BMB 462 Lecture 27 Outline of Last Lecture I Review of Nucleotide Excision Repair II Direct Repair III Recombinational Repair IV Error Prone Repair Mechanisms a Nonhomologous End Joining NHEJ b SOS repair V Damage that must be Repaired in the cell VI DNA Recombination a Homologous Recombination b Site Specific Recombination Outline of Current 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 Current Lecture Concepts to remembers from previous courses lectures I Overview of the Central Dogma of Molecular Biology a Information flows from DNA the storehouse of information When making proteins the DNA is then transcribed to mRNA That gets translated on ribosomes into a polypeptide form that gets folded into its final conformation II Comparing DNA and RNA 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 a Both are composed of a sugar phosphate backbone with bases attached b DNA has thymine while RNA has uracil The difference between these 2 bases is the methyl group found on the thymine i Adding that methyl group takes a little more energy so it s more expensive for the cell to make thymine But because deamination of cytosine results in uracil if the DNA used uracil as well the cell would have no way of distinguishing replication errors On the other hand the RNA doesn t have to be repaired because they are transient molecules in the cell The DNA is the storehouse and the source of information and must be preserved 1 There are even certain RNAs that are intentionally deaminated to change its function This is called RNA editing c The deoxyribose in DNA has a hydrogen atom on the 2 Carbon RNA s ribose has a hydroxyl group at that position That hydroxyl group is important in chemical reactions in vitro it makes RNA less stable in alkaline conditions In the presence of hydroxyl groups the 2 hydroxyl becomes more reactive causing the phosphodiester bond to break This quality can be used in research to break down the RNA strands so they are easier to separate from DNA d In vivo the 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 III Structure of RNA a Primary i RNA s primary structure forms a right handed helix due to base stacking You can determine it s a right handed helix due to the fact that the molecule is spiraling around the axis in a counterclockwise direction ii Once the primary structure is established secondary structure can form If there are complementary sequences running in an antiparallel fashion they can pair much like DNA These complementary sequences form Ahelices not the B helices found in DNA iii A form helices are a little shorter more dehydrated than the b form The A form double helices are quite stable increasing the stability of RNA double helices b Secondary i Structural elements of Complementary RNA sequences 1 Bulge a single base is mismatched causing a kink in the helix 2 Internal loop several base pairs are mismatched 3 Hairpin or Stem loop formed by inverted complementary strands base pairing a Inverted repeats in DNA when transcribed are what allow the hairpins to form in RNA ii Tertiary RNA structure can be visualized using tRNA 1 The secondary structure looks like a cloverleaf with a stem and 3 leaves formed by hairpins 2 In RNA it is very common for G to pair with U instead of the usual A U pairing The G U pairing forms 2 H bonds just like the A U pairing does iii The 3 end of the stem is where the amino acid attaches The anticodon is found on the leaf directly opposite that The anticodon is what pairs to the codon in the mRNA iv This structure is RNase P a ribozyme it is an RNA sequence associated with a protein component It is the RNA part that does the catalysis in a reaction the fact that the RNA does the catalysis is what makes it a ribozyme 1 Pairing does not have to occur between consecutive sequences Pairing between distal parts is what allows the formation of tertiary sequences c Tertiary i The tertiary structure of tRNA in the cell is L shaped not the secondary clover shape ii The functional ends of the molecule are at the ends of the L shape iii Tertiary folding creates a very compact highly complementary stable structure 1 Part of the tertiary structure is formed by a Adenine can bond with another purine dimethylguanine b Another example of an unusual hydrogen bond occurs between a hydroxyl group in a ribose and a Nitrogen atom in a base iv Unusual hydrogen bonding and base modification give variety and stability to the structure of tRNAs as well as other RNA molecules d Non Watson Crick base pairing i There are 40 50 tRNA molecules in the cell 1 Molecules called amino acyl tRNA synthases have to recognize the right tRNA and attach the correct amino acid to it a All tRNA are in the L shape the modified bases give the molecules variety so the enzymes can recognize them in addition to recognizing the anticodons b The modified bases also add stability to the RNA molecules methylating bases makes them more hydrophobic which allows them to stack better on top of each other increasing stability IV Ribozymes a 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 difference is that the RNA carries out the catalytic function b RNA World hypothesis because of the structural and functional diversity found in RNA with structures like ribozymes it is thought that RNAs might have been the first catalysts and first genes Before life as we know it RNAs might have been evolving and gaining catalytic function This could offer a solution to the Chicken egg problem you need the enzymes to replicate DNA but the DNA to code for the enzymes Perhaps neither of these came first the RNA first acted as catalysts c Steps of Creation in the RNA World hypothesis i 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
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