BIF401 Final Term Current Solved Papers

Current solved paper *BIF 401* (For Finals)

Q. Define Top down proteomics?

Answer: “Top down proteomics can handle whole proteins”. Top down proteomics measures the intact proteins followed by peptides after fragmentation.

Q. Need for Chau fasman algorithm?

Answer: Chau fasman algorithm is a propensity base method. The method is based on analyses of the relative frequencies of each amino acid in alpha helices, beta sheets, and turns based on known protein structures solved with X-ray crystallography. From these frequencies a set of probability parameter were derived.

Q. Write down an objective base method and clustering approach?

Answer: UPGMA is a clustering approach and least square distance is an objective base method.

Q. Differentiate between finger printing and short gun proteomics?

Answer: Shotgun proteomics digests the entire protein mix 1st followed by peptide analysis & protein database search

• Peptide mass fingerprinting involves protein separation followed by a single protein’s peptide analysis.

Q. what are substitutions and indels?

Answer: Indels: Removal and addition of amino acids in proteins and nucleotides in DNA, RNA by using Gaps named as Indels.

Substitution:

Replacement of a single or a specific pair of amino acid or nucleotide with other on in a sequence is called substitution.

Q. How can psuedonots detected in the prediction of RNA?

Answer: Tertiary or 3’ structure of RNA may form pseudoknots to detect the pseudoknots in RNA structure we need “circular plot” which is a graphical approach.

Q. Formation of protein sequence and limitation?

Answer: There are two basic techniques for sequence of a protein,

1. Edman degradation
2. Mass spectrometery

Edman degradation used to sequence the smaller length protein, about 40 – 50 amino acids. Large protein sequence is carried out by mass spectrometery. *Limitations ni mili,

Q. Uniprot and ESEMBL or EMBL?

Ans> Uniprot is a public data base which is used to find the sequence of protein. ESEMBLE is genome search engine which is used to search the genome of every recorded species. OR it might be EMBL so, Input to FASTA search can be in * EMBL*,= European molecular biology laboratory (EMBL)

Q. Mas spectrometer?

Ans> Mass spectrometer is used to measure mass/charge ratio of ionized proteins and peptides. Data output from the MS comprises of m/z ratios and intensities of each molecule that is measured.

Function of Tandem Ms:

Tandem MS helps in measurement of mass to the fragments as well. This process Substitutions ACGA GGA provides another step in further scoring and ranking and Protein identification thus becomes easier.

Q. Define Orthology?

Ans> it is a homologous gene present in two organisms that encode protein with same function. It is evolved by direct vertical descent.

Q. What does role of 5´ cap and 3´ poly A tail?

Answer: the 5´ end of molecule caped with 7 methyl guanosine tri phosphate and 3´ end poly A tail cap, both caps play major role to translate mRNA to ribosome, also protect mRNA. Q.: Explain applications of bioinformatics. There are some major applications of bioinformatics: In this field bioinformatics help us in gene finding, in assemblage of genes and forming of databases.

2.Proteomics:

It helps us to decoding protein sequences for better understanding about protein structure, protein to protein relationship, post translational changes and in generating databases for their sequence and structure.

3.Evolutionary study:

It can make phylogenetic trees to find evolutionary relationship between species, also show ancestry between them,

4.System biology:

Bioinformatics also helps us in regulatory mechanism in genes and proteins. So that we can better understand about regulators and treat them by evaluate drugs. Bioinformatics also help us in further many aspects like,

Drug development · Waste cleanup · Gene therapy

Preventative medicine etc.

Q=write types of phylogenetic trees ? no option

Rooted trees:

•  Each node with descendants represents the inferred most recent common