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 sequenced in 1976
RNA virus MS2; 5386 bp
First cellular genome sequenced in 1995
Haemophilus influenzae
The human genome contains…
3 billion bp and 25000 protein coding regions
sequencing
determining the precise order of nucleotides in a DNA or RNA molecule
generation
successive 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 overlaps
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 for comparative purposes
Majority of genes encode…
proteins
functional open reading frame (ORF)
encodes a protein
How do computer algorithms search for ORFs?
look for start/stop codons and Shine-Dalgarno sequences
hypothetical proteins
proteins that likely exists, but whose function is currently unknown and encode nonessential genes
noncoding RNA
RNA that does not code for protein; lack start codons and have multiple stop codons (tRNA, rRNA)
Unlike prokaryotes, eukaryotic genomes contain…
a large fraction of noncoding DNA
On average, a prokaryotic gene 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 viable cell is…
250-300 genes
Many genes can be identified by..
comparative analysis
comparative analysis
identifying sequence similarities to genes found in other organisms
most abundant class of genes
metabolic genes and genes 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% or less of total ORFs detected
Archaea typically devote a high percentage of they genomes to…than bacteria
energy and coenzyme production
Archaea contain fewer genes for…. than bacteria
carb metabolism or cytoplasmic membrane function
metagenome
total genetic complement of all cells present in a particular environment
epigenome
total number of possible epigenetic changes
methylome
total number of methylated sites on the DNA
mobilome
total number of mobile genetic elements in a cell
transcriptome
total RNA produced in an organism under a specific set of conditions
proteome
total set of proteins encoded by a genome
translatome
total set of proteins present under specific conditions
interactome
total set of interactions between proteins or other macromolecules
secretome
total set of proteins secreted by a cell
metabolome
total complement of small molecules and metabolic intermediates
glycome
total complement of sugars and other carbs
microbiome
total complement of microorganisms in an environment
virome
total complement of viruses in an environment
mycobiome
total complement of fungi in a natural environment
microarrays
small solid-state supports to which genes or portions of genes are fixed and arrayed spatially in a known pattern
metagenome
total gene content of the organisms present in an environment
RNA Seq
replacing microarrays for the analysis of gene expression
What info can be derived from microarrays?
- global gene expression
- expression of specific groups of genes under different conditions
- expression of genes with unknown function
- comparison of gene content in closely related organisms
- identification of specific organisms
homologous
elated sequences that implies common genetic ancestry
gene families
groups of gene homologs
paralogs
genes within an organism whose similarity 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
transfer of genetic info between organisms
vertical gene transfer
inheritance from parental organisms
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
proteomics
genome wide study of the structure, function, and regulation of an organisms proteins
2D polyacrylamide gel electrophoresis
technique for the separation, identification, and measurement of all proteins present in a sample
How are proteins separated in a 2D PAGE?
- horizontally, separated by difference in isoelectric points
- vertically, by size
protein domains
- distinct structural modules within proteins
- have characteristic functions that can reveal much about a protein’s role, even in absence of complete sequence homology
interactomes
complete set of interactions among molecules and data expressed in form of network diagrams
metabolome
complete set of metabolic intermediates and other small molecules produced in an organism
What is the primary technique for monitoring metabolites?
mass spectrometry (MALDI and TOF)
systems biology
integration of different fields of “comics” research
0compares data and builds a computer model of system being studied
