genome architeecture

Question 1

what is karyotype?

Answer 1

A karyotype is an individual’s complete set of chromosomes

/ number of chromosomes

Question 2

why are archaea hard to culture?

Answer 2

they are very elusive, only found in specific envriornents

through enivronmental DNA equencing (e.g. samplin sea water) we know they exisst!

Question 3

what are actin, histones and ubiquitin exampes of?

Answer 3

eukarytofi defining proteins

> actually derived from archeal lineage!

Question 4

describe the chromosome structurr of pro and euk?

Answer 4

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

Question 5

how does karyotype and viability of cells relate?

Answer 5

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

Question 6

do eukarytoes have mobilome?

Answer 6

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

Question 7

describe he average euk gene

Answer 7

2600 bp mRNA
66500bp gene length
145bp exon, 8 exons in a gene
10-800 kbp intron size
400 aa in a protein

Question 8

how are prokaryotic genes organised?

Answer 8

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

Question 9

how do prokaryotic genes comparmentalise?

Answer 9

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

Question 10

how are eukaryotic genes compartmentalised?

Answer 10

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

Question 11

what is the C-value paradox?

Answer 11

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

Question 12

what does the majority of human genome consist of?
A protein coding DNA
B repetitive DNA
C introns
D tRNA

Answer 12

OPTION B
only 1.2% of human genome is protein coding!

majority is repetitive sequence ~ 45%

Question 13

how do tandem and interspersed repeats differ?

Answer 13

they are both forms of repetitive DNA but tandem is shorter repeats in clusters whilst interspersed are longer and more spaced out

Question 14

when does most LINE1 transposition happen?

Answer 14

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

Question 15

where are the majority of human SINEs found? where do they derive from?

Answer 15

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

Question 16

what is a gene family

Answer 16

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

Question 17

WHAT IS DIFFERENCE BETWEEN ORTHOLOGUE AND PARALOGUE?

Answer 17

ortho - arise from species divergence

para - arise from gene duplication / same genome

Question 18

describe exon shuffling

Answer 18

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

Question 19

if a duplicated gene aqquires a new function this is called…?

Answer 19

neofunctionalism!!

Question 20

can you describe an example of neofunctionalisation?

Answer 20

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

Question 21

what is de novo generation

Answer 21

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

Question 22

which of these are examples of DNA fossils/evolutionary relics in humans?
A dna transposon
B LINE
C SINE
D pseudogene
E reverse transcriptase

Answer 22

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

Question 23

what types of mutations would cause haplosufficeny and haplo insufficenty?

Answer 23

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

Question 24

how does a duplicated and unitary psedogene differ?

Answer 24

duplicated- from duplication/ non functionalisation
unitary - just a gene that has aqquired null mutationss

both can be unprocessed(DNA derived) or processed (mRNA derived)

Question 25

what is an ultracocnerved element?

Answer 25

highly conserved regions of the genome (over 200bp) that are conserved between different species