Genome Anatomy Flashcards
what is genome anatomy?
genome anatomy is how the genome is organised and how it functions
how is almost all heritable information written and how is it organised?
in DNA sequences
3x10^9 nucleotides from father and mother and there is 750 megabytes of uncompressed date
where is other information found?
in chromatin features such as in epigenetics
where do data storage errors arise from?
genetic pathologies (genome goes wrong and genetic disease results) and this is why error correction methods (ensure that the DNA is copied correctly) are important
what is epigenetics?
changes in the genome that influence the genome and are not included in the DNA code
what is the difference between DNA and RNA?
the presence and absence of the hydroyxl group on the second carbon atom
what is the effect of the chemical groups on the carbon atoms?
this changes the stability of the molecule - RNA is less stable as the breakage is faster in the phosphodiester bond (intramolecular nucleophilic attack)
which direction are DNA sequences written in?
5’-3’ direction which is the direction that DNA and RNA are synthesised in
what determines the sequences?
the order of purine and pyrimidine bases sticking out the side of the chain
at which end do new nucleotides get added?
3’ end
how are strands arranged and how are they matched?
they are antiparallel and matched by base pairing
Abb(ns) nt and bp are what?
these are shorthand loosely interchangeable terms for DNA sequences
how is shorthand usually written?
with the sense strands (which can also relate to antisense as well)
in DNA replication what happens on the antisense (lagging) strand?
Okazaki fragments are found
how do they replicate?
they unwind the structure using a helicase and then synthesise a complimentary daughter strand
how long is DNA in one chromosome?
around 9 cm
what are chromosomes?
they are the packages in which the DNA is organised as it must fit into the nucleus
how many nucleotides are wrapped around histone proteins?
around 200
what order is standard karyotype?
largest to smallest
what does diploidy refer to?
diploidy is the human genome and means that we get one gene from mother and one from father
what is the centromere?
the centromere is where the chromosomes are attached to the spindle during cell division
what is found at the end of the chromosomes?
at the end of each arm of the chromosome (p being short and q long) there is a telomere - Ptel and Qtel are different
what is the telomeric repeat sequence?
TTAGGG and includes specialised replication machinery with telomerase and TERT
what happens in somatic cell division?
the telomeres shorter and therefore telomerase is inactive in somatic cells - there is a finite number of cell divisions until senescence known as ageing. Telomerase is only active in germ cells
what happens in a cancerous mechanism?
TERT reactivates
how does the end of the chromosome work?
it is single stranded and loops back round in a complex structure to stabilise the chromosome
in the chromosome ideogram how can abnormal chromosomes be identified?
stretching of chromosomes determines the visibility of bands and therefore when there are abnormal chromosomes they are shown up in bands
what does 2n=46 mean
the chromosome complement is diploid therefore n = 23 and 2n = 46.
what does haploinsufficiency mean?
haploinsufficiency is when 2 copies are needed and one is insufficient - dosage is important in these genes - the exception is the X chromosome
what are psudomonal regions?
information that is shared with the X and the Y regions
why are males hemizygous?
they only have one X chromsome and therefore only have one copy of many genes that are only found on the X chromosome
what happens to chromosomes after replication?
each chromosome becomes sister chromatids - 4n
what is the Y chromosome composed of compared to X?
the Y has the pseudomonal regions and then mostly heterochromatin, the X has the pseudomonal regions and the X unique genes
how much of the human genome is non coding?
> 90% - short and long non coding genes
how many protein coding genes are there?
around 20,000 with an average size of 50-100kb and average mRNA of 2kb
what are three different sequences classes and examples?
single copy sequences such as genes
repetitive sequences such as Alu repeats - interspersed repeats
satellite DNA such as heterochromatin and large blocks of repetitive sequence
describe mitochondrial genomes?
circular, not linear: this is an endosymbiotic remnant
cytoplasmic not nuclear due to maternal inheritance from oocyte
what do the genes in mitochondria do?
they encode for mitochondrial roles such as components of oxidative phosphorylation
how are mitochondrial pathologies inherited?
maternally
what is a gene?
it is a functional unit of DNA
what is the term used to describe the copying of DNA into RNA?
transcription. Translation is when RNA is turned into a protein.
what are the components of genes?
introns, exons and regulatory sequences (promtores, enhancers and locus control regions)
where is the DNA transported to after splicing?
after splicing the DNA is transported into the cytoplasm
which regions gets removed in splicing?
the intronic region
what is the term for when exons are spliced together in different orders or creating different proteins?
alternative splicing
what happens to the genome through evolution?
duplication and divergence
what does duplication produce?
two random arrangements of genes
what do mutations lead to?
mutations over millions of years lead to two random arrangements of genes diverging and producing different functions
what are pseudogenes?
they look the same as normal genes but they contain errors and are therefore non functional
what are processed genes?
intronless copies of other genes that are usually remote from parent genes. They occur via reverse transcription and reintegration. They will occasional remain functional but most are non functional
what are the classifications of repetitive DNA?
interspersed repeats (scattered around the genome) and satellite DNA
where is satellite DNA found?
satellite DNA is found with large blocks at the centromeres and heterochromatin chromosomal regions
what are simple tandemly repeated sequences?
there are many types - centromere repeats and chromosome specific
what does polymorphic relate to?
polymorphic means that the blocks of satellite DNA may vary in size
what type of satellite DNA is found at centromeres?
alphoid DNA - 171bp repeat unit. It is required for the assembly of the centromere and making it unique
what type of variation does alphoid DNA show?
it shows chromosome specific sequence variation
what is an alu repeat?
it i a SINE - short interspersed nuclear element that has a role in the generation of molecular pathology
how are alu repeats dispersed?
retrotransposition
