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MOLBIO LEC
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MOLBIO LEC
Genomics
Study
1
Question
What is the basis of Maxam-Gilbert method of sequencing?
Answer
Chemical modification of DNA and subsequent cleavage at specific bases.
2
Question
How is the sample labeled in Maxam-Gilbert sequencing?
Answer
Radioactively labeled with 32P ATP.
3
Question
How many tubes is the sample divided into in Maxam-Gilbert sequencing?
Answer
Four tubes.
4
Question
What is the most common method for DNA sequencing that is also known as Sanger sequencing?
Answer
ChainTermination sequencing or Dideoxy sequencing.
5
Question
What are the components required for ChainTermination sequencing?
Answer
Single-stranded DNA template, Sequencing primer, DNA polymerase, Radioactively labeled nucleotides (dNTPs), Chain terminating nucleotides (ddNTPs).
6
Question
What happens when a chain terminating nucleotide is incorporated in ChainTermination sequencing?
Answer
The synthesis stops.
7
Question
What is the advantage of Next Generation Sequencing (NGS) over manual sequencing?
Answer
Automated massively parallel methods where millions of sequencing reactions occur and are recorded simultaneously.
8
Question
What was the first commercially available Next Generation Sequencing (NGS) technology?
Answer
Roche 454 Pyrosequencing.
9
Question
What is the principle of Illumina/Solexa Sequencing?
Answer
Reversible Dye-Termination.
10
Question
What is the principle of Ion Torrent Sequencing?
Answer
Ion Conductance.
11
Question
What is the principle of ABi SOLiD Sequencing?
Answer
Sequencing by Ligation, requires 5 primers and a set of 16 dibase oligonucleotides with attached fluorescent probes.
12
Question
What are the two main characteristics of Third Generation Sequencing?
Answer
PCR is not needed before sequencing, Signal is captured in real-time.
13
Question
What is the principle of Oxford Nanopore sequencing?
Answer
Utilization of nanopore, Ionic flow is applied continuously, Current disruption is detected by standard electrophysiological techniques, Readout relies on the size difference between all deoxyribonucleoside monophosphates.
14
Question
What does Genome Sequencing refer to?
Answer
Sequencing of the whole genetic profile of an organism on a much larger scale than DNA sequencing.
15
Question
What was the first DNA genome to be sequenced?
Answer
Bacteriophage X174.
16
Question
What are the two approaches to Genome Sequencing?
Answer
Clone Contig Sequencing and Shotgun Sequencing.
17
Question
What is the process in clone contig sequencing approach?
Answer
In this approach, the genome is broken down into segments through partial restriction followed by cloning to a high-capacity cloning vector (BAC, YAC) and then subjected to shotgun sequencing with de novo assembly.
18
Question
What is another name for the hierarchical shotgun sequencing approach?
Answer
Hierarchical shotgun sequencing is also known as clone contig sequencing.
19
Question
What is the process in shotgun sequencing approach?
Answer
In shotgun sequencing, the genome is randomly broken into short fragments, ligated to a cloning vector randomly, amplified, and then assembled by identifying overlaps between sequences.
Molecular Phylogeny
Study
1
Question
What does 'Branch length' represent in phylogenetic analysis?
Answer
The number of changes that have occurred in the branch
2
Question
What are some examples of genes utilized in molecular phylogeny?
Answer
Ribosomal DNA (rDNA), Mitochondrial DNA (mtDNA), Chloroplast DNA (cpDNA) are commonly used in molecular phylogeny.
3
Question
What is the purpose of MEGA software in phylogenetic analysis?
Answer
It can construct a phylogenetic tree based on its algorithm
4
Question
What is molecular phylogeny and how is it different from traditional phylogeny?
Answer
Molecular phylogeny refers to phylogeny utilizing molecular sequence data, while traditional phylogeny was inferred using phenotypic characteristics or physical appearance.
5
Question
What are phylogenetic trees used for?
Answer
Phylogenetic trees are diagrams used for depicting evolutionary relationships, showing the common ancestor, taxonomic units represented by nodes, relationships between taxa through branches, and the number of changes represented by branch lengths.
6
Question
What are the two types of evolution that take place within a group of organisms connected by reproduction?
Answer
Anagenesis and Cladogenesis. Anagenesis refers to evolution taking place in a single lineage over time, while Cladogenesis refers to the splitting of one lineage into two.
