Spring 2015

Assignments from Spring 2015

Feb 09 Aqueous Solutions, Buffers

Reading (to be completed before class!)   

Chp 2: All (required)
Example Pre-Assignment      key

In Class Activities

Discussion of Syllabus and Basic Buffer Concepts

Worksheet: Properties of water     key

Class Summary (link)


Chp 2: 1, 2, 3, 5, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 20, 22, 24, 25, 26, 27, 33

Some Helpful review (solutions)


Feb 11 Amino Acids, Primary Structure

Reading (to be completed before class!)

Lehninger 6th ed (required review)
Chp 3: 3.1, 3.4
Chp 3: 3.2, 3,3 (these methods will be discussed in lab - you are responsible for them on the exam)


  1. PreAssignment Worksheet    Key
  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
Summary of the Discussion (link)


Deepview Assignment 1 - Views 1-8, DS-1 (view 9 with caption)
Due Tuesday the 17th at noon
Amino Acids
Memorize Names and 3 and 1 Letter AbbreviationsKnow 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 6th ed
Chp 3: 1, 2, 4, 11, 12, 13, 21, 22
Chp 3 (Methods Problems): 5, 10, 15*, 17
(These are review problems and not covered in class. Please see me ASAP if you need assistance)

Rework PreAssignment and InClass Worksheet  


Online Resource Amino Acids


Feb 13 Secondary Structure and Modeling

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!)

Required Review Reading
Lehninger 6th ed (required review)
Chp 3: 4.1, 4.2
Supplemental Reading
Berg Biochemistry
Chp 3: 3.2
Mostly repeat of above, however, it may help with understanding torsion angles,
cis and trans peptide bonds, and the Ramachandran plot.


Complete Deepview tutorials (1-8) and bring questions



Lehninger 6th ed
Chp 4: 1, 4, 5, 6, 10

Berg Biochemistry
Chp 3: problem 15

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. Activity

- Use Deepview to convert the octapeptide into

1) a 3-10 helix            > doc octapeptide
2) a α-helix
3) a β-strand              >  brief instructions

Feb 16 - Thermodynamics

Reading (to be completed before class!)

Whitford - Proteins: Structurer and Function: pages 53-58
This is the best prepartion for the worksheet

Voet 4th ed
Chp 3: all
Chp 8, Sect 4
We will pay careful attention to the role of thermodynamic principles in governing protein stability.
Weak Forces, Hydrophobic effect, clathrates, free energy changes. This is one of the most important sections since the principles govern protein-substrate and drug interactions, stability of DNA, RNA, and Lipid structures, etc.


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

Define the hydrophobic effect and explain how it can
influences protein folding?

Additional Review Questions

Explain the following statement

"The folding process can occur when the combination of the entropy associated with the hydrophobic effect and the enthalpy change associated with hydrogen bonds and van der Waals interactions makes the overall free energy negative."

In Class Activities

- BRING YOUR BOOK or have online reference available in CLASS

- Group Problem on Intermolecular forces, thermodynamics, and protein stability - Key


Your general chemistry chapter on thermodynamics


Class Summary (please contribute)


Feb 18 - 3D Structure of Proteins

Reading (to be completed before class!)

Required Review Reading

Lehninger 6th ed (required review)
Chp 4: 4.3
Supplemental Reading
Berg Biochemistry
Chp3: 3.3, 3.4, 3.5 Protein 3D Structure

- Jmol Animation on Protein Structure

Deepview Assignment 1 - reminder due feb 17th noon


Berg Chp 3 (5th ed): 2, 6, 7, 9

Voet: Chp8: 4 (also using Swiss PDBviewer), 18 (also support your answer using SwissPDBviewer), 22  Solutions

In Class Activities

- Molecular Modeling wih Swiss PdbViewer
Tutorials 7, 10 , 11 (Try tutorial 10 with 1 HHO.pdb , READ Note!)


