RNA Synthesis, Protein Production & Bioinformatics: In-depth Analysis - Prof. K. Sullivan, Study notes of Biology

Download RNA Synthesis, Protein Production & Bioinformatics: In-depth Analysis - Prof. K. Sullivan and more Study notes Biology in PDF only on Docsity! Chapter 8- Transcription, Translation, and Bioinformatics RNA Synthesis Transcription- making an RNA copy of part of a DNA strand Differences between DNA & RNA: DNA- made of made of deoxyribonucleotides • Double stranded • Thymine • Sugar- deoxyribose RNA- made of ribonucleotides • Single Stranded • Uracil • Sugar- ribose 3 main types of RNA: 1. Messenger RNA (mRNA) - Encode proteins - Average 1000-1500 bases long 2. Transfer RNA (tRNA) - Carries amino acids to the ribosome to build a protein during translation 3. Ribosomal RNA (rRNA) - Component of ribosomes (site of protein synthesis) mRNA and tRNA are never made into proteins • Template strand- DNA strand that is being copied into complementary mRNA • RNA polymerase • Enzyme that transcribes DNA into RNA by adding ribonucleotides onto 3’ end of growing RNA chain 1 • Needs no primer • Recognizes specific start sequence on DNA called the promoter & starts transcribing DNA into RNA at that site • Promoter is beginning of the gene** • Where transcription starts • Bacterial RNA polymerase - 4 subunits: α (2 Copies), β β’ σ - σ function is to help core enzyme locate Multiple sigma factors (over 100 known so far from numerous species) σ70 – “Housekeeping” sigma factor used for most essential genes • finding promoter for most genes – σ32 Active when cell is stressed by heat (heat-shock response) – Results in the formation of protective heat proteins Process of transcription 3 phases: 1. Initiation 2. Elongation 3. Termination Transcription Initiation • Sigma factors binds core RNA polymerase – Forms RNA polymerase holoenzyme 2 • More than one codon can encode the same amino acid • Redundant/regenerate • Ex. There are 3 codons for isoleucine: AUU, AUC, AUA • Codons for the same amino acid usually only differ in the last nucleotide of the codon • This “wobble” is partly due to the curvature of the anticodon loop • A single amino acid may be encoded by several different but related codons. First two bases are normally the same, but the last one is different. Transfer RNA (tRNA)  tRNA- small RNA molecules that act as adapters o carry amino acids  Each tRNA has a binding site for a codon at one end, and a binding site for an amino acid at the other end • There are tRNA molecules for 61 of the 64 codons- these are called sense codons. • The other 3 codons are called nonsense codons. • One or more transfer RNAs exist for each amino acid found in a protein. • Enzymes called aminoacyl-tRNA attach an amino acid to tRNAs. • There is one aminoacyl-tRNA transferase for each amino acid. Anticodon- 3 nucleotides at the bottom of the tRNA that are complementary to a codon on the mRNA 5 • In drawing above, the anticodon is UAC • What codon is this anticodon complementary to? AUG (usually the start codon) • AUG is the codon for which amino acid? Met • A codon will base-pair with a sequence of 3 bases on a tRNA called the anticodon • Translation of mRNA occurs from a start codon to a stop codon.  From start codon to stop codon is called an open reading frame (ORF). • Part of mRNA that is translated to a protein • Codon table- shows all possible codons & the amino acid each codes for. • Each of the 61 sense codons specify amino acids • There are tRNA’s for the 61 sense codons  There are no tRNA’s for the 3 nonsense codons- UAG, UGA, UAA • End of a protein The ribosome • Ribosome- large complex of proteins and RNA that links amino acids together to form proteins. • There are 2 ribosomal subunits, 30s and 50s in prokaryotes. • s stands for Svedberg unit, a measure of mass and shape • The 2 subunits together form a 70s ribosome. • There are three sites on the ribosome: 6 – acceptor (A) site, where the charged tRNA first binds – peptide (P) site where the growing polypeptide chain is held – exit (E) site Translation initiation • Shine-Dalgarno sequence/ribosome binding site- mRNA sequence that hybridizes to a sequence on the 16s rRNA of the ribosome to correctly position the mRNA for translation • Initiation factors bind ribosome to mRNA so there is 1 codon in the P site (AUG) and 1 codon in the A site • Aminoacylated tRNA’s with correct anticodons fit into these 2 sites & hydrogen bond with the mRNA codons. • Ribosome forms a peptide bond between the 2 amino acids- this is called the peptidyl- transferase activity of the ribosome. • After peptide bond forms, there is a chain of 2 amino acids hooked to the tRNA in the A site. Translation elongation • Translocation- ribosome moves up the mRNA 1 codon so the tRNA with the chain of amino acids is in the P site. • EF-Ts, EF-Tu, EF-G bring GTP energy • For polymerization & movement of ribosome along mRNA • A new aminoacylated tRNA binds to the vacant A site. • chain of amino acids is linked to the is linked to the amino acid in the A site • Now there is a chain of 3 amino acids • Ribosome moves up the mRNA 1 more codon & repeats the cycle until the complete chain is made. 7