Chap 4

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Chap 4

• Review of intermolecular forces
• That determine the structure of proteins

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• What is NSSE?
• The National Survey of Student Engagement (NSSE)
  is a short, reliable and easy to complete student
  survey. This spring NSSE will be sent to a
  sample of freshmen and seniors at ESU. The
  survey asks students questions about how they
  spend their time, what they feel they have gained
  from their ESU experience and to assess the
  quality of their interactions with others at ESU.
  See the attached NSSE benchmarks.
• When is NSSE?
• The first invitation was sent February 13th to
  student ESU email accounts.  The email will have
  the following subject line ESU Wants Your
  Feedback!  and will be from Student_at_NSSESurvey.or
  g    Follow-up reminders will be sent through the
  remainder of the spring semester with the first
  one scheduled in the next few days.  Students can
  complete the survey any time during the spring
  semester.
• Student Incentives
• Students are being offered incentives to complete
  this survey. One 100 incentive will be awarded
  for each 100 respondents. One 300 incentive
  will be awarded. Students can select the form
  their incentive takes either a gift certificate
  to the bookstore or as an addition to their
  e-card.

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Papers

• Topics Should be chosen Paper
• Biblio due Noon 29 Feb
• min 10 sources
• 5 less than 10 years
• Outlines Due Noon 26 Mar
• this is Wednesday
• Papers due Noon 16 April

4
Lab

• Wendnesday
• complete protein assays over the next two weeks
  (complete by spring break)
• If there is interest in a particular day I could
  be up over spring break.
• Short Report Due 2 school Weeks from today
• Wednesdays lab due Wednesday after spring break.
  
• Next weeks lab
• Column Chromo/size separtation
• I messed up and didnt get links up Mondays lab
  books due Monday morning by 900 AM, Wednesday
  due Noon Tues

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Study Goals for chapter 4 Intermolecular Forces
that Govern the Properties of Proteins

• Goal of the chapter
• Understand the molecular forces that fold
  proteins.
• Forces to understand
• Electro static
• Point charges
• Dipoles
• Vander Waals interaction
• Water
• Understand the Structure Of water
• Understand how the structure of water causes the
  hydrophobic effect.

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Note on chapter 3

• The latest cool thing in Cladistic evolutionary
  trees.
• Find your self a super computer
• You find a bunch of related proteins that have
  been crystallized.
• Lock in a point on the structure and overlap the
  structures as closely as possible.
• Calculate the root mean square deviation of the
  back bone.
• organize the tree from smallest deviation to
  largest.
• Helps to look at relationships between widely
  divergent sequences.

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Study Goals for chapter 4 Intermolecular Forces
that Govern the Properties of Proteins

• Understand the concept of effective
  concentration.
• Understand the concept of Cooperatively
• Chapter problems to spend time thinking about
• 1, 2, 3, 4, 6, 8, 11
• Exercises
• Draw the structure of hydrophobic droplet in
  water
• Arg and Glu do not associate with one another in
  aqueous solution Yet in proteins they are often
  found as salt bridges discuss the reasons for
  this discrepancey
• The heat of solvation for benzene in water is
  Negative by approximately 6 Kcals yet the
  solutions are immiscible. Explain

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Chapter 4 Summary

• Understanding the forces that fold proteins
• Electrostatic
• point charges
• dipoles
• H-bond
• Van der Waals
• Water
• understand the structure of water
• understand how the structure of water causes the
  hydrophobic effect
• Effective concentration and Cooperatively

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The Van der Waals interaction

• Both Repulsive and attractive portions.

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Van der Waals Radii and Repulsion

• The closest approach of non bonded atoms
• Varies depending on what things are bonded to
• Crevices in molecules are often inaccessable
  because they are smaller than the Van der Waals
  Radus

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Van der Waals interaction

• the ubiquitous force

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Electrostatic interactions

• Point Charges Salt Bridges
• in vacu
• DE(ZAZBe2)/rab
• 120 kcal/mol for Cl-and Na in optimum contact
• in real life
• DE(ZAZBe2)/D rab
• in real life Charge transfer minimizes DE
• so the dielectric maters

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Electrostatic interactions

• in real life
• DE(ZAZBe2)/D rab
• in real life Charge transfer minimizes DE
• so the dielectric maters

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Electrostatic interactions

• in real life side chains are not point charges

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Electrostatic interactions

• Solvent effects on Ionization
• The lower the dielectric the less a group will
  ionize

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Electrostatic interactions

• Dipoles
• Occur When charge is separated in a molecule
• Mathematically expressed as mDZd

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Electrostatic interactions

• Dipoles
• Possible interactions