The majority of this material should be review.
Thus, the focus for this class is to gain further expertise with an essential biochemistry tool, the molecular modeling program, and using it to help us understand the following concepts:

  • tertiary packing and the hydrophobic effect
  • stabilizing factors in 3o and 4o structure
  • working with oligomeric proteins
    • comparing hemoglobin and myoglobin


Feb 20 - Loops, Turns, Motifs

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
      • You do not have to focus on history of development of b-turns
  3. Voet
    • B. Tertiary Structure, a through i, p245-p256
    • Focus of this reading is on Motifs (supersecondary structure)


Topology and Turns

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

In Class Activities

  • In Class QUIZ (on material from week 1 and last Mon)
  • Discussion of Chou and Voet readings
  • Turns and loops as secondary structure analyzed - using molecular modeling software
    • Inspect the structures of the following protein.
      • 1TNF (Note: we actually did 1HEW in class)

Identify two β-turns (according to the nomenclature of Chou), identify the residues in the turn, and discuss an stabilizing interactions in the turn.

This material will be addressed later ...



Feb 23 - Writing Assignment Intro

Reading (to be completed before class!)

Writing Assignment (On Google Docs)

Voet Chp 15, Sect 4 on Drug Design

Hubbach, Writing Research Papers Across the Curriculum, Sect 4 A - G

If you plan to bring and use you won laptop read this

 Problems (Due before next library session)

In Class Activities

Discussion of the writing assignment, deadlines, and Hubbach

Continued work on Homology Models


Library's Biochemistry Subject Guide

ACS Style Guide

Example Papers


Feb 25th - Methods I - Crystallography

Reading (to be completed before class!)

Required Reading

PreQuiz (will discuss in class)

  • Updated slides (from 2015)
    • Large file, allow some download time.
    • This is a pdf but you can play it much like a movie, one slide at a time.
    • Old Lecture Video (no sound, just picts and most text shown in class)
  • My Notes

Use the notes with the slides to supplement the assigned reading


Additional Web Resources

X-ray diffraction


Feb 27 - Crystallography Models

Reading (to be completed before class!)

Required Reading

Asymmetric Unit

Online Dictionary of Crystallography

R-factor (definition)

Review of Steps in Crystallography



9. Judging the quality of models

Deepview Tutorial: Electron Density Maps

In Class Activities

QUIZ (key)

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

My Notes


Consider the following questions.
Submit answers to at least 3  
questions. If you have other questions from the reading please email
you instructor.

Mar 04 - Reading Crystallography Papers

Reading (to be completed before class!)


  • Section on reading crystallography papers

X-ray structure Article

  • Ray et al. Crystal structure of human thimet oligopeptidase provides insight into substrate recognition, regulation, and localization. J Biol Chem (2004) vol. 279 (19) pp. 20480-9
  • Prepare to Discuss the paper by reviewing the outline (in the problems) and preparing questions AND answers


Helpful Definitions

In Class Activities

Disussion of paper and reading


- Discussion of the paper

  • The intro section, what does it accomplish? Who is the audience?
    • Significance of the HEXXH metal binding motif
    • Specifically compared TOP and Thermolysin (discussed HEXXH motif, structure in relation to substrate type)
    • MEROPS database for classification of peptidases (know how to use the database to find information)
      • Discuss the significance of Clans and Families (where is TOP, what is its closest family member)
  • Experimental Section
    • Compared the information on crystallization and structure determination in the experimental section to that provided the reading in chapter 8
      • Crystal growth, space group, phases
      • Who is the audience for this section?
      • What information is provided related to the quality of the dataset and the model? What is missing that you would like to see?
    • Discuss the authors reference to the occupancy of the Zn ion and the thermal (B) factor
  • Results
    • What is the overall fold of the protein?
    • Why are some residues missing in the structure?
    • What is the significance of the gold region in figure 1A?
    • Can you view Fig1 in STEREO?
    • What is the evidence provided that TOP and Neurolysin bear strong structural similarity?
  • To Be Completed Individually
    • The authors discuss regions of flexibility in the enzyme? How could we check this?
    • Discuss fig 5 and the differences that the authors suggest influence substrate specificity.
    • What is the significance of the the structural elements important in substrate restriction and the modeled "unstructured" peptide substrate
    • What are the primary conclusions highlighed by the authors?


Mar 06 - Structural Bioinformatics

Reading (to be completed before class!)

