introns = 90 bp - 17.1 kbp

exons = 50 - 100 bp

Beta globin genes are a good example of a gene cluster family

psuedogenes- "dead" genes that have the same cluster intron/exon organization found in active genes. They are no longer expressed because they lack control elements.

active members- expressed at different times (e.g., ε in the embryo, β in the adult)

Alu emelent- 300 bp repeat sequence in the non transcribed spacer DNA b/t genes.

1.) DNA with tandem repeat arrays of 20 - 100 kbp

2.) Located in centromeres and telomeres

3.) for proper segergation of chromosomes (mitotic spindle attachement sites) and maintainance of chromosome ends (telomeres)

1.) Simple Sequence DNA with Tandem Repeats of 1-13 bp

2.) occasionally occur within transcription units where mutations that lead to expansion of the repeats is associated with a number of human diseases (e.g., myotonic dystrophy, spinocerebellar ataxia)

Simple Sequence DNA that is composed of 14 - 100 bp repeats in arrays of 1-5 kb long (20-50 repeats)

Micro Satelite sequence of repeat units is highly conserved among individuals but the number of repeats is highly variable

DNA fingerprinting makes use of PCR reactions with a mixture of primers flanking a number of different minisatellites resulting in a pattern of varying size bands the pattern uniquely identifies any individual with mathematical certainty

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1.) DNA transposons -are found in both bacteria and eukaryotes

2.) Retrotransposons- require an RNA intermediate, they are found only in eukaryotes and move by a process analogous to retrovirus genome insertion, and are evolutionarily related

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First descovered as spotaneous mutations duet to insertion of a DNA sequence into a coding region of a gene and called IS elements. These IS elements are 1-2 kbp and transpose at low frequencey most transpose anywhere at random into a host chromosome.

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Transposase makes blunt-end cuts next to the inverted repeat sequences in IS element. Transposase makes staggered cuts in target DNA and ligates unpaired stretch to IS element. DNA pol w/ ligation fills in cellular gap to generate short direct repeat target-site sequences. Size of short targe site repeats depend on on the particular IS element (5,9, 11 bp)

LTR (Long Terminal Repeat sequences) - 6 -11 kbp long that contain LTR and genes similar to those found in retroviruses targets 5-10 bp of direct repeats

Non-LTR retrotransposons- the largest element is 6 kbp (they are smaller) and they all lack LTR's and are distanly related to retroviruses, target A/T rich regions

1.) Retrovirus containing genomic ssRNA and Reverse Transcriptase enters the cell via fusion causing the loss of the protein coat which froms a viral nucleocapsid.

2.) The viral DNA is copied through reverse transcription

3.) The DNA is transported into the nucleus and integrated into the host chromosome creating a Provirus

4.) Transcription occurs creating retrovirus protiens

5.) Complete retroviruses emerge from the cell in a process called budding

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Transposase Enzyme = reverse transcriptase/integrase

and virus capsid proteins that lack the envelope proteins (defective)

Both contain Transcription control elements that are flanked by short direct repeats. Both are transcriped by RNA pol II. Both have LTR regions

LINES - long interspersed elements (900 bp)

SINES - short interspersed elements (100 -400 bp)

Both target A/T rich regions

L1,L2,L3

ORFs, truncated, mutations

Pseudogenes originate from gene duplication and unequal crossing over events.

Processed pseudogenes are derived from mRNA copied into DNA and then integrated.

Exon shuffling between different genes by recombination (ie. b/t Alu elements in introns).

They have contributed to generation of gene families and formation of complex regulatory regions to control gene expression.

BLAST - basic local alignment search tool

BLAST is an effective computer program that evalutates wheter any 2 or more sequences are related (protein or DNA), and then generates a stat score of significance for alignment that indicate whether or no the alignment could be due to chance.

Homologous - sufficiently similar to suggest common ancestry

Paralogous- genes reulted from gene duplication

Orthologous- result from speciation

1.) IS element (1-2 kb) with a protein coding region for transposase enzyme

2.) protein region is flanked by 50 bp inverted repeats (part of the IS element

3.) IS element is flanked by target-site direct repeats of (5-11 bp)

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LTR retrotransposon ( 6-11 kb) contains a protein coding region flanked by LTR reagions (250 - 600 bp) LTR regions are flanked by target-site direct repeats (5-10 bp)

LINES and SINES

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SINES do not encode proteins but contain Alu elements