Week 1 => Intro/origins of genes and genomes Flashcards
5 primary tools of the ‘omics’ revolution?
Genomics, transcriptomics, metagenomics, proteomics, metabolomics
Genomics
- Sequencing genomes of cultures or samples
- Re-sequencing
Transcriptomics
- Traditional approach => ESTs
- HAs evolved to RNA-seq technology
Metagenomics
- Culture-independent sequencing
- DNA isolated from a community of organisms, shotgun sequenced, and assembled
- Goal: to gain insight into the composition of the microbial community
Proteomics
- Generally refers to large-scale experimental analysis of proteins in complex mixtures, but smaller partially purified samples can be examined
- large-scale studies combine fragmentation of proteins, separation of proteins by liquid chromatography and detection by tandem mass spectrometry
- required a reference genomes with predicted proteins (digested in silico compared to predication)
Metabolomics
- Study of small-molecule metabolite profiles using gas chromatography, high Performance Liquid Chromatography (HPLC), etc., for sample separation, and mass spectrometry for detection
Can provide insight into the physiology of the cell as the time the sample was taken
Why is the genome of an individual not stable?
1) Copy number variation (CNV) between and WITHIN individuals (e.g., in the brain)
2) Cancer
Simplified order of gene concept evolution
1) Mendel determined basic rules of inheritance with discrete units passed between generations
2) Wilhelm Johansen coined word ‘gene’
3) Morgan’s work with gene placement of chromosomes => genes as beads on a string
4) Beadle and Tatum introduced the concept that one gene makes one enzyme
5) Oswald, Avery, MacLeod, Maclyn, and McCarty found that genes are made of DNA
6) Watson and Crick determine chemical structure of DNA (central dogma of molecules biology emerges from this)
7) Roberts and Sharp discover gene splicing (splicing or introns and exons)
8) The firs microRNA is identified in the worm Caenorhabditis elegans
9) GeneSweep: human geneticists come up with a definition for protein-coding genes in order to decide on a winner for a bet in the number of human genes
10) the idea that human genes are one lone continuum begins to emerge
What is the central dogma of molecular biology?
Information flows from DNA to RNA to protein
The ENCODE project
Encyclopedia of DNA Elements => goal to build a comprehensive parts list of FUNCTIONAL elements in the humans genome
do species have a genome?
Yes and no: there is overlapping and unique elements to each genome of a particular species
Pan-genome
Is the complete set of genes in a species (is also includes accessory genome, which is made up of gens that are present in some but not all members of the species)
Core-genome
IS the subset of gens shared by all members of that species
Re-sequencing
determining the sequence of a genome for the purpose of comparison to a reference genome
ESTs
expressed sequence tags - cDNAs derived from mRNA
RNA-seq technology
whole transcriptome shotgun sequencing (uses next-generation technologies to provide a comprehensive picture of the RNA present in a sample)
In silico
refers to scientific experiments conducted using computer simulations or modeling
Where do genes and genomes come from?
The first(s) living things
In vitro
“in glass”
In vivo
“in life”
Reasoning for where genes and genomes come from
Through comparing extant (liking) and extinct (via fossils and indirect evidence), we infer that shared traits originated in a common ancestor
What group has the largest/most branches in the phylogenic tree?
Prokaryotes
The RNA world timeline (__billion years ago)
4.5 Formation of Earth
4.2 Stable hydrosphere
4.2-4.0 Prebiotic chemistry
4.2-4.0 Pre-RNA world
4.2-3.8 RNA world
4.2-3.6 First DNA/protein life
3.6-present Diversification of life
RNA with catalytic activity would have:
1) Replicated itself
2) Synthesized peptides
