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On doing homework. Typed is nice if you have long answers - otherwise you can write it in by hand. Please print out your answers and bring them to class. (I don't want you to email your answers back to me unless absolutely necessary to get them in on time).

I do not want long sections cut form the web. Shorter and directed to answer the question is better.

The copy of the homework on the web will have active links to various pages. If you find any dead links please email me immediately.

Homework-1: Hand in Tuesday Sept 4; Introduction

Hand in questions 1 and 2
1) Use the text books on line (e.g.Molecular Cell Biology or Molecular Biology of the Cell.or just use Wikipedia or GOOGLE. Give me a brief definition and the source you use to get the information.
-a) Mitochondria and Chloroplast
-b) Heme and quinone
-c) van der Waals forces
-d) pKa of an acid
-e) protein backbone; protein side chain

2) Use: Oxidative Phosphorylation at the fin de siecle to answer.

a) Write out the reference to the paper as if you were writing this for a bibliography.
b) What is the overall reactant and product of oxidative phosphorylation?
c) 5 proteins are described as Complex I-V.
What are the products and reactants for each protein?
Each has a name which describes its function. Connect the functional name with each complex.
The answers for complex 1:
Complex I is known as the NADH: ubiquinone oxidoreductase - It takes electrons from NADH (oxidizing it) and gives them to ubiquinone (reducing that). This process is described by the name. Protons are pumped across the membrane when this happens (as seen by the blue arrow in figure 1).
d) List the non-amino acid cofactors shown for each protein.
The protein contains 1 flavin mononucleotide, seven or eight different FeS centers, covalently bound lipid and at least 3 bound quinonl molecules.
e) use in the membrane proteins of known structure to find the 4 letter code for one structure of each of the 5 proteins. When the structure was solved. How many different structures are available.
For complex I: 1M9C solved in 2010. Two structures are available from different organisms.
You may want to go look at one of the proteins in the Protein data bank

_____________EXTRA WEB SITES TO LOOK FOR INTRODUCTION __________________

Start with the web sites of interest page.
I suggest you download one of the molecular graphics packages (I will use PYMOL VMD, Rasmol, Swiss PDB viewer) are all ok. I will use PYMOL in class.Swiss PDB viewer is probably the easiest.
Look up amino acids in the MedLine online textbooks ,
Amino acid web sites Indiana State (basic chemistry of Biomolecules page), Image Library ,
Look at the protein chapter in the Indiana State (Protein structure and analysis)
Find a real cell biology or biochemistry text book and look up amino acids and protein synthesis.
Make sure you can download the figure for the amino acid homework.
Go to all the recommended links (Useful web sites ).

A bit more on protein synthesis: RNA>PROTEIN; and a lovely movie.

Papers that connect biology to chemistry
Can biological phenomena be understood by humans?pdf
The Biological Frontier of Physics. pdf

Web and utube pages that I showed in the first class
aquaporins
bacteriorhodopsin and another on bacteriorhodopsin-with a larger view
lipids and md simulation of lipid bilayer in water

HOMEWORK 2-Hand in Thurs Sept 13 (after homework 3) Lecture: Our proteins

You will use this information in questions 1-8 for your project.
1) Find the right protein
Find your protein at the membrane proteins of known structure web site
What is the 4 letter code for the pdb file for your protein in the protein databank?

2) Find some good references
What is the main reference suggestedthe membrane proteins of known structure web site?
Give a reference to a review article for the protein (look at pubmed and search for reviews).
You may need to find different papers for the structure and for the function. For some proteins you may find a better review for a protein in your group of protein rather than for your specific protein (eg Bacteriorhodopsin review will help you understand halorhodopsin; cytochrome c oxidase may help with quinol oxidase - these connections are noted in the handout sheet for your assigned proteins).
Give me the URL for a web site on line that is dedicated to your protein.
Give me the URL for a good site for information in an online text book

3) What does the protein do?
What is the function of your protein? What are the reactants and the products? (this may be chemical A + electrons go to chamical +B or it may be protons move from the cytoplasm to the periplasm. Draw a sketch of the reaction (giving me the reference you are using).
Does the reaction happen in several steps? If yes what are the intermediates?
Does the protein store energy in the membrane gradient - or does it use the membrane gradient as its energy source?
A nice review of electron transfer 'cofactors'

