genome architeecture Flashcards
what is karyotype?
A karyotype is an individual’s complete set of chromosomes
/ number of chromosomes
why are archaea hard to culture?
they are very elusive, only found in specific envriornents
through enivronmental DNA equencing (e.g. samplin sea water) we know they exisst!
what are actin, histones and ubiquitin exampes of?
eukarytofi defining proteins
> actually derived from archeal lineage!
describe the chromosome structurr of pro and euk?
pro- 90% circular chromosomes of essential and some extra junk/nonessential in the mobilome which drives HGT/evolutionary processes, HAPLOID
euk- variable numbers of linear chromosome pairs, some circles in mitch+chloro, DIPLOID/TRIPLOID/STERILE - so they are meotically active
how does karyotype and viability of cells relate?
they dont!
in a eukaryote, your number of chromosome pairs isn’t vital for cell function but helps with species identification + fertility of offspring
changes in karyotype help to drive evolution
do eukarytoes have mobilome?
yes! often made up of repear seqeuneces (satellite dna) and also long non coding sequences (LINE+SINE)
also introns, UTR, regulatory regions so the protein coding part of genome is quite small
describe he average euk gene
2600 bp mRNA 66500bp gene length 145bp exon, 8 exons in a gene 10-800 kbp intron size 400 aa in a protein
how are prokaryotic genes organised?
into OPERONS which are clusters of genes encoding enzymes in the asme metabolic pathway
> transcribed as a polycistronic mRNA molecule so multiple ORF present/ encodes multiple proteins on 1 mRNA molecule
how do prokaryotic genes comparmentalise?
they form the nucleoid which is DNA loosely interacting with Nucleoid Associated Proteins that bind very loosely to DNA
nucleoid can form macrodomains too which can help with superociling
how are eukaryotic genes compartmentalised?
wrapped up in histone proteins and form octamer/nucleosome which is the functional repeat unit of CHROMATIN
after mitosis, the chromatin may not fully decondense and instead form topologically associated domains
what is the C-value paradox?
the amount of DNA/genome size is not proportional to the the number of genes produced
> e.g a lungfish and pufferfish have very large genomes but are simple organisms
this could be due to the large number of repetitive DNA sequences present in their genomes
what does the majority of human genome consist of? A protein coding DNA B repetitive DNA C introns D tRNA
OPTION B
only 1.2% of human genome is protein coding!
majority is repetitive sequence ~ 45%
how do tandem and interspersed repeats differ?
they are both forms of repetitive DNA but tandem is shorter repeats in clusters whilst interspersed are longer and more spaced out
when does most LINE1 transposition happen?
during early embronyic develepoment
> there are around only 100 active LINE1 elements, the rest of them,lines 2 and 3 are inactive due to a lack of DNA on the 5’ end
where are the majority of human SINEs found? where do they derive from?
2/3 of SINEs found in introns (Alu main)
derive from tRNA and also 7SL rRNA
transpose by stealing Line1 rt/endonuclease and use copy/paste
what is a gene family
in human genes, these are genes that derive from a common ancestor like the keratins or olfactory recepeptors and Hb gene family
SO THEY ARE HOMOLOGUES
WHAT IS DIFFERENCE BETWEEN ORTHOLOGUE AND PARALOGUE?
ortho - arise from species divergence
para - arise from gene duplication / same genome
describe exon shuffling
a way that new genes can form/ gene families can expand
its when 2 exons from different genes will fuse together
This is one way to create a de novo gene
if a duplicated gene aqquires a new function this is called…?
neofunctionalism!!
can you describe an example of neofunctionalisation?
the antifreeze glycoprotein gene is likley to have derived from the trypsinogen gene (protease) which has a triple aa repeat before the 2nd exon
likely the gene was duplicated, expansion of triple repeat and then deletion of the other exons
what is de novo generation
its another way to increase size of gene family by having a non-coding DNA becoming coding DNA
> needs to aqquire an ORF and a function
which of these are examples of DNA fossils/evolutionary relics in humans? A dna transposon B LINE C SINE D pseudogene E reverse transcriptase
DNA transpons, pseudogenes and LINE2+3 are fossils, they are inactive
acquired mutations so unable to produce a functional protein/ carry out their function
100 Line1 elements and some SINE like Alu are active
what types of mutations would cause haplosufficeny and haplo insufficenty?
recessive LOF - haplosufficency, there is still enough gene product made for a normal phenotype
dominant LOF - haploinsuffiency, even a loss of 1 allele will result in a abnormal phenotype // these genes are indispensible
how does a duplicated and unitary psedogene differ?
duplicated- from duplication/ non functionalisation
unitary - just a gene that has aqquired null mutationss
both can be unprocessed(DNA derived) or processed (mRNA derived)
what is an ultracocnerved element?
highly conserved regions of the genome (over 200bp) that are conserved between different species
