Chapter 11: Microbial Genetics Flashcards
What are Homologs
evolutionarily linked genes or genes derived from the same ancestral gene
What are Paralogs
A homolog that has risen from a duplication event. Paralogs often differ in biochemical function in contrast with orthologs.
What are Orthologs
A homolog that has risen from a duplication event. Orthologs have the same function in
contrast with orthologs. In different genomes in contrast with paralogs
How does G+C content between microbes affect horizontal gene transfer
The more equivalent the G+C content, the higher likelihood of successful horizontal gene transfer
What is metagenomic or environmental genomics
DNA is extracted directly from microbial communities and analyzed as a composite mixture. Or Study of genomes isolated from environmental samples using cultivation-independent methods
genomics
Determination and study of complete genome sequences
automated sequencing
Technique based on Sanger sequencing that yields sequences of up to 1,000 nucleotides; see also cycle sequencing
cycle sequencing
Technique based on Sanger sequencing that yields sequence of up to 1,000 nucleotides within hours; see also automated sequencing
pyrosequencing
Next generation sequencing method in which incorporation of a pyrophosphate (PPi) drives a luciferase reaction, producing light that can be detected with a charge-coupled device (CCD) camera; see also 454 DNA sequencing
Sanger sequencing
Technique to determine DNA sequence that relies on incorporation of chain-terminating dideoxy nucleotides and includes cloning of the fragment to be sequenced, DNA synthesis, and gel electrophoresis; see also dideoxy sequencing
dideoxy sequencing
Technique to determine DNA sequence that relies on incorporation of chain-terminating dideoxy nucleotides and includes cloning of the fragment to be sequenced, DNA synthesis, and gel electrophoresis; see also Sanger sequencing
primer walking
Technique in which a DNA sequence obtained from an early sequencing run is used to design a new primer that will anneal farther along the fragment to be sequenced; consecutive runs allow sequencing of the entire DNA segment
high-throughput sequencing
or
next-generation sequencing
Use of post-Sanger-sequencing platforms to sequence many DNA fragments simultaneously and at a fraction of the cost of previous electrophoresis-based approaches; see also next-generation sequencing
454 pyrosequencing
High-throughput sequencing method in which incorporation of a pyrophosphate (PPi) drives a luciferase reaction, producing light that can be detected with a charge-coupled device (CCD) camera
Ion Torrent
A high-throughput sequencing method that measures a pH change with successive nucleotide additions to a growing DNA chain to identify many target DNA molecules simultaneously
Illumina sequencing
High-throughput sequencing approach that uses massively parallel synthesis of DNA fragments on a glass surface, with light emission, in order to sequence large numbers of DNA fragments simultaneously
PacBio
High-throughput sequencing method for sequencing relatively large DNA fragments of interest
shotgun sequencing
Technique for sequencing DNA that shears DNA into short fragments that are sequenced, after which computer programs are used to identify regions of sequence overlap; allows researchers to sequence complete genomes, starting with individual genome fragments.
bioinformatics
Field that uses computers to analyze large quantities of biological data, such as DNA or protein sequences; facilitates the analysis of genome sequences and the prediction of gene function
annotation
Use of computer programs to predict the beginning and end of protein-encoding sequences of DNA; helps identify ORFs
genomic library
Collection of cloned DNA fragments that comprise the entire genome of an organism
Northern blot
Use of nucleic acid probes specific to a gene of interest to identify the size of targeted RNA templates of interest
Southern blot
Technique for detecting specific DNA sequences by hybridization using labeled probes of complementary sequence
transcriptome
Set of transcripts encoded by each of the genes within a genome
microarray
Solid support on which single-stranded DNA molecules within a genome are fixed in position; can be used to study the transcriptional activity of all genes in the genome simultaneously; opposite of northern blot
RNA-seq
Methodology involving high-throughput sequencing of cDNA fragments derived from extracted RNA from an organism or sample of interest; involves direct sequencing of a cell’s transcriptome by using high-throughput sequencing of RNA-derived cDNA.
proteome
Collection of proteins within a cell under specific conditions
2D-PAGE
Two-dimensional polyacrylamide electrophoresis in which molecules are separated based on both isoelectric point and mass
mass spectrometry (MS)
Technique that involves ionization of target chemicals to characterize ions based on their corresponding mass to charge ratio
Individual polypeptides can be identified by
mass spectrometry (MS)
liquid chromatography-mass spectrometry (LC-MS)
An analytical chemistry approach using liquid chromatography for physical separation alongside mass analysis for measuring the mass of targeted molecules; can be combined to separate and identify individual proteins from a protein mixture.
X-ray crystallography and nuclear magnetic resonance (NMR)
can be used to determine the three-dimensional structure of proteins.
comparative genomics
Field of study that determines evolutionary relationships among organisms based upon DNA sequence data
genomic island
DNA sequence transferred from one species to another; result of horizontal gene transfer
pan-genome
Collection of all genes from multiple representatives from a single species or clade within specific bacteria or archaea pf interest
3 steps of Sanger Sequencing
- Cloning of the gene fragment to be sequenced
- DNA synthesis
- Electrophoresis
