Assignments 2018

Spring 2018

Assignment Pages for Spring 2018
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Foundations Feb 12

Reading (to be completed before class!)   

Lehninger
Chp 1: 1.1 Cellular Foundations
Chp 2: 2.2-2.4 Acid-base, buffers
 
Example Pre-Assignment

In Class Activities

Discussion of Syllabus and Basic Buffer Concepts

Worksheet: Acid-base biochemistry  key

Class Summary (link)

Problems

Lehninger
Chp 2: 1, 2a, 3b, 5, 8, 9, 10, 11, 12ce, 14, 15, 16, 17, 24, 26, 27, 28, 31

Some Helpful review (solutions)

 

A Note on Assessment

 


Aqueous Solutions Feb 14

Reading (to be completed before class!)   

Lehninger
Chp 2: 2.1 Aqueous solutions, weak interactions

Article
NATURE | VOL 430 | 1 JULY 2004.
Context-dependent contributions of backbone hydrogen bonding to β-sheet folding energetics.
READ abstract and text related to figures 1 and 2.
 
In-Class PreQuiz

In Class Activities

Worksheet: Properties of water

Problems

Lehninger
Chp 2: 1, 2a, 3b, 5, 8, 9, 10, 11, 12ce, 14, 15, 16, 17, 24, 26, 27, 28, 31

Some Helpful review (solutions)


 

Primary Structure with Intro to Molecular Modeling Feb 16

Reading (to be completed before class!)

Lehninger
Chp 3: 3.1, 3.2, 3.4 Amino Acids, Primary Structure
Chp 3: 3,3 (discussed in lab)
Chp 4: Sections 1-2, pages 115-125

Pre-Assignment

  1. PreAssignment Worksheet
  2. Download Deepview (SwissPDB viewer) to your computer.
    Read The Intro to the Deepview turorial and do parts 1 (Getting Started) and 2 (Windows)

In Class Activities

  1. Short lecture/discussion
  2. Activity
    • If you have one please BRING your LAPTOP to CLASS
    • Molecular Modeling wih Swiss PdbViewer 
      Tutorials 3-6, 8

Problems

  • If you have one please BRING your LAPTOP to CLASS
  • Molecular Modeling wih Swiss PdbViewer 
    Tutorials 3-6, 8  Please complete by Monday the 19th before class

Deepview Assignment 1 - Views 1-8, DS-1 (view 9 with caption)
Due Friday the 23rd end of day (pleases send all files via email or share with me in a Google folder)


Amino Acids

  • Memorize Names and 3 and 1 Letter Abbreviations
  • Know Categories to which each AA belongs (nonpolar, neutral polar charged, etc)
  • Be able to match structure of the AA to its name
  • Know approximate pKas for backbone amines and carboxylic acids, charged side chains

Lehninger
Chapter 3: 5, 10, 11, 13, 15, 21, 22
Chp 3 (Methods Problems): 5, 10, 15*, 17
(Methods problems are assigned to support lab. These are review problems and not covered in class. Please see me ASAP if you need assistance)


 

Secondary Structure and Molecular Modeling - Feb 19

Focus
Most of this material is review. In this class we will focus on
  • understanding phi and psi
  • relationship between phi and psi and structure
  • using the Ramachandran plot
  • working with the molecular modeling program to visualize structure

Reading (to be completed before class!)

Lehninger 7th ed (required review)
Chapter 4: Sections 1-3, pages 115-143

Supplemental Reading
Berg Biochemistry Chp 3: 3.2 (May help with torsion angles,
cis and trans peptide bonds, and the Ramachandran plot.)

Pre-Assignment

 

Problems

  • Lehninger 7th ed
    Chapter 4: 1, 4, 6, 7, 10, 13, 16
  • Voet 4th ed
    Chp 8: 2, 4
  • Begin to Browse the resources available a ExPASy*
    • Expert Protein Analysis System,
    • Molecular Biology computing tools.
    • available on Server in Geneva, Switzerland

In Class Activities

  1. In Class Activity Worksheet

- BRING your LAPTOP to CLASS
> octapeptide molecule (download)


Thermodynamics - Feb 23

Reading (to be completed before class!)

