1. many replication origins

2. two telomeres; repeated nucleotide sequences, cap ends.

3. centromere; specialized sequence that allows for separation of duplicated chromosomes at mitosis. keeps two chromosomes together prior to mitosis.

-Combination of DNA + associated proteins.

-Histones (about over a million) are associated with DNA.

-in interphase cell, DNA is packed into chromatin fibers (30 nm) thick

-subject to low salt conc-->"beads on a string" (become slightly unpacked)

• DNA makes 1.7 turns around histone core
• histones contain high proportion of positively charged amino acids (Lys, Arg)-->facilitate interaction w/ neg charged phosphate backbone of DNA
• Histones are some of most highly conserved proteins.
• Tails of histones--> N-terminal end of protein; regulate chromatin structure and gene expression

• Binds at point where DNA exits nucleosome
• pack DNA into beads on a string fiber
• pack nucleosomes even more densely

DNA double helix>>beads on a string form of chromatin>>30 nm chromatin fiber packed of nucleosomes>>extended loops>>condensed section of chromosome>>entire mitotic chromosome

- Bind to DNA/histones

-powered by ATP Hydrolysis, slide along DNA

---->moving or removing histones and decondensing local regions of DNA.

-inactivated during mitosis

• Tails of nucleosome core histones enzymatically modified
• acetylation
  • Lys sidechain; neutraliation of + charge (gene expression)
• methylation
  • Lys, Arg sidechains; spreads + charge over larger number of atoms (gene silencing)
• Phosphorylation
  • Occurs on hydroxyl group of Ser, Thr; adds negative charge (gene expression)

-more condensed chromatin; stains darkly

-tends to accumulate at periphery of nucleus

-includes a lot of non-gene coding DNA (centromeres telomeres)

-if chromosomal rearrangement places gene in region that is condensed to heterochromatin--> gene may be poorly expressed/completely repressed

-important example of chromatin condensation as gene regulation = X inactivation

-->one chromosome is permamently condensed to heterochromatin and is not expressed (silenced)

--->silencing is faithfully inherited in subsequent cell divisions

-->silenced X chromosome is visible in interphase nucleus. (barr body).

***inactivation patterns are inherited

• all Prokaryotic polymerases are capable of proofreading.
• eukaryotic = Gamma, detla , epsolon
• can remove a single nucleotide from teh brand new 3' end of newly synthesized strand.

-initiates DNA synthesis

-requires 3'-primer and template strand

-after adds ~20 nucleotides, falls off

-also has 5'-3' exonuclease activity, this is used to remove the RNA primer

-involved in DNA repair; deletion of Pol II does not interfere with growhth/replication

-main polymerase involved in replication of DNA

• involved in the initiation of DNA synthesis
• forms a complex with primase that makes the RNA primer
• Pol a adds ~20 nucleotides  falls off and delta and epsilon take over
• does not have proofreading activity or 5'-3' exonuclease activity.

• Involved in DNA repair (base excision repair)

• Involved in replication of mitochondrial DNA
• has 3'-5' exonuclease activity

• main DNA polymerases
• have 3'-5' exonuclease activity

removes primers.

gap is filled by Pol a

• acheives error rate of 1 in 10,000,000 b/c of proofreading
• after new nucleotide is added, polymerase checks to see if it is correct
  • if not, nuclease cleaves off, polymerase tries again
• p site: polymerization is carried out
• e site: error-checking takes place

• protein couples energy from atp hydrolysis to its transit across chain
• separates two strands as it moves along
• lagging trand is prevented from re-forming base pairs; single strand binding protein
• sliding clamp protein--->keeps DNA polymerase firmly attached to template
• ATP powered clamp loader

• uses Tyr hydroxyl group to insert into backbone, creating a Tyr-O-phosphate linkage
• no ATP is consumed
• attaches to DNA phosphate-->breaking phosphodiester linkage in DNA strand

• pulls one string through another

1. creates double-strand brank in one piece of DNA
2. causes intact double helix to pass through break
3. reseals break

