Biol3104 Key Terms

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Restriction endonuclease

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Enzymes that cleave DNA at specific nucleotide sequences
-Sequence recognized is often 4-6 nt long

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Isochizomer

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Restriction enzymes that recognize the same target sequence but do not make the same cut

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Temperate phage

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Bacteriophages that choose between lytic and lysogenic pathways of development

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Plaque

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Reveals the presence of virus-infected bacterial cells growing in a lawn on an agar plate

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Genomic library

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Collection of DNA from a single organism, not necessarily containing its entire genomic DNA
-DNA from source of interested is divided into multiple fragments packaged in cloning vectors that carries a portion
-Vectors can be inserted into host organisms for amplification and retrieval

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Taq polymerase

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Thermostable DNA poly named after thermophilic bacterium Thermus aquatics
-Frequently used in PCR for amplifying short segments of DNA

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Transition/transversion mutation

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Point mutations
Transition: changes purine to another purine (A, G), or pyrimidine to another pyrimidine (C, T)
Transversion: substitution of purine for pyrimidine or vice versa; more drastic consequences

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STS

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Sequence-tagged sites
-Short DNA sequence with a single occurrence in the genome whose location and base sequence are known
-Easily detected by PCR with specific primers
-Useful for constructing genetic and physical maps from sequence data from different labs
-Landmarks on developing physical map of genome

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SNP

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Single nucleotide polymorphism
-DNA sequence variation when a single nucleotide differs between members of a biological species or of paired chromosomes
-Almsot all common ones have only two alleles
-Usually occur in non-coding regions
-Can be predicted by presence of microsatellites
-Usually used to find out whether individuals carry alleles (ex. to find drug susceptibility) --> detection on PAGE

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5'-UTR and 3'-UTR

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Untranslated regions, on ends of mRNA, not translater into protein

5': from transcription start site to just before ATG translation initiation codon, sequences for regulating translation efficiency or mRNA stability
3': sequences for regulation of translation efficiency, mRNA stability, and polyadenylation signals

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Exon, intron

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Exon: any nucleotide sequence encoded by a gene that remains present within the final mature RNA product of that gene after removal of introns by RNA splicing, coding portion
-DNA sequence and RNA sequence

Intron: any nucleotide sequence within a gene that's removed by RNA splicing while the final mature RNA product of a gene is being generated, non-coding
-Both the DNA sequence within a gene and the corresponding RNA sequence

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Codon bias

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Differences in frequency of occurrence of synonymous codons in coding DNA
-Degeneracy of the genetic code

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Homolog

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The most closely related genes
-Orthologs
-Paralogs

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Paralog

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Genes that are related by gene duplication events in a genome

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Ortholog

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Homologs that are the same genetic locus inherited from a common ancestor

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Genome

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Entirety of an organism's hereditary information
-Encoded in either DNA or RNA (virus)
-Includes both genes and non-coding sequences of DNA/RNA

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Transcriptome

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Set of all RNA molecules including mRNA, rRNA, tRNA, and other non-coding RNA in one or a pop'n of cells

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Proteome

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Entire set of proteins expressed by a genome, cell, tissue or organism at a certain time
-Set of expressed proteins in a given type of cells or an organism at a given time under defined conditions

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Contig

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A set of overlapping DNA segments that together represent a consensus region of DNA
-Bottom-up sequencing: overlapping sequence data
-Top-down sequencing: overlapping clones that form a physical map of the genome used to guide sequencing and assembly

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"Counting experiment"

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Identifying overabundant transcripts in a mutant, comparing mutant and wt mRNA - cDNA - Solexa

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EST

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Expressed sequence tag
-Short sub-sequence of a cDNA sequence
-Can be used to identify gene transcripts, instrumental in gene discovery and gene sequence determination
-Result of one-shot sequencing of cloned cDNA

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Common ancestor

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Infers common descent of a group of organisms

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Protein domain

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Conserved part of a given protein sequence and structure that can evolve, function, and exist independently of the rest of the protein chain

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Protein family

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Group of evolutionarily-related proteins
-Descended from a common ancestor and have similar 2-D structures, functions, and significant sequence similarity

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Synteny

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Physical co-localization of genetic loci on the same chromosome within an individual or species
-Related to genetic linkage

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Epitope

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Small region of AA sequence of antigen recognized by antibody

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Antibody

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Immunoglobulin
-Y-shaped protein produced by B-cells
-Used by immune system to identify and neutralize foreign objects
-Recognizes epitope of foreign target (antigen)

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Antigen

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A substance that evokes the production of antibodies
-Can be from external enviro or formed within the body
-Immune sys will try to destroy or neutralize it if recognized as foreign and harmful

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Ribozyme

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RNAs with enzymatic activity, ex. self-splicing introns
-Proof of an RNA world

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Knockout

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Make a gene no longer active
-Ex. stick another gene inside to break it up (insertional mutagenesis)
-On/off switch

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Knock-down

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Not interrupting the DNA but instead inserting the complementary gene which is incorporated into RISC and results in many produced transcripts getting degraded after matching to RISC proteins
-Can regulate rate at which you produce gene without completely knocking out
-Dimer switch (or off depending on how much RNAi made)

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Nucleosome

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-Basic unit of DNA packaging in EU
-Segment of DNA wound in sequence around 4 histone protein cores

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Histone

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-Alkaline proteins found in EU cell nuclei that package and order the DNA into structural units called nucleosomes
-Chief protein components of chromatin

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Post-translational modification

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Chemical modification of protein after translation
-Later step of protein biosynthesis and gene expression

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COS

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For circularization and packaging of viral DNA in a bacteriophage