genetics for biologists (genomics 8)

includes both the genes (the coding regions) and the noncoding DNA, as well as mitochondrial DNA and chloroplast DNA.

set of all RNA transcripts, including coding and noncoding, in an individual or a population of cells

entire set of proteins that is expressed by a genome, cell, tissue, or organism at a certain time.

overlapping DNA-sequences 

First time a specific sequnce is obtained

Representative sequence

(Individual genomes are distinct in many places – single nucleotide polymorphisms (SNPs))

Sequencing of an individual genome, where a reference genome is already known

complete set of all polymorphisms within a species

requires fragmentation of DNA to be sequenced and an amplification step before sequencing

Do not require DNA amplification prior to sequencing and can sequence long DNA molecules

Single base changes in genome

Segments of DNA duplicated or deleted

usually begins with ATG and ends with STOP-codon

– structure of genes and genome organization

function of genes and their interplay with each other

gene relationships between species and within a genome

interactions of the environment with genetics and gene function

= Basic local alignment search tool

Used to screen databases and compare a sequence to a known sequence

Genes that are evolutionarily related; they share the same evolutionary origin

Homologous genes found in different species

are thought to have descended from a common ancestor but have largely equivalent molecular functions

Homologous genes in same species that have the same evolutionary origin but have distinct molecular functions

(Ion channels, membrane-spanning regions, secretion, and export signals, DNA binding domains)

indicates a function of the protein

(Helix-turn-helix, leucine zipper, or zinc- finger)

(recognition sequence for a specific transcription factor)

indicate how expression of the gene could be controlled

(in promoters or enhancers)

= Chromatin immunoprecipitation

used to determine where in the genome certain DNA binding or chromatin binding proteins are located

precipitating a protein out of solution using an antibody specific for that particular protein

a next generation sequencing method to obtain a global overview of the transcription state of a population of cells

initial step of converting RNA to DNA

(analytical technique)

used to measure the massto-charge ratio of ions

identifies which proteins are present in a complex mixture of proteins