***Driven by ATP hydrolysis

• Result of single nucleotide mutation in beta-globin gene
• Glu-->Val (hydrophobic) 
  • multiple hemoglobin molecules adhere to each other in insoluble fibrous precipitates and deform RBCs (fragile)
• Heterozygotes-->resistant to malaria
  • accounts for prevalence of gene

1. Replication errors that escape proofreading
2. post-replicative damage
   1. Depurination
   2. Deamination
   3. Thymine Dimerization
3. Double strand breaks

• mismatches that escape proofreading are detected by MutS (pro) and MSH2 (euk)
• when MSH2 detects problem--> MutL (pro) or MLH1 or MLH3 (euk) scans along DNA until it finds a nick.
• nuclease cleaves nucleotides off newly synthesized strand
• DNA polymerase rebuilds new strand
• ligase completes repair

-loss of purine bases

-leaves backbone intact, bu is free hydroxyl group at 1-position

-lead t loss of nucleotide pair

-cause frameshift in DNA code

-converts cytosine to uracil

-converts CG pair to AT pair

-stalls DNA replication machinery, inhibiting cell replication

-takes care of deamination, depurination, oxidative damage to DNA

-DNA glycosylase enzymes scan DNA, flipping out one base at a time and examine it.

-damaged base is recognied, glycosyl linkage is broken

-missing tooth recognized by endonuclease

--->deoxyribose phosphate removed

-DNA polymerase adds new nucleotide

-ligase joins nick

• larger structural damage
  
  • pyrimidine dimer
  • polycyclic aromati hydrocarbon addition (carcinogens0
• large multienzyme complex scans DNA for large distortions in double helix
• upon encounter, helicase removes damaged strand
• polymerase repairs/DNA ligase joins

-way to fix double-stranded breaks

-enzyme complex brings ends together and joins w/ligase

(some base pairs lost)_

"quick and dirty fix" but works since so little of DNA is carrying useful information.

• ensures no base pairs are lost
• repaired segments correspond in sequence to other chromosome, not original
• --->can result in loss of heterozygosity which can be detrimental to cell line.

• Branch points in homologous recombination
• set of recombination proteins stablizes junctions
  • helicase powered by ATP hydrolysis can cause branch point ot migrate along chain

-Jumping genes

-short specialized segments of DNA that contain information necessary for them to insert anywhere in genome (euk-->w/in cell)

Transposase gene = enzymatic activity to carry out

Insertion of whole segment into new location

DNA recognition sequences: end of each transposon

Recognized by transposase as boundaries of DNA to be moved

-can move by either cut and paste method

-or replicative

• Unique to eukaryotes; information flows from RNA to DNA
  • RNA polymerase makes RNA copy of retrotransposon.
  • reverse transcriptase makes DNA copy that can insert elsewhere in genome
• L1 elements = long (include gene for RT)
• Alu sequences = shorter, do not have gene for RT

• Mobile genetic elements that can escape from cells/infect other cells
• lack machinery to synthesize protein, use host

• use RNA in genomes, upon infecting host cell, must use reverse transcriptase to make DNA copy
• integrase = integrates new DNA into host cells DNA
  • latent form = provirus
    

• no proofreading cability
• man copies are mutated
• single mutation can sometimes alter a viral protein in such a way that it becomes resistant to drugs

drug cocktails: 3 different drugs targeting different viral enzymes.. probability of single copy of virus developing resistance to all three remains low

autosomal recessive

-sensitivity to sunglight w/development of carcinomas at early age

-neurologic sympotoms.... Santics-Cacchione syndrome

sulfur-deficient brittle hair; brittle hair/nails

physical/mental retardatio

photosensitivity

abnormal and slow growth and development

cachetic dwarfism

cutaneous photosensitivity

adult progeria

patients age rapidly following puberty

propensity to develop chromosomal aberrations

proportionate pre-and post natal growth deficiency

sun sensitive

predispositionto malignancy

chromosomal instability

hereditary dermatosis

atrophy

pigmentation

telangiectasia

chromosome instability and increased cancer susceptibility

genes linked to hereditary breast cancer

complex roles in cell growth regulation

associated w/repair of double strand breaks

mutations of strand-directed mismatch repair system

muations of MSH2 or MLH1