Term
| Ribosomal subunits in prokaryotes |
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Definition
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| Ribosomal subunits in eukaryotes |
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Definition
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23 s in 50 s ribozyme
transfers the peptide bond from the p site to the new trna in the a site |
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| E P A site what they stand for |
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Definition
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| structure based drug design |
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Definition
| The process of using basic information about cellular machinery to develop new antibiotics and other drugs |
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Term
| Initial transcribing complex |
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Definition
| the promoter polymerase complex shortly after the open complex where the rnts are released and before actual transcribing of the gene before the escape |
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Definition
contains enzyme dna and rna phase where elongation takes place
After initial transcribing complex |
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Definition
| how many transcripts it initiates at a given time which is influeneced by how well the promoter binds polymerase initially how efficiently it supports isomerization and how readily the pol can escape |
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Definition
| the transition from the closed to the open complex in rna pol does not require energy derived from atp and is instead the result of a spontaneous conformational change in the dna enzyme complex to a more energetically favorable form |
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Term
| Pyrophosphorolytic editing |
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Definition
| reincorporates pyrophosphate in a simple back reaction to catalyze removel of incorrect bp, can remove either correct or incorrect bps in this fashion but spends longer hovering over incorrect bps |
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Definition
| backtracks by one or more nts and cleaves rna product removing error containing sequence |
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Definition
| enhance hydrolytic editing function and serve as elongation stimulating factors |
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Definition
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Definition
| trigger the elongating pol to dissociate from the dna and release the rna chain it has made |
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Definition
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Definition
| 1957 zamecnik and hoagland |
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Term
| aminoacyl trna synthetase |
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Definition
| enzyme that hooks amino acid onto trna |
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Definition
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| process after ribosome is recruited and bound to mrna and moves along mrna until it encounters a 5’ aug 3’ start codon |
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Definition
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Definition
| refers to the minimal set of sequence elements required for accurate transcription initiation in vitro |
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Definition
| uas, enhancers, silencers, boundary elements and insulators |
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Definition
| 30 bp upstream of the start site |
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Definition
| 1. All living things are composed of cells. 2. At this point all cells come from pre-existing cells. |
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Definition
| can grow on minimal medium |
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Definition
| cannot grow on minimal medium |
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Term
| three methods of gene transfer |
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Definition
| conjugation, transformation, transduction |
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Definition
| a plasmid that can integrate into a cell's dna |
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| Hfr high frequency of recombination |
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Definition
| chromosome inside of cell |
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Definition
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Definition
| must be a temperate phage lambda is an example can only integrate in a specific spot carries rec + with it |
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Definition
| can only do lytic cycle and therefore cannot do specialized transduction |
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Definition
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Definition
| b is permissive k is restrictive |
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Definition
| 2(# plaques on K)/(# plaques on B) |
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Definition
| Precursor > enzyme X > ornithine > enzyme Y > citrulline > enzyme Z > arginine. |
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Definition
| The gene is viewed as the fundamental unit of structure. It is indivisible by crossing over |
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Term
| minimal recombination proportion between a pair of different mutant alleles |
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Definition
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Definition
| A deletion is a mutation which results from the loss of a portion of the DNA. |
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Definition
| anaximander 6th century bc |
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| western thought against the idea of evolutionary change. |
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| Enrolled at Christ College at Cambridge University. |
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| 22 years old five year voyage December 27 1831 |
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| 22 years old five year voyage December 27 1831 |
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Definition
| the correlations he made between the variation in geography and the variation in the characteristics of the organisms found in the various areas he visited. |
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| darwin primarily observed? |
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Definition
| living and recently dead things |
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Definition
| volcanic origin and is located approximately 900 km west of Ecuador in South America. |
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Term
| Darwins unique realization |
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Definition
| in realizing that if individuals of a species with superior characteristics reproduced more successfully and if their characteristics were inherited, the average character of the species would be altered. |
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Term
| Charles Darwin’s contribution to evolutionary theory |
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Definition
| fitness has to do with reproductive success not survival |
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Term
| Two major thesis of darwins book origin of species |
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Definition
: All species, living or extinct have descended without interruption from one or a few original forms of life.
