ortholog-paralog

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Orthologs are genes in different species that evolved from a common ancestral gene by speciation. Normally, orthologs retain the same function in the course of evolution. Identification of orthologs is critical for reliable prediction of gene function in newly sequenced genomes.

Paralogs are genes related by duplication within a genome. Orthologs retain the same function in the course of evolution, whereas paralogs evolve new functions, even if these are related to the original one.

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Different organisms often show particularpreferences for one of the several codons that encode the same amino acid- that is, a greater frequency of one will be found than expected by chance.

only a few codons are used to any significant extent in a given gene -over this window of 10 codons, what % of them are preferred protein coding codons=codon bias (one way of recognizing a gene)

A short strand of DNA that is a part of a cDNA molecule and can act as identifier of a gene. Used in locating and mapping genes

genes that are neutral don’t get selected for or against because they are non-coding -EST (expressed sequence tag) can be used to identify these

http://www.youtube.com/watch?v=gbSIBhFwQ4s&feature=related

Each eukaryotic chromosome contains a single, long, folded DNA molecule. 
In the progressive levels of chromosome packing, 
1. DNA winds onto nucleosome spools. 
2. The nucleosome chain coils into a solenoid. 
3. The solenoid forms loops, and the loops attach to a central scaffold. 
4. The scaffold plus loops arrange themselves into a giant supercoil. 

Under low salt, electron micrographs of chromatin appear to resemble 10 nm wide "beads on a string". 
As DNAse can be used to remove the "string", it is DNA. 
The beads are nucleosomes, which are each made up of an octomer of histone proteins  (two H2A, two H2B, two H3 and two H4). 
The DNA wraps around the histone core much like string on a spool. 
In turn the nucleosomes coil into a 30 nm solenoid structure and are stabilized by H1, another histone protein. 
To achieve higher order of coiling, the 30 nm solenoid loops around a cellular protein scaffolding.comprised mostly of topoisomease II. 
The enzyme topoisomease II allows one DNA strand to pass through another by cutting one strand while pushing another through and rejoining the cut strand. The chromosome binds to the scaffold protiens at special regions called the scaffold attachment regions (SARs).

-the tail regulates whether cell will be in hetero/U chromatin

histone tails plays an important role in the regulation of eukaryotic transcription, in the formation of repressive chromatin complexes, and in the inactivation of whole chromosomes. In addition, the tails and adjacent regions serve as recognition sites for chromatin assembly and transcription remodeling machinery and the interactions that occur may also be responsive to histone acetylation.

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The hypothesis is that chromatin-DNA interactions are guided by combinations of histone modifications. While it is accepted that modifications (such as methylation, acetylation, ADP-ibosylation, ubiquitination and phosphorylation) to histone tails alter chromatin structure, a complete understanding of the precise mechanisms by which these alterations to histone tails influence DNA-histone interactions remains elusive.

-chromatin-immuno precipitation: you can purify nucleosomes based on whether they are methylated or acetylated and then amplify it using PCR. Using this you can tell if the overall histone is methylated or acetlated -the crux of the problem: how does the acetyl/methylated? -we don’t know how the cell tells what region to acetyl/methylate. KNOW: *there is a histone code *we are starting to understand the histone code *there are specific enzymes for modifying the histones *all 4 histones are involved *we can examine the histone code using chromatin-immuno precipitation and PCR *in very few of these cases to we understand what that modification means

interphase chromosome loops are biologically active—capable of influencing the course of intrachromosomal recombination.

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-chromatin metabolism -protein scaffold with DNA sticking off of it -the histone code within a loop can be the same or offset -C,D,E,F,G, H have a different code than A,B

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-has been validated in ALL eukaryotes -there are boundary elements that bind to the nuclear scaffold -there is one control region that begins the pattern and that pattern spreads across the chromosome until it hits a boundary element=SAR or MAR -the boundary element keeps the code from spreading any further -if you have a gene that you want expressed all the time; flank it with a couple of SARS; flanked region cant be shut off

The nuclear lamina is a structure near the inner nuclear membrane and the peripheral chromatin. It is involved in most nuclear activities including DNA replication, RNA transcription, nuclear and chromatin organization, cell cycle regulation, cell development and differentiation, nuclear migration, and apoptosis.

