Download Exam 1 Study Guide – General Concepts

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;