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Midterm

vocab (midterm).docx

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Department
Biology (Sci)
Course
BIOL 200
Professor
Francois Fagotto
Semester
Fall

Description
BIOL 200- Vocabulary (Midterm) 5’ cap-structure: 7-methyl-G added to nascent RNA chain; stabilizes and protects Activator: Specific transcription factor that stimulates transcription Activation domain: Interacts with other proteins to stimulate transcription from a nearby promoter Amino acids: Monomers for building proteins Assay: Analysis to determine the presence, absence, or quantity of one or more components; Binding domain: A modular structure (protein domain) present in transcription factors that binds to specific DNA sequences in gene promoters and enhancers; sequence specific Chromatography: Biochemical technique for separating mixtures of molecules based on mass (filtration), charge (ion exchange) or ability to bind to specific other molecules (affinity) Codon: A sequence of three adjacent nucleotides constituting the genetic code that determines the insertion of a specific amino acid in a polypeptide chain Consensus sequence: Sequence of nucleotides or amino acids similar or identical between regions of homology in different but related DNA, RNA, or protein sequence. Control sequences: Recruit proteins which can activate transcription Co-transfection: Used to evaluate whether a protein encoded by a known gene is a transcription factor or not; simultaneous transfection with two separate, unrelated nucleic acid molecules, one of which may contain a gene that is easily assayed and acts as a marker. CpG island: Regions in vertebrae DNA ~100-1000 bp that have stretches of repeated C and G (phosphate linked), clustered around 5’ promoter region. Function as promoters for transcription initiation; to recruit RNA pol II (loosely) to start transcribing; can usually be initiated at multiple sites. CTD: Carboxyl-terminal domain; hangs off primary subunit of RNA pol II; series of repeats of amino acids (Tyr-Ser-Pro-Thr-Ser-Pro-Ser) that can be phosphorylated to help RNA pol initiate transcription and elongation Deletion analysis: Identification of control sequences for longer sequences situated farther from promoter; big chunks of DNA taken out of the sequence; deletion series are then put in a plasmid vector containing a reporter gene and gene expression is monitored Deletion constructs: Edited version of DNA molecule which lacks the region of interest Dimer/dimerization/heterodime A chemical compound composed of two identical or similar (not necessarily r: identical) subunits or monomers/the chemical reaction that joins two molecular subunits, resulting in the formation of a single dime/ dimer made up of two similar but not identical subunits. DNA: Long linear polymer composed of four kinds of deoxyribose nucleotides; carrier of genetic information. DNase I: Reveal specific binding sites for DNA binding proteins; used as an assay in transcription factor purification DNA binding-motifs: The part of a DNA-binding protein that makes contact with the double helix; common site which facilitates their binding to DNA (ex: leucine zippers, zinc finger proteins) Downstream: The direction RNA pol moves on a gene during transcription (5’ end of template strand) EMSA (gel shift): Used as an assay to detect DNA binding proteins during biochemical purification; DNA bound to proteins travels more slowly in a gel Enhancers: Regulatory sequence in eukaryotic DNA that may be located at a great distance from the gene it controls. Binding of specific proteins to an enhancer modulates the rate of transcription of the associated gene; part of larger class enhancer elements; made up of DNA-binding domains bound to several transcription factor-binding sites Exons: Segment of eukaryotic gene (or of primary transcript) that reaches the cytoplasm as part of a mature mRNA; coding sequence GTP/GTPase: An immediate precursor of guanine (GDP) nucleotides in RNA; similar to ATP, used as a source of energy during synthesis of proteins / one of a family of monomeric GTP-binding proteins Housekeeping genes: Constitutive genes (transcribed regularly) that are required for the maintenance of basic cellular function, and are expressed in all cells of an organism under normal conditions hnRNP: Heterogeneous Ribonucleoprotein Particles; are comprised of proteins and RNA and are present in the nucleus; they bind to pre-mRNA before it is transported out of the nucleus Initiator element: DNA sequence that specifies transcription initiation within the sequence Initiation factor: One of a group of non-ribosomal proteins that promote the proper association of ribosomes and mRNA that are require
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