chromosomes week 8 Flashcards
what is euchromatin
- open structure
- active genes
- the leg bits of chromosomes
what is heterochromatin
- condensed structure
- active genes
- at ends and centre of chromosomes
what are telomeres
the bits at the end of chromosomes
what direction is DNA synthesised
5’ to 3’
what does DNA polymerase need to initiate DNA synthesis
RNA primer
what happens to the lagging strand in DNA replication
it is synthesised in fragments (Okazaki fragments) which are stitched together by ligase
why do telomeres get shorter as eukaryotes age
in the lagging strand the removal of the RNA primer causes a gap which is filled with repeats and is resynthisised by telomerase
- but telomerase is only expressed in certain cell types which is why telomeres shorten
what is the centromere
- site of kinetochore which is the protein complex that binds to microtubules
what happens in S phase
DNA replication occurs
what percentage of our DNA is protein coding
2%
what are some extragenic sequences (non-coding)
- tandomly repeated DNA sequences (satellite DNA and minisatellite DNA)
- highly repeated interspersed DNA sequences (SINEs - short interspersed nuclear elements and LINEs - long)
what is a chromatin
DNA packaged with histone proteins forms chromatin
what charge do histone proteins have
positive charge
what are the unit packages in chromatins called
nucleosomes
what is at the core of the nucleosome
eight histone proteins collectively called octameric histone and DNA gets wrapped round this (146bp wrapped 1.8 turns)
what are the histone protein types in the octameric histone
- histone H2A
- histone H2B
- histone 3
- histone 4
so two of each make the core
what does histone 1 do
binds to the base of the nucleosome and helps fix the DNA in place
what does the wrapping of nucleosomes form
- solenoid strucure
- about 6 nucleosomes per turn
so what is each bit of the condensed chromatin structure
- nucleosome
- chromatin fibre
- fibre-scaffold complex
- chromosome
what is the purpose of packaging DNA
- negatively charged DNA neutralised by positive charged histone proteins
- DNA takes up less space
- inactive DNA can be folded into inaccessible locations until required
- inactive chromatin characterised by specific histone modification (e.g. methylation)
what is the shorter arm on a chromosome called
p or petite arm
what is the longer arm on a chromosome called
q arm
what is a metacentric chromosome
where centromere is close to being in the middle
what is a submetacentric chromosome
where centromere is displaced from centre
what is an acrocentric chromosome
the centromere is so far displaced that the petite arm contains no functional DNA
what is a karyotype
A karyotype is a preparation of the complete set of metaphase chromosomes sorted by length, centromere location and other features.
what is chromosome analysis
- blood taken
- remove red cells (no nucleus)
- culture white cells
- incubate
- colchicine added (mitotic inhibitor)
- separate off white cells
- saline added
- stain
- photograph
what is fluorescent in situ hybridisation (FISH)
a more detailed way of looking at specific chromosome sequences
sequence of interest labelled with fluorescent dye
what is meiosis
- cell division in germ cells
- diploid cells (ovaries/testes) divide to form haploid cells
- chromosome are passed on as re-arranged (recombined) copies
what is oogenesis
process of egg formation
what is spermatogenesis
process of sperm formation
when does gametogenesis happen in males and females
females - early embryonic life cells arrive at meiosis 1 and then at puberty cells go through meiosis 2
males - puberty
what is X inactivation
random inactivation of one X chromosome in females
what are the different types of chromosomal abnormalities
- numerical (wrong number)
- structural (scale rearrangement that’s apparent from karyotype)
- mutational (smaller scale - can range from small deletions to point mutations)
what is the most common type of abnormality in first trimester miscarriages
trisomy (think tri=trimester)
what is trisomy mutation
where there are three copies of a chromosome when there should only be two (so in total 47 chromosomes)
what is monosomy X
there is only a single sex chromosome (so 45 chromosomes total)
- first trimester miscarriages
what is triploidy mutation
where there are three whole copies of chromosomes (so 69 chromosomes)
- first trimester miscarriages
what is tetraploidy mutation
there are four copies of chromosomes (so 92 total)
- first trimester miscarriages
what are common chromosomal abnormalities in lovelorn infants
