L2: Genome Diversity and the organisation of DNA in chromsosomes

Question 1

Viral Genome (possible characteristics x5, approx. size range)

Answer 1

• 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)

Question 2

C-Value paradox - why might a genome be particularly large in eukaryotes?

Answer 2

• Genome size does NOT consistently correlate with organism complexity
• Genomes often have transposable elements, which can have many repeats, that increase genome size

Question 3

Intergenic regions (details, classification, contrast in euk vs bacteria)

Answer 3

• 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)

Question 4

Bacterial Chromosomes

Answer 4

• 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

Question 5

Lyme Disease (exception to typical bacterial chromosome)

Answer 5

• Linear
• One large ds DNA, 0.91 Mb
• 12 linear, 9 circular extrachromosomal element/plasmid (total 0.61 Mb)

Question 6

Organization of bacterial chr.s

Answer 6

• 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)

Question 7

Supercoiling in nucleoid

Answer 7

• ~400 independent negatively supercoiled looped domains
• each of ~10 Kb
• Generated by topoisomerases

Question 8

Organization of eukaryotic genomes

Answer 8

• Fixed no. Chr.s per cell
• Mostly diploid w/ haploid gametes
• 1 linear dsDNA molecule
• DNA complexed w/ proteins into chromatin

Question 9

Structure of nucleosome, about the histones

Answer 9

• 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

Question 10

Core histone ‘tails’

Answer 10

• 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

Question 11

Variant histones

Answer 11

• Can be incorporated into nucleosomes usually in case of DNA damage
• e.g. CENP-A (centromere protein-A), variant of H3

Question 12

10nm fiber

Answer 12

• Beads on a string
• Least compacted version (interphase)

Question 13

30nm fiber

Answer 13

• 10nm fiber wrapped up in solenoid fashion
• 50x more compact
• H1 binds to nucleosome, facilitating formation of 30nm fiber

Question 14

Further compaction

Answer 14

• 30nm chromatin fiber folded into looped domains via anchoring to central non-histone protein chr. scaffold
• Alternatively, packed w/ 10nm without 30nm IM

Question 15

Euchromatin and heterochromatin at interphase

Answer 15

• In interphase, not actively being transcribed, euchromatin, variation in compaction
• Both euchromatin (10nm) and heterochromatin (more compact)
• Histone modifications govern E vs H

Question 16

Heterochromatin rich regions

Answer 16

• Telomeres
• DNA at or near centromere

Rich in highly repetitive DNA sequences

Question 17

Histone modification (pairs of enzymes)

Answer 17

• Histone acetyltransferase (HATs) add acetyl to lysine side chains -> H (HDACs remove)
• Histone methyltransferases (HMTs) add methyl grps to lysine, arginine side chains -> E (histone demethylases reverse)
• Phosphates added by kinases, removed by phosphatases
• Ubiquitin added by chain of enzymatic rxns. removed by deubiquitinating enzyme

Question 18

Key chromosome elements + their functions

Answer 18

• ori:
  origin of replication. Sequences near ori determine distribution of replicated chr.s to daughter cells
• ter:
  specifies replication termination
• Centromeres (direct chr. segregation)
• Telomeres (stabilize Chr. ends)

Question 19

Centromeres - what are they made of, how are they inherited?

Answer 19

• H’in region
• most species have 1 per chr.
• inherited epigenetically, marked by H3 variant histone (CENP-A)
• *kinetochore

Question 20

Mitochondrial, chloroplasts genome (type of DNA and function)

Answer 20

• Circular, ds
• Code for proteins involved in their own functions