genome

complete DNA sequence

Shotgun Sequencing

-nomrally when sequencing genome of certain species for first time

-genome broken up into sets of overlapping fragments that are small enought to be sequences

-the regions of overlap are used as guides for putting sequenced fragments back together

BAC

-bacterial articfical chromosome

able to replicate large segments of DNA

BAC library

genomic library-a set of all DNA sequences in a praticular genome, split into small segments and inserted into cloning

Steps of Shotgun sequencing

(1) cut DNA at random locations into fragments of 160 k                                                    

(2) clone using BAC (insert frags into BAC; grow E Coli cells to obtain large # of  

                                        fragments      

(3) Cut into 1 kb fragments randomly (1 kb fragments overlap)

(4) clone using plasmids

(5) sequence each fragment (find where overlap)

(6) assemble all 1 kb framents (match overlaps)

(7) assemble all 160 kb framents from differen BACs                                                                                                        

bioinformatiics

fuses computer sci and biology 

genes

a segment of DNA that cods for an RNA or a protein product and that regulates thair production

Open reading frams (ORFs)

DNA segments that are identified based on sequences typical of promoters, operators or other regulatory sites

Homology

if genes are homologous

they are similar bc they are related by decent from common ancestor

-similar base sequences and frequently the same of similar functions

Why are eukaryotic genes harder to scan

-introns

-large stretches of noncoding DNA

how to identify genes in eukaryotic cells

need to isolate mRNAs from cells, use RT to produce cDNA

sequence a portion of resultin moleucle to produce an expresed sequence tage

expressed sequence tag

represents protein coding genes

(the exons)

correlation btwn size of genome and metabolic capabilites in bacteria

as genome size INC # proteins -encoding genes INC

Lateral gene transfer

movement of DNA from one species to another (via plasmid)

Environmental Sequencing

metagenomics

cataloging all of the genes present in a community of bacteria/archea

Transposable elements

-segments of DNA that are capable of being inserted into new locations or transposing in a genome

-neve leave host cell

-passed from parent to offspring

selfish gene

DNA sequence that survives and reproduces but does not increase the fitness of the host genome

Long interspersed nuclear elenemnt

(LINE)

transposable element similar to retroviruses

most dont actually fuction 

How Line transposable elements spread

1.- long interspersed nuclear element (LINE) exists in DNA

2.- RNA poly transcribes LINA, producing Line mRNA

3.- LINE mRNA exits in nucleus and is translated

4.- LINE mRNA and proteins enter nucleus

5.- R.T. makes LINE cDNA from mRNA then makes cDNA double stranded

6.- Integrase cutes chromosomal DNA and inserts LINE cDNA

7.- New copies of LINE is integrated into the genome

Short Tandem Repeats

(STRs)

eukaryotic genomes have these several thousand loci

-microsatellites

-minisatellites

microsatellites 

(simple sequence repeats)

repeating units that are just 1-5 bases long

originate when DNA poly skips or mistakenly adds extra base durin replication

Minisatellites

(variable # tandem repeats VNTRs)

repeating untis that are 500-600 bases long

origin unclear

Unequal crossover

-how micro and mini satellites have so many diff alleles

1. homologs pair

2. repeats misaling (during meoisis I)

3. Products unique

DNA fingerprinting

micro/mini satelilite sequences vary so much among individuals they are now the seqence in choice of DNA fingerprinting

take DNa sample and perform PCR using frpimers

Gene family

genes that are extrememly similar to each other in structure and function w/in a species

gene duplication

extra copy of gene is added to genome

(most occur as result of unequal crossover during meiosis)

Pseudogene

DNA sequence that closely resembles a functional gene but is not transcribed

thought it have arisen by duplication of functional gene followed by inactivation due to mutation