PDB

A protein database contains the information about ___________

1)

mRNA

DNA

3-D structure of proteins

RNA

2) The primary structure of a protein is made up of linear sequence of _______________

DNA

mRNA

nucleotide

amino acid

3) An example for protein secondary structure is _________

alpha helix

Cysteine

beta sheets

Both a and c

4) PDB is ___________

Protein Database Bank

Protein Detail Bank

Protein Data Bank

None of the above

5) Which of the following statement(s) are true

The PDB files contain experimentally decided 3-D structures of biological macromolecules

The molecular structures are obtained by X-ray crystallography or NMR spectroscopy

All data PDB are accessible to public

PDB is maintained by Worldwide Protein Data Bank

All of the above

1. Find out the best alignment among the two alignments with your own basic assumed scores?
2. Align two FASTA formatted Haemoglobin and Myoglobin protein sequences of Casuarina glauca (Genbank: CAA54776.1) and Equus
caballus (NP_001157488.1) extracted from ENTREZ database, find the maximum score and the best alignment

Assignment
1. Take the Insulin protein (amino acid) sequences of two organisms like Octodon degus (AAA40590.1) which is a species of
rodent (commonly called rat) and Cavia Porcellus (AAA37041.1), commonly called Guinea pig, also a species of rodent rat.
Align both of the protein sequences using local alignment method based on a online tool “EMBOSS-
water”(http://www.ebi.ac.uk/Tools/psa/emboss_water/) and find out the similarity percentage between the two protein
sequences.

2. Find out the similarity percentage of the nucleotide sequences of the two organisms given in first question?