Protein Sequencing Protein Evolution: Exam Review
Protein Sequencing Protein Evolution: Exam Review
Protein Sequencing Protein Evolution: Exam Review
(3) Fragment PP into smaller peptides Enzymes (Trypsin, Chymotrypsin, etc.) Chemical (CNBr)
(4) Determine the sequence Edman Degradation with PITC (5) Assemble a sequence
Q12. You must cleave the following peptide into smaller fragments. Which of the proteases listed in the table would be likely to yield the most fragments? The fewest? NMTQGRCKPVNTFVHEPLVDVQNVCFKE
Q15. Separate cleavage reactions of a polypeptide by CNBr and chymotrypsin yield fragments with the following amino acid sequences. What is the the sequence of the intact polypeptide? CNBr treatment Chymotrypsin 1. Arg-Ala-Tyr-Gly-Asn 1. Met-Arg-Ala-Tyr 2. Leu-Phe-Met 2. Asp-Met-Leu-Phe 3. Asp-Met 3. Gly-Asn
Q17. Treatment of a polypeptide with 2-mercaptoethanol yields two PP: 1. Ala-Val-Cys-Arg-Thr-Gly-Cys-Lys-Asn-Phe-Leu 2. Tyr-Lys-Cys-Phe-Arg-His-Thr-Lys-Cys-Ser Treatment of the intact PP with trypsin yields fragments with the following aa compositions: 3. (Ala, Arg, Cys2, Ser, Val) 4. (Arg, Cys2, Gly, Lys, Thr, Phe) 5. (Asn, Leu, Phe) 6. (His, Lys, Thr) 7. (Lys, Tyr) Indicate the positions of disulfide bonds in the intact PP.
http://us.expasy.org/
Tools and software packages Proteomics Similarity searches (BLAST)
Also try:
http://www.ncbi.nlm.nih.gov/BLAST/
A protein that is well adapted to its function, that is, one that is not subject to significant physiological improvement, nevertheless continues to evolve.
Homologous proteins (evolutionarily related proteins) Compare protein sequences: Conserved residues, i.e invariant residues reflect chemical necessities. Conserved substitutions, substitutions with similar chemical properties (Asp for Glu), (Lys for Arg), (Ile for Val) Variable regions, no requirement for chemical reactions etc.
0 2 6 9 9 7 19 8 11 17 22 27 44 46 45 50
5.1 0 6 8 8 6 18 9 11 17 21 26 44 46 45 50 0 12 10 10 21 11 13 18 24 28 47 49 46 51
0 2 3 19 8 11 17 23 28 46 47 46 51
0 3 20 8 12 18 24 27 46 48 45 50
0 17 7 11 17 22 27 46 46 46 51
gray whale
Man,chimp
cow,sheep
Tuna fish
worm fly
kangaroo
Chicken,
Bullfrog
silkworm
penguin
monkey
Donkey
rabbit
turtle
Horse
dog
Duck
Wheat
Candida
Yeast
Phylogenetic tree
Indicates the ancestral relationships among the organisms that produced the protein. Each branch point indicates a common ancestor. Relative evolutionary distances between neighboring branch points are expressed as the number of amino acid differences per 100 residues of the protein. PAM units or Percentage of Accepted Mutations
Although DNA mutates at a assumed constant rate. Some proteins cannot accept mutations because the mutations kill the function of the protein and thus are not viable.
Although insects have shorter generation times that mammals and many more numbers of replication, number of mutations appear to be independent of the number of generations but dependent upon time
Cytochrome c amino acid differences between mammals, insects and plants note the similar distances
Myoglobin:
is an oxygen storage protein it binds oxygen tightly and releases it when oxygen concentrations are very low