BMB 462Exam # 4 Study Guide Lectures: 27 - 39Lecture 27 Central dogma of molecular biology.Information flows from DNA, the storehouse of information. To make proteins, the DNA is transcribed to mRNA. That gets translated on ribosomes into a polypeptide that gets folded intoits final conformation.Compare and contrast RNA and DNA.Same:Sugar-phosphate backbone with bases attached. Different:DNA has thymine while RNA has uracil. The deoxyribose in DNA has a hydrogen atom on the 2' Carbon. RNA's ribose has a hydroxyl group at that position. RNA is less stable because it is susceptible to attack from ribonucleases (RNases). RNA is able to form secondary and tertiary structures, though, which protect the strands from attack and make it more stable.RNA primary, secondary, and tertiary structure.Primary:Right-handed helix from base stacking. Complementary sequences form A-helices.Structural elements of Complementary RNA sequences:-Bulge - a single base is mismatched, causing a kink in the helix-Internal loop - several base pairs are mismatched-Hairpin or Stem loop - formed by inverted complementary strands base pairing.Secondary:Appears as a clover leaf, with a stem and 3 "leaves" formed by hairpins.-In RNA, it is very common for G to pair with U, instead of the usual A-U pairing. The G-U pairingforms 2 H-bonds, just like the A-U pairing does.The 3' end of the stem is where the amino acid attaches. The anticodon is found on the leaf directly opposite that. Tertiary:L-shaped structure. The functional ends of the molecule are at the ends of the L-shape.Part of the tertiary structure is formed by-Adenine can bond with another purine, dimethylguanineRibozymes and the RNA World Hypothesis.A ribozyme is an RNA (such as RNase P) that folds into a distinct tertiary structure, bringing functional groups (like Hydroxyl groups) into position to bind a substrate and catalyze a reaction,much as an enzyme does. The RNA carries out the catalytic function.RNA World hypothesis - RNAs might have been the first catalysts and first genes. a. Steps of Creation in the RNA World hypothesisi. Creation of a prebiotic soup, including nucleotides from components of Earth's primitive atmosphere.ii. Production of short RNA molecules with random sequences; RNA molecules were produced through chemical reactions.iii. Selective replication of self-duplicating catalytic RNA segments. The catalytic RNA segments would be the first genes and catalysts.1. You could reverse the splicing process that breaks apart RNA chainsto get joining of RNA segments. The reversal of self-splicing could have created RNA catalysts.iv. Synthesis of specific peptides, catalyzed by RNA. This begins the connecting of amino acids to form peptides.1. We think this is possible because rRNA catalyzes peptide bond formation in ribosomes.a. Ribosomes are formed of rRNA and ribosomal proteins. At the catalytic site there are no ribosomal proteins; it's all rRNA that does the joining of peptide bonds.v. Increasing role of peptides in RNA replication; coevolution of RNA and protein.vi. Primitive translation system evelops, with RNA genome and RNA-protein catalysts. Evidence for RNA genomes comes from the presence of RNA viruses that never have a DNA change. RNA protein catalysts are evidenced by ribosomes.vii. Genomic RNA begins to be copied into DNA. This is evidenced by reverse trancriptase - synthesizing DNA from an RNA template.viii. DNA genome, translated on RNA-protein complex (ribosome) with protein catalysts. A membrane-bound DNA genome, translated on RNA…. becomes the first cell.RNA genomes in viruses.Types of RNA viruses:1. Those that don't have a DNA stage, i.e. influenza. They use RNA-dependent RNA polymerases to replicate the genome.2. Viruses that have a DNA intermediate stage; they translate the RNA genome into DNA then back to RNA, are called retroviruses. i.e. HIV. Many of these viruses are associated in cancer.Lecture 28Compare and Contrast RNA function.mRNA:-Carry the information from DNA as nucleotide triplet codons.- 5% of the total RNA in the cell - they are the least abundant-Many types: for each protein coded for in the DNA, you need a different mRNA-Variable in length (ranging from 100-1,000,000)-Single stranded, unstable.tRNA:-Adaptors between nucleic acids and proteins-Anticodon on one end, amino acid on the opposite end.-Complex methylation, and secondary/tertiary structures increases stability. -~15% of the total RNA in the cell-~40-50 different types; ~2-3 tRNA for each of the 20 amino acids.-They are about 75 nucleotides in length; fairly uniform structures.rRNA-Structural and functional component of ribosomes.-80% of all the RNA in the cell-3 types in bacteria and 4 types in eukaryotes-100-3,000 nucleotides long-Mostly double-stranded, making them stable structures (as does the association with proteins)Small Nuclear RNAs (snRNA) -Process mRNA in eukaryotic cells; they help splice out introns in the mRNARNase (ribonuclease) P -Ribozyme -Involved in tRNA processing.Small Nucleolar (snoRNA) -Involved in rRNA processing of rRNA.Small interfering RNA (siRNA) -Typically associated with viruses infecting a host cell-From outside the cellMicro RNAs (miRNA)-Produced within the cell.-Regulate ~1/3 of the genes in eukaryotic cells. -They typically effect the translation or stability of mRNAs.-Mediate RNA interference (RNAi)Telomere-Associated RNA for telomere synthesis-Telomerase is associated with a specific RNA sequence it uses as a templateDescribe a transcription unit.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. Everything in the gene is labeled relative to the +1; any base pairs before that point are considered upstream and are consecutively labeled with negative numbers. Everything to the right of the RNA +1 start is considered downstream and is labeled consecutively with positive values.The area between the start and stop codons is called the open reading frame (ORF), an open frame for translation.DNA contains a coding strand and a template strand. RNA polymerase uses the template strand as a reference to add a nucleotide that is complementary to the one in the DNA template strand. Explain the mechanism of RNA synthesis.RNA polymerase binds to the DNA, bending and opening it to access the template strand (transcription bubble).The active site in the polymerase contains the 3' end of the RNA where the new nucleotides willbe
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