BIF401 Final Term Solved Past Questions

MUHAMMAD IMRAN BIF401 -Bioinformatics I · MCQs&Questions final term Past papers /2019/2020 · 1. What Are Uses Of Mass Spectrometry? 2

Mass spectrometry (MS) is an analytical technique that ionizes chemical species and sorts the ions based on their mass-to-charge ratio. In simpler terms, a mass spectrum measures the masses within a sample. Mass spectrometry is used in many different fields and is applied to pure samples as well as complex mixtures.

2. Need For Chou Fasman Algorithms? 2

were calculated by considering the relative frequency of a given amino acid within a protein, its occurrence in a given type of secondary structure, and the fraction of residues occurring in that type of structure.

3. Three individual scores Integrative Scoring Scheme? 2

Three individual scores can be obtained including

1. MW Match Score
2. PST Match Score
3. In vitro & In silico Match Score.

4. Write benefits of phylogenetic studies marks • 03

5. Advantage of Folded Protein over Denatured Protein. 5

Difference Between Folding Protein and Denature Protein, / What Factors Are Used For Folding Proceeds?

Protein folding is the physical process by which a protein chain acquires its native 3-dimensional structure, a conformation that is usually biologically functional, in an expeditious and reproducible manner. Denaturation of proteins involves the disruption and possible destruction of both the secondary and tertiary structures. Since denaturation reactions are not strong enough to break the peptide bonds, the primary structure (sequence of amino acids) remains the same after a denaturation process. Protein folding is a process by which a polypeptide chain folds to become a biologically active protein in its native 3D structure. Protein structure is crucial to its function. Folded proteins are held together by various molecular interactions. ... The amino acid sequence of a protein determines its 3D structure. The forces involved in protein folding include: • Electrostatic interactions, • van der Waals interactions, • Hydrogen bonds, • Hydrophobic interactions

6. Score in Silico fragment scoring?.5

Count the matches between in silico and in vitro peaks. Give an equivalent score to the candidate protein. Weigh each of the aforementioned match by the mass error. Accumulate the score

7. How Loops Are Found After The Finding Of Alpha And Beta Sheets?5

Alpha helices and beta strands are connected by these turns and loops. ... Loops and turns generally lie on the surfaces of proteins so they often participate in interactions between proteins and other molecules. In a loop, there are no regular structures as can be found in helices or beta strands.

8. Tandem mass spectrometry

Tandem mass spectrometry (MS-MS) is a related technology in which compounds are separated by molecular weight by one mass spectrometer, fragmented as they exit, and identified on the basis of their fragments by a second mass spectrometer

Q9. Advantage and disadvantage of Ab initio method?

Advantages:

Ab Initio methods can fold any target sequence using only physical atomic properties. Predictions are mostly accurate and correctly describe the natural folding process. Disadvantages: Ab initio methods are the very difficult to design (energy function). These methods are slow due to the huge possibilities.

10. Types of secondary structures of RNA:

1. Single stranded:

3’end may fold on to the 5’ end.

2. Helices:

Double stranded RNA helix of stacked base pairs 3.

Hairpin loop:

The loop of the hairpin must at least four bases long to avoid steric hindrance with base-pairing in the stem part of the structure 4. Bulge Loops: Bulges, are formed when a double-stranded region cannot form base pairs perfectly.

5. Interior loop:

Interior loops are formed by an asymmetric number of unpaired bases on each side of the loop.

6. Junctions or intersections:

Junctions include two or more double-stranded regions converging to form a closed structure. The unpaired bases appear as a bulge

Q11. How homology modeling is used for knowing the sequence of unknown protein sequence?

If another protein which has a similar sequence also has its structure known, the structure of an unknown protein can be predicted based on that similar protein. So, it is then possible to identify unknown protein structures by just examining the homologous protein sequences. Good sequence alignment and identity ensures that homology modelling will give accurate results. Thus, Homology modeling is used to predict structures of proteins having high sequence similarity with other proteins with known structures:

Q12. Role of Amino Acid?

13. Write Down The Following Terms Of PDB (3)

Title (Title of the structure) Source (Identify which organism structure from) COMPND (Brief detail of the structure) REVEDAT (The data of last revision

Q14. What Happend When Ph Is Less Than The Pk Value?

If the pH is higher than the pKa, then the compound will be deprotonated. A further consideration is the charge on the compound. Acids are neutral when protonated and negatively charged (ionized) when deprotonated. Bases are neutral when deprotonated and positively charged (ionized) when protonated.

Q15. Chou Fasman Algorithm?

The Chou–Fasman method is an empirical technique for the prediction of secondary structures in proteins, originally developed in the 1970s by Peter Y. Chou and Gerald D. Fasman.

Q16. Function of Tandem MS?

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

Q17. Factors That Participate In Folding Protein?

The external factors involved in protein denaturation or disruption of the native state include temperature, external fields (electric, magnetic), molecular crowding, and even the limitation of space, which can have a big influence on the folding of proteins

Q18. Need For Chou Fasman Algorithms?

were calculated by considering the relative frequency of a given amino acid within a protein, its occurrence in a given type of secondary structure, and the fraction of residues occurring in that type of structure.

Q19. Optimal Energy Function In Protein?

Results: For a single protein sequence, the probability of success (i.e. the probability that the folded state is the lowest energy state) is derived. We then maximize the average probability of success for a set of proteins to obtain the optimal potential energy function

Q20. Silico Fragments Comparison?

Matching experimental fragments with in silico fragments is the final resort in protein search & identification

Q21. Chou – Fasman method?

It is a technique for the prediction of secondary structures in proteins i.e. Alpha Helices, Beta Sheets and Turns is Chou – Fasman technique. 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 parameters (in our handouts, it is propensity table) were derived For the appearance of each amino acid in each secondary structure type. To predict the probability that a given sequence of amino acids would form a helix, a beta strand, or a turn in a protein.

Chou-fasman algorithm (alpha helix):

For Alpha Helices, 4 contiguous amino acids are required. Their Alpha-Helix propensity should be more than 1.0 Once this propensity falls below 1.0, Alpha-Helix stops.

Q22. Improvements Of Chou Fasman Algorithm?

The Chou-Fasman algorithm, one of the earliest methods, has been successfully applied to the prediction. ... We improved Chou-Fasman method in three aspects. (a) Replace the nucleation regions with extreme values of coefficients calculated by the continuous wavelet transform.

Q23. What is hydrophobicity of amino acid?

In chemistry, hydrophobicity is the physical property of a molecule that is seemingly repelled from a mass of water. In contrast, hydrophiles are attracted to water. Hydrophobic molecules tend to be nonpolar and, thus, prefer other neutral molecules and nonpolar solvents.

Q24. how propensity table can helps us?

Q25. Seven Steps present in flow chart of homology modeling?

1. Template recognition and initial alignment.
2. Alignment correction.
3. Backbone generation.
4. Loop modeling.
5. Side-chain modeling.
6. Model optimization.
7. Model validation