Helpful Review
Voet 4th ed
Chp 3: all
Chp 8, Sect 4

In Class Activities

Problems

Voet Chp 3: 3, 9, 13
Voet Chp 8: 13, 14

Additional Problems: See worksheet

Interpret the table below to answer the following questions (adapted from Fiore et al. Biochem. 2009, 48, 2550): Thermodynamic parameters for folding of structured RNAs

  • Is the folding of these RNA molecules driven by the same forces as the peptides discussed in class? Justify your answer.
  • Calculate the ΔGo for each RNA (assume 298K). Is folding spontaneous?
     RNA  ΔHo (kcal/mol)  ΔSo (cal/mol*K)
    P4-P6 domain of Group I intron  -28 ± 3  -91 ± 8
       -4.1 ± 2.3  -9.6 ± 5.7

Loops, Turns, Motifs - Feb 26

Reading (to be completed before class!)

Reading on Loops and Turns

1) Whitford This first reading is very short but provides a nice introduction to the topic.

2) Chou Analytical Biochemistry 2000
- Read just through beta-turns
- Note there is a mistake in the phi and psi angles for residue i+1 in the type II' turn in table I. They should be phi = 60o psi = -120o

3) From EXPASY text Chp 1- The image of type I and II turns nicely compliment table I of Chou

  • You do not have to focus on history of development of b-turns

4) From EXPASY text Chp 2 - The image of type I' and type II' turns compliments table I nicely

5) Voet

  • B. Tertiary Structure, a through i, p245-p256
  • Focus of this reading is on Motifs (supersecondary structure) 

6) Loops and Turns Pre-Assignment Worksheet

In Class Activities

  • Discussion of Chou and Voet readings
  • Turns and loops as secondary structure analyzed - using molecular modeling software get worksheet
    • Inspect the structures of 1HEW, 1TNF, or 1RCP
      • Identify two β-turns (according to the nomenclature of Chou), identify the residues in the turn, and discuss an stabilizing interactions in the turn.

Problems
1)
Topology and Turns

2) You can practice looking at turns and loops using the identified structures from this paper
Protein Structure 1973 Lewis
Go to table II. Find some of the identified β-turns and then confirm in DeepView using the PDB structures of those enzymes

3) PDBsum. Please try out this tool and compare to the answers you assigned for 4CHA and other proteins. Help with the Codes in PDBsum, ProMotif.

4) Due Friday (see assignment in Worksheet)

 

 


 

Methods I - Crystallography - March 5th

PreClass Assignments (to be completed before class!)


 

 

Problems

Electron Density Map Tutorial in Deepview

  • Do Lysozyme Tutorial and Fitting Residues into Denisty Tutorial

Additional Crystallography Problems Worksheet with key

Additional Handy Web Resources

X-ray diffraction

     

Crystallography Models March 7th

Reading (to be completed before class!)
The goals of these two readings are linked.
The first reading, for Wed, will be applied to the Tzartos article on Fri.

  1. CCMC Chap 02
  2. Tzartos et. al.

Other Resources Online Dictionary of Crystallography      Refinement (definition)

R-factor (definition)   Structure Factor (defined)     Review of Steps in Crystallography

Problems

9. Judging the quality of models

Deepview Tutorial: Electron Density Maps

Pre-Assignments

  1. (Wed) Consider the following questions. This is a class collaboration.
    Submit answers as class discussion. Do not delete any answers.
  2. Tzartos PreAssignment for Fri

 

In Class Activities

9. Judging the quality of models 9a and 9b

Required Files                 My Notes

Exam I - March 14

Exam through X-ray (Fri Mar 9)

Study Guide             Exam Sign-Up Sheet


 

   

Homology Modeling - Mar 16

Reading (to be completed before class!)

Assignment

 

In Class Activities

Work on Homology Modeling Tutorial

Note!  Before doing the homology model tutorial you will need to create an
account in SwissModel. That is where your results are stored. SwissPDB viewer
communicates with SwissModel to a certain extent. 

Review

Chp9: Sect 3A,B

Make sure you have MASTERED Deepview tutorials 1-8, 10, 11

Methods II - Fluorescence and CD

Reading (to be completed before class!)

These will also be helpful

Pre-Assignment (Due in Class) Key

Why use Circular Dichroism ?