His theory of the causal elements of evolutionary change, his theory of natural selection |
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Definition
| is a group of organisms living in a particular area that have a higher probability of mating with each other and producing fertile offspring than they do with members of other such groups. |
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Definition
| Evolution is a change in the allelic proportions at a locus in a population of organisms from one generation to the next. |
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Definition
| Occurs whenever some individuals in a population reproduce more than others. |
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Term
| For efficient operation, cells must be able to do two things: |
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Definition
Cells must be able to turn on or turn off the transcription of loci.
Cells must be able to recognize environmental conditions in which they should activate or repress transcription of the relevant loci. |
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Term
| Activators and repressors |
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Definition
Activators (positive regulators), proteins that promote transcription
Repressors (negative regulators), proteins that inhibit transcription. |
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Term
| two classes of regulators |
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Definition
| activators and repressors |
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Term
| basal level of transcription |
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Definition
| This low level of transcription in the absence of regulatory proteins is called the constitutive or basal level of transcription |
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Term
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Definition
Typically the activator uses one domain to bind to a site on the DNA near the promoter. With another domain it interacts with RNA pol helping to bring RNA pol to the promoter.
This mechanism is called recruitment and it is an example of cooperative binding of proteins to DNA. |
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Definition
| a protein called an architectural protein binds between activator sites to assist in DNA bending. |
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Term
| the model for the lac operon in E. coli. |
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Definition
| 1950’s Francois Jacob and Jacques Monod |
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Term
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Definition
| is a cluster of loci whose control is under a single operator. It has the transcribed portion of the locus and sequences that RNA polymerase and proteins that regulate the binding of RNA polymerase bind to. |
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Definition
| disaccharide molecule made up of galactose and glucose |
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Definition
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Definition
| Cleaves lactose into to yield glucose and galactose.) |
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Definition
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Definition
| Transports lactose into the cell and as well as toxic thiogalactosides.) |
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Term
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Definition
| thiogalactoside transacetylase |
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Term
| thiogalactoside transacetylase |
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Definition
| rids the cell of toxic thiogalactosides. |
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Term
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Definition
| because each mRNA includes the information for more than one protein. |
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Term
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Definition
| A transcription factor is a protein that binds onto the DNA and either promotes the binding of RNA polymerase or inhibits it. |
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Definition
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Definition
| The process of the relief of repression for systems such as this one is called induction. |
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Term
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Definition
| The compound that causes the release of the repression is called the inducer |
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Term
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Definition
| A cis control element is a portion of the DNA that is on the same chromosome as the locus it controls. |
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Term
| A trans control element is |
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Definition
| A trans control element is a compound (usually a protein) that binds to the DNA and either promotes or inhibits the binding of RNA polymerase. |
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Term
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Definition
| Negative control occurs when a compound binds to the DNA and prevents or inhibits the binding of RNA pol. |
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Term
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Definition
| Positive control occurs when a compound binds to the DNA and promotes the binding of RNA pol. |
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Term
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Definition
| cyclic adenosine monophosphate |
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Definition
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Definition
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Definition
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| - is the sum total of the chemical reaction in an organism |
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Definition
| building up of something. ie amino acids into protein |
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Definition
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| example of signal integration. |
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Definition
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Definition
| coordinated with the expression of other loci |
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Definition
One example is the heat-shock σ32, that directs RNA pol to loci involved in protecting the cell from heat shock.
Bacteriophage SPO1 infects Bacillus subtilis. |
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Term
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Definition
| an excess of product leads to a shutdown of the production of the enzymes that synthesize that product. |
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Term
| example of a repressible system |
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Definition
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Definition
| a type of control found in the trp operon |
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Definition
Two life cycle possibilities.
Lytic cycle.
