Term
| Consists of a sugar (deoxyribose). It is devoid of a hydroxyl (OH) group on the 2 carbon (specialized sugar). It is a nitrogen containing ring/base (purine/pyrimidine) |
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Definition
| DNA (deoxyribonucleic acid) |
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Term
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Definition
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Term
| Ring and a sugar and a phosphate (PO4) group |
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Definition
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Term
| 2 rings consisting of adenine (A) and guanine (G) |
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Definition
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Term
| 1 ring consisting of thymine (T) and cytosine (C) |
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Definition
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Term
| The structure of DNA is this type of structure |
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Definition
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Term
| When nucleotides join by a covalent bond |
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Definition
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Term
| Energy (electron) is placed into the system and energy (electrons) is released during the breaking of these bonds |
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Definition
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Term
| There is a covalent bond between the ____ _____ with a _________ group and the _________ ________ with a _________ group |
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Definition
| 5' carbon, PO4; 3 carbon, OH |
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Term
| Energy for covalent bonds comes from PO4 bonds ______, _________, and _________ |
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Definition
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Term
| 2 strands that are complementary; antiparallel: one strand runs 5' to 3' and the other strand runs 3' to 5'; hydrogen bonds: strands are connected by these |
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Definition
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Term
| Form of DNA with a left handed rotation and 12 base pairs per turn, does not exist in nature |
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Definition
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Term
| Form of DNA that has a right handed rotation and 10 base pairs per turn, found in animals |
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Definition
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Term
| Form of DNA that has a right handed rotation and 11 base pairs per turn |
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Definition
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Term
| When a closed circular form of DNA is split at the phosphodiester bond |
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Definition
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Term
| When an open circular form of DNA is split at the phosphodiester bond |
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Definition
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Term
| Form of DNA that is supercoiled and a negative form |
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Definition
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Term
| The base pairs containing 2 hydrogen bonds between them |
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Definition
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Term
| The base pairs containing 3 hydrogen bonds between them |
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Definition
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Term
| Double-stranded (each strand used in replication), anti-parallel: 3' to 5', circular (negative): negative supercoil, semi-conservative: 1 strand used as template and new strand formed from that |
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Definition
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Term
| Nucleotide used as a precursor in DNA replication |
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Definition
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Term
| Enzyme which removes oxygen from the 2 carbon of ribose, Transforms ATP to dATP |
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Definition
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Term
| Enzyme that adds a PO4 group to nucleotides and transforms ADP to ATP |
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Definition
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Term
| The alpha PO4 group binds the 5' carbon to the OH group of the 3' carbon, which is the only direction they can bind; it synthesizes by reading the strand from 3' to 5'; the beta: alpha phosphate is removed because of formed covalent bond (energy); it needs a pre-existing 3'-OH (primer); cannot undergo de novo synthesis (creating something out of nothing); 5'-3' exonuclease (removes primer): degrades DNA and removes RNA; 3'-5'exonuclease (proof reading): removes 1 nucleotide after another and destroys DNA |
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Definition
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Term
| Main enzyme in DNA replication (5,000 bp/sec), used in synthesis, probability of mistakes increases |
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Definition
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Term
| Enzyme used in DNA replication to repair/proof read (5 bp/sec), Utilizes the Klenow fragment, corrects mistakes made by the main enzyme utilized in DNA replcation |
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Definition
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Term
| Used in DNA replication, Only has polymerase activity and not exonuclease activity |
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Definition
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Term
| Used in DNA replication, 245 base pair sequence, theta and Y replication (viruses do not undergo) |
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Definition
| Origin of replication initiation |
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Term
| Recognizes origin of replication initiation site; separates DNA strands; Breaks hydrogen bonds that hold the 2 strands together; ATP dependent: twists DNA strands in opposite directions to break hydrogen bonds; DNA becomes single-stranded |
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Definition
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Term
| single-stranded binding proteins |
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Definition
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Term
| Prevents 2 strands from binding back together in DNA replication |
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Definition
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Term
| RNA primer used in DNA replication that recognizes 3'-GTC-5' |
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Definition
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Term
| Strand in DNA replication where continuous replication occurs read from 3'-5' |
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Definition
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Term
| Strand of DNA where discontinous replication takes place in DNA replication, read from 5'-3', Okazaki fragments are utilized on this strand |
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Definition
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Term
| Enzyme in DNA replication that is ATP dependent and joins fragments together to seal fragments together and create a continuous strand |
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Definition
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Term
| Enzyme in DNA replication that breaks 1 strand of DNA, is a negative supercoil: relaxed form (got rid of knotted strand); No ATP is utilized or needed: potential energy is converted to kinetic energy in order to bind broken strand back together |
