Chapter 9 Flashcards
genome
entire complement of genetic info including genes, regulatory sequences and noncoding DNA
genomics
discipline of mapping, sequencing, analyzing and comparing genomes
first genome sequences in 1976
RNA citrus MS2; 5386 bp
first cellular genome sequenced in 1995
haemophilus influenzae
human genome contains..
3 billion pb and 25000 protein coding regions
sequencing
determine the precise order of nucleotides in a DNA or RNA molecule
generation
succesive major changes in sequencing technology that confer
-increase in speed, drop in cost of sequencing
sanger method
first generation sequencing
presently, most labs access _____ generation sequencing
second
shotgun sequencing
entire genome is cloned, and resultant clones are sequenced
-sequencing is redundant
genome assembly
connecting the DNA fragments in the correct order and eliminating overlap
annotation
converting raw sequence data into a list of genes present in the genome
bioinformatics
science that applies powerful computational tools to DNA and protein sequences for the purpose of analyzing, storing, and accessing the sequences of comparative purposes
majority of genes encode
proteins
functional open reading frame (ORF)
encodes a protein
how do computer algorithms search for ORFs?
looks for start/stop codon and Shine-Dalgarno sequences
hypothetical proteins
proteins that exists, but whose function is currently unknown and encode nonessential genes
noncoding RNA
RNA that does not code for proteins; lack start codon and have multiple stop codons (tRNA, rRNA)
unlike prokaryotes, eukaryotes genome contains….
large fraction of non coding DNA
on average a prokaryotic genome is ____ bp long
1000
as genome size increases, gene content….
proportionally increases
smallest cellular genomes belong to…
parasitic or endosymbiotic prokaryotes
estimates suggest minimum # of genes for a variable cell is…
250-300 genes
many genes can be identifies by….
comparative analysis
comparative analysis
identifying sequence similarities to genes found in other organisms
most abundant class of genes
metabolic genes and gene coding for protein sequences
what makes up a minor fraction of genome?
DNA replication and transcription genes
number of genes with role that can be identified in a given genome is…
70% > total ORFs detected
archaea typically devote a high percentage of their genomes to ___ than bacteria
higher
archaea contain fewer genes for ___ than bacteria
carbohydrate metabolism or cytoplasmic membrane functions
metagenome
total gene content of the organism present in an enviro
transcriptome
entire complement of RNA produced under a given set of conditions
interactome
- complete set of interactions among molecules
- data expressed in the form of network diagrams
metabolome
the complete set of metabolic intermediates and other small molecules produces in an organism
microbiome
- lyses and extract DNA
- sequence DNA
- assemble genomes
microarrays
hybridization techniques can be used in conjunction with genomic sequence data to measure gene expression
RNA sequence
deep sequencing of cDNAs allowing comprehensive quantitation of all RNAs in a cell
what info can be derived from microarray
- global gene expression
- expression of specific group of genes under different conditions
- expression of genes with unknown function
- comparison of gene expression
- identification of specific strains
homologous
related sequence that implies common genetic ancestry
gene families
group of gene homologs
paralogs
genes within organisms whose similarities to one or more genes in the same organism is the result of gene duplication
orthologs
genes found in one organism that are similar to those in another organism but differ because of speciation
gene analysis in the 3 domains suggests that…
many genes present in all organisms have common evolutionary roots
horizontal gene transfer
- transformation
- transduction
- conjugation
elements: plasmids, phage, transposons and insertion sequences (isoelectric points)
vertical gene transfer
gene replication and cell division (size)
core genome
shared by all strains of the species
pan genome
includes all the optional extras present in some but not all strains of the species
polyacrylamide gel electrophoresis
technique used for the separation, identification, and measurement of all proteins present in a sample
how are proteins separated in a 2D page?
- horizontal–> isoelectric points
2. vertical–> size
interactomes
- complete set of interaction among molecules
- data expressed in the form of network diagrams
what is the primary technique for monitoring metabolites?
mass spectrometry
systems biology
integration of different field of “ohms” research
- genomics
- proteomics
- transcriptomics
- metabolomics
