Term
| why protein synthesis is called translation |
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Definition
| because the 4 letter alphabet of nucleic acids is translated into the 20 letter alphabet of proteins |
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Term
| some characteristics of the genetic code |
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Definition
1: 3 nucleotides encode an amino acid
2: the code is nonoverlapping
3: the code has no punctuation; it is read sequentially from a fixed starting point without punctuation
4: the genetic code has directionality (5'-->3')
5: the genetic code is degenerate |
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Term
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Definition
| group of 3 bases that encodes an amino acid |
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Term
| is the genetic code overlapping or nonoverlapping? |
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Definition
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Term
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Definition
| sequentially from a fixed starting point with no punctuation |
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Term
| direction the genetic code is read |
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Definition
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Term
| how the genetic code is degenerate |
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Definition
| this means that some amino acids are encoded by more than 1 codon |
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Term
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Definition
| codons that specify the same amino acid |
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Term
| depiction of the genetic code |
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Definition
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Term
| why the degeneracy of the genetic code is advantageous |
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Definition
| because it minimizes the deleterious effects of mutations |
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Term
| why the genetic code is almost, but not entirely, universal |
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Definition
| because some codons translate differently in different organisms |
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Term
| why the genetic code of mitochondria differs from the rest of the cell |
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Definition
| because mitochondrial DNA encodes a distinct set of transfer RNAs, adaptor molecules that recognize the alternative codons |
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Term
| depiction of the distinctive codons of human mitochondria |
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Definition
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Term
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Definition
| serves as the adaptor molecule between the codon and its specified amino acid |
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Term
| how tRNA acts as an adaptor |
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Definition
| by binding to a specific codon and brings with it an amino acid for incorporation into the polypeptide chain |
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Term
| some features of all known transfer RNA molecules |
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Definition
1: single strand containing 73-93 ribonucleotides
2: the 3D molecule is L-shaped
3: contain many unusual bases, typically 7-15 per tRNA, such as methylated derivatives of A, U, C, and G
4: can be arranged in a clover leaf pattern when depicted in 2D; it also has about half the nucleotides base-paired to form double-helices; also has 5 groups of bases that are not base paired
5: the 5' end is phosphorylated, with the 5' residue usually being pG
6: the activated amino acid is attached to a hydroxyl group of the adenosine residue located at the end of the 3' CCA component of the acceptor stem
7: the anticodon is present in a loop near the center of the sequence |
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Term
| depiction of transfer RNA structure |
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Definition
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Term
| what methylation of certain bases does for tRNA |
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Definition
-prevents the formation of certain base pairs, rendering some of the bases accessible for for interactions with other components of the translation machinery
-gives some regions of tRNA hydrophobic character |
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Term
| the 5 groups of bases that are not base paired in tRNAs |
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Definition
-the 3' CCA terminal region, which is part of the acceptor system
-the TψC loop, which got its name from ribothymine-pseudouracil-cytosine
-the "extra arm," which contains a variable number of residues
-the DHU loop, which contains several dihydrouracil residues
-the anticodon loop |
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Term
| depiction of the general structure of transfer RNA molecules |
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Definition
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Term
| why some tRNAs can recognize more than 1 codon |
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Definition
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Term
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Definition
| states that some tRNAs can recognize more than 1 codon because of steric freedom in pairing of the 3rd base of the codon |
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Term
| depiction of allowed pairings at the third base of the codon according to the wobble hypothesis |
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Definition
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Term
| 2 generalizations that can be made concerning the codon-anticodon interaction |
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Definition
1: codons that differ in either of their first 2 bases must be recognized by different tRNAs
2: the first baser of an anticodon determines whether a particular tRNA molecule reads 1, 2, or 3 kinds of codons; thus, part of the degeneracy of the genetic code arises from imprecision in the pairing of the third base of the codon with the first base of the anticodon |
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Term
| part of the degeneracy of the genetic code arises from... |
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Definition
| imprecision in the pairing of the third base of the codon with the first base of the anticodon |
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Term
| the observed error rate of protein synthesis |
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Definition
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Term
| table of the accuracy of protein synthesis |
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Definition