  • determination of the secondary structure
  • tertiary structure
  • folding kinetics
  • determine whether an expressed, purified protein is folded
  • if a mutation affects its conformation or stability.
  • protein-protein interactions
  • ligand binding
  • CD measurementent
    Basic experiment.
  • Protein secondary structure determination

In Class Activities

  • Group discussion on UV-vis and fluorescence and CD applications
  • Class notes (from a previous class)

 

Problems

Fluorescence and CD problems

 

 

 

 

 

 

 

 

Homology Modeling Take II - April 4th

Reading (to be completed before class!)

Also scan the following tutorials we will be doing in class

Problems


 

In Class Activities

  1. CD Spectroscopy Catch Up (see assignment page)
  2. Work on Homology Modeling Tutorial

Note!  Before doing the homology model tutorial you will need to create an
account in SwissModel. That is where your results are stored. SwissPDB viewer
communicates with SwissModel to a certain extent. 

Review

Chp9: Sect 3A,B

Make sure you have MASTERED Deepview tutorials 1-8, 10, 11

Folding Thermodynamics and Kinetics - April 6th

Reading (to be completed before class!)

  • Lehninger p143-146
    • (this will provide a VERY brief overview of the topics (see goals)
  • Whitford, Chp 11, pp - 395-403
    • Fills in details on thermodynamics of folding and unfolding
  • Berg Ch6 3.6.2
    • I added this for the nice discussion on Cooperativity in Protein Folding

Pre-Assignment
Create an outline of the reading.
Within the outline, highlight two questions to share in class discussion.

Goals

In the next three sections we will look at three broad topics

  • Thermodynamics and equilibrium unfolding and stability of proteins
  • Folding Pathways and Kinetics of Folding
  • Determinants of Protein Folding
  • Techniques to measure folding

In Class Activities

Discussion

Discussion Slides (movie)

Past Class Outline

 Note: I supplemented my discussion of the reading from three sources (focus on the highlighted parts)
  •  Fersht. The sixth Datta Lecture. Protein folding and stability: the pathway of folding of barnase. FEBS Lett (1993) vol. 325 (1-2) pp. 5-16
  •  Gutin et al . A protein engineering analysis of the transition state for protein folding: simulation in the lattice model. Fold Des (1998) vol. 3 (3) pp. 183-94

  • Apetri and Surewicz. Kinetic intermediate in the folding of human prion protein. J Biol Chem (2002) vol. 277 (47) pp. 44589-92
    • We used the first pages of ths paper in class to expand on the discussion of the Chevron plots discussed in Whitford

Denaturation Paper - April 9th

Reading (to be completed before class!)

Review Reading

Folding of the SARS coronavirus spike glycoprotein immunological fragment (SARS_S1b): thermodynamic and kinetic investigation correlating with three-dimensional structural modeling.

Yu et al. Biochemistry (2005) vol. 44 (5) pp. 1453-63

or

http://pubs.acs.org/doi/abs/10.1021/bi0482396

Problems

 

Questions for class discussion

In Class Activities

Discuss paper -

Each group should present the figures from within their section and lead discussion of the meaning and significance of the results. You may need to refer to the experimental section or past class material and lectures on fluorsecnce CD, denaturation, etc.

You have to read all sections. But you will lead the discussion of your sections. I will have the figures displayed on the overhead for you to refer to.

Each team will have 3 minutes/person to present their section(s).


INTRODUCTION

  • (including figure 1) led by ...

RESULTS and DISCUSSION

  • Intrinsic Tryptophan Fluorescence (all of figure 2 and Table 1) - led by 
  • Temperature-Dependent CD Spectra (all of figure 3) led b
  • Unfolding under Equilibrium Conditions (including figure 4 and Table 1) - led by
  • Unfolding and Refolding Kinetics - (figure 5 and 6) led by
  • Structural Predictions - (including Figure 7) led by
 





 

Denaturation Paper / Unfolding Kinetics- April 11th

Catch-up day

We will conitinue our discussion of

Folding of the SARS coronavirus spike glycoprotein immunological fragment (SARS_S1b): thermodynamic and kinetic investigation correlating with three-dimensional structural modeling. Yu et al. Biochemistry (2005) vol. 44 (5) pp. 1453-63 (http://pubs.acs.org/doi/abs/10.1021/bi0482396)