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Definition
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Term
| Any of the short strands of DNA produced during discontinuous replication of the lagging strand |
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Definition
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Term
| Enzyme in DNA replication that breaks 2 strands; relaxed strand goes to a negative supercoil; is ATP dependent |
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Definition
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Term
| RNAs in DNA replication are removed by 5'-3' _________ |
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Definition
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Term
| DNA polymerase I utilizes these as proof reading factors in DNA replication |
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Definition
| dcm: methylate dCTP and dam: methylate dATP (inhibits exonuclease) |
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Term
| Synthesizes all RNA (mRNA, tRNA, and rRNA); makes complementary copy of DNA; 5'-3', does not require a primer |
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Definition
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Term
| RNA polymerase binds and recognizes to this DNA sequence; determines the efficiency and rate of transcription |
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Definition
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Term
| DNA sequence where repressor binds |
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Definition
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Term
| Subunit of RNA polymerase that aids in binding to promoter site (cannot bind to promoter without it) |
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Definition
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Term
| Most common promoter; template strands of DNA copied 3-GATCGATC-5; transcribed strand (3'-5'): 5-CUAGCUAG-3; other strand (coding strand - 5'-3'): 5-CTAGCTAG-3 (identical to transcribed RNA strand); Has a -35 site (TTGACA), 17 nucleotides (2 helix turns) in between and a -10 site (TATAAT); -10 and -35 are in the same plane and easy to bind to and they tell the relative position of the promoter; efficiency and rate of transcription severely decreases; weak promoter; cannot bind tightly; getting very few transcripts; RNA polymerase needs an activator to help it transcribe |
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Definition
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Term
| Bind adjacent to promoter so RNA polymerase can bind; increases efficiency |
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Definition
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Term
| Prevents and blocks transcription from proceeding |
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Definition
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Term
| Removes repressors to turn transcription on |
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Definition
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Term
| Termination step of transcription that involves RNA-DNA Helicase; binds to the carbon rich rut site and removes RNA polymerase so that transcription no longer takes place |
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Definition
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Term
| Termination step of transcription that involves the inverted repeat followed by several adenines; forms a secondary structure called a hairpin/stem loop; energy is greater than that of the RNA-DNA hybrid |
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Definition
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Term
| Protein involved in translation; Linear structure of amino acids; peptide bond |
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Definition
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Term
| Protein involved in translation; Alpha helices and beta sheets; hydrogen bond |
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Definition
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Term
| Protein involved in translation; Di-sulfide bond |
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Definition
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Term
| Protein involved in translation; More than 1 polypeptide coming together; alpha2 protein: gene; alphabeta protein: 2 different genes transcribed and translated to give subunits |
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Definition
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Term
| Ribosome, 70s, bacteria; 30s-16s + 21 proteins (small subunit) and 50s-23s + 5s + 31s (large subunit that joins amino acids) - composed of nucleotides of a non-linear scale |
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Definition
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Term
| Ribosomes are found in the cytoplasm in _______ __________ |
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Definition
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Term
| Ribosomes are found in the endoplasmic reticulum in _______ ________ |
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Definition
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Term
| Sequence of 3 nucleotides that encodes for a specific amino acid; Complementary to anticodons |
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Definition
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Term
| Enzyme involved in translation that recognizes a specific tRNA molecule and connects to it (charges tRNA) |
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Definition
| Aminoacyl-tRNA-synthetase |
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Term
| Ribosomal binding site in translation; codons are present here |
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Definition
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Term
| Binding of ribosome to mRNA; 30s binds (16s) first because of complementary base pairing; involves Shine-Dalgarno sequence; ribosomal binding site (AGGAGG): 4-10 base pairs up from start |
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Definition
| Initiation of translation |
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Term
| Purine (As and Gs) rich region, which contains a short sequence of six nucleotides usually 5’-AGGAGG-3’ |
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Definition
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Term
| During initiation of translation, the ________ binds after the ________ |
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Definition
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Term
| Help the assembly of the initiation complex during the initiation step of translation |
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Definition
| Initiation factors 1, 2 and 3 |
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Term
| Genes; begins with a start (initiation) codon and stops with a stop (nonsense) codon |
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Definition
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Term
| Proteins known as elongation factor Tu (Ef-Tu) and elongation factor G (Ef-G) usher the appropriate tRNA into the _________ _________ of the ribosome |
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Definition
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Term
| The complementary nucleotide sequences pair to form a double stranded RNA structure that binds the mRNA to the ribosome so that the start codon is placed at the _________ _________ |
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Definition
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Term
| The ribosome moves three nucleotides toward the 3’ end of the mRNA and the tRNAs move relative to the ribosome, because of codon-anticodon base-paring, and the uncharged tRNA is moved to the __________ ________ |
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Definition
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Term
