BMB 462 Lecture 28 Outline of Last Lecture I. Overview of the Central Dogma of Molecular BiologyII. Differences between DNA and RNAIII. Structure of RNAa. Primaryb. Secondaryc. Tertiaryd. Non-Watson-Crick base pairingIV. RibozymesV. RNA genomesOutline of Current Lecture I. Differentiating between the types of RNAsII. Varying RNA functionsIII. Structure of a typical transcription unitIV. Mechanism of transcription and RNA synthesisV. Role of topoisomerases in transcriptionCurrent LectureConcepts 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 RNAsa. 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-shapefolding) increases the stability of tRNA. Many of the bases are alsomethylated, 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 bondformation 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 functionsa. RNAs that function in RNA processing:i. Small Nuclear RNAs (snRNA) - process mRNA in eukaryotic cells; they helpsplice 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 synthesisi. 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 atemplate (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 crossthe membrane; aka protein targeting).III. Structure of a typical transcription unita. Genes are regions of DNA that transcribed into one of the types of RNA.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).b. Transcription is the first step in gene expression (and last step, if the gene is goingto 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 economicalto regulate things at the first step.c. Top strand is 5' to 3', the bottom strand is antiparallel to that.d. +1 indicates the transcription start site.
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