We will also go back to our discussion of unfolding kinetics

Whitford, Chp 11, pp - 404-415

Nice dscussion of the kinetics of protein folding and Leninthal's Paradox

Note: I supplemented my discussion of the reading from three sources (focus on the highlighted parts)

  •  Fersht. The sixth Datta Lecture. Protein folding and stability: the pathway of folding of barnase. FEBS Lett (1993) vol. 325 (1-2) pp. 5-16
  •  Gutin et al . A protein engineering analysis of the transition state for protein folding: simulation in the lattice model. Fold Des (1998) vol. 3 (3) pp. 183-94
  • Apetri and Surewicz. Kinetic intermediate in the folding of human prion protein. J Biol Chem (2002) vol. 277 (47) pp. 44589-92
    • We used the first pages of ths paper in class to expand on the discussion of the Chevron plots discussed in Whitford

Problems

See Past assignment pages for problems.

   





 

Biological NMR - April 16th

Reading (to be completed before class!)

Review your organic chem text on NMR
Carey Chp 14. Sect 14.1-14.19

New Reading
Whitford Chp 10 p 360-375

Problems

Perform this tutorial

  1. https://spdbv.vital-it.ch/TheMolecularLevel/SPVTut/text/STut09.html#9b
  2. Find another NMR derived structure from the PDB and analyze using it using the same metod

Determination of Angiotensin Analog via Proton NMT spectroscopy (handout)

In Class Activities

- Lecture and discussion on reading

 Additional Problems

 

 

 

Carbohydrates_review

Reading

Lehninger 7.1-7.4

Supplemental Reading Berg 5th ed, CHP 11

Problems

Berg 5th ed
Chp11 All

In Class Activity

Group Problem

Example answer to question 10

An oligosaccharide (shown in grey) bound in the binding site of a plant lectin (Griffonia simplicifolia isolectin IV in complex with the Lewis b blood group determinant). Only a part of the oligosaccharide (central, in grey) is shown for clarity.

An oligosaccharide (shown in grey) bound in the binding site of a plant lectin (Griffonia simplicifolia isolectin IV in complex with the Lewis b blood group determinant). Only a part of the oligosaccharide (central, in grey) is shown for clarity.

Carbohydrates_research April 18

Reading

Read as much as needed to help understand the application in the paper
FRET (quick intro)

Papers
Lamarre-Vincent and Hsieh-Wilson.  Dynamic glycosylation of the transcription factor CREB: A potential role in gene regulation . J Am Chem Soc (2003) vol. 125 (22) pp. 6612-6613

Gross et al.  A strategy to discover inhibitors of O-linked glycosylation . J Am Chem Soc (2008) vol. 130 (2) pp. 440-+

In Class
Leaders for each paper assigned.
FRET paper (Group C - Nick, Breanna; Group D - Mark, Ben)
CREB paper (Group B - Moises, Brandon, Kevin; Group A - Sarah, Belen, Ray)

Each group has 25 minutes to discuss the worksheets regarding their paper
After answering the questions the 2 groups will lead a 15 minute discussion about the article.

Unanswered questions or addtional questions and comments should at the end of your Google doc

CREB paper worksheet A

CREB paper worksheet B

FRET paper worksheet C

FRET paper worksheet D

FRET! April 27th

Reading

Lehninger, Box 12-3 (FRET special section), pages 448-449.

FRET (quick intro)

Campbell, Biophysical Techniques, pages 193-196.

From Lakowicz's Principles of Fluorerscence Spectroscopy

Wallrabe and Periasamy.
Imaging protein molecules using FRET and FLIM microscopy.
Curr. Opin. Biotech. 2005, 16, 19–27.

Homework

Cambell Problems: 5.5.1, 5.5.2, 5.5.3, 5.5.5, 5.5.6 (solutions)

 

Additional (Due At Exam Time): 15 pts

Access the article “Real-time monitoring of cyclic nucleotide signaling in neurons using genetically encoded FRET probes.” Brain Cell Biology. 2008, 36, 3.

Read the introduction, then look at the indicated figures to answer the questions below.