4) What is important, what is missing and what is extra in your pdb structure file?
What are the non-amino acid groups (cofactors, reactants, products) needed for the function of your protein? Find this in the review articles.
What are the non-amino acids found in the crystal structure? This is in the Ligand Chemical Component and Modified Residue section of the main page for your protein at the protein databank.
Match up the cofactors/reactants/products needed for function and the groups found in the structure. Do you have extra groups or missing groups.
How many polypeptide chains should your protein have (look in a review article). How many do you find in the structure? [Different organisms have different number of polypeptide subunits. Usually mammalian proteins have more subunits. If you have a choice use a smaller protein to start. However some proteins are missing important subunits. Others have extra proteins attached - Look out for proteins that are co-crystalized with an antibody. You do not want to look at the antibody!


5 - not about your protein) Use: The Biological Frontier of Physics. pdf to tell me how many moles ATP you synthesize each day. (You can modify this based on your caloric intake.)

_____________EXTRA WEB SITES TO LOOK FOR ELECTRON TRANSFER CHAINS__________________

Good web sites
general overview for Electron Transfer Chains here

Homework 3 Hand in Tues. Sept. 11 Lecture: Amino acid properties; peptide bonds
make use of the Introduction to protein structure chapter for this assignment.


Print out this figure;
(1) Label each side chain with its full name (e.g. Glycine); Three letter name (Gly); and its 1 letter name (G)
- Color each Oxygen red and each Nitrogen blue
- Label which are NP non-polar; P polar; + positively charged; - negatively charged
- Label which are S (small); M (medium); and L (large) in size (this is a bit subjective)

(2) Draw a valine amino acid (backbone and side chain). Draw a dipeptide Ala-Val. You need to combine 2 amino acids to form a peptide bond. Circle the peptide bond; circle each amino acid; and label each side chain.

(3) What distinguishes hydrophobic and hydrophilic amino acids? Give me the reference you used for the definition.

(4) Find a table of side chain physics properties (this can be found in some of the web references provided or the protein chapter I've given you)
4a) What is the molecular volume of and Ala, a Lys, a Val? Is this value for just the side chain or for the whole amino acid? (what reference did you use?)
4b) Look at the Suggested amino acid substitutions. Thre are 4 groups circled. For 2 of the circles say what properties these amino acids have in common.
4c) Make the following graphs. (1) Surface area vs solubility; (2) Volume vs solubility. Which has a better correlation? Use data at: Jena Library site. If you use another data source give me the reference.

4a) Give me a definition of the pK of an acid or base (and the reference you used).
4b) What amino acids have acidic side chains?
4c) Which ones have basic side chains?
4d) What is the pK of the side chain for these acidic and basic groups? (what reference did you use?). [do not give me the n-terminal or c-terminal site pK here].
4e) Every side chain (except proline) has a amino n-terminal and carboxylic acid c-terminal. What is the pK of the n-terminal and the c-terminal.

_____________EXTRA WEB SITES TO LOOK FOR AMINO ACIDS__________________
I will send you a copy of a chapter in preparation for a biophysics book.
Jena Library site- Individual properties of the 20 standard aa (including pKs);
Look at the ionic equilbria review page
A good list of properties. An introductory page.
pH dependence of residue charge: isolated aa
Membrane proteins. Look at the Experimentally determined hydrophobicity scales.
Look at the amino acids web sites suggested in the reading/homework for homework 1.

Homework 4- Hand in Tues Sept 20 (with homework 5) Lecture: Protein Motifs; 1°,2°,3° structures; visualization
make use of the Introduction to protein structure chapter for this assignment.

This is a very important excercise for your project - you will use this information for your project.
(1) Go to the The protein data bank (PDB) site..
1a) How many entries are currently in the protein data bank for all proteins?

You have each been given a protein. Find the structures for your protein. Each protein structure has a unique 4-letter code used in all of these sites.
Look up your protein in all these sites. (1) membrane protein site. (2) the protein databank and in the (3) Macromolecular Structure Database (use 'text' search'). (4) PubMed and go to STRUCTURE. Do a keyword search; (5) SCOP Do a Keywork search.

There may be multiple copies of the same protein - from different organisms, with different mutations, or with different bound molecules.
The RCSB site in particular will give you noise - in particular proteins that interact with your but are that protein.

