Biochemistry 7: RNA and the Genetic Cod The Genetic Code Central Dogma: States that DNA is transcribed to RNA, which is translated to protein. Degenerate Code: Allows for multiple codons to encode for the same amino acid. Start / Stop Initiation (start): AUG Codons: Termination (stop): UAA, UGA, UAG Wobble: 3rd base in the codon. Allows for mutations to occur ? without effects in the protein. Wobble base pairings are less stable. Point Mutations: Silent: Mutations with no effect on protein synthesis. Usually found in the 3rd base of a codon. Nonsense (truncation): Mutations that produce a premature STOP codon. Missense: Mutations that produce a codon that codes for a DIFFERENT amino acid. Frameshift Result from a nucleotide addition or deletion, and Mutations: change the reading frame of subsequent codons. RNA: Similar to DNA except: Ribose sugar instead of deoxyribose. Uracil instead of thymine. Single stranded instead of double stranded. 3 Types of RNA: Messenger RNA (mRNA): Transcribed from DNA in the nucleus, it travels into the cytoplasm for translation. Transfer RNA (tRNA): Brings in amino acids and recognizes the codon on the mRNA using its anticodon. Ribosomal RNA (rRNA): Makes up the ribosome and is enzymatically active. Transcription Translation * See appendix for full diagram tRNA: Translates the codon into the correct amino acid. Ribosomes: Factories where translation (protein synthesis) occurs. Eukaryotes: 80s ribosomes Prokaryotes: 70s ribosomes Initiation: Prokaryotes: When the 30S ribosome attaches to the Shine-Delgarno Sequence and scans for a start codon; it lays down N-formylmethionine in the P site of the ribosome. Eukaryotes: When the 40S ribosome attaches to the 5’ cap and scans for a start codon; it lays down methionine in the P site of the ribosome. Elongation: The addition of a new aminoacyl-tRNA into the A site of the ribosome and transfer of the growing polypeptide chain form the tRNA in the P site to the tRNA in the A site. The now uncharged tRNA pauses in the E site before exiting the ribosome. The A site tRNA moves to the P site. Termination: Occurs when the codon in the A site is a stop codon; release factor places a water molecule on the polypeptide chain and thus releases the protein. Posttranslational Folding by chaperones. Formation of quaternary Modifications: structure. Cleavage of proteins or signal sequences. Covalent addition of other biomolecules (phosphorylation, carboxylation, glycosylation, prenylation). DNA Ligase: Fuse the DNA strands together to create one strand. * See appendix for full diagram Helicase: Unwinds the DNA double helix. RNA Polymerase II: Binds to the TATA box within the promoter region of the gene (25 base pairs upstream from first transcribed base). hnRNA: Collective term for the unprocessed mRNA in nucleus. Posttranscriptional The process in eukaryotic cells where primary transcript Modification: RNA is converted into mature RNA. Introns cut out. Exons: Exit the nucleus and form mRNA. Introns: Spliced out so they stay in nucleus. Introns also enable alternative splicing. Alternative splicing: Usually introns are cut away and exons remain, but alternative splicing might change that. A certain exon may be cut out, or an intron may stay. This allows for the RNA segment to code for more than one gene. 5’ Cap and Poly-A tail are added to the mRNA. The cap and tail stabilize mRNA for translation. Prokaryotic cells can increase the variability of gene products from one transcript though polycistronic genes. There are multiple translation sites within the gene which leads to different gene products. Control of Gene Expression in Prokaryotes Jacob-Monod Model: Explains how Operons work. Operons: Inducible or repressible clusters of genes transcribed as a single mRNA. Inducible Systems: Under normal conditions, they are bonded to a repressor. They are turned on when an inducer pulls the repressor off. Example: Lac operon. Repressible Systems: Transcribed under normal conditions; they can be turned off by a corepressor coupling with the repressor and the binding of this complex to the operator site. Example: Trp operon Control of Gene Expression in Eukaryotes Transcription Search for promoter and enhancer regions in the DNA, Factors: then bind to the DNA and recruit RNA polymerase. Promotors: Are within 25 base pairs of the transcription start site. Enhancers: Are more than 25 base pairs away from the transcription start site. Modification of chromatin structure affects the ability of transcriptional enzymes to access the DNA through histone acetylation (increases accessibility) or DNA methylation (decreases accessibility).