Lysogenic cycle |
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Definition
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Definition
| Enhancers promote transcription when the appropriate trans-acting elements (activators) are bound to them. |
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Term
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Definition
| Silencers inhibit or prevent transcription when the appropriate trans-acting elements (repressors) are bound to them. |
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Term
| general transcription factors |
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Definition
| because they are the minimal requirement for RNA pol. II to initiate transcription (usually very weakly). |
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Term
| example of a trans-acting enhancer binding protein |
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Definition
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Term
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Definition
| upstream activating sequences |
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Term
| Loss-of-function dominant mutations |
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Definition
| Inactivation of one of the two copies of a gene reduces the output of transcript below a threshold level. Get a dominant appearing mutation where the diseased state is dominant |
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Term
| Gain-of-function mutations |
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Definition
| Dominant because misregulation produces a new property of the locus. Arise as a result of the fusion of the regulatory apparatus of one locus with another locus. A result of chromosomal rearrangements placing the promoter of a locus within the range of the enhancers of the other locus and these enhancers and effect both loci. |
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Term
| example of gain of function |
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Definition
| bar mutation in drosophila |
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Term
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Definition
| A hormone is a compound produced by cells in one part of the body that travels in the blood or body fluids to another part of the body where it effects certain cells. |
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Definition
| Changes in heritable characters that are not the result of changes in the DNA sequence. |
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Term
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Definition
| Alleles suffer irreversible changes as a result of being in a cell with another allele. |
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Definition
| : A gene is expresses only if that gene was inherited from a parent with a particular sex |
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Definition
| The use of the information in an mRNA molecule to order the amino acids in a protein. |
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Definition
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| mixed poly (U) with protein-synthesizing machinery and got synthetic protein |
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Definition
| 1961 Nirenberg and Heinrich Matthaei |
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Term
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Definition
| five prime to three prime |
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Term
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Definition
| 5’ D loop, anticodon, the variable arm, ψU loop, amino acid attachment site. 3’ |
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Term
| energy for formation of peptide bond |
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Definition
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Term
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Definition
| This relaxation of the pairing rules at the 5’ end of the anticodon is called wobble. |
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Definition
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Definition
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Definition
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| codons that do not designate an amino acid |
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Definition
| a measurement of sedimentary velocity |
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Definition
| The study of all the proteins that a genome can produce |
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Definition
| the production of RNAs and proteins. |
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| The central dogma of molecular biology was enunciated |
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Definition
| by Francis Crick in 1958. |
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Definition
The flow of information from loci to proteins
The flow is unidirectional
Information here means the precise determination of sequence. |
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Definition
| is the production of an RNA molecule using a DNA molecule as a template. |
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Definition
| The RNA product of transcription. |
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Definition
| : transports amino acids to the translation complex and aligns them at the correct location along the mRNA. |
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Definition
| Combine with proteins to make ribosomes. rRna’s do most of the catalytic functions of the ribosomes |
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Term
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Definition
| small nuclear RNA’s. combine with specific proteins to form ribonucleoprotein particles (snRNP’s |
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Term
| evolutionarily conserved. |
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Definition
The character is very important to the fitness of the life form.
The character is important to the fitness of the life forms in many species. |
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Term
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Definition
| A consensus sequence is a series of nucleotides in the DNA that is the same at many loci. Note must be in the same region as well |
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Term
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Definition
| The transition from the closed to the opening of the DNA is called isomerization. |
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Term
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Definition
Cleavage of the message
Addition of many adenine residues to the 3’ end of the transcript
And subsequently termination of transcription |
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Term
| Polyadenylation is mediated by the enzyme |
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Definition
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Term
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Definition
| 1. Protects against degradation. 2. Participates in the initiation of translation. |
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Term
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Definition
| 1. regulation of translation. 2. necessary for nucleocytoplasmic transport 3. protects against degradation. |
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Term
| The functions of the 5’ and 3’ UTRs include |
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Definition
| mRNA localization, regulation of RNA lifetime and translation control. |
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Term
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Definition
| Splicing is the removal of inton stretches and the subsequent splicing of the exons (the coding sequences) together. |
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Term
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Definition
| primary transcript before splicing |
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Term
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Definition
| Alternative splicing leads to different proteins being produced from the same locus. |
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Term
| 3 sequences at intron exon junctions |
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Definition
5' splice site:GU
3' splice site:AG
branch site-A |
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Term
| Two successive transesterification reactions occur |
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Definition
The first reaction is triggered by the 2’ OH of the conserved A at the branch site.
This group acts as nucleophile to attack the phosphoryl group of the conserved G in the 5’ splice site.
