BMB 462 Lecture 28 Outline of Last Lecture I Overview of the Central Dogma of Molecular Biology II Differences between DNA and RNA III Structure of RNA a Primary b Secondary c Tertiary d Non Watson Crick base pairing IV Ribozymes V RNA genomes Outline of Current Lecture I II III IV V Differentiating between the types of RNAs Varying RNA functions Structure of a typical transcription unit Mechanism of transcription and RNA synthesis Role of topoisomerases in transcription Current Lecture Concepts to remembers from previous courses lectures Review of RNA World Hypothesis o By chemical processes there could ve been created first nucleotides which then could ve been joined together in short oligonucleotides The first catalysts may have been RNAs It worked as a kind of reversal of what we see today with self splicing introns where RNAs are broken apart those reactions can actually be reversed resulting in RNAs joining together The concept of being able to join together RNAs gives rise to the idea that the first catalytic units were RNAs able to join together other RNAs in sort of self duplicating RNAs these were ribozymes o From there once the cell is able to make more complex ribozymes the idea is that they could begin connecting amino acids together and start making peptides the These 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 peptides would then grow into proteins the proteins would cooperate with RNAs resulting in the creation of ribosomes which are much more efficient at linking together amino acids and translating RNAs o The hypothesis also states that reverse transcriptase seen in retroviruses is what allowed the creation of the first DNA genome from an RNA genome I Differentiating between the types of RNAs a Differentiating between the different RNAs i mRNA carries the information from DNA as nucleotide triplet codons that specify amino acids 1 They make up 5 of the total RNA in the cell they are the least abundant 2 There are many types because for each protein coded for in the DNA you need a different mRNA a In E coli there are 4000 protein encoding genes so 4000 mRNAs In humans that increases to 23 000 3 Variable in length ranging from 100 1 000 000 4 Single stranded so they are unstable and typically get degraded by ribonucleases In prokaryotes the half life can be as short as minutes so they re rapidly turned over This half life is slightly longer in eukaryotes ii tRNAs are the adaptors between nucleic acids and proteins one end has an anticodon to associate with the nucleic acids in mRNA the other end can be charged with an amino acid to synthesize the protein 1 Complex secondary and tertiary structures the clover and L shape folding increases the stability of tRNA Many of the bases are also methylated increasing the hydrophobicity and the ability to stack which aids in stability 2 They make up 15 of the total RNA in the cell 3 There are 40 50 different types typically there are 2 3 tRNA for each of the 20 amino acids 4 They are about 75 nucleotides in length fairly uniform structures iii rRNA acts as a structural and functional component of ribosomes 1 It is the functional component because all though the rRNA associates with ribosomal proteins the site in which peptide bond formation is actually catalyzed it s a region of all rRNA The rRNA then is functioning like a ribozyme because it s carrying out catalysis in the ribosome 2 80 of all the RNA in the cell is rRNA you need a lot of ribosomes to make all the proteins needed by the cell 3 Only 3 types in bacteria and 4 types in eukaryotes 4 They range from 100 3 000 nucleotides long iv Mostly double stranded making them stable structures as does the association with proteins II Varying RNA functions a RNAs that function in RNA processing i Small Nuclear RNAs snRNA process mRNA in eukaryotic cells they help splice out introns in the mRNA ii RNase ribonuclease P a ribozyme since the RNA carries out the catalysis even though the molecule is complexed with a protein It is involved in tRNA processing iii Small Nucleolar snoRNA involved in the processing of rRNA since the nucleolus is where rRNA is produced b RNAs that have a role in Gene regulation i Small interfering RNA siRNA these are typically associated with viruses infecting a host cell the RNA comes from outside the cell ii Micro RNAs miRNA are produced from within the cell It is estimated that 1 3 of the genes in eukaryotic cells are regulated by miRNAs They typically effect the translation or stability of mRNAs 1 They can also mediate RNA interference RNAi c Telomere associated RNA for telomere synthesis i Telomeres the ends of chromosomes are very hard to replicate so the cell has a special enzyme called telomerase 1 The enzyme is associated with a specific RNA sequence it uses as a template telomerase is an enzyme not a ribozyme even though it carries around an RNA sequence The protein not the RNA is what catalyzes the reaction d RNA associated with the formation of ribonucleoprotein complexes RNPs i RNA comes together with a protein to carry out a function i e telomerase with its RNA template the rRNA in ribosomes snRNA in snRNPs snRNPs are the functional unit where you bring together snRNA and proteins to carry out the splicing of mRNAs RNA in the signal recognition particle the signal recognition particle is a complex of RNA and protein that recognizes the signal sequence on a protein when it begins to be translated and targets it to the membrane so that it can cross the membrane aka protein targeting III Structure of a typical transcription unit a Genes are regions of DNA that transcribed into one of the types of RNA b c d e i There are not just crunching and coding genes though these are the types that are typically thought of Some genes have a functional product that is just an RNA that performs a task in the cell i e rRNA Transcription is the first step in gene expression and last step if the gene is going to be a functional RNA It will go on to be translated if it s an mRNA i Transcription is often a regulated step in gene expression It is economical to regulate things at the first step Top strand is 5 to 3 the bottom strand is antiparallel to that 1 indicates the transcription start site This is where the RNA will begin i Everything in the gene is labeled relative to the 1 any base pairs before that point are considered upstream and are consecutively
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