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What is a genome

The entire complement of genetic information. Includes genes, regulatory sequences, and noncoding DNA


What is genomics

Discipline of mapping, sequencing, analyzing, and comparing genomes


What is shotgun sequencing

A technique used by virtually all genomic sequencing projects. Random fragments of entire genome are cloned or amplified and sequenced to produce millions of sequence "reads"


How can you sequence with shotgun sequencing

The organisms genome is broken up into random fragments, there will be so many fragments that every part of the genome will be sequenced. Computer algorithms assemble the overlapping reads into contiguous regions in order to produce the entire genome


What are some difficulties with shotgun sequencing

Assembly of complete circular chromosome


When sequencing a circular chromosome how are gaps between contigs filled

They can be filled using PCR or cloning techniques or by sequencing methods that will produce very long reads


What is a closed genome

A genome that is complete


What is a draft genome

A fast and cheap method of sequencing but will contain gaps


What is annotation

Converting raw sequence data into a list of genes present in the genome. The majority of genes encode proteins


What is a functional ORF

An open reading frame that encodes a protein. The ORFs are bounded by start/stop codons, Shine-Dalgarno sequences upstream of ATG start site.


How are ORFs used in genomics

You can compare new ORFs that have been identified by a computer to those previously found in other genomes, finding homologs suggests the gene is real


What is bioinformatics

Science that applies computational tools to DNA and protein sequences. Analyze, annotate, and compare homologs. And identify genes for metabolic pathways by comparison to those well-studied model organisms


What is comparative analysis and what is it used for

Identifying genes by comparing similarities between sequences with previously identified genes in other organisms. Allows for predictions of metabolic pathways and transport systems. Can be used to determine how to grown an organism in a lab


What are homologous genes

Genes that may have a common evolutionary ancestor


What are hypothetical genes and proteins

Only about 70% or less of total ORFs are detected and these are the uncharacterized ORFs. They encode for proteins that likely exist but whose function is unknown (nonessential genes). All essential genes have been identified


Describe a metagenome

The total gene content of all organisms present in an environment. Allow a variety of bioinformatic analyses to identify organisms, types of metabolisms, etc. Can be obtained by shotgun sequencing of total DNA from an environmental sample. Goal is to determine DNA sequences of organisms in a population and identify all of them. Sequencing the rRNA is primarily used.


Describe a transcriptome

Provides data on expressed genes by measuring RNA. The entire complement of RNA produced under a given set of growth conditions (temperature, nutrients, other organisms)


What are microarrays

Hybridization technique based on genomic sequence data for target organism. Thousands of gene probes are arrayed in a known pattern on solid-state chips or glass slides


What is RNA-seq

Direct shotgun sequencing of total RNA samples


What can be learned from transcriptomes

Gene expression patterns for every gene in genome under different conditions and in different mutants. And expression of specific groups of genes under different conditions can yield clues to possible roles of unknown genes.


What is proteomics

The study of all proteins present in cells/tissues under different conditions (proteins produce phenotypes). It combines genomic info with quantitative data on protein amounts


What are the techniques used in proteomics to obtain data of all the proteins present

2D gel electrophoresis, liquid chromatography, and mass spectrometry


Describe the 2D gel electrophoresis

On the horizontal acis they have been separated by their isoelectric point (the point where they have no charge) and on the vertical axis they have been separated by size.


Describe mass spectrometry

Can be used to cut out individual spots and determine what protein is in there


What are proteins with >50% sequence similarity

Typically have similar functions, and are probably homologs


What are proteins with >70% sequence similarity

Almost certainly have similar functions and are LIKELY homologs


What are protein domains

Distinct structural regions or functional modules within proteins (transcription repressor protein would have a DNA-binding domain and a co-repressor binding domain). Have characteristic functions that can reveal a protein's role/function, even in the absence of complete sequence homology


What is an interactome

Complete set of interactions among proteins. Proteins that physically interact are likely to be involved in the same process or pathway. Is the combination of genome info and experimental data on protein-protein interactions.


What is a metabolome

The complete set of metabolic substrates, products, and intermediates, and other small molecules in an organism


What is used to identify and measure metabolites

Mass spectrometry


What are homologous chromosomes

They are related in sequence to an extent that implies common genetic ancestry


What are gene families

Groups of gene homologs. The whole gene or part of a gene is homologous and related to other genes. They can all transport molecules but they use different molecules for transporting.


What are paralogs

Homologous genes within an organism, often the result of gene duplication. Ex. Cyanobacteria contain multiple psbA gnes: psbAI, psbAII, psbAIII. Often they all have the same function in a single species of bacteria but one gene may function better in the light while another gene may function better in the darkness


What are orthologs

Homologous genes found in different organisms. They are found in different organisms but will have the same function


What are gene duplications

They are the mechanism for the evolution of new genes.


Describe the mechanism of gene duplication in evolution

Two gene copies can evolve independently: One copy keeps the original function and the other copy can evolve to acquire a new function.


What is deletion

Deletions can eliminate genes no longer needed, genes that do not provide a selective advantage


Where are housekeeping genes found and what does that tell us

Many housekeeping genes are found in all three domains of life showing that all organisms have common evolutionary roots (these housekeeping genes were originally found in LUCA)


What is horizontal gene transfer

The transfer of genetic information between organisms, as opposed to vertical inheritance (from parental organisms). Can also occur between different species and different genera


What does crossing phylogenetic boundaries mean

Bacteria can pick up genetic material from something that is very different as long as the codon usage is not so different that the gene is not expressed


How do you detect horizontal gene flow

Presence of genes typically found only in distantly related species (finding a gene normally in G+ bacteria in just one strain of a G- bacteria). Presence of a DNA region with GC content or codon bias that differes significantly from remainder of genome. or presence of DNA sequence signatures that indicate mobile DNA element such as a transposon or virus


What are transposons and insertion sequences

Transposons can trasfer DNA between different organisms. Transposons and insertion sequences (IS) may also mediate large-scale chromosomal changes within a single organism. Multiple ISs are often found in a genome. Recombination between related IS elements can result in large-scale chromosomal rearrangements


What are chromosomal islands

Region of bacterial chromosome of foreign origin (HGT) that contains clustered genes. They usually contribute specialized functions not essential for growth


What are pathogenicity islands

Chromosomal islands containing genes for virulence


What are some specialized functions that are not essential for growth that chromosomal islands are responsible for

Virulence, biodegradation of unusual compounds and symbiosis