Lecture 1 - Higher Eukaryotic Chromosomes Flashcards
What is a Telomere?
Area of repetitive DNA and end of chromosomes
Are telomere stable?
Yes and they do not fuse with other chromosomes
What is a centomere?
Region or kinetocore where the cells spindle fibres attach
What are sister chromatids?
Identical copies formed in DNA replication - both copies are joined together by the centromere
How is DNA packaged into a nucleus?
DNA is wrapped to make ball like structures they then form chromatin fiber to form metaphase chromosome
What grooves open up when the DNA wraps around the nucleosome?
Minor groove
What makes the DNA relaxed?
The longer the linker DNA
What is found near the centromere?
Heterochromatin
What happens to telomeres with age?
Shorten
What is it called when the centromere is in the centre of the chromosome?
Metacentric chromosome
Where is the centromere in a submetacentric chromosome?
Top of the chromosome, makes a smaller short arm than long arm
What is it called when the centromere is at the very top of the chromosomes?
Acrocentric
What are satellites?
Secondary constriction site with small chromosomal segment
What does a secondary constriction site on a chromosome act as?
Acts as a nuclear organisation region (NOR)
What chromosomes do we find Satellites on?
13, 14, 15, 21 and 22
What is the stain used to distinguish between similar chromosomes?
Giemsa staining (g-banding)
When using giemsa staining what regions stain darker and why?
Heterochromatic regions (AT-rich) and are gene poor
When using giemsa staining why are some bands stained light?
GC rich and more active
What stops the protein from holding DNA together before giemsa can stain?
Trypsin
What is the international system of human cytogenetic nomenclature (ISCN)?
Database showing all the chromosome bands allowing us to locate specific regions and find abnormalities
Why do we have the international system of human cytogenetic nomenclature (ISCN)?
Good for accurate and consistent description of genomic changes as identified by karyotyping
What is the short arm labelled as?
XP
What is the king arm labelled as?
XQ
How do you accurately locate positions for specific genes?
FISH
How do you do fish?
Isolate metaphase chromosomes and spread in glass slide.
Meanwhile clone a gene of interest and make a DNA probe by adding it to a plasmid - fluorescent it label this.
Then add dye to the DNA (direct labelling) or add biotin then later the dye by adding streptavidin with dye on it which will react with biotin (indirect labelling).
Denature chromosomes and probe and the gene of interest will hybridise to the chromosome. You can now see the gene of interests location
Can you do FISH for more than one gene?
Yes - multicolour FIsH
How does digital karyotyping work?
Uses short sequence tags taken from specific genomic loci ti provide a quantitative and high-resolution view of copy number changes in a genome wide scale
How can Digital karyotyping help you see abnormalities and how does it work?
Genome fragmented into small pieces and labelled
Once labelled it’s hybridised too an array of DNA probes which span the wholes gene
A computer will then see the amount of fluorescence and you can see if there is any abnormalities
What is polyploidy?
One or more additional chromosomes sets e.g triploidy is 3 copies of the haploid chromosome
What is aneuploidy?
Loss or gain of genetic material from a single chromosome
In aneuploidy what is a monosomy?
Loss of one chromosome
In aneuploidy what is a trisomy?
Gain of one chromosome
What is the most common cause of aneuploidy?
Nondisjunction in meiosis
What are some structural abnormalities?
Deletions, duplications, inversions and translocations
What is nondisjunction?
Failure of the chromosomes to unjoin resulting in them going into the same daughter cells
What happens if nondisjunction happens in the first division?
One daughter cell gets both sets of chromosomes
What happens if nondisjunction happens in the 2nd meitotic division?
The Nondisjunction would leas ti one daughter cell having 2 chromosomes and one having non. However the 3rd and 4th could be normal depending on if only one daughter cell suffered the nondisjunction
What is Turner syndrome?
One copy of X chromosomes due to aneuploidy
What is Klinefelter syndrome?
