Genomics and Proteomics

CRISPR

clustered regularly interspersed short palindromic repeats

CAS 9 system

uses CAS 9 enzyme, a guide RNA, and PAM to cause gene interruption

PAM

protospacer adjacent motif

short DNA sequence that CAS9 enzymes recognize and bind to

non-homologous end joining

CAS9 crispr system response due to in/del events causing homologous recombination

homology directed repair

CAS9 crispr response caused by the introduction of new DNA causing stable integration

genomics

study of the genome

genetic map

layout of positional information of DNA based on linkage dataph

physical map

precise ordering and positioning of genes

typically marker assisted by trait conformation or chromosomal banding patterns

based on actual distance

purpose of genomic mpas

locate and position genes on chromosome

important for relational studies, evolutionary aspects, comparative biology

connecting phenotype and genotype

markers used in trait conformation studies for maps

STS, SSR, STR, SNP, RFLP

STS

sequence tagged site

SSR

simple sequence repeats

STR

short tandem repeats

SNP

single nucleotide polymorphisms

RFLP

restriction fragment length polymorphism

RFLP function

cut genome with restriction enzymes into specific banding patterns

allows allele identification and linkage studies

individuals contain how many alleles

two alleles

homozygous or heterozygous

STR function

number of repeats varies in a population, each number of repeats represents an allele

physical maps and STS

sequence based markers allow for determination of STR and RFLP loci

causes amplification of unique sequence sites in the genome

map-based sequencing

clone by clone sequencing

map based sequencing function

fragments entire genome, then clones

uses markers to identify clones and based on the clones presence, forms a contig

congtig

series of overlapping DNA segments

clone by clone sequencing assembly

based on overlap of contig

shotgun sequencing

fragments entire genome then sequences

computer used to align fragments

more analytically intensive

sequencing an SNP identification

some alleles only differ at single nucleotides around the genome, sequencing can help recognize those differences

DNA fingerprinting

identify individuals through unique patterns in their DNA

haplotyping

determining DNA sequences inherited from the parents

understanding relationship of individuals in a population based on association of SNPs

4 main haplotype sample populations

nigeria, japan, china, and western europe

changes in SNP derive from

mutations, but are overall stable

hap-map

map of genetic variations, focusing on SNP allele changes and the groups they are associated with

hap-map purpose

id haplotypes that allow genome assocation studies

discover genes associated with particular traits/diseases

metagenomics

identify species in a community

particularly important for bacteria

synthetic biology

synthetically creating a genome or designing new organisms

functional genomics

knowing the genomic sequence and why the genome is important and how phenotype is affected

transcriptome

identifing all expressed mRNA

proteome

identifing all expressed proteins

gene identification

through bioinformatics and the use of computers to store, sort, and analyze complex biological data

BLAST

basic local alignment search tool

identify genes based on their similarity to other genes

homologs

all genes are these

similar between different organisms and have evolved from a common ancestor

orthologs

same gene, different organisms

paralogs

similar genes within the same organism with slightly different function

identity

same amino acid

similarity

similar amino acid

score

likelihood of two sequences to match

microarray

collection of single genes or DNA fragments

microarray based on

hybridization, probe DNA immobilized on a slide

can be all known genes, series of genomic clones, or whole genome

microarray process

target cDNA or other DNA isolated from cells, labeled with fluorescent dye

target is then washed over a probe set, any matches will bind and be detected

microarray analysis

hybridize from two different target sets, allowing comparison to look for expression or diseases

evolutionary studies of organisms

variable genome size and number/position of genes

function of genes categorized via definitions from GO (gene ontology)

prokaryotic gene density

constant

larger genome= more complex

prokaryotic gene complexity

related to habitat utilization

specialists require larger genomes and more genes

eukaryotic gene density

not correlated with complexity

eukaryotic genomes

segmental duplications and multi gene families

high percent of non coding DNA

proteomics

all proteins present in a particular cell