Advanced Topics in Biochemistry CHEM 4723 On ACME

Advanced Topics in Biochemistry DNA topology • Overview of higher-order DNA structure • Implications

Advanced Topics in Biochemistry Voet, and Pratt (Ch. 23 -27) • • • Nucleic acid structure DNA compaction, replication, repair, and recombination Transcription and RNA processing Translation Regulation of gene expression 1/22/2022 S. A. Mc. Farland © 2008 4

Advanced Topics in Biochemistry CHEM 4720 L (the lab) • Molecular biology techniques used in biotechnology • Topological manipulation – Drug design – Forensics – Food industry 1/22/2022 S. A. Mc. Farland © 2008 5

Advanced Topics in Biochemistry Final assessment 1/22/2022 S. A. Mc. Farland © 2008 9

Advanced Topics in Biochemistry Responsibilities (undergrads) • Laboratory – Learn your Bio. Rad experiment – Prepare timeline, submit to your grad student – Perform your experiment with your grad student • Report – – – Your Bio. Rad experiment Biotechnology prodecure Science behind the biotechnology Real-world applications/examples of your biotechnology Potential/existing ethic/economic/social concerns Suggestions/comments for adapting this experiment as a 4 th-year university laboratory experiment • Presentation – Same outline/points as report 1/22/2022 S. A. Mc. Farland © 2008 10

Advanced Topics in Biochemistry Responsibilities (grads) • Laboratory – – – • Proposal (topic related to DNA topology) – – – – • Familiarize yourself with your undergrads’ experiments Revise (if needed) proposed timeline and submit Perform the experiment with your undergrads and ask lots of questions Submit an assessment of your undergraduates’ working knowledge of the experiment and theory Submit a report outline/summarizing a list of potential undergraduate experiments that relate to DNA topology General introduction Statement of the research proposal and objectives Recent progress in research related to the proposal Literature pertinent to the proposal Methods and proposed approach Anticipated significance of the work How this work might contribute to the training of young scientists (optional) Presentation – Research proposal 1/22/2022 S. A. Mc. Farland © 2008 11

Advanced Topics in Biochemistry Undergrad-grad pairs for Bio. Rad experiments • Elizabeth – Steph (GMO investigator) – Tim (Crime scene investigator) • Jimmy – Ashleigh (DNA fingerprinting) – Susan (Secrets of the rainforest) • Suzie – Lacey (Restriction digestion and analysis of Lambda DNA) – Sara (Transformation and plasmid purification) 1/22/2022 S. A. Mc. Farland © 2008 12

Advanced Topics in Biochemistry blah 1/22/2022 S. A. Mc. Farland © 2008 13

Advanced Topics in Biochemistry blah 1/22/2022 S. A. Mc. Farland © 2008 14

Advanced Topics in Biochemistry blah 1/22/2022 S. A. Mc. Farland © 2008 15

Advanced Topics in Biochemistry blah 1/22/2022 S. A. Mc. Farland © 2008 16

Advanced Topics in Biochemistry For this week… • Undergrads – Download. pdf supplement for your Bio. Rad kit (see link in 2008 -calendar -4723. xls on ACME/Notes for website) ASAP – Email the. pdf file to your grad student and myself – Figure out prep, experimental, and analysis time involved and organize the details in a file (by Tues. , Jan. 15, email your grad student this file and CC it to me) – Read posted information for this Friday’s intro lab • Grads – Get the. pdf from your undergrad and read it – Organize your own timeline to make sure your undergrads’ proposed timelines are reasonable – Submit the revised timeline to me as soon as it’s done (due Friday, Jan. 18) – Read posted information for this Friday’s intro lab 1/22/2022 S. A. Mc. Farland © 2008 17

DNA Information supermolecules 1/22/2022 S. A. Mc. Farland © 2008 18

DNA Instructions for biochemical processes 1/22/2022 S. A. Mc. Farland © 2008 19

DNA Information molecules are complex and expensive Hexokinase, MW ~96, 000 730 amino acids,

DNA Information molecules are complex and expensive Peptide bond cost ~21 k. J mol-1, catalyzed by relatively simple enzymes …to get a peptide bond between two specific amino acids, the cost is ~125 k. J mol-1 1/22/2022 S. A. Mc. Farland © 2008 21

DNA Information molecules are complex and expensive HK makes 729 specific peptide bonds so the cost exceeds 91, 000 k. J/mol-1! …and more than 200 enzymes, RNA molecules, and specialized proteins are required per bond 1/22/2022 S. A. Mc. Farland © 2008 22

DNA Information supermolecules are HUGE! Each amino acid is coded for by 3 consecutive nucleotides …a polypeptide chain of 730 amino acids corresponds to AT LEAST 2190 base pairs 1/22/2022 S. A. Mc. Farland © 2008 23

DNA Information supermolecules are HUGE! 1/22/2022 S. A. Mc. Farland © 2008 24

DNA from a lysed E. coli cell 1/22/2022 S. A. Mc. Farland © 2008

DNA Information supermolecules are HUGE! • Length of E. coli chromosome, 1. 7 mm • Length of typical E. coli cell, 2 μM • E. coli cells also contain extrachromosomal elements called plasmids (1000 -10, 000 bp) 1/22/2022 S. A. Mc. Farland © 2008 26

DNA Information supermolecules are HUGE but compact! • • 1/22/2022 46 human chromosomes, 2 m of DNA (end-to-end) Adult human (~1014 cells), 1 X 1011 km of DNA! Circumference of earth, 4 x 104 km Distance between earth and sun, 1. 5 x 108 km S. A. Mc. Farland © 2008 27