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BIO 184 Tom Peavy Fall 2007 EXAM 1 STUDY GUIDE – GENERAL CONCEPTS Molecular Structure of DNA & RNA Definitions of key topics (i.e. gene, allele, homologous chromosomes) Fundamental studies leading to our understanding Griffith’s expts with Rough vs Smooth virulent strains of bacteria Avery, MacLeod & McCarty’s expts (enzyme treatments such as DNase) Hershey & Chase bacteriophage expts Rosalind Franklin’s structural data (helix, 10 bp per turn, > 1 strand) Chargaff’s Rule(s) (A=T; G=C; and also corollary A+G = T+C) Structure of DNA/RNA (composition and structural features) Nucleotides (G,A, C, T or U), phosphate, sugar (deoxyribose/ribose) Right-handed double helix in antiparallel direction Complementarity Major & minor grooves 5’-3’ directionality RNA secondary structure (e.g. stem-loop structures) Chromosome Organization & Molecular Structure Bacteria nucleoid, loop domains, negative supercoiling, gyrase (creates supercoils; aka- topoisomerase II), topoisomerase I (relaxes supercoils) Eukaryotic Complexity of genome (i.e. repeats and other non-coding genetic material) Chromatin structure histone core, H1 linker, beads-on-a-string, 11nm fiber, 30nm fiber, radial loops that associate with nuclear matrix, facultative and constitutive heterochromatin, euchromatin DNA Replication Messelsen & Stahl’s expt to distinguish between the different replication models (Conservative, Semi-conservative, Dispersive) Bacterial DNA Replication bidirectional Leading & Lagging strand replication mechanics BIO 184 Tom Peavy Fall 2007 Polymerases (DNA Pol I and III) Helicase (and counteracting gyrase) Single stranded binding proteins DNA Primase Ligase Okazaki fragments Exonuclease activity (5’-3’ activity vs 3’-5’ proofreading) Eukaryotic DNA Replication Multiple origins of replication Telomeres Telomerase Transcription Prokaryotic (uses one RNA polymerase) Stages: Initiation- promoters, regulatory elements (operator) [note that both use consensus sequences], open vs closed complex Elongation- RNA polymerase uses the template strand (non-sense strand), Coding strand (sense strand) is the opposite and has the exact sequence as the mRNA (except for T vs U) Termination- rho-dependent vs rho independent (note that both use stem-loop structures) Colinear expression of genes (no introns) Eukaryotic (has 3 different RNA polymerases for transcription) - Still have promoters and regulatory elements (but promoters are less conserved and are shorter and regulatory elements are classified as enhancers & silencers) - RNA processing of heterogeneous RNA (primary transcript into mRNA) Intron splicing (alternative splicing also) 5’ end capping (7-methylguanosine) Poly A tail Factors that control expression for both can be either cis-acting elements (DNA sequences nearby genes) or trans-acting elements (regulatory proteins that bind DNA sequences) Translation Genetic code (codons, degeneracy, near universality) tRNAs complementarity to mRNA charged with amino acid via aminoacyl-tRNA synthetases wobble rule Ribosomes comprised of large and small subunits (note: sizes differ for prokaryotic vs BIO 184 Tom Peavy Fall 2007 eukaryotic) contain 3 discrete functional sites (A=aminoacyl site; P=peptidyl sites; E=exit site) Stages: Initiation- initiator tRNA (methionine), ribosome binding site (Shine-Dalgarno sequence) Elongation- peptide bond formation of amino acids into growing polypeptide chain via the ribosome functional sites A, P, E; Amino-terminus and Carboxy-terminus Termination- nonsense codons (stop codons), release factors Proteins- primary, secondary, tertiary and quartenary structure;