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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.

1- Mon Jan 31 -> Hand in on Feb. 7 Class outline; basic definitions; Start genetic code

:Look up amino acids in the MedLine online textbooks , The course on protein structure on line Birkbeck
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 found on class homepage).

Look at the movies showing myosin and tubulin moving down a filament.
A nice overview of what proteins are and do.

HAND IN answers to 1-3 Feb. 7
1) Look up papers by JE Walker using PubMed and Science Citation (for Science Citation choose 'Web of Science' Then 'Full Search' Then 'General Search'). You must be at a CUNY IP address to get onto Science Citation.
(See what happens if you look for Walker or for Walker J. Try to add the subject ATPase to your search).
1a) How many papers are listed for him in each database?
1b) Why are the numbers different in the different data bases?
1c) How many papers are listed for Related Papers (PubMed) or Cited Articles (Sci Cit)?
1d) How easy is it to find recent related articles in each database?
1e) What did Walker get the Nobel prize for?
Look at the paper Stock D, Gibbons C, Arechaga I, Leslie AG, Walker JE. The rotary mechanism of ATP synthase. Curr Opin Struct Biol. 2000 Dec; 10(6): 672-9
Use PubMed to see Related Articles. Use Science Citation for look for articles that cite this paper.
(for Science Citation choose 'Web of Science' Then 'Full Search' Then 'Cited Ref Search')
1f) How many papers cite this paper by Walker?
1g) Why is it useful to get articles that cite a paper?

2) Use the text books on line (EEGMolecular Cell Biology or Molecular Biology of the Cell Petsko & Ringe or some other source.. Give me the definition and the source you use.
-2a) Protein
-2b) Genome
-2c) Genetic code
-2d) Amide group in the protein backbone
-2e) Protein side chain
-2f) Define the 4 levels of protein structure: primary, secondary, tertiary, quaternary.

3) Use: Can biological phenomena be understood by humans? Nature (2000) 403 pg 345 to answer.

3a) What is the field of 'Structural Geonomics'?
3b) What would we want to learn about proteins by computation?'

2-Wed Feb. 2.-> Hand in Feb. 7 Lecture: Amino acids, Nucleic Acids, The genetic code; protein synthesis

References for protein synthesis and ribosome structure.
- P&R 1-2 and any cell biology or biochemistry textbook. Protein synthesis at Birbeck. Another good RNA>protein web site here

Web sources I used in lecture.
From The Cell: DNA
From The Cell: DNA replication
From the Cell: DNA to RNA
from The Cell: from RNA to proteinPrimer on the genome project

DNA structure
base pairs now in helix , and Transcription coding and Base pairing
Introns and exons and Multiple splice sites and signaling for splicing
One gene
Genetic code-aa perspective and NA perspective
Examples of reading the code
How tRNA translates from the NA alphabet to the AA alphabet and another view
tRNA structure
wobble
Linking 2 AA and Polymerization in general
Three roles of RNA in protein sysnthesis
Ribosome and tRNA binding sites
Cycle of peptide elongation

1-Use this reference to answer the questions Mechanics of the ribosome Nature (1999) 400 pg 811
1a) What 2 methods have been used to get information about the structure of ribosomes?
1b) What is bound to the 30S subunit of the ribosome when the 50S subunit binds?
1c) What are the 30S subunit and 50S subnits made up of?
Another interesting reference: Structure of a bacterial 30S ribosomal subunit at 5.5A resolution Nature (1999) 400 pg 833.

(2) Just for fun: Cut apart the individual nucleic acids.
Label them (A: C: T: G)
Paste them together showing the correct pairing for standard Watson-Crick base pairing. You can get this in any cell bio or biochemistry text book. Or try looking around on the web to find the answer.
Notice the pair sizes and the number of hydrogen bonds of the 2 pairs. Hydrogen bonds are formed between an O= and a H-N or an N (without a H) and an H-N.

(3) Find a table of the genetic code. (P&R, any cell bio or biochem text, on line)
Take the DNA sequence.

3' GTACACTTGTATTAATGG

3a) Write out the complementary DNA strand.
3b) Write out the complementary mRNA (messenger RNA) strand.
There are 6 possible protein sequences that can be read from this piece of DNA (one from the strand and one from its complement.) Write them out. The genetic code is for mRNA to protein. The message RNA is read from 5' to 3' end. (I will give you a hint - there are tools on the web to do this for you. If you use one give me it's URL. Then annotate one of your 6 answers so I know you understand how the RNA sequence is derived).

4a) Which amino acids have the most codons? Which have the fewest?
4b) Phe, Leu, Ile, Ala, and Val are hydrophobic amino acids while Arg, Lys, Asp and Glu are ionizable residues.
The na-> aa table can be organized grouping aa of different types together. This means their codons have some similarities.
4b-1) What do the codons of the hydrophobic residues have in common?
4b-2) What makes a residue hydrophobic?
4b-3) What makes a residue ionizable?

3- Feb. 5 -> Hand in Feb. 14 Lecture: Amino acid properties; peptide bonds
Look at the amino acids web sites suggested in the reading/homework for Jan 31.
Go to the Birbeck AA site; look at the text. A good list of properties. An introductary 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.

Lecture
Amino acids: the movie
Volume, pK, surface area
and hydrophobicity
One view of aa classifications
Best substitutions
sidechain conformation

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 1 and strand and another view
secondary structure
Berg Biochem on 2 structure
helix ; hbd in helix and strand and sheets

Ramachandran space restrictions on peptide conformations and overview in torsion space 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

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?).

Look at the Birbeck Protein Geometry pages

4- Feb. 9 -> Hand in Feb. 14 Lecture: Protein Motifs; 1°,2°,3° structures; visualization
Go here for homework.

Biochem book tertiary structure

5- Feb. 14 -> Hand in Feb. 28 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.

6-Feb. 16 -> Hand in Feb. 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: Birbeck, 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'?)

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.

7-Feb. 21. -> Hand in Feb. 28 Our proteins.
database of macromolecular motions

1) Getting started
1a) What is the function of your protein? (which protein).
1b) Find 2 web sites that provide information about your protein.
1c) Provide a reference for information about your protein from a textbook (hardcopy or on line).
1d) Provide 2 references to review papers about your protein.

2) Looking for conserved domains. Submit your sequence to NCBI CDD site
2a) What kind of proteins show up in the 'top listed sequences' and in the 'most diverse sequences'?
2b) What shows up in the 'Feature Display' options? List the residues where each feature is found (the # in the sequence).
2c) Going to 'Show Domain Relatives' click on 3 different domains found for related proteins. What domains are they.
2d) Click on one of the long red bars. What domain do you get?
2e) Look at the links for references. Tell me something you learned.

3) Use CDD site help.
3a) What is a conserved domain?
3b) What do the colors indicate in the alignment display?
3c) Define PSI-Blast

Last revised February 22, 2005