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NUCLEIC ACIDS Chapter readings Ch.8 Ch.24 Ch.25 Ch.26 Ch.27 Ch.9 all 947-971 975-1003 1021-1041, 1045-1049 1065-1072, 1075-1096, 1098 304-308, 315-327 Chapter Problems Ch.8 Ch.24 Ch.25 Ch.26 Ch.27 1,2,5,6,7,8,10,11,12,13,14 2,4,9 1,4,6,9,12 2,3,4,8,10,11 1-5,8,9,10 Scientific American article See website Learning Objectives - Nucleotides and Nucleic Acids Know the Three basic parts of nucleotides Be able to draw 5 nitrogenous bases (which are found in DNA? Which in RNA?) What is the difference between DNA and RNA nucleotides? Know the linkages in nucleic acids Understand the Hydrolysis reaction of RNA Know the Properties of nucleotides Hydrophobicity UV absorption Hydrogen bonding Know and be able to draw the Hydrogen bonding between nitrogenous bases (3 between G and C, 2 between A and T(U)) Know the basics of the Discovery of DNA Avery-MacLeod-McCarty Hershey-Chase Chargaff Franklin & Wilkins Watson & Crick Understand that DNA is a double helix (2 strands wrapped around each other), antiparallel strands (one strand 5'-3' the other 3'-5'), and complementarity between strands Know the differences between A-DNA vs. B-DNA vs. Z-DNA Know types of RNA structures that form Understand how nucleic acids can become denatured Be able to describe the Hypo (hyper) chromic effect Know how to determine the Melting temperature (Tm) for a nucleic acid Know the process of DNA sequencing Know the basics of Nucleotide synthesis and degradation Synthesis - from metabolic precursors or from recycled free bases Degradation - diseases (gout and ADA deficiency) Know how nucleic acids can act as Cancer drugs Learning Objectives - Genes & Chromosomes What is a chromosome? Gene? Genome? Chromatin? Know the difference between Introns and exons Understand how DNA is compacted in the nucleus 30 nm fiber “beads-on-a-string” what makes up a nucleosome Understand why supercoiling is important Learning Objectives - DNA metabolism Know the characteristics of DNA Replication Semi-conservative Bidirectional Leading vs. lagging strand synthesis (semidiscontinuous) Proofreading (3’5’ exonuclease) Understand how the Meselson-Stahl experiment was done and its results Know the importance of having an origin of replication Know some of the characteristics of DNA polymerases (processivity, roles, 5’3’-exo) Know the stages of replication Initiation (proteins involved) Elongation (proteins involved) Termination DNA repair Know the causes of DNA damage Mismatch repair (how it works, proteins involved) Understand how defects in DNA repair lead to cancers Learning Objectives - RNA metabolism Transcription Know the functions of rRNA, tRNA, mRNA Know the role of RNA polymerase Know all the things that happen at the Transcription bubble Know the roles of the subunits of E.Coli RNA polymerase Understand the difference between a closed vs. open complex What is the role of a Promoter? Prokaryotes: -10 region, Pribnow box -35 region Eukaryotes: -25 region, TATA box -75 region, CAAT box Know an example of a Transcription repressor and activator Understand the Termination of transcription Know examples of Inhibitors of RNA polymerase Translation Know that it occurs on ribosomes Know the Role of tRNA and how activation of tRNA occurs What is a Codon? (know stop codons) Know the characteristics of the Genetic code - nonoverlapping, sequential (reading frames), degenerate (wobble pair) How do Insertions or deletions affect the genetic code? Understand how a codon specifies which aminoacyl-tRNA binds to mRNA Know the Stages of translation: Activation of amino acids (amino acid + ATP + tRNA + synthetase) Initiation (N-formyl Methionine, AUG, Shine-Dalgarno sequence, 30S ribosome, 50S ribosome, mRNA, GTP, Init. Factors, A site, P site) Elongation (70S complex, Elong. Factors, GTP, tRNAs) Termination (codons, Release factors, ATP) What is a Polysome? Understand how prokaryotes couple transcription-translation Know examples of Inhibitors of translation RNA Processing & Catalysts Describe 5'-capping & polyadenylation Understand RNA splicing & editing What are ribozymes? Group I vs. hammerhead Define RNA interference Understand role of riboswitches
