout the genome?

A

No

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22
Q

What is a Cot renaturation curve?

A

Measures how much repetitive DNA is in a DNA sample

Used to study genome structure and organisation

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23
Q

What is repetitive DNA?

A

A sequence present more than once in a haploid genome

24
Q

What is a gene family?

A

Genes present in more than one copy in a haploid genome

25
Q

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

A

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

26
Q

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

A

Histone repeating units in sea urchins

27
Q

What are the 2 types of interspersed repeats?

A

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

28
Q

Where can SINEs be interspersed?

A

Within and between genes

29
Q

How do most interspersed repeats spread?

A

Retrotransposition

Integrated using reverse transcription - LINE encodes RT

30
Q

What are negative effects of interspersed repeats?

A

Can cause insertional mutagenesis and genome rearrangements

31
Q

What are VNTRs?

A 
Variable number tandem repeats
Can be:
Satellite - >100 bp
Minisatellite - 15-100bp
Microsatellite - <15bp
32
Q

Why are VNTR repeats variable in number?

A

Unequal crossing over
DNA replication slippage
DNA repair

33
Q

What is genetic fingerprinting?

A

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

34
Q

What causes triplet repeat diseases?

A

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

35
Q

What does epigenetic mean?

A

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

36
Q

What makes up chromatin?

A

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

37
Q

What is heterochromatin?

A

Tightly packed DNA, transcriptionally inactive

Constitutive and facultative forms

38
Q

What is euchromatin?

A

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

39
Q

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

A

The histone tail

40
Q

What does acetylation of lysine do?

A

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

41
Q

What does methylation of lysine residues do?

A

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

42
Q

What is ChIP?

A

Chromatin Immunoprecipitation

Detects DNA sequences associated with specific chromatin modifications

43
Q

Steps of ChIP

A 
Cell lysis
Sonication
Fragmented chromatin
Immunoprecipitation with antibody
DNA purification
Analysis - eg. sequencing
44
Q

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

A

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

45
Q

How is specificity achieved for kinetochore assembly?

A

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

46
Q

What causes Position Effect Variegation (PEV) in Drosophila?

A

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

47
Q

What do Suvar genes do?

A

Have a role in forming heterochromatin with HP1

48
Q

What are examples of highly methylated sequences?

A

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

49
Q

What does DNA methylation usually signify?

A

Repression

50
Q

Which sites are mostly methylated?

A

CG sites (70-80%)

51
Q

What CG sites aren’t methylated?

A 
CpG islands:
Around 1kb long
Mark promoters and 5' regions of genes
Open chromatin
Normally unmethylated even if not expressed
52
Q

How does methylation lead to chromatin modification?

A

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

53
Q

Why and how does X inactivation occur?

A

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

54
Q

What happens to CpG island in inactivated X

A

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

55
Q

What does Xist do?

A

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

MOG (7 decks)

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