For Past Papers Just Follow The Download Buttons, We have a large data for revision of Virtual University courses. You can also join following groups for study discussion . The best is We Recommend you to study your handouts and lectures, Prepare your all course then revise the past papers for your good grade.
Solved papers (plz correct if u see any mistake)
solved by Zareen Fatima
Define mutation (2)
- Replacement of amino acids with certain other amino acids in proteins
- Replacement of nucleotides with certain other nucleotides in DNA/RNA
Databases use for proteins (2)
Ans: uniport and swisport
Generally used databases and which type of information they store (3)
Genebank. Pdb, uniport swisport
- Accession number
- Molecular mass
- Journal etc.
Types of RNA and their functions (5)
RNA can be divided into two categories
- Coding RNAs
- Non-Coding RNAs
- Coding RNAs as is obvious from their name, code for Proteins
- Non-Coding RNAs regulate/assist in the process of translation Types of RNA
- Messenger RNA (mRNA) Messenger RNA (mRNA) carries the genetic information copied from DNA in the form of a series of three-basecode “words,” each of which specifies a particular amino acid
- Transfer RNA (tRNA) is the key to converting the code words in mRNA.
- Ribosomal RNA (rRNA) associates with a set of proteins to form ribosomes. These complex structures, which physically move along an mRNA molecule, catalyze the assembly of amino acids into protein chains. They also bind tRNAs and various accessory molecules necessary for protein synthesis.
- Micro RNAs (miRNA)
5. Small Interfering RNA (siRNA)
Small (or short) interfering RNA (siRNA) is the most commonly
used RNA interference (RNAi) tool for inducing short-term silencing of protein coding genes.siRNA is a synthetic RNA duplex designed to specifically target a particular mRNA for degradation.
Uses of clustalw 2
Ans: CLUSTALW can:
create multiple alignments
- profile analysis &
- create phylogenetic trees
Ans: • Tertiary or 3’ structures may form pseudoknots
- A simple graph-based approach “Circular Plot” can help us detect the pseudoknots
A pseudoknot is a nucleic acid secondary structure containing at least two stem-loop structures in which half of one stem is intercalated between the two halves of another stem. Pseudoknots fold into knot-shaped three-dimensional conformations but are not true topological knot
- Protein Sequences are reported from sequencing experiments
- This data is stored in protein sequence databases
- The famous ones include UniProt & SwissProt
Scoringatrix formula 5
s(a,b)=1/λlog pab /fafb
Pam matric steps5″
Step 1: Align proteins sequences which are 1-PAM unit diverged
Step 2: Let Ai,j be the number of times Ai is suabstituted by Aj
Step 3: Compute the frequency fi of amino acid Ai
Then, PAM1 = pij = PAM’n’ = ( PAM1 ) n
STEP OF BLOSUM?
How are Bulges Formed?
- Bulges, are formed when a double-stranded region cannot form base pairs perfectly
- Bulges can be asymmetric with varying number of base pairs on one side of the loop
Name three hydrophobic amino acid?
Ans: glycine (Gly), alanine (Ala), valine (Val), leucine (Leu), isoleucine (Ile), proline (Pro), phenylalanine (Phe), methionine (Met), and tryptophan (Trp).
2.rooted and unrooted tree difference?
Ans: Rooted and Unrooted trees can be used to show phylogenetic relationships between sequences
Rooted tree shows the phylogeny of ancestors
Phylogenetic trees take several forms: They can be rooted or unrooted, binary orgeneral, and may show, or not show, edge lengths. A rootedtree is a tree in which one of the nodes is stipulated to be the root, and thus the direction of ancestral relationships is determined
- Rooted trees reflect the most basal ancestor of the tree in question.
- Unrooted trees do not imply a known ancestral root.
dynammic programming to create scoring matrix?r 1 series sequence dia hua tha scoring matrix maloom krny k liy?
ans: From the large number of possible nucleotide combinations, it is hard to find the optimal one
• Dynamic Programming (DP) helps break the problem into smaller problems
Select a nucleotide from sequence
List all possible complementary position for the selected nucleotide in the complete sequence.
How DP works?
- DP exhaustively makes all possible nucleotide combinations
- DP then recombines such combinations in a process called “Traceback” to ensure that the highest coupled 2’ structure is reported
Complete the protein sequence .F-x(3)-x-R-F-K-x(4-5)-D-E-R?
clustering is used to build groups of genes with related expression patterns
Define system biology and its application?
. Systems Biology
- Model protein and gene interactions
- Dynamical analysis of such models
- Understand system properties
- Predict system level behaviors
Need for bioinformatics ?
1 An interdisciplinary field
- New but rapidly developing field
- Low requirement on infrastructure and research equipment
- Vast opportunities for scientific discovery
Life, evolution and disease can be better understood
• Drugs can be better developed after understanding molecular basis of life Possible contributions
- Solve important problems related to life
- Handle mammoth quantities of experimental data
- Develop efficient solutions towards these goals
Role of 5’ cap and poly a tail?
- The 5’ cap helps identify mRNAs at the Ribosomes
- The 5’ cap also acts as a shield against 5’ exonuclease, thus leading to an increase in mRNA stability
The 3’-end of mRNA has a polyA tail (around 30-200 adenylate residues) which help shield against 3’ exonucleases
Please write down the complete names of organisms renowed as “EMBL” and “EBJ”
Ans: European Molecular Biology Laboratory
Describe the types of phlylogenetic tree
Name any 3 hydrophobic aminoacids.
Elaborate the 4 steps to use Fasta algorithm to your nucleotide amino acid
Formula for scoring matrix.
Ans: topic 67
domain of protein ?
Ans: Examples of Protein Domains Background • Alpha Domains • Beta Domains • Alpha/Beta Domains • Alpha + Beta Domains • Alpha & Beta Multi-Domains
- Membrane & cell-surface proteins
what is positive & negative release of energy in molecule?
Application of bioinformatics
Ans: Introduction • Where can bioinformatics be applied specifically? • What are the avenues in biology that can benefit from this science? • What benefits can
it deliver to the society?
• DNA Sequencing • Gene Finding • Genome Assembly • Variation in Genomes • Transcription Data • Databases
2. Evolutionary Studies
- Evolutionary relationships • Evolutionary distances • Phylogenetics • Tree of life
Protein Sequencing • Protein Structures • Post-translational Modifications • Protein-Protein Interactions • Database Development
4. Systems Biology • Model protein and gene interactions
Dynamical analysis of such models • Understand system properties • Predict system level behaviors
q1: indel and substitution
Ans: Insertions or deletions (“indels”) result in gaps in alignments • Substitutions result in mismatches
q2: EXPASY STAND
Ans: export protein analysis
Q3: NEWICK ZRUTH
q4: need of bioinformatic
- An interdisciplinary field
- New but rapidly developing field 3. Low requirement on infrastructure and research equipment 4. Vast opportunities for scientific discovery
• Since genome and proteome information is publically available, you can process this information after downloading it
• If you carefully search this online data, with a little bit of biology background, it is a gold mine!
Quote Biology easily has 500 years of exciting problems to work on. Donald Knuth, Professor, Stanford University What can bioinformatics deliver? • Life, evolution and
disease can be better
understood • Drugs can be
better developed after
basis of life
- Solve important problems related to life • Handle mammoth quantities of experimental data • Develop efficient solutions towards these goals
- From gene sequences to protein sequences Bioinformatics is the way forward
- Protein structure, protein-protein interactions and systems biology are other research areas in bioinformatics
q5: field of bioinformatic
q6: similarity and identy and formula Ans: topic 28
Enumerate the clustering and objective based methods for constructing phlogenetic tree.