  1. The system you will be examining in the next question is shown in Figure 1B. What enzyme activity is being monitored? Is this upstream or downstream of cAMP signaling?
  2. Will FRET transfer increase or decrease during cAMP signaling?
  3. Now examine Figure 4. What ratio is being monitored? Is it higher or lower during cAMP signaling?
  4. How do the various neurotransmitters affect this ratio? What does this mean for cAMP signaling?
  5. Do all of the cells react the same? (How awesome is it that they can monitor all of them at once?!)

PreAssignment: FRET PreAssignment

In Class

In Class Worksheet ----- (solutions)

Slides

DNARNA Review April-30

Reading (to be completed before class!)

Required
  Lehninger, Chapter 8, pages 281-291

Suggested
  Berg

PreAssignment (based on Lehninger Reading DNA-RNA Pre)

In Class Activities

Group Problem - RNADNA

Two other group problems were also handed out

Class Google Doc of Discussion

Problems/Questions

Berg Problems
1, 2, 5, 6, 13, 14, 16, 19, 20, 23, 24

Additional Problems

 

Interactive Tutorials


Tour of the Ribosome - May 2nd

Reading (to be completed before class!)

Problems/Questions

Link to Student edited Questions (also in Group Google Doc)

 notes from class discussion

Additional Problems on RNA structure (answers)

 

 

 

Helpful Review (see class on DNA/RNA)

DNA structure, RNA structure, tRNA structure, Genetic Code

In Class Activities

Brief Lecture Slides on RNA Structure

Unedited Group Google Doc From Class

 

Writing Assignment Peer Review

Reading (to be completed before class!)

  • Read Assigned articles
  • PreAssignment - Complete Rubric for each Peer paper
  • RUBRIC

 

 

In Class Activities

Rountable Discussions of the Papers

 

Membrane Transport Systems - May 9th

Reading (to be completed before class!)

Review: Lehninger 10.1, 10.2 on Lipid Structure

Required: Chp 11.1-11.3

Supplemental reading and activities
Berg 5th: Chp 13
Intro - Sect 13.1- Sect 13.2- Sect 13.3
Sect 13.4 - Sect 13.5 - Sect 13.6
Summary

Pre-Assignment (7 pts)

In Class Activities

Original Group Worksheet

Student altered group worksheet

Worked Problem -  Cell Potential Problem        Key

Problems/Questions

Lehninger Chp 10: 1, 2, 3, 8, 9

Lehninger Chp 11: More TBD 13, 14, 15

Berg Chp 13 5th Ed: 10, 11, 14, 19


Additional Web Resources

Active Transport

Facilited Diffusion

Potassium Channels

   

ABC transporters

Reading (to be completed before class!)

Locher et al. Science (2002) vol. 296 (5570) pp. 1091-8
The E. coli BtuCD structure: a framework for ABC transporter architecture and mechanism.

Additional Cool Resources

Journal of Bioenergetics and Biomembranes
December 2001, Volume 33, Issue 6, pp 453-458
Overview: ABC Transporters and Human Disease

Multidrug Resistance Transporters (ABC cassette)

PreAssignment (6 pts)

Coming ...

Problems/Questions

TBD

In Class Activities

Transport Group Worksheet

Discuss Research Paper Led by instructor

 

   

Ion Channels

Reading (to be completed before class!)

Reading
Voet: Chp20, 2F (potassium channels),
Voet 4th: Chp 20, 5A, 5C (voltage gating, structure),
 (ligand gating, dopamine)

Review P-type ATPases (Lehninger)

***Structural basis for Ca21 selectivity of a
voltage-gated calcium channel
 (I will cover this paper in class. I have 
highlighted the sections relevant to what I discussed).

PreAssignment - 6 pts Ion Channels (from Voet 2F and 5A)

Additional Web Resources

Potassium Channels
Calcium Pumps

Begin Reading this paper. We will discuss in class on the 16th.

Calcium, Bioenergetics, and Neuronal Vulnerability
in Parkinson's Disease

 

Problems/Questions

Voet Chp20: 1, 4, 5, 6, 7, 10(assume 37C)
12, 14, 15, 16, 

In Class Activities

  • Structural Basis for Voltage gating
  • Example of selective channel (K+ channels)
  • Action potentials
  • Ca2+ channel (see Tang paper)

Slides (in movie format)

Original Group Worksheet

Student altered group worksheet

Slides from that day (also see highlighted parts of Tang)

   

 

 

 

 

 

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