BIO 344 1st EditionExam # 1 Study Guide Lectures: 1 -8 Lecture 1 (September 3)Genome Structure- organization of genetic informationo know bacteria gene characteristics vs humanso remember, gene number does not necessarily correlate to complexityBacterial Genome- open reading frames (orf)= frame of base pairs, begins with start codon, codes for a gene, and genes in one orf code for one protein- non protein coding genes= regulatory genes that code for tRNA- dense with coding sequence- functionally related genes are typically close together- can synthesize all amino acidsTrp Operon- operon= a unit made up of linked genes that regulates other genes responsible for protein synthesis- Trp operon= controls transcription of tryptophano Regulated by repressor (trans acting, represses via feedback system)- Know definition of polycistronic mRNA, horizontal gene transfer- Restriction enzyme = enzyme that cleaves DNA at a specific locus of sequenceHuman Genome- definition of epigenetics- low gene density, not organized by function, transcription factors are combinationalDNA structure- antiparallel, polarity, base pairs held together by H- bonding, know factors that denatureit-Lecture 2 (September 5)Topoisomerase- supercoils are formed to reduce strain of DNA unwinding in replication- positive supercoils vs negative supercoils- function of topoisomerase to relieve straino type I vs. Type II- gyrase present in bacteria since they do not have histonesReplication- initiation: know properties needed at the origin- DnaA, DnaB, and DnaC functiono Helicase hexomer- Leading vs. lagging strand (Okazaki fragments)- Processivity= what keeps polymerase associated to the DNA strando Primase= low processivity, polymerase= high processivityo Single strand binding protein= coats single stranded DNA at fork to keep from tangling- Know problems with replication: okazaki fragments, cantenation, completing the endso Telomeres= protective, stabilizing DNA ends; telomerase RNA= extends the end of telomeres so more DNA can be replicatedLecture 3 (September 10)DNA polymerization- utilizes 3’ end, needs –OH to bind, overall synthesis 5’3’o understand primer strand, template strand, nontemplate strand- know how cell differentiates between DNA and RNA- fidelity—exonuclease proofreading, mismatch repair- know how DNA polymerase are targets for chemotherapeutics- understand how we “see” DNA (i.e. radioactive and fluorescent labels)DNA sequencing- know these methods: Sanger, Gel electrophoresis, PCR, NextGenLecture 4 (September 12)- discussed how to examine papers (we all did this so we should know the steps first hand)- also know the gist of each paper- know Messelson Stahl experiment/paper on random dispersion of replicationLecture 5 (September 17)Gene Regulation- genomes have directed stable pathways—gene regulation is the mechanism for this- Lac Operon—metabolizing lactoseo Positive and negative control—need glucose absent and lactose presento Know role of beta galactosidase, X-gal, and that lactose is upstream from glucoseo Know complementation groupso Know which gene codes for beta galactosidase (lacY or lacZ) and how that information was obtained experimentally (end result is that its lacZ)o Know, experimentally, how we know how cells control their expression of their genes—how lacZ expression is latered in regulatory mutantso Constitutive vs. uninducible o lacI encodes the repressor and is trans working—know how this information was obtained experimentally repressor binds the operator operator is cis working—know how this is known experimentallyLecture 6 (September 19)Structure and Function of lac repressor - binding site is palindromico tells us lac repressor is a dimer- defining ligant binding domains—know what different mutations do- helix-turn-helix motifo alpha helix dimensions match the major groove- mutations in DNA binding domain are dominantStructure and function of lac operator- O1 is a binding siteo Know, experimentally, how it is known that O2 and O3 also function in regulationDNA binding site—recognition of target- specificity and affinityo dimers boost both—know how- understand Kon, Koff, equilibrium constant and how to calculateLigand- induced allostery—when lactose is present- allolactose is an inducer—know its function- cooperativityo ligand binding- negative regulationo ligands prefer different conformationsLecture 7 (September 24)Integrating glucose and lactose signals- prefers glucose as carbon source, using lactose costs energy- glucose repression is combinatorialo know relationships between glucose and lactose presence, if the operon is on or off, and why (CAP bound, lac repressor bound, or both?)o cAMP, CAP—know function of eachGeneralizing Regulation- relationships between negative/positive and inducible/repressible and effect on gene regulationGeneral Transcription- Start site at +1- Know RNAP function- Understand consensus sequences and how they effect expressiono -35 and -10- RNA enzymeo Holoenzyme and core enzyme Know composition and differencesTranscription Initiation- stages initiated by RNAP- closed complez, open complex, abortive initiation, elongation complex- sigma factor melts the -10 regionLecture 8 (September 26)Eukaryotic Transcription- stem cell research—pluripotent cellso metastable statesEukaryotic Transcription--- RNAP- three types RNA I, II, and III- RNAP IIo Shaped similar to bacterial RNAPo Promoters, enhancers, and transcription factors Core promoter= start site- TATA box, DPA, initiator elemento Know traits of each Transcription factors—TFIID function and composition- Binds to TATA and distorts DNA Enhancers- Tethering a protein to DNA- Combinatorial