In the second transesterification reaction, the 3’OH of the 5’ exon becomes a nucleophile that attacks the phosphoryl group at the 3’ splice site (Fig. 13-3). |
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| Self-splicing RNA experiment |
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Definition
| Thomas Cech and coworkers in Tetrahymena |
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Term
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Definition
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Term
| The snRNPs have three roles in splicing: |
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Definition
They recognize the 5’ splice site and the branch site
They bring those sites together as required
They cataylze or help to catalyze the RNA cleavage and joining reactions. |
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Term
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Definition
| Exonucleases can only degrade from the end of the nucleic acid polymer (RNA or DNA). |
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Term
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Definition
| Endonucleases can degrade nucleic acid polymers by cutting into the chain in areas other than the en |
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Term
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Definition
| Primase is a specialized RNA pol dedicated to making short, RNA primers (5-10) nucleotides long on a ssDNA template. |
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Term
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Definition
| recognizes and removes most of each RNA primer. |
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Term
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Definition
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Term
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Definition
| The combination of all the proteins that function at the replication fork is called the replisome. |
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Term
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Definition
| Holoenzyme is a general name for a multiprotein complex in which the core enzyme activity is associated with additional components that enhance function. |
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Term
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Definition
| The specific sites at which DNA unwinding and initiation of replication occur are called origins of replication. |
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Term
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Definition
| all the DNA replicated from a particular origin as a replicon. |
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Term
| The replicon has two components, |
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Definition
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Term
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Definition
| The replicator is defined as the entire set of cis-acting DNA sequences that is sufficient to direct the initiation of DNA synthesis. |
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Term
| The single replicator for E. coli |
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Definition
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Term
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Definition
| The 9-mer motif is the binding site for the initiator, DnaA protein, and is repeated five times at oriC |
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Term
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Definition
| The 13-mer motif, repeated 3 times is the initial site of ssDNA formation. |
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Term
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Definition
| initiator, helicase, helicase loader |
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Term
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Definition
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Term
| where is active telomerase |
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Definition
| germ line and young cells |
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Term
| example of a ribonucleoprotein |
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Definition
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Term
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Definition
| 1.5 complementary TAACCCTAA |
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Term
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Definition
| a class of DNA polymerases that can use RNA as a template to produce DNA called reverse transcriptases. |
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Term
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Definition
| ribosome binding site shine dalgarno sequence |
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Term
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Definition
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Term
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Definition
| the phenomenon of linked translation between overlapping orfs |
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Term
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Definition
| unusuall 5' to 5' linkage |
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Term
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Definition
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Term
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Definition
| refers to the transfer of amp |
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Term
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Definition
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Term
| driving force for adenylylation |
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Definition
| hydrolysis of pyrophosphate |
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Term
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Definition
| accept the same amino acid (trna) |
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Term
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Definition
| accept the same amino acid (trna) |
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Term
| areas of recognition of trna |
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Definition
acceptor arm (discriminator base)
anticodon loop |
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Term
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Definition
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Term
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Definition
| removes formyl group from amino terminus |
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Term
| translation initiation factors |
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Definition
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Term
| what binds to poly a binding protein in circularizing eukaryotic mrna |
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Definition
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Term
| moving the mrna through the ribosome |
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Definition
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Term
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Definition
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Term
| why do we study rna pol 2 |
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Definition
| most studied and transcribes for most genes |
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Term
| metal ions in transcription |
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Definition
| mg 2+ active site has one and the other comes in with each new nucleotide |
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Term
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Definition
| initiation elongation and termination |
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Term
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Definition
| a promoter is the dna sequence that initially bind the rna polymerase |
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Term
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Definition
| once an enzyme has made a transcript of longer thn ten nucleotides |
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Term
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Definition
| how well polymerase binds to it how efficiently it supports isomerization and how readily the pol can escape |
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Term
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Definition
| runs into pol usually causing it to dissociate then trcf recruits repair enzymes |
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Term
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Definition
| refers to the minimal set of sequence elements required for accurate transcription initiation by the pol 2 machinery as measured in vitro. |
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Term
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Definition
| help pol binds to the promoter and melts the dna and help pol to escape from the promoter |
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Term
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Definition
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Term
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Definition
| the complete set of general transcription factors and polymerase bound to gether at the promoter and poised for initiation is called the preinitiation complex |
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Term
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Definition
| hydrolyzes atp and promoter melting transition from preinitiation complex to open complex |
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Term
| word order for pol 2 core promoter drawing |
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Definition
| bre, tata inr, dcex2, dpe, dce |
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Term
| sequences at intron exon boundaries drawing sequence of nts |
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Definition
| c/aggua/g...ynyuray...agg |
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