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Clemson BCHM 3050 - Translation and Protein Synthesis

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BCHM 3050 1st Edition Lecture 23Outline of Last Lecture I. Transcription in EukaryotesII. Eukaryotic RNA PolymerasesIII. Eukaryotic PromotersIV. Initiation of Eukaryotic TranscriptionV. EnhancersVI. RNA ProcessingVII. 5’ Cap of Eukaryotic mRNAVIII. mRNAPolyadenylationIX. mRNA SplicingOutline of Current Lecture I. Introduction to TranslationII. Cracking of the Genetic CodeIII. The Complete mRNA Genetic CodeIV. Codons vs. AnticodonsV. The “Wobble” HypothesisVI. Formation of Aminoacyl-tRNAsVII. Requirements for Protein SynthesisVIII. Ribosome StructureIX. Formation of the Prokaryotic Initiation ComplexX. Peptide ElongationCurrent LectureI. Introduction to TranslationThese notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute.a. HIV is a virus that has genetic material; it has RNA at first and once it gets into a host, it makes the RNA into DNA and it integrates this DNA into the genome of the hostb. Translation – the “coded” mRNA-dependent synthesis of protein (or the use of the genetic directions encoded in mRNA to synthesize proteins)II. Cracking of the Genetic Codea. Bacterial extract contains all components/co-factors required for protein synthesis (including tRNA’s, ribosomes, amino acids, ATP, GTP) except mRNA.b. Similar experiments were performed with other mRNA’s (e.g. poly A’s à poly-lysine; poly C’s à poly-proline; other triplet combinations gave other peptides.c. Eventually, all possible combinations of triplet (tri-nucleotide) codons were tested and assigned their corresponding amino acid.d. Several scientists came to this same conclusion but Nirenberg and Matthaei “wonthe race”e. Everything needed for translation in is the bacterial extract, except mRNA, which has to be made new everytimef. The key difference between DNA polymerase and RNA polymerase is that RNA polymerase does not need a primer; DNA polymerase requires a primer in order to start extending a DNA chaing. 1st observation à there is a code; the nitrogenous bases code for specific amino acidsh. Then, when they put 2 different alternating bases in a sequence, they got 2 different amino acids, and 2 different amino acid sequence combinationsi. 2 different base sequences à UCU-CUC-UCU-CUC & CUC-UCU-CUC-UCUj. They determined that there is probably more than one combination that codes for a specific amino acidk. Then, they put 3 nucleotides together, and they were able to figure out that 3 bases = 1 amino acidIII. The Complete mRNA Genetic Codea. The start “AUG” in eukaryotes codes for methionine; in prokaryotes it codes for N-formyl methionine.b. Note: All other AUG codons elswhere in the transcript always code for methionine.c. Some amino acids are coded for by more than 1 tripletd. Leucine is the most abundant amino acid in the body (so it has the most amount of different triplet codes)e. Methionine (AUG) is the start codon and must be present in order for amino acids to be coded in the body; start translating where there is an AUG, and ignoreeverything that comes before this start codonf. The stop codons end translationg. The start and stop codons are where translation starts and where translation stopsh. Promoter and terminator are present for transcription and they start and stop transcriptioni. Each amino acid has about 4 codons that code for it; the third position of the codons varies, while the first and second positions are the same between the 4 different codons; the 3rd nitrogenous base is called a degenerative basej. There is only 1 codon that codes for tryptophan, so it is likely the least abundant amino acidk. All of the codons are read 5’à3’l. The more codons that code for a specific amino acid, the more abundant that amino acid isIV. Codons vs. Anticodonsa. Make sure you read the tRNAs 5’à3’ when trying to code for an amino acidb. 5’CAU3’ à anti-codonc. 3’GUA5’ à mRNA codond. So the amino acid you code for is methionine (AUG)e. 64 total codons and 20 total amino acidsf. In order to find the total number of possible base combinations of an organism, you must take the total number of bases and raise it to the power of the number of bases that have to be combined to make an amino acid; so if you have 4 nucleotide bases and 3 together make a codon, than 43 = 64, which gives you the total number of possible base combinations, or codonsV. The “Wobble” Hypothesisa. “wobble rules” of base pairing will allow a minimum of 31 codons required to provide code combinations for the amino acids (32 codons including a stop)VI. Formation of Aminoacyl-tRNAsa. tRNA Charging (i.e. synthesis of aminoacyl-tRNA’s) is essentially irreversible because of the hydrolysis of pyrophosphate.b. There are 20 special enzymes that are specialized for the 20 amino acidsVII. Requirements for Protein Synthesisa. mRNA transcriptb. Large and small ribosome subunitsc. Assorted initation and elongation factorsd. Assorted supply of aminoacyl-tRNase. GTP energyi. Need energy, both ATP and GTPii. GTP serves are the primary energy source rather than ATPf. Three Stages:i. Initiationii. Elongationiii. TerminationVIII. Ribosome Structurea. There are 3 main spots in the ribosomeb. Which codon is sitting in which spot tells you how translation will proceedc. 2 tRNAs take up A and P sites and the two tRNAs transfer amino acids to form a peptided. The acceptor site accepts new tRNA all of the timee. The 1st codon (amino acid) sits at the P Sitef. The 2nd and 3rd codons (amino acids) sit at the A Site (the A Site has 2 amino acids)IX. Formation of the Prokaryotic Initiation Complexa. Shine-Delgarno sequence is a purine rich mRNA sequence just upstream from theAUG start codon.b. This is facilitated by base pairing with the 16s rRNA.c. This insures that protein synthesis starts at the true start codon and not at some internal methionine codon.d. Shine-Dalgarno sequence is a purine rich mRNA sequence just upstream from theAUG start codon.e. This is facilitated by base pairing with the 16s rRNA.f. This insures that protein synthesis starts at the true start codon and not at some internal methionine codon.X. Peptide Elongationa. EF-Tu is a GTP binding (Elongation Factor) protein. It carries aminoacyl-tRNA’s to the ribosome and positions them in the empty A site.b. GTP is hydrolyzed causing release of EF-Tu-GDP from the ribosome.c. GDP of EF-Tu is replaced by GTP.d. EF-Tu-GTP


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