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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 Sept 7; Introduction and Our Proteins

:Look up amino acids in the MedLine online textbooks ,
Amino acid web sites Indiana State , Image Library ,
Look at the protein chapter in the biophysical society web text
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 ).

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

Hand in questions 1 and 2 and 3
1) Use the text books on line (e.g.Molecular Cell Biology or Molecular Biology of the Cell.or just use GOOGLE. Give me a brief definition and the source you use to get the information.
-a) Mitochondria and Chloroplast
-b) Heme and quinone
-c) Amide group in the protein backbone
-d) Cytochrome
-e) Protein side chain
-f) Define the 4 levels of protein structure: primary, secondary, tertiary, quaternary
-g) pK.

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 product of oxidative phosphorylation?
c) 5 proteins are described as Complex I-V. Each has a name which describes its function. Connect the functional name with each complex.
d) What are the products and reactants for each protein?
e) List the non-amino acid cofactors shown for each protein.

3) 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.)

Getting ahead in the class:
I) Look at these molecular graphics packages and download one of them.:
In order of ease of use (inversely proportional to its power) SwissPdbViewer - Rasmol - Pymol
I recommend pymol or rasmol
Molecular visulization: PYMOL & Rasmol & Swiss Pdb Viewer
Site to get protein structures: Protein Data Bank

2)Look at the protein references here
I will assign proteins at the next class. If you have a preference email it to me by Mon Sept 4.

2-Tues Sept 5.->Hand in Sept 14 Lecture: Mitochondria and Bioenergetics Overview

You have been given a protein.
1) What is its function?
2) Give me a review article describing what it does.
You may want to start with the papers I referenced (here). Look at our web references for a place to start. Pubmed and Science Citation Index can be used to find paper that are related to a reference you already have.
3) Give me the URL for a web site on line that is dedicated to your protein.
4) Give me the URL for a good site for information in an online text book
5) Using the information you have tell me what non-amino acid groups are used in the function of your protein.
6) Draw me a sketch of the reaction (giving me the reference you are using).

Good web sites
general overview here

3- Thurs Sept 7-> Hand in Sept. 14 Lecture: Amino acid properties; peptide bonds
Look at the amino acids web sites suggested in the reading/homework for homework 1.
A good list of properties. An introductory page.

-The amino acids have different properties that in some way determine the folded structure
Some are big others small
Some are non-polar (hydrophobic), polar (neutral dipoles), or by binding or loosing H+ are positive or negative
-As we will learn in the 'forces' section of the course: there are penalties for atomic overlap; for holes; opposite charges attract; dipoles line up (+-)(+-) ; and non-polar atoms move out of water. These rules determine the best structure for a given sequence of amino acids.

Homework

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)
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?)

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 side chain pK for these acidic and basic groups? (what reference did you use?).
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.

Web sites of interest
Amino acids: the movie
Volume, pK, surface area
and hydrophobicity
One view of aa classifications
Best substitutions

Thornton site for aa geometries
AA chemistry and pH dependence of residue charge: isolated aa
Biochem text (Stryer) AA and Sequence yields structure and what we can learn from sequences

Peptide bond
helix and sheet
Berg Biochem on 2 structure
helix ; hbd in helix and strand and sheets

Ramachandran space restrictions on peptide conformations and for helix and sheet plots
Fig and fig 1. and cpk for different angles

di-Sulfide bridges
picture and Ribonuclease and immunoglobin and insulin and multiple disulfides in one protein

Secondary structure prediction
frequency

Helical wheel
Draw one

Membrane proteins
one example and hydropathy plots and

4- Tues Sept 12-> Hand in Sept 21 Lecture: Protein Motifs; 1°,2°,3° structures; visualization
Go here for homework.

Biochem book tertiary structure

5- Thurs Sept 14-> Hand in Sept 21 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 assigned in the 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.
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.

Reading
What is the period of the hydrogen bonds in the helixand sheet ; Answer questions 4 on helix page.

6-Tues Sept 19-> Hand in Thurs Sept 28. Matching primary sequences.

Nucleic Acids Research 1997 25 3389-3402 (If you are interested in how BLAST works and how hits are scored).
Conservative mutation: The substituted residues are similar. They could be all small; or all large; or all polar; all positive; all charged; all non-polar etc.

Blast - matching sequences

Check these sites out for glossaries: Blast Statistics,

1) Using Blosum62 matrix find the raw score for comparison of

TEFKAGSAKKGATLFKTRCLQ
and

TEFKAGSAKGATLFKTRCLQ

TEFKAGSAKLGATLFKTRCLQ

TEFKAGSAKGATLFKTRCLQ

TEPRAGSAKGATLFKTRCLQ

TEFKAGSAKKKGAGATLFKTRCLQ

Do these by hand (eq. with a spread sheet)
then do these at the NCIB web site for 2-sequence comparisons make sure you're using BLASTP
and report
score = __ (bits __), expect = __
identities = ___ Positives = ____ Gaps = _____

2) Using the Protein Data Bank site find the 2 proteins you used in homework 4 (the one I gave you and the one you found..
What proteins are these? What is the source? How are they classified in SCOP?
Get their sequences in FASTA format. You can use PDB site or MSD site.
Past FASTA format sequences into 2-sequence comparisons site
Report: score etc.
The 2 sequences are aligned to each other
- How many residues are identical (report first 10 identical residues)
-How many residues are similar (report all pairs of similar residues - do you agree these residues are 'similar'?)

Hints for question 2
-When you do a sequence match use sequences from 2 different species, otherwise they will be identical - or different only because of a mutation or because some pieces of the structure are missing in one structure.
-Submit only 1 chain. Go for a chain that is important for function. So this should be the one with all the cofactors bound or where the reaction happens. There are lots of places to get a FASTA output for all the chains to use to paste into the BLAST search.
-If you don't have a 2nd structure from a close relative then think a bit wider - Think about proteins you have been told are related in structure and function and try them (so move up a level in SCOP). Or if your protein is a 'heterodimer' with 2 similar but non-identical chains then compare them.
-If you don't find any neighbors then just submit the most important subunit to BLAST. (Look for Protein-Protein Blast on Blast home page). See what are the sequence neighbors of your protein. (that is go to question 3).
-Always remember to check that you are using BLASTp not BLASTn (you may need to change this on the page you are working from).

3) Do a BLAST search of your protein. What other similar proteins are reported? Did any of these types of proteins show up in your search of SCOP families or superfamilies.
4) Give me the URL for the BLAST home page.

7-Sept. 26. -> A short talk Our proteins.

For the Tuesday class please prepare a brief (5 minute) presentation which describes the function of your protein.
I'd like to see a schematic diagram of the protein - with the working parts (important residues or cofactors) labeled.
Then you will have a chance to tell us what the reaction mechanism is in your protein. If you want to send me a powerpoint with 1-2 pictures that would be fine.

.
Call the file: name.prot.ppt using use for protein hr, br, ox (for oxidase), f0, f1, psi, psii, rc to identify your protein.
eg gunner.hr.ppt if i was doing halorhodopsin

Last revised September 27, 2006