Chapter 6*

the various proteins encoded by alternatively spliced mRNAs expressed from one gene

98.5%

sequences that can copy themselves and move throughout the genome

complex of DNA and the proteins that organize it; can be visualized as individual chromosomes during mitosis

transcriptional control regions; in eukaryotes, can be 50 bases or more away from exon coding regions

• 1) tRNA
• 2) rRNA
• 3) microRNA (regulate mRNA stability and translation)

each mRNA molecule encodes a single protein (what most eukaryotic genomes are); unlike bacterial genomes which are polycistronic, meaning a single mRNA includes a coding region for several proteins (that often function together in a biological process)

protein coding regions

type of DNA transcript that yields a single type of mRNA (primary transcript) which goes on to be translated into a sinlge protein

primary RNA transcript can be processed in a variety of different ways, leading to the formation of mRNAs composed of different exons (made from teh same DNA template); common in multicellular organisms

explands the number of proteins encoded in the genomes of higher level organisms

a set of duplicated genes that encode proteins with similar but not identical amino acid sequences; the then encoded/closely related homologous proteins are called a protein family

nonfunctional gene sequences, aka lost protein coding ability or are otherwise not expressed in the cell

the process by which these sequences are copied and inserted into a new site in the genome

• 1) those that transpose directly as DNA (transposons)
• 2) those that transpose via an RNA intermediate transcribed from the mobile element by RNA polymerase then converted back to DNA via reverse transcriptase (retrotransposons)

similar b/c retrotransposons make an RNA copy of themselves, introduce this new copy into another site in the genome (using reverse transcriptase) while also remaining at their original location; this is the same mechanism by which retroviruses spread; retroviruses can be thought of as retrotransposons that evolved genes encoding viral coats

DNA; in contrast, most mobile elements in eukaryotes are retrotransposons

• 1) direct-repeat sequence: 5 - 11 b.p.'s, most outer ends of transposon, sequence dictates which target site the element will be inserted into
• 2) inverted repeat: 50 b.p.'s, region flanking central protein-coding region; define the boundaries of transposon
• 3) protein-coding region: encodes transposase (enzyme REQUIRED for transposition of the sequence to its new site)

• 1) precisely exises the transposon element in the donor DNA (blunt-end cuts)
• 2) makes staggered cuts in target DNA
• 3) ligates the 3' ends of the transposon to the 5' ends of the cut target DNA

-transposition is completed by the host-cell's DNA polymerase and ligase first filling in the missing nucleotides at the 3' ends of the target DNA (creating the direct repeats) and then joining the free ends

-S phase of the cell cycle is when DNA synthesis occurs; if the donor DNA is in the region of the daughter cell that has already replicated and the target DNA is in a region that has yet to be replicated, then there is a net increase in transposon sequences in that daughter cell's DNA; one of 4 germ cells has an extra copy of the transposon

those with and those WITHOUT long terminal repeats (LTRs)

~250-600 b.p.; flank central protein coding region of retrotransposon, important for the incorporation of element into target site; leftward LTR functions as promoter and directs host RNA polymerase to initiate transcription (at the 5' nucleotide of the R sequence???)

constitute 8% of human DNA; difference between retrotransposons and retroviruses is that retrotransposons don't code for envelope protein so they can't bud from host cell; can still transpose to new DNA target sites

retrotransposons lacking LTR's

cytosol; DNA is then transported into the nucleus via a complex involving INTEGRASE: an enzyme encoded by retrotransposon that integrates the double stranded DNA into its target site via a similar mechanism as that used by transcriptase (for DNA transposons)

transposons that lack LTRs; form two classes in mammalian genome: LINEs and SINEs

about 6 kb.'s long; are three major families (L1, L2, L3) in human DNA and L1 is the only one that transposes in the contemporary genome; make ip 21% of total human DNA

• composed of:
• -short direct repeats
• -contain 2 long open reading frames:
• 1) ORF1: ~1 kb long, encodes RNA binding protein
• 2) ORF2: ~4 kb long, encodes protein similar to reverse transcriptase and exhibits endonuclease activity

300 b.p.'s long;