Berg 5th ed: Chp3: 3.6 The Amino Acid Sequence Determines 3D Structure
Review Voet B. Tertiary Structure, p245 - p256
Voet: Chp8: Sect 3C; Chp9: Sect 3A,B


  • Go to the protein data bank and find a PDB file for Thimet Oligopetidase
  • "Play" with the page. In other words, analyse the information and tools provided.
    For instance, try to view the structure in 3D. Determine CATH and SCOP classification of the enzyme.
    • Your text and Voet have information of SCOP and CATH
  • Find a protein or enzyme of interest to you. Bring a summary of your findings to share in class.


Extra Problem

Voet 3rd ed (note that DALI is now SSM)
Chp8: 10
Chp9: 10, 12

Nomenclature, Sequence and Structure Problems

Web Resources


1) Swiss Institute of Bioinformatics

ExPASy (Expert Protein Analysis System) Tools
(the tools can be accessed by category or by resources A-Z)  

  • Sequence Alignment tools
    - BLAST (BLASTp)
  • ENZYME (repository of information relative to the nomenclature of enzymes)
  • Compute pI/MW and ProtParam (calculate pI, % composition, e280nm, etc)
    - HelixWheel (this is no longer on the ExPASy site, use Helical Wheel)
  • Secondary
    ProtScale - allows you to compute and represent the profile produced by any
    amino acid scale on a selected protein. For instance, you can enter the Accession
    number for a protein and predict the secondary structure content based on the
    amino acid sequence using Chou-Fasman parameters.
    -----Use the following Excel file to assist in the prediction of secondary structure using Chou-Fasman parameters
    ----- Compare the actual secondary structure of Goose Lysozyme to that prediced using Chou-Fasman parameters within ProtScale
  • Tertiary structure analysis tools - http://expasy.org/structural_bioinformatics

2) European Bioinformatics Institute

Tools for Multiple and pairwise protein stuctural comparison and sequence alignment

In Class Activities

Discussion of Structural Informatics Tools


3D Structure of Proteins
- Berg 5th ed: Chp2: 2.3-2.6 Protein 3D Structure
- Cox 5th ed Chp 4.2, 4.3

Mar 09 - Homology Modeling

Reading (to be completed before class!)

Also scan the following tutorials we will be doing in class


Assignment 2, Exercise 4 of the Deepview Tutorial


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. 


Chp9: Sect 3A,B

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

Mar 16 - Methods III - CD

Read the following tutorial sections on Circular Dichroism spectroscopy

  • Reading Gore Chapter 4
  • From The Circular Dichroism Site
    • Introduction
      What is Circular Dichroism ?
      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.

These will also be helpful


Mar 13 - Exam I

Exam through Homology Modeling (Mon Mar 9)


Take Home       Due Thursday March 19th at 10pm by email (This email address is being protected from spambots. You need JavaScript enabled to view it.).

It is attached as a word file. You can insert answers directly in the document.

NO collaboration. No discussing the exam with anyone but me.
It is open book and resource.

if you observe any mistakes email me ASAP! Thanks!!

(Note: Homology Model project will be moved to due one week later on March 26th, same time)



March 23 - Library Workshop II

Reading and Pre-Class Assignment

In Class Activities

- Meet in the Wildenradt Theatre

- Presentation and activity by Linda Wobbe


  • Read Section 2 from How to Write Like a Chemist:Graphics, References, and Final Stages of Writing
  • Complete draft 1 of you paper - due April 9th
    • On April 11th you will be assigned two drafts of peer papers to read
    • Peer draft review sheets will be due April 17
  • Use Google Calendar (same as from Lab) to Sign Up for one-on-one meeting in week 11 (April 20-24) to discuss draft 1

Mar 27 - Folding Kinetics

Reading (to be completed before class!)

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



In Class Activities

- Lecture and discussion on reading

Summary of the topics and order of material covered in class

Movie Ab initio protein folding

Discussion Slides (Movie)

Summary slide of introductory material to protein kinetics (adapted from Fersht and Gutin)
Summary Slide of Mutational Analysis 





April 8th-10th - Denaturation Paper

Reading (to be completed before class!)

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




Questions taken from 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 6-8 minutes to discuss their section(s) and the relevance of the findings to the conclusions.