7
Question
What is an 'Optimality criterion' in phylogenetic analysis?
Answer
It examines different tree topologies for a given number of taxa in the search for the one that optimizes a specific criterion
8
Question
What does 'Node' signify in phylogenetics?
Answer
That the two organisms have similar characteristics, such as being mammals
9
Question
What is a 'Clade' in phylogenetics?
Answer
A group of two or more taxa that includes both their common ancestor and all their descendants
10
Question
Why are human and mouse grouped together in phylogenetic analysis?
Answer
Because both of them are mammals
11
Question
What does 'Branch' define in phylogenetic analysis?
Answer
Relationship between the taxa in terms of descent and ancestry
12
Question
Why is the fly not grouped with mammals in phylogenetic analysis?
Answer
Because it is an arthropod, not a mammal
13
Question
What is MEGA in phylogenetic analysis?
Answer
MEGA stands for Molecular Evolutionary Genetics Analysis and is a software developed for phylogenetic studies
14
Question
What is a 'Distance matrix' used for in phylogenetic analysis?
Answer
To differentiate between the distance between two organisms using a particular statistical tool
15
Question
What is a 'Clustering algorithm' in phylogenetic analysis?
Answer
It gradually clusters taxa into a single tree using distance matrix to compute branch lengths
16
Question
What is the definition of biological evolution?
Answer
Biological evolution is the change in allelic frequencies in a population caused by mutation, migration, genetic drift, and natural selection.
17
Question
What is the molecular clock hypothesis based on?
Answer
The molecular clock hypothesis is based on the assumption that the rate of change in DNA or amino acid sequence is relatively constant, and genetic difference between species is proportional to the time since they last shared a common ancestor.
18
Question
What does 'Root' represent in phylogenetic analysis?
Answer
The common ancestor
Bioinformatics
Study
1
Question
What is bioinformatics?
Answer
A field that converges computer science, molecular biology, and statistics to analyze biological data
2
Question
What are the applications of bioinformatics?
Answer
Analyzing genetic and protein sequence data, studying macromolecules like proteins and nucleic acids
3
Question
What is genomics?
Answer
Study of an organism's whole set of DNA
4
Question
What is transcriptomics?
Answer
Study of the whole messenger RNA of an organism
5
Question
What is proteomics?
Answer
Study of an organism's whole set of proteins encoded from the transcriptome mRNA
6
Question
What is epigenomics?
Answer
Study of the epigenetics of the cell, focusing on how DNA is packaged into chromosomes and its effect on gene expression
7
Question
What is metabolomics?
Answer
Study of the networks or communication between proteins in an organism
8
Question
What is microbiomics?
Answer
Study of microorganisms in a host or human body, including symbiotic, commensal, and pathogenic ones
9
Question
What is NCBI GenBank?
Answer
A public repository of biomedical data containing annotated and identified DNA sequence information
10
Question
What is Expasy UniProt?
Answer
A resource of protein sequences and functional information, providing comprehensive and free access to protein data
11
Question
What is the Protein Data Bank (PDB)?
Answer
A major repository of 3D structural information about biological macromolecules, such as proteins and nucleic acids
12
Question
What is the Protein Information Resource (PIR)?
Answer
A public bioinformatics resource supporting genomic, proteomic, and systems biology research
13
Question
What is the GenBank format optimized for?
Answer
Reading by humans, not suited for large-scale data processing
14
Question
What does the Locus in GenBank format provide?
Answer
Locus name, size of nucleotide sequence, nature of the molecule, and its topology
15
Question
What information does the Accession in GenBank format provide?
Answer
Unique identifier number within and across various databases
16
Question
What information does the Locus section of a GenBank entry provide?
Answer
Locus gives the locus name, size of the nucleotide sequence in base pairs, the nature of the molecule, and its topology.
17
Question
What is the locus information for NG009549 in GenBank format?
Answer
NG009549 locus, 15944 bp, size of the gene DNA, linear topology of the gene.
18
Question
What does the Definition section in a GenBank entry provide?
Answer
Provides a short definition of the gene that corresponds to the entry sequence.
19
Question
What information does the Accession section of a GenBank entry provide?
Answer
Lists the accession number, a unique identifier within and across various databases.
20
Question
What are the keywords in a GenBank entry used for?
Answer
Introduce a list of terms that broadly characterize the entry.
