Study Guide Exam 3: Recombinant DNA Technology & Microbial Genomics

Vocabulary flashcards for Exam 3 covering key concepts in Recombinant DNA Technology, Microbial Genomics, and other related topics.

Biotechnology

Use of living organisms to create products that are useful to humans.

Genetic engineering

The deliberate modification of an organism's genome sequence.

Recombinant DNA technology

Set of procedures used to combine genetic material from multiple sources and create DNA sequences not found in organisms.

Cloning

Generation of a larger number of identical DNA molecules from a single DNA molecule.

Restriction enzymes

A type of endonuclease that allows scientists to cut up DNA at specific sites.

Sticky ends

Single-stranded DNA sequences produced by staggered cuts made by restriction enzymes.

Ligase

Enzyme that forms covalent bonds between the cloned gene and the plasmid.

Reverse transcriptase

Enzyme that creates double-stranded DNA from a single-stranded RNA template.

cDNA

Complementary DNA created from an RNA template.

Gel electrophoresis

A technique that separates nucleic acids and proteins based on their size and electrical charge.

Phosphate backbones

The components of nucleic acids that carry a negative charge.

Ethidium bromide

Dye used to stain DNA during gel electrophoresis.

PCR

Polymerase Chain Reaction, a technique to quickly make many copies of DNA.

Taq polymerase

DNA polymerase derived from Thermus aquaticus, a thermophilic bacterium.

DNA of interest

The specific DNA segment that is targeted for amplification in PCR.

Primers

Short single-stranded sequences used to initiate DNA synthesis in PCR.

Hydrogen bonds

Bonds that hold the two strands of DNA together and are broken by heat during PCR.

Cloning vector

A tool used to transfer genetic material into another cell.

Origin of replication

Site where replication of the vector DNA begins.

Selectable marker

Gene that allows for the identification of cells that have taken up the cloning vector.

Polylinkers

Unique restriction sites found in cloning vectors for inserting DNA.

Plasmids

Self-replicating pieces of extrachromosomal DNA found commonly in prokaryotes.

Bacteriophages

Viruses that infect bacteria.

Cosmids

Hybrid vectors that are between plasmids and bacteriophages.

Artificial chromosomes

Synthetic chromosomes containing DNA fragments integrated into a host.

Genomic library

A collection of an organism’s entire genomic DNA.

Transformation

The uptake of naked DNA from the environment by a bacterial host.

Electroporation

A technique that uses electrical shock to make cells competent to uptake DNA.

Polyhistidine Tagging

A technique used to isolate or visualize the protein product of a cloned gene.

Fluorescent labeling

A method to visualize the expression patterns of proteins.

Genomics

Study of the organization of genomes, the information they store, and the gene products they code for.

Sanger sequencing

A method that determines the nucleotide sequence of DNA based on chain termination.

dideoxyribonucleotide

A nucleotide that halts DNA synthesis during Sanger sequencing.

Next-generation sequencing

Technologies that enable fast and inexpensive sequencing of DNA.

Functional genomics

The study of the function of genes.

Transcriptome

The entire set of mRNA transcripts in a given cell.

Transcriptomics

The study of transcriptomes.

Proteome

The entire set of proteins expressed by a genome.

Proteomics

The study of proteomes.

Metagenomics

The study of genetic material recovered from environmental samples.

Metatranscriptomics

The study of RNA found in environmental samples.

Metabolomics

The study of the metabolome, the complete set of small-molecule metabolites.

Lipidomics

The study of the lipidome, the complete lipid profile of a cell.

Glycomics

The study of the glycome, the complete set of sugars.

DNA microarray analysis

A tool to observe the pattern of gene expression for thousands of genes at one time.

RNA-Seq

A method developed to overcome issues with microarray analysis.

Genomic Encyclopedia of Bacteria and Archaea Project

A project aimed at sequencing the genomes of various cultured microorganisms.

Bioinformatics

The use of computers to study and analyze genomes.

Annotation

The process of determining where genes start and end on a genome.

Paralogs

Genes that have similar nucleotide sequences within the same genome, usually due to gene duplication.

Orthologs

Genes with similar sequences found in different organisms due to speciation.

BLAST

A program that compares gene sequences and identifies regions of similarity.

Systems biology

An interdisciplinary field that studies cells holistically.

Comparative genomics

The study of similarities in nucleotide and amino acid sequences among organisms to infer function and evolution.

Pan-genome

The entire set of genes found across all strains in a species.

Core genome

The minimal number of genes necessary for the survival of a species.

Genomic islands

Mobile gene elements that integrate into bacterial genomes.

Pathogenicity island

Genomic islands that encode for virulence factors.

Synteny

The study of the order of orthologous genes in genomes.

Taxonomy

The science of biological classification.

Classification

Arrangement of organisms into groups called taxa.

Nomenclature

The assignment of names to taxa.

Identification

Determining which taxon an organism belongs to.

Carolus Linnaeus

The scientist who developed the first formal system of classification in the 1700s.

Phenetic classification

Grouping organisms based on similar phenotypes.

Genotypic classification

Comparing genetic similarity between organisms.

Phylogenetic classification

Based on the evolutionary relationships between organisms.

Hierarchical classification system

Arrangement from Domain, Phylum, Class, Order, Family, Genus, to Species.

Species

A collection of strains sharing stable properties differing from other strains.

Strain

A population descending from a single organism or culture isolate.

Biovars

Same species with biochemical or physiological differences.

Morphovars

Same species with morphological differences.

Serovars

Same species with different antigenic properties.

Type strain

The strain that is often the first discovered and most fully characterized.

Binomial system

The naming system gives each organism a scientific name based on genus and species.

Morphological features

Characteristics like cell shape and size used for classification.

Physiological features

Traits such as nutritional types and oxygen relationships used for classification.

Ecological features

Traits reflecting habitat preferences and symbiotic relationships for classification.

Molecular methods

Techniques providing robust analyses of microbial evolution.

G + C content

The proportion of guanine and cytosine in DNA, indicating species similarity.

DNA melting temperature

The temperature at which half of double-stranded DNA separates.

DNA-DNA hybridization

Process of heating DNA strands to create single-stranded DNA for complementary base pairing.

Genetic fingerprinting

Method for analyzing genetic relatedness through DNA fragmentation patterns.

Phylogenetic tree

A diagram showing inferred evolutionary relationships among organisms.

Horizontal gene transfer

Movement of genes across different domains complicating phylogenetic construction.

LUCA

Last Universal Common Ancestor, classified as a member of Bacteria.

Endosymbiotic hypothesis

Theory describing the origin of organelles like mitochondria and chloroplasts.

Mitochondrion origin

Evolved from Rickettsiae bacteria.

Hydrogenosomes origin

Evolved from mitochondrial ancestors.

Chloroplasts origin

Derived from cyanobacteria.

Gold standard assignment

Criteria to confirm the assignment of two organisms as the same species.

Genetic drift

Small, random genetic changes over generations leading to microevolution.

Bergey’s Manual

The most accurate classification scheme for prokaryotes.

Symbiosis

A stable association of one organism with another.

Mutualism

Both organisms benefit and depend on each other for survival.

Cooperation

Both organisms benefit but do not need to interact for survival.

Commensalism

One organism benefits while the other is neither harmed nor benefited.

Predation

One organism (predator) attacks and kills another (prey).

Parasitism

One organism (parasite) benefits at the expense of another (host).

Amensalism

One organism negatively impacts another organism.