Lecture 6_091124 Protein Secondary Structure Ch 4 - PDF

Wednesday, Sept 11 Psalm 56:8 THE HOMIEGLOBINS Rutledge Feltel You have kept count of my Jennifer Gates tossings (wanderings, Emma Jackson sorrows, troubles) and put Cole Pickle my tears in your bot...

Wednesday, Sept 11 Psalm 56:8 THE HOMIEGLOBINS Rutledge Feltel You have kept count of my Jennifer Gates tossings (wanderings, Emma Jackson sorrows, troubles) and put Cole Pickle my tears in your bottle (wineskin). Are they not in your book (ledger)?  Ch. 2-12 “the stuff of life” Announcements Today: – Achieve updates Lehninger’s Ch 4:1-2 – Study Group Guidelines – Using Primary Structure – SWWN reports due – Secondary Structure Thursday Our Achieve Course: homework HW assignments and due dates Our Achieve Course: other resources Not assigned. Optional!! Each chapter has: “Skills you Need” “Adaptive Quiz” Abbreviated and Extended Solutions to Textbook Problems  Our Achieve Course: utilize the resources tab For help with problem solving/troubleshooting a specific question Our Achieve Course: does have its glitches! e.g. HW2B Q4. Would not accept the correct answer 9.8! If this happens to you in the future, don’t waste time on it. Alert me to it by sending an email (a screenshot is great too). Achieve HW3A Q4: Steps to solve: 1. Identify ionizable protons on peptide and designate pKa’s. (Hint: there are 5) 2. Determine charge changes for protonated→deprotonated groups. (Hint: amines are +1→0; carb acids are 0→-1) 3. Solve the 3 pH problems below. (Hint: ask—what is the charge on each group at this pH?) 4. For finding the pI, consider where the molecule is net neutral. The pI will be the average of the 2 neighboring pKa’s. Video solution posted on Canvas. I will open it tomorrow.  Achieve HW4B Q4: Description says researcher increases the poly(Glu) solution pH from 3 to 7… while question states pH increases from 6 to 7… Study Groups: pH PATROL FRI 2:15 PM HOMIE-GLOBINS WED 8:20 PM EEJA MON 7:00 PM HEMOGLOBIN HOMIES THUR 1:15 PM MACROMOLE-COOLS THUR 4:30 PM GENE-IES FRI 2:15 PM DELL inc TUES 2:00 PM BIOCHEM BUFFS MON 8:30 PM 1. Meet weekly for 1 hour (minimum) 2. Fill out the Study Group Log (available on Canvas) and turn it in 3 times during the semester (on Exam dates). 3. Submit feedback a few times during the semester when Dr B. asks for it (especially prior to exam review sessions).  Swans (SWWNs) So What? What’s New? on Canvas in “SWWN” module Biochem Buffs “Biochem Buffs” Kyle Johnson Audrey Lazar Davis Reeves Emma Wasson 1. Find a source of information (news article, video, scientific report, nutrition fact, etc.) that allows you to gain further insight into topics we have studied or will be studying in the coming week. 2. Write a paragraph ( 99.95%) Peptide bonds involving proline: a few are in the cis configuration (~ 6%) Most of these 6% involve tight -turns. Recall: peptide bond is rigid and planar. Proline isomerization 180 ° is catalyzed by proline isomerases 0° Interactions promoting protein stabilization What promotes folding of a protein chain into these structures? Hydrogen bonds – How did we see Hydrogen bonding contribute to stabilization of secondary structures? Van der Waals Be specific with regard to -helix, -sheet, -turn Electrostatic interactions With a couple Disulfide bonds of your nearest neighbors, Hydrophobic effect discuss this. Interactions promoting protein stabilization How do we see Hydrogen bonds contribute to stabilizing secondary structures? Interaction of N-H and C=O of the backbone amides The -helix between residue i and i+4 The -sheet between residues farther apart on the polypeptide (across strands of the sheet) The -turn between residues 1 and 4  Examining Protein Structures -helical proteins -sheet proteins  Predicting Protein Structure The  helix: Protein secondary structure prediction began in 1951 when Pauling and Corey predicted No glycine, usually no proline helical and sheet conformations MALEK: Met, Ala, Leu, Glu, Lys for protein polypeptide backbone favor helix even before the first protein structure was determined! The  sheet: All these years later, powerful new methods breathe new life No proline into this field. The highest accuracy is now at 82–84%, a Similar properties of aa side chains every other residue number unthinkable just a few years ago. https://academic.oup.com/bib/article/19/3/482/2769436 Predicting Protein Structure Which of the following peptides are likely to form an  helix structure, and why? LKAENDEAARAMSEA CRAGGFPWDQPGTSN KSLKDTIKSSWELVKSM Will any of these peptides form an amphipathic helix?  for today (9/11) In class today, we sought to: – Recognize the usefulness of primary structure (sequence) – Examine the basis for the formation of secondary structure – Define angles of rotation in the peptide backbone – Discuss the 2 main secondary structures: -helices and -sheets and the types of bonds that allow their stabilization – Use protein sequence to predict secondary structure