Protein scaffold of intermediate filaments that lines inside of nuclear membrane and holds it inside. centromere and telomeres may be involved. most heterochromatin on outside of nucleus which is where centromeres and telomeres are.

The treatment of chromosomes to reveal characteristic patterns of horizontal bands like bar codes.The banding patterns lend each chromosome a distinctive appearance so the 22 pairs of human nonsex chromosomes and the X and Y chromosomes can be identified and distinguished without ambiguity. Banding also permits the recognition of chromosome deletions (lost segments), chromosome duplications (surplus segments) and other types of structural rearrangements of chromosomes.

N-banding, G-banding staining technique for the metaphase chromosome. allows us to see banding patterns to differentiate between chromosomes and to locate the centromere. label p-arm and longer one is q-arm, this is important for hybridization. Allows you to notice downsydrome or leukemia.

In genetics, a chromosome translocation is a chromosome abnormality caused by rearrangement of parts between nonhomologouschromosomes. A gene fusion may be created when the translocation joins two otherwise separated genes, the occurrence of which is common in cancer.[image]

based on banding patterns we can see translocation. noticed during metaphase. chromosome breakage is normal though body can fix it, but if two are near one another and break then translocation may occur. if a chromosome that breaks contains immunity and the other an oncogene and they fuse. then uncontrolled expression of oncogene occurs since it needs to be regulated.

Some insects, such as Drosophila melanogaster have highly replicated polytene chromosomes in some tissues such as the salivary glands. 
Polytene chromosomes are a giant chromosome containing non-separated multiple copies of replicated DNA. 
Chromocentre is the point where polytene chromosomes appear to be attached. Along the length of the  polytene chromomes several features such as bands, puffs and Balbiani rings are present.

 dark regions are heterochromatin. light regions are uchromatin be expressed. Drosophila Larvae Salivary Glands • Biotin labeled probe for gene – detected with Streptavidin-Alk Phos no one knows why just in salivary glands.

A centromere is a region of DNA typically found near the middle of a chromosome where two identical sister chromatids come closest in contact. It is involved in cell division as the point of mitotic spindle attachment

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no more than 150 base pairs in length. consists of 2 highly defined sequences. centromere function allows for accurate divison during mitosis. centromeres are not origins, need origin and centromere for stable episome plasmid. long repeats make up centromeres

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 lower example, integrate into the host chromosome

A genetic element in bacteria that can replicate free in the cytoplasm (has a different number of copies) or can be inserted into the main bacterial chromosome and replicate with the chromosome. Plasmids are an example.

.piece of DNA that exists in addition to chromosome--yeast plasmid. highly unstable and can be lost during division b/c no distributed during mitosis. 

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to create ions that are suspended in a vacuum to apply electric field and measure speed they fly.

TOF stands for time of flight. Because ions are very reactive and short-lived, their formation and manipulation must be conducted in a vacuum.

spot sample-vacuum-laser it. if you just spot proteins-laser will burn them up and no one wants to study burnt product. boil matrix-vaporize.

never methylated, but can be spontaneously methylated and deaminated.

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examples of deamination which involves the removal of an amino group.  Accidental deamination may change the cytosine to uracil, or the methylated cytosine to thymine.

contains the origin of replication in the yeast genome. A segment of a DNA molecule necessary for the initiation of its replication; generally a site recognized and bound by the proteins of the replication system.

For replication-ARS (autonomously replicating sequences)or plasmid; believed to be chromosomal origins of replication w/eukaryotes-several origins of replication during S phase--bidirectional. ARS-chromosome origin of replication in yeast cells. only some work.

differential centrifugation: put proteins in tube and spin. it seperates them by size. do over and over to get smaller sizes. 

Rate-Zonal centrifugation: use sucrose to separate proteins by mass. smaller size on top, larger ones on bottom. only have to do once. 

2d

does electrophoresis twice. first by using isoelectric focusing-to seperate by charge (isoelectric point). 

then SDS electrophoresis which seperates by size.