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Module 0 - Important Information

Module 0 - Important Information. Faculty and instructor offices, phones and email, pages 4 & 5 Guidelines for problem based exercises (PBEs), pages 5 & 6 Exams and exam preparation, pages 6-8 Grading, page 8 Lecture schedule, pages 9-12 PBE schedule, pages 13-14.

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Module 0 - Important Information

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  1. Module 0 - Important Information • Faculty and instructor offices, phones and email, • pages 4 & 5 • Guidelines for problem based exercises (PBEs), pages 5 & 6 • Exams and exam preparation, pages 6-8 • Grading, page 8 • Lecture schedule, pages 9-12 • PBE schedule, pages 13-14

  2. Welcome to Human Biochemistry! • Jim Keck, Biomolecular Chemistry - Protein biochemist • Contact info: jlkeck@wisc.edu, 263-1815 (office in am) 265-4247 (?) (office after class), 2264 HSLC • Office hours: Each day after class; 12-1 in 2264 HSLC and by appointment • This section is organized in three major parts: fundamentals of protein structure and function (lect. 1-6) specific examples of protein function (lect. 7-10) future perspectives in protein biochemistry (lect. 11-13).

  3. Welcome to Human Biochemistry! • I am a protein biochemist teaching protein biochemistry, which can be dangerous. So if something is confusing or goes by too fast PLEASE STOP ME! • Please fill out the form on the last page of Module 0 indicating your previous experience in biochemistry courses. • Turn this end at the end of class today. • PBE and literature search information has been distributed to your mailboxes -- pre-PBE homework must be turned in prior to 8:00 am on the morning of your first meeting!

  4. Welcome to Human Biochemistry! • Lecture presentations will be available on our website prior to the day of the lecture. Modified lecture presentations will also be posted after the lecture; these will be designated with a “prime” symbol (e.g. lecture1’.ppt) and will include any announcements, review, and repairs. • Additional materials, including problem sets and last year’s exam will be made available to you. Going through these example problems is optional.

  5. Lecture 1: Fundamentals of Protein Structure

  6. Frank Lloyd Wright

  7. Levels of Protein Structure

  8. Primary structure = order of amino acids in the protein chain

  9. Anatomy of an amino acid

  10. Non-polar amino acids

  11. Polar, non-charged amino acids

  12. Negatively-charged amino acids

  13. Positively-charged amino acids

  14. Charged and polar R-groups tend to map to protein surfaces

  15. Non-polar R-groups tend to be buried in the cores of proteins Myoglobin Blue = non-polar R-group Red = Heme

  16. protonated unprotonated ( ) Some R-groups can be ionized The Henderson-Hasselbalch equation allows calculation of the ratio of a weak acid and its conjugate base at any pH

  17. General protein pK’ values • Approximate pK' • Group In a “Typical” Protein • -carboxyl (free) 3 (C-terminal only) • -carboxyl (Asp) 4 • -carboxyl (Glu) 4 • imidazole (His) 6 • sulfhydryl (Cys) 8 • 1˚-amino (free) 8 (N-terminal only) • -amino (Lys) 10 • hydroxyl (Tyr) 10 • 2˚-amino (Pro)(free) 9 (N-terminal only) • guanido (Arg) 12

  18. An example of a Henderson-Hasselbalch calculation • What is the structure of the histidine side chain at pH 4? 4 = 6.0 - log [HB]/[B-] -2 = -log [HB]/[B-] 2 = log [HB]/[B-] 100 = [HB]/[B-] • So, in a solution of histidine at pH 4, the majority structure is that of the protonated form.

  19. Some R-groups can modified

  20. Amino Acids Are Joined By Peptide Bonds In Peptides - a-carboxyl of one amino acid is joined to a-amino of a second amino acid (with removal of water) - only a-carboxyl and a-amino groups are used, not R-group carboxyl or amino groups

  21. Chemistry of peptide bond formation

  22. The peptide bond is planar This resonance restricts the number of conformations in proteins -- main chain rotations are restricted tof and y.

  23. small hydrophobic large hydrophobic polar positive charge negative charge DnaG E. coli ...EPNRLLVVEGYMDVVAL... DnaG S. typ ...EPQRLLVVEGYMDVVAL... DnaG B. subt ...KQERAVLFEGFADVYTA... gp4 T3 ...GGKKIVVTEGEIDMLTV... gp4 T7 ...GGKKIVVTEGEIDALTV... : : * * * : : : : Primary sequence reveals important clues about a protein • Evolution conserves amino acids that are important to protein structure and function across species. Sequence comparison of multiple “homologs” of a particular protein reveals highly conserved regions that are important for function. • Clusters of conserved residues are called “motifs” -- motifs carry out a particular function or form a particular structure that is important for the conserved protein. motif

  24. Generally only a limited amount of a protein’s surface is well conserved Invariant (the residue is always the same, e.g. Asp) Conserved (the residue is generally similar, e.g. negatively charged) Not conserved (can be many different residues in different species)

  25. Secondary structure = local folding of residues into regular patterns

  26. The a-helix • In the a-helix, the carbonyl oxygen of residue “i” forms a hydrogen bond with the amide of residue “i+4”. • Although each hydrogen bond is relatively weak in isolation, the sum of the hydrogen bonds in a helix makes it quite stable. • The propensity of a peptide for forming an a-helix also depends on its sequence.

  27. The b-sheet • In a b-sheet, carbonyl oxygens and amides form hydrogen bonds. • These secondary structures can be either antiparallel (as shown) or parallel and need not be planar (as shown) but can be twisted. • The propensity of a peptide for forming b-sheet also depends on its sequence.

  28. b turns • b-turns allow the protein backbone to make abrupt turns. • Again, the propensity of a peptide for forming b-turns depends on its sequence.

  29. Which residues are common for a-helix, b-sheet, and b-turn elements?

  30. Ramachandran plot -- showsf and yangles for secondary structures

  31. Tertiary structure = global folding of a protein chain

  32. Tertiary structures are quite varied

  33. Quaternary structure = Higher-order assembly of proteins

  34. Example of tertiary and quaternary structure - PriB homodimer Example is PriB replication protein solved at UW: Lopper, Holton, and Keck (2004) Structure12, 1967-75.

  35. Example of quaternary structure - Sir1/Orc1 heterodimer Example is Sir1/Orc1 complex solved at UW: Hou, Bernstein, Fox, and Keck (2005) Proc. Natl. Acad. Sci.102, 8489-94.

  36. Examples of other quaternary structures TetramerHexamerFilament SSBDNA helicaseRecombinase Allows coordinated Allows coordinated DNA binding Allows complete DNA binding and ATP hydrolysis coverage of an extended molecule

  37. Classes of proteins Functional definition: Enzymes: Accelerate biochemical reactions Structural: Form biological structures Transport: Carry biochemically important substances Defense: Protect the body from foreign invaders Structural definition: Globular: Complex folds, irregularly shaped tertiary structures Fibrous: Extended, simple folds -- generally structural proteins Cellular localization definition: Membrane: In direct physical contact with a membrane; generally water insoluble. Soluble: Water soluble; can be anywhere in the cell.

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