MC170200997 ALMAIDAH MAHMOOD

MC170200997
ALMAIDAH MAHMOOD

(Q.1) Explain how computer algorithms can be used to predict the primary, secondary and tertiary structures of proteins.5
Solution:-
Algorithm mean modified for speed enhancement or problem solving, computer algorithms means the those problems which are solved by the computers . computer algorithms are used for the prediction of protein structure. Different algorithms are used for the prediction of the protein.
Primary structure:
These are some methods used for the prediction of the primary structure of the protein.
Tandem mass spectrophotometery:
In the process of the tandem mass spectrophotometery the protein sequences are breakdown by the protease enzyme known as trypsin into the smaller fragments are known as peptides and then by the application of this process these smaller fragments are then degraded into further smaller fragments.
Secondary structure :
these are some methods used for the prediction of the secondary structure of protein .
SPIDER2:
This is the mopdel used for the prediction of neural network of the secondary structure of protein.this model were initially released in 2015.
RaptorX-SS8
This is the model used for the prediction of the secondary structure in the 3-state and 8-state . it is also used in the neural prediction of the secondary structure of the protein.
Frag1D:
It is a model used for the prediction of the secondary structure of the protein but it also predict the shape strings of the protein. This model were initially released in 2010.
Tertiary structure of protein:-
These are the some methods discussed below used for the prediction of tertiary protein structure:
IntFOLD:
This is the model used for the prediction of the tertiary structure of protein. With the prediction of the tertiary structure it also predict the 3D modelling , domain prediction and helpful in a lot more predictions.
It is automated webserver.
Ab intio method :
Ab intio method or the de novo protein structure prediction method is used for the prediction of the tertiary structure of protein .for better prediction this method requires more algorithm such as Blue Gene.

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(Q.2) detail note the problems occur during of peptide sequencing. 5
Solution:-
Protein sequencing is done by the process of mass spectrometery . in the whole process the enzyme trypsin change the protein into peptides and then by the process of mass spectrometer these peptides are converted into the small fragments in a very short time and it measures the mass of each of these small fragments . the mass spectrum of these peptides is the collection of masses of these fragments . the protein sequencing problem is to derive the sequence of a peptide given in its mass spectrum. In the ideal mass spectrometer the peptide sequencing problem is simple , however the fragmentation process is not ideal, a mass spectrophotometer is measure the mass with some imprecision ,thees details makes peptide sequencing difficult. So the problem is to contsruct the amino acid sequencing of the peptides from the masses of the broken pieces so this strategy is used by using the tendem mass spectrophotometer and it measures the amount of the ion present in the smaller fragments and these can be used to sequence the proteins of different sizes. Although mass spectrometer has facilitated in the sequencing of proteins but there are some problems in that process so when the mass spectrometer breaks the small fragments into further smaller the problem is that despite of having the small fragments some molecules that are with the molecules they removed so the mass is calculated by the machine is different from the mass of actual amino acids or peptides .
So if we consider that
A={a1, a2, …….,a20}
This is the set of 20 amino acids and molecular mass of this set is suppose m(ai) ,
And as we know the protein molecule is break into peptide , suppose peptide sequence is
P={p1, p2,……………,pn}
The sequence of amino acid with paernt mass m(P)=
and we can denote the partial N-terminal peptide as p1,……..,pi of mass
In this case pi is the partial C-terminal peptide pi+1,…..,pn of the mass and
m(P)n-mi as p-I , 1?i?n.
And we know that mass spectra is obtained by the tendem mass spectrophotometery consist predominantly of partial N-terminal peptides and C- terminal peptides and we know that every protein is linear chain and connected by peptides bonds between the amino acids.
Mass spectrophotometer typically breaks the peptides into smaller fragments which we gave name as p1,p2,……pn
At different peptides bonds and detect the masses of resultant partial N-terminal and C-terminal peptides .
(Q.3) write down the applications of Smith-Waterman Algorithm. 5
Solution :-
These are the algorithms used for sequence alignment and used to determine the similar region between the protein sequence and the string of nucleic acid.
Basically the smith waterman algorithm(modified for speed enhancement) used to calculate the local algorithms .
These are the algorithms used to find the similar segments between two sequence.
Another benefit of this algorithm is that no negative scores are obtained during the whole process of scoring system.
One more use of this algorithm is that it determine how two sequences are aligned and also use to determine their optimal alignment.
The one of the important application of the smith waterman algorithm is to DNA testing of the sequence match or protein sequence match against the genome database.
It is used to find comparison between the different segments of length and by scoring method if find the segment which is actually maximizing the scoring measurements.
It use dynamic programming for the scoring.
Only significant matches are re-analyzed using smith waterman algorithm.
(Q.4) what is DNA Arrays, detail note on types and applications of microarray 5
Solution:-
DNA arrays:-
DNA micro arrays are the solid substrates (usually of glass or silicon )upon thousands of DNA molecules are attached in organized grid fashion.
Each sample of DNA spot is called as probe which represent the single gene present on the DNA.
Several other names also given to DNA micro arrays as some of these are DNA chips , gene array or biochip etc.
Types of DNA arrays:-
These are the two types of DNA micro arrays, discussed below
cDNA micro array :
Glass cDNA micro arrays involves spotting the fragments on the glass .
A kind of DNA synthesized from single stranded RNA template catalyzed by the enzyme to change into cDNA . it is a DNA produced by the retrovirus.
Oligonucleotides arrays :
In this type chips involves involves in situ synthesized arrays .
In the oligonucleotides arrays the probe are sequence are design such that the can match the sequence of the part of known or predicted ORF.
These arrays are although used in the spotted microarrays but their specific term is commonly referred to these arrays.
These sequence are designed by the sequencing of short oligonucleotides sequence to represent the single gene by synthesizing this sequence directly onto the array surface instead of depositing intact sequence.
Applications of DNA micro arrays:-
These are the some application for the DNA micro array:
Gene expression:
One of the most important application of the DNA micro array is that it Is used to measure the gene expression.
Pharmaceutical :
Micro arrays are used in the research of cancer and it approaches to the treatments of the several diseases , as we can say that it helps in the pharmaceutical .
Labeling :-
Several micro arrays are used in the labeling f the cRNA or cDNA .
Genotyping :
It used to measure the expression of the genotype of multiple regions.
Wide records of data:-
It is used to analyze the wide amount of data to take help in any kind of disease search or for other things .