BIOL1000 - Chapter 4 – Nucleic Acids and the RNA World PDF

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Nucleic acids, nucleotides, and the RNA world....

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Chapter 4 – Nucleic Acids and the RNA World  

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Nucleic Acids o Nucleic acids are polymers formed from nucleotide monomers. Nucleotides o Phosphate Group o Pentose Sugar  Each carbon atom is labelled with a number and a prime symbol.  The nitrogenous base is attached to the 1’ carbon while the phosphate group is attached to the 5’ carbon.  Ribonucleotides contain an -OH group bonded to the 2’ carbon while deoxyribonucleotides contain a single -H group bonded to the 2’ carbon. o Nitrogenous Base  Purines  Double ringed nucleotides; adenine and guanine  Pyrimidines  Single ringed nucleotides; cytosine, thymine, and uracil o Naming  Nucleotides are named and classified based on their nitrogenous bases, number of phosphate groups, and type of pentose sugar.  ATP (adenosine), CTP (cytidine), GTP (Guanosine), and UTP (uridine) are all NTPs (nucleoside triphosphates). These are the nucleotides used to make RNA.  dATP, dCTP, dGTP, and dTTP (thymidine) are all dNTPs (deoxynucleoside triphosphates). These are the nucleotides used to make DNA.  AMP (adenosine monophosphate) contains adenine, ribose, and one phosphate group while dADP (deoxyadenosine diphosphate) contains adenine, deoxyribose, and two phosphate groups. Nucleotide Polymerization o Phosphodiester Bonds  Covalent bonds that form between the hydroxyl group on 3’ carbon of the sugar component and the hydroxyl group of the 5’ phosphate component of another nucleotide.  Phosphodiester bonds allow nucleotides to polymerize and form nucleic acids. In order for these bonds to form, a dehydration synthesis reaction occurs. o DNA and RNA strands are Directional  One end of the strand has an unlinked 5’ phosphate while the other end has an unlinked 3’ hydroxyl.  The order of nucleotides forms the primary structure of the nucleic acid. By convention the order is always written in the 5’ -> 3’ direction.

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DNA Structure and Function o Primary Structure  Sequences of dATP, dCTP, dGTP, and dTTP nucleotides attached to a sugarphosphate backbone connected to each other via phosphodiester bonds. o Secondary Structure  Early Clues  Chemists had worked out the structure of nucleotides and the process of DNA polymerization via phosphodiester bonds.  Erwin Chargaff had established that the number of purines in a given molecule is equal to the number of pyrimidines and that there is an equal T’s and A’s and an equal number of C’s and G’s.  Rosalind Franklin and Maurice Wilkins used X-ray crystallography and found a regular repeating pattern (distances of 0.34 nm, 2.0 nm, and 3.4 nm) which suggested a helical structure.  The Antiparallel Double Helix  Watson and Crick used all the previous research to form a complete model of DNA structure.  They arranged two strands of DNA with the bases facing the inside and concluded that only purine-pyrimidine pairs could fit within the 2.0-nmwide structure.  This pairing allows hydrogen bonds to form between specific bases known as complementary base pairing. Adenine will form two bonds with thymine and guanine will form three bonds with cytosine.  This bonding can only occur if the two strands are antiparallel meaning one strand runs 5’ -> 3’ and the other runs 3’ to 5’. These antiparallel strands were predicted to form a double helix.  Every 10 bases, the structure completes a full helical turn which was the 3.4-nm distance observed and the distance between each bases is 0.34 nm.  The outside structure of the helix contains a wide major groove, where most proteins bind, and a smaller minor groove. o Tertiary Structure  DNA often forms compact and organized tertiary structures by wrapping around certain proteins. o Function  DNA stores the information required for an organism’s growth and reproduction.

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RNA Structure and Function o Primary Structure  Similar to DNA with a few differences.  Instead of dNTPs, RNA consists of NTPs (ATP, GTP, CTP, and UTP)  RNA contains ribose instead of deoxyribose  RNA contains uracil instead of thymine o Secondary Structure  Like DNA, RNA has a secondary structure that results from complementary base pairing. However, rather than two strands pairing together, RNA bases undergo pairing on the same strand.  Adenine forms two bonds with uracil and guanine forms three bonds with cytosine.  One of the most common structures is the hairpin structure where a region of the RNA molecule is unpaired and forms a loop with a stem containing the paired bases. Different lengths and arrangements produce different structures. o Tertiary Structure  RNA forms tertiary structures when the secondary structure folds to form a 3-D shape. o Functions  Since RNA is made of nucleotides it also carries information. This is useful in transcription, translation, and protein synthesis.  RNA can also catalyze reactions because of the large variety of potential structures. These catalysts are called ribozymes. In Search of the First Life Form o The theory of chemical evolution relies on the premise that life began as a self-replicator – a molecule that existed separately without being enclosed in a membrane. o In order for this molecule to replicate it needed to have a template for replication and it needed to be able to polymerize reactions that would link monomers into a copy of that template. Because RNA is capable of both processes, it’s thought that the first life form was an RNA. The RNA World o The RNA world hypothesis can be tested by establishing an environment in a lab that selects for ribozymes that catalyze key reactions required for an RNA world....