chromosones and genomes (pre midterm)

lec 10-12

what state does dna exist in during interphase

chromatin

how does dna behave in isotonic vs low salt buffers

• low salt: dna strongly attracts proteins so dna<protein

  • beads on a string

• isotonic: native chromatin structure is preserved, 1:1 ratio of protein:dna

nucleosome

• histones with dna wrapped around

• beads separated bt linker dna

• each protein core has 147 bp wrapped around

how many subunits do histones have

8, 2 of each:

• H2A

• H2B

• H3

• H4

solenoid and two-start helix model

• made of condensed fibre like chromatin

• stabilized by H1

how is chromatin condensation regulated

• modyfying histone tails at the N or C terminals

how can the charges of side chains be changed?

• methylation

• phosphorylation

• ubiquitination

• acetylation of lysine (neutralizes positive amino)

polytene chromsones

• on drosophila salivary glands

• interphase chromosones

• repeated replication without separation leads to parallel chromatids

polytene chromosones and transcription

• chromosone shoes econdensation with transcription activation

• puffs are linked with active RNA pol II

SMC proteins

• moderate looping of chromatin

• klesin is widely conserved in evolution by euks and bacteria

who condeses chromosones during metaphase?

condensins (SMCs)

• condensin II forms central scaffold with loop around it

• condensin I further compacts the loops

what structure do mitotic chromosones have

• series of loops wrapped around a protein core

3 requirements for replicaton and inheritance

1. origin of replication

2. centromere

3. 2 telomeres

we havee these 3 things in each mitotic chromsone

how does telomerase work

• reverse transcriptase

• has its own RNA template compliment to the telomeric DNA

• give primase more template DNA to prime on

CENP-A

• centromeric protein A

• centromere specific histone variant that links to the kinetochore

• replacement for H3 histone

• kinetochore connects to centromeres and microtubules

what do control regions consist of

• promoters

• cis-regulatory factors

isoforms

• made when genes are alternitavely processed and transcribed to get multiple different transcripts from the same gene

gene family

• set of related genes formed by duplication of an orginal single copy gene

ortholog vs paralog genes

• ortholog: same protein in a different species

• paralog: closely related protein in the same species

  • duplication occurs then they evolve differently

simple sequence repeats (SSR)

• 6% of our genome

• noncoding

• minisatellite dna

• microsatellite dna

• hypervariable nature is exploited for fingerprinting

minisatellite dna

• SSRs

• repeats 14-100 bp

  • longer than those of microsatellites

• arrays are 1kbp-5kbp long

• often in centromere/telomere region

microsatellites

• repeats are 1-4bp long

• formed by dna slippage

• arrays are 600bp, much shorter than minisatellite

• seen in transcription units

what cauzes neuromuscular diseases

• expansion of microsatellite dna through replication slippage

how much of dna is transposons and what type?

• 40% retrotranposon

• 3% DNA transposon

how do DNA transposons work

• dna transposase is cut anx paste into new dna segment

• target dna is cut to have sticky ends

• donor dna is cut bluntly

• causes 9bp duplication

LTR retrotransposons

• long terminal repeats, 8% of genome

• cannot form infectious particles or coat proteins so cannot leave the cell

• similar to retroviruses

• encode reverse transcriptase and integrase

how do LTRs work

• trancribed into and RNA copy

• retrotranscriptase turns rna into dna in the cytoplasm

  • uses trna as primer

• dna is moved to nucleus, then integrase mediates insertion into genome

LINEs and SINEs

• lines are longer

• both are nonviral dna retrotransposons

• LINEs are 21% of genome

• SINEs are 13%

ORF1 and ORF2

• regions on LINEs and SINEs

• orf1 encodes rna binding protein

• ORF2 encodes reverse transcriptase and a nuclease

how often are protein coding genes solitary/single copy

• 25-50% of the time

• rest occur in multiple copies

how do LINEs insert dna

• rna is made and exported from nucleus

• ORF1/2 translate and bind the rna

• rna protein complex goes to nucleus

• nucleae cuts dna strand at an AT rich area

  • dna end are used as primase

gramm negative bacteria

• have outer membrane arond cell wall

  • opposite of most bacteria

how many chromosones do most bacterial cells have

1

which direction are genes translated in bacteria

• highly transcribed genes are translated in the same direction as th replication fork progression so that mistakes are head to tail

operons

• regions that share a promotor and are transcribed together

• form polysctrinic mrna

polycistrinic mrna

• formed by operons

• code for multiple proteins

who folds bacterial dna

• gyrase (DNA topoisomerase) introduces torsion to compact dna

• SMC proteins form loops with the dna

• no histones involved

nucleoid

• structure bacterial dna is folded into by proteins

• can have the origin of replication in the centre or at the poles

which organelles are endosymbionts

• chloroplast and mitochondria

what about organellar dna resembles prokaryotes?

• circular shape

• lack of introns

• gene products resemble prokaryotic rnas and proteins

human mtDNA

• encodes 37 genes

• lacks introns

• encodes stuff for respiraton and translation

• gene products stay in mitochondria

cpDNA

• chloroplast genome

• much larger than mtDNA genome

• encodes 100-200genes

ricksettsia genus

• mitochondrial ancestor

lokiarchaea

• close relative of eukarotes ancestor cell

inheritance in mtDNA

• cytoplasmic inheritance

• mitochondria are evenly (number) and randomly (type) split between daughter cells