BSCI222 Chromosome Structure & Transposable Elements

HU protein

prokaryotic

binds to the DNA and each other for bending of DNA and the formation of loops (similar to histones in eukaryotes)

Supercoiling

the spinning of the circular DNA after breaking it, to create bends, making the DNA shorter and further compacted (carried out by DNA Gyrase)

Positive supercoiling

turning the DNA in the same direction as the DNA

Negative supercoiling

turning the DNA in the different direction as the DNA (“unwinding” makes opening and transcription easier)

Chromatin

eukaryotic

complex of DNA and proteins

chromosomes are made of condensed chromatin

Proteins involved in chromatin structure

eukaryotic

histones

non-histone chromosomal proteins

Histones

eurkaryotic

positively charged

DNA wrapped around 8 histone proteins to form a nucleosome

H1 histone helps pull the nucleosomes together to further compact (one H1 per core nucleosome)

H2a H2b H3 H4 (2 of each forms a nucleosome)

Condensin

eukaryotic

binds same DNA to form loops

when chromosomes decondense, they fall into territories rather than a mixture of random places

Euchromatin

eukaryotic

chromatin packing

less packed

undergoes process of normal condensation and decondensation (decondenses during interphase into territories)

light in a scan

easier for transcription

Heterochromatin

eukaryotic

chromatin packing

more packed

stays condensed throughout the cycle

dark in a scan

compacted during interphase

Histone acetylation

eukaryotic

adds acetyl group, making histones LESS positive —> DNA binds less tightly

open chromatin structure

Histone deacetylation

eukaryotic

removes acetyl group, making histones more positive —> DNA binds more tightly

compacted chromatin structure

Eukaryotic Origin of replication

part of eukaryotic chromosome

allows replication of a DNA in S phase

specific sequence where DNA synthesis starts

multiple ones on each chromosome

Centromere

part of eukaryotic chromosome

allows segregation in meiosis and mitosis

site of kinetochore - spindle microtubule attachment

holds sister chromatids together

constricted due to satellite DNA packed as heterochromatin

lower eukaryote: specific centromere sequence

higher eukaryote: more complex sequence -satellite repeats, no genes

instead of H3, has CENP-A histone

pinched structure for rmicrotubule attachment

Telomere

part of eukaryotic chromosome

protects ends of linear DNA

repeats at ends needed for DNA replication problem of 5’ ends (shorter 5’ ends of newly replicated strands — on the lagging strand)

telomerase protein expands repeats to solve the problem^

shelterin protein and folding over of DNA protects ends from degradation & triggering repair enzymes

unique DNA

~50%

includes genes and introns

highly repetitive DNA

short sequenes tandemly repeated many times

satellite

minisatellite

microsatellite

moderately repetitive DNA

functional genes needed in large numbers- rRNA, tRNA, often tandem arrays in places around genome

transposable elements

satellite DNA

5-150bp

forms chunks found around CENTROMERES

minisatellites

10-60bp

scattered in smaller chunks over GENOME

microsatellites

1-6bp repeated 10-100 times

scattered over GENOME

variable number of repeats due to mistake sin replication or repair

useful for CODIS- Forensic DNA fingerprint 13 STR

if in genes- variable # of aa: Huntington’s & Fragile X

DNA transposons

cuts & pastes

transposable element

transposase- enzyme that cuts and pastes

bacteria IS (insertion sequences) elements and transposable elements (captured gene)

corn (maize) - Ac element hops in and out

Drosophila P element

Retroelements

copies & pastes

uses RNA intermediate

related to retrovirus

• reverse transcriptase (RT) copies RNA virus to DNA, which inserts in DNA

• Transcription forms RNA copy

Types of retroelements

Endogenous retroviruses (ERV)

LINE

SINE

ERV

defective retroviruses 8-9 Kbp

has RT that allows to make RNA transcript into a DNA that gets inserted elsewhere in genome

LINE

has no terminal repeat, 6-8 Kbp

has RT that allows to make RNA transcript into a DNA that gets inserted elsewhere in genome

SINE

example: Alu element (short 80-630 bp) related to 7S signal particle

NO RT gene, relies on LINE or ERV’s RT to move

Genetic effects of tranposons

can disrupt a gene when hops into/near it

changing regulation of gene

^can reverse potentially when it hops out

creates sites for recombination of nonhomologous chromosomes or different parts in the same chromosome