| Attaches tRNA to A site and it knows to bind because of the codon |
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Definition
| Elongation factor Tu (Ef-Tu) |
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Term
| Trans locates to the P site |
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Definition
| Elongation factor G (Ef-G) |
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Term
| Enzyme that forms a peptide bond between 2 adjacent amino acids for the 23s |
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Definition
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Term
| Aminoacyl-tRNA-synthetase utilizes _________ in order for translation to occur |
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Definition
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Term
| During the termination step of translation, these do not encode for an amino acid |
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Definition
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Term
| Stop codons pause because there is no tRNA and no polypeptides available to bind to the amino acid |
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Definition
| UAA (most common), UGA, UAG |
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Term
| Only codes for 1 amino acid (Methionine); most common |
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Definition
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Term
| Proteins that recognize and bind to the stop codons and bring the polypeptide synthesis to a stop |
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Definition
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Term
| Recognizes the stop codons UAA and UAG |
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Definition
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Term
| Recognizes the UAA and UGA stop codons |
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Definition
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Term
| Catalyzes the release of RF1 and RF2 at the end of the termination process of translation by binding with either RF1 or RF2, depending upon the stop codon being used |
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Definition
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Term
| Cuts covalent bond between last amino acid and removes tRNA from the polypeptide and releases the polypeptide from the ribosome to become a newly synthesized protein |
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Definition
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Term
| The ribosome release factors move down the __________ ________ ________ while the P site and the A site activity takes place and the ribosome dissociates into its large (50S) and small (30S) subunits |
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Definition
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Term
| A single DNA unit enabling the concurrent regulation of the three structural genes—lacZ, lacY, and lacA—in response to environmental changes; utilizes a negative regulation system |
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Definition
| lac (the ability to utilize lactose) operon |
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Term
| 2 or more open reading frames under the control of a single promoter |
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Definition
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Term
| Encodes β-galactosidase, an enzyme that cleaves the disaccharide lactose into glucose and galactose |
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Definition
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Term
| Encodes β-galactoside permease, a membrane-bound transport protein that causes additional lactose to come into the cell |
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Definition
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Term
| Encodes β-galactoside transacetylase, an enzyme that transfers an acetyl group from acetyl-CoA to β-galactosides |
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Definition
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Term
| Only _____ and _______ appear to be prudent for the breaking down of lactose |
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Definition
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Term
| Utilizes the repressor protein ______ to inhibit the expression of the genes involved in the coding for proteins by impeding RNA polymerase from transcribing mRNA on the open reading frame sequence by preventing it from binding; also inhibits the production of β-galactosidase during the absence of lactose and the genes are only repressed when lactose is not present in the cell; binds to the DNA sequence near O causing RNA polymerase not to bind to P, which is a weak σ70 promoter; When lactose is present in the cell, allolactose (a combination of glucose and galactose) binds to ______ and __________ does not bind to O and RNA polymerase is able to transcribe the open reading frame |
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Definition
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Term
| Glucose utilizes the __________ _________ _________ to increase production of β-galactosidase when glucose is not present in the cell |
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Definition
| Catabolite activator protein (CAP) |
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Term
| A signal molecule whose prevalence is inversely proportional to that of glucose and it binds to CAP so that CAP can bind to the CAP binding site (a site 16 base pairs upstream from the P) |
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Definition
| Cyclic adenosine monophosphate (cAMP) |
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Term
| Activator of the lac operon |
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Definition
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Term
| The _______ gene encodes for ___________, which produces cyclic AMP and requires ATP in order to be produced |
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Definition
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Term
| The gene _______ encodes for CAP |
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Definition
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Term
| The activator binds adjacent to the ________ and stabilizes RNA polymerase so that it can bind to the ________ and the presence of glucose inhibits LacY by uncoupling entergetics and not allowing lactose to come into the cell |
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Definition
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Term
| There will not be an ________ present in the cell during the presence of glucose for the lac operon |
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Definition
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Term
| Glucose essentially removes the ________ and allows LacI to bind to the Operator of the cell |
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Definition
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Term
| In the absence of glucose, the cAMP concentration is ________ and binding of CAP-cAMP to the open reading frame _________ the production of β-galactosidase, enabling the cell to digest lactose and release galactose and glucose. |
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Definition
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Term
| The lac operon utilizes a ________ regulation system |
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Definition
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Term
| The ara operon utilizes a ________ regulation system |
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Definition
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Term
| The activator of the ara operon |
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Definition
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Term
| The inducer of the ara operon |
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Definition
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Term