Males have one extra X chromosome (XXY)
What happens in trisomy X
Females have an extra X chromosomes (XXX)
And makes get an extra y (XYY).
What is seen in spontaneous abortions?
Every possible trisomy
Example of trisomy?
Down syndrome
Examples of lethal trisomy’s?
Patau syndrome and Edward syndrome
What are the 4 ways chromosomes can be rearranged ti cause structural abnormalities?
Duplication, deletion, inversion and translocation
What happens in a duplication?
Prices of genome duplicated
What happens in a deletion?
Chromosome fragment lost
What happens in inversion?
DNA fragment reversed
What happens in translocation?
Chromosome fragment moved to different strand
What is reciprocal translocation?
Two DBA fragments have changed their position
What are Consequences if rearranged chromosomes?
Change in gene dosage in deletion and duplication leading to unbalanced genes
Why are inversions easier ti tolerate than duplication and deletions?
The gene dosage remains the same so no unbalanced chromosomes
What is a Paracentric inversion?
Centromeres are parallel which conserves location if centromeres
What does pericentric mean with inversion?
The centromeres aren’t parallel which changes the order of genes and the location of centromeres
This affects meiosis and next generation
Where are low copy repeats found and what does non-allergic homologous recombination (NAHR) between two LCR’s lead ti?
These are interspersed throughout the genome and a NAHR between 2 LCRs can lead ti deletion or tandem duplications of the flanking area of the genome
Can you get crossover between homologous but non-alleic LCR?
Yes
What are low copy repeats?
DNA sequences which appear the same in lots of different places in the genome
In a duplication how many copies of a gene will you get?
3
In a deletion how many copies of a gene is there?
1 copy deleted in one allele and one normal in the other allele
Where are LCR’s found?
In hotspots
What are balanced reciprocal translocations?
When a gene translocated with another gene and this doesn’t create a duplication or a deletion.
What happens to carriers of balanced reciprocal translocations?
They are healthy and fertile but can transmit the unbalanced form to offspring.
What would happen if the 4 chromosome reciprocal translocation structure was split adjacent 2 (vertically)?
It would be unbalanced
What would happen to the 4 chromosomal structure reciprocal translocation is it was split horizontally (adjacent)?
Unbalanced
What would happen if the 4 chromosomal reciprocal translocation structure was split alternatively?
It would be balanced
What determines whether or not reciprocal translocations would lead to unbalanced or balanced segregation?
Depends of how they are segregated
What are robertsonian translocations?
Centric fusion of two Acrocentric chromosomes
How do robertsonian translocations work?
The long arm fuses with another arm of a different chromosomes when the DNA breaks.
What arm has more genes?
Long arm.
In robertsonian translocation what product is lost and why?
Short arm as there is no essential genea
Is the robertsonian translocation balanced?
Yes
What disease is caused by robertsonian translocation?
Down syndrome
What is an example of a reciprocal translocation and how is it done and what does it cause?
Philadelphian chromosome where long arm of chromosome 9 fuses with chromosome 22. This can cause leukaemia.
How do you diagnose the Philadelphia chromosome?
FISH
What are copy number variations?
Small variations only seen through genome sequencing and causes human variation
Are CNV’s lethal or neutral?
Both
Do duplications of CNV’s go in tandem?
Yes
What are the two CNV groups?
Long and short repeats
Example of segmental duplication and evolution: AMY-1
People adapted to get more energy from starch food
What do fixed segmental duplications generate?
Redundant genes free to evolve and can generate de novo rearrangements
What do karyotypes need to evolve?
They need to be fixed and passed through the germ line through meiosis
Do chromosomes from different species have the same ancesterol chromosome?
Yea
If something is described as being syntenic what does this mean?
A situation in which genes are arranged in similar blocks in different species and the conserved order of genes between species
When looking at blocks how can you tell how close the evolution is?
The smaller the number of blocks
When looking at syntenic blocks between 2 species what does more conserved syntenic blocks mean?
There is more evolutionary rearrangement and they are close in evolution