- trisomy 13
- trisomy 18
- trisomy 21 (down’s)
- 45 X
- 47 XXY
- 47 XYY
what is trisomy 13
patua’s syndrome
- 47 XX
what is trisomy 18
Edward’s syndrome
- 47 XY
what is trisomy 21
Down’s syndrome
- 47 XX
what is 47 XXY
Klinefelter
what is monosomy 45X
turner
what is an autosome
non-sex chromosome
are sex chromosome abnormalities often from maternal or paternal origin
paternal
- 45X
are autosomal abnormalities more often from maternal or paternal origin
maternal
- trisomy 21
down’s syndrome
- trisomy 21
- 1 in 650
- IQ can be less than 50
- Alzheimer’s later in life
- facial dysmorphologies
patua syndrome
- trisomy 13
- 1 in 5000
- multiple dysmorphic features and mental retardation
- few survive beyond first year
Edward’s syndrome
- trisomy 18
- 1 in 3000
- severe developmental problems, most patients die within first year, many within first month
turner syndrome
- 45 X
- 1 in 5000 to 1 in 10,000 (liveborn)
- incidence at conception much greater but 97% result in spontaneous loss
- female of short stature and infertile
- neck webbing and wide spaced nipples
- intelligence and lifespan normal
klinefelter syndrome
- 47 XXY
- 1 in 1000
- tall stature and long limbs
- male but infertile
- small testes
- 50% gynaecomastia (man boobs)
- mild learning difficulties
what are the different types of structural abnormalities
- balanced or unbalanced rearrangements
- translocations (reciprocal or robertsonian)
- deletions
- insertions
- inversions
what is a translocation mutation
where material is exchanged between two chromosomes
what are the two types of translocation mutations
- reciprocal - involving breaks in two chromosomes, these broken segments swap and so info exchanged
- robertsonian - fusion of two Acrocentric chromosomes
when is a reciprocal translocation said to be unbalanced
when there is additional DNA or DNA mission
- so i.e. more from dad than mum when it should be equal
- this can result in partial trisomy and partial monosomy in the same cell because only one and a half chromosomes from mum and two and a half from dad
what happens in a robertsonian translocation
- two Acrocentric chromosomes fuse
- loss of short arms (which have no coding DNA anyway)
- this can result in trisomy/monosomy
who has a predisposition to having children with Down’s syndrome
individual with robertsonian translocation
what is paracentric inversion
inversion of bit of chromosomal arm
what is pericentric inversion
inversion of centromere
what are some types of genetic mutations
- non-coding
- coding
- silent - CGA (Arg) to CGC (Arg)
- missense - CGA (Arg) to GGA (Gly)
- nonsense - CGA (Arg) to TGA (stop)
- frameshift (deletion/insertion)
what is Cys64Arg
a cystine changed to an arginine at position 64
what is M252X
methane 252 and X means stop codon
what is 1294del40
amino acid 1294 deletion of 40
what is 662-42C>T
the closest ending exon position is 662 and so 662-42 because it is 42 nucleotides before this
what is IVS2+12insG
intervening sequence 2 so that will be the second intron in the +12 position within that intervening sequence and we have insertion of a G
what techniques can you use to detect mutations
- PCR
- gel electrophoresis
- restriction fragment length polymorphism (RFLP)
- amplification refractory mutation system (ARMS)
- DNA sequencing
what do you need for PCR
- sequence information
- oligonucleotide primers
- DNA
- nucleotides
- thermoresistant DNA polymerase
what are the steps in PCR
- denature 93-95 degrees
- anneal (heat then cool) 50-70 degrees
- extend using DNA polymerase to add nucleotides
70-75 degrees
what is gel electrophoresis
- separating DNA fragments by size by applying an electric field
- you do this after PCR
what is amplification refractory mutation system (ARMS)
- type of PCR
- if you use normal primer with normal nucleotide then DNA will be amplified with the help of a constitutive primer
- if you use mutant primer with normal nucleotide no DNA amplification (e.g. A-G not work)
- mutant primer with mutant nucleotide will work (e.g. A-T works)
what are restriction endonucleases
- enzymes from bacterial cells
- protective mechanism
- degrade DNA of invading viruses
- recognise specific DNA sequences
- usually recognises 4-8bp
- always cuts DNA at same site
what is RFLP analysis
so restriction enzyme can recognise and cut normal DNA but it cannot recognise mutant DNA
- simple and cheap
what is DNA sequencing
- chain termination method
- use of dideoxynucleotides
- there is a H group at the three prime position of the carbon ring instead of OH
- expensive