| The repressor of the ara operon |
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Definition
| Ara C (regulatory protein) |
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Term
| The activator of the ara operon |
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Definition
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Term
| If arabinose is ________, it builds a complex: AraC and arabinose, This complex is needed for RNA polymerase to bind to the promoter and transcribe the ara operon; Also for activation the binding of another structure to araI is needed: CAP and cyclic AMP; So the activation depends on the __________ of arabinose and cAMP |
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Definition
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Term
| If arabinose is __________, the AraC protein assumes a different conformation. In this conformation the AraC protein binds to the araI DNA region as well as to the araO DNA region. This causes the DNA to form a loop, preventing transcription of the downstream ara operon elements. |
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Definition
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Term
| A ________ _________ must be formed in order for the positive expression of the arabinose operon to occur |
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Definition
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Term
| High levels of _______ in the environment will repress the arabinose operon due to low levels of the cAMP molecule |
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Definition
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Term
| The arabinose operon consists of three structural genes _____, ______, _______ that code for the catabolic enzymes: kinase, isomerase and epimerase respectively and a C gene, a conventional gene that produces a protein product that combines with arabinose and acts positively to “turn on” the arabinose operon |
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Definition
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Term
| Two promoter sites of the ara operon |
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Definition
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Term
| Two operator sites of the ara operon |
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Definition
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Term
| The regulatory protein of the ara operon that has three binding sites, O1, O2 and ara I |
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Definition
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Term
| In the _________ of arabinose the regulatory protein binds simultaneously to the ara I and O2 regions causing the operon to fold on itself thereby blocking transcription of the ara B, A and D genes |
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Definition
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Term
| When arabinose is ________, it binds to the ara C gene product and stimulates the transcription of the structural B, A and D genes. The cAMP-CAP complex acts by promoting a rearrangement of the ara C gene and in rearrangement, it represses transcription to a state in which it activates the promoter, Pbad of the ara B, A and D genes. |
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Definition
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Term
| Only when the levels of its gene product become _________, does the ara C gene activate its promoter, Pc and code for its gene product regardless of the levels of arabinose present in the environment |
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Definition
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Term
| Arabinose creates xyulose-5-phosphate which is a ___________ ___________ __________ |
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Definition
| Pentose phosphate pathway |
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Term
| Carbon is a _______ for the ara operon when a loop is formed and this can only occur when carbon is bound to the O2 site |
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Definition
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Term
| The ara operon will not have a repressor if ______ is not present |
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Definition
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Term
| In order for BAD to be expressed in the ara operon, _______ and ________ must be present |
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Definition
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Term
| When carbon binds to OI and O2, carbon is a repressor for ________ |
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Definition
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Term
| BAD is not expressed when ______ is present because adenyl cyclase is inhibited and no cAMP or CAP is present |
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Definition
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Term
| The operator of induction of the ara operon |
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Definition
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Term
| BAD is always being made in the ara operon but it is _________ _________ with the presence of carbon |
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Definition
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Term
| Carbon is not permanently bound to the operator sites and any time carbon falls off of the operator sequence, another operator site is at _______ or ________ |
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Definition
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Term
| Carbon's affinity to OI is _________ |
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Definition
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Term
| Carbon's affinity to O2 is ________ in the presence of arabinose |
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Definition
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Term
| Carbon has a _______ affinity for O2 in the absence of O2 |
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Definition
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Term
| Presence of arabinose causes a ___________ __________ |
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Definition
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Term
| ara operon has ________ regulation because carbon is always present, just not always bound, turning on transcription/translation |
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Definition
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Term
| lac operon has __________ regulation because when LacI is bound to the operator site, LacZ, LacY, and LacA are impeded, turning off transcription/translation |
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Definition
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Term
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Definition
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Term
| When there is a closed conformation loop, Ara C is a __________ for BAD |
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Definition
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Term
| When there is an open conformation, Ara C is an _________ for BAD |
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Definition
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Term
| Ara C can act as a _________ for C and an ___________ for BAD when arabinose is present and the activator is present and carbon is bound to the O2 site and the O1 site |
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Definition
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Term
| The third stage of protein biosynthesis in which the sequence of nucleotides in a messenger RNA (mRNA), produced by transcription, directs the assembly of the correct sequence of an amino acid chain in the corresponding polypeptide; this polypeptide will later be formed into a protein |
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Definition
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