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20 Cards in this Set
- Front
- Back
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Nucleosome
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"beads on a string"
DNA wrapped 2x around nucleosome - aggregates of 8 histone proteins -core particles: H2A, H2B, H3, and H4 H1 is linker between nucleosomes Histones are + charge and DNA is - = 200 bp condensation of DNA 10:1 |
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Solenoid
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Spinal coil 5-6 nucleosomes per turn
structure mediated by H1 histone -condensation 50:1 |
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Dark Giemsa stain (G bands)
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stains most dense, tightly packed DNA
replicate late in S phase Less active in transcription |
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Light Giemsa stain (R bands)
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Loosely packed loops
often rich in G and C more transcriptional activity |
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DNA double helix
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Human DNA 3 billion bp (3 x 10^9)
Double helix has major and minor groove (3.4 angstroms) replication = synthesis of new DNA strand |
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Transitions
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purine to purine (A to G; G to A)
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Transversions
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purine to pyrimidine (A to T; C to G)
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Deamination
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most common type of mutation
- deamination happens to cytosines - if "normal" cytosine - becomes uracil -can be repaired by cutting out U with Uracil-DNA glycosylase |
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Deamination of methylated C
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becomes Thymine
-more difficult to find and repair - many "recurring" mutations are this type -occurs in m5CpG |
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Stop Codons
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DNA: TGA, TAA, TAG
RNA: UGA, UAA, UAG |
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Post-translational modifications
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Phosphorylation: addition of a phosphate; mostly T (threonine) and S (serine); also Y (tyrosine; important for protein signaling
Glycosylation: addition of sugar groups; N-linked most common; O-linked less but important for development Meristylation, palmitoylation: covalent addition of lipids; important for protein-signaling |
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LOD score
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LOD > 0 = favor of linkage
LOD < 0 = evidence against linkage LOD = 3.0 statistically significant evidence of linkage LOD < -2.0 statistically significant against linkage 1% recombinate rate = 1 cM = 1 million bp |
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Knock in/knock out mouse transgenics
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- recombination with endogenous locus
- modulate mouse gene - requires embryonic stem cells, homologous recombination/ selection - stem cells are then introduced into blastocyst; chimera produced - breed to get transmission; knock-outs - recessive (typically loss of function) |
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"classical" mouse transgenics
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- Add new gene to mouse genome
- can be anything (human, mouse, bacterial) - generally random integration, multiple copies - over-expression, or controlled/tissue-specific expression -Dominant (expresses new protein) |
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Retroviruses
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ADA deficiency; require dividing cells
stable integration into genome can cause leukemia due to integration at oncogene site |
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Adenoviruses
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larger packaging; significant immune reaction
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AAV (Adenoassociated virus)
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parasite of other viruses; generally only virus that is "good for us"
limited packaging ex. HPV |
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SNPs
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single nucleotide polymorphisms
- single letter change - often arranged in haplotypes - typically 2-10 haplotypes in specific populations - over regions of 10kb-200kb SNP is not a VNTR (variable number tandem repeats) |
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STRs
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Short tandem repeats
- CA repeats - trinucleotide repeats - generally in non-coding; rare exceptions of causing disease (ex. trinucleotide repeats; AR receptor is normally polymorphic for glutamines in protein, expansion causes Kennedy's disease) STRs are subset of VNTRs |
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GWAS
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genome-wide association studies
- using common polymorphisms for common traits ex. Type 2 diabetes (associated subphenotypes include blood pressure, LDL too high, HDL too low, insulin resistance, central adiposity); Macular degeneration - GWAS typically massively parallel genotyping (100K to 1 million SNPs) - need large case/control cohorts, need replication, hidden stratification, lack of HWE, allele frequency (generally > 5-10%), relative risks typically 1.1-1.2 fold environment typically a major confounder; difficult to control for |
