L2: Genome Diversity and the organisation of DNA in chromsosomes Flashcards
1
Q
Viral Genome (possible characteristics x5, approx. size range)
A
- Relatively small but significant variation in size (5000nt to 200k bp)
- DNA or RNA
- ss or dsDNA
- Circular or linear
- Genes can overlap
- in some cases, genome can be split across multiple molecules (e.g. rotavirus)
2
Q
C-Value paradox - why might a genome be particularly large in eukaryotes?
A
- Genome size does NOT consistently correlate with organism complexity
- Genomes often have transposable elements, which can have many repeats, that increase genome size
3
Q
Intergenic regions (details, classification, contrast in euk vs bacteria)
A
- Don’t include any functional DNA
- historically called ‘junk’
- A large proportion of it is transposable elements which can copy themselves to different locations in the genome
- Includes DNA coding for RNA species that aren’t translated
- Classified by abundance
- Prok: mostly unique sequence, coding DNA
- Euk: mix of unique and repetitive (~50:50)
4
Q
Bacterial Chromosomes
A
- Typically single, circular dsDNA e.g. E.coli, 4.6 Mb
- Chromosomal DNA is localized to the nucleoid
- May contain extrachromosomal pieces (plasmids) -> nonessential BUT potentially advantageous
5
Q
Lyme Disease (exception to typical bacterial chromosome)
A
- Linear
- One large ds DNA, 0.91 Mb
- 12 linear, 9 circular extrachromosomal element/plasmid (total 0.61 Mb)
6
Q
Organization of bacterial chr.s
A
- Compacted into nucleoid
- Binding small positively charged proteins along DNA, counteracting negative charge
- NAPS (bacterial nucleoid associated proteins) bend DNA and hold loops together…
- e.g. Integration host factor (IHF) bends DNA, also FIS, HU, H-NS, SMC (structural maint. of chr.s)
7
Q
Supercoiling in nucleoid
A
- ~400 independent negatively supercoiled looped domains
- each of ~10 Kb
- Generated by topoisomerases
8
Q
Organization of eukaryotic genomes
A
- Fixed no. Chr.s per cell
- Mostly diploid w/ haploid gametes
- 1 linear dsDNA molecule
- DNA complexed w/ proteins into chromatin
9
Q
Structure of nucleosome, about the histones
A
- Histones pack euk. DNA into nucleosomes
- 4 conserved histones, rich in + lysine, arginine, counteract - charge of phosphate on DNA. Charges stabilise histone-DNA interaction
- Wraps anticlockwise 1.75x around octamer; 2xH3-H4 dimers associate w/ DNA, then join 2xH2A-H2B dimers
- Removing histone leaves negative supercoiling
10
Q
Core histone ‘tails’
A
- Each has an N-terminal tail, extends out of nucleosome between the DNA coils
- Interact w/ other nucleosomes to further compact DNA
- Can be chemically modified
11
Q
Variant histones
A
- Can be incorporated into nucleosomes usually in case of DNA damage
- e.g. CENP-A (centromere protein-A), variant of H3
12
Q
10nm fiber
A
- Beads on a string
- Least compacted version (interphase)
13
Q
30nm fiber
A
- 10nm fiber wrapped up in solenoid fashion
- 50x more compact
- H1 binds to nucleosome, facilitating formation of 30nm fiber
14
Q
Further compaction
A
- 30nm chromatin fiber folded into looped domains via anchoring to central non-histone protein chr. scaffold
- Alternatively, packed w/ 10nm without 30nm IM
15
Q
Euchromatin and heterochromatin at interphase
A
- In interphase, not actively being transcribed, euchromatin, variation in compaction
- Both euchromatin (10nm) and heterochromatin (more compact)
- Histone modifications govern E vs H