You can answer these questions from The protein data bank (PDB) site. or Macromolecular Structure Database. In each case just type your 4 letter code in and play around. The membrane protein site is the simplest way to get a workable 4 letter code. Then go to the protein databank site (this is linked in the membrane protein site.

For the PDB file for your protein you have chosen:
From the SUMMARY page.
1b) What is the 'source'. What's the common name for this organism?
1c) How many atoms in the protein?
1e) How many residues?
1f) How many polypeptide chains (subunits)?
1g) What is the resolution? Low values of resolution are better. Below 2 Å is not too bad.
1h) What non-amino acid groups are bound to this protein (list the ligands and prosthetic groups)?
On the Derived Data Page
1i) What is the SCOP fold?
From the SEQUENCE Page
1j) How many helices are there? What percent is helical?
From the Sequence Similarity page
1k) How many proteins are 100% similar (identical).
1l) How many proteins are on the list of 30% similarity. Tell me what some of them are.
In the Geometry page.
1m) Find the Ramachandran plot for your protein. MolProbity Ramachadran Plot or Procheck in the Structure Analysis/Geometry section of PDB site.
1n) Make a sketch pointing out the helical and sheet regions. Are all residues at the optimum position for the 2° structure type?
Use 'LIGAND EXPLORER' (this is on the right side of the RCSB site or pymol or other molecular visualization software.
1o) What Ligands are found? Look at the amino acids that make a HYDROGEN BOND and METAL INTERACTIONS to your ligand. If you have many ligands use your (growing) knowledge of your protein to tell me about the ligands that are important for function - you can ask me about this if you don't know yet.
Click through the other tabs at the PDB site.

2) Look up the function of your protein.
2a) What does your protein do?
2b) Give me the reference to a review article about your protein.
Try using PubMed, Google Scholar, (or when on campus ISI web of knowledge or Science Direct). You can use the citation for your pdb file or use 'related articles' in pubmed to find some papers. Use keyword 'review' to narrow your seach.

_____________EXTRA WEB SITES TO LOOK FOR PROTEIN STRUCTURES__________________
Biochem book tertiary structure
Peptide bond
helix ; hbd in helix and strand and sheets
Ramachandran space cpk for different angles

Homework 5 Hand in Sept 20 (with homework 4) Lecture: Protein folds and families

1a) Compare the classification system of SCOP and CATH (SCOP has Class ->Fold -> Superfamily -> Family, CATH starts with Architecture). What levels correspond in the 2 systems. Define what each level describes.
1b) How many topologies are there in CATH? How many folds are in SCOP?

2) Use the pdb file for your protein you started looking at in homework 4.
2a) Compare the classification of your proein in SCOP and CATH.
2b) How many domains are found for each chain of your protein?
2c) What other kinds of proteins are found in the same SCOP superfamily?
2d) What other kinds of proteins are found in the same SCOP family?

A - Evolution of the Protein Repertoire Science (2003) 300 pg 1701
B-One thousand families for the molecular biologist Nature (1992) 357 pg 543-4
C-CATH-a hierarchic classification of protein domain structures Structure (1997) 5 pg 1093-1108. A more recent paper Dessaily et al.
D-From protein sequence to function Curr Opin Struct Biol (1999) 9 pg 363-376.
E- SCOP JMB reference

-3a) What is a protein domain? (Give a definition from ref A and from another source).
-3b) How do CATH and SCOP handle proteins with multiple domains?
-3c) What are the 2 alternative ways for evolution to occur described in ref 1 and which one does Chothia support?
-3d) What do protein families have in common?
-3e) Have all the genomes discussed here in 1992 been sequenced? Give me the URL for the web site for one of them?
-3f) How many proteins are now available at the Protein Data Bank?
-3g) How many protein families did Chothia think there would be in 1992? How good was his prediction?
-3h) How much does the structure tell us about the function? Give 2 examples described in ref 4.

_____________EXTRA WEB SITES TO LOOK FOR PROTEIN MOTIFS__________________

6-. Membranes and the difference between membrane and soluable proteins.
More information about membrane proteins from Steve White on membrane proteins and on lipids.

7-Tues Oct 2. Powerpoint slide for the structure of your protein. template
Submit a one page writeup about your protein. This summarizes the work you have done in the homeworks for this section of the class.

Last revised September 4, 2012