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Translation
Terms from Translation unit of 04-350 at NW
| Term | Definition |
|---|---|
| amino acid | monomeric subunit used to form a polypeptide or protein |
| amino group | NH3+, functional group that is part of an amino acid. You could consider this the head of the monomer. |
| carboxyl group | COOH, functional group that is part of an amino acid. Considered the tail of the monomer. |
| variable group | side chain of the amino acid that distinguishes one amino acid from another |
| radical group | another term for the variable group that distinguishes one amino acid from another |
| alpha carbon | the central carbon atom of an amino acid, with an amino group at one end, carboxyl group at the other and variable group |
| peptide bond | covalent bond that links amino acids together in a chain, extending from the carboxyl group of the first amino acid to the amino acid of the second. formed by peptidyl transferase during translation |
| thymidine | a nucleoside that may be found in RNA after chemical modification has occurred. found in the T loop of tRNA |
| dihydroxyuridine | a nucleoside that may be found in RNA after chemical modification has occurred. Found in the D loop of tRNA |
| inosine | a nucleoside that may be found in RNA after chemical modification has occurred. found in the anticodon of tRNA in particular |
| tRNA secondary structure | stem loops and hairpins of tRNA due to internal base pairing. greatly influenced by rare chemically modified bases |
| tRNA tertiary structure | overall 3D shape of a tRNA when stem loops are twisted and contorted. greatly influenced by rare chemically modified bases. determines which amino acyl synthetase will charge that tRNA |
| anticodon | three nucleotides forming a loop at the bottom of the tRNA. Responsible for binding with the mRNA codon when the genetic code is read. |
| D loop | loop of a tRNA closes to the 5' end of the molecule. Contains dihydroxyuridine |
| T loop | loop of a tRNA closest to the 3' end of the molecule. Contains a thymidine due to chemical modification |
| variable loop | Loop of a tRNA that may or may not be present. Has a big impact on overall shape |
| acceptor stem | CCA sequence added to the 3' end of the tRNA after it has been transcribed. Serves as the connection point for the amino acid when charging occurs |
| charging | process by which amino acids are attached to the acceptor stem of a tRNA. Requires the consumption of energy. |
| amino acyl tRNA synthetase | Enzyme responsible for charging the tRNA... one for each amino acid. Recognizes the tRNA with the proper shape and uses them as a substrate for the charging reaction. |
| codon | sequence of three nucleotides found within the mRNA that specifies which amino acid will be incorporated into the polypeptide during translation |
| triplet | the fact that the code contains three bases to make up one codon |
| nonambiguous | one codon sequence always codes for the same amino acid |
| non overlapping | a single base in a codon is part of only one codon... not multiple |
| non punctuated | the genetic code is not broken up using markers to distinguish one codon from the other |
| redundant | the genetic code has multiple codons that code for the same amino acid. also known as a degenerate code |
| universal | the genetic code is interpreted in the same way in nearly all organisms |
| start codon | AUG sequence that serves as the first codon in all open reading frames |
| stop codon | a sequence in the mRNA that indicates where translation will stop. not recognized by any tRNA but recognized by release factors instead. also known as nonsense codons |
| ORF | open reading frame, a string of consecutive codons that begin with a start codon and concludes with a stop |
| sense codon | a codon that codes for an amino acid |
| non Watson Crick base pairng | possibility of improper complementary base pairing that violates Chargaff's Rules, of A-U, and C-G pairing. Possible but not thermodynamically stable. Occurs during mutation and wobble. |
| wobble | improper pairing between bases at the third position of the codon and the first position of the anticodon |
| Svedberg unit | S, unit of measure that includes not only mass but factors related to density. How likely will a molecule sink through a density gradient |
| ribosome | machinery for protein synthesis, composed of two subunits (one large and one small) |
| small ribosomal subunit | complex of rRNA and protein that serves as one half of a functional ribosome |
| large ribosomal subunit | complex of rRNA and protein that serves as one half of a functional ribosome |
| A site | amino acyl site, binding site on the ribosome where new tRNA deliver amino acids during translation |
| P site | peptidyl site, binding site in the middle of the ribosome where the first tRNA is in place but subsequent tRNA enter this site during translation |
| E site | exit site, exit channel where uncharged tRNA will leave the ribosome after being used in translation |
| factor binding center | portion of the large ribosomal subunit that makes contact with elongation factors to insure the proper tRNA is in the A site |
| peptidyl transferse | ribozyme that is part of the large ribosomal subunit, responsible for making the peptide bonds between amino acids during translation |
| 5' UTR | 5' untranslated region, portion of the mRNA at the 5' end that does not contain codons, upstream of the start codon |
| 3' UTR | 3' untranslated region, portion of the mRNA after the stop codon that does not contain codons that will be translated |
| monocistronic | a mRNA that contains a single ORF |
| polycistronic | a mRNA that contains multiple ORF so a single RNA is responsible for multiple proteins |
| ribosomal binding site | also known as the Shine Dalgarno sequence, prokaryotic sequence found in the 5' UTR adjacent to the start codon. The sequence is complementary to the sequence found in the rRNA of the small ribosomal subunit |
| initiator tRNA | first tRNA used to initiate translation, binds to the start codon. In eukaryotes it carries methionine and in prokaryotes it carries a chemically modified version of methionine (fMet) |
| fMet | chemically modified methionine used during initiation of prokaryotic translation carried by the initiator tRNA |
| Methionine | unmodified amino acid used in the middle of a prokaryotic protein and as the first amino acid or internal amino acid in eukaryotic polypeptides |
| IF1 | initiation factor 1, in prokaryotes used to keep the A site free until the ribosome assembles |
| IF2 | initiation factor 2, protein in prokaryotes that holds the initiator tRNA in place until the ribosome assembles |
| IF3 | initiation factor 3, protein in prokaryotes that keeps lrge and small ribosomal subunits apart until they recognize a mRNA |
| GTP | guanosine triphosphate, RNA monomer, also a high energy molecule used to drive various steps of translation |
| methyl guanosine cap | 5' end of mature mRNA, binding site of eukaryotic initiation factors of translation, where the ribosome will assemble |
| Kozak sequence | consensus sequence found in eukaryotic 5' UTR adjacent to the start codon, used to indicate which start codon should be used for initiation |
| cap binding proteins | eukaryotic translation initiation factors that bind to the methyl guanosine cap, mark the assembly point for eukaryotic ribosomes |
| EF-Tu | Elongation factor Tu, protein that guides new charged tRNA into the A site of the ribosome, carrying GTP, make contact with the factor binding center if all proper pairing of codon and anticodon occurs to stimulate peptidyl transferase |
| EF-G | elongation factor G, protein that burns GTP while associated with the small ribosomal subunit that causes the ribosome to move one codon during the translocation step of translation |
| release factor | proteins involved in termination of translation, either bind to the stop codon or disassemble the stalled ribosome |
| mRNA looping | interaction between cap binding proteins and poly A binding proteins causes eukaryotic mRNA to loop over on itself, increases rate of ribosomal recycling |
| post translational modification | alterations to polypeptides after translation has been completed, may include adding sugars or phosphate or removing segments of amino acids |
Created by:
jthorns
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