Transcription, Translation and Bioinformatics - Lecture Notes | BIOL 2051, Study notes of Biology

Download Transcription, Translation and Bioinformatics - Lecture Notes | BIOL 2051 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 (one short segment of DNA is copied into a section or RNA) Differences between DNA & RNA: DNA- made of deoyribonucleotides • Double stranded • Thymine in DNA not found in RNA • Sugar-deoyribose RNA- made of ribonucelotides (leave of deoxy) • Single stranded • Nitrogen base uracil (so where the is T in DNA there is a U in RNA) • Sugar- ribose Three types of RNA: 1. mRNA Contains information used to make proteins (Eventually translated into proteins) 2. tRNA a. Carries amino acids to build the polypeptide during translation 3. rRna a. Component of ribosomes (site of protein synthesis) • Template strand- DNA strand that is being copied into complementary mRNA • RNA polymerase- enzyme that transcribes DNA into RNA • Bacterial RNA polymerase 4 subunits: a (2 compies), a beta, a beta prime, and an Process of transcription 3 phases: 1. Initiation a. Start tanscibition 2. Elongation 1 a. Add on to it 3. Termination a. End the process • Transcription of RNA from DNA involves the enzyme RNA polymerase, which adds ribonucleotides onto 3’ end of growing RNA chain • Does not need a primer, can start a RNA chain all by itself • Unlike DNA polymerase, RNA polymerase needs no primer • RNA polymerase recognizes a specific start sequence on the DNA called the promoter and starts transcribing DNA into RNA at that site Transcription Initiation • Sigma factor binds RNA polymerase – Forms RNA polymerase holoenzyme • RNA polymerase binds promoter – Sequence on DNA – 10 and 35 bases upstream of start site • Polymerase unwinds the DNA at promoter – Open complex • Once complex is opened , the Sigma factor released • Promoters • Specific DNA sequences indicating start site of transcription • Two important regions: (in Bacteria) • -35 sequence • -10 sequence (Pribnow box) • (- means upstream of start site) • Prokaryotes have a single RNA polymerase with a sigma subunit (it only job it to help find the promoter) The sigma factor binds to the promoter to initiate transcription . Multiple sigma factors 2 Codons: • There are 20 amino acids found in proteins • How can 4 RNA bases (A,U,G,C) code for 20 amino acids? • A group of 3 RNA bases code for each amino acid- this is called a codon –a group of 3 mRNA bases and each group of there codes for one amino acid The genetic code is degenerate • There are 64 possible codons, but only 20 amino acids • Some amino acids that have several codons • Ex. There are 3 codons for isoleucine: AUU, AUC, AUA (don’t have to memorize) • A single amino acid may be encoded by several different but related codons The “wobble” concept • Base pairing between tRNA and mRNA is more flexible for the third base than the first two • This allows some tRNA to recognize more than one codon • For example: – Arg codons are CGU, CGC, CGA, CGG Transfer RNA (tRNA)  tRNA- small RNA molecules that acts as adapters in the process of translation  Each tRNA has a binding site for a codon at one end and a binding site for an amino acid • There are tRNA molecules for 61 of the 64 codons- these are called sense codons • The other 3 codons are called nonsense codons, (have no tRNA that will code to them )they end the process of translation 5 • One or more transfer RNAs exist for each amino acid found in a protein. • Enzymes called aminoacyl-tRNA synthetases attach an amino acid to a tRNA. The anticodon • 3 nucleotides at the bottom of the tRNA that are complementary to a codon on the mRNA • In drawing above, the anticodon is UAC • The anticodon is written from 3’ to 5’ • 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 (AUG) to a stop codon (3 different stop codons)  From start codon to stop codon is called an open reading frame (ORF) • Codon table- shows all possible codons & the amino acid that each on codes for (look at one and make sure you know how to use one) • Each of the 61 sense codons that all specify amino acids 6 • There are tRNA molecules for the 61 sense codons  There are no tRNA’s for the 3 nonsense codons (UAG, UGA, UAA) The ribosome • Ribosome- large complex of proteins and RNA that links amino acids together to form proteins(location of protein synthesis) • 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 (merege together in such a way that you end up with a 70s ribosome) There are three sites on the ribosome: – acceptor (A) site, where the charged tRNA (t RNA which has a charge attached to it) first binds – peptide (P) site where the growing polypeptide chain is held – exit (E) site, where the tRNA exit from Translation initiation, so intiation in the first step • Shine-Dalgarno sequence/ribosome binding site- mRNA sequence involved in binding of the mRNA to the ribosomes • The mRNA fits into a groove in the 30s subunit of the ribosome • The 50s has 3 “holes”, called the P (peptide) site, the A (acceptor) site, and the E (exit) site. • Initiation factors bind ribosome to mRNA so there is one codon in the P site (AUG) and one codon in the A site • Aminoacylated tRNA’s with correct anticodons fit into these 2 sites & form hydrogen bond with the mRNA codons • Ribosomes forms a peptide bond between the 2 amino acids 7