  • (including figure 1) led by Sigman


  • Intrinsic Tryptophan Fluorescence (all of figure 2 and Table 1) - led by Trevor, Tessa, Shane
  • Temperature-Dependent CD Spectra (all of figure 3) led by Kayla, Amanda
  • Unfolding under Equilibrium Conditions (including figure 4 and Table 1) - led by Hans, Alina
  • Unfolding and Refolding Kinetics - (figure 5 and 6) led by Julian, Erika
  • Structural Predictions - (including Figure 7) led by Hamida, Sasha




Apri 13 - Protein Folding and Misfolding

Reading (to be completed before class!)

Prepare to lead discussion


In Class Activities

- Class produced Google Doc Summary of Group discussion of the papers


  1. The first section in article by Dobson reviews protein folding kinetics. Based on the reading put together a summary of the protein folding process.
  2. According to Dobson what parameter of the protein structure has the most significant correlation with folding rate?
  3. What is the "modular mechanism" of folding?
  4. From Taylor et al, what are the two strategies to prevent and deal with protein misfolding?
  5. List two enzymes involved in increasing the rate of protein folding. What reactions do they catalyze?
  6. Based on both papers properties do all the misfolded proteins associated with these diseases have in common? How do these the misfolded protein differ from normal, globular proteins both in structure and formation? Related to this is the fact that the ability to form fibrils is common to all proteins.
  7. The Dobson paper suggests that familial forms of disorders like ALS and Alzheimer's, proteins have an increased propensity to misfold. Discuss some possibilities and, when possible, link them to specific diseases.

Summary of Class Answers to the questions, from 2014



April 17 - DNARNA

Reading (to be completed before class!)


In Class Activities

Group Problem -  RNADNA

Two other group problems were also handed out

Class Google Doc of Discussion


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


April 20-22 - Tour of the Ribosome

Reading (to be completed before class!)


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

 notes from class discussion




Helpful Review (see class on DNA/RNA)

DNA structure

RNA structure

tRNA structure

Genetic Code

In Class Activities

Unedited Group Google Doc From Class


April 27 - Membrane Transport Systems

Reading (to be completed before class!)

Required reading and activities
Berg 5th: Chp 13
Sect 13.1
Sect 13.2
Sect 13.3
Sect 13.4
Sect 13.5
Sect 13.6

Additional Web Resources

Active Transport


Multidrug Resistance Transporters (ABC cassette)

Calcium Pump (P-type)

Facilited Diffusion

Potassium Channels


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

Voet TBD



In Class Activities

Original Group Worksheet

Student altered group worksheet

Worked Problem -  Cell Potential Problem


April 29 - ABC transporters

Reading (to be completed before class!)

Review reading

Berg 5th: Chp 13
Sect 13.3

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 Web 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)




In Class Activities

Finish previous group problem

Original Group Worksheet

Student altered group worksheet

Discuss Research Paper Led by instructor



May 1 - Drug Targets


Robertson, J. G. Mechanistic Basis of Enzyme-Targeted Drugs. Biochemistry 44, 5561–5571 (2005). 
Get Paper


Questions from discussion


In Class Activity

Seminar Style Discussion


May 4th - Quinolone Action


Aldred, K. J., Kerns, R. J. & Osheroff, N. Mechanism of quinolone action and resistance.
Biochemistry 53, 1565–1574 (2014). Get Paper


Questions from discussion


In Class Activity

Please come with questions about the paper. We will compare and record questions and then answer questions as a class. We will also divide into smal groups to address the paper in the context of the writing assignment


May 8th - Drug Targets


Robertson, J. G. Mechanistic Basis of Enzyme-Targeted Drugs. Biochemistry 44, 5561–5571 (2005). 
Get Paper


Questions from discussion


In Class Activity

Seminar Style Discussion


May 12 - Carbohydrates_Articles


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

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 A - Huma, Sasha, Shane, Kayla, Julian)
CREB paper (Group B - Trevor, Erika, Tessa, Hans, Alina, Amanda)

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.

CREB worksheet

FRET worksheet


Week 1

Assignments for the first week

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Week 3
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Week 4
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Week 5
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Week 7
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Week 9
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Week 10
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Week 13
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