Study Guide for Final Paper | Biochemistry III | BCHM 465, Study notes of Biochemistry

Download Study Guide for Final Paper | Biochemistry III | BCHM 465 and more Study notes Biochemistry in PDF only on Docsity! BCHM 465 Spring, 2005 Study Guide for the Final Exam Final Exam: Tuesday, May 17, 8:00 am - 10:00 Here is a list of the major topics and concepts that were covered during the semester, as a reminder of what you should study in preparation for the final exam. The overall format of the final will be similar to the two mid-term exams. Some questions will try to tie together points that came up in different sections of the course. Questions addressing material that came up since the second exam are likely to address details. Questions on material from the earlier part of the course will probably not address details as much. General: Know structures (see below). Concepts that arose repeatedly in different biological concepts, such as: error avoidance, fidelity, and proofreading processivity use of ATP by many enzymes, in various steps of replication, translation, etc. use of GTP in translation. Review experiments that were discussed in lecture, that supported various conclusions. I. DNA and RNA structure and chemistry Structures: be sure that you know (and can draw): complete structures of bases, nucleosides, and nucleotides structure of a polynucleotide chain (phosphodiester bonds) Watson-Crick base pairs Nomenclature of bases, nucleosides, nucleotides Chemical properties Approximate pKa’s of ionizable groups enol-keto tautomerization, cyclic forms of sugars glycosidic bond RNA hydrolysis mechanism B-DNA structure properties of helical structures - pitch, twist, helix axis, handedness, major/minor grooves, etc. syn-anti conformations, sugar pucker What are they? What is the chemical basis? A, Z-DNA structures What are major differences, similarities, among A, B, and Z forms (at the level of the overall helical structure, and at the level of individual base pairs)? 2 Hoogsteen base pairing. Triple, quadruple helices. H-DNA RNA structure - secondary and tertiary structure. Definitions. Interactions typical of each. Denaturation/renaturation Absorbance methods for analysis. Melting curve. Definition of melting temperature (Tm) Factors that affect Tm - pH, salt, DNA concentration, length, number and sequence of base pairs. Base stacking, relevance for Tm DNA supercoiling Linking number, twist, writhe Lk = Tw + Wr Interconversion of twist and writhe. Compensatory changes. Relaxed DNA. Negative and positive supercoils Energetics Strand separation, cruciforms, and Z-DNA in negatively supercoiled DNA Topoisomerases. Topoisomerase reaction mechanisms. Functions of topoisomerases in, e.g., DNA replication Gel electrophoresis to analyze DNA topoisomers. Ethidium bromide. How can (has) DNA topology been used as a tool to understand mechanisms of DNA replication and transcription? II. DNA replication III. DNA repair and recombination See Exam 2 Study Guide distributed earlier in semester (available on BCHM 465 web- site: http://www.chem.umd.edu/courses/spring05/bchm465/index.html IV. RNA synthesis Transcription mechanism RNA polymerase subunits, overall structure Promoter structure in bacteria Initiation - promoter binding. Closed and open complexes. Role of sigma factor. Transcription elongation. Transcription bubble. Termination - rho-independent, rho-dependent Regulation promoter strength sigma factors repressors and activators; inducers, co-repressors, co-activators Lac operon repression/induction activation by CRP-cAMP.