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Term
| aminoacyl-tRNA synthetases |
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Definition
| catalyze the activation of amino acids |
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Term
| 2 reasons the specific linkages between amino acids and specific tRNAs are crucial |
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Definition
1: the attachment of a given amino acid to a particular tRNA establishes the genetic code
2: the formation of a peptide bond is not thermodynamically favorable, so the amino acid must first be activated |
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Term
| what establishes the genetic code? |
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Definition
| the attachment of a given amino acid to a particular tRNA |
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Term
| why an amino acid must be activated before being added to the polypeptide chain |
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Definition
| because the formation of that bond is thermodynamically unfavorable |
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Term
| the activated intermediates in protein synthesis |
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Definition
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Term
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Definition
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Term
| aminoacyl-tRNA aka charged tRNA |
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Definition
| an amino acid ester of tRNA |
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Term
| amino acids are activated by... |
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Definition
| attachment to transfer RNA |
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Term
| depiction of aminoacyl-tRNA |
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Definition
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Term
| amino acids are first activated by... |
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Definition
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Term
| the first step in the activation of amino acids |
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Definition
| the formation of an aminoacyl adenylate from the amino acid and the ATP |
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Term
| depiction of aminoacyl adenylate aka aminoacyl-AMP |
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Definition
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Term
| the 2 steps of activation of an amino acid by adenylation |
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Definition
1: formation of an aminoacyl adenylate from an amino acid and ATP
2: the transfer of the aminoacyl group to a particular tRNA molecule to form aminoacyl-tRNA |
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Term
| the net rxn of the activation of amino acids |
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Definition
| amino acid + ATP + tRNA + H2O --> aminoacyl-tRNA + AMP + 2 Pi |
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Term
| the energy consumed in the synthesis of aminoacyl-tRNA |
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Definition
| equivalent of 2 molecules of ATP consumed in the synthesis of each aminoacyl-tRNA |
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Term
| how translation takes place |
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Definition
| takes place with the formation of the ester linkage between an amino acid and a specific tRNA |
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Term
| the actual translators of the genetic code |
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Definition
| the aminoacyl-tRNA synthetases |
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Term
| how aminoacyl-tRNA synthetases are specific in their binding |
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Definition
| they have highly discriminating amino acid activation sites |
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Term
| depiction of the active site of threonyl-tRNA synthetase |
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Definition
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Term
| one way the fidelity of protein synthesis is increased |
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Definition
| proofreading by aminoacyl-tRNA syntyhetases |
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Term
| how the aminoacyl-tRNA can be edited without dissociating from the synthetase |
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Definition
| the CCA arm with the amino acid attached to it can swing out of the activation site and into the editing site, which hydrolyzes the bond between the amino acid and the tRNA, providing an opportunity for correction |
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Term
| depiction of the editing of aminoacyl-tRNA |
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Definition
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Term
| the point at which translation takes place |
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Definition
| synthetases choosing their tRNA partners |
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Term
| depiction of the recognition sites on tRNA |
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Definition
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Term
| depiction of the ribosome at high resolution |
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Definition
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Term
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Definition
| the molecular machines that coordinate the interplay of aminoacyl-tRNAs, mRNA, and proteins |
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Term
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Definition
-large subunit
-small subunit
-both subunits made of nearly 2/3 RNA and 1/3 protein |
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Term
| depiction of ribosomal RNA folding pattern |
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Definition
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Term
| the catalytic sites in the ribosome are composed almost entirely of... |
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Definition
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Term
| one reason it's advatageous for mRNA to be translated in the 5' --> 3' direction |
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Definition
| allows for translation to take place as it's being transcribed |
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Term
| a key feature of bacterial gene expression |
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Definition
| translation and transcription are closely coupled in space and time |
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Term
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Definition
| a group of ribosomes bound to an mRNA molecule |
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Term
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Definition
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