21
Question
What information does the Source section in a GenBank entry provide?
Answer
Divulges the common name of the relevant organism to which the sequence belongs.
22
Question
What do the Features in a GenBank entry include?
Answer
Source (where the sequence is in the chromosome), Gene (reconstruction of various mRNA), mRNA (representation of alternative splicing patterns), Exon (position of the sole exon present), CDS (coding sequence).
23
Question
What does the FASTA format retain from a GenBank record?
Answer
It retains some sequence information - the header consists of the contents from ACCESSION and DEFINITION of a GenBank format, the genomic sequence follows.
24
Question
What is the purpose of Sequence Alignment?
Answer
Pairwise alignment to find similarities between sequences and determine the most similar sequence to a query sequence.
25
Question
What are the two factors that govern every alignment in Sequence Alignment?
Answer
Alignment algorithm (global, local, semiglobal) and Alignment scoring parameters (numerical values that tune the arrangement).
26
Question
What is the difference between Global alignment and Local alignment?
Answer
Global alignment attempts to align all residues in a sequence, while Local alignment focuses on aligning only a part of a sequence in search for similar sequence motifs.
27
Question
What are some examples of Sequence Alignment Tools?
Answer
CLUSTAL, EMBOSS, Bioedit, MEGA, RStudio.
28
Question
What is CLUSTAL and how is it used in sequence alignment?
Answer
CLUSTAL is an umbrella tool for different sequence alignment services, utilizing a matrix-based algorithm to make multiple sequence alignments.
29
Question
What is Emboss and how is it used in sequence alignment?
Answer
EMBOSS (European Molecular Biology Open Software Suite) is a free open-source software package for sequence alignment, developed by the European Bioinformatics Institute.
30
Question
What is BioEdit and how is it used in sequence alignment?
Answer
BioEdit is a software program for nucleic acid/protein sequence editing and alignment.
Proteomics
Study
1
Question
What is the purpose of column chromatography in protein separation techniques?
Answer
To separate proteins based on different properties such as size, charge, or specific binding properties.
2
Question
What is the stationary phase in size exclusion chromatography composed of?
Answer
Cross-linked gel particles made of dextran, agarose, or polyacrylamide.
3
Question
How does affinity chromatography separate proteins?
Answer
By utilizing the specific binding properties of proteins to a ligand on the stationary phase.
4
Question
What is the principle behind ion exchange chromatography in protein separation?
Answer
Separating proteins based on their charge interactions with the ion exchange resin in the stationary phase.
5
Question
What distinguishes high-performance liquid chromatography (HPLC) from traditional liquid chromatography?
Answer
The use of high-resolution columns that can operate under high pressures for improved separation.
6
Question
What is the basis of electrophoresis in protein separation techniques?
Answer
The movement of charged particles in an electric field towards an oppositely charged electrode.
7
Question
What is the purpose of sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE)?
Answer
To separate proteins based on their size by denaturing them with SDS before electrophoresis.
8
Question
How does isoelectric focusing separate substances in protein analysis?
Answer
Based on the isoelectric points of proteins, allowing separation by their relative charges.
9
Question
What is the significance of two-dimensional gel electrophoresis in protein analysis?
Answer
It combines two separate electrophoresis techniques to provide a more detailed protein separation and analysis.
10
Question
What is the method of protein identification known as Edman Degradation used for?
Answer
To determine the amino acid sequence of a protein by sequentially removing and identifying amino acids.
11
Question
What information can be obtained from the amino acid analysis after complete hydrolysis of a protein sample?
Answer
The presence and molar ratios of different amino acids in the protein sequence.
12
Question
How is the presence of specific amino acids confirmed in a protein sample using 1-fluoro-2,4-dinitrobenzene treatment?
Answer
By forming derivatives of amino acids that can be detected through chromatography.
13
Question
What is the significance of free tyrosine detection in protein analysis using chymotrypsin digestion followed by chromatography?
Answer
It indicates the presence of tyrosine as a constituent amino acid in the protein sequence.
14
Question
In protein analysis, why is the relative ratio of amino acids important in determining the sequence of the peptide?
Answer
It provides insight into the order and composition of amino acids in the protein sequence.
15
Question
What role does primary structure identification by chemical degradation play in protein analysis?
Answer
It helps in determining the sequence of amino acids in a protein by breaking it down into individual components.